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Resolving the complexity of the human genome using single-molecule sequencing

Identifieur interne : 001598 ( Main/Exploration ); précédent : 001597; suivant : 001599

Resolving the complexity of the human genome using single-molecule sequencing

Auteurs : Mark J. P. Chaisson [États-Unis] ; John Huddleston [États-Unis] ; Megan Y. Dennis [États-Unis] ; Peter H. Sudmant [États-Unis] ; Maika Malig [États-Unis] ; Fereydoun Hormozdiari [États-Unis] ; Francesca Antonacci [Italie] ; Urvashi Surti [États-Unis] ; Richard Sandstrom [États-Unis] ; Matthew Boitano [États-Unis] ; Jane M. Landolin [États-Unis] ; John A. Stamatoyannopoulos [États-Unis] ; Michael W. Hunkapiller [États-Unis] ; Jonas Korlach [États-Unis] ; Evan E. Eichler [États-Unis]

Source :

Nature [ 0028-0836 ] ; 2014.

RBID : PMC:4317254

Descripteurs français

English descriptors

KwdEn :
- Chromosome Inversion (genetics), Chromosomes, Human, Pair 10 (genetics), Cloning, Molecular, GC Rich Sequence (genetics), Genetic Variation (genetics), Genome, Human (genetics), Genomics, Haploidy, Humans, Mutagenesis, Insertional (genetics), Reference Standards, Sequence Analysis, DNA (methods), Tandem Repeat Sequences (genetics).
MESH :
- genetics : Chromosome Inversion, Chromosomes, Human, Pair 10, GC Rich Sequence, Genetic Variation, Genome, Human, Mutagenesis, Insertional, Tandem Repeat Sequences.
- methods : Sequence Analysis, DNA.
- Cloning, Molecular, Genomics, Haploidy, Humans, Reference Standards.

Abstract

The human genome is arguably the most complete mammalian reference assembly^1–3 yet more than 160 euchromatic gaps remain^4–6 and aspects of its structural variation remain poorly understood ten years after its completion^7–9. In order to identify missing sequence and genetic variation, we sequenced and analyzed a haploid human genome (CHM1) using single-molecule, real-time (SMRT) DNA sequencing¹⁰. We closed or extended 55% of the remaining interstitial gaps in the human GRCh37 reference genome—78% of which carried long runs of degenerate short tandem repeats (STRs) often multiple kilobases in length embedded within GC-rich genomic regions. We resolved the complete sequence of 26,079 euchromatic structural variants at the basepair level, including inversions, complex insertions, and long tracts of tandem repeats. Most have not been previously reported with the greatest increases in sensitivity occurring for events less than 5 kbp in size. Compared to the human reference, we find a significant insertional bias (3:1) in regions corresponding to complex insertions and long STRs. Our results suggest a greater complexity of the human genome in the form of variation of longer and more complex repetitive DNA that can now be largely resolved with the application of this longer-read sequencing technology.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317254

DOI: 10.1038/nature13907
PubMed: 25383537
PubMed Central: 4317254

Affiliations:

Le document en format XML

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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosome Inversion (genetics)</term>
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<term>GC Rich Sequence (genetics)</term>
<term>Genetic Variation (genetics)</term>
<term>Genome, Human (genetics)</term>
<term>Genomics</term>
<term>Haploidy</term>
<term>Humans</term>
<term>Mutagenesis, Insertional (genetics)</term>
<term>Reference Standards</term>
<term>Sequence Analysis, DNA (methods)</term>
<term>Tandem Repeat Sequences (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN ()</term>
<term>Chromosomes humains de la paire 10 (génétique)</term>
<term>Clonage moléculaire</term>
<term>Génome humain (génétique)</term>
<term>Génomique</term>
<term>Haploïdie</term>
<term>Humains</term>
<term>Inversion chromosomique (génétique)</term>
<term>Mutagenèse par insertion (génétique)</term>
<term>Normes de référence</term>
<term>Séquence riche en GC (génétique)</term>
<term>Séquences répétées en tandem (génétique)</term>
<term>Variation génétique (génétique)</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosome Inversion</term>
<term>Chromosomes, Human, Pair 10</term>
<term>GC Rich Sequence</term>
<term>Genetic Variation</term>
<term>Genome, Human</term>
<term>Mutagenesis, Insertional</term>
<term>Tandem Repeat Sequences</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Chromosomes humains de la paire 10</term>
<term>Génome humain</term>
<term>Inversion chromosomique</term>
<term>Mutagenèse par insertion</term>
<term>Séquence riche en GC</term>
<term>Séquences répétées en tandem</term>
<term>Variation génétique</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Cloning, Molecular</term>
<term>Genomics</term>
<term>Haploidy</term>
<term>Humans</term>
<term>Reference Standards</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Clonage moléculaire</term>
<term>Génomique</term>
<term>Haploïdie</term>
<term>Humains</term>
<term>Normes de référence</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p id="P1">The human genome is arguably the most complete mammalian reference assembly<sup><xref rid="R1" ref-type="bibr">1</xref>
–<xref rid="R3" ref-type="bibr">3</xref>
</sup>
 yet more than 160 euchromatic gaps remain<sup><xref rid="R4" ref-type="bibr">4</xref>
–<xref rid="R6" ref-type="bibr">6</xref>
</sup>
 and aspects of its structural variation remain poorly understood ten years after its completion<sup><xref rid="R7" ref-type="bibr">7</xref>
–<xref rid="R9" ref-type="bibr">9</xref>
</sup>
. In order to identify missing sequence and genetic variation, we sequenced and analyzed a haploid human genome (CHM1) using single-molecule, real-time (SMRT) DNA sequencing<sup><xref rid="R10" ref-type="bibr">10</xref>
</sup>
. We closed or extended 55% of the remaining interstitial gaps in the human GRCh37 reference genome—78% of which carried long runs of degenerate short tandem repeats (STRs) often multiple kilobases in length embedded within GC-rich genomic regions. We resolved the complete sequence of 26,079 euchromatic structural variants at the basepair level, including inversions, complex insertions, and long tracts of tandem repeats. Most have not been previously reported with the greatest increases in sensitivity occurring for events less than 5 kbp in size. Compared to the human reference, we find a significant insertional bias (3:1) in regions corresponding to complex insertions and long STRs. Our results suggest a greater complexity of the human genome in the form of variation of longer and more complex repetitive DNA that can now be largely resolved with the application of this longer-read sequencing technology.</p>
</div>
</front>
</TEI>
<affiliations><list><country><li>Italie</li>
<li>États-Unis</li>
</country>
<region><li>Californie</li>
<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"><region name="Washington (État)"><name sortKey="Chaisson, Mark J P" sort="Chaisson, Mark J P" uniqKey="Chaisson M" first="Mark J. P." last="Chaisson">Mark J. P. Chaisson</name>
</region>
<name sortKey="Boitano, Matthew" sort="Boitano, Matthew" uniqKey="Boitano M" first="Matthew" last="Boitano">Matthew Boitano</name>
<name sortKey="Dennis, Megan Y" sort="Dennis, Megan Y" uniqKey="Dennis M" first="Megan Y." last="Dennis">Megan Y. Dennis</name>
<name sortKey="Eichler, Evan E" sort="Eichler, Evan E" uniqKey="Eichler E" first="Evan E." last="Eichler">Evan E. Eichler</name>
<name sortKey="Eichler, Evan E" sort="Eichler, Evan E" uniqKey="Eichler E" first="Evan E." last="Eichler">Evan E. Eichler</name>
<name sortKey="Hormozdiari, Fereydoun" sort="Hormozdiari, Fereydoun" uniqKey="Hormozdiari F" first="Fereydoun" last="Hormozdiari">Fereydoun Hormozdiari</name>
<name sortKey="Huddleston, John" sort="Huddleston, John" uniqKey="Huddleston J" first="John" last="Huddleston">John Huddleston</name>
<name sortKey="Huddleston, John" sort="Huddleston, John" uniqKey="Huddleston J" first="John" last="Huddleston">John Huddleston</name>
<name sortKey="Hunkapiller, Michael W" sort="Hunkapiller, Michael W" uniqKey="Hunkapiller M" first="Michael W." last="Hunkapiller">Michael W. Hunkapiller</name>
<name sortKey="Korlach, Jonas" sort="Korlach, Jonas" uniqKey="Korlach J" first="Jonas" last="Korlach">Jonas Korlach</name>
<name sortKey="Landolin, Jane M" sort="Landolin, Jane M" uniqKey="Landolin J" first="Jane M." last="Landolin">Jane M. Landolin</name>
<name sortKey="Malig, Maika" sort="Malig, Maika" uniqKey="Malig M" first="Maika" last="Malig">Maika Malig</name>
<name sortKey="Sandstrom, Richard" sort="Sandstrom, Richard" uniqKey="Sandstrom R" first="Richard" last="Sandstrom">Richard Sandstrom</name>
<name sortKey="Stamatoyannopoulos, John A" sort="Stamatoyannopoulos, John A" uniqKey="Stamatoyannopoulos J" first="John A." last="Stamatoyannopoulos">John A. Stamatoyannopoulos</name>
<name sortKey="Sudmant, Peter H" sort="Sudmant, Peter H" uniqKey="Sudmant P" first="Peter H." last="Sudmant">Peter H. Sudmant</name>
<name sortKey="Surti, Urvashi" sort="Surti, Urvashi" uniqKey="Surti U" first="Urvashi" last="Surti">Urvashi Surti</name>
</country>
<country name="Italie"><noRegion><name sortKey="Antonacci, Francesca" sort="Antonacci, Francesca" uniqKey="Antonacci F" first="Francesca" last="Antonacci">Francesca Antonacci</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

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Resolving the complexity of the human genome using single-molecule sequencing

Resolving the complexity of the human genome using single-molecule sequencing

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