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Test Code D1300
Test Summary

Diagnostic whole exome and mitochondrial genome sequencing of the proband and 2 family members

Turn-Around-Time (TAT)* 4 - 6 weeks
Acceptable Sample Types
Whole Blood (EDTA)
DNA, Isolated
Dried Blood Spots
Saliva
Acceptable Billing Types
Self (patient) Payment
Institutional Billing
NY Approved Yes
Self (patient) Price $2000.00
Institutional Price $2000.00
CPT Codes** 81415 (x1), 81416 (x1), 81479 (x2), 81460 (x1)
Revvity Omics Tax ID: 25-1645804
*TAT starts after the sample and all required sample information is received at Revvity Omics.
**The CPT codes listed are in accordance with Current Procedural Terminology, a publication of the American Medical Association, and are provided for informational purposes only. CPT coding is the sole responsibility of the billing party.

Whole Exome Sequencing includes:

  • Mean coverage of 100X with complete coverage of more than 97% of the exome at greater than 20X coverage
  • Enhanced coverage of known disease-causing genes and regions with inclusion of curated, pathogenic deep-intronic and promoter variants
  • Exon-level copy number variant (CNV) calling with reliable detection of the CNVs 3 exons or greater as well as the use of custom breakpoint capture baits to ensure inclusion of common deletion events
  • Mitochondrial genome sequencing and analysis of SNVs

All variants are analyzed according to American College of Medical Genetics and Genomics (ACMG) guidelines, and pathogenic, likely pathogenic, and variants of uncertain significance (VOUS) are reported. Variant analysis is phenotype-driven to minimize the reporting of VOUS.

Familial testing for VOUS is complimentary for up to two variants in two family members.

Complimentary opt-in for additional reports:

  • ACMG Recommended Secondary Findings - pathogenic and likely pathogenic variants in genes recommended for reporting based on well-defined, highly-penetrant phenotypes with clinical actionability
  • Pharmacogenetic Variants - select allele haplotypes recommended by the Association for Molecular Pathology pharmacogenomics working group and classified as Clinical Pharmacogenetics Implementation Consortium (CPIC) level A and PharmGKB level 1A
  • Carrier Status - 330+ genes associated with disorders whose inheritance pattern is autosomal recessive or X-linked
  • Diagnostic findings in all disease-associated genes - pathogenic and likely pathogenic variants are reported in genes associated with disease unrelated to clinical presentation

One complimentary reanalysis is included and can be requested at any time.

Access to raw data is included and available via electronic transfer.

  • Genetically heterogeneous disease caused by likely pathogenic/pathogenic findings in multiple genes
  • Condition suggestive of a genetic disorder with a long differential diagnosis list
  • Unclear or atypical presentation of a genetic disorder
  • Previous genetic testing did not yield a diagnosis

This testing includes whole exome sequencing, copy number variant analysis, and mitochondrial genome sequencing. Sequencing is performed on genomic DNA enriched for the exome using a sequence capture method. Direct sequencing of the amplified captured regions was performed using 2X150bp reads on Illumina next-generation sequencing (NGS) systems. A base is considered to have sufficient coverage at 20X and an exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered at 20X or more. A list of low coverage regions, if any, is available upon request. Alignment to the human reference genome (GRCh37) is performed and annotated variants are identified in the targeted region. Variants reviewed have a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Indels and single nucleotide variants (SNVs) may be confirmed by Sanger sequence analysis before reporting at director discretion. Mitochondrial DNA is sequenced and analyzed using the same pipeline. This assay cannot detect variants in regions of the exome that are not covered, such as deep intronic, promoter, and enhancer regions, and areas containing large numbers of tandem repeats. Genes and/or exons located in pseudogene regions are not covered in this assay. Copy number variation (CNV) analysis detects deletions and duplications; in some instances, due to the size of the exons, sequence complexity, or other factors, not all CNVs may be analyzed or may be difficult to detect. When reported, copy number variant size is approximate. Actual breakpoint locations may lie outside of the targeted regions. This assay does not interrogate CNVs in mitochondrial DNA. CNV analysis will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), methylation abnormalities, triploidy, and genomic imbalances in segmentally duplicated regions. This assay is not designed to detect mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. Primary data analysis is performed using Illumina bcl2fastq converter v2.19. Secondary analysis is performed using Illumina DRAGEN Bio-IT Platform v.3.10.8. Tertiary data analysis is performed using SnpEff v5.0 and Revvity Omics' internal ODIN v.1.01 software. CNV and absence of heterozygosity are assessed using BioDiscovery’s NxClinical v6.1 software.

