Single haplotype assembly of the human genome from a hydatidiform mole.
Identifieur interne : 001306 ( Main/Exploration ); précédent : 001305; suivant : 001307Single haplotype assembly of the human genome from a hydatidiform mole.
Auteurs : Karyn Meltz Steinberg [États-Unis] ; Valerie A. Schneider [États-Unis] ; Tina A. Graves-Lindsay [États-Unis] ; Robert S. Fulton [États-Unis] ; Richa Agarwala [États-Unis] ; John Huddleston [États-Unis] ; Sergey A. Shiryev [États-Unis] ; Aleksandr Morgulis [États-Unis] ; Urvashi Surti [États-Unis] ; Wesley C. Warren [États-Unis] ; Deanna M. Church [États-Unis] ; Evan E. Eichler [États-Unis] ; Richard K. Wilson [États-Unis]Source :
- Genome research [ 1549-5469 ] ; 2014.
Descripteurs français
- KwdFr :
- Allèles, Analyse de séquence d'ADN, Biologie informatique (), Cartographie chromosomique, Chromosomes artificiels de bactérie, Duplications génomiques segmentaires, Femelle, Grossesse, Génome humain, Génomique (), Haplotypes, Humains, Hétérozygote, Môle hydatiforme (génétique), Polymorphisme de nucléotide simple, Séquences répétées d'acides nucléiques, Séquençage nucléotidique à haut débit.
- MESH :
- génétique : Môle hydatiforme.
- Allèles, Analyse de séquence d'ADN, Biologie informatique, Cartographie chromosomique, Chromosomes artificiels de bactérie, Duplications génomiques segmentaires, Femelle, Grossesse, Génome humain, Génomique, Haplotypes, Humains, Hétérozygote, Polymorphisme de nucléotide simple, Séquences répétées d'acides nucléiques, Séquençage nucléotidique à haut débit.
English descriptors
- KwdEn :
- 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.
- MESH :
- genetics : Hydatidiform Mole.
- methods : Computational Biology, Genomics.
- Alleles, Chromosome Mapping, Chromosomes, Artificial, Bacterial, Female, Genome, Human, Haplotypes, Heterozygote, High-Throughput Nucleotide Sequencing, Humans, Polymorphism, Single Nucleotide, Pregnancy, Repetitive Sequences, Nucleic Acid, Segmental Duplications, Genomic, Sequence Analysis, DNA.
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.
DOI: 10.1101/gr.180893.114
PubMed: 25373144
Affiliations:
- États-Unis
- Pennsylvanie, Washington (État)
- Pittsburgh, Seattle
- Université de Pittsburgh, Université de Washington
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Le document en format XML
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Schneider</name><affiliation wicri:level="1"><nlm:affiliation>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA;</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894</wicri:regionArea><wicri:noRegion>Maryland 20894</wicri:noRegion></affiliation></author><author><name sortKey="Graves Lindsay, Tina A" sort="Graves Lindsay, Tina A" uniqKey="Graves Lindsay T" first="Tina A" last="Graves-Lindsay">Tina A. Graves-Lindsay</name><affiliation wicri:level="1"><nlm:affiliation>The Genome Institute at Washington University, St. Louis, Missouri 63108, USA;</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Genome Institute at Washington University, St. Louis, Missouri 63108</wicri:regionArea><wicri:noRegion>Missouri 63108</wicri:noRegion></affiliation></author><author><name sortKey="Fulton, Robert S" sort="Fulton, Robert S" uniqKey="Fulton R" first="Robert S" last="Fulton">Robert S. Fulton</name><affiliation wicri:level="1"><nlm:affiliation>The Genome Institute at Washington University, St. Louis, Missouri 63108, USA;</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Genome Institute at Washington University, St. Louis, Missouri 63108</wicri:regionArea><wicri:noRegion>Missouri 63108</wicri:noRegion></affiliation></author><author><name sortKey="Agarwala, Richa" sort="Agarwala, Richa" uniqKey="Agarwala R" first="Richa" last="Agarwala">Richa Agarwala</name><affiliation wicri:level="1"><nlm:affiliation>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA;</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894</wicri:regionArea><wicri:noRegion>Maryland 20894</wicri:noRegion></affiliation></author><author><name