Whole Exome Sequencing

WES is the analysis of the protein-coding regions of all ~20,000 genes of the human genome (known as the exome) using next-generation sequencing technologies. While the exome constitutes only ~1% of the whole genome, ~85% of all established disease-causing variants are located within the exome.

The diagnostic yield of WES is higher than many traditional genetic diagnostic methods such as multi-gene panels. A diagnosis is made in 20% to 60% of cases with severe, early onset disorders having the highest diagnostic rates.

WES is most suitable for individuals with:

  • A complex, nonspecific genetic disorder with multiple differential diagnoses
  • A genetically heterogeneous disorder where stepwise testing of genes significantly increases costs
  • A suspected genetic disorder where a specific genetic test is not available
  • Previous genetic testing that has not been diagnostic
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Our flagship WES offering is the Whole Exome Family Plus test, which includes WES for the index patient and biological parents. Other family members can be analyzed upon request. Details include:

  • WES and deletion/duplication (copy number variant) analysis for the proband and the biological parents
  • Including parental samples provides the following benefits:
    • Improved variant filtering and analysis
    • Reduced rate of uncertain findings
    • Increased diagnostic rate
    • Reduced overall turnaround time

In addition, we also offer the following options:

  • Whole Exome Plus – Proband only WES and deletion/duplication (copy number variant) analysis
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Test Test code Considerations
Whole Exome Plus WE0301
  • When biological parents are NOT available
Whole Exome Family Plus WE0401
  • Both biological parents are available
  • The most comprehensive reporting and interpretation of variants is desired at the time the report is issued
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High-quality exome capture is performed using an in-house–designed WES platform and the Illumina NovaSeq sequencing system.

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We have performed an extensive assay validation to determine the coverage, accuracy and precision of our WES data.

Highly uniform sequencing depth across all protein-coding genes:

  • On average, median sequencing depth of 174X
  • On average, ≥99.4% of the base pairs (bp) in target coding regions covered at ≥20X

Highly sensitive and specific detection of SNVs and indels

  • 99.7% sensitivity and >99.99 specificity for SNV detection within target coding regions
  • 97% sensitivity and >99.99% specificity for indel detection within target coding regions (up to 220 bp)

Excellent sensitivity for the detection of copy number variants (CNVs)

  • Most 1 exon deletions detected and >99% sensitivity to detect 5 exon del/dup
  • 100% sensitivity to detect known microdeletion and microduplication syndromes

Deep intronic disease-causing variants included in every WES

  • Assessment of >1500 noncoding disease-causing variants listed in ClinVar and HGMD are included in every WES

Assay performs with high precision

  • The within run precision (repeatability) is 99.7% for SNVs
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Yes. The median sequencing depth and ≥20x coverage are reported for each individual included in the WES analysis. In addition, we include a coverage plot detailing the target region coverage for each individual included in the WES analysis.

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Yes, Blueprint Genetics includes assessment of deletions or duplications (CNVs) for all of our Whole Exome products. The detection limit for Del/Dup (CNV) analysis varies throughout the genome depending on exon size, sequencing coverage, and sequence content. In our validation study, 92% of single exon deletions were detected.

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Our WES products detect variants in nuclear encoded mitochondrial genes. At this time, mtDNA variants are not targeted in our WES.

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WES generates thousands of variants. Our proprietary bioinformatics pipeline distinguishes disease-relevant variants from the many benign variants present in the exome. The pipeline determines the consequence of variants and performs filtering steps to remove common variants based on allele frequencies in population cohorts. We review the literature and various databases to determine the association between the identified variants and 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 which are collected and curated in-house, and/or accessed from the public domain or licensed from commercial sources.

The analysis of the WES data is individually tailored. During the analysis process, the clinical and family history of the patient, including symptoms, age of onset, prevalence, and inheritance patterns are taken into consideration. The precise filters used in the variant analysis are then selected based on this information.

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Blueprint Genetics analyzes WES data using a ‘genotype-first’ approach. In the genotype-first approach, the genetic data are primarily utilized to establish the diagnosis. This is in contrast to the ‘phenotype-first’ approach where WES data are filtered for genes that are known to be associated with the symptoms observed in the patient. The genotype-first approach allows for a diagnosis of an unexpected or atypical presentation of a disorder associated with previously established disease genes.

The WES data are first analyzed for variants in genes that are known to be associated with conditions showing overlap with that of the patient. If this is inconclusive, the data are then analyzed for variants that are not located within known clinically associated genes, but have properties that make them candidates for potentially disease–causing variants.

Variants are reported based on the clinical information provided. It is therefore extremely important to provide detailed clinical information with the patient sample to maximize the diagnostic yield of the genotype-first approach.

If, over time, other patients with similar phenotypes and variants in the same gene are identified, the variant may be reclassified as a likely cause of the disorder. In this circumstance, an updated report will be sent to the ordering clinician.

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As WES includes all protein-coding genes of the genome, it detects variants in genes that are not related to the indication for performing WES but are of medical value for patient care. These variants are known as secondary findings.

