Groken 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. All samples are processed with the highest standards of quality, accuracy and consistency in the College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory which located in the USA. 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:

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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:

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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.

Groekn 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 Groken’s 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.

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

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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.

Using orthogonal technologies, Invitae confirms all clinically significant findings (e.g., pathogenic or likely pathogenic and sufficient to explain the patient’s phenotype) that do not meet stringent NGS quality metrics. The confirmation techniques we use include Sanger sequencing, PacBio sequencing of circularized amplicons, array comparative genome hybridization (aCGH), and multiplex ligation-dependent probe amplification (MLPA).