Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.
Identifieur interne : 000B29 ( Main/Exploration ); précédent : 000B28; suivant : 000B30Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.
Auteurs : Dirk D. Dolle [Royaume-Uni] ; Zhicheng Liu [Royaume-Uni] ; Matthew Cotten [Royaume-Uni] ; Jared T. Simpson [Canada] ; Zamin Iqbal [Royaume-Uni] ; Richard Durbin [Royaume-Uni] ; Shane A. Mccarthy [Royaume-Uni] ; Thomas M. Keane [Royaume-Uni]Source :
- Genome research [ 1549-5469 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- genetics : Genome, Human, INDEL Mutation.
- methods : Sequence Alignment, Whole Genome Sequencing.
- Alleles, Data Compression, Genomics, Genotype, Humans, Sequence Analysis, DNA, Software.
Abstract
We are rapidly approaching the point where we have sequenced millions of human genomes. There is a pressing need for new data structures to store raw sequencing data and efficient algorithms for population scale analysis. Current reference-based data formats do not fully exploit the redundancy in population sequencing nor take advantage of shared genetic variation. In recent years, the Burrows-Wheeler transform (BWT) and FM-index have been widely employed as a full-text searchable index for read alignment and de novo assembly. We introduce the concept of a population BWT and use it to store and index the sequencing reads of 2705 samples from the 1000 Genomes Project. A key feature is that, as more genomes are added, identical read sequences are increasingly observed, and compression becomes more efficient. We assess the support in the 1000 Genomes read data for every base position of two human reference assembly versions, identifying that 3.2 Mbp with population support was lost in the transition from GRCh37 with 13.7 Mbp added to GRCh38. We show that the vast majority of variant alleles can be uniquely described by overlapping 31-mers and show how rapid and accurate SNP and indel genotyping can be carried out across the genomes in the population BWT. We use the population BWT to carry out nonreference queries to search for the presence of all known viral genomes and discover human T-lymphotropic virus 1 integrations in six samples in a recognized epidemiological distribution.
DOI: 10.1101/gr.211748.116
PubMed: 27986821
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 000E47
- to stream PubMed, to step Curation: 000E47
- to stream PubMed, to step Checkpoint: 000A69
- to stream Ncbi, to step Merge: 001887
- to stream Ncbi, to step Curation: 001887
- to stream Ncbi, to step Checkpoint: 001887
- to stream Main, to step Merge: 000B32
- to stream Main, to step Curation: 000B29
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.</title><author><name sortKey="Dolle, Dirk D" sort="Dolle, Dirk D" uniqKey="Dolle D" first="Dirk D" last="Dolle">Dirk D. Dolle</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SA</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Zhicheng" sort="Liu, Zhicheng" uniqKey="Liu Z" first="Zhicheng" last="Liu">Zhicheng Liu</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SA</wicri:noRegion></affiliation></author><author><name sortKey="Cotten, Matthew" sort="Cotten, Matthew" uniqKey="Cotten M" first="Matthew" last="Cotten">Matthew Cotten</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SA</wicri:noRegion></affiliation></author><author><name sortKey="Simpson, Jared T" sort="Simpson, Jared T" uniqKey="Simpson J" first="Jared T" last="Simpson">Jared T. Simpson</name><affiliation wicri:level="1"><nlm:affiliation>Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3</wicri:regionArea><wicri:noRegion>Ontario M5G 0A3</wicri:noRegion></affiliation></author><author><name sortKey="Iqbal, Zamin" sort="Iqbal, Zamin" uniqKey="Iqbal Z" first="Zamin" last="Iqbal">Zamin Iqbal</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN</wicri:regionArea><wicri:noRegion>Oxford OX3 7BN</wicri:noRegion></affiliation></author><author><name sortKey="Durbin, Richard" sort="Durbin, Richard" uniqKey="Durbin R" first="Richard" last="Durbin">Richard Durbin</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SA</wicri:noRegion></affiliation></author><author><name sortKey="Mccarthy, Shane A" sort="Mccarthy, Shane A" uniqKey="Mccarthy S" first="Shane A" last="Mccarthy">Shane A. Mccarthy</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SA</wicri:noRegion></affiliation></author><author><name sortKey="Keane, Thomas M" sort="Keane, Thomas M" uniqKey="Keane T" first="Thomas M" last="Keane">Thomas M. Keane</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SA</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:27986821</idno><idno type="pmid">27986821</idno><idno type="doi">10.1101/gr.211748.116</idno><idno type="wicri:Area/PubMed/Corpus">000E47</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000E47</idno><idno type="wicri:Area/PubMed/Curation">000E47</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000E47</idno><idno type="wicri:Area/PubMed/Checkpoint">000A69</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000A69</idno><idno type="wicri:Area/Ncbi/Merge">001887</idno><idno type="wicri:Area/Ncbi/Curation">001887</idno><idno type="wicri:Area/Ncbi/Checkpoint">001887</idno><idno type="wicri:Area/Main/Merge">000B32</idno><idno type="wicri:Area/Main/Curation">000B29</idno><idno type="wicri:Area/Main/Exploration">000B29</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.