Literature DB >> 19029539

Fast and flexible simulation of DNA sequence data.

Gary K Chen1, Paul Marjoram, Jeffrey D Wall.   

Abstract

Simulation of genomic sequences under the coalescent with recombination has conventionally been impractical for regions beyond tens of megabases. This work presents an algorithm, implemented as the program MaCS (Markovian Coalescent Simulator), that can efficiently simulate haplotypes under any arbitrary model of population history. We present several metrics comparing the performance of MaCS with other available simulation programs. Practical usage of MaCS is demonstrated through a comparison of measures of linkage disequilibrium between generated program output and real genotype data from populations considered to be structured.

Mesh：

Substances：

Year:  2008        PMID： 19029539      PMCID： PMC2612967          DOI： 10.1101/gr.083634.108

Source DB:  PubMed          Journal:  Genome Res        ISSN： 1088-9051            Impact factor:   9.043


  33 in total

1.  The coalescent with gene conversion.

Authors:  C Wiuf; J Hein
Journal:  Genetics       Date:  2000-05       Impact factor: 4.562

2.  Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels.

Authors:  L Frisse; R R Hudson; A Bartoszewicz; J D Wall; J Donfack; A Di Rienzo
Journal:  Am J Hum Genet       Date:  2001-08-29       Impact factor: 11.025

3.  On the number of segregating sites in genetical models without recombination.

Authors:  G A Watterson
Journal:  Theor Popul Biol       Date:  1975-04       Impact factor: 1.570

4.  Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.

Authors:  Na Li; Matthew Stephens
Journal:  Genetics       Date:  2003-12       Impact factor: 4.562

5.  SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history.

Authors:  Guillaume Laval; Laurent Excoffier
Journal:  Bioinformatics       Date:  2004-04-29       Impact factor: 6.937

6.  Variant of transcription factor 7-like 2 (TCF7L2) gene confers risk of type 2 diabetes.

Authors:  Struan F A Grant; Gudmar Thorleifsson; Inga Reynisdottir; Rafn Benediktsson; Andrei Manolescu; Jesus Sainz; Agnar Helgason; Hreinn Stefansson; Valur Emilsson; Anna Helgadottir; Unnur Styrkarsdottir; Kristinn P Magnusson; G Bragi Walters; Ebba Palsdottir; Thorbjorg Jonsdottir; Thorunn Gudmundsdottir; Arnaldur Gylfason; Jona Saemundsdottir; Robert L Wilensky; Muredach P Reilly; Daniel J Rader; Yu Bagger; Claus Christiansen; Vilmundur Gudnason; Gunnar Sigurdsson; Unnur Thorsteinsdottir; Jeffrey R Gulcher; Augustine Kong; Kari Stefansson
Journal:  Nat Genet       Date:  2006-01-15       Impact factor: 38.330

7.  Exploring population genetic models with recombination using efficient forward-time simulations.

Authors:  Badri Padhukasahasram; Paul Marjoram; Jeffrey D Wall; Carlos D Bustamante; Magnus Nordborg
Journal:  Genetics       Date:  2008-04       Impact factor: 4.562

8.  Ancestral inference from samples of DNA sequences with recombination.

Authors:  R C Griffiths; P Marjoram
Journal:  J Comput Biol       Date:  1996       Impact factor: 1.479

9.  Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.

Authors:  David J Begun; Alisha K Holloway; Kristian Stevens; Ladeana W Hillier; Yu-Ping Poh; Matthew W Hahn; Phillip M Nista; Corbin D Jones; Andrew D Kern; Colin N Dewey; Lior Pachter; Eugene Myers; Charles H Langley
Journal:  PLoS Biol       Date:  2007-11-06       Impact factor: 8.029

