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Genetic Testing, Including Chromosomal Microarray Analysis and Next-Generation Sequencing Panels, for Prenatal Evaluation and the Evaluation of Children With Developmental Delay/Intellectual Disability or Autism Spectrum Disorder
DESCRIPTIONChromosomal microarray (CMA) testing has been proposed for detection of genetic imbalances in infants or children with characteristics of developmental delay/intellectual disability (DD/ID) or autism spectrum disorder (ASD). G-banded karyotyping has for many years been the standard first-line test for this purpose. G-banded karyotyping allows visualization and analysis of chromosomes for chromosomal rearrangements including genomic gains and losses. Chromosomal microarray (CMA) analysis performs a similar, although non-visual, analysis at a much higher resolution. As a result, CMA has the potential to increase the diagnostic yield in this population and change clinical interpretation in some cases.
Children with signs of neurodevelopmental delays or disorders in the first few years of life may eventually be diagnosed with mental retardation or autism syndromes, serious and lifelong conditions that present significant challenge to families and to public health. Cases of developmental delay / mental retardation and of autism are associated with genetic abnormalities. For children with clear, clinical symptoms and / or physiologic evidence of syndromic neurodevelopmental disorders, diagnoses are based primarily on clinical history and physical examination, and then may be confirmed with genetic testing. However, for children who do not present with obvious syndrome, who are too young for full expression of a suspected syndrome, or who may have an atypical presentations, genetic testing is used as a basis for establishing a diagnosis.
Current guidelines for these patients, such as those published by the American Academy of Pediatrics (AAP) and the American Academy of Neurology (AAN), recommend cytogenetic evaluation to look for certain kinds of chromosomal abnormalities that may be causally related to their condition. The AAN guidelines note that only in occasional cases will an etiologic diagnosis lead to specific therapy that improves outcomes but suggest the more immediate and general clinical benefits of achieving a specific genetic diagnosis from the clinical viewpoint, as follows (1):
AAP and AAN guidelines also emphasize the importance of early diagnosis and intervention in an attempt to ameliorate or improve behavioral and cognitive outcomes over time.
Most commonly, genetic abnormalities associated with neurodevelopmental disorders are deletions and duplications of large segments of genomic material, which are called "copy number variants" or CNVs. For many well-described syndromes, the type and location of the chromosomal abnormality has been established with the study of large number of cases and constitutes a genetic diagnosis; for others, only a small number of patients with similar abnormalities may exist to support a genotype-phenotype correlation. Finally, for some patients, cytogenetic analysis will discover entirely new chromosomal abnormalities that will require additional study to determine their clinical significance.
Conventional methods pf cytogenetic analysis, including karyotyping (e.g., G-banded) and fluorescence in situ hybridization (FISH), have relatively low resolution and a low diagnostic yield (i.e., proportion of tested patients with clinically relevant genomic abnormalities), leaving the majority of cases without identification of a chromosomal abnormality associated with the child's condition.
CMA analysis is a newer cytogenetic analysis method that increases the chromosomal resolution for detection of CNVs, and, as a result, increases the genomic detail beyond that of conventional methods and may increase the diagnostic yield. Array CGH results are clinically informative in the same way as results derived from conventional methods and thus CMA represents an extension of standard methods with increased resolution.
CMA Analysis to Determine Genetic Etiology
CMA analysis detects CNVs by comparing a reference genomic sequence (“normal”) with the corresponding patient sequence. Each sample has a different fluorescent label so that they can be distinguished, and both are co-hybridized to a sample of a specific reference (also normal) DNA fragment of known genomic locus. If the patient sequence is missing part of the normal sequence (deletion) or has the normal sequence plus additional genomic material within that genomic location (e.g., a duplication of the same sequence), the sequence imbalance is detected as a difference in fluorescence intensity. For this reason, standard CMA (non-single nucleotide polymorphisms (SNP), see following) cannot detect balanced CNVs (equal exchange of material between chromosomes) or sequence inversions (same sequence is present in reverse base pair order) because the fluorescence intensity would not change.
