Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases

Abstract

Purpose: Genomic sequencing has become an increasingly powerful and relevant tool to be leveraged for the discovery of genetic aberrations underlying rare, Mendelian conditions. Although the computational tools incorporated into diagnostic workflows for this task are continually evolving and improving, we nevertheless sought to investigate commonalities across sequencing processing workflows to reveal consensus and standard practice tools and highlight exploratory analyses where technical and theoretical method improvements would be most impactful.

Methods: We collected details regarding the computational approaches used by a genetic testing laboratory and 11 clinical research sites in the United States participating in the Undiagnosed Diseases Network via meetings with bioinformaticians, online survey forms, and analyses of internal protocols.

Results: We found that tools for processing genomic sequencing data can be grouped into four distinct categories. Whereas well-established practices exist for initial variant calling and quality control steps, there is substantial divergence across sites in later stages for variant prioritization and multimodal data integration, demonstrating a diversity of approaches for solving the most mysterious undiagnosed cases.

Conclusion: The largest differences across diagnostic workflows suggest that advances in structural variant detection, noncoding variant interpretation, and integration of additional biomedical data may be especially promising for solving chronically undiagnosed cases.

Fig. 1. Representative clinical workflow to uncover disease-causing genetic variants in undiagnosed patients.

Upon acceptance to the Undiagnosed Diseases Network (UDN), (a) an affected patient has an in-person clinical evaluation where extensive phenotyping and additional tests are performed as needed. (b) Before or during the clinical evaluation, samples of relevant affected and unaffected individuals in a family are sent for genomic sequencing. (c,d) Sequencing data provided by the sequencing center are analyzed in conjunction with other information in a back-and-forth process between bioinformaticians, clinicians, and genetic counselors to highlight variants that are likely to explain the patient’s disease. (e) Matches to the strong candidate explanatory variants identified in (c) are searched for in databases containing human genetic variant and corresponding symptom information (e.g., Matchmaker Exchange) or in databases containing animal genetic variants and corresponding phenotype information (e.g., MARRVEL). Strong candidate variants are also introduced into model organisms or cell lines where possible to assess in vivo phenotypic impact. (f) Once a candidate variant has been confirmed as disease causal, a molecular diagnosis is provided that can subsequently be used to tailor clinical management and molecular therapeutics. (g–j) Recurring steps in computational workflows to process genomic sequencing data to call, filter, and prioritize genetic variants that explain the affected individual’s disease symptoms.