Coverage Policy Manual - Arkansas Blue Cross and Blue Shield

Genetic Test: Whole Exome and Whole Genome Sequencing

Description:

CLINICAL CONTEXT AND TEST PURPOSE

Whole exome sequencing (WES) is targeted sequencing of the subset of the human genome that contains functionally important sequences of protein-coding DNA, while whole genome sequencing (WGS) uses next-generation sequencing (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. (Dixon-Salazar, 2012). The search for a diagnosis may thus become a time-consuming and expensive process. 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 20,000 genes and 180,000 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 mutations. 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: 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 greater ability to detect large deletions or duplications in protein-coding regions compared to WES, but requires greater data analytics. Technical aspects of WES and WGS are evolving, including 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 develop standard terminology for describing sequence variants (Richards, 2015). Guidelines developed by this workgroup, published in 2015, describe criteria for classifying pathogenic and benign sequence variants based on types of data into 5 categories: pathogenic, likely pathogenic, uncertain significance, likely benign, and benign.

AVAILABLE WES AND WGS TESTING SERVICES

Several laboratories offer WES and WGS as a clinical service. Illumina offers 3 TruGenome tests: the TruGenome Undiagnosed Disease Test (indicated to find the underlying genetic cause of an undiagnosed rare genetic disease of single-gene etiology), TruGenome Predisposition Screen (indicated for healthy patients interested in learning about their carrier status and genetic predisposition toward adult-onset conditions), and the TruGenome Technical Sequence Data (WGS for labs and physicians who will make their own clinical interpretations). Ambry Genetics offers 2 WGS tests, the ExomeNext and ExomeNext-Rapid, which sequence both the nuclear and the mitochondrial genomes. GeneDx offers WES with its XomeDx™ test. Medical centers may also offer WES and WGS as a clinical service.

The following labs offer WES sequencing Ambry Genetics (Aliso Viejo, CA), GeneDx (Gaithersburg, MD), Baylor College of Medicine (Houston, TX), Illumina (San Diego, CA), University of California Los Angeles Health System, EdgeBio (Gaithersburg, MD), Children’s Mercy Hospitals and Clinics (Kansas City, MO) and Emory Genetics Laboratory (Atlanta, GA).

Policy/
Coverage:

EFFECTIVE APRIL 2017

Does Not Meet Primary Coverage Criteria Or Is Investigational For Contracts Without Primary Coverage Criteria

Whole exome and whole genome sequencing for all indications does not meet member benefit certificate primary coverage criteria that there be scientific evidence of effectiveness in improving health outcomes.

For members with contracts without primary coverage criteria, whole exome and whole genome sequencing is considered investigational for all indications. Investigational services are specific contract exclusions in most member benefit certificates of coverage.

EFFECTIVE PRIOR TO APRIL 2017

Whole exome sequencing for all indications does not meet member benefit certificate primary coverage criteria that there be scientific evidence of effectiveness in improving health outcomes.

For members with contracts without primary coverage criteria, Whole exome sequencing is considered investigational for all indications. Investigational services are specific contract exclusions in most member benefit certificates of coverage.

Rationale:

Analytic validity

Whole exome sequencing has not yet been well-standardized for the clinical laboratory and has not been fully characterized in publicly available documents with regard to the analytic validity for the various types of relevant mutations. The few existing professional guidelines give only high-level direction. Technical limitations include error rates due to uneven sequencing coverage and gaps in exon capture prior to sequencing, and the variability contributed by the different platforms and procedures used by different clinical laboratories offering exome sequencing as a clinical service is unknown.

Clinical utility

The clinical utility of exome sequencing lies in the influence of the results on medical decision-making and patient outcomes. There are several ways in which clinical utility can be demonstrated.

WES may detect additional mutations that are missed by other testing methods, thus leading to a definitive diagnosis.

If the establishment of a definitive diagnosis leads to management changes that improve outcomes, then clinical utility has been established.
If the establishment of a definitive diagnosis leads to avoidance of other tests that are unnecessary, then this is another example of clinical utility.

If WES is at least as accurate as other methods of sequencing, then an improvement in the efficiency of workup (diagnosis obtained more quickly and/or at less cost), then clinical utility has been established.

WES in characterizing Mendelian disorders

Typically, when a phenotype/history suggests a genetic etiology, microdeletions/duplications should be excluded by chromosomal microarray analysis and, if clinically appropriate, other possible disorders like inborn errors of metabolism should also be excluded. If these tests are negative, the potential uses of WES include facilitating the accurate diagnosis of individuals with a suspected monogenic (Mendelian) disorder that presents with an atypical presentation or multiple congenital anomalies, is difficult to confirm with clinical or laboratory criteria alone (e.g. when disease characteristics are shared among multiple disorders, leading to potentially overlapping differential diagnoses [clinical heterogeneity]), and when there is a long list of possible candidate genes (Bamshad, 2011).

An additional potential use of WES is when a clinical presentation is suggestive of a specific genetic condition, but targeted testing is negative or unavailable. In this situation, the yield of a definitive diagnosis can be used to evaluate the clinical utility of WES, also considering whether management changes occur that improve outcomes.

Currently there are no published studies that systematically examine potential outcomes of interest such as changes in medical management (including revision of initial diagnoses), and changes in reproductive decision-making after a diagnosis of a Mendelian disorder by WES. A small number of studies of patient series, and a larger number of very small series or family studies report anecdotal examples of medical management and reproductive decision-making outcomes of exome sequencing in patients who were not diagnosed by traditional methods. These studies show that over and above traditional molecular and conventional diagnostic testing, exome sequencing can lead to a diagnosis that influences patient care and/or reproductive decisions, but give no indication of the proportion of patients for which this is true. The publication of a large number of small diagnostic studies with positive results but few with negative results, raise the possibility of publication bias—the impact of which is unknown.

