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GeneSeq®PLUS

CPT: Call client services.
Updated on 06/29/2020

Synonyms

  • Follow-up gene sequencing
  • Full gene sequencing
  • Partner gene sequencing

Special Instructions

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



Related Documents

For more information, please view the literature below.

Inheritest®500 PLUS Panel Brochure

    For more information, please view the literature below.

    Inheritest®500 PLUS Panel Brochure

    For more information, please view the literature below.

    Inheritest®500 PLUS Panel Brochure


    Specimen Requirements


    Specimen

    Whole blood


    Volume

    8.5 mL

    8.5 mL

    8.5 mL

    8.5 mL

    8.5 mL


    Container

    Yellow-top (ACD-A) tube or lavender-top (EDTA) tube


    Storage Instructions

    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


    Test Details


    Use

    Full gene sequencing is available for the majority of genes included in the Inheritest®500 PLUS Panel. For SMN1, use Spinal Muscular Atroophy (SMA Carrier Testing) [450010]; for FMR1, use Fragile X Syndrome, PCR With Reflex to Southern Blot [511919].


    Limitations

    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.


    Methodology

    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 15 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%.

    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.

    NGS Reported Variants: Pathogenic, likely pathogenic, and variants of uncertain significance variants 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. Likely benign and benign variants are not reported. Variant classification is consistent with ACMG standards and guidelines. When provided, carrier rates and detection rates are derived from gnomAD and ClinVar. For unknown or mixed ethnicities, the ethnic background with the most conservative risk estimate is used. For a complete list of residual risks for all genes on this panel, visit www.integratedgenetics.com.


    References

    den Dunnen JT. Describing Sequence Variants Using HGVS Nomenclature. Methods Mol Biol. 2017;1492:243-251.27822869
    Monaghan KG, Lyon E, Spector EB; American College of Medical Genetics and Genomics. ACMG Standards and Guidelines for fragile X testing: a revision to the disease-specific supplements to the Standards and Guidelines for Clinical Genetics Laboratories of the American College of Medical Genetics and Genomics. Genet Med. 2013 Jul;15(7):575-586.23765048
    Richards S, Aziz N, Bale S. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015 May;17(5):405-424.25741868

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