Whole Exome Sequencing and Whole Genome Sequencing

Whole exome sequencing (WES) is targeted next-generation sequencing (NGS) of the subset of the human genome that contains functionally important sequences of protein-coding DNA, while whole genome sequencing (WGS) uses NGS techniques to sequence both coding and noncoding regions of the genome. WES and WGS have been proposed for use in patients presenting with disorders and anomalies not explained by standard clinical workup. Potential candidates for WES and WGS include patients who present with a broad spectrum of suspected genetic conditions.

Given the variety of disorders and management approaches, there are a variety of potential health outcomes from a definitive diagnosis. In general, the outcomes of a molecular genetic diagnosis include (1) impacting the search for a diagnosis, (2) informing follow-up that can benefit a child by reducing morbidity, and (3) affecting reproductive planning for parents and potentially the affected patient.

The standard diagnostic workup for patients with suspected Mendelian disorders may include combinations of radiographic, electrophysiologic, biochemical, biopsy, and targeted genetic evaluations.^1, The search for a diagnosis may thus become a time-consuming and expensive process.

Whole Exome Sequencing and Whole Genome Sequencing Technology

WES or WGS using NGS technology can facilitate obtaining a genetic diagnosis in patients efficiently. WES is limited to most of the protein-coding sequence of an individual (»85%), is composed of about 20000 genes and 180000 exons (protein-coding segments of a gene), and constitutes approximately 1% of the genome. It is believed that the exome contains about 85% of heritable disease-causing variants. WES has the advantage of speed and efficiency relative to Sanger sequencing of multiple genes. WES shares some limitations with Sanger sequencing. For example, it will not identify the following: intronic sequences or gene regulatory regions; chromosomal changes; large deletions; duplications; or rearrangements within genes, nucleotide repeats, or epigenetic changes. WGS uses techniques similar to WES but includes noncoding regions. WGS has a greater ability to detect large deletions or duplications in protein-coding regions compared with WES but requires greater data analytics.

Technical aspects of WES and WGS are evolving, including the development of databases such as the National Institutes of Health’s ClinVar database (http://www.ncbi.nlm.nih.gov/clinvar/) to catalog variants, uneven sequencing coverage, gaps in exon capture before sequencing, and difficulties with narrowing the large initial number of variants to manageable numbers without losing likely candidate mutations. The variability contributed by the different platforms and procedures used by different clinical laboratories offering exome sequencing as a clinical service is unknown.

In 2013, the American College of Medical Genetics and Genomics, Association for Molecular Pathology, and College of American Pathologists convened a workgroup to standardize terminology for describing sequence variants. In 2015, guidelines developed by this workgroup describe criteria for classifying pathogenic and benign sequence variants based on 5 categories of data: pathogenic, likely pathogenic, uncertain significance, likely benign, and benign.^2,

Regulatory Status

Clinical laboratories may develop and validate tests in-house and market them as a laboratory service; laboratory-developed tests must meet the general regulatory standards of the Clinical Laboratory Improvement Amendments (CLIA). WES or WGS tests as a clinical service are available under the auspices of the CLIA. Laboratories that offer laboratory-developed tests must be licensed by the CLIA for high-complexity testing. To date, the U.S. Food and Drug Administration (FDA) has chosen not to require any regulatory review of this test.

Related Policies

• Genetic Testing for Facioscapulohumeral Muscular Dystrophy (Policy #088 in the Pathology Section)
• Genetic Testing for Epilepsy (Policy #102 in the Pathology Section)
• Genetic Testing for Limb-Girdle Muscular Dystrophies (Policy #125 in the Pathology Section)
• Genetic Testing for Developmental Delay/Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies (Policy #047 in the Pathology Section)
• Genetic Testing for the Diagnosis of Inherited Peripheral Neuropathies (Policy #087 in the Pathology Section)

For Medicare Advantage, Medicaid and FIDE-SNP, please refer to the Coverage Sections below for coverage guidance.)

1. Standard whole exome sequencing, with trio testing when possible (see Policy Guidelines), is considered medically necessary for the evaluation of unexplained congenital or neurodevelopmental disorder in children when ALL of the following criteria are met:

a. Documentation that the member has been evaluated by a clinician with expertise in clinical genetics, including at minimum a family history and phenotype description, and counseled about the potential risks of genetic testing.
b. There is potential for a change in management and clinical outcome for the individual being tested.
c. A genetic etiology is considered the most likely explanation for the phenotype despite previous genetic testing (e.g., chromosomal microarray analysis and/or targeted single-gene testing), OR when previous genetic testing has failed to yield a diagnosis, and the affected individual is faced with invasive procedures or testing as the next diagnostic step (e.g., muscle biopsy).

a. At least one of the following criteria is met:
i. Multiple congenital anomalies (see Policy Guidelines);
ii. An abnormal laboratory test or clinical features suggests a genetic disease or complex metabolic phenotype (see Policy Guidelines);
iii. An abnormal response to standard therapy for a major underlying condition;
b. None of the following criteria apply regarding the reason for admission to intensive care:
i. An infection with normal response to therapy;
ii. Isolated prematurity;
iii. Isolated unconjugated hyperbilirubinemia;
iv. Hypoxic Ischemic Encephalopathy;
v. Confirmed genetic diagnosis explains illness;
vi. Isolated Transient Neonatal Tachypnea;or
vii. Nonviable neonates.

For members enrolled in Medicaid and NJ FamilyCare plans, Horizon BCBSNJ applies the above medical policy.

FIDE SNP:

For members enrolled in a Fully Integrated Dual Eligible Special Needs Plan (FIDE-SNP): (1) to the extent the service is covered under the Medicare portion of the member’s benefit package, the above Medicare Coverage statement applies; and (2) to the extent the service is not covered under the Medicare portion of the member’s benefit package, the above Medicaid Coverage statement applies.

Policy Guidelines: (Information to guide medical necessity determination based on the criteria contained within the policy statements above.)

The policy statements are intended to address the use of whole exome and whole genome sequencing for the diagnosis of genetic disorders in patients with suspected genetic disorders and for population-based screening.

This policy does not address the use of whole exome and whole genome sequencing for preimplantation genetic diagnosis or screening, prenatal (fetal) testing, or testing of cancer cells.

Rapid Sequencing

In the NSIGHT1 trial (Petrikin, 2018) rapid Whole Genome Sequencing (rWGS) provided time to provisional diagnosis by 10 days with time to final report of approximately ~ 17 days although the trial required confirmatory testing of WGS results which lengthened the time to rWGS diagnosis by 7–10 days. The WGS was performed in ‘rapid run’ mode with minimum depth of 90 Gb per genome and average depth of coverage of 40X.

For rapid WES or WGS, the patient should be critically ill and in the NICU or PICU when the test is ordered but may be discharged before results are delivered.

Copy number variation (CNV) analysis should be performed in parallel with rWGS using chromosomal microarray analysis (CMA) or directly within rWGS if the test is validated for CNV analysis.

Examples of specific malformations highly suggestive of a genetic etiology, include but are not limited to any of the following :

• Choanal atresia
• Coloboma
• Hirschsprung disease
• Meconium ileus

• Abnormal newborn screen
• Conjugated hyperbilirubinemia not due to total parental nutrition (TPN) cholestasis
• Hyperammonemia
• Lactic acidosis not due to poor perfusion
• Refractory or severe hypoglycemia

• Significant hypotonia; or
• Persistent seizures.
• Infant with high risk stratification on evaluation for a Brief Resolved Unexplained Event (BRUE) (see below) with any of the following features:
  • Recurrent events without respiratory infection
  • Recurrent witnessed seizure like events
  • Required Cardiopulmonary Resuscitation (CPR)
  • Significantly abnormal chemistry including but not limited to electrolytes, bicarbonate or lactic acid, venous blood gas, glucose, or other tests that suggest an inborn error of metabolism
• Significantly abnormal electrocardiogram (ECG), including but not limited to possible channelopathies, arrhythmias, cardiomyopathies, myocarditis or structural heart disease
• Family history of:
  • Arrhythmia
  • BRUE in sibling
  • Developmental delay
  • Inborn error of metabolism or genetic disease
  • Long QT syndrome (LQTS)
  • Sudden unexplained death (including unexplained car accident or drowning) in first- or second-degree family members before age 35, and particularly as an infant

Brief Resolved Unexplained Event (BRUE) was previously known as Apparent Life Threatening Event (ALTE). In a practice guideline from the American Academy of Pediatrics (AAP), BRUE is defined as an event occurring in an infant younger than 1 year of age when the observer reports a sudden, brief (usually less than one minute), and now resolved episode of one or more of the following:

• Absent, decreased, or irregular breathing
• Altered level of responsiveness
• Cyanosis or pallor
• Marked change in tone (hyper- or hypotonia)

Trio Testing

The recommended option for testing when possible is testing of the child and both parents (trio testing). Trio testing increases the chance of finding a definitive diagnosis and reduces false-positive findings.

Trio testing is preferred whenever possible but should not delay testing of a critically ill patient when rapid testing is indicated. Testing of one available parent should be done if both are not immediately available and one or both parents can be done later if needed.

Genetics Nomenclature Update

The Human Genome Variation Society nomenclature is used to report information on variants found in DNA and serves as an international standard in DNA diagnostics. It is being implemented for genetic testing medical policy updates starting in 2017 (see Table PG1). The Society’s nomenclature is recommended by the Human Variome Project, the HUman Genome Organization, and by the Human Genome Variation Society itself.

The American College of Medical Genetics and Genomics and the Association for Molecular Pathology standards and guidelines for interpretation of sequence variants represent expert opinion from both organizations, in addition to the College of American Pathologists. These recommendations primarily apply to genetic tests used in clinical laboratories, including genotyping, single genes, panels, exomes, and genomes. Table PG2 shows the recommended standard terminology¾“pathogenic,” “likely pathogenic,” “uncertain significance,” “likely benign,” and “benign”¾to describe variants identified that cause Mendelian disorders.

Table PG1. Nomenclature to Report on Variants Found in DNA

Previous	Updated	Definition
Mutation	Disease-associated variant	Disease-associated change in the DNA sequence
	Variant	Change in the DNA sequence
	Familial variant	Disease-associated variant identified in a proband for use in subsequent targeted genetic testing in first-degree relatives

Table PG2. ACMG-AMP Standards and Guidelines for Variant Classification

Variant Classification	Definition
Likely pathogenic	Likely disease-causing change in the DNA sequence
Pathogenic	Disease-causing change in the DNA sequence
Variant of uncertain significance	Change in DNA sequence with uncertain effects on disease
Likely benign	Likely benign change in the DNA sequence
Benign	Benign change in the DNA sequence

ACMG: American College of Medical Genetics and Genomics; AMP: Association for Molecular Pathology.

Genetic Counseling

Experts recommend formal genetic counseling for patients who are at risk for inherited disorders and who wish to undergo genetic testing. Interpreting the results of genetic tests and understanding risk factors can be difficult for some patients; genetic counseling helps individuals understand the impact of genetic testing, including the possible effects the test results could have on the individual or their family members. It should be noted that genetic counseling may alter the utilization of genetic testing substantially and may reduce inappropriate testing; further, genetic counseling should be performed by an individual with experience and expertise in genetic medicine and genetic testing methods.


[RATIONALE: The policy was created in 2014 and has been updated regularly with searches of the MEDLINE database. The most recent literature update was performed through January 31, 2020. Evidence reviews assess whether a medical test is clinically useful. A useful test provides information to make a clinical management decision that improves the net health outcome. That is, the balance of benefits and harms is better when the test is used to manage the condition than when another test or no test is used to manage the condition.

The first step in assessing a medical test is to formulate the clinical context and purpose of the test. The test must be technically reliable, clinically valid, and clinically useful for that purpose. Evidence reviews assess the evidence on whether a test is clinically valid and clinically useful. Technical reliability is outside the scope of these reviews, and credible information on technical reliability is available from other sources.

Overview

This review was informed in part by a TEC Special Report (2013) on exome sequencing for patients with suspected genetic disorders.^3,

In 2018, Smith et al reported a scoping review of genome and exome sequencing as a diagnostic tool for pediatric patients. ^4, The authors identified 171 publications) although 131 were case reports. They concluded that diagnostic yield was the only consistently reported outcome. The median diagnostic yield in publications including more than single case reports was 33% but varied by broad clinical categories and test type.

The following sections review evidence by test type (WES and WGS), broad type of disorder and care setting (intensive care vs. not intensive care).

Whole Exome Sequencing for Children with Multiple Congenital Anomalies or a Neurodevelopmental Disorder of Unknown Etiology Following Standard Workup; Patients who are not Critically Ill
Clinical Context and Test Purpose

The purpose of whole exome sequencing (WES) in children who have multiple unexplained congenital anomalies or a neurodevelopmental disorder of unknown etiology following standard workup is to establish a molecular diagnosis. The criteria under which diagnostic testing for a genetic or heritable disorder may be considered clinically useful are as follows:

• A definitive diagnosis cannot be made based on history, physical examination, pedigree analysis, and/or standard diagnostic studies or tests;
• The clinical utility of a diagnosis has been established (eg, by demonstrating that a definitive diagnosis will lead to changes in clinical management of the condition, changes in surveillance, or changes in reproductive decision making, and these changes will lead to improved health outcomes); and
• Establishing the diagnosis by genetic testing will end the clinical workup for other disorders.

