Whole Exome Plus

Test code: WE0301

Whole Exome Plus includes high-quality Whole Exome sequence analysis of single patient cases, coupled with Whole Exome Deletion/Duplication analysis. Whole Exome Plus allows detection of single-nucleotide and indel variants, as well as larger deletions/duplications.

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 analysed 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.

Availability

Whole Exome Plus test is available with TAT of 8-10 weeks.

Test strength

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

Test limitations

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.

The test targets all protein coding exons and ± 20 base pairs from the exon-intron boundary. In addition, the test includes selected non-coding, deep intronic variants (listed in Appendix 8 in the electronic version of the exome report).

The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. The proprietary automated bioinformatics pipeline developed and employed at Blueprint Genetics enables detection of single-nucleotide, small indel variants from WES data but also large copy-number variants (³1 exon level) when Plus analysis type is requested.

WES data are primarily analyzed for changes in genes that are known to be associated with human disease. 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. We have incorporated a number of reference population databases and mutation databases such as, but not limited, to 1000 Genomes Project, gnomADClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as SIFTPolyPhenMutationTaster are used to assist with variant classification.

Through our online ordering and statement reporting system, Nucleus, the customer has an access to details of the analysis, including patient specific sequencing metrics. This reflects our mission to build fully transparent diagnostics where customers have easy access to crucial details of the analysis process.

In the WES analysis we are primarily looking for an explanation for all or a subset of patient’s symptoms. Therefore, analysis and reporting focus on what is likely directly relevant for patient’s disease, such as known/possibly disease causing heterozygous variants in AD genes or homozygous/compound heterozygous variants in AR genes at least partly matching the patient´s phenotype. I.e. carrier statuses of variants in AR genes are not specifically analysed and are rarely reported. 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. Therefore, it is important that the clinical and family history information delivered to us in as detailed as possible when ordering the test.

Analysis of WES data is primarily focused on established disease genes that have been previously associated with genetic disorders. The genes with known clinical association include those curated by Blueprint Genetics (BpG) and included in BpG diagnostic panels. These genes are supplemented with genes included in The Clinical Genomics Database and the Developmental Disorders Genotype-Phenotype Database (DD2GP). Total number of genes that are considered as clinically associated is around 3800 at the moment and the number is constantly updated. We use a variant-driven approach, referred to as ‘genotype-first’ strategy in the literature, and it is considered as one of the major benefits what WES or WGS has to offer. It means e.g. that we are not pre-filtering the data against predefined set of genes that are thought to be associated with patient’s disease, but we are including variants in all known disease genes. The genotype-first approach takes into proper consideration the fact that many exome cases may have either 1) atypical presentation of a relatively well-known syndrome, 2) a genetically highly heterogeneous syndrome, 3) very rare disease with a clinical picture not yet well-established.

 

If analysis of variants in previously established disease genes is inconclusive, exome data is also analyzed for variants that are not located within known clinically associated genes but have properties that make them candidates for potentially disease-causing variants using the following scheme: 1) For probands who were whole-exome sequenced with parents, all coding region de novo variants are evaluated as potential candidate variants; 2) Novel heterozygous, truncating variants in genes predicted to be intolerant for loss-of-function variation based on ExAC variant data (probability of loss-of-function intolerance score pLI>=0.9); 3) Rare, truncating homozygous or possibly compound heterozygous variants, or a combination of rare truncating and rare missense variant that is predicted deleterious by multiple in silico tools; 4) Only variants in genes with expression pattern and known function considered relevant for the phenotype are included.

We aim to provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. In our statements, we provide a comprehensive description of our rationale for the classification of the variant. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

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.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references used, congress abstracts and mutation databases to help our customers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counseling.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratory is therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.

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.

Find more info in Support
$
Whole Exome Plus
$ 3100
Total $
Order in Nucleus

ICD & CPT codes

CPT codes

81415, 81229

Accepted sample types

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)

Label the sample tube with your patient's name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. Read more about our sample requirements here.

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