Wanqing Shao from Boston Children’s Hospital presented at the Nanopore Community Meeting on “Maximizing the power of genomic sequencing in pediatric rare disease.” Shao is a Genomics Scientist working in a collaborative team: the Children’s Rare Disease Collaborative (CRDC). They are interested in rare and complex diseases that are often misdiagnosed. Shao also noted that about 80% of rare diseases are associated with genetic variants. The CRDC was established in 2018 and unifies 100+ physician-scientists and provides sequencing to thousands of families. The CRDC designed a platform streamlining data generation, analysis, and organization. To increase the diagnostic yield, they initiated a project with 350+ families with prior negative genetic testing. Long-read data can capture the short-read WGS SNVs and provide new insights. The team is sequencing the data on PromethION 24/48 at various locations, including ONT in California. Dorado and minimap2 are used, and then the EPI2ME human variation workflow is used. Custom tools were developed to further support CNVs and SVs. In one example, Shao presented a de novo 6 kb deletion in the 3′ UTR of HMGA2 was found. The phenotype of this case is overgrowth. The second example Shao presented was a set of compound heterozygous variants in NEB. In this case, the parental data was not available. The phenotype is nemaline myopathy, and long-read sequencing helped solve this case. I did not know about this project and collaboration. I wonder what tools they are developing and if they will be implemented in future EPI2ME workflows.