The following PICO was used to select literature to inform this review.

Patients

The relevant population of interest is children presenting with multiple unexplained congenital anomalies or a neurodevelopmental disorder that are suspected to have a genetic basis but are not explained by standard clinical workup.

Intervention

The relevant intervention of interest is WES with trio testing when possible.

Comparators

The following practice is currently being used to diagnose multiple unexplained congenital anomalies or a neurodevelopmental disorder: standard clinical workup without WES.

A standard clinical workup for an individual with a suspected genetic condition varies by patient phenotype but generally involves a thorough history, physical exam (including dysmorphology and neurodevelopmental assessment, if applicable), routine laboratory testing, and imaging. If the results suggest a specific genetic syndrome, then established diagnostic methods relevant for that syndrome would be used.

Outcomes

There is no reference standard for the diagnosis of patients who have exhausted alternative testing strategies, therefore diagnostic yield will be the clinical validity outcome of interest.

The health outcomes of interest are reduction in morbidity due to appropriate treatment and surveillance, the end of the diagnostic odyssey, and effects on reproductive planning for parents and potentially the affected patient.

False-positive test results can lead to misdiagnosis and inappropriate clinical management. False-negative test results can lead to a lack of a genetic diagnosis and continuation of the diagnostic odyssey.

Study Selection Criteria

For the evaluation of clinical validity of WES, studies that met the following eligibility criteria were considered:

• Reported on the diagnostic yield or performance characteristics such as sensitivity and specificity of WES;
• Patient/sample clinical characteristics were described; children with congenital abnormalities or neurodevelopmental disorders were included;
• Patient/sample selection criteria were described;
• Included at least 20 patients.

Assessment of technical reliability focuses on specific tests and operators and requires review of unpublished and often proprietary information. Review of specific tests, operators, and unpublished data are outside the scope of this policy and alternative sources exist. This policy focuses on the clinical validity and clinical utility.

Clinically Valid

A test must detect the presence or absence of a condition, the risk of developing a condition in the future, or treatment response (beneficial or adverse).

A number of studies have reported on the use of WES in clinical practice (see Table 1). Typically, the populations included in these studies have had suspected rare genetic disorders, although the specific populations vary.

Series have been reported with as many as 2000 patients. The most common reason for referral to a tertiary care center was an unexplained neurodevelopmental disorder. Many patients had been through standard clinical workup and testing without identification of a genetic variant to explain their condition. Diagnostic yield in these studies, defined as the proportion of tested patients with clinically relevant genomic abnormalities, ranged from 25% to 48%. Because there is no reference standard for the diagnosis of patients who have exhausted alternative testing strategies, clinical confirmation may be the only method for determining false-positive and false-negative rates. No reports were identified of incorrect diagnoses, and how often they might occur is unclear.

When used as a first-line test in infants with multiple congenital abnormalities and dysmorphic features, diagnostic yield may be as high as 58%. Testing parent-child trios has been reported to increase diagnostic yield, to identify an inherited variant from an unaffected parent and be considered benign, or to identify a de novo variant not present in an unaffected parent. First-line trio testing for children with complex neurologic disorders was shown to increase the diagnostic yield (29%, plus a possible diagnostic finding in 27%) compared with a standard clinical pathway (7%) performed in parallel in the same patients.^5,

Table 1. Diagnostic Yields of Whole Exome Sequencing for Congenital Anomalies or a Neurodevelopmental Disorder

Study	Patient Population	N	Design	Yield, n (%)	Additional Information
Cordoba et al (2018)6,	Patients suspected of having a neurogenetic condition: typical findings of known neurogenetic diseases and/or hints of monogenic etiology such as familial aggregation or chronic and progressive courseMean age was 23 yrs	40	Prospective Consecutive patients selected from a Neurogenetic Clinic of a tertiary Hospital in ArgentinaUnclear how many were trio testing	16 (40)	Results led to altered treatment in 14 patients
Ewans et al (2018)7,	Patients from families with a distinctive phenotype likely to have a monogenic etiology with a family structure consistent with Mendelian inheritance. Prior diagnostic testing had all been negative.. The majority of disorders were intellectual disability or neurological (62%) but 13% were skeletal and 11% were hematologicalTwo-thirds pediatric	37 families	54 individuals from 37 families recruited from clinical genetics units in NewSouth Wales from 2013 to 2014. Proband plus family members(s) underwent WES.	11 (30)	Reanalysis at 12 mos improved diagnostic success from 30 to 41%
Powis et al (2018) 8,	Neonates (birth to 1 mo of age). The majority had multiple congenital anomalies or dysmorphic features.	66	Trio or singleton WES6 infants received rapid WES	Overall: 25 (38)rapid WES: 3 (50)	VUS noted in 6 patients
Wright et al (2018)9,, re-analysisWright et al (2015)10,, original analysis	Children with severe undiagnosed NDDs and/or congenital anomalies, abnormal growth parameters, dysmorphic features, and unusual behavioral phenotypes	1133	Consecutive family trios from U.K.-wide patient recruitment network	454 (40), re-analysis 311 (27), original analysis	Wright et al (2018) is reanalysis of existing data from earlier Wright et al (2015) publication from DDD study using improved variant calling methodologies, novel variant detection algorithms, updated variant annotation, evidence-based filtering strategies, and newly discovered disease-associated genes
Nambot et al (2018)11,	Children with congenital anomalies and intellectual disability with negative prior diagnostic workup	461	Consecutive cases meeting criteria referred to specialty clinic in France	31%	Initial yield in y 1: 22%, reanalysis led to increase yield
Tsuchida et al (2018)12,	Children with epilepsy (»63% with early-onset epileptic encephalopathies) with no causative SNV in known epilepsy-associated genes	168	Consecutive unsolved cases referred to a single-center	18 (11)	Performed WES with CNV detection tools
Evers et al (2017)13,	Children with undiagnosed NDDs (63%), neurometabolic disorders, and dystonias	72	Prospective study, referral and selection unclear	36% in NDD 43% in neurometabolic disorders 25% in dystonias	Results reported to be important for family planning, used for a prenatal diagnostic procedure in 4 cases, management changes reported in 8 cases; surveillance for other disease-associated complications initiated in 6 cases
Vissers et al (2017)5,	Children with complex neurologic disorders of suspected genetic origin	150	Prospective comparative study at a tertiary center	44 (29) conclusive 41 (27) possible	First-line WES had 29% yield vs. 7% yield for standard diagnostic workupb
Nolan and Carlson (2016)14,	Children with unexplained NDDs	50	Pediatric neurology clinic	41 (48)	Changed medication, systemic investigation, and family planning
Allen et al (2016)15,	Patients with unexplained early-onset epileptic encephalopathy	50 (95% <1 y)	Single-center	11 (22)	2 VUS for follow-up, 11 variants identified as de novo
Stark et al (2016)16,	Infants (≤2 y) with suspected monogenic disorders with multiple congenital abnormalities and dysmorphic features	80 overall;37 critically ill	Prospective comparative study at a tertiary center	46 (58) overall;19 (51) in critically ill infants	First-line WES increased yield by 44%, changed clinical management and family planning.
Tarailo-Graovac et al (2016)17,	Intellectual developmental disorders and unexplained metabolic phenotypes (all ages)	41	Consecutively enrolled patients referred to a single-center	28 (68)	WES diagnosis affected the clinical treatment of 18 (44%) probands
Farwell et al (2015)18,	Unexplained neurologic disorders (65% pediatric)	500	WES laboratory	152 (30)	Trio (37.5% yield) vs. proband only (20.6% yield); 31 (7.5% de novo)
Yang et al (2014)19,	Suspected genetic disorder (88% neurologic or developmental)	2000 (45% <5 y; 42% 5-18 yrs; 12% adults)	Consecutive patients at single-center	504 (25)	Identification of novel variants. End of the diagnostic odyssey and change in management
Lee et al (2014)20,	Suspected rare Mendelian disorders (57% of children had developmental delay; 26% of adults had ataxia)	814 (49% <5 y; 15% 5-18 y; 36% adults)	Consecutive patients at single-center	213 (26)	Trio (31% yield) vs. proband only (22% yield)
Iglesias et al (2014)21,	Birth defects (24%); developmental delay (25%); seizures (32%)	115 (79% children)	Single-center tertiary clinic	37 (32)	Discontinuation of planned testing, changed medical management, and family planning
Soden et al (2014)22,	Children with unexplained NDDs	119 (100 families)	Single-center databasea	53 (45)	Change in clinical care or impression in 49% of families
Srivastava et al (2014)23,	Children with unexplained NDDs	78	Pediatric neurogenetics clinic	32 (41)	Change in medical management, prognostication, and family planning
Yang et al (2013)24,	Suspected genetic disorder (80% neurologic)	250 (1% fetus; 50% <5 y; 38% 5-18 yrs; 11% adults)	Consecutive patients at single-center	62 (25)	Identification of atypical phenotypes of known genetic diseases and blended phenotypes

CNV: copy number variant; DDD: Deciphering Developmental Disorders; NDD: neurodevelopmental disorder; SNV: single nucleotide variants; VUS: variant of uncertain significance; WES: whole exome sequencing.
^a Included both WES and whole genome sequencing.
^b Standard diagnostic workup included an average of 23.3 physician-patient contacts, imaging studies, muscle biopsies or lumbar punctures, other laboratory tests, and an average of 5.4 sequential gene by gene tests.
Clinically Useful

A test is clinically useful if the use of the results informs management decisions that improve the net health outcome of care. The net health outcome can be improved if patients receive correct therapy, or more effective therapy, or avoid unnecessary therapy, or avoid unnecessary testing.

Direct Evidence

Direct evidence of clinical utility is provided by studies that have compared health outcomes for patients managed with and without the test. Because these are intervention studies, the preferred evidence would be from randomized controlled trials (RCTs).

No RCTs assessing the use of WES to diagnose multiple unexplained congenital anomalies or a neurodevelopmental disorder were identified.

Chain of Evidence

Indirect evidence on clinical utility rests on clinical validity. If the evidence is insufficient to demonstrate test performance, no inferences can be made about clinical utility.

Cohort studies following children from presentation to outcomes have not been reported. There are considerable challenges conducting studies of sufficient size given the underlying genetic heterogeneity, and including follow-up adequate to observe final health outcomes. Studies addressing clinical utility have reported mainly diagnostic yield and management changes. Thus, it is difficult to quantify lower or upper bounds for any potential improvement in the net health outcome owing in part to the heterogeneity of disorders, rarity, and outcome importance that may differ according to identified pathogenic variants. Actionable items following testing in the reviewed studies (see Table 2) included family planning, change in management, change or avoidance of additional testing, surveillance for associated morbidities, prognosis, and ending the diagnostic odyssey.

The evidence reviewed here reflects the accompanying uncertainty, but supports a perspective that identifying a pathogenic variant can (1) impact the search for a diagnosis, (2) inform follow-up that can benefit a child by reducing morbidity and rarely potential mortality, and (3) affect reproductive planning for parents and later potentially the affected child. When recurrence risk can be estimated for an identified variant (eg, by including parent testing), future reproductive decisions can be affected. Early use of WES can reduce the time to diagnosis and reduce the financial and psychological burdens associated with prolonged investigation.

Section Summary: Whole Exome Sequencing for Children with Multiple Congenital Anomalies or a Neurodevelopmental Disorder of Unknown Etiology Following Standard Workup

The evidence on WES in children who have multiple congenital anomalies or a developmental disorder with a suspected genetic etiology of unknown etiology following standard workup includes case series. These series have reported diagnostic yields of WES ranging from 22% to 58%, depending on the individual’s age, phenotype, and previous workup. Comparative studies have reported an increase in diagnostic yield compared with standard testing strategies. Thus, for individuals who have a suspected genetic etiology but for whom the specific genetic alteration is unclear or unidentified by standard clinical workup, WES may return a likely pathogenic variant. A genetic diagnosis for these patients is reported to change management, including medication changes, discontinuation of or additional testing, ending the diagnostic odyssey, and family planning.

Whole Exome Sequencing for Children with a Suspected Genetic Disorder other than Multiple Congenital Anomalies or a Neurodevelopmental Disorder of Unknown Etiology Following Standard Workup; Patients who are not Critically Ill
Clinical Context and Test Purpose

Most of the literature on WES is on neurodevelopmental disorders in children; however, other potential indications for WES have been reported (see Table 3). These include limb-girdle muscular dystrophy, inherited retinal disease, and other disorders including mitochondrial, endocrine, and immunologic disorders.

The purpose of WES in patients who have a suspected genetic disorder other than multiple unexplained congenital anomalies or a neurodevelopmental disorder of unknown etiology following standard workup is to establish a molecular diagnosis. The criteria under which diagnostic testing for a genetic or heritable disorder may be considered clinically useful are stated above.

The question addressed in this policy is: Does WES improve health outcomes when used for the diagnosis of a suspected genetic condition other than multiple congenital anomalies or a neurodevelopmental disorder of unknown etiology following standard workup?

The following PICO was used to select literature to inform this review.

Patients

The relevant population of interest is children presenting with a disorder other than multiple unexplained congenital anomalies or a neurodevelopmental disorder that is suspected to have a genetic basis but is not explained by standard clinical workup.

Intervention

The relevant intervention of interest is WES. Specific tests were described in the preceding section on WES.

Comparators

The following practice is currently being used to diagnose a suspected genetic disorder other than multiple unexplained congenital anomalies or a neurodevelopmental disorder: standard clinical workup without WES.

Standard clinical workup was described in a preceding section.

Outcomes

There is no reference standard for the diagnosis of patients who have exhausted alternative testing strategies, therefore diagnostic yield will be the clinical validity outcome of interest.

The health outcomes of interest are reduction in morbidity due to appropriate treatment and surveillance, the end of the diagnostic odyssey, and effects on reproductive planning for parents and potentially the affected patient.

Study Selection Criteria

For the evaluation of clinical validity of WES, studies that met the following eligibility criteria were considered:

• Reported on the diagnostic yield or performance characteristics such as sensitivity and specificity of WES;
• Patient/sample clinical characteristics were described;
• Patient/sample selection criteria were described;
• Included at least 20 patients.

Assessment of technical reliability focuses on specific tests and operators and requires review of unpublished and often proprietary information. Review of specific tests, operators, and unpublished data are outside the scope of this policy and alternative sources exist. This policy focuses on the clinical validity and clinical utility.

Clinically Valid

A test must detect the presence or absence of a condition, the risk of developing a condition in the future, or treatment response (beneficial or adverse).

Studies have assessed WES for a broad spectrum of disorders. The diagnostic yield in patient populations restricted to specific phenotypes ranges from 3% for colorectal cancer to 60% for unexplained limb-girdle muscular dystrophy (see Table 2). Some studies used a virtual gene panel that is restricted to genes associated with the phenotype, while others have examined the whole exome, either initially or sequentially. An advantage of WES over individual gene or gene panel testing is that the stored data allows reanalysis as new genes are linked to the patient phenotype. WES has also been reported to be beneficial in patients with atypical presentations.

Table 2. Diagnostic Yields of Whole Exome Sequencing for Conditions Other Than Multiple Congenital Anomalies or a Neurodevelopmental Disorder

Study	Patient Population	N	Design	Yield,n (%)	Additional Information
Hauer et al (2018)25,	Short stature in whom common nongenetic causes had been excluded	200 (mostly children)	Randomly selected from a consecutive series of patients referred for workup; trio testing performed	33 (17)	Standard diagnostic approach yield: 13.6% in original cohort of 565 WES results had possible impact on treatment or additional preventive measurements in 31 (16%) families
Rossi et al (2017)26,	Patients with autism spectrum disorder diagnosis or autistic features referred for WES	163	Selected from 1200 consecutive retrospective samples from commercial lab	42 (26)	66% of patients already had a clinician-reported autism diagnosis VUS in 12%
Walsh et al (2017)27,	Peripheral neuropathy in patients ranging from 2-68 y	23 children 27 adults	Prospective research study at tertiary pediatric and adult centers	19 (38)	Initial targeted analysis with virtual gene panel, followed by WES
Miller et al (2017)28,	Craniosynostosis in patients who tested negative on targeted genetic testing	40	Research study of referred patientsa	15 (38)	Altered management and reproductive decision making
Posey et al (2016)29,	Adults (overlap of 272 patients reported by Yang et al [2014]),19, includes neurodevelopmental and other phenotypes	486 (53% 18-30 y; 47% >30 y)	Review of lab findings in consecutive retrospective series of adults	85 (18)	Yield in patients 18-30 y (24%) vs. those >30 y (10.4%)
Ghaoui et al (2015)30,	Unexplained limb-girdle muscular dystrophy	60 families	Prospective study of patients identified from specimen bank	27 (60)	Trio (60% yield) vs. proband only (40% yield)
Valencia et al (2015)31,	Unexplained disorders: congenital anomalies (30%), neurologic (22%), mitochondrial (25%), endocrine (3%), immunodeficiencies (17%)	40 (<17 y)	Consecutive patients in a single-center	12 (30)	Altered management including genetic counseling and ending diagnostic odyssey VUS in 15 (38%) patients
Wortmann et al (2015)32,	Suspected mitochondrial disorder	109	Patients referred to a single-center	42 (39)	57% yield in patients with high suspicion of mitochondrial disorder
Neveling et al (2013)33,	Unexplained disorders: blindness, deafness, movement disorders, mitochondrial disorders, hereditary cancer	186	Outpatient genetic clinic; post hoc comparison with Sanger sequencing	3%-52%	WES increased yield vs. Sanger sequencing Highest yield for blindness and deafness

WES: whole exome sequencing; VUS: variant of uncertain significance.
^a Included both WES and whole genome sequencing.

The purpose of the limitations tables (see Tables 3 and 4) is to display notable limitations identified in each study. This information is synthesized as a summary of the body of evidence and provides the conclusions on the sufficiency of the evidence supporting the position statement.

Table 3. Relevance Limitations for Studies Assessing Whole Exome Sequencing for Conditions Other Than Multiple Congenital Anomalies or a Neurodevelopmental Disorder

Study	Populationa	Interventionb	Comparatorc	Outcomesd	Duration of Follow-Upe
Hauer et al (2018)25,
Rossi et al (2017)26,	4. Most patients had a clinical diagnosis; only 33% had testing for specific ASD genes before WES
Walsh et al (2017)27,		3. Proband testing only
Miller et al (2017)28,
Posey et al (2016)29,	3. Included highly heterogeneous diseases	3. Proband testing only
Ghaoui et al (2015)30,
Valencia et al (2015)31,	3. Included highly heterogeneous diseases	2. Unclear whether WES performed on parents
Wortmann et al (2015)32,		3. Proband testing only
Neveling et al (2013)33,	3. Included highly heterogeneous diseases	3. Proband testing only

The study limitations stated in this table are those notable in the current review; this is not a comprehensive limitations assessment.
ASD: autism spectrum disorder; WES: whole exome sequencing.

^a Population key: 1. Intended use population unclear; 2. Clinical context is unclear; 3. Study population is unclear; 4. Study population not representative of intended use.

^b Intervention key: 1. Classification thresholds not defined; 2. Version used unclear; 3. Not intervention of interest.

^c Comparator key: 1. Classification thresholds not defined; 2. Not compared to credible reference standard; 3. Not compared to other tests in use for same purpose.

^d Outcomes key: 1. Study does not directly assess a key health outcome; 2. Evidence chain or decision model not explicated; 3. Key clinical validity outcomes not reported (sensitivity, specificity, and predictive values); 4. Reclassification of diagnostic or risk categories not reported; 5. Adverse events of the test not described (excluding minor discomforts and inconvenience of venipuncture or noninvasive tests).

^e Follow-Up key: 1. Follow-up duration not sufficient with respect to natural history of disease (true-positives, true-negatives, false-positives, false-negatives cannot be determined).

Table 4. Study Design and Conduct Limitations for Studies Assessing Whole Exome Sequencing for Conditions Other Than Multiple Congenital Anomalies or a Neurodevelopmental Disorder

Study	Selectiona	Blindingb	Delivery of Testc	Selective Reportingd	Data Completenesse	Statisticalf
Hauer et al (2018)25,
Rossi et al (2017)26,
Walsh et al (2017)27,
Miller et al (2017)28,	2. Selection not random or consecutive
Posey et al (2016)29,
Ghaoui et al (2015)30,
Valencia et al (2015)31,
Wortmann et al (2015)32,	1,2. Unclear how patients were selected from those eligible
Neveling et al (2013)33,	1,2. Unclear how patients were selected from those referred

The study limitations stated in this table are those notable in the current review; this is not a comprehensive limitations assessment.
WES: whole exome sequencing.

^a Selection key: 1. Selection not described; 2. Selection not random or consecutive (ie, convenience).

^b Blinding key: 1. Not blinded to results of reference or other comparator tests.

^cTest Delivery key: 1. Timing of delivery of index or reference test not described; 2. Timing of index and comparator tests not same; 3. Procedure for interpreting tests not described; 4. Expertise of evaluators not described.

^d Selective Reporting key: 1. Not registered; 2. Evidence of selective reporting; 3. Evidence of selective publication.

^e Data Completeness key: 1. Inadequate description of indeterminate and missing samples; 2. High number of samples excluded; 3. High loss to follow-up or missing data.

^f Statistical key: 1. Confidence intervals and/or p values not reported; 2. Comparison with other tests not reported.

Clinically Useful

A test is clinically useful if the use of the results informs management decisions that improve the net health outcome of care. The net health outcome can be improved if patients receive correct therapy, or more effective therapy, or avoid unnecessary therapy, or avoid unnecessary testing.

Direct Evidence

Direct evidence of clinical utility is provided by studies that have compared health outcomes for patients managed with and without the test. Because these are intervention studies, the preferred evidence would be from RCTS.

No RCTs assessing the use of WES to diagnose a suspected genetic disorder other than multiple unexplained congenital anomalies or a neurodevelopmental disorder were identified.

Chain of Evidence

Indirect evidence on clinical utility rests on clinical validity. If the evidence is insufficient to demonstrate test performance, no inferences can be made about clinical utility.

A genetic diagnosis for an unexplained disorder can alter management in several ways: such a diagnosis may lead to including genetic counseling and ending the diagnostic odyssey and may affect reproductive decision making.

Because the clinical validity of WES for this indication has not been established, a chain of evidence cannot be constructed.

Section Summary: WES for a Suspected Genetic Disorder Other Than Multiple Congenital Anomalies or a Neurodevelopmental Disorder

There is an increasing number of reports assessing use of WES identify a molecular basis for disorders other than multiple congenital anomalies or neurodevelopmental disorders. The diagnostic yields in these studies ranged from 3% for colorectal cancer to 60% for trio (parents and child) analysis of limb-girdle muscular dystrophy. Some studies have reported on the use of a virtual gene panel with restricted analysis of disease-associated genes, and the authors noted that WES data allows reanalysis as new genes are linked to the patient phenotype. Overall, a limited number of patients have been studied for any specific disorder, and study of WES in these disorders is at an early stage with uncertainty about changes in patient management.

Whole Genome Sequencing for Children with Multiple Congenital Anomalies or a Neurodevelopmental Disorder of Unknown Etiology Following Standard Workup; Patients who are not Critically Ill

The purpose of whole genome sequencing (WGS) in patients with a suspected genetic disorder of unknown etiology following standard workup is to establish a molecular diagnosis from either the coding or noncoding regions of the genome. The criteria under which diagnostic testing for a genetic or heritable disorder may be considered clinically useful are stated above.

The question addressed in this policy is: Does WGS improve health outcomes when used for the diagnosis of patients with a suspected genetic disorder of unknown etiology following standard workup without WES or WGS?

The following PICO was used to select literature to inform this review.

Patients

The relevant population of interest is:

• Children who are not critically ill with multiple unexplained congenital anomalies or a neurodevelopmental disorder of unknown etiology following standard workup.

The relevant interventions being considered include:

• WGS with trio testing when possible

The median time for standard WGS is several weeks.

Note that this policy does not address the use of WGS for preimplantation genetic diagnosis or screening, prenatal (fetal) testing, or for testing of cancer cells.

Comparators

The following practice is currently being used to diagnose a suspected genetic disorder: standard clinical workup without WES or WGS.

Standard clinical workup was described in a preceding section.

Outcomes

Outcomes of interest are as described above for use of WES in patients with multiple congenital anomalies or a neurodevelopmental disorder.

Study Selection Criteria

For the evaluation of clinical validity of WGS, studies that met the following eligibility criteria were considered:

• Reported on the diagnostic yield or performance characteristics such as sensitivity and specificity of rapid WGS or WGS;
• Patient/sample clinical characteristics were described;
• Patient/sample selection criteria were described;
• Included at least 20 patients.

Assessment of technical reliability focuses on specific tests and operators and requires review of unpublished and often proprietary information. Review of specific tests, operators, and unpublished data are outside the scope of this policy and alternative sources exist. This policy focuses on the clinical validity and clinical utility.

Clinically Valid

A test must detect the presence or absence of a condition, the risk of developing a condition in the future, or treatment response (beneficial or adverse).

Studies have shown that WGS can detect more pathogenic variants than WES, due to an improvement in detecting copy number variants, insertions and deletions, intronic single-nucleotide variants, and exonic single-nucleotide variants in regions with poor coverage on WES. A majority of studies described methods for interpretation of WGS indicating that only pathogenic or likely pathogenic variants were included in the diagnostic yield and that VUS were not reported. In some studies, the genes examined were those previously associated with the phenotype, while other studies were research-based and conducted more exploratory analysis.^34, It has been noted that genomes sequenced with WGS are available for future review when new variants associated with clinical diseases are discovered.

The use of WGS has been studied in children who are not critically ill with multiple unexplained congenital anomalies or a neurodevelopmental disorder of unknown etiology following standard workup in several observational studies, both prospective and retrospective. Studies are described in Table 5. The diagnostic yield of WGS has been between 20% and 40%. Additional indirect evidence is available from studies reporting diagnostic yield of WES in a similar population as summarized above, and it is reasonable to expect that WGS is likely to result in similar or better diagnostic yield for pathogenic or likely pathogenic variants as compared with WES.

Table 5. Diagnostic Yields with Whole Genome Sequencing in Children who are not Critically Ill with Multiple Unexplained Congenital Anomalies or a Neurodevelopmental Disorder of Unknown Etiology Following Standard Workup

Study	Patient Population	N	Design	Yield,n (%)	Additional Information
Lionel et al (2018)34,	Well-characterized but genetically heterogeneous cohort of children <18 y that had undergone targeted gene sequencing Referral clinic: 44% metabolic, 23% ophthalmology, 15% Joint laxity/hypermobility	103	ProspectiveTrio WGS testing for patients recruited from pediatric nongenetic subspecialists	42 (41)	Compared with a 24% yield with standard diagnostic testing and a 25% increase in yield from WES Limited information on change in management
Costain et al (2018), re-analysis35, Stavropoulos et al (2016)36,, original analysis	Children (<18 y) with an undiagnosed congenital malformations and neurodevelopmental disorders Presentation: abnormalities of the nervous system (77%), skeletal system (68%), growth (44%), eye (34%), cardiovascular (32%) and musculature (27%)	64, re-analysis 100, original analysis	Prospective, consecutive Proband WGS was offered in parallel with clinicalCMA testing	7 (11), re-analysis 34 (34), original analysis	Costain (2018) is re-analysis of undiagnosed patients from Stavropoulos et al (2016) CMA plus targeted gene sequencing yield was 13%WGS yield highest for developmental delay 39% (22/57) and lowest (15%) for connective tissue disorders Change in management reported for some patients 7 incidental findings
Hiatt et al (2018) 37, re-analysisBowling et al (2017)38, original analysis	Children with developmental and/or intellectual delays of unknown etiology 81% had genetic testing prior to enrollment	Original analysis included 244 Re-analysis includes additional 123, for a total cohort of 494	Retrospective, selection method and criteria unclear Trio WGS in a referral center	54 (22)1, original analysis	Re-analysis:Re-analysis yielded pathogenic or likely pathogenic variants that were not initially reported in 23 patients Downgraded 3 'likely pathogenic' and 6 VUS Original analysis:Compared to 30% yield for WES1 Changes in management not reported 11% VUS in WGS
Gilissen et al (2014)39,	Children with severe intellectual disability who did not have a diagnosis after extensive genetic testing that included whole exome sequencing	50	Trio WGS testing including unaffected parents	201 (42)	Of 21 with positive diagnosis, 20 had de novo variants Changes in management not reported

VUS: variant of uncertain significance; WGS: whole genome sequencing; WES: whole exome sequencing; CMA: chromosomal microarray analysis.

¹ SNV/indel

Tables 6 and 7 display notable limitations identified in each study.

Table 6. Relevance Limitations for Studies of Whole Genome Sequencing

Study	Populationa	Interventionb	Comparatorc	Outcomesd	Duration of Follow-Upe
Lionel et al (2018)34,	3. Included highly heterogeneous diseases	3. Proband testing only
Costain et al (2018), re-analysis35,		3. Proband testing only
Bowling et al (2017)38,	4. 19% had no prescreening performed
Gilissen et al (2014)39,

The study limitations stated in this table are those notable in the current review; this is not a comprehensive limitations assessment.
WGS: whole genome sequencing.
^a Population key: 1. Intended use population unclear; 2. Clinical context is unclear; 3. Study population is unclear; 4. Study population not representative of intended use.
^bIntervention key: 1. Classification thresholds not defined; 2. Version used unclear; 3. Not intervention of interest.
^c Comparator key: 1. Classification thresholds not defined; 2. Not compared to credible reference standard; 3. Not compared to other tests in use for same purpose.
^d Outcomes key: 1. Study does not directly assess a key health outcome; 2. Evidence chain or decision model not explicated; 3. Key clinical validity outcomes not reported (sensitivity, specificity, and predictive values); 4. Reclassification of diagnostic or risk categories not reported; 5. Adverse events of the test not described (excluding minor discomforts and inconvenience of venipuncture or noninvasive tests).
^e Follow-Up key: 1. Follow-up duration not sufficient with respect to natural history of disease (true-positives, true-negatives, false-positives, false-negatives cannot be determined).

Table 7. Study Design and Conduct Limitations for Studies of Whole Genome Sequencing

Study	Selectiona	Blindingb	Delivery of Testc	Selective Reportingd	Data Completenesse	Statisticalf
Lionel et al (2018)34,	1,2. Unclear how patients were selected from those eligible
Costain et al (2018), re-analysis35,
Bowling et al (2017)38,	1,2. Unclear how patients were selected from those eligible
Gilissen et al (2014)39,

The study limitations stated in this table are those notable in the current review; this is not a comprehensive limitations assessment. WGS: whole genome sequencing.
^a Selection key: 1. Selection not described; 2. Selection not random or consecutive (ie, convenience).
^b Blinding key: 1. Not blinded to results of reference or other comparator tests.
^c Test Delivery key: 1. Timing of delivery of index or reference test not described; 2. Timing of index and comparator tests not same; 3. Procedure for interpreting tests not described; 4. Expertise of evaluators not described.
^d Selective Reporting key: 1. Not registered; 2. Evidence of selective reporting; 3. Evidence of selective publication.
^e Data Completeness key: 1. Inadequate description of indeterminate and missing samples; 2. High number of samples excluded; 3. High loss to follow-up or missing data.
^f Statistical key: 1. Confidence intervals and/or p values not reported; 2. Comparison with other tests not reported.

Clinically Useful

A test is clinically useful if the use of the results informs management decisions that improve the net health outcome of care. The net health outcome can be improved if patients receive correct therapy, or more effective therapy, or avoid unnecessary therapy, or avoid unnecessary testing.

Direct Evidence

Direct evidence of clinical utility is provided by studies that have compared health outcomes for patients managed with and without the test. Because these are intervention studies, the preferred evidence would be from RCTs.

No RCTs assessing the use of WGS to diagnose multiple unexplained congenital anomalies or a neurodevelopmental disorder outside of critical care were identified.

Chain of Evidence

Indirect evidence on clinical utility rests on clinical validity. If the evidence is insufficient to demonstrate test performance, no inferences can be made about clinical utility.

Clinical validity is established based on the meaningful diagnostic yield associated with WGS when a genetic etiology is uncertain after standard workup. Studies onWGS report changes in management that would improve health outcomes. The effect of WGS results on health outcomes are the same as those with WES, including avoidance of invasive procedures, medication changes to reduce morbidity, discontinuation of or additional testing and initiation of palliative care or reproductive planning.

Section Summary: Whole Genome Sequencing for Children with Multiple Congenital Anomalies or a Neurodevelopmental Disorder of Unknown Etiology Following Standard Workup; Patients who are not Critically Ill

WGS has been studied in non-critically ill children with congenital abnormalities and development delays of unknown etiology following standard workup. The diagnostic yield for WGS has been reported between 20% and 40%. Additional indirect evidence is available from studies reporting diagnostic yield and change in management results of WES in a similar population, and WGS may result in similar or better diagnostic yield for pathogenic or likely pathogenic variants compared with WES although few direct comparisons are available.

Whole Genome Sequencing for a Suspected Genetic Disorder Other Than Multiple Congenital Anomalies or a Neurodevelopmental Disorder; Patients who are not Critically Ill

The purpose of WGS in patients with a suspected genetic disorder of unknown etiology following standard workup is to establish a molecular diagnosis from either the coding or noncoding regions of the genome. The criteria under which diagnostic testing for a genetic or heritable disorder may be considered clinically useful are stated above.

The question addressed in this policy is: Does WGS improve health outcomes when used for the diagnosis of patients with a suspected genetic disorder of unknown etiology following standard workup without WES or WGS?

The following PICO was used to select literature to inform this review.

Patients

The relevant population of interest is:

• Children with a suspected genetic disorder other than multiple unexplained congenital anomalies or a neurodevelopmental disorder of unknown etiology following standard workup.

The relevant interventions being considered include:

• WGS with trio testing when possible

The median time for standard WGS is several weeks.

Note that this policy does not address the use of WGS for preimplantation genetic diagnosis or screening, prenatal (fetal) testing, or for testing of cancer cells.

Comparators

The following practice is currently being used to diagnose a suspected genetic disorder: standard clinical workup without WES or WGS.

Standard clinical workup was described in a preceding section.

Outcomes

Outcomes of interest are as described above for use of WES in patients with multiple congenital anomalies or a neurodevelopmental disorder.

Study Selection Criteria

For the evaluation of clinical validity of WGS, studies that met the following eligibility criteria were considered:

• Reported on the diagnostic yield or performance characteristics such as sensitivity and specificity of rapid WGS or WGS;
• Patient/sample clinical characteristics were described;
• Patient/sample selection criteria were described;
• Included at least 20 patients.

Assessment of technical reliability focuses on specific tests and operators and requires review of unpublished and often proprietary information. Review of specific tests, operators, and unpublished data are outside the scope of this policy and alternative sources exist. This policy focuses on the clinical validity and clinical utility.

Clinically Valid

A test must detect the presence or absence of a condition, the risk of developing a condition in the future, or treatment response (beneficial or adverse).

The use of WGS has been studied in children with a suspected genetic disorder other than multiple unexplained congenital anomalies or a neurodevelopmental disorder in several observational studies, both prospective and retrospective. Studies are described in Table 8. The diagnostic yield of WGS has been between 9% and 55%. However, these studies include mixed indications with heterogeneous populations and include little information about associated changes in management following genetic diagnosis.

Table 8. Diagnostic Yields with Whole Genome Sequencing in Children with a Suspected Genetic Disorder other than Multiple Unexplained Congenital Anomalies or a Neurodevelopmental Disorder of Unexplained Etiology Following Standard Workup

Study	Patient Population	N	Design	Yield,n (%)	Additional Information
Thiffault et al (2019)40,	Patients with suspected genetic disorders referred for genetic testing between 2015 and 2017. The majority had previous genetic testing without diagnosis.The mean age was 7 yrs.	80	Prospective. The majority underwent trio sequencing; WGS was performed for the proband and WES was done for both parents	19 (24)	2 partial gene deletions detected with WGS that would not be detectable with WES
Alfares et al (2018)41,	Undiagnosed patients (91% pediatric) who had a history of negative WES testing 70% Consanguinity	154 recruited; 108 included in analysis	Retrospective, selection method and criteria unclear	10 (9%)	Reported incremental yield of WGS in patients with negative CGH and WES
Carss et al (2017)42,	Unexplained inherited retinal disease; ages not specified	605	Retrospective NIHR-BioResource Rare Diseases Consortium	331 (55)	Compared with a detection rate of 50% with WES (n=117)
Ellingford et al (2016)43,	Unexplained inherited retinal disease; ages not specified	46	Prospective WGS in patients referred to a single-center	24 (52)	Estimated 29% increase in yield vs. targeted NGS
Taylor et al (2015)44,	Broad spectrum of suspected genetic disorders (Mendelian and immunological disorders)	217	Prospective, multicenter series Clinicians and researchers submitted potential candidates for WGS and selections were made by a scientific Steering Committee. Patients were eligible if known candidate genes and large chromosomal copy number changes had been excluded. Trio testing for a subset of 15 families.	46 (21)	34% yield in Mendelian disorders; 57% yield in trios
Yuen et al (2015)45,	Patients with diagnosed autism spectrum disorder	50	Prospective; unclear how patients were selected; quartet testing of extensively phenotyped families (parents and 2 ASD-affected siblings)	21 (42%)	12/20 had change in management; 1/20 had change in reproductive counseling

ASD: autism spectrum disorder;CGH: comparative genomic hybridization; NGS: next-generation sequencing; NIHR: National Institute for Health Research;WGS: whole genome sequencing; WES: whole exome sequencing;
¹ SNV/indel

Tables 9 and 10 display notable limitations identified in each study.

Table 9. Relevance Limitations for Studies of Whole Genome Sequencing

Study	Populationa	Interventionb	Comparatorc	Outcomesd	Duration of Follow-Upe
Thiffault et al (2019)40,	3. Included heterogeneous diseases
Alfares et al (2018)41,	3: Clinical characteristics not described4: 70% consanguinity	3. Appears to be proband testing only but not clear
Carss et al (2017)42,	4. 25% had no prescreening performed
Ellingford et al (2016)43,		3. Proband testing only
Taylor et al (2015)44,	3. Included highly heterogeneous diseases
Yuen et al (2015)45,	4: All patients had a clinical diagnosis		3: Results of standard diagnostic methods not discussed

The study limitations stated in this table are those notable in the current review; this is not a comprehensive limitations assessment.
WGS: whole genome sequencing.
^a Population key: 1. Intended use population unclear; 2. Clinical context is unclear; 3. Study population is unclear; 4. Study population not representative of intended use.
^bIntervention key: 1. Classification thresholds not defined; 2. Version used unclear; 3. Not intervention of interest.
^c Comparator key: 1. Classification thresholds not defined; 2. Not compared to credible reference standard; 3. Not compared to other tests in use for same purpose.
^d Outcomes key: 1. Study does not directly assess a key health outcome; 2. Evidence chain or decision model not explicated; 3. Key clinical validity outcomes not reported (sensitivity, specificity, and predictive values); 4. Reclassification of diagnostic or risk categories not reported; 5. Adverse events of the test not described (excluding minor discomforts and inconvenience of venipuncture or noninvasive tests).
^e Follow-Up key: 1. Follow-up duration not sufficient with respect to natural history of disease (true-positives, true-negatives, false-positives, false-negatives cannot be determined).