sortKey="Huddleston, John" sort="Huddleston, John" uniqKey="Huddleston J" first="John" last="Huddleston">John Huddleston</name><affiliation wicri:level="4"><nlm:affiliation>Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA;</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195</wicri:regionArea><orgName type="university">Université de Washington</orgName><placeName><settlement type="city">Seattle</settlement><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Shiryev, Sergey A" sort="Shiryev, Sergey A" uniqKey="Shiryev S" first="Sergey A" last="Shiryev">Sergey A. Shiryev</name><affiliation wicri:level="1"><nlm:affiliation>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA;</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894</wicri:regionArea><wicri:noRegion>Maryland 20894</wicri:noRegion></affiliation></author><author><name sortKey="Morgulis, Aleksandr" sort="Morgulis, Aleksandr" uniqKey="Morgulis A" first="Aleksandr" last="Morgulis">Aleksandr Morgulis</name><affiliation wicri:level="1"><nlm:affiliation>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA;</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894</wicri:regionArea><wicri:noRegion>Maryland 20894</wicri:noRegion></affiliation></author><author><name sortKey="Surti, Urvashi" sort="Surti, Urvashi" uniqKey="Surti U" first="Urvashi" last="Surti">Urvashi Surti</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pathology and Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA;</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology and Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15260</wicri:regionArea><orgName type="university">Université de Pittsburgh</orgName><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName></affiliation></author><author><name sortKey="Warren, Wesley C" sort="Warren, Wesley C" uniqKey="Warren W" first="Wesley C" last="Warren">Wesley C. Warren</name><affiliation wicri:level="1"><nlm:affiliation>The Genome Institute at Washington University, St. Louis, Missouri 63108, USA;</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Genome Institute at Washington University, St. Louis, Missouri 63108</wicri:regionArea><wicri:noRegion>Missouri 63108</wicri:noRegion></affiliation></author><author><name sortKey="Church, Deanna M" sort="Church, Deanna M" uniqKey="Church D" first="Deanna M" last="Church">Deanna M. Church</name><affiliation wicri:level="1"><nlm:affiliation>Personalis, Inc., Menlo Park, California 94025, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Personalis, Inc., Menlo Park, California 94025</wicri:regionArea><wicri:noRegion>California 94025</wicri:noRegion></affiliation></author><author><name sortKey="Eichler, Evan E" sort="Eichler, Evan E" uniqKey="Eichler E" first="Evan E" last="Eichler">Evan E. Eichler</name><affiliation wicri:level="4"><nlm:affiliation>Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA;</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195</wicri:regionArea><orgName type="university">Université de Washington</orgName><placeName><settlement type="city">Seattle</settlement><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Wilson, Richard K" sort="Wilson, Richard K" uniqKey="Wilson R" first="Richard K" last="Wilson">Richard K. Wilson</name><affiliation wicri:level="1"><nlm:affiliation>The Genome Institute at Washington University, St. Louis, Missouri 63108, USA;</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Genome Institute at Washington University, St. Louis, Missouri 63108</wicri:regionArea><wicri:noRegion>Missouri 63108</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genome research</title><idno type="eISSN">1549-5469</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles</term><term>Chromosome Mapping</term><term>Chromosomes, Artificial, Bacterial</term><term>Computational Biology (methods)</term><term>Female</term><term>Genome, Human</term><term>Genomics (methods)</term><term>Haplotypes</term><term>Heterozygote</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Hydatidiform Mole (genetics)</term><term>Polymorphism, Single