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Concert Genetic Testing: Exome and Genome Sequencing for the Diagnosis
of Genetic Disorders
V1.2025
Date of Last Revision: 11/24

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Coding Implications

CONCERT GENETIC TESTING:

EXOME AND GENOME SEQUENCING
FOR THE DIAGNOSIS OF GENETIC
DISORDERS

See Important Reminder at the end of this policy for important regulatory and legal
information.

OVERVIEW

Exome sequencing (ES) (also known as ‘whole exome sequencing (WES)’) involves sequencing
and copy number variant (CNV) analysis of the portion of the genome that contains protein-coding
DNA, which are termed exons. Together, all of the exons in a genome are known as the exome,
which constitutes approximately 1% of the genome and is currently estimated to contain about 85%
of heritable disease-causing variants.

Genome sequencing (GS) (also known as ‘whole genome sequencing (WGS)’) is a comprehensive
method that sequences both coding and noncoding regions of the genome. GS has a greater ability
to detect large deletions or duplications in protein-coding regions compared to ES, as well as the
ability to detect variants that may be missed by ES, such as copy-number variants (CNV), mid-size
insertions and deletions (ca. 10-500 bp), nucleotide repeat expansion mutations, deeper intronic
mutations, structural variants(e.g., translocations, inversions), and variants that result in
methylation defects and uniparental disomy. GS requires greater data analysis but less DNA
preparation prior to sequencing.

ES and GS have been proposed for use in patients presenting with disorders and anomalies not
immediately explained by standard clinical workup. Potential candidates for ES and GS include

patients who present with a broad spectrum of suspected genetic conditions. GS has been shown to
have a higher diagnostic yield compared to ES when used as a first line test.

ES reanalysis is often performed approximately 18 months to 2 years following initial,
uninformative ES. Studies have shown that the diagnostic yield of ES reanalysis is comparable to
performing GS after an uninformative ES.

Rapid exome sequencing (rES) and rapid genome (rGS) sequencing involves sequencing of the
exome or genome, respectively, in an accelerated time frame. Preliminary results can typically be
returned in less than 7 days, and a final report in less than two weeks. Studies suggest that the use
of rES or rGS in acutely-ill infants, presenting with complex phenotypes that are likely rare genetic
conditions, can identify a genetic diagnosis more quickly, allowing clinicians and family members
to change acute medical or surgical management options and end the diagnostic odyssey.

Trio testing is preferred whenever possible. Testing of one available parent is a valid alternative if
both are not immediately available and one or both parents can be done later if needed. Exome
sequencing or genome sequencing can reveal incidental findings or secondary findings. These
findings are defined as results that are not related to the indication for undergoing the sequencing,
but may be of medical value or utility. Disclosure of these findings has been a topic of intense
debate within the medical genetics community. In 2013, ACMG published recommendations for
reporting secondary findings that included a list of conditions to be included. The list currently
includes 59 genes that confer highly-penetrant and medically actionable conditions.

Pre-test and post-test genetic counseling that facilitates informed decision-making, the possibility
to identify secondary finding with the option to ‘opt out’ of receiving these results, elicits patient
preferences regarding secondary and/or incidental findings if possible, and formulates a plan for
returning such results before testing occurs is strongly advised.

If a genetic diagnosis is not found by ES or GS, periodic reanalysis of the previously obtained
genomic sequence is recommended. Reevaluation can occur on the variant-level or case-level. Any
variants identified and reported prior to the current ACMG variant classification standards should
be reevaluated using the current ACMG standards.

POLICY REFERENCE TABLE

Coding Implications

This clinical policy references Current Procedural Terminology (CPT®. CPT is a registered
trademark of the American Medical Association. All CPT codes and descriptions are copyrighted
2023, American Medical Association. All rights reserved. CPT codes and CPT descriptions are
from the current manuals and those included herein are not intended to be all-inclusive and are
included for informational purposes only. Codes referenced in this clinical policy are for
informational purposes only. Inclusion or exclusion of any codes does not guarantee coverage.
Providers should reference the most up-to-date sources of professional coding guidance prior to
the submission of claims for reimbursement of covered services.

The tests, associated laboratories, CPT codes, and ICD codes contained within this document
serve only as examples to help users navigate claims and corresponding criteria; as such, they are
not comprehensive and are not a guarantee of coverage or non-coverage. Please see the Concert
Platform for a comprehensive list of registered tests.

Criteria Sections	Example Tests (Labs)	Common CPT Codes	Common ICD Codes	Ref
Standard Exome Sequencing	Genomic Unity Exome Analysis - Proband (Variantyx)	81415	F70-F79, F80.0-1, 3, 5, F89, Q00.0- Q99.9, R56.9, R62.0, R62.50, R62.51, G40.909	7, 8, 12, 13
	Genomic Unity Exome Analysis - Comparator (Duo or Trio) (Variantyx Inc.)	81416
	XomeDx - Proband (GeneDx)	81415
	Exome - Proband Only (Invitae)
	XomeDx - Duo (GeneDx)	81415, 81416
	XomeDX - Trio (GeneDx)
	Exome - Duo (Invitae)
	Exome - Trio (Invitae)
Reanalysis of Exome or Genome Sequencing Data	Exome Reanalysis (Ambry)	81417	F70-F79, F80- F89, Q00.0- Q99.9, R56.9, R62.0, R62.50, R62.51, G40.909	4, 9, 10, 12
	Whole Genome Reanalysis (ARUP)	81427
Rapid Exome	XomeDxXpress (GeneDx)	81415, 81416	F70-F79, F80-	1, 3, 5,

| | PGxome RAPID Exome Test (PreventionGenetics, part of Exact Sciences) | | | |

| | STAT Whole Exome Sequencing (PerkinElmer Genomics) | | | |

| | Genomic Unity® Whole Genome Analysis - Comparator (Variantyx Inc.) | 0213U | | |

| | GenomeSeqDx (GeneDx) | 81425, 81426 | | |

| | Whole Genome Sequencing (PerkinElmer Genomics) | | | |

| | Praxis Whole Genome Sequencing (Praxis Genomics LLC) | 0265U | | |

| | Rapid Whole Genome Sequencing, Comparator Genome (Rady Children’s Institute for Genomic Medicine) | 0425U | | |

| | Ultra-Rapid Whole Genome Sequencing (Rady Children’s Institute for Genomic Medicine) | 0426U | | |

| | STAT Whole Genome Sequencing (PerkinElmer Genomics) | 81425, 81426 | | |

This policy document provides criteria for exome and genome sequencing for the diagnosis of
genetic disorders in patients with suspected genetic disorders and for population-based screening.
Please refer to:

