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- Follow-up gene sequencing
- Full gene sequencing
- Partner gene sequencing
This assay is not currently available in New York state.
Contact an Integrated Genetics laboratory genetic coordinator at 800-255-7357 with any questions. Indicate the specific gene(s) to be analyzed on the test request form. Failure to indicate gene(s) will result in testing delays.
Expected Turnaround Time
14 - 21 days
Turnaround time is defined as the usual number of days from the date of pickup of a specimen for testing to when the result is released to the ordering provider. In some cases, additional time should be allowed for additional confirmatory or additional reflex tests. Testing schedules may vary.
- Fragile X Syndrome, PCR With Reflex to Southern Blot
- GeneSeq®PLUS without VUS
- Inheritest® Carrier Screen, Ashkenazi Jewish Panel (48 Genes)
- Inheritest® Carrier Screen, Comprehensive Panel (144 Genes)
- Inheritest® Carrier Screen, Society-guided Panel (14 Genes)
- Inheritest® Gene-specific Sequencing, NGS
- Spinal Muscular Atrophy (SMA) Carrier Testing
- α-Thalassemia, DNA Analysis
Yellow-top (ACD-A) tube or lavender-top (EDTA) tube
Maintain at room temperature or refrigerate at 4°C.
Causes for Rejection
Frozen specimen; quantity not sufficient for analysis; improper container; yellow-top (ACD-B) tube
Full gene sequencing is available for genes included in the Inheritest®500 PLUS panel. See related Inheritest® test codes: Inheritest® Carrier Screen, Comprehensive (144 genes) (451950); Inheritest® Carrier Screen, Ashkenazi Jewish (48 genes) (451920); Inheritest® Carrier Screen, Society-guided (14 genes) (451960).
For HBA1 and HBA2 (alpha-thalassemis) see α-Thalassemia, DNA Analysis (511172); for SMN1 see Spinal Muscular Atrophy (SMA) Carrier Testing (450010); and for FRM1 see Fragile X Syndrome, PCR with Reflex to Southern Blot (511919). Links to these tests are in Related Information.
Technologies used do not detect germline mosaicism and do not rule out the presence of large chromosomal aberrations, including rearrangements, gene fusions, or variants in regions or genes not included in this test, or possible inter/intragenic interactions between variants. Variant classification and/or interpretation may change over time if more information becomes available. False positive or false negative results may occur for reasons that include: rare genetic variants, sex chromosome abnormalities, pseudogene interference, blood transfusions, bone marrow transplantation, somatic or tissue-specific mosaicism, mislabeled samples, or erroneous representation of family relationships.
Single Nucleotide Polymorphism and Small Indel Sequencing Assessment: Genomic regions of interest are selected using a custom capture reagent for target enrichment and sequenced via the Illumina® next generation sequencing platform. Sequencing reads are aligned with the human genome reference GRCh37/hg19 build. Regions of interest include all exons and intron/exon junctions (+/-20 nucleotides) for each gene analyzed. A minimum of 99% of bases are covered at >15X. Analytical sensitivity is estimated to be >99% for single nucleotide variants, >97% for insertions/deletions less than six base pairs, and >95% for insertions/deletions between six and fifteen base pairs. Uncovered regions with known pathogenic variants are sequenced in a targeted manner. All reported variants are confirmed by a second method.
Copy Number Variant Assessment: Next Generation Sequencing is performed and the data are assessed with Illumina’s DRAGEN (Dynamic Read Analysis for GENomics) Bio-IT Platform. Reported variants are confirmed by a second method. Analytical sensitivity is estimated to be >95%.
Spinal Muscular Atrophy: This analysis will detect the copy number of exon 7 of the SMN1 gene. When no copies of SMN1 exon 7 are detected, SMN2 exon 7 copy number is assessed and reported. This test is unable to differentiate between two copies of the SMN1 gene on one allele (in cis) versus two copies of the gene on different alleles (in trans). When two copies of SMN1 exon 7 are detected, the data are assessed for the presence of the c.*3+80T>G “silent carrier” variant.
Congenital Adrenal Hyperplasia: This analysis will detect most large rearrangements/deletions/duplications within the CYP21A2 gene, as well as the presence of seven of the most common pathogenic variants in the gene: 1) c.518T>A (p.Ile173Asn), Chr6:32007203; 2) c.713T>A (p.Val238Glu); Chr6:32007587; 3) c.719T>A (p.Met240Lys); Chr6:32007593; 4) c.923dup (p.Leu308Phefs); Chr6:32007966; 5) c.293-13C/A>G; Chr6:32006858; 6) c.332_339delGAGACTAC (p.Gly111Valfs); Chr6:32006910-32006917; 7) c.-113G>A; Chr6:32006087. Other point mutations and small indels and reciprocal changes between CYP21A2 and CYP21A1P are not detected by this analysis. The analytical sensitivity of this assay is estimated to be >99%.
Alpha thalassemia: Variants included in the analysis of the alpha-globin (HBA) gene cluster are the Constant Spring non-deletion variant and the following deletions: -alpha3.7, -alpha4.2, --alpha20.5, --SEA, --FIL, --THAI, --MED, and the HS-40 regulatory region.
Reported Variants: Pathogenic variants, likely pathogenic variants, and variants of uncertain significance are reported after confirmation by an appropriate technology. NEB variants occurring in exons 82-105 may not be reliably detected by this analysis and are not reported. Nondeletion variants are specified using the numbering and nomenclature recommended by the Human Genome Variation Society. Benign and likely benign variants are not reported. Variant classification is consistent with ACMG standards and guidelines.