Processing frozen cells for population-scale Oxford Nanopore long-read DNA sequencing SOP v1

Author:

Alvarez Jerez Pilar

Abstract

Processing frozen cells for population-scale Oxford Nanopore long-read DNA sequencing SOP At the NIH's Center for Alzheimer's and Related Dementias (CARD)https://card.nih.gov/research-programs/long-read-sequencingwe will generate long-read sequencing data from roughly 4000 patients with Alzheimer's disease, frontotemporal dementia, Lewy body dementia, and healthy subjects. With this research, we will build a public resource consisting of long-read genome sequencing data from a large number of confirmed people with Alzheimer's disease and related dementias and healthy individuals. For this project the long-read sequencing data will be derived from brain tissue, but for benchmarking purposes we also developed a protocol for processing frozen cells. The frozen cell protocol was developed to generate long-read sequencing data for the Coriell human-genome cell-lines that is comparable to the data output of the brain based protocol described herehttps://www.protocols.io/view/processing-human-frontal-cortex-brain-tissue-for-p-kxygxzmmov8j/v2) i.e. targeting an N50 of ~30kb and ~30X coverage. †Correspondence to: Kimberley Billingsleybillingsleykj@nih.govand Cornelis Blauwendraatcornelis.blauwendraat@nih.gov Acknowledgements: We would like to thank the Nanopore team (Androo Markham &Hannah Lucio), Circulomics Inc team (Jeffrey Burke, Michelle Kim, Duncan Kilburn & Kelvin Liu) and the whole CARD long-read team listed below =>UCSC: Benedict Paten, Mikhail Kolmogorov, Miten Jain, Kishwar Shafin, Trevor Pesout;NHGRI: Adam Phillippy, Arang Rhie; Baylor: Fritz Sedlazeck;JHU: Winston Timp; NINDS: Sonja Scholz;NIA: Cornelis Blauwendraat, Kimberley Billingsley, Pilar Alvarez Jerez, Frank Grenn, Bryan Traynor, Shannon Ballard, Caroline Pantazis. Laksh Malik, Edmund Roberts;CZI: Paolo Carnevali.

Publisher

ZappyLab, Inc.

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