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PMID: 25373144 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Single haplotype assembly of the human genome from a hydatidiform mole.

Genome research ·Vol. 24 ·No. 12 ·2014-00-00 ·Pages 2066-76

Steinberg KM, Schneider VA, Graves-Lindsay TA, Fulton RS, Agarwala R, Huddleston J, Shiryev SA, Morgulis A, Surti U, Warren WC, Church DM, Eichler EE, Wilson RK

Abstract

A complete reference assembly is essential for accurately interpreting individual genomes and associating variation with phenotypes. While the current human reference genome sequence is of very high quality, gaps and misassemblies remain due to biological and technical complexities. Large repetitive sequences and complex allelic diversity are the two main drivers of assembly error. Although increasing the length of sequence reads and library fragments can improve assembly, even the longest available reads do not resolve all regions. In order to overcome the issue of allelic diversity, we used genomic DNA from an essentially haploid hydatidiform mole, CHM1. We utilized several resources from this DNA including a set of end-sequenced and indexed BAC clones and 100× Illumina whole-genome shotgun (WGS) sequence coverage. We used the WGS sequence and the GRCh37 reference assembly to create an assembly of the CHM1 genome. We subsequently incorporated 382 finished BAC clone sequences to generate a draft assembly, CHM1_1.1 (NCBI AssemblyDB GCA_000306695.2). Analysis of gene, repetitive element, and segmental duplication content show this assembly to be of excellent quality and contiguity. However, comparison to assembly-independent resources, such as BAC clone end sequences and PacBio long reads, indicate misassembled regions. Most of these regions are enriched for structural variation and segmental duplication, and can be resolved in the future. This publicly available assembly will be integrated into the Genome Reference Consortium curation framework for further improvement, with the ultimate goal being a completely finished gap-free assembly.

MeSH Terms
Alleles Chromosome Mapping Chromosomes, Artificial, Bacterial Computational Biology/methods Female Genome, Human Genomics/methods Haplotypes Heterozygote High-Throughput Nucleotide Sequencing Humans Hydatidiform Mole/genetics Polymorphism, Single Nucleotide Pregnancy Repetitive Sequences, Nucleic Acid Segmental Duplications, Genomic Sequence Analysis, DNA
Authors & Affiliations
13 authors, click to expand affiliations / ORCID
Steinberg Karyn Meltz
The Genome Institute at Washington University, St. Louis, Missouri 63108, USA;
Schneider Valerie A
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA;
Graves-Lindsay Tina A
The Genome Institute at Washington University, St. Louis, Missouri 63108, USA;
Fulton Robert S
The Genome Institute at Washington University, St. Louis, Missouri 63108, USA;
Agarwala Richa
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA;
Huddleston John
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA;
Shiryev Sergey A
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA;
Morgulis Aleksandr
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA;
Surti Urvashi
Department of Pathology and Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA;
Warren Wesley C
The Genome Institute at Washington University, St. Louis, Missouri 63108, USA;
Church Deanna M
Personalis, Inc., Menlo Park, California 94025, USA.
Eichler Evan E
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA;
Wilson Richard K
The Genome Institute at Washington University, St. Louis, Missouri 63108, USA;
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1549-5469
DOI
10.1101/gr.180893.114
Published
2014-00-00
Epub
2014-00-04
Pages
2066-76
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC4248323
Subset
IM
Grants
NHGRI NIH HHS · U41 HG007635 · United States
Howard Hughes Medical Institute · United States
NHGRI NIH HHS · 5P01HG004120 · United States
NHGRI NIH HHS · 2R01HG002385 · United States
NHGRI NIH HHS · R01 HG002385 · United States
NHGRI NIH HHS · P01 HG004120 · United States
Databases
SRA
SRP017546, SRX533609
figshare
10.6084/m9. figshare.1091429
External Links
PubMed source DOI: 10.1101/gr.180893.114 PMC Full Text View journal details
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