Oncology: Molecular Analysis of Solid Tumors and Hematologic Malignancies for
criteria related to exome and genome sequencing of solid tumors and hematologic
malignancies.
Genetic Testing: Multisystem Inherited Disorders, Intellectual Disability, and
Developmental Delay for criteria related to diagnostic genetic testing performed after a
child has been born.
Genetic Testing: Prenatal and Preconception Carrier Screening for criteria related to
prenatal carrier screening, preimplantation genetic testing, or preconception carrier
screening.
Genetic Testing: Prenatal Diagnosis (via Amniocentesis, CVS, or PUBS) and Pregnancy
Loss for coverage related to prenatal exome sequencing.
Genetic Testing: General Approach to Genetic and Molecular Testing for criteria related
to exome and genome sequencing that is not specifically discussed in this or another non-
general policy, including known familial variant testing.

CRITERIA

It is the policy of health plans affiliated with Centene Corporation® that the specific genetic testing
noted below is medically necessary when meeting the related criteria:

STANDARD EXOME SEQUENCING

I. Standard exome sequencing (81415, 81416, 0214U, 0215U), with trio testing when
possible, is considered medically necessary when:

A. The member/enrollee has not previously had genome sequencing, AND
B. Alternate etiologies have been considered and ruled out when possible (e.g.,
environmental exposure, injury, infection, isolated prematurity), AND
C. Clinical presentation does not fit a well-described syndrome for which single-gene
or targeted multi-gene panel testing is available, AND
D. The member/enrollee’s personal and family histories have been evaluated by a
Medical Geneticist, Genetic Counselor or an Advanced Practice Nurse in Genetics
(APGN), AND
E. The member/enrollee meets at least one of the following clinical findings:

The member/enrollee has unexplained epilepsy diagnosed at any age, OR
The member/enrollee has global developmental delay or intellectual
disability with onset prior to age 18 years, OR
The member/enrollee was diagnosed with at least one congenital anomaly
(functional and/or structural), OR
The member/enrollee has at least TWO of the following:
a) Bilateral sensorineural hearing loss of unknown etiology, OR
b) Symptoms of a complex neurological disorder (e.g., dystonia,
hemiplegia, spasticity, epilepsy, myopathy, muscular dystrophy), OR
c) Family history suggestive of a genetic etiology, including
consanguinity, OR
d) Clinical or laboratory findings suggestive of an inborn error of
metabolism, OR
e) Autism, OR
f) Severe neuropsychiatric condition (e.g., schizophrenia, bipolar
disorder, Tourette syndrome, self-injurious behavior, reverse sleep-
wake cycles), OR

g) Period of unexplained developmental regression (unrelated to
epilepsy or autism).

II. Repeat standard exome sequencing (81415, 81416, 0214U, 0215U) is considered

**investigational**.

III. Standard exome sequencing (81415, 81416, 0214U, 0215U) is considered investigational

 for all other indications, including screening asymptomatic/healthy individuals for genetic  
 disorders.

REANALYSIS OF EXOME OR GENOME SEQUENCING DATA

I. Reanalysis of exome or genome sequencing data (81417, 81427) is considered medically
necessary when*:

A. The member/enrollee had exome or genome sequencing at least 18 months ago, OR
B. The member/enrollee’s phenotype has expanded to include clinical findings** that

  were not present at the time of the initial exome or genome sequencing analysis,  
  AND  

  1. Results of prior exome or genome sequencing do not explain these new  
     clinical findings.

II. Reanalysis of exome or genome sequencing data (81417, 81427) is considered

**investigational** for all other indications.

*If reanalysis of exome data is not possible, see the genome sequencing criteria for additional coverage information.
**See Standard Exome Sequencing or Standard Genome Sequencing criteria for qualifying clinical findings.

RAPID EXOME SEQUENCING

I. Rapid exome sequencing (rES) (81415, 81416), with trio testing when possible, is
considered medically necessary when:

A. The member/enrollee is an acutely-ill infant (12 months of age or younger), AND
B. The member/enrollee has not previously had genome sequencing, AND
C. Alternate etiologies have been considered and ruled out when possible (e.g.,

  environmental exposure, injury, infection, isolated prematurity), AND

D. Clinical presentation does not fit a well-described syndrome for which rapid single-

  gene or targeted multi-gene panel testing is available, AND

E. The member/enrollee’s personal and family histories have been evaluated by a

  Medical Geneticist, Genetic Counselor or an Advanced Practice Nurse in Genetics  
  (APGN), AND

F. The member/enrollee meets at least one of the following clinical findings:

  1. The member/enrollee has unexplained epilepsy, OR  
  2. The member/enrollee has **global developmental delay**, OR  
  3. The member/enrollee was diagnosed with at least one **congenital anomaly**  
     (functional and/or structural), OR  
  4. The member/enrollee has at least TWO of the following:  

     a) Bilateral sensorineural hearing loss of unknown etiology, OR  
     b) Symptoms of a complex neurological disorder (e.g., dystonia,  
        hemiplegia, spasticity, epilepsy, myopathy, muscular dystrophy), OR  
     c) Family history suggestive of a genetic etiology, including  
        consanguinity, OR  
     d) Clinical or laboratory findings suggestive of an inborn error of  
        metabolism, OR  

  e) Severe neuropsychiatric condition (e.g., schizophrenia, bipolar  
     disorder, Tourette syndrome, self-injurious behavior, reverse sleep-  
     wake cycles), OR  
  f) Period of unexplained developmental regression (unrelated to  
     epilepsy or autism).

II. Rapid exome sequencing (rES) (81415, 81416) is considered investigational for all other

indications, including screening asymptomatic/healthy individuals for genetic disorders.