Summary

Whole exome sequencing (WES) using next-generation sequencing has been recently introduced as a laboratory-developed diagnostic clinical laboratory test. A potential major indication for use is molecular diagnosis of patients with a phenotype that is suspicious for a genetic disorder or for patients with known genetic disorders that have a large degree of genetic heterogeneity involving substantial gene complexity. Such patients may be left without a clinical diagnosis of their disorder despite a lengthy diagnostic work-up involving a variety of traditional molecular and other types of conventional diagnostic tests. For some of these patients, WES, after initial conventional testing has failed to make the diagnosis, may return a likely pathogenic variant.

However, at this time, there are many technical limitations to WES that prohibit its use in routine clinical care. The limited experience with WES on a population level leads to gaps in understanding and interpreting ancillary information and variants of uncertain significance. As a result, the risk/benefit ratio of WES testing is poorly defined.

Practice Guidelines and Position Statements

The American College of Medical Genetics (ACMG) states that diagnostic testing with WES (and whole genome sequencing [WGS]) should be considered In the clinical diagnostic assessment of a phenotypically affected individual when:

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.

The ACMG states that for screening purposes:

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 states that WGS/WES should not be used at this time as an approach to prenatal screening, or as a first-tier approach for newborn screening.

https://www.acmg.net/StaticContent/PPG/Clinical_Application_of_Genomic_Sequencing.pdf

In March 2013, an ACMG board finalized approval of their recommendations for reporting incidental findings in whole genome and whole exome sequencing (Green, 2013). A working group determined that reporting some incidental findings would likely have medical benefit for the patients and families of patients undergoing clinical sequencing and recommended 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. A full list of the specified conditions can be found at:

https://www.acmg.net/docs/ACMG_Releases_Highly- Anticipated_Recommendations_on_Incidental_Findings_in_Clinical_Exome_and_Genome_Sequencing.p df

2016 Update

A literature search conducted through February 2016 did not reveal any new information that would prompt a change in the coverage statement. The key identified literature is summarized below.

Analytic Validity

Whole Exome Sequencing

There is relatively little data specific to the analytic validity of whole exome sequencing (WES). The next-generation sequencing (NGS) techniques used for WES are generally expected to have high accuracy for mutation detection, NGS platforms differ in terms of the depth of sequence coverage, methods for base calling and read alignment, and other factors. These factors contribute to potential variability across the different platforms and procedures used by different clinical laboratories offering exome sequencing as a clinical service The American College of Medical Genetics has clinical laboratory standards for NGS, including WES (Rehm, 2013). The guidelines outline the documentation of test performance measures that should be evaluated for NGS platforms, and note that typical definitions of analytic sensitivity and specificity do not apply for NGS.

Depending on the platform and variant call method used, WES may not accurately detect large insertions and deletions, large copy number variants (CNVs), and structural chromosome rearrangements due to the short sequence read lengths (Rehm, 2013).

Whole Genome Sequencing

Whole genome sequencing (WGS) is subject to the same considerations related to potential variability in technical performance as WES.

With advances in sequencing capacity, novel sequence variants associated with genetic disorders are rapidly being described. Sequence variants detected on WES/WGS, or any form of NGS, must be classified on a spectrum from almost certainly pathogenic to almost certainly benign. In 2013, the ACMG, Association for Molecular Pathology, and College of American Pathologists convened a workgroup to develop standard terminology for describing sequence variants (Richards, 2015). Guidelines developed by this workgroup, published in 2015, describe criteria for classifying pathogenic and benign sequence variants based on a variety of population, computational and predictive, functional and data, segregation data into 5 categories: pathogenic, likely pathogenic, uncertain significance, likely benign, and benign.

WES/WGS for Identifying Novel Mutations

Since publication of the 2013 TEC Special Report, studies continue to demonstrate that WES can be used to identify novel genetic mutations in a range of clinical conditions. In particular, WES/WGS has been evaluated for disorders associated with significant genetic heterogeneity (Greenway, 2014; Jiang, 2013; Kim, 2013; Zhou, 2014).

WES/WGS in Clinical Practice

Several studies have reported on the use of WES and, less frequently, WGS in clinical practice. Typically the populations included in these studies are those with suspected rare genetic disorders, although the specific patient populations varu.

In 2015, Lee and colleagues reported on a large (n=814) single-center cohort of patients with undiagnosed, suspected genetic conditions who underwent WES (Lee, 2015). The investigators used a “trio-CES [clinical exome sequencing]” technique which involves sequencing of the proband and 2 family members, typically unaffected parents. For the first approximately 300 cases, all reported variants were confirmed by Sanger sequencing with more than 99% confirmation. After that, variants were evaluated with a QUAL score, a scaled probability of a variant existing at a given site, and only clinically significant mutations with a QUAL score lower than 500 were confirmed. Variants found were annotated to provide information about their effect on protein function, allele frequency in the general population, and prior evidence of disease causality and filtered to select likely pathogenic DNA variants. For variants in probands, with family member testing available, variants were categorized as de novo (usually heterozygous in the patient and potentially causing an autosomal dominant condition), homozygous, compound heterozygous, and inherited variants. Variants were evaluated in the context of a “primary gene list” which was determined based on phenotypic key words included in referring clinician notes. Of the 814 patients included, 520 patients (64%) were children, and 254 of those were younger than 5 years at testing. The most common clinical indication for testing was developmental delay in the entire population and in the childhood group (37% and 53%, respectively). In the adult group, ataxia was the most common indication for testing (26%). Overall, a molecular diagnosis with a causative variant in a well-established clinical gene was provided for 213/814 cases (26%; 95% CI 23 to 29%). Of the 264 variants reported in 213 cases, 188 were reported as “likely pathogenic” and 73 were reported as “pathogenic” variants..