CMA analysis uses thousands of cloned or synthesized DNA fragments of known genomic locus immobilized on a glass slide (microarray) to conduct thousands of comparative reactions at the same time. The prepared sample and control DNA are hybridized to the fragments on the slide, and CNVs are determined by computer analysis of the array patterns and intensities of the hybridization signals. Array resolution is limited only by the average size of the fragment used and by the chromosomal distance between loci represented by the reference DNA fragments on the slide.
There are some differences in CMA technology, most notably in the various types of microarrays. They can differ first by construction; earliest versions were used of DNA fragments cloned from bacterial artificial chromosomes (BAC). These have been largely replaced by oligonucleotide (oligos; short, synthesized DNA) arrays, which offer better reproducibility. Finally, arrays that detect hundreds of thousands of single nucleotide polymorphisms (SNP) across the genome have some advantages as well. Oligo/SNP hybrid arrays have been constructed to merge the advantages of each. Regardless of the array components used, all microarrays allow the deposition of many thousands of short, DNA probe sequences on a small, solid surface in an orderly fashion. The location of each known probe sequence allows the identification of the test sequence bound to it, and when compared to a control sequence, the identification of missing sequences or sequences with extra copies (i.e. copy number variants).
Microarrays may be prepared by the laboratory utilizing the technology, or, more commonly by commercial manufacturers, and sold to laboratories that must qualify and validate the product for use in their assay, in conjunction with computerized software for interpretation. The proliferation of in-house developed and commercially available platforms prompted the American College of Medical Genetics (ACMG) to publish guidelines for the design and performance expectations for clinical microarrays and associated software in the postnatal setting. (2)
Targeted CMA analysis provides high-resolution coverage of the genome primarily in areas containing known, clinically significant CNVs. The ACMG guideline for designing microarrays recommends probe enrichment in clinically significant areas of the genome to maximize detection of known abnormalities but also recommends against the use of targeted arrays in the postnatal setting. Rather, a broad genomic screen is recommended to identify atypical, complex, or completely new rearrangements, and to accurately delineate breakpoints.
Whole-genome CMA analysis has allowed the characterization of several new genetic syndromes, with other potential candidates currently under study. However, the whole-genome arrays also have the disadvantage of potentially high numbers of apparent false-positive results, because benign CNVs are also found in phenotypically normal populations; both benign and pathogenic CNVs are continuously cataloged and to some extent made available in public reference databases to aid in clinical interpretation. Additionally, some new CNVs are neither known to be benign nor causal; these CNVs may require detailed family history and family genetic testing to determine clinical significance and/or may require confirmation by subsequent accumulation of similar cases and so, for a time, may be considered a CNV of undetermined significance (some may eventually be confirmed true positives or causal, others false positives or benign).
To determine clinical relevance (consistent association with a disease) of CNV findings, the following actions are taken:
ACMG has also published guidelines for the interpretation and reporting of CNVs in the postnatal setting, in order to promote consistency among laboratories and CMA results. (10) Three categories of clinical significance are recommended for reporting: pathogenic, benign, and uncertain clinical significance.
In 2008, the International Standards for Cytogenomic Arrays (ISCA) Consortium was organized (Available online at: https://www.iscaconsortium.org/index.php); to date, it has established a public database containing de-identified whole genome microarray data from a subset of the ISCA Consortium member clinical diagnostic laboratories. Array analysis was carried out on individuals with phenotypes including intellectual disability, autism, and developmental delay. As of November 2011, there are over 28,500 total cases in the database. Additional members are planning to contribute data; participating members use an opt-out, rather than an opt-in approach that was approved by the National Institutes of Health (NIH) and participating center institutional review boards. The database is held at NCBI/NIH and curated by a committee of clinical genetics laboratory experts.
Use of the database includes an intralaboratory curation process, whereby laboratories are alerted to any inconsistencies amongst their own reported CNVs or other mutations, as well as any not consistent with the ISCA “known” pathogenic and “known” benign lists. The intralaboratory conflict rate was initially about 3% overall; following release of the first ISCA curated track, the intralaboratory conflict rate decreased to about 1.5%. A planned interlaboratory curation process, whereby a group of experts curates reported CNVs/mutations across laboratories, is currently in progress.
