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Clinical Exome Sequencing


Test Information

Test Method

DNA extraction (if applicable) and ultrasonic fragmentation; targeted capture of the coding regions and intron/exon boundaries of protein coding RefSeq genes using the Agilent Clinical Research Exome kit; next generation sequencing (NGS) on an Illumina HiSeq 2500 instrument; alignment to the human reference genome (GRCh37/hg19) using the Burrows-Wheeler Aligner (bwa); variant calling using GATK; Sanger sequencing to confirm low quality and/or complex indel variants related to the specified phenotype(s); Review of sequence data for the specified genes by multiple staff members; Variant classification following ACMG criteria (if applicable). Bioinformatic analysis was performed using DDL pipeline DDL.CRExome.v1.2018_04_18.

Clinical Sensitivity

The clinical sensitivity of this assay is dependent on the phenotypic information provided to the laboratory. A causative genetic variant is identified in approximately 20-30% of affected individuals (Farwell et al., 2015, PMID 25356970; Retterer et al., 2016, PMID 26633542; Yang et al., 2013, PMID 24088041). Variants in the ACMG list of secondary findings genes are identified in approximately 1-4% of individuals (Kalia, et al., 2017, PMID 27854360; Olfson et al., 2015, PMID 26332594; Schwarz, et al., 2018, PMID 30100086). This test is only validated for inherited gene alterations associated with the specified phenotype(s).

Analytic Sensitivity

> 99% for single nucleotide and >92% for small insertion/deletion variants for the nucleotides evaluated. Lower limit of detection: Single nucleotide variants: 25% allele frequency (>96% sensitivity), Small insertion/deletion variants: 50% allele frequency (>94% sensitivity). This test is not validated to identify deletions/insertions of greater than 20bp, copy number changes, nucleotide repeat expansions, mitochondrial DNA variants or mosaicism. Disease-associated variants in regions that are not captured and/or sufficiently sequenced will not be detected by this assay.

Sample Requirements

3-6ml whole blood in EDTA (purple topped) tubes
Saliva collected in an appropriate collection device (Oragene®-DNA 500 or 600 device)
DNA extracted from fibroblast or lymphocyte cell line (must be extracted in a CLIA-certified laboratory)

Turn Around Time

Approximately 6-8 weeks

Fee and CPT Codes

Exome Proband-Only: $5600
Exome Duo: $6350
Exome Trio: $7100
Exome Quad: $7850

CPT Code: 81415 and 81416
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