In 2014, Yang and colleagues reported on a single-center observational study that included 2000 consecutive patients referred for clinical WES for a suspected genetic disorder (Yang, 2014). This report excluded 250 patients reported in an earlier publication. The majority of the samples were from pediatric patients, with 900 from children under 5 years (45.0%), 845 from children/adolescents aged 5 to 18 years (42.2%), 244 from adults (12.2%), and 11 fetal samples. The most common indications for testing were neurological disorders or developmental delay (87.8%). Molecular diagnoses were reported for 504 patients (25.2%, 95% CI 23.3% to 27.2%), with a total of 708 presumptive causative variants. Most of the identified disease-associated variants were novel (409/708; 57.8%). Overall, 95 medically-actionable incidental findings were reported in 92 patients (4.6%), most of which (n=59) were included in the American College of Medical Genetics list of 56 genes recommended to be disclosed to patients.

Tammimies and colleagues reported on the results of chromosomal microarray analysis (CMA) and WES in a sample of children with autism spectrum disorders (Tammimies, 2015). The patient cohort included 258 consecutively enrolled patients, stratified into three groups based on the presence of major congenital abnormalities and minor physical anomalies (n=168, 37, and 53 considered essential, equivocal, and complex, respectively). All probands underwent CMA testing. WES was performed for 95 proband-parent trios. Among the 95 patients undergoing WES, 8 children (9 mutations) were received an ASD-related molecular diagnosis (8.4%, 95% CI 3.7% to 15.9%). Incidental or medically-actionable findings were reported in 8/95 (8.4%) probands tested with WES, 6 of which were considered medically-actionable.

Other studies have reported the yield of WES/WGS testing in clinical populations, varying depending on the population. Taylor and colleagues report a yield of 21% for disease-causing variants with WES in a population of 217 patients with suspected genetic disorders with no pathogenic variants on prior screening (Taylor, 2015). Among 11 subjects with cardiomyopathy, Golbus and colleagues reported a yield of 82% for pathogenic variants using WGS (Golbus, 2014).

Clinical Utility: Change in Patient Management with WES/WGS

Several studies have reported on potential benefits, in terms of medical management changes or avoidance of alternative testing, following WES/WGS. Soden and ciolleagues reported on the use of WGS and/or WES in parent-child trios for 119 children with neurodevelopmental disorders (Soden, 2014). A definitive molecular diagnosis of an established genetic disorder was identified in 45 of the 100 families with children affected by neurodevelopmental disorders (53 of 119 affected children). Chart reviews and interviews with referring physicians were used to assess changes in short-term management following WES/WGS, and changed patient management and/or clinical impression was reported in 22/45 families (49%). In a retrospective study of 78 children with neurodevelopmental disorders with a prior unrevealing workup who underwent WES, Srivastava and colleagues reported a presumptive diagnostic testing rate of 41% (Srivastava, 2014). Results of WES changed patient management in all cases, most often related to reproductive planning (n=27), along with additional disease monitoring in 4 cases, further workup for systemic involvement in 6 cases, and 7 medication changes.

Iglesias et al reported on clinical changes that occurred after WES/WGS in a broader population of 115 patients with a genetically undefined disorder (Iglesias, 2014). The most common indications for WES evaluation were birth defects, developmental delay, and seizures, in 24.3%, 25.2%, and 14% of patients, respectively. A definitive diagnosis was made in 37 cases (32.2%). The clinical implications of testing are described qualitatively for patients with a genetic diagnosis. In 6 cases, it was noted that genetic information was used for reproductive planning; in 11 cases, patients were noted to have a change in medical management or surveillance or testing for related conditions.

With wider genome coverage in sequencing comes an increased likelihood that testing will identify potentially clinically-significant gene mutations that may be unrelated to the phenotype being evaluated. The ACMG issued recommendations in 2013 outlining 56 genes associated with 24 conditions that should be reported to patients when known or likely pathogenic variants are detected (Green. 2013). The risks and benefits of WES/WGS in terms of detection of clinically actionable incidental findings should be evaluated on an individual basis.

Ongoing and Unpublished Clinical Trials

Some currently unpublished trials that might influence this review are listed below:

Ongoing

(NCT01969370) NCGENES: North Carolina Clinical Genomic Evaluation by NextGen Exome Sequencing; planned enrollment 750; completion date December 2015.

(NCT02175264) Genetic Basis of Non Syndromic Congenital Diaphragmatic Hernia; planned enrollment 78; completion date July 2016

(NCT02067962) Identification of Genes Involved in Juvenile Idiopathic Arthritis by Whole Exome Sequencing; planned enrollment 30; completion date December 2017.

(NCT02077894) Whole Exome and Whole Genome Sequencing for Genotyping of Inherited and Congenital Eye Cond; planned enrollment 150; completion date September 2018.

(NCT01087320) Whole Genome Medical Sequencing for Gene Discovery; planned enrollment 400; completion No Date

(NCT00340626) Genetic Analysis of Hereditary Non-Syndromic Oral Clefts; planned enrollment 1000; completion No date

(NCT01952275) Assessment of the Enrichment of Rare Coding Genetic Variants in Patients Affected by Neutrophil-Mediated Inflammatory Dermatoses; planned enrollment 660; completion date January 2020.

