Background

The Exome Sequencing test aims to end the diagnostic odyssey for individuals with rare genetic disorders, ultimately guiding clinical care for patients and their families. This test provides physicians with high quality exome sequencing, as well as unparalleled data interpretation. Results will be returned to the ordering physician in a concise report featuring an overall test result and in-depth phenotype-driven interpretation of known or plausible genetic causes of disease. Patients have the option to expand the report to include incidental findings (unrelated to the primary indication for testing) in genes recommended by the American College of Medical Genetics (https://www.ncbi.nlm.nih.gov/clinvar/docs/acmg/). Analysis of additional incidental finding genes is also available upon request.

Exome Sequencing Consultation

If you would like assistance in determining the appropriateness of exome sequencing for your patient, you may contact us by phone or submit pages 2–3 of our requisition form, along with your contact information, and we will contact you.

Indication for Testing

Testing is currently recommended for individuals with a suspected genetic disorder in whom traditional genetic testing has not yielded a result, despite a suspected genetic etiology. Exome sequencing may also be considered as a first-line testing strategy for conditions with a high degree of genetic heterogeneity for which panel-based testing is either limited or unavailable.

Requirements, Pricing and TAT

1. Exome Sequencing requisition form, completed and sent with specimen.
2. Acceptable Specimens:

    

   • 7mL of whole blood collected in a lavender (K₂EDTA/K₃EDTA) top tube.
     OR
   • DNA sample: 5–10 µg extracted DNA at a concentration of 50 ng/µl in Tris-EDTA (TE) buffer with OD_260/280 between 1.8–2.0.

    

Methodology

Exome sequence is generated from extracted genomic DNA that is fragmented, barcoded, and subjected to solution phase hybridization with an enhanced Agilent SureSelect Human All Exon V5 Plus probe set. Sequencing is performed on the Illumina HiSeq 2500 platform (rapid mode). Exomes are sequenced to an average target coverage of 125X with 90-95% of bases sequenced to at least 20X coverage. Reads are aligned to the NCBI reference sequence (GRCh37), using the Burrows-Wheeler Aligner (BWA), and variant calls are made using the Genomic Analysis Tool Kit (GATK). Data is filtered based upon automated annotations and case-specific measures, including suspected inheritance patterns and clinical features where appropriate. All reported variants are confirmed via an orthogonal method.

Limitations

Specific types of genetic variation, such as triplet repeat expansions, translocations, large copy number events, and mitochondrial variation are currently not reliably detected by Exome Sequencing. Because Exome Sequencing only covers the coding regions of the genome, any genetic changes residing outside of the targeted region will not be detected. Furthermore, not all coding regions are sufficiently covered and variants in regions of low coverage may not be reliably detected. Gene-level coverage information for both tests is available online and details regarding the coverage of genes associated with a specific indication can be determined upon request.

For additional questions, you also may visit our Frequently Asked Questions page.