Technical development of rapid whole genome nanopore sequencing and variant identification pipeline

Andrew Carroll
Ankit Sethia
Benedict Paten
Christopher Wright
Daniel R Garalde
Dianna G. Fisk
Elizabeth Spiteri
Euan Ashley
Fritz J. Sedlazeck
Gunjan Baid
Jean Monlong
Jeffrey W Christle
John E. Gorzynski
Jonathan A Bernstein
Joseph Guillory
Karen P. Dalton
Katherine Xiong
Kishwar Shafin
Maria Nattestad
Maura RZ Ruzhnikov
Megan E. Grove
Mehrzad Samadi
Miten Jain
Sneha D. Goenka
Tanner D. Jensen
Tong Zhu
Trevor Pesout
Nature Biotechnology (2022)

Abstract

Whole genome sequencing can identify pathogenic variants for genetic disease but the time
required for sequencing and analysis has been a barrier to its use in acutely ill patients. Here,
we develop an approach to ultra-rapid nanopore whole genome sequencing that combines an
efficient sample preparation protocol, distributed sequencing over 48 flow cells, near real-time
base calling and alignment, accelerated variant calling, and fast variant filtration. We show
that this framework provides accurate variant prioritization in less than half the fastest time
recorded for an equivalent analysis to date.

Research Areas