NDLI: Sample Reproducibility of Genetic Association Using Different Multimarker TDTs in Genome-Wide Association Studies: Characterization and a New Approach

Content Provider	PubMed Central
Author	Abad-grau, Mara M. Medina-medina, Nuria Montes-soldado, Rosana Matesanz, Fuencisla Vineet, Bafna
Editor	Bader, Joel S.
Copyright Year	2012
Abstract	Multimarker Transmission/Disequilibrium Tests (TDTs) are very robust association tests to population admixture and structure which may be used to identify susceptibility loci in genome-wide association studies. Multimarker TDTs using several markers may increase power by capturing high-degree associations. However, there is also a risk of spurious associations and power reduction due to the increase in degrees of freedom. In this study we show that associations found by tests built on simple null hypotheses are highly reproducible in a second independent data set regardless the number of markers. As a test exhibiting this feature to its maximum, we introduce the multimarker -Groups TDT ( ), a test which under the hypothesis of no linkage, asymptotically follows a distribution with degree of freedom regardless the number of markers. The statistic requires the division of parental haplotypes into two groups: disease susceptibility and disease protective haplotype groups. We assessed the test behavior by performing an extensive simulation study as well as a real-data study using several data sets of two complex diseases. We show that test is highly efficient and it achieves the highest power among all the tests used, even when the null hypothesis is tested in a second independent data set. Therefore, turns out to be a very promising multimarker TDT to perform genome-wide searches for disease susceptibility loci that may be used as a preprocessing step in the construction of more accurate genetic models to predict individual susceptibility to complex diseases.
Related Links	http://dx.doi.org/10.1371/journal.pone.0029613
Starting Page	29613
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	2
Volume Number	7
Language	English
Publisher	Public Library of Science
Publisher Date	2012-02-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies

Analysis of Genome-Wide Association Studies with Multiple Outcomes Using Penalization

Discovery, Validation and Characterization of Erbb4 and Nrg1 Haplotypes Using Data from Three Genome-Wide Association Studies of Schizophrenia

Genome-Wide Association Studies Using Haplotypes and Individual SNPs in Simmental Cattle

New Components of Drosophila Leg Development Identified through Genome Wide Association Studies

SNP Set Association Analysis for Genome-Wide Association Studies

Accuracy of Predicting the Genetic Risk of Disease Using a Genome-Wide Approach

A Genome-Wide Association Study of Neuroticism in a Population-Based Sample

Computational Characterization of Osteoporosis Associated SNPs and Genes Identified by Genome-Wide Association Studies

Sample Reproducibility of Genetic Association Using Different Multimarker TDTs in Genome-Wide Association Studies: Characterization and a New Approach

Similar Documents

A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies

Analysis of Genome-Wide Association Studies with Multiple Outcomes Using Penalization

Discovery, Validation and Characterization of Erbb4 and Nrg1 Haplotypes Using Data from Three Genome-Wide Association Studies of Schizophrenia

Genome-Wide Association Studies Using Haplotypes and Individual SNPs in Simmental Cattle

New Components of Drosophila Leg Development Identified through Genome Wide Association Studies

SNP Set Association Analysis for Genome-Wide Association Studies

Accuracy of Predicting the Genetic Risk of Disease Using a Genome-Wide Approach

A Genome-Wide Association Study of Neuroticism in a Population-Based Sample

Computational Characterization of Osteoporosis Associated SNPs and Genes Identified by Genome-Wide Association Studies

Sample Reproducibility of Genetic Association Using Different Multimarker TDTs in Genome-Wide Association Studies: Characterization and a New Approach