STANDARD GENOME SEQUENCING

I. Standard genome sequencing (81425, 81426, 0212U, 0213U, 0265U), with trio testing
when possible, is considered medically necessary when:

A. Alternate etiologies have been considered and ruled out when possible (e.g.,

  environmental exposure, injury, infection, isolated prematurity), AND

B. Clinical presentation does not fit a well-described syndrome for which single-gene

  or targeted multi-gene panel testing is available, AND

C. The member/enrollee’s personal and family histories have been evaluated by a

  Medical Geneticist, Genetic Counselor or an Advanced Practice Nurse in Genetics  
  (APGN), AND

D. The member/enrollee meets at least one of the following clinical findings:

  1. The member/enrollee previously had uninformative exome sequencing (ES),  
     AND  

     a) ES reanalysis is not possible, OR  
  2. The member/enrollee has unexplained epilepsy diagnosed at any age, OR  
  3. The member/enrollee has **global developmental delay** or **intellectual  
     disability** with onset prior to age 18 years, OR

The member/enrollee was diagnosed with at least one congenital anomaly
(functional and/or structural), OR
The member/enrollee has at least TWO of the following:
a) Bilateral sensorineural hearing loss of unknown etiology, OR
b) Symptoms of a complex neurological disorder (e.g., dystonia,
hemiplegia, spasticity, epilepsy, myopathy, muscular dystrophy), OR
c) Family history suggestive of a genetic etiology, including
consanguinity, OR
d) Clinical or laboratory findings suggestive of an inborn error of
metabolism, OR
e) Autism, OR
f) Severe neuropsychiatric condition (e.g., schizophrenia, bipolar
disorder, Tourette syndrome, self-injurious behavior, reverse sleep-
wake cycles), OR
g) Period of unexplained developmental regression (unrelated to
epilepsy or autism).

Repeat standard genome sequencing (81425, 81426, 0212U, 0213U, 0265U) is considered

**investigational**.

III. Standard genome sequencing (81425, 81426, 0212U, 0213U, 0265U) is considered

 **investigational** for all other indications, including screening asymptomatic/healthy  
 individuals for genetic disorders.

Note: When genome sequencing is performed, the mitochondrial genome is assumed to be included as a part of the
analysis.

Concert Genetic Testing: Exome and Genome Sequencing for the Diagnosis
of Genetic Disorders
V1.2025
Date of Last Revision: 11/24
CENTENE Corporation

RAPID GENOME SEQUENCING

I. Rapid genome sequencing (rGS) (81425, 81426, 0094U, 0425U, 0426U), with trio testing when possible, is considered medically necessary when:

A. The member/enrollee is an acutely-ill infant (12 months of age or younger), AND  
B. Alternate etiologies have been considered and ruled out when possible (e.g., environmental exposure, injury, infection, isolated prematurity), AND  
C. Clinical presentation does not fit a well-described syndrome for which rapid single-gene or targeted multi-gene panel testing is available, AND  
D. The member/enrollee’s personal and family histories have been evaluated by a Medical Geneticist, Genetic Counselor or an Advanced Practice Nurse in Genetics (APGN), AND  
E. The member/enrollee meets at least one of the following clinical findings:  
    1. The member/enrollee has unexplained epilepsy, OR  
    2. The member/enrollee has multiple congenital abnormalities (functional and/or structural) affecting unrelated organ systems, OR  
    3. The member/enrollee has epileptic encephalopathy, OR  
    4. The member/enrollee has at least TWO of the following:  
        a) Abnormality affecting at least one organ system, OR  
        b) Symptoms of a complex neurological condition (e.g., dystonia, hemiplegia, spasticity, epilepsy, hypotonia, myopathy, muscular dystrophy, global developmental delay, intellectual disability), OR  
        c) Family history suggestive of a genetic etiology, including consanguinity, OR  
        d) Laboratory findings suggestive of an inborn error of metabolism, OR  
        e) Abnormal response to standard therapy.

Concert Genetic Testing: Exome and Genome Sequencing for the Diagnosis
of Genetic Disorders
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Date of Last Revision: 11/24
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II. Rapid genome sequencing (rGS) (81425, 81426, 0094U, 0425U, 0426U) is considered investigational for all other indications, including screening asymptomatic/healthy individuals for genetic disorders.

Note: When genome sequencing is performed, the mitochondrial genome is assumed to be included as a part of the analysis.

DEFINITIONS

Exome Sequencing (ES): A genomic technique for sequencing all of the protein-coding regions of genes in the genome (also known as the exome).
Genome Sequencing (GS): A genomic technique for sequencing the complete DNA sequence, which includes protein coding as well as non-coding DNA elements.
Trio Testing: Testing of the child and both biological/genetic parents, which increases the chances of finding a definitive diagnosis while reducing false-positive findings.
Congenital anomalies: According to ACMG, congenital anomalies are multiple anomalies not specific to a well-delineated genetic syndrome. These anomalies are structural or functional abnormalities usually evident at birth, or shortly thereafter, and can be consequential to an individual’s life expectancy, health status, physical or social functioning, and typically require medical intervention.
Global Developmental delay: An individual that is slow-to-meet or not reaching milestones in the expected way for a child’s age in at least two of the areas of development (communication, gross/fine motor, cognition, social-emotional, or adaptive skills)
Intellectual disability (ID): Defined by the DSM-V as an individual who meets all of the following:
a. Deficits in intellectual functions, such as reasoning, problem solving, planning, abstract thinking, judgment, academic learning, and learning from experience, confirmed by both clinical assessment and individualized, standardized intelligence testing.

Concert Genetic Testing: Exome and Genome Sequencing for the Diagnosis
of Genetic Disorders
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b. Deficits in adaptive functioning that result in failure to meet developmental and sociocultural standards for personal independence and social responsibility. Without ongoing support, the adaptive deficits limit functioning in one or more activities of daily life, such as communication, social participation, and independent living, across multiple environments, such as home, school, work, and community.
c. Onset of intellectual and adaptive deficits during the developmental period.

Exome sequencing (ES) reanalysis may not be possible in some situations. Sequencing platforms may have changed substantially enough that the performing lab can no longer use the data from the original ES in their pipeline. Specifically, ES reanalysis may not be possible if there have been improvements in technology/chemistry (e.g., new methods for DNA capture and/or sequencing), bioinformatics advancements, or there is new information regarding the genetic etiology of a condition that could explain the patient’s clinical features and would not have been able to be detected by the previous exome sequencing.

