Algorithms for inferring haplotypes

Genetic Epidemiology
Tianhua Niu

Abstract

Haplotype phase information in diploid organisms provides valuable information on human evolutionary history and may lead to the development of more efficient strategies to identify genetic variants that increase susceptibility to human diseases. Molecular haplotyping methods are labor-intensive, low-throughput, and very costly. Therefore, algorithms based on formal statistical theories were shown to be very effective and cost-efficient for haplotype reconstruction. This review covers 1) population-based haplotype inference methods: Clark's algorithm, expectation-maximization (EM) algorithm, coalescence-based algorithms (pseudo-Gibbs sampler and perfect/imperfect phylogeny), and partition-ligation algorithm implemented by a fully Bayesian model (Haplotyper) or by EM (PLEM); 2) family-based haplotype inference methods; 3) the handling of genotype scoring uncertainties (i.e., genotyping errors and raw two-dimensional genotype scatterplots) in inferring haplotypes; and 4) haplotype inference methods for pooled DNA samples. The advantages and limitations of each algorithm are discussed. By using simulations based on empirical data on the G6PD gene and TNFRSF5 gene, I demonstrate that different algorithms have different degrees of s...Continue Reading

References

Jan 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·G A ChurchillS D Tanksley
Dec 1, 1996·Nucleic Acids Research·S Michalatos-BeloinG Ruano
May 13, 1999·Nature Genetics·M J RiederD A Nickerson
Mar 25, 2000·American Journal of Human Genetics·C I AmosW Wang
Jul 11, 2000·Nature Biotechnology·A T WoolleyC M Lieber
Mar 10, 2001·Nature·R SachidanandamUNKNOWN International SNP Map Working Group
Mar 20, 2001·American Journal of Human Genetics·M StephensP Donnelly
Mar 29, 2001·Proceedings of the National Academy of Sciences of the United States of America·X B ZhongD C Ward
Sep 6, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·D Gusfield
Oct 10, 2001·Genome Research·J S LiuN Risch
Dec 4, 2001·Nature Genetics·Gonçalo R AbecasisLon R Cardon
Dec 13, 2001·American Journal of Human Genetics·Tianhua NiuJun S Liu
Dec 26, 2001·Nucleic Acids Research·Stéphane Le CromPhilippe Marc
Apr 6, 2002·Human Genetics·Chun-Fang XuIan J Purvis
May 7, 2002·American Journal of Human Genetics·Dajun Qian, Lars Beckmann
Jul 26, 2002·Nucleic Acids Research·Ester InbarAriel Darvasi
Oct 3, 2002·European Journal of Human Genetics : EJHG·Katherine M Kirk, Lon R Cardon
Oct 22, 2002·American Journal of Human Genetics·Daniel J SchaidStephen N Thibodeau
Nov 5, 2002·Nature Reviews. Genetics·Pak ShamMichael Owen
Nov 27, 2002·BioTechniques·Jacob OdebergMathias Uhlén
Jan 1, 2003·Genetic Epidemiology·Shuang WangHongyu Zhao
Jan 2, 2003·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Peining LiJerry N Thompson
Apr 2, 2003·Human Molecular Genetics·Patrick G KehoeJonathan A Prince
Apr 15, 2003·Bioinformatics·Ren Hua Chung, Dan Gusfield
Apr 24, 2003·BMC Bioinformatics·Josephine HohJurg Ott
Jun 5, 2003·Proceedings of the National Academy of Sciences of the United States of America·Yaning YangJurg Ott
Jul 23, 2003·Genetics·Guohua ZouHongyu Zhao
Aug 14, 2003·Proceedings of the National Academy of Sciences of the United States of America·Stephen N WhiteJames E Womack
Aug 27, 2003·European Journal of Human Genetics : EJHG·Tim Becker, Michael Knapp
Sep 10, 2003·Nature Biotechnology·Giulia C KennedyKeith W Jones

❮ Previous
Next ❯

Citations

Sep 20, 2007·Archives of Toxicology·Klaus GolkaSilvia Selinski
Apr 6, 2006·Breast Cancer Research and Treatment·Mia M GaudetMarilie D Gammon
Jan 7, 2009·Genetics Research·Matti PirinenMikko J Sillanpää
May 21, 2010·Journal of Human Genetics·Yumi Yamaguchi-KabataNaoyuki Kamatani
Nov 17, 2005·Bioinformatics·Dumitru Brinza, Alexander Zelikovsky
Aug 31, 2010·Bioinformatics·Anthony Y C KukYaning Yang
Feb 1, 2013·Molecular Biology and Evolution·Darren KessnerJohn Novembre
Oct 14, 2005·Nucleic Acids Research·Sarah J LindsayMatthew E Hurles
Nov 14, 2006·Annals of Human Genetics·K Van SteenG Molenberghs
Aug 30, 2005·Annual Review of Genomics and Human Genetics·Dana C CrawfordDeborah A Nickerson
Jan 28, 2009·Human Heredity·Guimin GaoIna Hoeschele
Jan 31, 2008·BMC Bioinformatics·Bruno F BettencourtJácome Bruges-Armas
May 21, 2005·BMC Genetics·Claire BardelEmmanuelle Génin
Jun 4, 2005·BMC Genetics·Audrey Sabbagh, Pierre Darlu
Oct 28, 2006·BMC Genetics·Cédric CoulongesJean-François Zagury
Mar 18, 2006·BMC Genomics·Simon BoitardBrigitte Mangin
Mar 9, 2006·Genome Biology·Ralph Snyderman, Jason Langheier
Nov 3, 2010·Genome Biology·Amy L WilliamsDavid K Gifford
Feb 1, 2012·PLoS Genetics·Daniel John LawsonDaniel Falush
Oct 20, 2007·Genetics·Xiang Dong DingQin Zhang
Dec 1, 2007·Proceedings of the National Academy of Sciences of the United States of America·Xiang ChenHeping Zhang
Jun 24, 2008·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Fengyu Zhang, Diane Wagener
Aug 19, 2009·Biometrical Journal. Biometrische Zeitschrift·Wensheng ZhuJianhua Guo
Apr 21, 2007·Tissue Antigens·P A GourraudD Middleton
Jan 6, 2009·Molecular Ecology·Daniel James WhiteNeil John Gemmell
May 19, 2006·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·C FluryH Simianer

❮ Previous
Next ❯

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