The Whole Exome Sequencing is a customized analysis of the human exome based on a combination of the patient’s clinical presentation and the variants found within his/her exome.

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Our exome combines rigorous bioinformatics with detailed phenotypic and clinical information to yield relevant information for your patient.

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We will analyze:

After sequencing the exome, variants identified that meet the following criteria will be interpreted according to American College of Medical Genetics and Genomics criteria:

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1. All variants in genes specifically requested in the order and which are covered by the assay, plus

2. Variants detected in genes:

   • that are likely to be disruptive (e.g., cause premature truncation events, interfere with canonical splice sites, initiator, frameshift, or whole-exon deletions), or

   • for which there are two variants detected in a single gene associated with a condition that is autosomal recessive, plus

3. Variants detected in genes associated with Mendelian conditions that correspond to the patient’s presentation that:

   • are reported to cause disease in publications but are absent in frequency databases

4. For a trio analysis (when samples from both parents are provided for analysis),

   • variants shown to be de novo in the patient, or

   • variants segregating as X-linked, or

   • autosomal recessive.

 

We will report:

Of the variants interpreted, only variants that are deemed likely to have medical implications for the patient (e.g., pathogenic/likely pathogenic, or highly suspicious variants of uncertain significance) will be reported.

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In addition, a proband and/or parents may choose to have an additional analysis for secondary findings as recommended by the American College of Medical Genetics (Kalia et al 2017) at no additional charge. A separate report for each individual will be generated evaluating pathogenic/likely pathogenic variants in this set of 59 genes. The decision of a proband and each family member to opt in to this additional analysis is required at the time the test is ordered by a clinician. The additional reports evaluating these 59 genes will be released as companion reports.

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Test description:

The Whole Exome Sequencing detects single nucleotide variants, indels less than 50 bp, and intragenic copy number variants across >18,000 genes. However, in contrast to gene panel sequencing where single-exon del/dups are detected, the greater variability in depth of coverage across an exome permits reliable detection of del/dups spanning 4 exons or more with high confidence; smaller events may be detected and will be reported when sufficient resolution exists.

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To ensure high sensitivity and specificity, the exome is sequenced to an average depth of 150x (per base). Over 18,000 genes of the mappable exome are called at high quality (depth ≥20x). Joint calling is performed to maximize sensitivity.

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The assay is not intended to detect large copy number variations (cytogenetic events), indels >50 bp, or mosaic/somatic events constituting less than 20% of the total calls in that tissue. The assay does not detect variants in mitochondrial DNA.

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Sample requirement: 6ml EDTA

TAT: 8 weeks

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