BACKGROUND AND RATIONALE

Standard Exome Sequencing

American College of Medical Genetics and Genomics (ACMG)

In 2021, ACMG (Manickam, 2021) published an evidence-based clinical practice guideline on exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability, which included the following:

“We strongly recommend ES and GS as a first- or second-tier test… for patients with one or more congenital anomalies prior to one year of age, or for patients with intellectual disability/developmental delay with onset prior to 18 years of age. (p. 2031)
“Isolated autism without ID or congenital malformation is formally out of scope for this recommendation but evaluation of exome/genome studies is ongoing.” (p. 2034)

In 2020, ACMG (Malinowski, et al) released a systematic evidence-based review, which “provide[d] indirect evidence of the clinical and personal utility of ES/GS for patients with CA/DD/ID and their family members, noting that a “change in clinical management” resulted in over half of the patients examined as a result of their ES/GS results. (p. 1001)

Concert Genetic Testing: Exome and Genome Sequencing for the Diagnosis
of Genetic Disorders
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Date of Last Revision: 11/24
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In 2022, ACMG (Li, et al) released a clinical practice resource for the clinical evaluation of hearing loss published, which states that first-line genetic testing for individuals with exam findings that suggest a syndromic hearing loss etiology may include a variety of tests, including genome sequencing, depending on clinical presentation. For individuals without physical findings that suggest a syndromic hearing loss etiology, they recommend a tiered approach, starting with comprehensive hearing loss gene panel testing unless a more specific genetic etiology is evident for which targeted testing is appropriate. (p. 1400)

National Society for Genetic Counselors

The National Society for Genetic Counselors (NSGC) released a position statement (2013, updated 2020, reaffirmed 2023) stating the following in regard to secondary and incidental findings in genetic testing:
“The National Society of Genetic Counselors strongly advises pre-test counseling that facilitates informed decision-making, elicits patient preferences regarding secondary and/or incidental findings if possible, and formulates a plan for returning such results before testing occurs”

The National Society of Genetic Counselors (NSGC) published evidence-based practice guidelines for individuals with unexplained epilepsy (Smith et al, 2022). The NSGC recommendations are as follows (p. 4):

Individuals with unexplained epilepsy should be offered genetic testing, without limitation of age.
Multi-gene, comprehensive testing, such as exome sequencing, genome sequencing or a multigene panel as a first-tier test is strongly recommended.

Patient-Centered Laboratory Utilization Guidance Services

In the PLUGS July 2023 guidelines entitled “Genomic Sequencing for Rare Disease,” the following clinical criteria are recommended for exome sequencing and genome sequencing.
“Exome sequencing or genome sequencing (ES/GS) is considered medically necessary when ALL of the following criteria are met: …

The etiology of the patient’s features is not known, and a genetic etiology is considered a likely explanation for the phenotype, based on one of the following…
a. Epilepsy of unexplained etiology with onset at any age, OR

Concert Genetic Testing: Exome and Genome Sequencing for the Diagnosis
of Genetic Disorders
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Date of Last Revision: 11/24
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b. Confirmed bilateral sensorineural hearing loss of unknown etiology and panel testing is unrevealing, OR
c. Intellectual disability, following formal assessment by a developmental pediatrician or neurologist, defined as moderate/severe/profound by Diagnostic and Statistical Manual of Mental Disorders (DSM-5) criteria, diagnosed by 18 years of age, OR
d. Global developmental delay, following formal assessment by a developmental pediatrician or neurologist, defined as significant delay in younger children, under age five years, in at least two of the major developmental domains: gross or fine motor; speech and language; cognition; social and personal development; and activities of daily living, OR
e. Multiple congenital anomalies affecting unrelated organ systems, OR
f. At least TWO of the following criteria are met:

i. Abnormality affecting at minimum a single organ system  
ii. Autism  
iii. Severe neuropsychiatric condition (e.g., schizophrenia, bipolar disorder, Tourette syndrome, self-injurious behavior, reverse sleep-wake cycles)  
iv. Symptoms of a complex neurological condition (e.g., dystonia, hemiplegia, spasticity, hypotonia, myopathy, muscular dystrophy)  
v. Family history strongly suggestive of a genetic etiology, including consanguinity  
vi. Period of unexplained developmental regression (unrelated to epilepsy or autism)  
vii. Laboratory findings suggestive of an inherited metabolic disorder

Alternate etiologies have been considered and ruled out, when possible (e.g., MRI abnormalities/brain malformations, environmental exposure, injury, infection, isolated prematurity), AND
Clinical presentation does not fit a well-described syndrome for which more targeted testing is available.” (p. 7)

Belanger, et al

A review of the evaluation of children with global developmental delay and intellectual disability by Belanger et al (2018) defines global developmental delay (GDD) as the following:

Significant delay (at least 2 standard deviations below the mean) in at least two developmental domains (gross or fine motor, speech/language, cognition, social/personal or activities of daily living. (p. 404)

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of Genetic Disorders
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Reanalysis of Exome or Genome Sequencing Data

Tan, et al

A study from 2020 examined data from 58 unsolved cases referred for any indication to evaluate the systematic reanalysis of singleton exome sequencing (ES). The authors performed a reanalysis at multiple timepoints following initial testing, and ultimately suggest that an interval of greater than 18 months from the original report may be optimal for reanalysis. (p. 1)

Alfares, et al

This study from 2018 compared the detection rates of whole-exome sequencing (WES) and whole-genome sequencing (WGS) in a clinical setting. The study included 108 patients with negative array CGH and negative or inconclusive WES results. WGS was performed on all patients, and the results of the study showed that 30% of the positive cases identified by WGS could be identified by reanalyzing WES raw data, and WGS achieved an only 7% higher detection rate. (p. 1328) The paper concluded that, although WGS is a more powerful tool than WES, in this study, “we showed that WGS has additional, but limited, clinical utility compared with reanalyzing WES data, and until the cost of WGS approximates that of WES, reanalyzing WES raw data is recommended before performing WGS.” (p. 1333)

American College of Medical Genetics

A statement from ACMG (Deignan, 2019) included considerations for case-level exome re-analysis, which include the following:

Significant improvements have been made to bioinformatics handling of the data (alignment/variant calling and/or the automated filtering processes)
Updated clinical and family history information, which may result in the identification of additional variants that are associated with the indication(s) for testing. (p. 1269)

Patient-Centered Laboratory Utilization Guidance Services

The PLUGS July 2023 guidelines entitled “Genomic Sequencing for Rare Disease” state the following regarding reanalysis of exome or genome sequencing data:
“Periodic reanalysis of previously obtained exome or genome sequence has the potential for additional diagnostic yield because of expanding variant databases, as well as periodic novel

Concert Genetic Testing: Exome and Genome Sequencing for the Diagnosis
of Genetic Disorders
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Date of Last Revision: 11/24
CENTENE Corporation

gene discovery and publication. A review of twenty-seven peer-reviewed articles revealed a median new diagnosis rate via reanalysis of 15% and median reanalysis timeframe of 22 months. The authors suggest that an interval of greater than 18 months from the original report may be optimal for reanalysis.” (p. 3)

The guidelines also state: “Re-analysis of previously obtained exome or genome sequence has the potential for additional diagnostic yield because of expanding variant databases, as well as periodic novel gene discovery and publication. Re-analysis could be considered prior to additional genomic sequencing, particularly if there has been onset or identification of additional symptoms that broadens the clinical phenotype assessed during the original ES/GS analysis…” (p. 8)

Rapid Exome Sequencing

American College of Medical Genetics and Genomics (ACMG)

In 2021, ACMG (Manickam, et al) published an evidence-based clinical practice guideline on exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability.), which included the following:

“We strongly recommend ES and GS as a first- or second-tier test… for patients with one or more congenital anomalies prior to one year of age, or for patients with intellectual disability/developmental delay with onset prior to 18 years of age. (p. 2031).
“Isolated autism without ID or congenital malformation is formally out of scope for this recommendation but evaluation of exome/genome studies is ongoing.” (p. 2034)

Concert Genetic Testing: Exome and Genome Sequencing for the Diagnosis
of Genetic Disorders
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National Society for Genetic Counselors

Individuals with unexplained epilepsy should be offered genetic testing, without limitation of age.
Multi-gene, comprehensive testing, such as exome sequencing, genome sequencing or a multigene panel as a first-tier test is strongly recommended.

Patient-Centered Laboratory Utilization Guidance Services

The etiology of the patient’s features is not known, and a genetic etiology is considered a likely explanation for the phenotype, based on one of the following…
a. Epilepsy of unexplained etiology with onset at any age, OR
b. Confirmed bilateral sensorineural hearing loss of unknown etiology and panel testing is unrevealing, OR
c. Intellectual disability, following formal assessment by a developmental pediatrician or neurologist, defined as moderate/severe/profound by Diagnostic and Statistical Manual of Mental Disorders (DSM-5) criteria, diagnosed by 18 years of age, OR
d. Global developmental delay, following formal assessment by a developmental pediatrician or neurologist, defined as significant delay in younger children, under age five years, in at least two of the major developmental domains: gross or fine

Concert Genetic Testing: Exome and Genome Sequencing for the Diagnosis
of Genetic Disorders
V1.2025
Date of Last Revision: 11/24
CENTENE Corporation

motor; speech and language; cognition; social and personal development; and activities of daily living, OR
e. Multiple congenital anomalies affecting unrelated organ systems, OR
f. At least TWO of the following criteria are met:

i. Abnormality affecting at minimum a single organ system  
ii. Autism  
iii. Severe neuropsychiatric condition (e.g., schizophrenia, bipolar disorder, Tourette syndrome, self-injurious behavior, reverse sleep-wake cycles)  
iv. Symptoms of a complex neurological condition (e.g., dystonia, hemiplegia, spasticity, hypotonia, myopathy, muscular dystrophy)  
v. Family history strongly suggestive of a genetic etiology, including consanguinity  
vi. Period of unexplained developmental regression (unrelated to epilepsy or autism)  
vii. Laboratory findings suggestive of an inherited metabolic disorder

Alternate etiologies have been considered and ruled out, when possible (e.g., MRI abnormalities/brain malformations, environmental exposure, injury, infection, isolated prematurity), AND
Clinical presentation does not fit a well-described syndrome for which more targeted testing is available.” (p. 7)

Rehm et al (2023)

A 2023 paper by Rehm et al demonstrated that exome and genome sequencing had a significantly lower VUS rate (22.5%) compared to multigene panels (32.6%). (p. 5 and 6)

Kingsmore SF, Cakici JA, Clark MM et al. 2019

The NSIGHT2 study, a prospective randomized, controlled, blinded trial (RCT) in acutely ill infants, found that 24% of infants undergoing rapid exome sequencing had genetic disease. They conclude that diagnostic testing in infants with diseases of unknown etiology, rapid genomic sequencing, including rapid exome sequencing can be performed as a first tier test in infants with diseases of unknown etiology at time of admission to ICUs. In unstable infants and in those whom a genetic diagnosis was likely to impact immediate management, rapid genomic sequencing had optimal analytic and diagnostic performance by virtue of shortest time to results. (p. 725)

Belanger, et al

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CENTENE Corporation

A review of the evaluation of children with global developmental delay and intellectual disability by Belanger et al (2018) defines global developmental delay (GDD) as the following:

Significant delay (at least 2 standard deviations below the mean) in at least two developmental domains (gross or fine motor, speech/language, cognition, social/personal or activities of daily living. (p. 404)

Standard Genome Sequencing

American College of Medical Genetics and Genomics (ACMG)

“We strongly recommend ES and GS as a first- or second-tier test… for patients with one or more congenital anomalies prior to one year of age, or for patients with intellectual disability/developmental delay with onset prior to 18 years of age. (p. 2031)
“Isolated autism without ID or congenital malformation is formally out of scope for this recommendation but reevaluation of exome/genome studies is ongoing. (p. 2034)

In 2020, ACMG (Malinowski et al) released a systematic evidence-based review (Malinowski, 2020), which “provide[d] indirect evidence of the clinical and personal utility of ES/GS for patients with CA/DD/ID and their family members, noting that a “change in clinical management” resulted in over half of the patients examined as a result of their ES/GS results. (p. 1001)