10.  A second generation human haplotype map of over 3.1 million SNPs.

Authors:  Kelly A Frazer; Dennis G Ballinger; David R Cox; David A Hinds; Laura L Stuve; Richard A Gibbs; John W Belmont; Andrew Boudreau; Paul Hardenbol; Suzanne M Leal; Shiran Pasternak; David A Wheeler; Thomas D Willis; Fuli Yu; Huanming Yang; Changqing Zeng; Yang Gao; Haoran Hu; Weitao Hu; Chaohua Li; Wei Lin; Siqi Liu; Hao Pan; Xiaoli Tang; Jian Wang; Wei Wang; Jun Yu; Bo Zhang; Qingrun Zhang; Hongbin Zhao; Hui Zhao; Jun Zhou; Stacey B Gabriel; Rachel Barry; Brendan Blumenstiel; Amy Camargo; Matthew Defelice; Maura Faggart; Mary Goyette; Supriya Gupta; Jamie Moore; Huy Nguyen; Robert C Onofrio; Melissa Parkin; Jessica Roy; Erich Stahl; Ellen Winchester; Liuda Ziaugra; David Altshuler; Yan Shen; Zhijian Yao; Wei Huang; Xun Chu; Yungang He; Li Jin; Yangfan Liu; Yayun Shen; Weiwei Sun; Haifeng Wang; Yi Wang; Ying Wang; Xiaoyan Xiong; Liang Xu; Mary M Y Waye; Stephen K W Tsui; Hong Xue; J Tze-Fei Wong; Luana M Galver; Jian-Bing Fan; Kevin Gunderson; Sarah S Murray; Arnold R Oliphant; Mark S Chee; Alexandre Montpetit; Fanny Chagnon; Vincent Ferretti; Martin Leboeuf; Jean-François Olivier; Michael S Phillips; Stéphanie Roumy; Clémentine Sallée; Andrei Verner; Thomas J Hudson; Pui-Yan Kwok; Dongmei Cai; Daniel C Koboldt; Raymond D Miller; Ludmila Pawlikowska; Patricia Taillon-Miller; Ming Xiao; Lap-Chee Tsui; William Mak; You Qiang Song; Paul K H Tam; Yusuke Nakamura; Takahisa Kawaguchi; Takuya Kitamoto; Takashi Morizono; Atsushi Nagashima; Yozo Ohnishi; Akihiro Sekine; Toshihiro Tanaka; Tatsuhiko Tsunoda; Panos Deloukas; Christine P Bird; Marcos Delgado; Emmanouil T Dermitzakis; Rhian Gwilliam; Sarah Hunt; Jonathan Morrison; Don Powell; Barbara E Stranger; Pamela Whittaker; David R Bentley; Mark J Daly; Paul I W de Bakker; Jeff Barrett; Yves R Chretien; Julian Maller; Steve McCarroll; Nick Patterson; Itsik Pe'er; Alkes Price; Shaun Purcell; Daniel J Richter; Pardis Sabeti; Richa Saxena; Stephen F Schaffner; Pak C Sham; Patrick Varilly; David Altshuler; Lincoln D Stein; Lalitha Krishnan; Albert Vernon Smith; Marcela K Tello-Ruiz; Gudmundur A Thorisson; Aravinda Chakravarti; Peter E Chen; David J Cutler; Carl S Kashuk; Shin Lin; Gonçalo R Abecasis; Weihua Guan; Yun Li; Heather M Munro; Zhaohui Steve Qin; Daryl J Thomas; Gilean McVean; Adam Auton; Leonardo Bottolo; Niall Cardin; Susana Eyheramendy; Colin Freeman; Jonathan Marchini; Simon Myers; Chris Spencer; Matthew Stephens; Peter Donnelly; Lon R Cardon; Geraldine Clarke; David M Evans; Andrew P Morris; Bruce S Weir; Tatsuhiko Tsunoda; James C Mullikin; Stephen T Sherry; Michael Feolo; Andrew Skol; Houcan Zhang; Changqing Zeng; Hui Zhao; Ichiro Matsuda; Yoshimitsu Fukushima; Darryl R Macer; Eiko Suda; Charles N Rotimi; Clement A Adebamowo; Ike Ajayi; Toyin Aniagwu; Patricia A Marshall; Chibuzor Nkwodimmah; Charmaine D M Royal; Mark F Leppert; Missy Dixon; Andy Peiffer; Renzong Qiu; Alastair Kent; Kazuto Kato; Norio Niikawa; Isaac F Adewole; Bartha M Knoppers; Morris W Foster; Ellen Wright Clayton; Jessica Watkin; Richard A Gibbs; John W Belmont; Donna Muzny; Lynne Nazareth; Erica Sodergren; George M Weinstock; David A Wheeler; Imtaz Yakub; Stacey B Gabriel; Robert C Onofrio; Daniel J Richter; Liuda Ziaugra; Bruce W Birren; Mark J Daly; David Altshuler; Richard K Wilson; Lucinda L Fulton; Jane Rogers; John Burton; Nigel P Carter; Christopher M Clee; Mark Griffiths; Matthew C Jones; Kirsten McLay; Robert W Plumb; Mark T Ross; Sarah K Sims; David L Willey; Zhu Chen; Hua Han; Le Kang; Martin Godbout; John C Wallenburg; Paul L'Archevêque; Guy Bellemare; Koji Saeki; Hongguang Wang; Daochang An; Hongbo Fu; Qing Li; Zhen Wang; Renwu Wang; Arthur L Holden; Lisa D Brooks; Jean E McEwen; Mark S Guyer; Vivian Ota Wang; Jane L Peterson; Michael Shi; Jack Spiegel; Lawrence M Sung; Lynn F Zacharia; Francis S Collins; Karen Kennedy; Ruth Jamieson; John Stewart
Journal:  Nature       Date:  2007-10-18       Impact factor: 49.962
View more
  165 in total

