A macaque's-eye view of human insertions and deletions: Differences in mechanisms
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作者:
Kvikstad, Erika M.
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Kvikstad, Erika M.
Tyekucheva, Svitlana
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Tyekucheva, Svitlana
Chiaromonte, Francesca
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Chiaromonte, Francesca
Makova, Kateryna D.
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Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Makova, Kateryna D.
[1
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机构:
[1] Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
[2] Penn State Univ, Dept Biol, University Pk, PA 16802 USA
[3] Penn State Univ, Dept Stat, University Pk, PA 16802 USA
Insertions and deletions (indels) cause numerous genetic diseases and lead to pronounced evolutionary differences among genomes. The macaque sequences provide an opportunity to gain insights into the mechanisms generating these mutations on a genome-wide scale by establishing the polarity of indels occurring in the human lineage since its divergence from the chimpanzee. Here we apply novel regression techniques and multiscale analyses to demonstrate an extensive regional indel rate variation stemming from local fluctuations in divergence, GC content, male and female recombination rates, proximity to telomeres, and other genomic factors. We find that both replication and, surprisingly, recombination are significantly associated with the occurrence of small indels. Intriguingly, the relative inputs of replication versus recombination differ between insertions and deletions, thus the two types of mutations are likely guided in part by distinct mechanisms. Namely, insertions are more strongly associated with factors linked to recombination, while deletions are mostly associated with replication-related features. Indel as a term misleadingly groups the two types of mutations together by their effect on a sequence alignment. However, here we establish that the correct identification of a small gap as an insertion or a deletion (by use of an outgroup) is crucial to determining its mechanism of origin. In addition to providing novel insights into insertion and deletion mutagenesis, these results will assist in gap penalty modeling and eventually lead to more reliable genomic alignments.
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Blanchette, M
Kent, WJ
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Kent, WJ
Riemer, C
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Riemer, C
Elnitski, L
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Elnitski, L
Smit, AFA
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Smit, AFA
Roskin, KM
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Roskin, KM
Baertsch, R
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Baertsch, R
Rosenbloom, K
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Rosenbloom, K
Clawson, H
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Clawson, H
Green, ED
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Green, ED
Haussler, D
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Haussler, D
Miller, W
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机构:
Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Blankenberg, Daniel
Taylor, James
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Taylor, James
Schenck, Ian
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机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Schenck, Ian
He, Jianbin
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机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
He, Jianbin
Zhang, Yi
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机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Zhang, Yi
Ghent, Matthew
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Ghent, Matthew
Veeraraghavan, Narayanan
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Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Veeraraghavan, Narayanan
Albert, Istvan
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机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Albert, Istvan
Miller, Webb
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h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Miller, Webb
Makova, Kateryna D.
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h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Makova, Kateryna D.
Hardison, Ross C.
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机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Hardison, Ross C.
Nekrutenko, Anton
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机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Blanchette, M
Kent, WJ
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Kent, WJ
Riemer, C
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h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Riemer, C
Elnitski, L
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Elnitski, L
Smit, AFA
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h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Smit, AFA
Roskin, KM
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Roskin, KM
Baertsch, R
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Baertsch, R
Rosenbloom, K
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Rosenbloom, K
Clawson, H
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h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Clawson, H
Green, ED
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h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Green, ED
Haussler, D
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Haussler, D
Miller, W
论文数: 0引用数: 0
h-index: 0
机构:
Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Blankenberg, Daniel
Taylor, James
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h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Taylor, James
Schenck, Ian
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h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Schenck, Ian
He, Jianbin
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h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
He, Jianbin
Zhang, Yi
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h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Zhang, Yi
Ghent, Matthew
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h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Ghent, Matthew
Veeraraghavan, Narayanan
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h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Veeraraghavan, Narayanan
Albert, Istvan
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h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Albert, Istvan
Miller, Webb
论文数: 0引用数: 0
h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Miller, Webb
Makova, Kateryna D.
论文数: 0引用数: 0
h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Makova, Kateryna D.
Hardison, Ross C.
论文数: 0引用数: 0
h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Hardison, Ross C.
Nekrutenko, Anton
论文数: 0引用数: 0
h-index: 0
机构:
Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA