Who benefits from clinical genome sequencing?
Testing is useful for patients with rare inherited disorders or with complex clinical presentations lacking a clear diagnosis.
Ideally, sequencing can contribute to a diagnosis, potentially getting answers that have been elusive. The medical provider can then use that diagnosis to avoid additional tests and develop a treatment plan. Sequencing and analysis could also shed light on recurrence risk factors and assist with family planning.
Patients under consideration should be evaluated by medical providers with expertise in the patient’s condition to help the laboratory correlate patient symptoms and family history with the variants identified from sequencing. The provider should consider patients with an undiagnosed disorder with a suspected genetic cause. Patients with rare or distinctive symptoms or a strong family history with multiple affected members may derive the most benefit.
What do patients need to know about genetic sequencing?
Consider directing patients to the Smith Family Clinic’s Frequently Asked Questions for more information. The Smith Family Clinic for Genomic Medicine, LLC is located on HudsonAlpha’s campus and works with the CSL for clinical genomic sequencing. You might also consider directing patients to the clinic’s fundamental information on genetic sequencing.
How does the CSL handle data and privacy?
The lab is HIPAA compliant, and the reports are only released to the ordering physician or other entities that are specified by the patient. The Clinical Services Lab, LLC recognizes that patients own their data and can request it at any time. The CSL does not sell sequencing data to third parties. For more information on data and sample storage, contact the CSL.
What are the specimen requirements?
Blood or DNA samples may be submitted for analysis for whole genome sequencing.
Blood Sample Requirements
Collect 2-4 ml of whole blood in EDTA (lavender top) tube. 2 EDTA tubes containing 2-4 ml of whole blood per patient preferred.
For infants, collect a minimum of 1 ml of blood.
Possible reason for sample rejection:
Quantity less than one ml
Specimen collected in wrong tube
DNA Sample Requirements
DNA Samples are ONLY accepted from CLIA-certified laboratories. You can find more information on CLIA labs here.
Required: CLIA License Number (Federal and state, if applicable)
- DNA quantitated via spectrometry. Submit a screw cap tube of at least 5ug of purified DNA at a concentration of at least 60ng/ul with a 260/280 purity ratio of 1.75 – 2.0.
- DNA quantitated via fluorometric assay (PicoGreen). Submit a screw cap tube of at least 3 ug of purified DNA at a concentration of at least 50 ng/ul
- DNA may be shipped at room temperature. Label the specimen with at least two identifiers; patient name and date of birth are preferred. To maintain clinical level testing, genomic DNA from CLIA laboratories is required. Products of whole genome amplification reactions or other amplification reactions.
Label the specimen with at least two identifiers; patient name and date of birth are preferred.
Ship blood in tubes at room temperature in an insulated container.
Specimen should be submitted within 48 hours of collection to allow extraction within 5-7 days of draw.
Possible reason for sample rejection:
Sample not extracted in CLIA laboratory
Low DNA concentration
What can patients expect from a report?
A genomics report will include rare variants that are suspected to cause disease in genes that are associated with the patient’s symptoms. The patient may elect to have additional findings in the report (secondary findings) such as variants associated with later onset diseases, carrier status or pharmacogenetics.
How long will it take? Most reports are given to physicians within 45-60 days.
How do I ship a sample?
- Please contact us at email@example.com or through our contact form to have your facility registered as a provider. Basic information as well as provider ID will be required.
- Samples may be submitted from a clinical collection lab as blood or purified DNA. For submission of blood, Beckton Dickinson ® Vacutainer EDTA Tubes are requested (lavender or pink) with lavender preferred. Also accepted is BD Vacutainer Specialty Tube (yellow). Heparin is a powerful PCR inhibitor and co-purifies with DNA. Therefore, blood collected in Heparin-coated tubes should not be submitted.
- Label samples with two unique identifiers, typically a patient’s name and date of birth.
- Package the forms, the sample and include a signed medical provider order (required for clinical sample processing). You can find the CSL’s test request form here.
- Print and sign the Hazardous Declaration Form to include with your shipment. Samples shipped without this document will be discarded.
- Pack samples as diagrammed at the side.
- Ship samples overnight to the address below. We advise shipping no later in the week than Wednesday in case a carrier delay causes samples to sit over the weekend.
- Shipping address: HudsonAlpha Clinical Services Lab, LLC, 601 Genome Way, Room 3023, Huntsville, AL 35806
How long does the process take?
The turnaround time for clinical genome sequencing with the final report ranges between 45 and 60 days. The final report includes variants in genes related to patient symptoms that may be clinically relevant and are confirmed by a different (orthogonal) method. Rapid genomes with a preliminary report between five and ten days may be available. Please contact the laboratory for details.
What can I expect to get back?
For interpreted genome sequencing, a clinical report will be provided to the requesting medical provider with a list of variants identified that are relevant to a patient’s symptoms. If a patient consents, the report will also include secondary findings unrelated to symptoms and/or pharmacogenomic variants.
Upon agreement with the CSL, medical providers that perform their own interpretation will receive the relevant sequencing files (FASTQ, BAM, and/or VCF) and a report of sequencing performance metrics.
The clinical report comes in a PDF signed by the director or associate director of the Clinical Services Lab. Reports may also be faxed.
Primary findings include variants in genes related to patient symptoms that are pathogenic, likely pathogenic or of uncertain significance. Secondary findings, when requested with patient consent, include dominant disorders for childhood and adulthood, carrier status for recessive disorders and pharmacogenomic variants for CPIC level 1A/1B evidence.
Under the HIPAA Privacy Rule, patients, patients’ designees and patients’ personal representatives can see or be given a copy of the patient’s protected health information, including an electronic copy, with limited exceptions. The patient or the personal representative must put their request in writing and pay for the cost of copying, mailing, or electronic media on which the information is provided. Copies will be sent to the patient within 30 days of his or her request. Clinical Laboratory Improvement Amendments of 1988 (CLIA) regulations to allow laboratories to give a patient, or a person designated by the patient (his or her “personal representative”) access to the patient’s completed test reports on the patient’s or patient’s personal representative’s request.
How much does sequencing and analysis from the CSL cost?
Our sequencing and analysis is offered at a competitive price for patients, grant-funded researchers and institutions. Patients may even receive funding opportunities through the Smith Family Clinic for Genomic Medicine. Please contact the laboratory for details.