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Literature DB >> 18492685

MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.

Mamoru Kato¹, Yusuke Nakamura, Tatsuhiko Tsunoda.

Abstract

UNLABELLED: Detailed analyses of the population-genetic nature of copy number variations (CNVs) and the linkage disequilibrium between CNV and single nucleotide polymorphism (SNP) loci from high-throughput experimental data require a computational tool to accurately infer alleles of CNVs and haplotypes composed of both CNV alleles and SNP alleles. Here we developed a new tool to infer population frequencies of such alleles and haplotypes from observed copy numbers and SNP genotypes, using the expectation-maximization algorithm. This tool can also handle copy numbers ambiguously determined, such as 2 or 3 copies, due to experimental noise. AVAILABILITY: http://emu.src.riken.jp/MOCSphaser/MOCSphaser.zip.

Entities: Species

Mesh：

Year: 2008 PMID： 18492685 PMCID： PMC2638261 DOI： 10.1093/bioinformatics/btn242

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

8 in total

Review 1. Algorithms for inferring haplotypes.

Authors: Tianhua Niu
Journal: Genet Epidemiol Date: 2004-12 Impact factor: 2.135

Review 2. Structural variants: changing the landscape of chromosomes and design of disease studies.

Authors: Lars Feuk; Christian R Marshall; Richard F Wintle; Stephen W Scherer
Journal: Hum Mol Genet Date: 2006-04-15 Impact factor: 6.150

3. Multiplex PCR-based real-time invader assay (mPCR-RETINA): a novel SNP-based method for detecting allelic asymmetries within copy number variation regions.

Authors: Naoya Hosono; Michiaki Kubo; Yumiko Tsuchiya; Hiroko Sato; Takuya Kitamoto; Susumu Saito; Yozo Ohnishi; Yusuke Nakamura
Journal: Hum Mutat Date: 2008-01 Impact factor: 4.878

4. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.

Authors: L Excoffier; M Slatkin
Journal: Mol Biol Evol Date: 1995-09 Impact factor: 16.240

5. Global variation in copy number in the human genome.

Authors: Richard Redon; Shumpei Ishikawa; Karen R Fitch; Lars Feuk; George H Perry; T Daniel Andrews; Heike Fiegler; Michael H Shapero; Andrew R Carson; Wenwei Chen; Eun Kyung Cho; Stephanie Dallaire; Jennifer L Freeman; Juan R González; Mònica Gratacòs; Jing Huang; Dimitrios Kalaitzopoulos; Daisuke Komura; Jeffrey R MacDonald; Christian R Marshall; Rui Mei; Lyndal Montgomery; Kunihiro Nishimura; Kohji Okamura; Fan Shen; Martin J Somerville; Joelle Tchinda; Armand Valsesia; Cara Woodwark; Fengtang Yang; Junjun Zhang; Tatiana Zerjal; Jane Zhang; Lluis Armengol; Donald F Conrad; Xavier Estivill; Chris Tyler-Smith; Nigel P Carter; Hiroyuki Aburatani; Charles Lee; Keith W Jones; Stephen W Scherer; Matthew E Hurles
Journal: Nature Date: 2006-11-23 Impact factor: 49.962

6. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays.

Authors: Daisuke Komura; Fan Shen; Shumpei Ishikawa; Karen R Fitch; Wenwei Chen; Jane Zhang; Guoying Liu; Sigeo Ihara; Hiroshi Nakamura; Matthew E Hurles; Charles Lee; Stephen W Scherer; Keith W Jones; Michael H Shapero; Jing Huang; Hiroyuki Aburatani
Journal: Genome Res Date: 2006-11-22 Impact factor: 9.043

Review 7. The population genetics of structural variation.

Authors: Donald F Conrad; Matthew E Hurles
Journal: Nat Genet Date: 2007-07 Impact factor: 38.330

8. 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

8 in total

10 in total

MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.

Review 1. Algorithms for inferring haplotypes.

Review 2. Structural variants: changing the landscape of chromosomes and design of disease studies.

3. Multiplex PCR-based real-time invader assay (mPCR-RETINA): a novel SNP-based method for detecting allelic asymmetries within copy number variation regions.

4. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.

5. Global variation in copy number in the human genome.

6. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays.

Review 7. The population genetics of structural variation.

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

1. Inferring combined CNV/SNP haplotypes from genotype data.

2. Inference of chromosome-specific copy numbers using population haplotypes.

3. Inferring haplotypes of copy number variations from high-throughput data with uncertainty.

4. A sequential Monte Carlo framework for haplotype inference in CNV/SNP genotype data.

5. Haplotype phasing and inheritance of copy number variants in nuclear families.

6. Human CCL3L1 copy number variation, gene expression, and the role of the CCL3L1-CCR5 axis in lung function.

7. Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances.

8. Population-genetic nature of copy number variations in the human genome.

9. Hardy-Weinberg equilibrium revisited for inferences on genotypes featuring allele and copy-number variations.

10. A method for calling copy number polymorphism using haplotypes.