(NCT01858285) Genetics of Epilepsy and Related Disorders; planned enrollment 500; completion date December 2020.

(NCT02014961) Worm Study: Identification of Modifier Genes in a Unique Founder Population With Sudden Cardiac Death; planned enrollment 223; completion date April 2025.

2017 Update

A literature search conducted using the MEDLINE database through March 2017 did not reveal any new information that would prompt a change in the coverage statement.

The following clinical trials are ongoing:

NCT02340871 Finding Genes With NGS Techniques in Whom Mutations Cause Neurological Diseases
NCT 02418377 Whole-exome Sequencing to Identify Genetic Variants Associated With Severe Childhood Obesity, and Tracking the Changing Prevalence of Obesity Related Complications
NCT02826694 North Carolina Newborn Exome Sequencing for Universal Screening
NCT02077894 Whole Exome and Whole Genome Sequencing for Genotyping of Inherited and Congenital Eye Cond
NCT01087320 Whole Genome Medical Sequencing for Gene Discovery
NCT01952275 Assessment of the Enrichment of Rare Coding Genetic Variants in Patients Affected by Neutrophil-Mediated Inflammatory Dermatoses
NCT 02769975 Evaluation of Children With Endocrine and Metabolic-Related Conditions

2018 Update

Annual policy review completed with a literature search using the MEDLINE database through February 2018. No new literature was identified that would prompt a change in the coverage statement. The key identified literature is summarized below.

WHOLE EXOME SEQUENCING IN PATIENTS WITH MULTIPLE CONGENITAL ANOMALIES OR A NEURODEVELOPMENTAL DISORDER

There are relatively few data specific to the analytic validity of WES. NGS techniques used for WES are expected to have high accuracy for mutation detection. However, NGS platforms differ regarding the depth of sequence coverage, methods for base calling and read alignment, and other factors. These factors contribute to potential variability across the platforms and procedures used by different clinical laboratories offering exome sequencing as a clinical service. The American College of Medical Genetics and Genomics has clinical laboratory standards for NGS, including WES (Rehm, 2013).The guidelines outline the documentation of test performance measures that should be evaluated for NGS platforms, and note that typical definitions of analytic sensitivity and specificity do not apply for NGS.

Depending on the platform and variant call method used, WES may not accurately detect large insertions and deletions, large copy number variants, and structural chromosome rearrangements due to the short sequence read lengths (Rehm, 2013). WES may be less sensitive for the detection of copy number variants than high-resolution microarray testing (de Ligt, 2013). NGS also has poorer coverage for A/T-rich, G/C-rich, and pseudogene regions, as well as homopolymer stretches (Mu, 2016; Hamilton, 2016).

A number of studies have reported on the use of WES in clinical practice. Typically, the populations included in these studies have suspected rare genetic disorders, although the specific populations vary. Series have been reported with as many as 2000 patients. The largest 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 as many as 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 (Vissers, 2017).

WHOLE GENOME SEQUENCING IN PATIENTS WITH A SUSPECTED GENETIC DISORDER

2019 Update

Annual policy review completed with a literature search using the MEDLINE database through February 2019. No new literature was identified that would prompt a change in the coverage statement.

2020 Update

A literature search was conducted through February 2020. There was no new information identified that would prompt a change in the coverage statement.

2021 Update

Annual policy review completed with a literature search using the MEDLINE database through February 2021. No new literature was identified that would prompt a change in the coverage statement. The key identified literature is summarized below.

Kingsmore et al 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 (Kingsmore, 2019). 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. 95 infants were randomized to rWES and 94 to rWGS; in addition 24 infants who were gravely ill received ultra-rapid whole-genome sequencing (urWGS). The initial Kingsmore et al 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 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).

2022 Update

Annual policy review completed with a literature search using the MEDLINE database through February 2022. No new literature was identified that would prompt a change in the coverage statement. The key identified literature is summarized below.

A 2020 Health Technology Assessment conducted by Ontario Health, with literature searches conducted in January 2019, included a comparative review of the diagnostic yield of WES and WGS in children with unexplained developmental disabilities or multiple congenital anomalies (Vandersluis, 2020). The diagnostic yield across all studies was 37% (95% confidence interval [CI] 34% to 40%). More studies, with an overall larger sample size, were included in the examination on WES (34 studies, N=9,142) than on whole genome sequencing (9 studies, N=648). Confidence intervals for studies using WES versus WGS overlapped (37%; 95% CI, 34% to 40%, vs. 40%; 95% CI 32% to 49%). Diagnostic yield ranged between 16% and73%, with variation attributed largely to technology used and participant selection. The overall quality of the evidence was rated as very low, downgraded for risk of bias, inconsistency, indirectness, and imprecision.

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 have described methods for interpretation of WGS indicating that only pathogenic or likely pathogenic variants were included in the diagnostic yield and that variants of uncertain significance (VUS) were not reported. Five studies included in the Ontario HTA review provided data on the yield of VUS, with an overall yield of 17%. Only 1 of the 5 studies used WGS, however. The review authors noted, "Whole genome sequencing always results in substantially longer lists of variants of unknown significance than whole exome sequencing does. Interpreting and acting upon variants of unknown clinical significance is the single greatest challenge identified by clinicians…” (Vandersluis, 2020).

Several laboratories offer WES or WGS as a clinical service. Medical centers may also offer rWES or rWGS or standard WES or WGS as a clinical service. The median time for standard WGS is several weeks. In its 2021 guideline, ACMG defines rapid and ultrarapid testing as 6 to 15 days and 1 to 3 days, respectively (Manickam, 2021).