Table 10. Study Design and Conduct Limitations for Studies of Whole Genome Sequencing

Study	Selectiona	Blindingb	Delivery of Testc	Selective Reportingd	Data Completenesse	Statisticalf
Thiffault et al (2019)40,	1,2: Unclear how patients were selected from those eligible
Alfares et al (2018)41,	1,2: Unclear how patients were selected from those eligible
Carss et al (2017)42,
Ellingford et al (2016)43,
Taylor et al (2015)44,
Yuen et al (2015)45,	1,2. Unclear how patients were selected from those eligible

The study limitations stated in this table are those notable in the current review; this is not a comprehensive limitations assessment. WGS: whole genome sequencing.
^a Selection key: 1. Selection not described; 2. Selection not random or consecutive (ie, convenience).
^b Blinding key: 1. Not blinded to results of reference or other comparator tests.
^c Test Delivery key: 1. Timing of delivery of index or reference test not described; 2. Timing of index and comparator tests not same; 3. Procedure for interpreting tests not described; 4. Expertise of evaluators not described.
^d Selective Reporting key: 1. Not registered; 2. Evidence of selective reporting; 3. Evidence of selective publication.
^e Data Completeness key: 1. Inadequate description of indeterminate and missing samples; 2. High number of samples excluded; 3. High loss to follow-up or missing data.
^f Statistical key: 1. Confidence intervals and/or p values not reported; 2. Comparison with other tests not reported.

Clinically Useful

A test is clinically useful if the use of the results informs management decisions that improve the net health outcome of care. The net health outcome can be improved if patients receive correct therapy, or more effective therapy, or avoid unnecessary therapy, or avoid unnecessary testing.

Direct Evidence

Direct evidence of clinical utility is provided by studies that have compared health outcomes for patients managed with and without the test. Because these are intervention studies, the preferred evidence would be from RCTs.

No RCTs assessing the use of WGS to diagnose a suspected genetic disorder other than multiple unexplained congenital anomalies or a neurodevelopmental disorder were identified.

Chain of Evidence

Indirect evidence on clinical utility rests on clinical validity. If the evidence is insufficient to demonstrate test performance, no inferences can be made about clinical utility.

A genetic diagnosis for an unexplained disorder can alter management in several ways: such a diagnosis may lead to including genetic counseling and ending the diagnostic odyssey and may affect reproductive decision making.

Because the clinical validity of WGS for this indication has not been established, a chain of evidence cannot be constructed.

Section Summary: Whole Genome Sequencing for a Suspected Genetic Disorder Other Than Multiple Congenital Anomalies or a Neurodevelopmental Disorder; Patients who are not Critically Ill

WGS has also been studied in children with a suspected genetic disorder other than multiple unexplained congenital anomalies or a neurodevelopmental disorder of unknown etiology following standard workup. The diagnostic yield of WGS has been between 9% and 55%. However, these studies include mixed indications with heterogeneous populations and include little information about associated changes in management following genetic diagnosis.

Rapid Whole Exome or Genome Sequencing in Critically Ill Infants or Children

The purpose of rapid whole exome sequencing (rWES) or rapid whole genome sequencing (rWGS) in critically ill patients with a suspected genetic disorder of unknown etiology is to establish a molecular diagnosis from either the coding or noncoding regions of the genome. The criteria under which diagnostic testing for a genetic or heritable disorder may be considered clinically useful are stated above.

The most common cause of death in neonates in the United States is genetic disorders. Currently, critically ill neonates with suspected genetic diseases are frequently discharged or deceased without a diagnosis. There are thousands of rare genetic disorders. The presentation of many of these disorders in neonates may be nonspecific or differ from the presentation in older patients and the disorder may produce secondary involvement of other systems due to the fragility of the neonate that obscures the primary pathology..

The neonatal intensive care unit (NICU) treatment of suspected genetic diseases is often empirical. Rapid diagnosis is critical for delivery of interventions that reduce morbidity and mortality in genetic diseases for which treatments exist. For many genetic diseases there is no effective treatment and timely diagnosis limits futile intensive care.

The question addressed in this policy is: Does rWES or rWGS improve health outcomes when used for the diagnosis ofcritically ill infants or children with a suspected genetic disorder of unknown etiology without WES or WGS?

The following PICO was used to select literature to inform this review.

Patients

The relevant population of interest is:

• Critically ill infants presenting with any of a variety of disorders and anomalies suspected to have a genetic basis but not explained by standard workup. For example, patients may have a phenotype that does not correspond with a specific disorder for which a genetic test targeting a specific gene is available. Specifically for critically ill infants, the population would also include patients for whom specific diagnostic tests available for that phenotype are not accessible within a reasonable timeframe. Petrikin (2018) identified the critically ill infants that are appropriate for rapid testing as meeting the following inclusion criteria: multiple congenital anomalies; abnormal laboratory test suggests a genetic disease or complex metabolic phenotype; abnormal response to standard therapy for a major underlying condition; significant hypotonia; or persistent seizures. Exclusion criteria included: an infection with normal response to therapy; isolated prematurity; isolated unconjugated hyperbilirubinemia; Hypoxic Ischemic Encephalopathy; confirmed genetic diagnosis explains illness; Isolated Transient Neonatal Tachypnea; or nonviable neonates.

The relevant interventions being considered include:

• rapid WES with trio testing when possible
• rapid WGS with trio testing when possible

The median time for standard WGS is several weeks. The median time-to-result for rWES or rWGS is approximately 5 days or less.

Note that this policy does not address the use of WES or WGS for preimplantation genetic diagnosis or screening, prenatal (fetal) testing, or for testing of cancer cells.

Comparators

The following practice is currently being used to diagnose a suspected genetic disorder: standard clinical workup without WES or WGS.

Standard clinical workup was described in a preceding section.

Outcomes

Outcomes of interest are as described above for use of WES in patients with multiple congenital anomalies or a neurodevelopmental disorder. For critically ill infants, rapid diagnosis is important therefore, in addition to the outcomes described in the previous section, time to diagnosis and time to discharge are also outcomes of interest.

Of course, mortality is a compelling outcome. However, many of the conditions are untreatable and diagnosis of an untreatable condition may lead to earlier transition to palliative care but may not prolong survival

Study Selection Criteria

For the evaluation of clinical validity of rWES or rWGS, studies that met the following eligibility criteria were considered:

• Reported on the diagnostic yield or performance characteristics such as sensitivity and specificity ofrWES or rWGS;
• Patient/sample clinical characteristics were described;
• Patient/sample selection criteria were described;
• Included at least 20 patients.

Assessment of technical reliability focuses on specific tests and operators and requires review of unpublished and often proprietary information. Review of specific tests, operators, and unpublished data are outside the scope of this policy and alternative sources exist. This policy focuses on the clinical validity and clinical utility.

Clinically Valid

A test must detect the presence or absence of a condition, the risk of developing a condition in the future, or treatment response (beneficial or adverse).

The use ofrWES and rWGS has been studied in critically ill children in several observational studies, both prospective and retrospective, and 1 RCT. Studies are described in Table 11. The RCT is discussed in more detail in the following ‘Clinically useful’ section. One study included only infants with cardiac defects and had a diagnostic yield of 6% with WGS. The remaining studies included phenotypically diverse but critically ill infants and had yields of between 30% and 60%.

Table 11. Diagnostic Yields With Rapid Whole Exome or Whole Genome Sequencing in Critically Ill Infants or Children With a Suspected Genetic Disorder of Unknown Etiology

Study	Patient Population	N	Design	Yield,n (%)	Additional Information
rapid WES
Wu et al (2019)46,	Pediatric patients (< 18 yr old) who were critically ill (PICU; 68%) and suspected of having a genetic disease or newborns who were suspected of having a serious genetic disease after newborn screening. The primary phenotypes were neurologic (35%), cardiac (22.5%), metabolic (15%), and immunological (15%). Ages ranged from 0.2 mos to 13 yrs.	40	Eligibility and selection from eligible patients were unclear. Trio testing was performed.	21 (52.5%)	Clinical management was changed for 81%: medications were recommended for 10 patients (48%), transplantation was advised for 5 (13%), and hospice care was suggested for 2 (5%)
Elliott et al (2019) 47,RAPIDOMICS	NICU neonates with unexplained seizures, metabolic disturbances (4%), neurological disorders (28%), multiple congenital anomalies (56%), or significant physiological disturbance for which diagnosis would likely change clinical management	25	Patient were evaluated for enrolment by a clinical geneticist and a neonatologist and approved by the research team. Trio analysis was performed.. All patients with suspected definitely, possibly, or partially causal variants generated by rWES underwent Sanger validation	15 (60%)	3 additional patients diagnosed with multi-gene panel testing or chromosomal microarray analysis 34 discrete and immediate medical decisions were identified for 15 of the 18 diagnosed patients
Gubbels et al (2019) 48,	Infants age <6 mos admitted to ICU admission with recent presentation of seizures (20%), hypotonia (40%), multiple congenital anomalies (72%), complex metabolic phenotype (32%) or other.	50	New ICU admissions were triaged daily by a patient selection algorithm developed by a multidisciplinary medical team (neonatology, genetics, and neurology). whole-blood samples were collected from probands and parents for trio-based exome sequencing.	29 (58%)	Results informed medical management changes in 24 of 29 patients. For 21 patients there was an acute impact on care: switch to comfort care, specialist referral, decision not to pursue further diagnostic testing
Stark et al (2018)49,	Acutely unwell pediatric patients with suspected monogenic disorders; 22% congenital abnormalities and dysmorphic features; 43% neurometabolic disorder; 35% other.	40	Recruited during clinical care by the clinical genetics services at the 2 tertiary pediatric hospitals; panel of study investigators reviewed eligibility; Used singleton rWES.	21 (53)	Clinical management changed in 12 of the 21 diagnosed patients (57%) Median time to report of 16 days (range, 9 to 109)
Meng et al (2017)50,	Critically ill infants within the first 100 days of life who were admitted to a tertiary care center between 2011 and 2017 and who were suspected to have genetic disorders. 208 infants were in NICU or PICU at time of sample.	278 overall; 208 in NICU or PICU; 63 received rWES	Referred to tertiary care; proband WES in 63%, trio WES in 14; critical trio rWES in 23%.	102 (37) overall;32 (51) for rWES	Molecular diagnoses directly affected medical management in 53 of 102 patients (52%) overall and in 23 of 32, 72% who received rWES
rapid WGS
French et al (2019)51,	Infants and children in NICU and PICU admitted between 2016 and 2018 with a possible single gene disorder. Exclusion criteria for infants included: admitted for short stay post-delivery surveillance, prematurity without additional features, babies with a clear antenatal or delivery history suggestive of a non-genetic cause and those babies where a genetic diagnosis was already made.Median age, NICU: 12 days, PICU: 24 mos	Overall: 195NICU: 106PICU: 61Pediatric neurology or clinical genetics department: 28	Trio WGS testing (when available) for prospective cohort of families recruited in NICU and PICU at a single site in the U.K.	Overall: 40 (21)NICU: 13PICU: 25	Diagnosis affected clinical management in more than 65% of cases (83% in neonates) including modification of treatments (13%) and care pathways (35% in PICU, 48% in NICU) and/or informing palliative care decisions. For at least 7cases, distinguishing between inherited and de novo variants informed reproductive decisions.VUS in 2 (1%)
Sanford et al (2019)52,	Children 4 mos to 18 yrs admitted to single-center PICU between 2016 and 2018 with suspicion for an underlying monogenic disease.Median age: 3 yrsPrimary reasons for admission: respiratory failure (18%), shock (16%), altered mental status (13%), and cardiac arrest (13%)	38	Trio rWGS testing (when available) in retrospective cohort study of, consecutive children who had rWGS after admission to a single-center tertiary hospital in the U.S.	17 (45)	VUS identified in all cases but were not reported to patients.Changes in ICU management in 4diagnosed children (24%), 3 patients had medication changes, 14 children had a subacute (non-ICU) change in the clinical management had implications for family screening
Hauser et al (2018)53,	Neonatal and pediatric patients born with a cardiac defect in whom the suspected genetic disorder had not been found using conventional genetic methods	34	TriorWGS testing for patients recruited from the NICU, PICU, or general inpatient pediatric ward of a single-center	2 (6)	VUS in 10 (26%)
Farnaes et al (2018)54,	Critically ill infants with undiagnosed, highly diverse phenotypes. Median age 62 days (range 1-301 days). Multiple congenital anomalies, 29%; Neurological, 21%; Hepatic, 19%	42	Retrospective; comparative (receivedrWGS and standard testing (mostly commonly CMA)Trio testing (when available) usingrWGS	18 (43)	10% were diagnosed by standard test Change in management after WGS in 13 of 18 (72%) patients with new genetic diagnosis Estimated that rWGS reduced length of stay by 124 days
Mestek-Boukhibar et al (2018)55,	Acutely ill infants with suspected underlying monogenetic disease. Median age 2.5 mos. Referred from Clinical genetics, 42%; Immunology 21%; intensive care, 13%	24	Prospective;rWGS trio testing in a tertiary children's hospital PICU and pediatric cardiac intensive care unit.	10 (42)	Change in management:In 3 patients
Van Diemen (2018)56,	Critically ill infants with undiagnosed illness excluding those with clear clinical diagnosis for which a single targeted test or gene panel was available; median age 28 days. Presentation: cardiomyopathy, 17%, severe seizure disorder, 22%, abnormal muscle tone, 26%, 13% liver failure	23	ProspectiverWGS Trio testing of patients from NICU/PICU; decision to include a patient was made by a multidisciplinary team; regular genetic and other investigations were performed in parallel	7 (30)	2 patients required additional sequencing data 1 incidental findingWGS led to the withdrawal of unsuccessful intensive care treatment in 5 of the 7 children diagnosed
Willig (2015)57,	Acutely ill infants with undiagnosed illness, suspected genetic etiology; 26% congenital anomalies; 20% neurological; 14% cardiac; 11% metabolic; Median age 26 days	35	Retrospective; enrolled in a research biorepository (nominated by treated physician, reviewed by panel of experts); hadrWGS and standard diagnostic tests to diagnose monogenic disorders of unknown cause; trio testing	20 (57)	had diagnoses with ‘strongly favorable effects on management’Palliative care initiated in 6 infantsof 20 WGS diagnoses were diseases that were not part of the differential at time of enrollment