Blueprint Genetics follows the ACMG recommendations for reporting secondary findings in clinical exome and genome sequencing to seek and report clinically actionable variants in the pre­determined genes by ACMG. These guidelines are followed if the patient or caregiver has opted­infor analysis and reporting of secondary findings. This can be attached to the order in Nucleus or sent to our laboratory via fax or land mail. For more information and the consent form click here.

If parents or other family members are also participating in the WES analysis, they also have the option to opt-in for analysis and reporting of secondary findings.

Secondary findings for additional family members are reported in a separate clinical statement than that of the index patient and are independent of the secondary findings reported in the index patient. This also requires a signed consent form for every individual who opts in.

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We do not currently report variants other than those that are considered to be associated with the indication for performing WES or that are within the ACMG-defined list of secondary findings genes.

We also do not report carrier status of variants in autosomal or X-linked recessive disease genes that are not linked with the indication for performing WES for the patient.

Lastly, pharmacogenetic variants are currently not reported.

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To view a sample WES report, please click here.

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Family members can be tested for variants identified by WES as part of our Familial Variant Testing (FVT) service. For more information, please click here.

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If samples are received on the index patient and one or more family members, all variants and segregation analysis relating to the cause of the index patient’s phenotype are reported in the index patient’s report.  

Secondary findings for family members participating in WES are reported in separate, individual reports if the family member chooses to receive this information. Otherwise, there will not be separate family member reports. 

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At this time, we do not accept prenatal samples for WES from ongoing pregancies; however, we are able to accept fetal samples for WES from a deceased fetus.

Please note, only extracted fetal DNA is accepted at this time. In addition, Blueprint Genetics currently does not offer maternal cell contamination (MCC) studies. Therefore, ordering clinicians need to ensure that any prenatal sample sent to Blueprint Genetics has MCC studies done locally.

Blueprint Genetics will accept prenatal samples for panel testing or Family Member Testing (FMT) at our standard fee when requested.

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An extensive WES Re-analysis service is available. For additional information, please read more here or contact our Support team.

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Yes, we provide raw data for WES orders. Read more about raw data here.

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What are the limitations of WES?

  • At present, it is not possible to capture and sequence 100% of the exome. We cover, on average, >99.4% of base pairs with at least 20X depth within the target coding regions.
  • WES is not optimized to detect certain variants such as trinucleotide repeats and may not reliably detect variants in genes with pseudogenes or segmental duplication.
  • At this time, we are not targeting variants in mtDNA.
  • This test is not designed to detect complex inversions, gene conversions, or balanced translocations.
  • This test is not designed to detect variants in regulatory or noncoding (intronic variants located deeper than 20 nucleotides from the exon-intron boundary) regions, however, we are specifically targeting almost 2000 noncoding disease-causing variants listed in ClinVar and HGMD.
  • This test may not reliably detect low-level mosaicism or stretches of mononucleotide repeats.
  • A negative result does not exclude a genetic condition.
  • It is possible that a variant is identified in a gene not currently known to be associated with disease. Given the incomplete knowledge of the function of all the genes in the genome, this variant may not be recognized as a factor in a patient’s disease.
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  • Sample from the index patient (see below for sample types accepted).
  • Completed requisition for the index patient.
  • Completed consent form for the index patient. To receive the reporting of secondary findings, please ensure the correct box is selected for opting in, and the form is sent to Blueprint Genetics before we begin analysis.
  • Detailed clinical information including consult notes, symptoms, and age(s) of onset pedigree, previous test results (genetic and others like ECG, MRI, etc). It is strongly preferred that these are provided in English.
  • Samples from additional family members, if applicable.
  • Consent forms for additional family members, if applicable.

If Whole Exome Family is being ordered, please send parental/familial and index patient samples at the same time.

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  • Blood (min. 1 mL) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Please see the accepted saliva kits on our Sample Requirements page)

Read more about our sample requirements here.

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Discordant relatedness occurs when the estimated degree of relatedness between two individuals is inconsistent with the reported relationship, and we have ruled out an internal sample mix-up to the best of our ability. Discordant relatedness could be identified for several reasons including but not limited to sample mix-up, undisclosed bone marrow or stem cell transplant, and non-paternity.

As part of our Quality Control (QC) process, a relatedness algorithm is run as part of our pipeline for all WES family and family variant tests (FVT) to ensure the sequenced samples belong to individuals who are blood relatives. This process estimates the degree of relatedness (1st degree, 2nd degree, etc) and is not a formal assessment of maternity/paternity. For WES family cases, the relatedness data is reviewed during interpretation when there is a suggestion of a discordant relationship (for example, if an unusual number of variants are called as de novo).

If discordant relatedness is identified, the ordering provider will be contacted to discuss the next steps including the option of submitting a new sample for the individual implicated. A plan on how to proceed if repeat testing continues to identify discordant relatedness will be discussed, either at the time of the initial conversation or during a follow-up conversation.

Content last modified: 27 February 2024