For the patient with a rare phenotype, when the constellation of clinical findings is not recognized as part of a known syndrome, yet the clinician investigator would like to investigate a particular set of genes that are known to contribute to a particular phenotype, “panel on demand” sequencing is a cost-efficient and precise approach to diagnostic testing for rare inherited disease. Examples of panels might include a neurodevelopmental gene panel, hereditary cancer panel, cardiomyopathy gene panel or others. Study of the custom panel of genes from the DNA of a single individual is used to identify sequence variants with a very low population frequency, with nucleotide conservation across species and likely pathogenic consequence. Testing of a family trio facilitates filtering of sequence variants and reduces the number of potential candidates by looking for the same sequence alteration in an unaffected parent(s).
Reflex to Exome Sequencing: If a causative or potentially causative variant is not identified by this exome panel test it is possible to order a REFLEX clinical exome. The full exome sequence will be analyzed as is done for our Clinical Exome Sequencing test using the data obtained from the exome panel test. Submission of parental samples, and or other family members may be needed to assist in the interpretation of sequence variants. Order REFLEX to EXOME SEQUENCING.
Next generation DNA sequencing is performed to identify nucleotide variants in the coding portion of the genome. >99% of the coding regions and the canonical splice sites are sequenced to a read coverage of greater than 20X and compared to the human reference genome. Variants are assessed for pathogenicity using available information from the following databases (ClinVar, HGMD, 1000 Genomes, dbSNP and EXAC), published literature, clinical correlation, segregation analysis, functional studies and predicted functional or splicing impact using evolutionary conservation analysis and computational tools.
Procedure: Genomic DNA was extracted from blood using standard procedures. A library of DNA fragments was constructed and enriched for protein and RNA coding portions of the human genome using the Exome v1.0 (Integrated DNA Technologies) capture system. Paired-end sequencing of the enriched library was performed using rapid run v2.0 (Illumina) chemistry on a HiSeq 2500 (Illumina) sequencer according to the manufacturer’s recommended protocol. Resulting sequences were aligned to the human genome reference (hg19) using the Burrows-Wheeler Aligner (BWA) and variants identified with the Genome Analysis Took Kit (GATK). A modified version of the SeattleSeq tool was used to annotate variants found within these genes.
Limitations of Methodology: The test does not detect large deletions or duplications and has limited ability to identify small insertions and deletions. This test has limited ability to detect mosaicism. The assay does not detect variants located: 1) outside the captured exome, 2) in regions of insufficient coverage, 3) in regions containing paralogous genes or pseudogenes, or 4) where the reference genome is inaccurate or contains gaps and insertions.
BLOOD is the Preferred Specimen drawn in a lavender top tube (EDTA):
PLUS 7 cc of blood drawn in yellow- top tube (acid citrate dextrose) for transforming lymphoblasts in case of the need for additional DNA. If necessary, whole blood may be stored up to 5-7 days in the refrigerator before shipping.
You may submit DNA (5ug at >20ng/uL) or saliva (Oragene kit acceptable) if necessary. If there are difficulties with arranging for laboratory blood draw and shipment, please contact the laboratory for more details and blood tube kits.
Please label the sample tubes with two identifiers: 1) the patient’s full name and 2) date of birth. If possible, please include the patient’s medical record number. Clinical information outlining the indication for the requested tests and pertinent medical history and family history is a necessary component of testing. The requisition form is formatted to allow for easy summary of the patient’s history and to note any suspected diagnoses and earlier negative testing.
For Medicaid billing, the following is required: A pre-authorization letter from Medicaid, with the effective dates of coverage (attach to requisition form)
How to Order
It may be helpful for the clinician to phone or contact us to discuss the patient with the laboratory director, Dr. Michael Dorschner (206-685-5488 or email@example.com) or the genetic counselors, Sam Bailey (206-543-5464 or firstname.lastname@example.org) or Dru Leistritz (206-543-5464 or email@example.com), to determine if testing is appropriate and which test to select. After selecting the test, please follow these steps to order it:
1. Complete Required Forms
2. Complete Billing Information
3. Collect Specimen
4. Ship specimen to NCGL
Center for Precision Diagnostics
Northwest Clinical Genomics Laboratory
1959 NE Pacific St., HSC H-561
Seattle, WA 98195
Phone: 206.221.2140; FAX: 206.221.7509
5. Receive Results
Results will be faxed to you at the contact points you provided on the requisition form.
Note: Orders cancelled after they have been submitted will incur a prorated charge based on the work that has been completed as of the time of cancellation.
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CPT Code & Cost81479