An efficient design for whole genome trio sequencing identifies key variants in rare neurological disorder cases

Abstract

We sequenced nine trios in which the probands in an underserved population were affected by a rare and undiagnosed disorder with neurological features. Sequencing was performed with one trio per flowcell on a benchtop sequencing instrument, leveraging the design of sequencing the proband at twice the coverage of the parents. The reduced coverage in the parents led to sequencing efficiencies while retaining the benefits of trio sequencing: the ability to discover de novo variants and the ability to trace inheritance patterns of rare variants. Once the sequencing data was generated, our two teams used independent informatics pipelines for variant calling and interpretation. In five of the nine cases, both teams found a single SNV or small indel that was deemed causal pending clinical validation. In three of the nine cases, neither team had a significant finding. In the final case, an additional scan for large CNVs performed by one of the teams identified a de novo deletion and duplication in the proband which is the likely cause of the underlying disease. The results across cases with significant findings showed a variety of affected genes (CFAP52, DYNC1H1, FANCE, TCF4, and TOP3A), variant types, and inheritance patterns. All findings were clinically validated, after which the families were counseled about disease management, current research studies (i.e. gene therapy), and family planning. With six of nine families receiving findings, the study demonstrated an efficient and effective trio sequencing design strategy.