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Cited by 803Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalitiesSingle-cell and spatial transcriptomics

Direct determination of diploid genome sequences

Open access
Weisenfeld, Neil I., Kumar, Vijay, Shah, Preyas, Church, Deanna M., Jaffe, David B.·2017·Genome Research
DOI 10.1101/gr.214874.116PMC PMC5411770

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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 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.

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  • New genome assemblies have been arriving at a rapidly increasing pace, due to decreases in sequencing costs and improvements in third-generation sequencing technologies.

    “New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies1–3.”

    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [2]

    The Discussion (page unavailable) says the low cost of the authors’ assembly method makes it applicable to large-scale projects. It does not establish that new assemblies were arriving at a rapidly increasing pace, or attribute such a trend to falling sequencing costs and improvements in third-generation sequencing technologies. (LLM, conf=0.78)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Weisenfeld, N. I., Kumar, V., Shah, P., Church, D. M., & Jaffe, D. B.
Affiliations
10X Genomics (United States) (US)
ORCID
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2017-04-05
Volume
27
Issue
5
Pages
757-767
ISSN
  • 1088-9051 (ISSN-L)
  • 1549-5469
DOI
10.1101/gr.214874.116
PMC
PMC5411770
OpenAlex
W2950682063
Cited by
803
References
2
Citations by year
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Type
posted content
Language
en
Open access
Locations
  • Genome Research (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HighWire Press Open Archive (submittedVersion)
Funders
NIH
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Keywords
diploid genome assembly, de novo genome assembly, 10x Genomics, human genome, reference bias, high molecular weight DNA
MeSH terms
Diploidy, Humans, Software, Genomic Library, Genome, Human, Sequence Analysis, DNA, Contig Mapping, Microfluidics

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