Introduction

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 2 d 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.

Publications

  1. Direct determination of diploid genome sequences.
    Cite this
    Weisenfeld NI, Kumar V, Shah P, Church DM, Jaffe DB, 2017-05-01 - Genome research

Credits

  1. Neil I Weisenfeld
    Developer

    10x Genomics, Pleasanton, United States of America

  2. Vijay Kumar
    Developer

    10x Genomics, Pleasanton, United States of America

  3. Preyas Shah
    Developer

    10x Genomics, Pleasanton, United States of America

  4. Deanna M Church
    Developer

    10x Genomics, Pleasanton, United States of America

  5. David B Jaffe
    Investigator

    10x Genomics, Pleasanton, United States of America

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Summary
AccessionBT003646
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByDavid B Jaffe