Haplotype inference from diploid sequence data: evaluating performance using non-neutral MHC sequences

Hereditas
David H BosJ Andrew Dewoody

Abstract

The direct sequencing of PCR products from diploid organisms is problematic because of ambiguities associated with phase inference in multi-site heterozygotes. Several molecular methods such as cloning, SSCP, and DGGE have been developed to empirically reduce diploid sequences to their constitutive haploid components, but in theory these empirical approaches can be supplanted by analytical treatment of diploid sequences. Analytical approaches are more desirable than molecular methods because of the added time and expense required to generate molecular data. A variety of analytical methods have been developed to address this issue, but few have been rigorously evaluated with empirical data. Furthermore, they all assume that the sequences under consideration are evolving in a neutral fashion and assume a moderate number of heterozygous sites. Here, we use non-neutral major histocompatibility complex (MHC) sequences comprised of large numbers of heterozygous sites that are under strong balancing selection to evaluate the performance of the popular Bayesian algorithm implemented by the program PHASE. Our results suggest that PHASE performs admirably with non-neutral sequences of moderate length with numerous heterozygous sites typi...Continue Reading

References

May 28, 1992·Nature·M P BelichP Parham
Sep 24, 1998·Immunogenetics·I B JakobsenS Easteal
Feb 3, 1999·Annual Review of Genetics·A L Hughes, M Yeager
Sep 15, 2000·Journal of Immunological Methods·D A Vignali
Feb 24, 2001·The Journal of Immunology : Official Journal of the American Association of Immunologists·B P ShumP Parham
Mar 20, 2001·American Journal of Human Genetics·M StephensP Donnelly
Apr 6, 2002·Human Genetics·Chun-Fang XuIan J Purvis
Oct 19, 2002·American Journal of Human Genetics·Shin LinAravinda Chakravarti
Jan 15, 2003·Annual Review of Medicine·Mary Carrington, Stephen J O'Brien
Oct 24, 2003·American Journal of Human Genetics·Matthew Stephens, Peter Donnelly
Dec 17, 2004·Human Genomics·Laurent ExcoffierDavid Balding
Mar 3, 2005·Genome Research·Stefan WeckxPeter De Rijk
Jun 15, 2006·American Journal of Human Genetics·Hua TangNeil Risch
Jul 11, 2006·American Journal of Human Genetics·Yu ZhangJun S Liu
Aug 1, 1998·Trends in Ecology & Evolution·S V Edwards, P W Hedrick

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Citations

May 1, 2009·Molecular Ecology Resources·Wiesław BabikJacek Radwan
Nov 1, 2008·Molecular Ecology Resources·Ryan J HarriganMichael D Sorenson
Mar 12, 2008·Evolution; International Journal of Organic Evolution·David H BosJ Andrew Dewoody
Jun 12, 2012·Journal of Avian Biology·Danielle J WhittakerEllen D Ketterson
Mar 1, 2010·Molecular Ecology Resources·W Babik
May 7, 2015·Molecular Ecology·Anna Fijarczyk, Wiesław Babik

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