In 2021, the American College of Medical Genetics and Genomics (ACMG) published a clinical practice guideline for the use of WES and WGS and made the following recommendation: "We strongly recommend ES and GS as a first-tier or second-tier test (guided by clinical judgment and often clinician-patient/family shared decision making after CMA or focused testing) for patients with one or more CAs prior to one year of age or for patients with DD/ID with onset prior to 18years of age" (Manickam, 2021). The recommendation was informed by a systematic evidence review and a health technology assessment conducted by Ontario Health.

In 2020, Dimmock et al reported results of the primary endpoint of NSIGHT2: clinician perception that rWGS was useful and clinician-reported changes in management (Dimmock, 2020). Clinicians provided perceptions of the clinical utility of diagnostic genomic sequencing for 201 of 213 infants randomized (94%). In 154 (77%) infants, diagnostic genomic sequencing was perceived to be useful or very useful; perceptions of usefulness did not differ between infants who received rWES and rWGS, nor between ultra-rWGS and rWES/rWGS. Thirty-two (15%) of 207 clinician responses indicated that diagnostic genomic sequencing changed infant outcomes (by targeted treatments in 21 [10%] infants, avoidance of complications in 16 [8%], and institution of palliative care in 2 [1%] infants). Changes in outcome did not differ significantly between infants randomized to rWES and rWGS, although ultra rWGS was associated with a significantly higher rate of change in management than rWES/rWGS (63% vs. 23%; p=.0001).

In the NICU Seq RCT, Krantz et al compared rWGS (test results returned in 15 days) to a delayed reporting group (WGS with test results returned in 60 days) in 354 infants admitted to an ICU with a suspected genetic disease at 5 sites in the US (Krantz, 2021). In 76% of cases, both parents were available for trio testing. Overall, 82 of 354 infants received a diagnosis (23%), with a higher yield in the 15-day group. The primary outcome was change in management, measured at day 60. Significantly more infants in the rWGS group had a change in management compared with the delayed arm (21.1% vs 10.3%; p=.009; odds ratio 2.3; 95% CI, 1.22 to 4.32). Changes in management included subspecialty referral (21 of 354, 6.0%), changes to medication (5 of 354, 1.4%), therapeutics specific to the primary genetic etiology (7 of 354;2.0%) and surgical interventions (12 of 354; 3.4%). Survival and length of stay did not differ between the groups.

2023 Update

Annual policy review completed with a literature search using the MEDLINE database through February 2023. No new literature was identified that would prompt a change in the coverage statement. The key identified literature is summarized below.

Dai et al conducted a systematic review to determine the diagnostic yield of sequencing reanalysis of data from cases with no diagnosis following an initial WES or WGS test (Dai, 2022). The primary measure of efficacy was the proportion of undiagnosed individuals reaching a positive diagnosis on reanalysis after first round sequencing and analysis. The overall diagnostic yield was 0.10 (95% CI, 0.06 to 0.13). Using the GRADE framework, the certainty of the evidence for this outcome was rated moderate certainty. Confidence in the estimate was downgraded due to significant heterogeneity across studies that could not be explained by subgroup analyses. The researchers performed subgroup analyses on the basis of time interval between the original analysis and reanalysis (<24months compared with ≥24 months), sequencing methodology (WES vs WGS), study sample size (<50, 50-100, >100 patients), sequencing of family members for segregation analysis, whether research validation of novel variants/genes were conducted, and whether any AI-based tools were used in variant curation. These subgroup analyses did not identify any statistically significant differences in diagnostic yield estimates.

Twenty-three of 29 studies (representing 429 individuals) provided the reasons for achieving a diagnosis with re-analysis. In 62%of these cases the reason was a new gene discovery, in 15% the reasons were unknown or unspecified, and in 11% the reason was validation of candidate variants through research or external collaboration. Other reasons included bioinformatic pipeline improvements (3.3%), laboratory errors/misinterpretations (2.8%), updated clinical phenotypes (2.1%), copy number variants (1.9%), and additional segregation studies in relatives (1.2%).

Only 7 of 29 studies provided individual clinical information of sequenced probands (e.g., diagnosed variant, or timing of reanalysis) but instead reported summary data of the overall population. There were 11 studies that reported the finding of VUS and/or variants in novel genes but only 8 studies provided research evidence confirming their pathogenicity. Only 3 studies discussed whether a genetic diagnosis led to management changes, and the impact on management was only described in a subgroup of individuals. To address uncertainties in the evidence, the review authors recommended best practices for future research including detailed inclusion and exclusion criteria, detailed clinical information on each case, clear documentation of methodology used for initial and re-analysis, and reporting of the rationale for attribution of pathogenicity.

Below is a summary of nonrandomized studies published after the Dai et al systematic review. The diagnostic yield in these studies was consistent with previous studies. Study limitations were similar to those identified in previous studies.

Ewans et al conducted a nonrandomized study of 54 affected individuals, unaffected parents, or other affected relatives from 37 families (Ewans, 2022). The design was Prospective cohort conducting initial WES analysis, then repeated WES at 12 months in undiagnosed families. The yield was Initial WES: 11/37 (30%) and Re-analysis at 12 months in undiagnosed individuals: 4/26 (15.4%).

Halfmeyer et al conducted a nonrandomized study of individuals with disorders who had been analyzed via WES between February 2017 and January 2022 (Halfmeyer, 2022). It consisted of 1040 affected individuals from 983 families. The design was a retrospective cohort. The yield was Initial WES: 155/1040; Re-analysis: 7/885 0.8%of all nondiagnostic cases (9 variants were identified; 7 were disease-causing).

