Genetic association mapping under founder heterogeneity via weighted haplotype similarity analysis in candidate genes

Genetic Epidemiology
K YuD C Rao

Abstract

Taking advantage of increasingly available high-density single nucleotide polymorphism (SNP) markers within genes and across genomes, more and more genetic association studies began to use multiple closely linked markers in candidate genes. A practical analytical challenge arising in such studies is the possibility that not all case chromosomes have inherited disease-causing mutations from a common ancestral chromosome (founder heterogeneity). To alleviate the problem, we propose a method that applies a clustering algorithm to haplotype similarity analysis. The method identifies a sequence of nested subsets of case chromosomes by a peeling procedure, where each subset is relatively homogeneous. The average similarity score estimated from each subset in the sequence is compared to that estimated in controls, and a raw (unadjusted for multiple comparisons) P value is obtained. The test for the association between the trait and the candidate gene is based on the minimum raw P value observed in the comparison sequence, with its significance level estimated by a permutation procedure. The method can be applied to both haplotype and genotype data. Simulation studies suggest that our method has the correct type I error rate, and is ge...Continue Reading

References

Mar 11, 2000·American Journal of Human Genetics·C J MacLeanK S Kendler
Dec 5, 2000·American Journal of Human Genetics·C BourgainF Clerget-Darpoux
Mar 27, 2001·Annual Review of Pharmacology and Toxicology·H L McLeod, W E Evans
Apr 21, 2001·European Journal of Human Genetics : EJHG·J AkeyM Xiong
Jun 21, 2001·Annals of Human Genetics·C BourgainF Clerget-Darpoux
Dec 13, 2001·American Journal of Human Genetics·Tianhua NiuJun S Liu
Jan 16, 2002·American Journal of Human Genetics·Daniel J SchaidGregory A Poland
Apr 2, 2002·American Journal of Human Genetics·Momiao XiongEric Boerwinkle
May 23, 2002·Annals of Human Genetics·C BourgainF Clerget-Darpoux
Oct 18, 2002·Genetic Epidemiology·Richard W Morris, Norman L Kaplan
Mar 1, 2003·American Journal of Human Genetics·Jung-Ying TzengKathryn Roeder
Mar 21, 2003·American Journal of Human Genetics·Ruzong Fan, Michael Knapp
Aug 21, 2003·American Journal of Human Genetics·Shuanglin ZhangRenfang Jiang

❮ Previous
Next ❯

Citations

Jul 15, 2005·Human Heredity·Tim Becker, Michael Knapp
Apr 29, 2006·BMC Bioinformatics·Hsin-Chou YangCathy S J Fann
Apr 17, 2008·BMC Bioinformatics·Hsin-Chou YangCathy S J Fann
Oct 10, 2006·Genetics·Mikko J Sillanpää, Madhuchhanda Bhattacharjee
May 7, 2008·Genetics·Yuehua CuiWenjiang Fu
Dec 2, 2014·Genome Génome / Conseil National De Recherches Canada·Marwan DiapariBunyamin Tar'an
Feb 13, 2009·Biometrics·Jung-Ying TzengMarie Davidian
Apr 1, 2009·Genetic Epidemiology·Kai YuNilanjan Chatterjee
Feb 13, 2010·Genetic Epidemiology·Anke SchulzLars Beckmann
Oct 20, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Petteri SevonVesa Ollikainen
Dec 21, 2005·American Journal of Human Genetics·Jung-Ying TzengChuhsing Kate Hsiao
Jun 3, 2005·American Journal of Human Genetics·Jinying ZhaoMomiao Xiong
Oct 13, 2006·American Journal of Human Genetics·Jennifer Wessel, Nicholas J Schork
Apr 23, 2013·Journal of Bioinformatics and Computational Biology·María M Abad-GrauFuencisla Matesanz
Feb 24, 2005·Genetic Epidemiology·Jung-Ying Tzeng
Jul 6, 2005·Annals of Human Genetics·Kai YuMichael Province
Oct 22, 2005·Genetic Epidemiology·Tim BeckerMichael Knapp

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.