| Test Code | D2310E | |
| Test Summary | STAT whole genome sequencing and mitochondrial genome sequencing of the fetus and 2 family members |
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| Turn-Around-Time (TAT)* | 10 - 14 days | |
| Acceptable Sample Types | Cultured Amniocytes Cultured Chorionic Villi DNA, Isolated Products of Conception |
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| Acceptable Billing Types |
Self (patient) Payment Institutional Billing
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|
| NY Approved | No | |
| Self (patient) Price | $7000.00 | |
| Institutional Price | $8100.00 | |
| CPT Codes** | 81243 (x1), 81425 (x1), 81426 (x1), 81479 (x2), 81265 (x1), 81266 (x1), 81329 (x1), 81460 (x1), 88235 (x1) |
STAT Prenatal Genome Sequencing includes:
- Mean coverage of 30X or greater with complete coverage of more than 99% of the exome, including over 5,400 disease-associated genes
- Analysis of single nucleotide variants (SNVs), deletions, and duplications in coding and non-coding regions of the genome
- Reliable detection of large-scale copy number variants (CNVs), including microdeletions and other gene- and chromosomal-level events
- Mitochondrial genome sequencing and analysis of SNVs as low as 5% heteroplasmy
- Rule-out of short tandem repeat (STR) expansion in more than 30 genes, including those associated with intellectual disability, epilepsy, and neuromuscular and movement disorders
- Spinal Muscular Atrophy (SMA) screening via SMN1 copy number characterization
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.
ACMG recommended secondary findings may be requested; however, a report will not be issued for an ongoing pregnancy.
One complimentary reanalysis is included and can be requested at any time.
Access to raw data is included and available via electronic transfer.
- Increased nuchal translucency
- Cystic hygroma
- Fetal anomaly
The purpose of this test is to find the underlying genetic cause for prenatal findings.
Whole genome sequencing is performed on genomic DNA using 2X150bp reads on Illumina next-generation sequencing (NGS) systems at a mean coverage of 40X. 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. Revvity Omics has curated deep intronic pathogenic variants in public databases and these are tagged for identification during analysis. 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 the director’s discretion. Mitochondrial DNA is sequenced and analyzed using the same pipeline. 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. 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 and tandem repeats analysis are 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. SMA testing and repeat expansion disorder screening are performed using in-house bioinformatics tools based on published literature with modification (PMID: 28125085, 32092542, 28887402).
Please contact a PKIG Laboratory genetic counselor for these requests.
Two T-25 flasks
All prenatal specimens will be tested for maternal cell contamination (MCC). Send maternal blood (EDTA tube) for comparison. If blood is unavailable, we will accept genomic DNA and Saliva sample types.
For prenatal samples, PerkinElmer will provide a shipping label to use for shipping the sample to our lab. Please call 1 (866) 354-2910 to arrange this. At this time, you will also be connected to a laboratory genetic counselor to answer any questions about the testing.
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.
- 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 prior to 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.
Sterile, screw-top container filled with tissue culture transport medium.
All prenatal specimens will be tested for maternal cell contamination (MCC). Send maternal blood (EDTA tube) for comparison. Transport products of conception and/or fresh tissue (minimum: 10 mg) in sterile, screw-top container filled with tissue transport medium. Do not place in formalin. If specimen is too large for normal collection tube, a larger sterile container can be used.
For prenatal samples, PerkinElmer will provide a shipping label to use for shipping the sample to our lab. Please call 1 (866) 354-2910 to arrange this. At this time, you will also be connected to a laboratory genetic counselor to answer any questions about the testing.