Background:
The human exome contains all protein coding regions of the genome encoding ~22,000 genes. Current estimations are that 85% of the disease causing mutations resides within the exome. Our exome sequencing test has been designed to give genetic sequencing information for the entire exome in addition to coverage in genes that are known to be associated with diseases. Exome sequencing has proven to be valuable in diagnosing rare hereditary diseases, especially when the patient’s physical exam and medical history strongly suggest a genetic etiology. It can be ordered early in a proband’s evaluation, or following extensive negative genetic or metabolic tests.. With the addition of biological parental/relative testing, (i.e. trio analysis) clinical diagnosis can be further improved by identifying de novo variants present in the affected child, but not in either parent/relative.
Reasons for Referral:
- Diagnostic Testing
- Negative results from targeted panel testing
Methodology:
Next generation sequencing using Illumina NextSeq 500 technology and preparing samples using hybridization probes to enrich exonic regions; extra probes are added to enrich clinically relevant genes. This assay does not assess regions of insufficient coverage, introns and promoter regions; pseudogenes; where the reference genome is inaccurate or contains gaps and insertions; and regions of high GC or polynucleotide repeats, but may contain variants that impact gene function.
Exon-level deletion/duplication analysis is performed by running the same NGS data through the Genome Analysis Toolkit (GATK) Germline CNV best practices pipeline from a GATK version. The pipeline has been validated in-house to detect deletion and duplication events as large as full chromosomes and as small as three exons. Detection of events involving one or two exons may occur but are not guaranteed within our validated parameters. If deemed reportable, deletions and duplications of <3 exons or with lower quality scores may be confirmed by orthogonal methods.
Specimen Requirements:
Three (3) samples to be collected:
- Proband
- Biological Relative #1
- Biological Relative #2
Blood: EDTA or ACD (Solution A or B):
- Adult: 5mL
- Child: 5mL
- Infant: 2-3mL
Saliva: 2 ORAgene Saliva Kits (OGR-500) used according to manufacturer instructions. Please contact KDL Client Services for a Saliva Collection Kit for patients that cannot provide a blood sample.
Assisted Saliva: 4 ORAgene Assisted Saliva Kits (OGR-575) used according to manufacturer instructions. Please contact KDL Client Services for an Assisted Saliva Collection Kit for patients that cannot provide a blood sample.
DNA: 10µg at a minimum of 60-100ng/µL (DNA must be extracted in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or CMS)
For routine testing of blood and saliva (or DNA extracted from them), KDL does NOT accept samples from patients within two (2) weeks of a packed cell/platelet transfusion or within four (4) weeks of a whole blood transfusion. For extraordinary circumstances, where testing must be performed outside of the above windows, please contact our lab.
A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES. Please include detailed clinical information, including ethnicity, clinical history, and family history.
Exome Sequencing Consent Form must be filled out and must accompany all samples.
Test Performed (Days):
Weekly
Turn Around Time:
Approximately 8-10 weeks
Shipment Sensitivity Requirements:
- Package and ship specimen to remain cold, but not frozen.
- Ship via overnight express, using the FedEx priority overnight label provided.
- Contact Client Services for shipping kits and instructions at (855) 535-1522.
References:
Additional Info: