Book ChapterDOI
A fast and accurate heuristic for the single individual snp haplotyping problem with many gaps, high reading error rate and low coverage
Loredana M. Genovese,Filippo Geraci,Marco Pellegrini +2 more
- pp 49-60
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TLDR
A new heuristic method is described that is able to tackle the case of many gapped fragments and retains its effectiveness even when the input fragments have high rate of reading errors and low coverage.Abstract:
Single nucleotide polymorphism (SNP) is the most frequent form of DNA variation. The set of SNPs present in a chromosome (called the haplotype) is of interest in a wide area of applications in molecular biology and biomedicine, including diagnostic and medical therapy. In this paper we propose a new heuristic method for the problem of haplotype reconstruction for (portions of ) a pair of homologous human chromosomes from a single individual (SIH). The problem is well known in literature and exact algorithms have been proposed for the case when no (or few) gaps are allowed in the input fragments. These algorithms, though exact and of polynomial complexity, are slow in practice. Therefore fast heuristics have been proposed. In this paper we describe a new heuristic method that is able to tackle the case of many gapped fragments and retains its effectiveness even when the input fragments have high rate of reading errors (up to 20%) and low coverage (as low as 3). We test our method on real data from the HapMap Project.read more
Citations
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Journal ArticleDOI
RadixHap: a radix tree-based heuristic for solving the single individual haplotyping problem
TL;DR: A greedy approach to reconstruct reliable Single Individual Haplotypes, named RadixHap, is introduced, to handle data sets with high error rates and the experimental results show that RadxHap can generate highly reliable results in most cases.
Proceedings ArticleDOI
A Hopfield-Type Neural Network for Haplotype Assembly Problem
Xinshun Xu,Jun Ma,Jiahai Wang +2 more
TL;DR: A Hopfield-type neural network based on the minimum fragment removal (MFR) model, which constructs a pair of haplotypes by deleting minimum fragments from the data set so that left fragments can be classified into two sets in which there is no confliction.
Journal ArticleDOI
Examination of The Students' Mistakes of Oral Reading
Murat Başar,Zekerya Batur +1 more
TL;DR: In this article, the authors examined the level of oral reading of the students studying on their 3rd degree, who are at the age range of 60-66 months, and the students who completed their 72nd month and started primary school.
Book ChapterDOI
Reconstruction of Infectious Bronchitis Virus Quasispecies from NGS Data
Bassam Tork,Ekaterina Nenastyeva,Alexander Artyomenko,Nicholas Mancuso,Mazhar I. Khan,Rachel J. O’Neill,Ion I. Mandoiu,Alexander Zelikovsky +7 more
TL;DR: A computational pipeline for quasispecies (closely related variants to ancestral genome) reconstruction consisting of 3 phases, which shows that varying the parameter settings gets better results in terms of Average Distance to Clones, and Average Prediction Error.
Journal ArticleDOI
Matrix Completion and Performance Guarantees for Single Individual Haplotyping
Somsubhra Barik,Haris Vikalo +1 more
TL;DR: A binary matrix factorization formulation of the single individual haplotyping problem is considered and shown to outperform existing methods when applied to synthetic as well as real-world Fosmid-based HapMap NA12878 datasets.
References
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Journal ArticleDOI
A haplotype map of the human genome
John W. Belmont,Andrew Boudreau,Suzanne M. Leal,Paul Hardenbol,Shiran Pasternak,David A. Wheeler,Thomas D. Willis,Fuli Yu,Huanming Yang,Gao Yang,H. B. 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,Jun Zhou,Rachel Barry,Brendan Blumenstiel,Amy L. Camargo,Matthew Defelice,Maura Faggart,Mary Goyette,Supriya Gupta,Jamie Moore,Huy Nguyen,Melissa Parkin,Jessica Roy,Erich Stahl,Ellen Winchester,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 Kwok-Wing Tsui,Hong Xue,J. Tze Fei Wong,Launa M. Galver,Jian-Bing Fan,Sarah S. Murray,Arnold 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,Kelly A. Frazer,Dennis G. Ballinger,David R. Cox,David A. Hinds,Laura L. Stuve,Pui-Yan Kwok,Dongmei Cai,Daniel C. Koboldt,Raymond D. Miller,Ludmila Pawlikowska,Patricia Taillon-Miller,Ming Xiao,Lap-Chee Tsui,William Mak,Pak C. Sham,You-Qiang Song,Paul K.H. Tam,Yusuke Nakamura,Takahisa Kawaguchi,Takuya Kitamoto,Takashi Morizono,Atsushi Nagashima,Yozo Ohnishi,Akihiro Sekine,Toshihiro Tanaka,Panos Deloukas,Christine P. Bird,Marcos Delgado,Emmanouil T. Dermitzakis,Rhian Gwilliam,Sarah E. Hunt,Jonathan Morrison,Don Powell,Barbara E. Stranger,Pamela Whittaker,David R. Bentley,Paul I.W. de Bakker,Jeffrey C. Barrett,Ben Fry,Julian Maller,Steve McCarroll,Nick Patterson,Itsik Pe'er,Shaun Purcell,Daniel J. Richter,Pardis C. Sabeti,Richa Saxena,Stephen F. Schaffner,Patrick Varilly,Lincoln Stein,Lalitha Krishnan,Albert V. Smith,Gudmundur A. Thorisson,Aravinda Chakravarti,Peter E. Chen,David J. Cutler,Carl S. Kashuk,Shin Lin,Gonçalo R. Abecasis,Weihua Guan,Heather M. Munro,Zhaohui S. Qin,Daryl J. Thomas,Gilean McVean,Leonardo Bottolo,Susana Eyheramendy,Colin Freeman,Jonathan Marchini,Simon Myers,Chris C. A. Spencer,Matthew Stephens,Peter Donnelly,Lon R. Cardon,Geraldine M. Clarke,David M. Evans,Andrew P. Morris,Bruce S. Weir,Tatsuhiko Tsunoda,James C. Mullikin,Stephen T. Sherry,Michael Feolo,Houcan Zhang,Changqing Zeng,Hui Zhao,Ichiro Matsuda,Yoshimitsu Fukushima,Darryl Macer,Eiko Suda,Charles N. Rotimi,Clement Adebamowo,Ike Ajayi,Toyin Aniagwu,Patricia A. Marshall,Chibuzor Nkwodimmah,Charmaine D.M. Royal,Mark Leppert,Missy Dixon,Andy Peiffer,Renzong Qiu,Alastair Kent,Kazuto Kato,Norio Niikawa,Isaac F. Adewole,Bartha Maria Knoppers,Morris W. Foster,Ellen Wright Clayton,Jessica Watkin,Richard A. Gibbs,Donna M. Muzny,Lynne V. Nazareth,Erica Sodergren,George M. Weinstock,Imtiaz Yakub,Stacey Gabriel,Robert C. Onofrio,Liuda Ziaugra,Bruce W. Birren,Mark J. Daly,Richard K. Wilson,Lucinda Fulton,Jane Rogers,John Burton,Nigel P. Carter,C M Clee,Mark Griffiths,Matthew C. Jones,Kirsten McLay,Robert W. Plumb,Mark T. Ross,Sarah Sims,David Willey,Zhu Chen,Hua Han,L. 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,Christianne R. Bird,Mark S. Guyer,Patrick J. Nailer,Vivian Ota Wang,Jane Peterson,Michael Shi,Jack Spiegel,Lawrence M. Sung,Jonathan Witonsky,Lynn F. Zacharia,Francis S. Collins,Karen Kennedy,Ruth Jamieson,John Stewart +232 more
TL;DR: A public database of common variation in the human genome: more than one million single nucleotide polymorphisms for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted.
Journal ArticleDOI
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
Ravi Sachidanandam,David Weissman,Steven Schmidt,Jerzy M. Kakol,Lincoln Stein,Gabor T. Marth,Steve Sherry,James C. Mullikin,Beverley J. Mortimore,David Willey,Sarah E. Hunt,Charlotte G. Cole,Penny Coggill,Catherine M. Rice,Zemin Ning,Jane Rogers,David R. Bentley,Pui-Yan Kwok,Elaine R. Mardis,Raymond T. Yeh,Brian Schultz,Lisa Cook,Ruth Davenport,Michael Dante,Lucinda Fulton,LaDeana W. Hillier,Robert H. Waterston,John Douglas Mcpherson,Brian Gilman,Stephen F. Schaffner,William J. Van Etten,David Reich,John M. Higgins,Mark J. Daly,Brendan Blumenstiel,Jennifer Baldwin,Nicole Stange-Thomann,Michael C. Zody,Lauren Linton,Eric S. Lander,David Altshuler +40 more
TL;DR: This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.
Book ChapterDOI
SNPs Problems, Complexity, and Algorithms
TL;DR: It is shown that the general SNPs Haplotyping Problem is NP-hard for mate-pairs assembly data, and polynomial time algorithms for fragment assembly data are designed, and the Minimum SNPs Removal problem amounts to finding the largest independent set in a weakly triangulated graph.
Journal ArticleDOI
Haplotype reconstruction from SNP fragments by minimum error correction
TL;DR: To improve the MEC model for haplotype reconstruction, a new computational model is proposed, which simultaneously employs genotype information of an individual in the process of SNP correction, and is called MEC with genotypes information (shortly, MEC/GI).
Book ChapterDOI
Fast hare: A fast heuristic for single individual SNP haplotype reconstruction
Alessandro Panconesi,Mauro Sozio +1 more
TL;DR: A simple heuristic is introduced and it is proved experimentally that is very fast and accurate and when compared with a dynamic programming of [8] it is much faster and also more accurate.
Related Papers (5)
Fast hare: A fast heuristic for single individual SNP haplotype reconstruction
Alessandro Panconesi,Mauro Sozio +1 more