Paula Saffie from Clinica Santa Maria in Chile presented at the Nanopore Community Meeting in Boston on “Long-read sequencing: bridging the diagnostic gap for undiagnosed cases in Chile.” Saffie is a clinician and is working on a Ph.D. in Parkinson’s. Saffie wants to study the genetic diseases that their patients suffer. They spoke about rare genetic diseases and the difficulty of studying them. Saffie is interested in diseases caused by repeat expansion. They highlighted the cost of investigating difficult cases, even after whole genome short-read exome sequencing. Saffie worked with the NIH CARD on a pilot project as part of their sabbatical. They went to the NIH and collected samples from their Ph.D. project of patients with Parkinson’s in Chile… but their DNA arrived with … low nanogram amount. Saffie struggled and learned how to work in the lab to extract HMW DNA from blood. The samples were size selected with the BluePippin. Library prep was performed manually with the LSK114 kit. One flow-cell (PromethION) was run per sample: 3 loads x 20 fmol per flow-cell. Data output average was 129 Gbases with 43X coverage. Three pipelines were used: one for structural variants, single nucleotide variants, and structural variants. They found known ataxia variants and now want to develop an adaptive sampling approach. At the time of recording, Saffie was preparing to finish doctoral studies and continue learning about the genomics of rare diseases.