CMA: chromosomal microarray analysis; ICU: intensive care unit; NICU: neonatal intensive care unit; PICU: pediatric intensive care unit; RAPIDOMICS: rapid genome-wide sequencing in a neonatal intensive care unit-successes and challenges; rWGS: rapid whole genome sequencing;
rWES: rapid whole exome sequencing;
WGS: whole genome sequencing; WES: whole exome sequencing; VUS: variant of uncertain significance.

Tables 12 and 13 display notable limitations identified in each study.

Table 12. Relevance Limitations for Studies of Rapid Whole Exome or Whole Genome Sequencing

Study	Populationa	Interventionb	Comparatorc	Outcomesd	Duration of Follow-Upe
Wu et al (2019)46,			3: Results of standard diagnostic methods not discussed
Elliott et al (2019) 47,
Gubbels et al (2019) 48,			3: Results of standard diagnostic methods not discussed
Stark et al (2018)49,	3. Included highly heterogeneous diseases	3. Proband testing only	3: Results of standard diagnostic methods not discussed
Meng et al (2017)50,		3: Not all patients received rapid testing	3: Chromosomal microarray analysis was completed for 85% but results not discussed
French et al (2019)51,			3: No comparator
Sanford et al (2019)52,			3: No comparator
Hauser et al (2018)53,			3: No comparator
Farnaes et al (2018)54,	3. Included highly heterogeneous diseases
Mestek-Boukhibar et al (2018)55,	3. Included highly heterogeneous diseases		3: No comparator
Van Diemen (2018)56,	3. Included highly heterogeneous diseases		3: Results of standard diagnostic methods not discussed; were available afterrWGS
Willig et al (2015)57,	3. Included highly heterogeneous diseases		3: Results of standard diagnostic methods not discussed
Gilissen et al (2014)39,

The study limitationsstated in this table are those notable in the current review; this is not a comprehensive limitations assessment.
rWES: rapid whole exome sequencing;rWGS: rapid whole genome sequencing.
^a Population key: 1. Intended use population unclear; 2. Clinical context is unclear; 3. Study population is unclear; 4. Study population not representative of intended use.
^b Intervention key: 1. Classification thresholds not defined; 2. Version used unclear; 3. Not intervention of interest.
^c Comparator key: 1. Classification thresholds not defined; 2. Not compared to credible reference standard; 3. Not compared to other tests in use for same purpose.
^d Outcomes key: 1. Study does not directly assess a key health outcome; 2. Evidence chain or decision model not explicated; 3. Key clinical validity outcomes not reported (sensitivity, specificity and predictive values); 4. Reclassification of diagnostic or risk categories not reported; 5. Adverse events of the test not described (excluding minor discomforts and inconvenience of venipuncture or noninvasive tests).
^e Follow-Up key: 1. Follow-up duration not sufficient with respect to natural history of disease (true-positives, true-negatives, false-positives, false-negatives cannot be determined).

Table 13. Study Design and Conduct Limitations for Studies of Rapid Whole Exome or Whole Genome Sequencing

Study	Selectiona	Blindingb	Delivery of Testc	Selective Reportingd	Data Completenesse	Statisticalf
Wu et al (2019)46,	1: Criteria for selection unclear
Elliott et al (2019)47,	2: Potential enrollees selected by a panel
Gubbels et al (2019)48,	2: New ICU admissions were triaged 1 team and enrollment criteria were applied by a panel
Stark et al (2018)49,	2: Eligibility determined by panel; a minimum of 2 clinical geneticists had to agree rWES was appropriate for a patient to be enrolled
Meng et al (2017)50,	1,2 Unclear if the patients were randomly or consecutively chosen from those who were eligible
French et al (2019)51,	1,2. Unclear how patients were selected from those eligible
Sanford et al (2019)52,
Hauser et al (2018)53,
Farnaes et al (2018)54,	2: Patients nominated by clinicians
Mestek-Boukhibar et al (2018)55,	2: Eligibility criteria established after first 10 enrolled.
Van Diemen (2018)56,	2: Decision to include a patient was made by a multidisciplinary team
Willig et al (2015)57,	2: Nominated by treated physician, reviewed by panel of experts for inclusion
Gilissen et al (2014)39,

The study limitationsstated in this table are those notable in the current review; this is not a comprehensive limitations assessment. rWES: rapid whole exome sequencing; rWGS: rapid whole genome sequencing.
^a Selection key: 1. Selection not described; 2. Selection not random or consecutive (ie, convenience).
^bBlinding key: 1. Not blinded to results of reference or other comparator tests.
^cTest Delivery key: 1. Timing of delivery of index or reference test not described; 2. Timing of index and comparator tests not same; 3. Procedure for interpreting tests not described; 4. Expertise of evaluators not described.
^d Selective Reporting key: 1. Not registered; 2. Evidence of selective reporting; 3. Evidence of selective publication.
^e Data Completeness key: 1. Inadequate description of indeterminate and missing samples; 2. High number of samples excluded; 3. High loss to follow-up or missing data.
^f Statistical key: 1. Confidence intervals and/or p values not reported; 2. Comparison with other tests not reported.

Clinically Useful

A test is clinically useful if the use of the results informs management decisions that improve the net health outcome of care. The net health outcome can be improved if patients receive correct therapy, or more effective therapy, or avoid unnecessary therapy, or avoid unnecessary testing.

Direct Evidence

Direct evidence of clinical utility is provided by studies that have compared health outcomes for patients managed with and without the test. Because these are intervention studies, the preferred evidence would be from RCTs.

Kingsmore et al (2019) reported early results of A Randomized, Blinded, Prospective Study of the Clinical Utility of Rapid Genomic Sequencing for Infants in the Acute-care Setting (NSIGHT2) trial^58,. NSIGHT2 was a randomized, controlled, blinded trial of the effectiveness of rapid whole-genome or -exome sequencing (rWGS or rWES, respectively) in seriously ill infants with diseases of unknown etiology primarily from the NICU, pediatric intensive care unit (PICU), and cardiovascular intensive care unit (CVICU) at a single hospital in San Diego. Details of the study are provided in Table 14and results are shown in Table 15. 95 infants were randomized to rWES and 94 to rWGS; in addition 24 infants who were gravely ill received ultrarapid whole-genome sequencing (urWGS). The initial Kingsmore et al (2019) publication included only the diagnostic outcomes. Other outcomes are expected in future publications. The registration for the study (NSIGHT2; NCT03211039) indicates that 1000 infants are expected to be enrolled; the Kingsmore et al (2019) publication does not specify whether enrollment is continuing. The diagnostic yield of rWGS and rWES was similar (19% vs. 20%, respectively), as was time (days) to result (median, 11 vs. 11 days). Although the urWGS was not part of the randomized portion of the study, the proportion diagnosed by urWGS was (11 of 24 [46%]) and time to result was a median of 4.6 days. The incremental diagnostic yield of reflexing to trio testing after inconclusive proband analysis was 0.7% (1 of 147).

Petrikin et al (2018) reported on the Prospective Randomized Trial of the Clinical Utility of Rapid Next Generation Sequencing in Acutely Ill Neonates(NSIGHT1; NCT02225522) RCT of rWGS to diagnose suspected genetic disorders in critically ill infants.^59, In brief,NSIGHT1 was an investigator-initiated (funded by National Human Genome Research Institute and Eunice Kennedy Shriver National Institute of Child Health and Human Development), blinded, and pragmatic trial comparing trio rWGS with standard genetic tests to standard genetic tests alone with a primary outcome of proportion of NICU/PICU infants receiving a genetic diagnosis within 28 days. Parents of patients and clinicians were unblinded after 10 days and compassionate cross-over to rWGS occurred in 5 control patients. The study was designed to enroll 500 patients in each group but was terminated early due to loss of equipoise on the part of study clinicians who began to regard standard tests alone as inferior to standard tests plus trio rWGS. Intention-to-treat analyses were reported, ie, crossovers were included in the group to which they were randomized. The trial required confirmatory testing of WGS results which lengthened the time to rWGS diagnosis by 7–10 days. Study characteristics are shown in Table 14 and results are shown in Table 15.

Table 14. Characteristics of RCTs of Rapid Whole Genome Sequencing in Critically Ill Infants

Study; Trial	Countries	Sites	Dates	Participants	Interventions1
					Active	Comparator
Kingsmore et al (2019)58,NSIGHT2 (NCT03211039)	U.S.	1	2017 to 2018	Acutely ill infants, primarily from the NICU, PICU, and CVICU; age <4 mos; time from admission or time from development of a feature suggestive of a genetic condition of <96 h; excluding infants in whom there was a very low likelihood that a genetic disease diagnosis would change management.	N=94, rWGS initially performed with proband sequences alone; if diagnosis was not made analysis was performed again, with parental samples	N=95, rWES initially performed with proband sequences alone; if diagnosis was not made analysis was performed again, with parental samples
Petrikin (2018)59,;NSIGHT1 (NCT02225522)	U.S.	1	2014 to 2016	Infants (<4m) in the NICU/PICU with illnesses of unknown etiology and: 1. genetic test order or genetic consult; 2. major structural congenital anomaly or at least 3 minor anomalies; 3. abnormal laboratory test suggesting genetic disease; or 4. abnormal response to standard therapy for a major underlying condition.Primary system involved:CA/musculoskeletal, 35%Neurological, 25%Cardiovascular,17%Respiratory, 6%	N=32 rWGS on specimens from both biological parents and affected infants simultaneously	N=33 Standard clinical testing for genetic disease etiologies was performed in infants based on physician clinical judgment, assisted by subspecialist recommendations

CA: congenital anomalies; CVICU: cardiovascular intensive care unit; NICU: neonatal intensive care unit ; NSIGHT1: Prospective Randomized Trial of the Clinical Utility of Rapid Next Generation Sequencing in Acutely Ill Neonates; NSIGHT2; A Randomized, Blinded, Prospective Study of the Clinical Utility of Rapid Genomic Sequencing for Infants in the Acute-care Setting; PICU: pediatric intensive care unit; RCT: randomized controlled trial; rWES: rapid whole exome sequencing; rWGS: rapid whole genome sequencing.

Table 15 Results of RCTs of Rapid Whole Genome Sequencing in Critically Ill Infants

Study	Diagnostic yield	Time to diagnosis	Age at at discharge	Changes in management	Mortality
Kingsmore et al (2019) 58,NSIGHT2	Genetic diagnosis, timing unspecified (%)	Proportion of results reported within 7 days (%)			Mortality at 28 days (%)
N	189	189	NR	NR	189
rWGS	20%	11%			3%
rWES	19%	4%			0%
Treatment effect (95% CI)	p=0.88	p=0.10			p=0.25
Petrikin et al (2018)59,;NSIGHT1	Genetic diagnosis within 28 days of enrollment (%)	Time (days) to diagnosis from enrollment, median	Age (days) at hospital discharge, mean	Change in management related to test results (%)	Mortality at 180 days (%)
N	65	65	65	65	65
rWGS	31%	13	66.3	41%1	13%
Standard testing	3%	107	68.5	24%1	12%
Treatment effect (95% CI)	p=0.003	p=0.002	p=0.91	p=0.11	NR

CI: confidence interval: RCT: randomized controlled trial; NR: not reported; NSIGHT1: Prospective Randomized Trial of the Clinical Utility of Rapid Next Generation Sequencing in Acutely Ill Neonates;
NSIGHT2; A Randomized, Blinded, Prospective Study of the Clinical Utility of Rapid Genomic Sequencing for Infants in the Acute-care Setting;
rWES: rapid whole exome sequencing; rWGS: rapid whole genome sequencing.
¹ Includes changes related to positive result (diagnosis); does not include impact of negative test results on management.

