Genome Sequencing Test Details
The Genome 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 genome 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.
Genome Sequencing Consultation
If you would like assistance in determining the appropriateness of genome 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. Genome 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
- Genome Sequencing requisition form, completed and sent with specimen.
- Acceptable Specimen:
- 4-8mL of whole blood collected in PAXgene Blood DNA tube
- 7mL of whole blood collected in a lavender (K2EDTA/K3EDTA) top tube
Single Genome: $9,000
Trio Genome: $18,000
Current turn-around time for reporting Genome Sequencing is anticipated to be ~16 weeks, but may vary depending upon the complexity of the case and the volume of cases within the laboratory. Please contact us for current turn-around times.Less
The technical component of the Genome Sequencing service is conducted on the HiSeq platform, using 100bp paired-end reads at the Illumina CLIA laboratory located in San Diego, CA. Genomes are sequenced to at least 30X mean coverage, and a minimum of 95% of bases are sequenced to at least 8X coverage. Computational analyses are performed at the Laboratory for Molecular Medicine (LMM). 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 at the Laboratory for Molecular Medicine.
Specific types of genetic variation, such as triplet repeat expansions, translocations, large copy number events, and mitochondrial variation are currently not reliably detected by Genome Sequencing. Additionally, while Genome Sequencing covers ~95% of the genome; there are certain regions for which the assay may fail to adequately generate sequence information. 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.
Genome Sequencing offers a unbiased look at patients’ genetic makeup that can provide them with information about the diseases they have, as well as risks for other diseases.
Interested in Genome Sequencing
For further information, please contact the
Laboratory for Molecular Medicine
Fax: (617) 768-8513
Amy Lovelette Hernandez, MS, CGC
Director of Genetic Counseling
Phone: (617) 768-8516
Ozge Birsoy, PhD
Assistant Laboratory Director
Phone: (617) 768-8396