DeNovoGear: de novo indel and point mutation discovery and phasing

被引：127

作者：

Ramu, Avinash ^{[1
]}

Noordam, Michiel J. ^{[1
]}

Schwartz, Rachel S. ^{[2
]}

Wuster, Arthur ^{[3
]}

Hurles, Matthew E. ^{[3
]}

Cartwright, Reed A. ^{[2
,4
]}

Conrad, Donald F. ^{[1
,5
]}

机构：

[1] Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA

[2] Arizona State Univ, Biodesign Inst, Ctr Evolutionary Med & Informat, Tempe, AZ USA

[3] Wellcome Trust Sanger Inst, Genome Mutat & Genet Dis Grp, Cambridge, England

[4] Arizona State Univ, Sch Life Sci, Tempe, AZ USA

[5] Washington Univ, Dept Pathol & Immunol, Sch Med, St Louis, MO USA

来源：

NATURE METHODS | 2013年 / 10卷 / 10期

基金：

英国惠康基金;

关键词：

GENOME; FRAMEWORK; SPECTRUM; RATES;

D O I：

10.1038/nmeth.2611

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We present DeNovoGear software for analyzing de novo mutations from familial and somatic tissue sequencing data. DeNovoGear uses likelihood-based error modeling to reduce the false positive rate of mutation discovery in exome analysis and fragment information to identify the parental origin of germ-line mutations. We used DeNovoGear on human whole-genome sequencing data to produce a set of predicted de novo insertion and/or deletion (indel) mutations with a 95% validation rate.

引用

页码：985 / +

页数：5

共 16 条

[1] Dindel: Accurate indel calls from short-read data
Albers, Cornelis A.
Lunter, Gerton
MacArthur, Daniel G.
McVean, Gilean
Ouwehand, Willem H.
Durbin, Richard
[J]. GENOME RESEARCH, 2011, 21 (06) : 961 - 973
[2] An integrated map of genetic variation from 1,092 human genomes
Altshuler, David M.
Durbin, Richard M.
Abecasis, Goncalo R.
Bentley, David R.
Chakravarti, Aravinda
Clark, Andrew G.
Donnelly, Peter
Eichler, Evan E.
Flicek, Paul
Gabriel, Stacey B.
Gibbs, Richard A.
Green, Eric D.
Hurles, Matthew E.
Knoppers, Bartha M.
Korbel, Jan O.
Lander, Eric S.
Lee, Charles
Lehrach, Hans
Mardis, Elaine R.
Marth, Gabor T.
McVean, Gil A.
Nickerson, Deborah A.
Schmidt, Jeanette P.
Sherry, Stephen T.
Wang, Jun
Wilson, Richard K.
Gibbs, Richard A.
Dinh, Huyen
Kovar, Christie
Lee, Sandra
Lewis, Lora
Muzny, Donna
Reid, Jeff
Wang, Min
Wang, Jun
Fang, Xiaodong
Guo, Xiaosen
Jian, Min
Jiang, Hui
Jin, Xin
Li, Guoqing
Li, Jingxiang
Li, Yingrui
Li, Zhuo
Liu, Xiao
Lu, Yao
Ma, Xuedi
Su, Zhe
Tai, Shuaishuai
Tang, Meifang
[J]. NATURE, 2012, 491 (7422) : 56 - 65
[3] Tandem repeats finder: a program to analyze DNA sequences
Benson, G
[J]. NUCLEIC ACIDS RESEARCH, 1999, 27 (02) : 573 - 580
[4] A Family-Based Probabilistic Method for Capturing De Novo Mutations from High-Throughput Short-Read Sequencing Data
Cartwright, Reed A.
Hussin, Julie
Keebler, Jonathan E. M.
Stone, Eric A.
Awadalla, Philip
[J]. STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY, 2012, 11 (02):
[5] Variation in genome-wide mutation rates within and between human families
Conrad, Donald F.
Keebler, Jonathan E. M.
DePristo, Mark A.
Lindsay, Sarah J.
Zhang, Yujun
Casals, Ferran
Idaghdour, Youssef
Hartl, Chris L.
Torroja, Carlos
Garimella, Kiran V.
Zilversmit, Martine
Cartwright, Reed
Rouleau, Guy A.
Daly, Mark
Stone, Eric A.
Hurles, Matthew E.
Awadalla, Philip
[J]. NATURE GENETICS, 2011, 43 (07) : 712 - U137
[6] A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, Mark A.
Banks, Eric
Poplin, Ryan
Garimella, Kiran V.
Maguire, Jared R.
Hartl, Christopher
Philippakis, Anthony A.
del Angel, Guillermo
Rivas, Manuel A.
Hanna, Matt
McKenna, Aaron
Fennell, Tim J.
Kernytsky, Andrew M.
Sivachenko, Andrey Y.
Cibulskis, Kristian
Gabriel, Stacey B.
Altshuler, David
Daly, Mark J.
[J]. NATURE GENETICS, 2011, 43 (05) : 491 - +
[7] The allele distribution in next-generation sequencing data sets is accurately described as the result of a stochastic branching process
Heinrich, Verena
Stange, Jens
Dickhaus, Thorsten
Imkeller, Peter
Krueger, Ulrike
Bauer, Sebastian
Mundlos, Stefan
Robinson, Peter N.
Hecht, Jochen
Krawitz, Peter M.
[J]. NUCLEIC ACIDS RESEARCH, 2012, 40 (06) : 2426 - 2431
[8] Rate of de novo mutations and the importance of father's age to disease risk
Kong, Augustine
Frigge, Michael L.
Masson, Gisli
Besenbacher, Soren
Sulem, Patrick
Magnusson, Gisli
Gudjonsson, Sigurjon A.
Sigurdsson, Asgeir
Jonasdottir, Aslaug
Jonasdottir, Adalbjorg
Wong, Wendy S. W.
Sigurdsson, Gunnar
Walters, G. Bragi
Steinberg, Stacy
Helgason, Hannes
Thorleifsson, Gudmar
Gudbjartsson, Daniel F.
Helgason, Agnar
Magnusson, Olafur Th.
Thorsteinsdottir, Unnur
Stefansson, Kari
[J]. NATURE, 2012, 488 (7412) : 471 - 475
[9] A Likelihood-Based Framework for Variant Calling and De Novo Mutation Detection in Families
Li, Bingshan
Chen, Wei
Zhan, Xiaowei
Busonero, Fabio
Sanna, Serena
Sidore, Carlo
Cucca, Francesco
Kang, Hyun M.
Abecasis, Goncalo R.
[J]. PLOS GENETICS, 2012, 8 (10):
[10] A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
Li, Heng
[J]. BIOINFORMATICS, 2011, 27 (21) : 2987 - 2993

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