Tables 16 and 17 display notable limitations identified in each study.

Table 16. Relevance Limitations of RCTs of Rapid Whole Genome Sequencing in Critically Ill Infants

Study	Populationa	Interventionb	Comparatorc	Outcomesd	Follow-Upe
Kingsmore et al (2019) 58,NSIGHT2				1: Initial publicaion includes only diagnostic outcomes5: No discussion of clinically significant differences	1,2: Follow-up unclear
Petrikin et al (2018)59,

The study limitations stated in this table are those notable in the current review; this is not a comprehensive limitations assessment. RCT: randomized controlled trial; NSIGHT2; A Randomized, Blinded, Prospective Study of the Clinical Utility of Rapid Genomic Sequencing for Infants in the Acute-care Setting; rWGS: rapid whole genome sequencing.
^a Population key: 1. Intended use population unclear; 2. Clinical context is unclear; 3. Study population is unclear; 4. Study population not representative of intended use.
^b Intervention key: 1. Not clearly defined; 2. Version used unclear; 3. Delivery not similar intensity as comparator; 4.Not the intervention of interest.
^c Comparator key: 1. Not clearly defined; 2. Not standard or optimal; 3. Delivery not similar intensity as intervention; 4. Not delivered effectively.
^d Outcomes key: 1. Key health outcomes not addressed; 2. Physiologic measures, not validated surrogates; 3. No CONSORT reporting of harms; 4. Not establish and validated measurements; 5. Clinical significant difference not prespecified; 6. Clinical significant difference not supported.
^e Follow-Up key: 1. Not sufficient duration for benefit; 2. Not sufficient duration for harms.

Table 17. Study Design and Conduct Limitations of RCTs of Rapid Whole Genome Sequencing in Critically Ill Infants

Study	Allocationa	Blindingb	Selective Reportingd	Data Completenesse	Powerd	Statisticalf
Kingsmore et al (2019)58,NSIGHT2	3: Allocation concealment not described				1: Power calculations not reported; clinicaltrials.gov listing indicates that 1000 infants were expected but only 189 were reported in the initial report	4 :Only p-values reported; no treatment effects
Petrikin et al (2018)59,		1: Parents/clinicians unblinded at day 10 but analyses were intention-to-treat so crossovers would bias toward null			4: Trial stopped early, power for secondary outcomes will be very low	3, 4: Only p-values reported with no treatment effects or CIs

The study limitations stated in this table are those notable in the current review; this is not a comprehensive limitations assessment. CI: confidence interval; RCT: randomized controlled trial; NSIGHT2; A Randomized, Blinded, Prospective Study of the Clinical Utility of Rapid Genomic Sequencing for Infants in the Acute-care Setting; rWGS: rapid whole genome sequencing; rWGS: rapid whole genome sequencing.
^a Allocation key: 1. Participants not randomly allocated; 2. Allocation not concealed; 3. Allocation concealment unclear; 4. Inadequate control for selection bias.
^b Blinding key: 1. Not blinded to treatment assignment; 2. Not blinded outcome assessment; 3. Outcome assessed by treating physician.
^c Selective Reporting key: 1. Not registered; 2. Evidence of selective reporting; 3. Evidence of selective publication.
^d Data Completeness key: 1. High loss to follow-up or missing data; 2. Inadequate handling of missing data; 3. High number of crossovers; 4. Inadequate handling of crossovers; 5. Inappropriate exclusions; 6. Not intent to treat analysis (per protocol for noninferiority trials).
^e Power key: 1. Power calculations not reported; 2. Power not calculated for primary outcome; 3. Power not based on clinically important difference; 4: Target sample size not achieved.
^f Statistical key: 1. Analysis is not appropriate for outcome type: (a) continuous; (b) binary; (c) time to event; 2. Analysis is not appropriate for multiple observations per patient; 3. Confidence intervals and/or p values not reported; 4. Comparative treatment effects not calculated.

Chain of Evidence

Indirect evidence on clinical utility rests on clinical validity. If the evidence is insufficient to demonstrate test performance, no inferences can be made about clinical utility. Two case series with approximately 100 infants are available to estimate performance characteristics of rWES in the NICU setting.

Studies on rapid WGS report changes in management that would improve health outcomes.The effect of WGS results on health outcomes are the same as those with WES, including avoidance of invasive procedures, medication changes to reduce morbidity, discontinuation of or additional testing and initiation of palliative care or reproductive planning. A chain of evidence linking meaningful improvements in diagnostic yield and changes in management expected to improve health outcomes supports the clinical value of WGS for critically ill infants.

Section Summary: Rapid Whole Exome or Genome Sequencing in Critically Ill Infants or Children

For critically ill infants, disease may progress rapidly and genetic diagnoses must be made quickly. Results of rWES have been reported in two cases including approximately 100 infants and children. Due to the limited data available, diagnostic yield and management changes are not well characterized.

Rapid WGS has increased coverage compared to WES. One RCT comparingtriorWGS with standard genetic tests to diagnose suspected genetic disorders in critically ill infants funded by National Institutes of Health has been conducted. The study was terminated early due to loss of equipoise on the part of study clinicians who began to regard standard tests alone as inferior to standard tests plus trio rWGS. The rate of genetic diagnosis within 28 days of enrollment was higher for rWGS versus standard tests (31% vs. 3%; p=0.003) and the time to diagnosis was shorter (13 days vs. 107 days; p=0.002). The age at hospital discharge and mortality rates were similar in the 2 groups. However, many of the conditions are untreatable and diagnosis of an untreatable condition may lead to earlier transition to palliative care but may not prolong survival. A second RCT compared rWGS to rWES in seriously ill infants with diseases of unknown etiology from the NICU, PICU, and CVICU. Only the diagnostic outcomes have currently been reported. The diagnostic yield of rWGS and rWES was similar (19% vs. 20%, respectively), as was time (days) to result (median, 11 vs. 11 days).. Several retrospective and prospective observational studies with sample sizes ranging from about 20 to more than 275 and in total including more than 450 critically ill infants or children reporting on diagnostic yield for rWGS ior rWES included phenotypically diverse but critically ill infants and had yields of between 30% and 60% and reports of changes in management such as avoidance of invasive procedures, medication changes, discontinuation of or additional testing and initiation of palliative care.

Summary of Evidence

For individuals who are children who are not critically ill with multiple unexplained congenital anomalies or a neurodevelopmental disorder of unknown etiology following standard workup who receive WES with trio testing when possible, the evidence includes large case series and within-subject comparisons. Relevant outcomes are test validity, functional outcomes, changes in reproductive decision making, and resource utilization. Patients who have multiple congenital anomalies or a developmental disorder with a suspected genetic etiology, but whose specific genetic alteration is unclear or unidentified by standard clinical workup, may be left without a clinical diagnosis of their disorder, despite a lengthy diagnostic workup. For a substantial proportion of these patients, WES may return a likely pathogenic variant. Several large and smaller series have reported diagnostic yields of WES ranging from 25% to 60%, depending on the individual’s age, phenotype, and previous workup. One comparative study found a 44% increase in yield compared with standard testing strategies. Many of the studies have also reported changes in patient management, including medication changes, discontinuation of or additional testing, ending the diagnostic odyssey, and family planning. The evidence is sufficient to determine that the technology results in a meaningful improvement in the net health outcome.

For individuals who are children with a suspected genetic disorder other than multiple congenital anomalies or a neurodevelopmental disorder of unknown etiology following standard workup who receive WES with trio testing when possible, the evidence includes small case series and prospective research studies. Relevant outcomes are test validity, functional outcomes, changes in reproductive decision making, and resource utilization. There is an increasing number of reports evaluating the use of WES to identify a molecular basis for disorders other than multiple congenital anomalies or neurodevelopmental disorders. The diagnostic yields in these studies range from as low as 3% to 60%. Some studies have reported on the use of a virtual gene panel with restricted analysis of disease-associated genes, and WES data allows reanalysis as new genes are linked to the patient phenotype. Overall, a limited number of patients have been studied for any specific disorder, and clinical use of WES for these disorders is at an early stage with uncertainty about changes in patient management. The evidence is insufficient to determine the effects of the technology on health outcomes.

For individuals who are children who are not critically ill with multiple unexplained congenital anomalies or a neurodevelopmental disorder of unknown etiology following standard workup who receive WGS with trio testing when possible, the evidence includes case series. Relevant outcomes are test validity, functional outcomes, changes in reproductive decision making, and resource utilization. In studies of children with congenital abnormalities and development delays of unknown etiology following standard clinical workup, the yield of WGS has been between 20% and 40%. Additional indirect evidence is available from studies reporting diagnostic yield and change in management results of WES in a similar population. WGS may result in similar or better diagnostic yield for pathogenic or likely pathogenic variants as compared with WES but few direct comparisons are available. The evidence is insufficient to determine the effects of the technology on health outcomes..

For individuals who are children with a suspected genetic disorder other than multiple unexplained congenital anomalies or a neurodevelopmental disorder of unknown etiology following standard workup who receive who receive WGS with trio testing when possible, the evidence includes case series. Relevant outcomes are test validity, functional outcomes, changes in reproductive decision making, and resource utilization. WGS has also been studied in other genetic conditions with yield ranging from 9% to 55%. Overall, a limited number of patients have been studied for any specific disorder, and clinical use of WGS as well as information regarding meaningful changes in management for these disorders is at an early stage. The evidence is insufficient to determine the effects of the technology on health outcomes.

For individuals who are critically ill infants with a suspected genetic disorder of unknown etiology following standard workup who receive rapid WGS (rWGS) or rapid WES (rWES) with trio testing when possible, the evidence includes randomized controlled trials (RCTs) and case series. Relevant outcomes are test validity, functional outcomes, changes in reproductive decision making, and resource utilization. One RCT comparing rapid trio WGS (rWGS) with standard genetic tests to diagnose suspected genetic disorders in critically ill infants was terminated early due to loss of equipoise. The rate of genetic diagnosis within 28 days of enrollment was higher for rWGS versus standard tests (31% vs. 3%; p=0.003). Changes in management due to test results were reported in 41% vs. 21% (p=0.11) of rWGS vs control patients; however, 73% of control subjects received broad genetic tests (eg, next-generation sequencing panel testing, WES, or WGS) as part of standard testing. A second RCT compared rWGS to rWES in seriously ill infants with diseases of unknown etiology from the neonatal intensive care unit, pediatric intensive care unit, and cardiovascular intensive care unit. Only the diagnostic outcomes have currently been reported. The diagnostic yield of rWGS and rWES was similar (19% vs. 20%, respectively), as was time (days) to result (median, 11 vs. 11 days). Several retrospective and prospective studies including more than 800 critically ill infants and children in total have reported on diagnostic yield for rWGS or rWES including phenotypically diverse but critically ill infants and had yields of between 30% and 60% for pathogenic or likely pathogenic variants. Studies have also reported associated changes in patient management for patients receiving a diagnosis from rWGS or rWES, including avoidance of invasive procedures, medication changes to reduce morbidity, discontinuation of or additional testing and initiation of palliative care or reproductive planning. A chain of evidence linking meaningful improvements in diagnostic yield and changes in management expected to improve health outcomes supports the clinical value of rWGS or rWES. The evidence is sufficient to determine that the technology results in a meaningful improvement in the net health outcome.

SUPPLEMENTAL INFORMATION

Practice Guidelines and Position Statements

American College of Medical Genetics and Genomics

In 2012, the American College of Medical Genetics and Genomics (ACMG) has recommended that diagnostic testing with whole exome sequencing (WES) and whole genome sequencing (WGS) should be considered in the clinical diagnostic assessment of a phenotypically affected individual when^60,:

a. "The phenotype or family history data strongly implicate a genetic etiology, but the phenotype does not correspond with a specific disorder for which a genetic test targeting a specific gene is available on a clinical basis.
b. A patient presents with a defined genetic disorder that demonstrates a high degree of genetic heterogeneity, making WES or WGS analysis of multiple genes simultaneously a more practical approach.
c. A patient presents with a likely genetic disorder but specific genetic tests available for that phenotype have failed to arrive at a diagnosis.
d. A fetus with a likely genetic disorder in which specific genetic tests, including targeted sequencing tests, available for that phenotype have failed to arrive at a diagnosis."

WGS/WES may be considered in preconception carrier screening, using a strategy to focus on genetic variants known to be associated with significant phenotypes in homozygous or hemizygous progeny.