Sun et al conducted a nonrandomized study of 100 children with global developmental delay/intellectual disability who had undergone CMA and/or ES and remained undiagnosed (Sun, 2022). The study consisted of 100 affected individuals of which 62 had received nondiagnostic WES. The design was a Prospective cohort. The yield was Overall: 21/100 (21%), CMA only: (64.3%, 9/14), WES only families: 9.7%,6/62, CMA + WES families:6/24 25.0%.

Lindstrand et al conducted a retrospective cohort comparing diagnostic yield from 3 genetic testing approaches (WGS 1st line, WGS 2nd line, and CMA/FMRI) (Lindstrand, 2022). The study consisted of 229 individuals with an ID diagnosis or a strong clinical suspicion of ID. The yield was WGS 1st line: 47 variants in 43 individuals (35%); WGS 2nd line: 48variants in 46 individuals (26%); CMA/FMRI: 51 variants in 51 individuals (11%). Several variants of uncertain significance were discovered: WGS 1st line: 12 of 47 variants were VUS; WGS 2nd line: 14 of 34 variants were VUS; CMA/FMRI: 4/47 variants were VUS.

van der Sanden et al conducted a prospective cohort with both SOC (including WES) and WGS with TRIO testing (van der Sanden, 2023). Participants included 150 individuals with neurodevelopmental delay of suspected genetic origin; clinical geneticist had requested a genetic diagnostic test to identify the molecular defect underlying the individual's phenotype. Yield - SOC/WES:43/150 (28.7%) and WGS: 45/150 (30.0%). VUS: WGS identified a possible diagnosis for 35 individuals of which 31 were also identified by the ES-based SOC pathway.

2024 Update

Annual policy review completed with a literature search using the MEDLINE database through February 2024. No new literature was identified that would prompt a change in the coverage statement.

2024 Update

Annual policy review completed with a literature search using the MEDLINE database through March 2024. No new literature was identified that would prompt a change in the coverage statement.

CPT/HCPCS:

0010U	Infectious disease (bacterial), strain typing by whole genome sequencing, phylogenetic based report of strain relatedness, per submitted isolate
0012U	Germline disorders, gene rearrangement detection by whole genome next generation sequencing, DNA, whole blood, report of specific gene rearrangement(s)
0013U	Oncology (solid organ neoplasia), gene rearrangement detection by whole genome next generation sequencing, DNA, fresh or frozen tissue or cells, report of specific gene rearrangement(s)
0014U	Hematology (hematolymphoid neoplasia), gene rearrangement detection by whole genome next generation sequencing, DNA, whole blood or bone marrow, report of specific gene rearrangement(s)
0016M	Oncology (bladder), mRNA, microarray gene expression profiling of 209 genes, utilizing formalin-fixed paraffin-embedded tissue, algorithm reported as molecular subtype (luminal, luminal infiltrated, basal, basal claudin-low, neuroendocrine-like)
0036U	Exome (ie, somatic mutations), paired formalin fixed paraffin embedded tumor tissue and normal specimen, sequence analyses
0056U	Hematology (acute myelogenous leukemia), DNA, whole genome next generation sequencing to detect gene rearrangement(s), blood or bone marrow, report of specific gene rearrangement(s)
0094u	Genome (eg, unexplained constitutional or heritable disorder or syndrome), rapid sequence analysis
0211U	Oncology (pan-tumor), DNA and RNA by next-generation sequencing, utilizing formalin-fixed paraffin-embedded tissue, interpretative report for single nucleotide variants, copy number alterations, tumor mutational burden, and microsatellite instability, with therapy association
0212U	Rare diseases (constitutional/heritable disorders), whole genome and mitochondrial DNA sequence analysis, including small sequence changes, deletions, duplications, short tandem repeat gene expansions, and variants in non uniquely mappable regions, blood or saliva, identification and categorization of genetic variants, proband
0213U	Rare diseases (constitutional/heritable disorders), whole genome and mitochondrial DNA sequence analysis, including small sequence changes, deletions, duplications, short tandem repeat gene expansions, and variants in non uniquely mappable regions, blood or saliva, identification and categorization of genetic variants, each comparator genome (eg, parent, sibling)
0214U	Rare diseases (constitutional/heritable disorders), whole exome and mitochondrial DNA sequence analysis, including small sequence changes, deletions, duplications, short tandem repeat gene expansions, and variants in non-uniquely mappable regions, blood or saliva, identification and categorization of genetic variants, proband
0215U	Rare diseases (constitutional/heritable disorders), whole exome and mitochondrial DNA sequence analysis, including small sequence changes, deletions, duplications, short tandem repeat gene expansions, and variants in non uniquely mappable regions, blood or saliva, identification and categorization of genetic variants, each comparator exome (eg, parent, sibling)
0265U	Rare constitutional and other heritable disorders, whole genome and mitochondrial DNA sequence analysis, blood, frozen and formalin-fixed paraffinembedded (FFPE) tissue, saliva, buccal swabs or cell lines, identification of single nucleotide and copy number variants
0266U	Unexplained constitutional or other heritable disorders or syndromes, tissuespecific gene expression by wholetranscriptome and next-generation sequencing, blood, formalin-fixed paraffinembedded (FFPE) tissue or fresh frozen tissue, reported as presence or absence of splicing or expression changes
0267U	Rare constitutional and other heritable disorders, identification of copy number variations, inversions, insertions, translocations, and other structural variants by optical genome mapping and whole genome sequencing
0297U	Oncology (pan tumor), whole genome sequencing of paired malignant and normal DNA specimens, fresh or formalin fixed paraffin embedded (FFPE) tissue, blood or bone marrow, comparative sequence analyses and variant identification
0298U	Oncology (pan tumor), whole transcriptome sequencing of paired malignant and normal RNA specimens, fresh or formalin fixed paraffin embedded (FFPE) tissue, blood or bone marrow, comparative sequence analyses and expression level and chimeric transcript id
0299U	Oncology (pan tumor), whole genome optical genome mapping of paired malignant and normal DNA specimens, fresh frozen tissue, blood, or bone marrow, comparative structural variant identification
0300U	Oncology (pan tumor), whole genome sequencing and optical genome mapping of paired malignant and normal DNA specimens, fresh tissue, blood, or bone marrow, comparative sequence analyses and variant identification
0329U	Oncology (neoplasia), exome and transcriptome sequence analysis for sequence variants, gene copy number amplifications and deletions, gene rearrangements, microsatellite instability and tumor mutational burden utilizing DNA and RNA from tumor with and DNA from normal blood or saliva for subtraction, report of clinically significant mutation(s) with therapy associations
0331U	Oncology (hematolymphoid neoplasia), optical for copy number alterations and gene rearrangements utilizing DNA from blood or bone marrow, report of clinically significant alternations
0335U	Rare diseases (constitutional/heritable disorders), whole genome sequence analysis, including small sequence changes, copy number variants, deletions, duplications, mobile element insertions, uniparental disomy (UPD), inversions, aneuploidy, mitochondrial genome sequence analysis with heteroplasmy and large deletions, short tandem repeat (STR) gene expansions, fetal sample, identification and categorization of genetic variants
0336U	Rare diseases (constitutional/heritable disorders), whole genome sequence analysis, including small sequence changes, copy number variants, deletions, duplications, mobile element insertions, uniparental disomy (UPD), inversions, aneuploidy, mitochondrial genome sequence analysis with heteroplasmy and large deletions, short tandem repeat (STR) gene expansions, blood or saliva, identification and categorization of genetic variants, each comparator genome (eg, parent)
0410U	Oncology (pancreatic), DNA, whole genome sequencing with 5-hydroxymethylcytosine enrichment, whole blood or plasma, algorithm reported as cancer detected or not detected
0413U	Oncology (hematolymphoid neoplasm), optical genome mapping for copy number alterations, aneuploidy, and balanced/complex structural rearrangements, DNA from blood or bone marrow, report of clinically significant alterations
0425U	Genome (eg, unexplained constitutional or heritable disorder or syndrome), rapid sequence analysis, each comparator genome (eg, parents, siblings)
0426U	Genome (eg, unexplained constitutional or heritable disorder or syndrome), ultra rapid sequence analysis
0507U	Oncology (ovarian), DNA, wholegenome sequencing with 5 hydroxymethylcytosine (5hmC) enrichment, using whole blood or plasma, algorithm reported as cancer detected or not detected
81349	Cytogenomic (genome wide) analysis for constitutional chromosomal abnormalities; interrogation of genomic regions for copy number and loss of heterozygosity variants, low pass sequencing analysis
81415	Exome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis
81416	Exome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis, each comparator exome (eg, parents, siblings) (List separately in addition to code for primary procedure)
81417	Exome (eg, unexplained constitutional or heritable disorder or syndrome); re evaluation of previously obtained exome sequence (eg, updated knowledge or unrelated condition/syndrome)
81425	Genome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis
81426	Genome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis, each comparator genome (eg, parents, siblings) (List separately in addition to code for primary procedure)
81427	Genome (eg, unexplained constitutional or heritable disorder or syndrome); re evaluation of previously obtained genome sequence (eg, updated knowledge or unrelated condition/syndrome)

References:

Bamshad MJ, Ng SB, Bigham AW et al.(2011) Exome sequencing as a tool for Mendelian disease gene discovery. Nature reviews. Genetics 2011; 12(11):745-55.

Biesecker LG.(2012) Opportunities and challenges for the integration of massively parallel genomic sequencing into clinical practice: lessons from the ClinSeq project. Genetics in medicine : official journal of the American College of Medical Genetics 2012; 14(4):393-8.

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

Dai P, Honda A, Ewans L, et al.(2022) Recommendations for next generation sequencing data reanalysis of unsolved cases with suspected Mendelian disorders: A systematic review and meta-analysis. Genet Med. Aug 2022; 24(8): 1618-1629. PMID35550369

Dimmock DP, Clark MM, Gaughran M, et al.(2020) An RCT of Rapid Genomic Sequencing among Seriously Ill InfantsResults in High Clinical Utility, Changes in Management, and Low Perceived Harm. Am J Hum Genet. Nov 052020; 107(5): 942-952. PMID 33157007

Dixon-Salazar TJ, Silhavy JL, Udpa N et al.(2012) Exome sequencing can improve diagnosis and alter patient management. Science translational medicine 2012; 4(138):138ra78.

Ewans LJ, Schofield D, Shrestha R, et al.(2018) Whole-exome sequencing reanalysis at 12 months boosts diagnosis and is cost-effective when applied early in Mendelian disorders. Genet Med. Dec 2018; 20(12): 1564-1574. PMID 29595814

Golbus JR, Puckelwartz MJ, Dellefave-Castillo L, et al.(2014) Targeted analysis of whole genome sequence data to diagnose genetic cardiomyopathy. Circ Cardiovasc Genet. Dec 2014;7(6):751-759. PMID 25179549

Green RC, Berg JS, Grody WW et al.(2013) ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genetics in medicine : official journal of the American College of Medical Genetics 2013; 15(7):565-74.

