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Direct determination of diploid genome sequences

Neil I. Weisenfeld, Vijay Kumar, Preyas Shah, Deanna M. Church, David B. Jaffe
doi: https://doi.org/10.1101/070425
Neil I. Weisenfeld
10x Genomics, Pleasanton CA, USA 94566
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Vijay Kumar
10x Genomics, Pleasanton CA, USA 94566
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Preyas Shah
10x Genomics, Pleasanton CA, USA 94566
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Deanna M. Church
10x Genomics, Pleasanton CA, USA 94566
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David B. Jaffe
10x Genomics, Pleasanton CA, USA 94566
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ABSTRACT

Determining the genome sequence of an organism is challenging, yet fundamental to understanding its biology. Over the past decade, thousands of human genomes have been sequenced, contributing deeply to biomedical research. In the vast majority of cases, these have been analyzed by aligning sequence reads to a single reference genome, biasing the resulting analyses and, in general, failing to capture sequences novel to a given genome.

Some de novo assemblies have been constructed, free of reference bias, but nearly all were constructed by merging homologous loci into single ‘consensus’ sequences, generally absent from nature. These assemblies do not correctly represent the diploid biology of an individual. In exactly two cases, true diploid de novo assemblies have been made, at great expense. One was generated using Sanger sequencing and one using thousands of clone pools.

Here we demonstrate a straightforward and low-cost method for creating true diploid de novo assemblies. We make a single library from ~1 ng of high molecular weight DNA, using the 10x Genomics microfluidic platform to partition the genome. We applied this technique to seven human samples, generating low-cost HiSeq X data, then assembled these using a new ‘pushbutton’ algorithm, Supernova. Each computation took two days on a single server. Each yielded contigs longer than 100 kb, phase blocks longer than 2.5 Mb, and scaffolds longer than 15 Mb. Our method provides a scalable capability for determining the actual diploid genome sequence in a sample, opening the door to new approaches in genomic biology and medicine.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted August 19, 2016.
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Direct determination of diploid genome sequences
Neil I. Weisenfeld, Vijay Kumar, Preyas Shah, Deanna M. Church, David B. Jaffe
bioRxiv 070425; doi: https://doi.org/10.1101/070425
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Direct determination of diploid genome sequences
Neil I. Weisenfeld, Vijay Kumar, Preyas Shah, Deanna M. Church, David B. Jaffe
bioRxiv 070425; doi: https://doi.org/10.1101/070425

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