© 2019 by Groken Bioscience Ltd.

  • Facebook - Grey Circle

Head Office:

Suite 2611, Office Tower Langham Place,

8 Argyle Street, MongKok,

Kowloon, Hong Kong

Tel: +852-3111 3369 (HK) / +853-6545 3135(Macau)
Fax: +852-3585 6699

Email: info@grokenbioscience.com

Groken Whole Exome Sequencing  

高勤全外顯子基因檢測 

Test description

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.

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:

  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.

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.

Technical description

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.

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.

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.

Variant analysis and interpretation

  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

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).

Limitations

Groken Whole Exome Sequencing is not intended for research or gene discovery.

This test is only appropriate for identifying conditions with Mendelian (single-gene) etiologies; complex conditions such as lupus, type 2 diabetes, psychiatric disorders, or fibromyalgia are examples of conditions in which genetic variants may affect risk, but are not appropriately evaluated with the Invitae Boosted Exome. This test is not indicated for hereditary cancer analysis or individuals with no personal history of disease.

Currently, this analysis does not include detection of large cytogenetic events, mitochondrial DNA variants, or methylation/imprinting abnormalities. Additionally, this test will not not detect triplet repeats and may not detect mosaic/somatic variants.

What is included in the report?

Groken Whole Exome Sequencing report is designed to summarize the most salient information, focusing on variants that are likely to have medical implications for the patient. These include pathogenic and likely pathogenic variants related to the indication for testing and variants of uncertain significance that follow an appropriate inheritance mode and/or where the condition associated with a gene has overlapping features that match the patient’s phenotype. A clinical summary describing the relevant findings is followed by a detailed description of reportable variants that are found within genes associated with Mendelian conditions that correspond to the patient’s presentation and additional genes you indicate, through analyses for truncating and loss of function variants, and through analyses of inheritance patterns.

Variants fulfilling reportable criteria will appear with a full variant description and citations. For trios, inheritance patterns of variants will be indicated.

If the proband and/or family chooses to opt in to the secondary findings companion analysis, each individual will receive a separate report for those analyses. The decision to opt in or opt out of this additional, separate analysis should be discussed and decided on with the ordering clinician at the time the exome order is placed.

Background information

What is Whole Exome Sequencing?

Whole exome sequencing is a genetic test that uses next-generation sequencing technology to analyze the coding regions of approximately 20,000 genes. This test identifies DNA changes in an attempt to pinpoint an individual’s genetic diagnosis. These coding regions are called exons and all of the exons together are called an exome. It is estimated that the vast majority of disease-causing DNA changes are found in the exons, which is why the test focuses on these regions. The test also includes analysis of approximately 10 base pairs of DNA into the introns of each gene. While the introns are considered to be non-coding, changes to these regions can alter the expression and function of the exons, thereby causing disease.

When is exome sequencing appropriate?

Exome sequencing is often ordered when individuals present with complex, often syndromic symptoms that have a suspected genetic etiology. Exome sequencing offers an efficient method to target approximately 20,000 genes at once, thus providing a cost-effective, timely tool to assess multiple genes at once. In addition, it can provide a means to determine the diagnosis for patients who have undergone other forms of testing with no informative results. Results from exome sequencing can directly inform medical treatment, determine recurrence risks for patients and family members, and end the need for additional costly or invasive tests and procedures.

In contrast, when a patient has a well-defined phenotype that is highly suggestive of a single, known genetic condition, single-gene or panel testing is typically indicated. If you would like assistance in determining whether exome sequencing is the best choice over single-gene testing or a gene panel for your patient.