In 2022, ACMG (Li et al) released a clinical practice resource for the clinical evaluation of hearing loss published, which states that first-line genetic testing for individuals with exam findings that suggest a syndromic hearing loss etiology may include a variety of tests, including genome sequencing, depending on clinical presentation. For individuals without physical findings that suggest a syndromic hearing loss etiology, they recommend a tiered approach, starting with comprehensive hearing loss gene panel testing unless a more specific genetic etiology is evident for which targeted testing is appropriate. (p. 1400)

National Society for Genetic Counselors

Concert Genetic Testing: Exome and Genome Sequencing for the Diagnosis
of Genetic Disorders
V1.2025
Date of Last Revision: 11/24

The National Society for Genetic Counselors (NSGC) released a position statement (2013, updated
2020, reaffirmed 2023) stating the following in regard to secondary and incidental findings in
genetic testing:

“The National Society of Genetic Counselors strongly advises pre-test counseling that
facilitates informed decision-making, elicits patient preferences regarding secondary and/or
incidental findings if possible, and formulates a plan for returning such results before
testing occurs.”

The National Society of Genetic Counselors (NSGC) published evidence-based practice
guidelines for individuals with unexplained epilepsy (Smith et al, 2022). The NSGC
recommendations are as follows (p. 4):

- Individuals with unexplained epilepsy should be offered genetic testing, without
  limitation of age.
- Multi-gene, comprehensive testing, such as exome sequencing, genome sequencing or a
  multigene panel as a first-tier test is strongly recommended.

Patient-Centered Laboratory Utilization Guidance Services

In the PLUGS July 2023 guidelines entitled “Genomic Sequencing for Rare Disease,” the
following clinical criteria are recommended for exome sequencing and genome sequencing.

“Exome sequencing or genome sequencing (ES/GS) is considered medically necessary when
ALL of the following criteria are met: ...

1. The etiology of the patient’s features is not known, and a genetic etiology is considered a
   likely explanation for the phenotype, based on one of the following...
   a. Epilepsy of unexplained etiology with onset at any age, OR
   b. Confirmed bilateral sensorineural hearing loss of unknown etiology and panel
      testing is unrevealing, OR
   c. Intellectual disability, following formal assessment by a developmental
      pediatrician or neurologist, defined as moderate/severe/profound by Diagnostic
      and Statistical Manual of Mental Disorders (DSM-5) criteria, diagnosed by 18
      years of age, OR
   d. Global developmental delay, following formal assessment by a developmental
      pediatrician or neurologist, defined as significant delay in younger children, under
      age five years, in at least two of the major developmental domains: gross or fine
      motor; speech and language; cognition; social and personal development; and
      activities of daily living, OR
   e. Multiple congenital anomalies affecting unrelated organ systems, OR
   f. At least TWO of the following criteria are met:
      i. Abnormality affecting at minimum a single organ system
      ii. Autism
      iii. Severe neuropsychiatric condition (e.g., schizophrenia, bipolar disorder,
           Tourette syndrome, self-injurious behavior, reverse sleep-wake cycles)
      iv. Symptoms of a complex neurological condition (e.g., dystonia,
          hemiplegia, spasticity, epilepsy, hypotonia, myopathy, muscular dystrophy)
      v. Family history strongly suggestive of a genetic etiology, including
         consanguinity
      vi. Period of unexplained developmental regression (unrelated to epilepsy or
          autism)
   vii. Laboratory findings suggestive of an inherited metabolic disorder
2. Alternate etiologies have been considered and ruled out, when possible (e.g., MRI
     abnormalities/brain malformations, environmental exposure, injury, infection, isolated
     prematurity), AND
3. Clinical presentation does not fit a well-described syndrome for which more targeted
   testing is available.” (p. 7)

Rehm et al (2023)

A 2023 paper by Rehm et al demonstrated that exome and genome sequencing had a significantly
lower VUS rate (22.5%) compared to multigene panels (32.6%). (p. 5 and 6)

Belanger, et al

A review of the evaluation of children with global developmental delay and intellectual disability
by Belanger et al (2018) defines global developmental delay (GDD) as the following:
- Significant delay (at least 2 standard deviations below the mean) in at least two
  developmental domains (gross or fine motor, speech/language, cognition, social/personal or
  activities of daily living. (p. 404)

Rapid Genome Sequencing
Patient-Centered Laboratory Utilization Guidance Services

In the PLUGS June 2022 guidelines entitled “Rapid Genome Sequencing,” the following clinical
criteria are recommended for coverage for “acutely-ill individuals” who meet “ALL of the
following criteria”:

“1. The etiology of the patient’s features is not known and a genetic etiology is considered a
   likely explanation for the phenotype, based on one of the following:
   a) Multiple congenital abnormalities affecting unrelated organ systems, OR
   b) Epileptic encephalopathy, OR
   c) TWO of the following criteria are met:
      - abnormality affecting at minimum a single organ system
      - symptoms of a complex neurological condition (e.g., dystonia, hemiplegia,
        spasticity, epilepsy, hypotonia, myopathy, muscular dystrophy, global
        developmental delay, intellectual disability)
      - family history strongly suggestive of a genetic etiology, including
        consanguinity
      - laboratory findings suggestive of an inborn error of metabolism
      - abnormal response to standard therapy
2. Alternate etiologies have been considered and ruled out when possible (e.g., MRI
   abnormalities/brain malformations, environmental exposure, injury, infection, isolated
   prematurity), AND
3. rGS is more efficient and economical than the separate single-gene tests or panels that would
   be recommended based on the differential diagnosis (e.g., genetic conditions that demonstrate a
   high degree of genetic heterogeneity)…” (p. 3 and 4)

National Society for Genetic Counselors

The National Society for Genetic Counselors (NSGC) released a position statement (2013, updated
2020, reaffirmed 2023) stating the following in regard to secondary and incidental findings in
genetic testing:

“The National Society of Genetic Counselors strongly advises pre-test counseling that
facilitates informed decision-making, elicits patient preferences regarding secondary and/or
incidental findings if possible, and formulates a plan for returning such results before
testing occurs.”