Nucleotide</term><term>Pregnancy</term><term>Repetitive Sequences, Nucleic Acid</term><term>Segmental Duplications, Genomic</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Allèles</term><term>Analyse de séquence d'ADN</term><term>Biologie informatique ()</term><term>Cartographie chromosomique</term><term>Chromosomes artificiels de bactérie</term><term>Duplications génomiques segmentaires</term><term>Femelle</term><term>Grossesse</term><term>Génome humain</term><term>Génomique ()</term><term>Haplotypes</term><term>Humains</term><term>Hétérozygote</term><term>Môle hydatiforme (génétique)</term><term>Polymorphisme de nucléotide simple</term><term>Séquences répétées d'acides nucléiques</term><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Hydatidiform Mole</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Môle hydatiforme</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Genomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Chromosome Mapping</term><term>Chromosomes, Artificial, Bacterial</term><term>Female</term><term>Genome, Human</term><term>Haplotypes</term><term>Heterozygote</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Polymorphism, Single Nucleotide</term><term>Pregnancy</term><term>Repetitive Sequences, Nucleic Acid</term><term>Segmental Duplications, Genomic</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Allèles</term><term>Analyse de séquence d'ADN</term><term>Biologie informatique</term><term>Cartographie chromosomique</term><term>Chromosomes artificiels de bactérie</term><term>Duplications génomiques segmentaires</term><term>Femelle</term><term>Grossesse</term><term>Génome humain</term><term>Génomique</term><term>Haplotypes</term><term>Humains</term><term>Hétérozygote</term><term>Polymorphisme de nucléotide simple</term><term>Séquences répétées d'acides nucléiques</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Pennsylvanie</li><li>Washington (État)</li></region><settlement><li>Pittsburgh</li><li>Seattle</li></settlement><orgName><li>Université de Pittsburgh</li><li>Université de Washington</li></orgName></list><tree><country name="États-Unis"><noRegion><name sortKey="Steinberg, Karyn Meltz" sort="Steinberg, Karyn Meltz" uniqKey="Steinberg K" first="Karyn Meltz" last="Steinberg">Karyn Meltz Steinberg</name></noRegion><name sortKey="Agarwala, Richa" sort="Agarwala, Richa" uniqKey="Agarwala R" first="Richa" last="Agarwala">Richa Agarwala</name><name sortKey="Church, Deanna M" sort="Church, Deanna M" uniqKey="Church D" first="Deanna M" last="Church">Deanna M. Church</name><name sortKey="Eichler, Evan E" sort="Eichler, Evan E" uniqKey="Eichler E" first="Evan E" last="Eichler">Evan E. Eichler</name><name sortKey="Fulton, Robert S" sort="Fulton, Robert S" uniqKey="Fulton R" first="Robert S" last="Fulton">Robert S. Fulton</name><name sortKey="Graves Lindsay, Tina A" sort="Graves Lindsay, Tina A" uniqKey="Graves Lindsay T" first="Tina A" last="Graves-Lindsay">Tina A. Graves-Lindsay</name><name sortKey="Huddleston, John" sort="Huddleston, John" uniqKey="Huddleston J" first="John" last="Huddleston">John Huddleston</name><name sortKey="Morgulis, Aleksandr" sort="Morgulis, Aleksandr" uniqKey="Morgulis A" first="Aleksandr" last="Morgulis">Aleksandr Morgulis</name><name sortKey="Schneider, Valerie A" sort="Schneider, Valerie A" uniqKey="Schneider V" first="Valerie A" last="Schneider">Valerie A. Schneider</name><name sortKey="Shiryev, Sergey A" sort="Shiryev, Sergey A" uniqKey="Shiryev S" first="Sergey A" last="Shiryev">Sergey A. Shiryev</name><name sortKey="Surti, Urvashi" sort="Surti, Urvashi" uniqKey="Surti U" first="Urvashi" last="Surti">Urvashi Surti</name><name sortKey="Warren, Wesley C" sort="Warren, Wesley C" uniqKey="Warren W" first="Wesley C" last="Warren">Wesley C. Warren</name><name sortKey="Wilson, Richard K" sort="Wilson, Richard K" uniqKey="Wilson R" first="Richard K" last="Wilson">Richard K. Wilson</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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