Clinical statement

 

 

The Blueprint Genetics clinical statement provided for the customers is a thorough report of the whole diagnostic process and fulfils ISO 15189 quality requirements. Our clinical statement is accessible through our online portal Nucleus, or upon request a printed pdf version of the statement is sent to the customer via regular mail or fax.

The most relevant tests results are concisely presented on the first page of the statement. Additional pages include basic information of variant’s allele frequencies in reference populations and in-silico predictions. Most important part is the careful literature review presenting all the evidence gathered for the variant classification such as number of patients with the same variant, their phenotype, available segregation data, citations (publications/mutation databases), and list of possible additional analysis used such as paralogue annotation. Finally, we also provide information about known pathogenic/likely pathogenic variants in near-by residues if rational.

For clarity, the statement is split into sections. Some information of the used technologies and detailed sequencing coverage is available only in the electronic report at our online portal, Nucleus.

All customers, even those who order results by mail or fax, have access to test results in Nucleus.

On the front page, we show the test result, identified relevant genetic variants, sequencing performance metrics and a list of the genes in the panel. Variants and their classification are clearly stated under the subheading test result. Additionally, clinically relevant variants are presented in a variant table with more detailed information. The table displays the gene, variant’s genomic position, variant id, codon, predicted consequence of the change, Genbank accession number for the transcript the mutation nomenclature is based on, mutation nomenclature according to HGVS guidelines, zygosity, minor allele and the minor allele frequency in the 1000 Genomes control cohort, and the classification for the variant. Sequencing performance metrics display the requested panel, full gene list, panel version, target region and coverage.

The statement

The patient’s clinical history provided by the customer is recapped in the beginning of the statement. This information is extremely valuable in the interpretation process.

The clinical report begins with the most relevant finding. If more than one significant variant is detected, they are described in the order of significance in relation to the clinical history and the phenotype of the patient. The first paragraph of the clinical report gives the core information regarding the variant. It covers the in silico predictions of variant’s potential pathogenicity when applicable (non-synonymous variants), and the minor allele frequency detected in control cohorts, or number of individuals carrying the same variant, principally in the Exome Aggregation Consortium (ExAC), comprised of over 60,000 individuals in total.

Review of literature opened in the clinical report outlines the literature and databases assessed in the interpretation process with references. For clarity, the review of literature first focuses specifically on the variant in question. Following the variant-specific literature review, more information on the gene, associated disease(s) and other additional/supporting information is offered. Comprehensive assessment of the literature is essential in the interpretation process and to explain the rationale behind variant classification. Please review our variant classification scheme here. Reporting of variants follows the ACMG guidelines and mutation nomenclature is based on the HGVS guidelines.

Concluding remarks tie and recap the evidence presented in the clinical report and clarifies the rationale for the classification of the identified variant(s). The utility of the genetic test results and possible recommendations for further actions are given. The conclusion also includes recommendations for genetic counselling and offers recommendations for family member testing. Test results with benign and likely benign variants are considered negative and therefore, these variants are not generally reported.

Pathogenic and likely pathogenic variants are always confirmed with bi-directional Sanger sequencing. Other variants are confirmed upon judgment. Customers are distinctly informed about the variants that were confirmed using Sanger sequencing.

Every report is signed by the clinical evaluation team, geneticists and physicians, who have together evaluated the sequencing results.

 

Download a report: Blueprint Genetics Sample Report