The Consortium recently proposed “an evidence-based approach to guide the development of content on chromosomal microarrays and to support interpretation of clinically significant copy number variation.” The proposal defines levels of evidence (from the literature and/or the ISCA and other public databases) that describe how well or how poorly detected mutations or CNVs are correlated with phenotype. The consortium will apparently coordinate a volunteer effort to describe the evidence for targeted regions across the genome.
The consortium is also developing vendor-neutral recommendations for standards for the design, resolution, and content of cytogenomic arrays using an evidence-based process and an international panel of experts in clinical genetics, clinical laboratory genetics, genomics, and bioinformatics.
CMA analysis is commercially available from several laboratories as a laboratory-developed test. Laboratory-developed tests performed by laboratories licensed for high complexity testing under the Clinical Laboratory Improvement Amendments (CLIA) do not require U.S. Food and Drug Administration (FDA) clearance for marketing.
At a meeting hosted by the FDA in July 2010, the FDA indicated that the Agency will in the future require microarray manufacturers to seek clearance in order to sell their products for use in clinical cytogenetics. Criteria for clearance, however, have not yet been published.
POLICYChromosomal microarray analysis may be considered medically necessary for diagnosing a genetic abnormality in children with apparent nonsyndromic cognitive developmental delay/intellectual disability (DD/ID) or autism spectrum disorder (ASD) according to accepted Diagnostic and Statistical Manual of Mental Disorders-IV criteria when all of the following conditions are met (see Policy Guidelines for definitions):
Chromosomal microarray analysis is considered investigational in all other cases of suspected genetic abnormality in children with developmental delay/intellectual disability or autism spectrum disorder.
Chromosomal microarray analysis to confirm the diagnosis of a disorder or syndrome that is routinely diagnosed based on clinical evaluation alone (see Policy Guidelines) is not medically necessary.
Chromosomal microarray analysis is considered investigational for prenatal genetic testing.
Panel testing using next-generation sequencing is considered investigational in all cases of suspected genetic abnormality in children with developmental delay/intellectual disability or autism spectrum disorder.
Chromosomal microarray analysis is considered investigational for prenatal genetic testing.
POLICY GUIDELINESDefinitions, from the American College of Medical Genetics Guideline, Evaluation of the Newborn with Single or Multiple Congenital Anomalies:
Investigative service is defined as the use of any treatment procedure, facility, equipment, drug, device or supply not recognized by certifying boards and / or approving or licensing agencies or published peer review criteria as standard, effective medical practice for the treatment of the condition being treated and as such therefore is not considered medically necessary.
The coverage guidelines outlined in the Medical Policy Manual should not be used in lieu of the Member's specific benefit plan language.
POLICY HISTORY03/25/2010: Approved by Medical Policy Advisory Committee
04/11/2012: Changed "Array Comparative Genomic Hybridization (aCGH)" to "Chromosomal Microarray (CMA) Analysis" in the policy title and throughout the policy. Policy statement revised to state that testing may be considered medically necessary for infants and children with developmental delay, intellectual disability, or autism spectrum disorder under certain conditions. Also changed "mental retardation" to "intellectual disability" throughout the policy and in the title. Added 81228 and 81229 to the Code Reference section and moved S3870 to the Covered Codes table.
04/18/2013: Policy reviewed; no changes.
07/11/2014: Policy title changed from "Chromosomal Microarray (CMA) Analysis for the Genetic Evaluation of Patients with Developmental Delay/Intellectual Disability or Autism Spectrum Disorder" to "Genetic Testing, Including Chromosomal Microarray Analysis and Next-Generation Sequencing Panels, for Prenatal Evaluation and the Evaluation of Children With Developmental Delay/Intellectual Disability or Autism Spectrum Disorder." Policy statement updated to add the following: 1) Panel testing using next-generation sequencing is considered investigational in all cases of suspected genetic abnormality in children with developmental delay/intellectual disability or autism spectrum disorder. 2) Chromosomal microarray analysis is considered investigational for prenatal genetic testing.
SOURCESBlue Cross Blue Shield Association Policy # 2.04.59
CODE REFERENCEThis may not be a comprehensive list of procedure codes applicable to this policy.
The code(s) listed below are ONLY medically necessary if the procedure is performed according to the "Policy" section of this document.