NDLI: Examining the effect of linkage disequilibrium between markers on the Type I error rate and power of nonparametric multipoint linkage analysis of two-generation and multigenerational pedigrees in the presence of missing genotype data

Please wait, while we are loading the content...

Examining the effect of linkage disequilibrium between markers on the Type I error rate and power of nonparametric multipoint linkage analysis of two-generation and multigenerational pedigrees in the presence of missing genotype data

Year: 2007, Volume: 31

Year: 2005, Volume: 29

Year: 2004, Volume: 26

Year: 1990, Volume: 7

Examining the effect of linkage disequilibrium between markers on the Type I error rate and power of nonparametric multipoint linkage analysis of two-generation and multigenerational pedigrees in the presence of missing genotype data

Content Provider	PubMed Central
Author	Kim, Yoonhee Duggal, Priya Gillanders, Elizabeth M. Kim, Ho Bailey-wilson, Joan E.
Abstract	Since most multipoint linkage analysis programs currently assume linkage equilibrium (LE) between markers when inferring parental haplotypes, ignoring linkage disequilibrium (LD) may inflate the Type I error rate. We investigated the effect of LD on the Type I error rate and power of nonparametric multipoint linkage analysis of two-generation and multigenerational multiplex families. Using genome wide single nucleotide polymorphism (SNP) data from the Collaborative Study of the Genetics of Alcoholism (COGA), we modified the original dataset into 30 total data sets in order to consider 6 different patterns of missing data for 5 different levels of SNP density. To assess power, we designed simulated traits based on existing marker genotypes. For the Type I error rate, we simulated 1,000 qualitative traits from random distributions, unlinked to any of the marker data. Overall, the different levels of SNP density examined here had only small effects on power (except sibpair data). Missing data had a substantial effect on power, with more completely genotyped pedigrees yielding the highest power (except sibpair data). Most of the missing data patterns did not cause large increases in the Type I error rate if the SNP markers were more than 0.3 cM apart. However, in a dense 0.25 cM map, removing genotypes on founders and/or founders and parents in the middle generation caused substantial inflation of the Type I error rate, which corresponded to the increasing proportion of persons with missing data. Results also showed that long high-LD blocks have severe effects on Type I error rates.
Related Links	http://dx.doi.org/10.1002/gepi.20260
Ending Page	51
Page Count	11
Starting Page	41
File Format	PDF
ISSN	07410395
e-ISSN	10982272
Journal	Genetic epidemiology
Issue Number	1
Volume Number	32
Language	English
Publisher Date	2008-01-01
Access Restriction	Open
Subject Keyword	Genetics(clinical) Epidemiology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Epidemiology Genetics (clinical)

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

Linkage Disequilibrium Inflates Type I Error Rates in Multipoint Linkage Analysis when Parental Genotypes Are Missing

Precision and type I error rate in the presence of genotype errors and missing parental data: a comparison between the original transmission disequilibrium test (TDT) and TDTae statistics

Examining the effect of linkage disequilibrium on multipoint linkage analysis

Precision and type I error rate in the presence of genotype errors and missing parental data: a comparison between the original transmission disequilibrium test (TDT) and TDTae statistics

Examining the effect of linkage disequilibrium on multipoint linkage analysis

Impact of genotyping errors on type I error rate of the haplotype-sharing transmission/disequilibrium test (HS-TDT).

Ignoring Intermarker Linkage Disequilibrium Induces False-Positive Evidence of Linkage for Consanguineous Pedigrees when Genotype Data Is Missing for Any Pedigree Member

An evaluation of power and type I error of single-nucleotide polymorphism transmission/disequilibrium-based statistical methods under different family structures, missing parental data, and population stratification.

Multipoint Lods Provide Reliable Linkage Evidence Despite Unknown Limiting Distribution: Type I Error Probabilities Decrease with Sample Size for Multipoint Lods and Mods

Examining the effect of linkage disequilibrium between markers on the Type I error rate and power of nonparametric multipoint linkage analysis of two-generation and multigenerational pedigrees in the presence of missing genotype data

Similar Documents

Linkage Disequilibrium Inflates Type I Error Rates in Multipoint Linkage Analysis when Parental Genotypes Are Missing

Precision and type I error rate in the presence of genotype errors and missing parental data: a comparison between the original transmission disequilibrium test (TDT) and TDTae statistics

Examining the effect of linkage disequilibrium on multipoint linkage analysis

Precision and type I error rate in the presence of genotype errors and missing parental data: a comparison between the original transmission disequilibrium test (TDT) and TDTae statistics

Examining the effect of linkage disequilibrium on multipoint linkage analysis

Impact of genotyping errors on type I error rate of the haplotype-sharing transmission/disequilibrium test (HS-TDT).

Ignoring Intermarker Linkage Disequilibrium Induces False-Positive Evidence of Linkage for Consanguineous Pedigrees when Genotype Data Is Missing for Any Pedigree Member

An evaluation of power and type I error of single-nucleotide polymorphism transmission/disequilibrium-based statistical methods under different family structures, missing parental data, and population stratification.

Multipoint Lods Provide Reliable Linkage Evidence Despite Unknown Limiting Distribution: Type I Error Probabilities Decrease with Sample Size for Multipoint Lods and Mods

Examining the effect of linkage disequilibrium between markers on the Type I error rate and power of nonparametric multipoint linkage analysis of two-generation and multigenerational pedigrees in the presence of missing genotype data