ACMG has also recommended that WGS and WES not be used at this time as an approach to prenatal screening or as a first-tier approach for newborn screening.

In 2014, ACMG guidelines on the clinical evaluation and etiologic diagnosis of hearing loss stated that for individuals with findings suggestive of a syndromic genetic etiology for hearing loss, “pretest genetic counseling should be provided, and, with patient’s informed consent, genetic testing, if available, should be ordered to confirm the diagnosis—this testing may include single-gene tests, hearing loss sequencing panels, WES, WGS, chromosome analysis, or microarray-based copy number analysis, depending on clinical findings.”^61,

In 2016, ACMG updated its recommendations on reporting incidental findings in WGS and WES testing.^62, ACMG determined that reporting some incidental findings would likely have medical benefit for the patients and families of patients undergoing clinical sequencing, recommending that, when a report is issued for clinically indicated exome and genome sequencing, a minimum list of conditions, genes, and variants should be routinely evaluated and reported to the ordering clinician. The 2016 update added 4 genes and removed 1 gene resulting in an updated secondary findings minimum list including 59 medically actionable genes recommended for return in clinical genomic sequencing.

American Academy of Neurology et al

In 2014, the American Academy of Neurology and American Association of Neuromuscular and Electrodiagnostic Medicine issued evidence-based guidelines on the diagnosis and treatment of limb-girdle and distal dystrophies, which made the following recommendations (see Table 18).^63,

Table 18. Guidelines on Limb-Girdle Muscular Dystrophy

Recommendation	LOE
Diagnosis
For patients with suspected muscular dystrophy, clinicians should use a clinical approach to guide genetic diagnosis based on the clinical phenotype, including the pattern of muscle involvement, inheritance pattern, age at onset, and associated manifestations (eg, early contractures, cardiac or respiratory involvement).	B
In patients with suspected muscular dystrophy in whom initial clinically directed genetic testing does not provide a diagnosis, clinicians may obtain genetic consultation or perform parallel sequencing of targeted exomes, whole-exome sequencing, whole-genome screening, or next-generation sequencing to identify the genetic abnormality.	C
Management of cardiac complications
Clinicians should refer newly diagnosed patients with (1) limb-girdle muscular dystrophy (LGMD)1A, LGMD1B, LGMD1D, LGMD1E, LGMD2C–K, LGMD2M–P, … or (2) muscular dystrophy without a specific genetic diagnosis for cardiology evaluation, including electrocardiogram (ECG) and structural evaluation (echocardiography or cardiac magnetic resonance imaging [MRI]), even if they are asymptomatic from a cardiac standpoint, to guide appropriate management.	B
If ECG or structural cardiac evaluation (eg, echocardiography) has abnormal results, or if the patient has episodes of syncope, near-syncope, or palpitations, clinicians should order rhythm evaluation (eg, Holter monitor or event monitor) to guide appropriate management.	B
Clinicians should refer muscular dystrophy patients with palpitations, symptomatic or asymptomatic tachycardia or arrhythmias, or signs and symptoms of cardiac failure for cardiology evaluation.	B
It is not obligatory for clinicians to refer patients with LGMD2A, LGMD2B, and LGMD2L for cardiac evaluation unless they develop overt cardiac signs or symptoms.	B
Management of pulmonary complications
Clinicians should order pulmonary function testing (spirometry and maximal inspiratory/expiratory force in the upright and, if normal, supine positions) or refer for pulmonary evaluation (to identify and treat respiratory insufficiency) in muscular dystrophy patients at the time of diagnosis, or if they develop pulmonary symptoms later in their course.	B
In patients with a known high risk of respiratory failure (eg, those with LGMD2I …), clinicians should obtain periodic pulmonary function testing (spirometry and maximal inspiratory/expiratory force in the upright position and, if normal, in the supine position) or evaluation by a pulmonologist to identify and treat respiratory insufficiency.	B
It is not obligatory for clinicians to refer patients with LGMD2B and LGMD2L for pulmonary evaluation unless they are symptomatic.	C
Clinicians should refer muscular dystrophy patients with excessive daytime somnolence, nonrestorative sleep (eg, frequent nocturnal arousals, morning headaches, excessive daytime fatigue), or respiratory insufficiency based on pulmonary function tests for pulmonary or sleep medicine consultation for consideration of noninvasive ventilation to improve quality of life.	B

LOE: level of evidence; LGMD: limb-girdle muscular dystrophy.

U.S. Preventive Services Task Force Recommendations

Not applicable.

Ongoing and Unpublished Clinical Trials

Some currently unpublished trials that might influence this review are listed in Table 19.

Table 19. Summary of Key Trials

NCT No.	Trial Name	Planned Enrollment	Completion Date
Ongoing
NCT02826694	North Carolina Newborn Exome Sequencing for Universal Screening	400	Jun 2019(ongoing)
NCT03211039	Prenatal Precision Medicine (NSIGHT2): A Randomized, Blinded, Prospective Study of the Clinical Utility of Rapid Genomic Sequencing for Infants in the Acute-care Setting	1000	Aug 2019
NCT03290469	NICUSeq: A Prospective Trial to Evaluate the Clinical Utility of Human Whole Genome Sequencing (WGS) Compared to Standard of Care in Acute Care Neonates and Infants	355	Jul 2019
NCT02699190	LeukoSEQ: Whole Genome Sequencing as a First-Line Diagnostic Tool for Leukodystrophies	450	Aug 2020
NCT03829176	Investigating the Feasibility and Implementation of Whole Genome Sequencing in Patients With Suspected Genetic Disorder	200	Jun 2020
NCT02422511	Genomic Sequencing for Childhood Risk and Newborn Illness (The BabySeq Project)	1440	Apr 2020
NCT03525431	Genomic Sequencing to Aid Diagnosis in Pediatric and Prenatal Practice: Examining Clinical Utility, Ethical Implications, Payer Coverage, and Data Integration in a Diverse Population	800	May 2021
NCT03548779	North Carolina Genomic Evaluation by Next-generation Exome Sequencing, 2	1700	May 2021
NCT03918707	Utility of Rapid Whole Genome Sequencing in the NICU: A Pilot Study	115	Jan 2022
NCT01736566	The MedSeq Project Pilot Study: Integrating Whole Genome Sequencing Into the Practice of Clinical Medicine	213	Apr 2022
NCT04170985	NeuroSeq: A Prospective Trial to Evaluate the Diagnostic Yield of Human Whole Genome Sequencing (WGS) Compared to Standard of Care in Adults With Suspected Genetic Neurological Disorders	100	Jun 2022
NCT04154891	Genome Sequencing Strategies for Genetics Diagnosis of Patients With Intellectual Disability (DEFIDIAG)	3825	Nov 2023
NCT03632239	The Genomic Ascertainment Cohort (TGAC)	1000	Dec 2028
NCT00410241	ClinSeq: A Large-Scale Medical Sequencing Clinical Research Pilot Study	2650	Not reported
NCT03385876	Rapid Whole Genome Sequencing (rWGS): Rapid Genomic Sequencing for Acutely Ill Patients and the Collection, Storage, Analysis, and Distribution of Biological Samples, Genomic and Clinical Data	100000	Dec 2050
Unpublished
NCT02380729	Mutation Exploration in Non-acquired, Genetic Disorders and Its Impact on Health Economy and Life Quality	200	Dec 2017 (completed)

NCT: national clinical trial.]
________________________________________________________________________________________

Horizon BCBSNJ Medical Policy Development Process:

This Horizon BCBSNJ Medical Policy (the “Medical Policy”) has been developed by Horizon BCBSNJ’s Medical Policy Committee (the “Committee”) consistent with generally accepted standards of medical practice, and reflects Horizon BCBSNJ’s view of the subject health care services, supplies or procedures, and in what circumstances they are deemed to be medically necessary or experimental/ investigational in nature. This Medical Policy also considers whether and to what degree the subject health care services, supplies or procedures are clinically appropriate, in terms of type, frequency, extent, site and duration and if they are considered effective for the illnesses, injuries or diseases discussed. Where relevant, this Medical Policy considers whether the subject health care services, supplies or procedures are being requested primarily for the convenience of the covered person or the health care provider. It may also consider whether the services, supplies or procedures are more costly than an alternative service or sequence of services, supplies or procedures that are at least as likely to produce equivalent therapeutic or diagnostic results as to the diagnosis or treatment of the relevant illness, injury or disease. In reaching its conclusion regarding what it considers to be the generally accepted standards of medical practice, the Committee reviews and considers the following: all credible scientific evidence published in peer-reviewed medical literature generally recognized by the relevant medical community, physician and health care provider specialty society recommendations, the views of physicians and health care providers practicing in relevant clinical areas (including, but not limited to, the prevailing opinion within the appropriate specialty) and any other relevant factor as determined by applicable State and Federal laws and regulations.

___________________________________________________________________________________________________________________________

Index:
Whole Exome and Whole Genome Sequencing for Diagnosis of Genetic Disorders
Whole Exome and Whole Genome Sequencing for Diagnosis of Patients with Suspected Genetic Disorders
Whole Exome Sequencing
Exome Sequencing
Whole Genome Sequencing
Genome Sequencing
TruGenome Undiagnosed Disease Test
TruGenome Predisposition Screen
TruGenome Technical Sequence Data

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3. Blue Cross and Blue Shield Association Technology Evaluation Center (TEC). Special Report: Exome Sequencing for Clinical Diagnosis of Patients with Suspected Genetic Disorders. TEC Assessments. 2013;Volume 28:Tab 3.

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22. Soden SE, Saunders CJ, Willig LK, et al. Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders. Sci Transl Med. Dec 3 2014;6(265):265ra168. PMID 25473036

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27. Walsh M, Bell KM, Chong B, et al. Diagnostic and cost utility of whole exome sequencing in peripheral neuropathy. Ann Clin Transl Neurol. May 2017;4(5):318-325. PMID 28491899

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29. Posey JE, Rosenfeld JA, James RA, et al. Molecular diagnostic experience of whole-exome sequencing in adult patients. Genet Med. Jul 2016;18(7):678-685. PMID 26633545

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31. Valencia CA, Husami A, Holle J, et al. Clinical impact and cost-effectiveness of whole exome sequencing as a diagnostic tool: a pediatric center's experience. Front Pediatr. Aug 2015;3:67. PMID 26284228

32. Wortmann SB, Koolen DA, Smeitink JA, et al. Whole exome sequencing of suspected mitochondrial patients in clinical practice.J Inherit Metab Dis. May 2015;38(3):437-443. PMID 25735936

33. Neveling K, Feenstra I, Gilissen C, et al. A post-hoc comparison of the utility of Sanger sequencing and exome sequencing for the diagnosis of heterogeneous diseases. Hum Mutat. Dec 2013;34(12):1721-1726. PMID 24123792

34. Lionel AC, Costain G, Monfared N, et al. Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test. Genet Med. Apr 2018;20(4):435-443. PMID 28771251

35. Costain G, Jobling R, Walker S, et al. Periodic reanalysis of whole-genome sequencing data enhances the diagnostic advantage over standard clinical genetic testing. Eur J Hum Genet. May 2018;26(5):740-744. PMID 29453418

36. Stavropoulos DJ, Merico D, Jobling R, et al. Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine. NPJ Genom Med. Jan 13 2016;1. PMID 28567303

37. Hiatt SM, Amaral MD, Bowling KM, et al. Systematic reanalysis of genomic data improves quality of variant interpretation. Clin. Genet. 2018 Jul;94(1). PMID 29652076

38. Bowling KM, Thompson ML, Amaral MD, et al. Genomic diagnosis for children with intellectual disability and/or developmental delay. Genome Med. May 30 2017;9(1):43. PMID 28554332

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41. Alfares A, Aloraini T, Subaie LA, et al. Whole-genome sequencing offers additional but limited clinical utility compared with reanalysis of whole-exome sequencing. Genet Med. Nov 2018;20(11):1328-1333. PMID 29565419

42. Carss KJ, Arno G, Erwood M, et al. Comprehensive rare variant analysis via whole-genome sequencing to determine the molecular pathology of inherited retinal disease. Am J Hum Genet. Jan 05 2017;100(1):75-90. PMID 28041643

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46. Wu ET, Hwu WL, Chien YH, et al. Critical Trio Exome Benefits In-Time Decision-Making for Pediatric Patients With Severe Illnesses. Pediatr Crit Care Med. 2019 Nov;20(11). PMID 31261230

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63. Narayanaswami P, Weiss M, Selcen D, et al. Evidence-based guideline summary: diagnosis and treatment of limb-girdle and distal dystrophies: report of the guideline development subcommittee of the American Academy of Neurology and the practice issues review panel of the American Association of Neuromuscular & Electrodiagnostic Medicine. Neurology. Oct 14 2014;83(16):1453-1463. PMID 25313375

Codes:
(The list of codes is not intended to be all-inclusive and is included below for informational purposes only. Inclusion or exclusion of a procedure, diagnosis, drug or device code(s) does not constitute or imply authorization, certification, approval, offer of coverage or guarantee of payment.)

CPT*

81415
81416
81417
81425
81426
81427
0036U