Whole Exome Family Plus
Test code: WE0401
Whole Exome Family Plus includes high-quality Whole Exome sequence analysis of an index patient and parents (trio) or other family members, coupled with Whole Exome Deletion/Duplication analysis. Whole Exome Family Plus is essential tool for detecting de novo mutations and copy number variants, which underlie many of the early-onset diseases.
Whole-exome sequencing (WES) is a robust and one of the most comprehensive genetic tests to identify the disease-causing changes in a large variety of genetic disorders. In WES, protein-coding regions of all genes (~20,000) of the human genome, i.e. exome, are sequenced using next-generation sequencing technologies. While the exome constitutes only ~1% of the whole genome, 85% of all disease-causing mutations are located there.
WES is most suitable for individuals with:
- a complex, unspecific genetic disorder with multiple differential diagnoses.
- a genetically heterogeneous disorder.
- a suspected genetic disorder where a specific genetic test is not available.
- unsuccessful previous genetic testing.
Blueprint Genetics Whole Exome tests have been developed to maximize diagnostic yields, first of all, by generating high-quality and uniform sequencing data. The sequencing data are analyzed using in-house, state-of-the art bioinformatics pipeline. Furthermore, the genetic information of patients is carefully interpreted by our team of geneticists and clinicians, utilizing information from latest publications and up-to-date databases.
Whole Exome Family Plus test is available with TAT of 8-10 weeks.
The strengths of this test include:
- CAP and ISO-15189 accreditations covering all operations at Blueprint Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
- CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
- Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
- Careful construction of clinically effective and scientifically justified gene panels
- Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
- Our publically available analytic validation demonstrating complete details of test performance
- ~1,500 non-coding disease causing variants in Blueprint WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
- Our rigorous variant classification based on modified ACMG variant classification scheme
- Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
- Our comprehensive clinical statements
Genes with partial, or whole gene, segmental duplications in the human genome are listed in our website (https://blueprintgenetics.com/pseudogene/) if they overlap with the UCSC pseudogene regions. The technology may have limited sensitivity to detect variants in these genes.
This test does not detect the following:
- Complex inversions
- Gene conversions
- Balanced translocations
- Mitochondrial DNA variants
- Repeat expansion disorders unless specifically mentioned
- Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).
This test may not reliably detect the following:
- Low level mosaicism (variant with a minor allele fraction of 14.6% is detected with 90% probability)
- Stretches of mononucleotide repeats
- Indels larger than 50bp
- Single exon deletions or duplications
- Variants within pseudogene regions/duplicated segments
The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.
For additional information, please refer to the Test performance section and see our Analytic Validation.
We utilize whole exome capture technology and Next-Generation Sequencing methods to obtain clinical-grade WES data, maximizing coverage of clinically relevant genes.
- Highly uniform sequencing depth across all protein-coding genes of the genome
- Mean sequencing coverage on average 174x at guaranteed 100M sequencing reads
- On average, 99.4 % of base pairs in genes’ coding regions and selected intronic variants covered at least 20x
- Highly sensitive and specific detection of single-nucleotide variants and indels
- 99.7% sensitivity and >99.99% specificity for single-nucleotide variant detection within coding regions of genes and selected intronic variants.
- 97.0% sensitivity and >99.99% specificity for indel detection within coding regions of genes and selected intronic variants.
- Deletions up to 220bp detected, insertions up to 221bp
- Assay performs with high precision
- Within-run precision (repeatability) 99.7%, intermediate precision (reproducibility) 99.7%
- Sensitive and specific detection of copy number variants (CNVs)
- Most of the single exon deletion events are detected and the sensitivity at five exon CNV level is >99% and specificity >99.9%. Segmentally duplicated genomic regions may have reduced sensitivity. The exact boundaries of the copy number aberration cannot be determined with this test.
Analysis of WES data is a complex process, imposing challenging requirements both in terms of computing resources and software. The proprietary automated bioinformatics pipeline developed and employed at Blueprint Genetics enables fast, reliable and highly accurate results.
We utilize state-of-the-art algorithms for quality control and processing of sequence reads as well as for detection of single-nucleotide, small indel variants as well as larger deletions and duplications from WES data. Furthermore, the pipeline employs accurate methods to determine consequence of variants as well as filtering steps to remove common variants based on allele frequencies in population cohorts.
WES data are primarily analysed for changes in genes that are known to be associated with conditions showing overlap with the one observed in the patient. We monitor recent literature and up-to-date databases to link genes observed in patients with up-to-date information regarding the genes’ association with relevant diseases. To further aid the process of variant interpretation, observed variants are matched against a comprehensive set of databases of disease-related mutations, collected and curated in-house, and accessed from the public domain or licensed from commercial sources.
WES data analysis needs to be tailored on individual basis. In the analysis process, we consider the clinical and family history of the patient, including symptoms, age of onset and prevalence and inheritance pattern of the disease. The applied filters for variant analysis are then selected based on this information to achieve an accurate diagnosis. Therefore, it is important that the clinical and family history information is delivered to us in as much as detail as possible when ordering the test.
A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. Other variants are confirmed upon judgment. Customers are distinctly informed about the variants that were confirmed using Sanger sequencing.
We provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.
In our statements, we provide a comprehensive description of our rationale for the classification of the variant. Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Please review our variant classification scheme here.
The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling the following criteria are not Sanger confirmed: the variant quality score is above the internal threshold for a true positive call and visual check-up of the variant at IGV is in-line with the variant call. Reported variants of uncertain significance are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size <10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at Blueprint Genetics.
We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic tests and clinical statements remain the most up-to-date on the market.
As WES covers all protein-coding genes of the genome, it enables detection of variants that are not associated with the indication for ordering the sequencing but are of medical value for patient care. These kind of findings are called secondary or incidental findings. We follow the ACMG Recommendations for Reporting Incidental Findings in Clinical Exome and Genome Sequencing to seek and report clinically actionable mutations of specified types in 59 genes determined by ACMG, if the patient or the caregiver has opted-in for analysis and reporting of secondary findings. If parents or other family members are also subjected to WES, they also have the possibility to opt-in for analysis and reporting of secondary findings. Secondary findings are reported in a separate statement. All reported secondary findings variants are based on high-quality variant calls in NGS data but these variants do not go through Sanger confirmation, which is in-line with the ACMG policy. Secondary findings are not analyzed or reported for deceased individuals or fetal samples.
ICD & CPT codes
Accepted sample types
For Whole Exome tests, sample requirements are:
- EDTA blood, min. 1 ml
- Purified DNA, min. 3 μg* in TE buffer or equivalent
- Saliva (Oragene DNA OG-500 kit)
When Whole Exome Family or Whole Exome Family Plus product is ordered, we require to send samples from first-degree relatives of the index patient at the start of testing.