Whole Blood (EDTA) (Preferred sample type)
Collection Container(s):

EDTA (purple top)

Collection:

Infants (< 2-years): 2 to 3 mL; Children (>2-years): 3 to 5 mL; Older children and adults: Minimum 5mL. The blood tube should be inverted several times immediately after blood collection to prevent coagulation.

Condition: Store at ambient temperature. Do not refrigerate or freeze.
Shipping: Ship overnight at ambient temperature ensuring receipt within 5-days of collection.
SPECIAL INSTRUCTIONS
Clotted or hemolyzed samples are not accepted.
DNA, Isolated
Collection:

Required DNA Quantity by Test Type*:

  • Next Generation Sequencing (NGS): Send >1000 ng total gDNA @ >15 ng/μL. Please ship samples in 10mM Tris. Do not use EDTA.
  • Sanger Sequencing: Send >500 ng total gDNA @ >15 ng/μL (varies by the size of the gene and the variants requested).
  • Non-Sanger Sequencing Tests: Send >500 ng total gDNA @ >15 ng/μL.

 

Condition: * Required DNA Quality: High molecular weight DNA (>12kb). A260/A280 reading should be ≥ 1.8. A260/230 a ratio range of 1.8 to 2.2. Contact the laboratory for specific amounts if total ng cannot be met.
Shipping: Ship overnight at ambient temperature.
SPECIAL INSTRUCTIONS
  • Research Laboratories: DNA extracted in research laboratories is not acceptable. Only under exceptional circumstances (e.g., proband not available) will DNA extracted in a research laboratory be accepted for clinical testing. Additional testing (e.g., of other family members) may be required to confirm results.
  • Laboratories outside the United States: Non-US laboratories are not subject to CLIA regulations and will be reviewed on a case-by-case basis. Please call to speak with a laboratory genetic counselor before submitting a DNA sample from any non-CLIA-certified laboratory.
  • Special Notes: If extracted DNA is submitted, information regarding the method used for extraction should be sent along with the sample.
Dried Blood Spots
Collection Container(s):

Dried blood spot card

Collection:

Follow kit instructions. Briefly, allow blood to saturate the card until indicated areas are filled and blood has soaked through the card. Air dry the card at ambient temperature for at least 3 hours.

  • NBS: Please contact Revvity Omics to request the StepOne® kit.
  • Gene Sequencing: Please contact Revvity Omics to request the DBS collection kit.
  • For pre-punched DBS: The required minimum is 6 punches
Condition: Follow the instructions provided with the collection set. Store the dried blood at ambient temperature for up to two days. If the specimen cannot be sent as soon as it is dry, the filter paper should be placed in a sealable plastic bag and stored in a refrigerator (≤ 8°C) or preferably in a freezer.
Shipping: Follow kit instructions. Double bag and ship overnight at ambient temperature.
Saliva
Collection Container(s):

Oragene™ Saliva Collection Kit or ORAcollect-Dx kit

Collection:

Collect saliva on an Oragene™ Saliva Collection Kit ORAcollect-Dx kit according to the manufacturer’s instructions. 

Condition: Store at ambient temperature. Do not refrigerate or freeze.
Shipping: Ship overnight at ambient temperature.
SPECIAL INSTRUCTIONS
Please contact Revvity Omics to request the saliva collection kit for patients who cannot provide a blood sample as whole blood is the preferred sample. Testing using Saliva swabs is currently not available for customers in India. Contact the Revvity Omics laboratory for more information.

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