Review 1.  Computer simulations: tools for population and evolutionary genetics.

Authors:  Sean Hoban; Giorgio Bertorelle; Oscar E Gaggiotti
Journal:  Nat Rev Genet       Date:  2012-01-10       Impact factor: 53.242

2.  Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia.

Authors:  Mait Metspalu; Irene Gallego Romero; Bayazit Yunusbayev; Gyaneshwer Chaubey; Chandana Basu Mallick; Georgi Hudjashov; Mari Nelis; Reedik Mägi; Ene Metspalu; Maido Remm; Ramasamy Pitchappan; Lalji Singh; Kumarasamy Thangaraj; Richard Villems; Toomas Kivisild
Journal:  Am J Hum Genet       Date:  2011-12-09       Impact factor: 11.025

3.  Inferring coancestry in population samples in the presence of linkage disequilibrium.

Authors:  M D Brown; C G Glazner; C Zheng; E A Thompson
Journal:  Genetics       Date:  2012-01-31       Impact factor: 4.562

Review 4.  An overview of population genetic data simulation.

Authors:  Xiguo Yuan; David J Miller; Junying Zhang; David Herrington; Yue Wang
Journal:  J Comput Biol       Date:  2011-12-09       Impact factor: 1.479

5.  Simulating gene-environment interactions in complex human diseases.

Authors:  Bo Peng
Journal:  Genome Med       Date:  2010-03-23       Impact factor: 11.117

6.  Natural selection and the distribution of identity-by-descent in the human genome.

Authors:  Anders Albrechtsen; Ida Moltke; Rasmus Nielsen
Journal:  Genetics       Date:  2010-06-30       Impact factor: 4.562

7.  A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination.

Authors:  Joshua S Paul; Yun S Song
Journal:  Genetics       Date:  2010-06-30       Impact factor: 4.562

8.  SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples.

Authors:  Si Quang Le; Richard Durbin
Journal:  Genome Res       Date:  2010-10-27       Impact factor: 9.043

9.  Genotype Imputation with Millions of Reference Samples.

Authors:  Brian L Browning; Sharon R Browning
Journal:  Am J Hum Genet       Date:  2016-01-07       Impact factor: 11.025

10.  Genome-Wide Analysis of SNPs Is Consistent with No Domestic Dog Ancestry in the Endangered Mexican Wolf (Canis lupus baileyi).

Authors:  Robert R Fitak; Sarah E Rinkevich; Melanie Culver
Journal:  J Hered       Date:  2018-05-11       Impact factor: 2.645
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.