A community-driven and open-source pipeline to annotate and prioritize germline variants in schwannomatosis
Purpose: Schwannomatosis is a rare genetic disorder that causes the development of nerve sheath tumors. Germline mutations in SMARCB1 and LZTR1 are causal in a subset of cases, but in some cases the cause of the condition is unknown. The goal of the Schwannomatosis Open Research Collaborative (SORC) is to uncover genomic variants and other genomic features that contribute to disease etiology and heterogeneity in schwannomatosis.
Methods: Germline variants from 33 whole exome sequencing and 6 whole genome sequencing samples from the Synodos for Schwannomatosis initiative (Mansouri et al., 2021) are available to SORC researchers via Synapse and the NF Data Portal (nfdataportal.org). These samples were processed using the nf-core sarek 2.7.1 pipeline which called germline variants using GATK HaplotypeCaller, DeepVariant, and Strelka.
Results: In a collaboration between SORC and the Bioinformatics Research Network, we developed a pipeline to annotate and prioritize germline single nucleotide variants in schwannomatosis patients in order to identify variants for further study. The pipeline takes a VCF file as input and annotates variants with scores from 9 different tools using OpenCRAVAT. To better capture splicing variants, we also annotated variants with scores from SpliceAI v1.3.1 and SQUIRLS v2.0.0, which are both advanced machine learning methods that together offer a complimentary approach for predicting splice-disrupting variants. Next, we integrated all of the annotated scores to identify variants that are most likely to impact gene expression.
Conclusions: Our pipeline is meant to be a first step in filtering low-impact variants before proceeding with additional genomic analyses, thus increasing the power of downstream analyses compared to genome-wide analyses. The pipeline will be applied to the schwannoma germline variants that are available to SORC researchers in order to generate a list of likely expression-altering variants that may be used to identify novel genes or druggable pathways in schwannomatosis. Future SORC analyses will utilize these variants as part of integrated analyses with available gene expression and DNA methylation data. Information about the SORC and information on joining this initiative can be found at www.synapse.org/swnts.
