Increased Power for Detection of Parent-of-Origin Effects via the Use of Haplotype Estimation

American Journal of Human Genetics
Richard HoweyHeather J Cordell

Abstract

Parent-of-origin (or imprinting) effects relate to the situation in which traits are influenced by the allele inherited from only one parent and the allele from the other parent has little or no effect. Given SNP genotype data from case-parent trios, the parent of origin of each allele in the offspring can often be deduced unambiguously; however, this is not true when all three individuals are heterozygous. Most existing methods for investigating parent-of-origin effects operate on a SNP-by-SNP basis and either perform some sort of averaging over the possible parental transmissions or else discard ambiguous trios. If the correct parent of origin at a SNP could be determined, this would provide extra information and increase the power for detecting the effects of imprinting. We propose making use of the surrounding SNP information, via haplotype estimation, to improve estimation of parent of origin at a test SNP for case-parent trios, case-mother duos, and case-father duos. This extra information is then used in a multinomial modeling approach for estimating parent-of-origin effects at the test SNP. We show through computer simulations that our approach has increased power over previous approaches, particularly when the data con...Continue Reading

References

Jun 12, 1999·American Journal of Human Genetics·C R Weinberg
Apr 21, 2001·Biometrics·B Devlin, K Roeder
Jul 2, 2005·Trends in Genetics : TIG·Ian M MorisonHamish G Spencer
Oct 15, 2005·Human Heredity·Suzanne M LealBertram Müller-Myhsok
Apr 7, 2009·Annals of Human Genetics·Min ShiClarice R Weinberg
Oct 8, 2009·European Journal of Human Genetics : EJHG·Nadezhda M BelonogovaYurii S Aulchenko
Jun 3, 2010·Nature Reviews. Genetics·Jonathan Marchini, Bryan Howie
Nov 19, 2010·Nature Protocols·Carl A AndersonKrina T Zondervan
Sep 22, 2011·Clinical Genetics·A Guilmatre, A J Sharp
Jan 9, 2013·Human Molecular Genetics·Heather J CordellJudith A Goodship
Aug 7, 2013·Nature Reviews. Genetics·Heather A LawsonJason B Wolf
Jan 21, 2014·Cell·Richard MottJonathan Flint

❮ Previous
Next ❯

Citations

Jun 17, 2016·Journal of Neurodevelopmental Disorders·Kerry A PettigrewSilvia Paracchini
Oct 3, 2019·Autism Research : Official Journal of the International Society for Autism Research·Ron NudelThomas Werge
Nov 3, 2017·Annals of Human Genetics·Miriam GjerdevikHåkon K Gjessing
Jan 17, 2020·Statistics in Medicine·Miriam GjerdevikRolv T Lie
Feb 23, 2020·European Journal of Human Genetics : EJHG·Fangyuan Zhang, Shili Lin
Sep 26, 2020·The Journal of Maternal-fetal & Neonatal Medicine : the Official Journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians·Tsegaselassie WorkalemahuMichelle A Williams

❮ Previous
Next ❯

Methods Mentioned

BETA
histone acetylation

Software Mentioned

UNPHASED
SHAPEIT2
PREMIM
HAPLORE
SimPed
HAPLIN
PLINK
EMIM

Related Concepts

Related Feeds

Atopic Dermatitis

Atopic dermatitis is a chronic inflammatory genetically determined disease of the skin marked by increased ability to form reagin (IgE), with increased susceptibility to allergic rhinitis and asthma, and hereditary disposition to a lowered threshold for pruritus. Discover the latest research on atopic dermatitis here.