The National Society of Genetic Counselors (NSGC) published evidence-based practice
guidelines for individuals with unexplained epilepsy (Smith et al, 2022). The NSGC
recommendations are as follows (p. 4):

- Individuals with unexplained epilepsy should be offered genetic testing, without
  limitation of age.
- Multi-gene, comprehensive testing, such as exome sequencing, genome sequencing or a
  multigene panel as a first-tier test is strongly recommended.

Kingsmore SF, Cakici JA, Clark MM et al. 2019

This report is from the NSIGHT2 study, a prospective randomized, controlled, blinded trial (RCT)
in acutely ill infants, primarily from the NICU, PICU, and CVICU at Rady Children’s Hospital,
San Diego (RCHSD) to compare the effectiveness and outcomes between rWGS and rWES, with
analysis as singleton probands and familial trios. The inclusion criteria for the 1,248 ill infants
defined the maximum age at the time of admission as four months. They found that 24% of infants
undergoing rapid exome sequencing had genetic disease. They conclude that diagnostic testing in
infants with diseases of unknown etiology, rapid genomic sequencing, including rapid exome
sequencing can be performed as a first tier test in infants with diseases of unknown etiology at time
of admission to ICUs. In unstable infants and in those whom a genetic diagnosis was likely to
impact immediate management, rapid genomic sequencing had optimal analytic and diagnostic
performance by virtue of shortest time to results. (p. 725)

Rehm et al (2023)

A 2023 paper by Rehm et al demonstrated that exome and genome sequencing had a significantly
lower VUS rate (22.5%) compared to multigene panels (32.6%). (p. 5 and 6)

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| Reviews, Revisions, and Approvals | Revision Date | Approval Date |
|----------------------------------|---------------|---------------|
| Policy developed.                | 03/23         | 03/23         |
| Semi-annual review. Updated title to reflect V1.2024 version. Throughout policy: replaced “coverage criteria” with “criteria”. Overview, coding, reference-table, background and references updated. For Overview: added “GS has been shown to have...”. For Other Related Policies: added “and Molecular”. For Standard Exome | 10/23         | 10/23         |
Sequencing: under I.A.1. added “diagnosed”; under I.A.2. removed “etiology of the member/enrollee’s features...” and replaced with “member/enrollee has developmental delay...”; under I.A.3. added “The member/enrollee was diagnosed...”; added I.A.4. added “The etiology of the member/enrollee’s features,...”; under I.A.4.b. removed “criteria are met” and added “Abnormality of at least one”; under I.B. added “The member/enrollee has not previously...”; under I.F. removed “during the hospitalization”; under I.G. replaced “Board Certified...” with “Medical Geneticist...” and added “(APGN)”; under I.H. removed “Board Certified...” and added “Genetic Counselor”; under II. removed “For the above indications...” is considered not medically necessary; removed II.A. “Significant new symptoms...”; removed II.B. “The member/enrollee has been re-evaluated...”; removed II.C. “There have been improvements...”; removed III. “Repeat standard exome...” and added “Standard exome sequencing...”; added “Reanalysis of Whole Exome Sequencing Data...”. For Rapid Exome Sequencing: under I.B. removed “Board Certified...” and replaced with “Medical Geneticist...”; under I.B. added “AND”; under I.C. added “Non-genetic etiologies...”; under I.D.2. removed “criteria are met”; under I.2.a. removed “significantly” and “minimum a single”; under I.C.2.d. removed “Dysmorphic features, OR”; for I.D. removed “Alternate etiologies, ...”; under I.F. removed “standard” and added “and other standard laboratory...”; under I.H. removed “Board Certified” and added “(APGN)”; For Standard Genome Sequencing Panel: removed “0209U...” and added “0212U...”; under I.A. added “The member/enrollee previously had...” under I.A.1. “WES reanalysis...”; under I.B. added “The member/enrollee meets...” under I.B.1. “The member/enrollee has unexplained...”; under I.B.2. added “The member/enrollee has developmental...”; under I.B.3. added “The member/enrollee was diagnosed...”; under I.B.4. added “The etiology of the member/enrollee’s...”; under I.B.4.a. added “Multiple congenital abnormalities...”; under I.B.4.b. added “TWO of the following...”; under I.B.4.b.1. added “Abnormality...”; under I.B.4.b.2. added “Dysmorphic features...”; under I.B.4.b.3. added “Encephalopathy...”; under I.B.4.b.4. added “Symptoms of a complex...”; under I.B.4.b.5. added “Family history strongly...”; under I.B.4.b.6. added “Clinical or laboratory...”; under I.B.5. added “Alternate etiologies...”; under I.B.6. added “Clinical presentation...”; under I.B.7. added “There is a predicted...”; under I.B.8. added “Pre- and post-test...”; under I.C. added “Standard genome sequencing...”; For Rapid Exome Sequencing: under I.B. removed “Board-Certified...” and added “Genetic Counselor”; under I.C.2. removed “criteria are met”; under I.C.2.a. removed “significantly” and “minimum a single” and added “least one”; under I.I.1. removed “Board Certified” and added “(APGN)”; under I.J. replaced “acutely ill infant” with “member/enrollee” and removed “diagnoses”; For Clinical Considerations: removed “While trio sequencing...”; removed “When appropriate, retesting...”; removed “Variant-level reanalysis...”; removed “Case-level
reanalysis...”. For Background and Rationale: added “which included the following:”; added “for patients”; added “Of note, ACMG...”; removed “In regards to repeat exome sequencing...”; removed “UpToDate...”; removed “Rapid Genome Sequencing...”; added “Traditional genetic testing...”; added “Reanalysis of Whole Exome Sequencing Data...”; added “Rapid Exome Sequencing...”; for Standard Genome Sequencing: added “A 2021 revision...”; removed “Sequencing may be performed...”; removed “(section E.6); added “Abul-Husn, et al...”; added “Chung, et al...”; added “Patient-centered Laboratory...”; added “National Society of Genetic Counselors...”; added “Rehm et al (2023).... For Rapid Genome Sequencing: removed “(p.3)”; added “Rehm et al (2023)....”

Added CPT codes 0425U, 0426U to the policy reference table and criteria for Rapid Genome Sequencing. | 11/23 |               |
| Semi-annual review. Updated title to reflect V2.2024 version. In Reanalysis of Exome or Genome Sequencing Data criteria, expanded to allow a path to approval for patient to get reanalysis prior to 18 months if they have new qualifying findings (supported by PLUGS). In Standard Exome Sequencing criteria, minor expansion in coverage in response to client feedback to remove burdensome criteria and better align with guidelines (e.g., bilateral sensorineural hearing loss of unknown etiology plus one other eligible finding is now covered under the policy). In Standard Exome Sequencing criteria, minor restriction – changed developmental delay definition to “global developmental delay” based on medical director feedback and to be consistent with guidelines. In Rapid Exome Sequencing criteria, minor expansion in coverage in response to client feedback to remove burdensome criteria and better align with guidelines (e.g., bilateral sensorineural hearing loss of unknown etiology plus one other eligible clinical finding is now covered under the policy). In Rapid Epilepsy Sequencing criteria, removed “diagnosed at any age” from unexplained epilepsy statement, since rapid exome sequencing is only appropriate for individuals 12 months of age or younger. Removed “intellectual disability” and “autism” from criteria set, since rapid exome sequencing is only appropriate for individuals 12 months of age or younger and these cannot be diagnosed until an older age Minor restriction – changed developmental delay definition to “global developmental delay” based on medical director feedback and to be consistent with guidelines. In Standard Genome Sequencing criteria, minor expansion in coverage in response to client feedback to remove burdensome criteria and better align with guidelines (e.g., bilateral sensorineural hearing loss of unknown etiology plus one other eligible clinical finding is now covered under the policy). In Standard Genome Sequencing criteria, minor restriction – changed developmental delay definition to “global developmental delay” based on medical director feedback and to be consistent with guidelines. In Rapid Genome Sequencing criteria, minor expansion in coverage in response to client feedback to
remove burdensome criteria and better align with guidelines (e.g., Epileptic encephalopathy is now an eligible clinical finding covered under the policy). In Reanalysis of Exome or Genome Sequencing Data criteria, criteria set name changed (formerly “Reanalysis of Whole Exome Sequencing Data”). Minor rewording for clarity throughout. Coding, reference-table, background and references updated. |               |               |
| Semi-annual review. Updated title to reflect V1.2025 version. Standard Genome Sequencing: Replaced PLA codes for an exome + mitochondrial test with more relevant exome tests in the Standard Exome section of policy reference table; Added phrase “with trio testing when possible” to criteria to guide providers and provide clarity; Streamlined content in Background and Rationale for clarity and brevity. Standard Exome Sequencing: Streamlined content in Background and Rationale for clarity and brevity; Updated references in Policy Reference Table. Rapid Exome Sequencing: Streamlined portions of Background and Rationale section for brevity. Rapid Genome Sequencing: Streamlined portions of Background and Rationale section for brevity. | 11/24         | 11/24         |



## Important Reminder

This clinical policy has been developed by appropriately experienced and licensed health care
professionals based on a review and consideration of currently available generally accepted
standards of medical practice; peer-reviewed medical literature; government agency/program
approval status; evidence-based guidelines and positions of leading national health professional
organizations; views of physicians practicing in relevant clinical areas affected by this clinical
policy; and other available clinical information. The Health Plan makes no representations and
accepts no liability with respect to the content of any external information used or relied upon in
developing this clinical policy. This clinical policy is consistent with standards of medical practice
current at the time that this clinical policy was approved. “Health Plan” means a health plan that
has adopted this clinical policy and that is operated or administered, in whole or in part, by Centene
Management Company, LLC, or any of such health plan’s affiliates, as applicable.

The purpose of this clinical policy is to provide a guide to medical necessity, which is a component
of the guidelines used to assist in making coverage decisions and administering benefits. It does not
constitute a contract or guarantee regarding payment or results. Coverage decisions and the
administration of benefits are subject to all terms, conditions, exclusions, and limitations of the
coverage documents (e.g., evidence of coverage, certificate of coverage, policy, contract of
insurance, etc.), as well as to state and federal requirements and applicable Health Plan-level
administrative policies and procedures.

This clinical policy is effective as of the date determined by the Health Plan. The date of posting
may not be the effective date of this clinical policy. This clinical policy may be subject to
applicable legal and regulatory requirements relating to provider notification. If there is a
discrepancy between the effective date of this clinical policy and any applicable legal or regulatory
requirement, the requirements of law and regulation shall govern. The Health Plan retains the right
to change, amend or withdraw this clinical policy, and additional clinical policies may be
developed and adopted as needed, at any time.

This clinical policy does not constitute medical advice, medical treatment, or medical care. It is not
intended to dictate to providers how to practice medicine. Providers are expected to exercise
professional medical judgment in providing the most appropriate care and are solely responsible for
the medical advice and treatment of member/enrollees. This clinical policy is not intended to
recommend treatment for member/enrollees. Member/enrollees should consult with their treating
physician in connection with diagnosis and treatment decisions.

Providers referred to in this clinical policy are independent contractors who exercise independent
judgment and over whom the Health Plan has no control or right of control. Providers are not
agents or employees of the Health Plan.

This clinical policy is the property of the Health Plan. Unauthorized copying, use, and distribution
of this clinical policy or any information contained herein are strictly prohibited. Providers,
member/enrollees, and their representatives are bound to the terms and conditions expressed herein
through the terms of their contracts. Where no such contract exists, providers, member/enrollees
and their representatives agree to be bound by such terms and conditions by providing services to
member/enrollees and/or submitting claims for payment for such services.

Note: For Medicaid member/enrollees, when state Medicaid coverage provisions conflict with
the coverage provisions in this clinical policy, state Medicaid coverage provisions take precedence.
Please refer to the state Medicaid manual for any coverage provisions pertaining to this clinical
policy.

Note: For Medicare member/enrollees, to ensure consistency with the Medicare National
Coverage Determinations (NCD) and Local Coverage Determinations (LCD), all applicable NCDs
and LCDs and Medicare Coverage Articles should be reviewed prior to applying the criteria set
forth in this clinical policy. Refer to the CMS website at http://www.cms.gov for additional
information.

©2018 Centene Corporation. All rights reserved. All materials are exclusively owned by Centene
Corporation and are protected by United States copyright law and international copyright law. No
part of this publication may be reproduced, copied, modified, distributed, displayed, stored in a
retrieval system, transmitted in any form or by any means, or otherwise published without the
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