Green RC, Berg JS, Grody WW, et al.(2013) ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med. Jul 2013;15(7):565-574. PMID 23788249

Greenway SC, McLeod R, Hume S, et al.(2014) Exome sequencing identifies a novel variant in ACTC1 associated with familial atrial septal defect. Can J Cardiol. Feb 2014;30(2):181-187. PMID 24461919

Halfmeyer I, Bartolomaeus T, Popp B, et al.(2022) Approach to Cohort-Wide Re-Analysis of Exome Data in 1000 Individuals with Neurodevelopmental Disorders. Genes (Basel). Dec 22 2022; 14(1). PMID 36672771

Iglesias A, Anyane-Yeboa K, Wynn J, et al.(2014) The usefulness of whole-exome sequencing in routine clinical practice. Genet Med. Dec 2014;16(12):922-931. PMID 24901346

Jiang YH, Yuen RK, Jin X, et al.(2013) Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing. Am J Hum Genet. Aug 8 2013;93(2):249-263. PMID 23849776

Kim HJ, Won HH, Park KJ, et al.(2013) SNP linkage analysis and whole exome sequencing identify a novel POU4F3 mutation in autosomal dominant late-onset nonsyndromic hearing loss (DFNA15). PLoS One. 2013;8(11):e79063. PMID 24260153

Kingsmore SF, Cakici JA, Clark MM, et al.(2019) A Randomized, Controlled Trial of the Analytic and Diagnostic Performance of Singleton and Trio, Rapid Genome and Exome Sequencing in Ill Infants. Am J Hum Genet. Oct 03 2019; 105(4): 719-733. PMID 31564432

Krantz ID, Medne L, Weatherly JM, et al.(2021) Effect of Whole-Genome Sequencing on the Clinical Management ofAcutely Ill Infants With Suspected Genetic Disease: A Randomized Clinical Trial. JAMA Pediatr. Dec 01 2021;175(12): 1218-1226. PMID 34570182

Lee H, Deignan JL, Dorrani N, et al.(2014) Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA. Nov 12 2014;312(18):1880-1887. PMID 25326637

Lindstrand A, Ek M, Kvarnung M, et al.(2022) Genome sequencing is a sensitive first-line test to diagnose individuals with intellectual disability. Genet Med. Nov 2022; 24(11): 2296-2307. PMID 36066546

Manickam K, McClain MR, Demmer LA, et al.(2021) Exome and genome sequencing for pediatric patients withcongenital anomalies or intellectual disability: an evidence-based clinical guideline of the American College ofMedical Genetics and Genomics (ACMG). Genet Med. Nov 2021; 23(11): 2029-2037. PMID 34211152

McLaughlin HM, Ceyhan-Birsoy O, Christensen KD, et al.(2014) A systematic approach to the reporting of medically relevant findings from whole genome sequencing. BMC Med Genet. 2014;15:134. PMID 25714468

Rehm HL, Bale SJ, Bayrak-Toydemir P, et al.(2013) ACMG clinical laboratory standards for next-generation sequencing. Genet Med. Sep 2013;15(9):733-747. PMID 23887774

Richards S, Aziz N, Bale S, et al.(2015) Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. May 2015;17(5):405-424. PMID 25741868

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

Srivastava S, Cohen JS, Vernon H, et al.(2014) Clinical whole exome sequencing in child neurology practice. Ann Neurol. Oct 2014;76(4):473-483. PMID 25131622

Sun Y, Peng J, Liang D, et al.(2022) Genome sequencing demonstrates high diagnostic yield in children with undiagnosed global developmental delay/intellectual disability: A prospective study. Hum Mutat. May 2022; 43(5): 568-581. PMID 35143101

Tammimies K, Marshall CR, Walker S, et al.(2015) Molecular Diagnostic Yield of Chromosomal Microarray Analysis and Whole-Exome Sequencing in Children With Autism Spectrum Disorder JAMA. Sep 1 2015;314(9):895-903. PMID 26325558

Taylor JC, Martin HC, Lise S, et al.(2015) Factors influencing success of clinical genome sequencing across a broad spectrum of disorders. Nat Genet. Jul 2015;47(7):717-726. PMID 25985138

van der Sanden BPGH, Schobers G, Corominas Galbany J, et al.(2023) The performance of genome sequencing as a first-tier test for neurodevelopmental disorders. Eur J Hum Genet. Jan 2023; 31(1): 81-88. PMID 36114283

Vandersluis S, Li CM, Cheng L, et al.(2020) Genome-Wide Sequencing for Unexplained Developmental Disabilities or Multiple Congenital Anomalies: A Health Technology Assessment. Ont Health Technol Assess Ser. 2020; 20(11): 1-178. PMID 32194879

Weeke P, Mosley JD, Hanna D, et al.(2014) Exome sequencing implicates an increased burden of rare potassium channel variants in the risk of drug-induced long QT interval syndrome. J Am Coll Cardiol. Apr 15 2014;63(14):1430-1437. PMID 24561134

Yang Y, Muzny DM, Xia F, et al.(2014) Molecular findings among patients referred for clinical whole-exome sequencing. JAMA. Nov 12 2014;312(18):1870-1879. PMID 25326635

Zhou Q, Yang D, Ombrello AK, et al.(2014) Early-onset stroke and vasculopathy associated with mutations in ADA2. N Engl J Med. Mar 6 2014;370(10):911-920. PMID 24552284

Group specific policy will supersede this policy when applicable. This policy does not apply to the Wal-Mart Associates Group Health Plan participants or to the Tyson Group Health Plan participants.
CPT Codes Copyright © 2024 American Medical Association.