</title><author><name sortKey="Dolle, Dirk D" sort="Dolle, Dirk D" uniqKey="Dolle D" first="Dirk D" last="Dolle">Dirk D. Dolle</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SA</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Zhicheng" sort="Liu, Zhicheng" uniqKey="Liu Z" first="Zhicheng" last="Liu">Zhicheng Liu</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SA</wicri:noRegion></affiliation></author><author><name sortKey="Cotten, Matthew" sort="Cotten, Matthew" uniqKey="Cotten M" first="Matthew" last="Cotten">Matthew Cotten</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SA</wicri:noRegion></affiliation></author><author><name sortKey="Simpson, Jared T" sort="Simpson, Jared T" uniqKey="Simpson J" first="Jared T" last="Simpson">Jared T. Simpson</name><affiliation wicri:level="1"><nlm:affiliation>Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3</wicri:regionArea><wicri:noRegion>Ontario M5G 0A3</wicri:noRegion></affiliation></author><author><name sortKey="Iqbal, Zamin" sort="Iqbal, Zamin" uniqKey="Iqbal Z" first="Zamin" last="Iqbal">Zamin Iqbal</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN</wicri:regionArea><wicri:noRegion>Oxford OX3 7BN</wicri:noRegion></affiliation></author><author><name sortKey="Durbin, Richard" sort="Durbin, Richard" uniqKey="Durbin R" first="Richard" last="Durbin">Richard Durbin</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SA</wicri:noRegion></affiliation></author><author><name sortKey="Mccarthy, Shane A" sort="Mccarthy, Shane A" uniqKey="Mccarthy S" first="Shane A" last="Mccarthy">Shane A. Mccarthy</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SA</wicri:noRegion></affiliation></author><author><name sortKey="Keane, Thomas M" sort="Keane, Thomas M" uniqKey="Keane T" first="Thomas M" last="Keane">Thomas M. Keane</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SA</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genome research</title><idno type="eISSN">1549-5469</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles</term><term>Data Compression</term><term>Genome, Human (genetics)</term><term>Genomics</term><term>Genotype</term><term>Humans</term><term>INDEL Mutation (genetics)</term><term>Sequence Alignment (methods)</term><term>Sequence Analysis, DNA</term><term>Software</term><term>Whole Genome Sequencing (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences ()</term><term>Allèles</term><term>Analyse de séquence d'ADN</term><term>Compression de données</term><term>Génome humain (génétique)</term><term>Génomique</term><term>Génotype</term><term>Humains</term><term>Logiciel</term><term>Mutation de type INDEL (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome, Human</term><term>INDEL Mutation</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Génome humain</term><term>Mutation de type INDEL</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Alignment</term><term>Whole Genome Sequencing</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Data Compression</term><term>Genomics</term><term>Genotype</term><term>Humans</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Allèles</term><term>Analyse de séquence d'ADN</term><term>Compression de données</term><term>Génomique</term><term>Génotype</term><term>Humains</term><term>Logiciel</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We are rapidly approaching the point where we have sequenced millions of human genomes. There is a pressing need for new data structures to store raw sequencing data and efficient algorithms for population scale analysis. Current reference-based data formats do not fully exploit the redundancy in population sequencing nor take advantage of shared genetic variation. In recent years, the Burrows-Wheeler transform (BWT) and FM-index have been widely employed as a full-text searchable index for read alignment and de novo assembly. We introduce the concept of a population BWT and use it to store and index the sequencing reads of 2705 samples from the 1000 Genomes Project. A key feature is that, as more genomes are added, identical read sequences are increasingly observed, and compression becomes more efficient. We assess the support in the 1000 Genomes read data for every base position of two human reference assembly versions, identifying that 3.2 Mbp with population support was lost in the transition from GRCh37 with 13.7 Mbp added to GRCh38. We show that the vast majority of variant alleles can be uniquely described by overlapping 31-mers and show how rapid and accurate SNP and indel genotyping can be carried out across the genomes in the population BWT. We use the population BWT to carry out nonreference queries to search for the presence of all known viral genomes and discover human T-lymphotropic virus 1 integrations in six samples in a recognized epidemiological distribution.</div></front></TEI><affiliations><list><country><li>Canada</li><li>Royaume-Uni</li></country></list><tree><country name="Royaume-Uni"><noRegion><name sortKey="Dolle, Dirk D" sort="Dolle, Dirk D" uniqKey="Dolle D" first="Dirk D" last="Dolle">Dirk D. Dolle</name></noRegion><name sortKey="Cotten, Matthew" sort="Cotten, Matthew" uniqKey="Cotten M" first="Matthew" last="Cotten">Matthew Cotten</name><name sortKey="Durbin, Richard" sort="Durbin, Richard" uniqKey="Durbin R" first="Richard" last="Durbin">Richard Durbin</name><name sortKey="Iqbal, Zamin" sort="Iqbal, Zamin" uniqKey="Iqbal Z" first="Zamin" last="Iqbal">Zamin Iqbal</name><name sortKey="Keane, Thomas M" sort="Keane, Thomas M" uniqKey="Keane T" first="Thomas M" last="Keane">Thomas M. Keane</name><name sortKey="Liu, Zhicheng" sort="Liu, Zhicheng" uniqKey="Liu Z" first="Zhicheng" last="Liu">Zhicheng Liu</name><name sortKey="Mccarthy, Shane A" sort="Mccarthy, Shane A" uniqKey="Mccarthy S" first="Shane A" last="Mccarthy">Shane A. Mccarthy</name></country><country name="Canada"><noRegion><name sortKey="Simpson, Jared T" sort="Simpson, Jared T" uniqKey="Simpson J" first="Jared T" last="Simpson">Jared T. Simpson</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000B29 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000B29 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:27986821
|texte= Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:27986821" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |