Treatment of uninformative families in mean allele sharing tests for linkage

Indranil Mukhopadhyay, Eleanor Feingold, Tao Wang, Robert C. Elston, Daniel E. Weeks

Research output: Contribution to journalArticle

Abstract

Using affected sibling pairs, the mean allele sharing statistic tests for linkage by testing if the mean proportion of alleles that are identical-by-descent (IBD) is equal to a half. The behavior of some versions of the mean allele sharing test statistic depends on whether or not families that are uninformative for their IBD status are included; the SIBPAL version provides less significant values when all families (informative and uninformative) are used than when only informative families are used. Here, we investigate this behavior both analytically and by simulation. Our investigation shows that the main issue is the choice of the variance estimator in the denominator of the statistic. The choice of the denominator is very important and is still not totally resolved. Our mathematical explanation supported by our simulation study might aid in the search for an optimum solution.

Original languageEnglish (US)
Article number13
JournalStatistical Applications in Genetics and Molecular Biology
Volume5
Issue number1
StatePublished - May 12 2006
Externally publishedYes

Fingerprint

Linkage
Sharing
Alleles
Statistics
Denominator
Descent
Test Statistic
Variance Estimator
Statistic
Proportion
Simulation Study
Testing
Family
Simulation

Keywords

  • Linkage analysis
  • Mean allele sharing tests
  • SIBPAL

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Statistics and Probability
  • Computational Mathematics

Cite this

Treatment of uninformative families in mean allele sharing tests for linkage. / Mukhopadhyay, Indranil; Feingold, Eleanor; Wang, Tao; Elston, Robert C.; Weeks, Daniel E.

In: Statistical Applications in Genetics and Molecular Biology, Vol. 5, No. 1, 13, 12.05.2006.

Research output: Contribution to journalArticle

Mukhopadhyay, Indranil ; Feingold, Eleanor ; Wang, Tao ; Elston, Robert C. ; Weeks, Daniel E. / Treatment of uninformative families in mean allele sharing tests for linkage. In: Statistical Applications in Genetics and Molecular Biology. 2006 ; Vol. 5, No. 1.
@article{003510c325944d50898dcd1e98d965cd,
title = "Treatment of uninformative families in mean allele sharing tests for linkage",
abstract = "Using affected sibling pairs, the mean allele sharing statistic tests for linkage by testing if the mean proportion of alleles that are identical-by-descent (IBD) is equal to a half. The behavior of some versions of the mean allele sharing test statistic depends on whether or not families that are uninformative for their IBD status are included; the SIBPAL version provides less significant values when all families (informative and uninformative) are used than when only informative families are used. Here, we investigate this behavior both analytically and by simulation. Our investigation shows that the main issue is the choice of the variance estimator in the denominator of the statistic. The choice of the denominator is very important and is still not totally resolved. Our mathematical explanation supported by our simulation study might aid in the search for an optimum solution.",
keywords = "Linkage analysis, Mean allele sharing tests, SIBPAL",
author = "Indranil Mukhopadhyay and Eleanor Feingold and Tao Wang and Elston, {Robert C.} and Weeks, {Daniel E.}",
year = "2006",
month = "5",
day = "12",
language = "English (US)",
volume = "5",
journal = "Statistical Applications in Genetics and Molecular Biology",
issn = "1544-6115",
publisher = "Berkeley Electronic Press",
number = "1",

}

TY - JOUR

T1 - Treatment of uninformative families in mean allele sharing tests for linkage

AU - Mukhopadhyay, Indranil

AU - Feingold, Eleanor

AU - Wang, Tao

AU - Elston, Robert C.

AU - Weeks, Daniel E.

PY - 2006/5/12

Y1 - 2006/5/12

N2 - Using affected sibling pairs, the mean allele sharing statistic tests for linkage by testing if the mean proportion of alleles that are identical-by-descent (IBD) is equal to a half. The behavior of some versions of the mean allele sharing test statistic depends on whether or not families that are uninformative for their IBD status are included; the SIBPAL version provides less significant values when all families (informative and uninformative) are used than when only informative families are used. Here, we investigate this behavior both analytically and by simulation. Our investigation shows that the main issue is the choice of the variance estimator in the denominator of the statistic. The choice of the denominator is very important and is still not totally resolved. Our mathematical explanation supported by our simulation study might aid in the search for an optimum solution.

AB - Using affected sibling pairs, the mean allele sharing statistic tests for linkage by testing if the mean proportion of alleles that are identical-by-descent (IBD) is equal to a half. The behavior of some versions of the mean allele sharing test statistic depends on whether or not families that are uninformative for their IBD status are included; the SIBPAL version provides less significant values when all families (informative and uninformative) are used than when only informative families are used. Here, we investigate this behavior both analytically and by simulation. Our investigation shows that the main issue is the choice of the variance estimator in the denominator of the statistic. The choice of the denominator is very important and is still not totally resolved. Our mathematical explanation supported by our simulation study might aid in the search for an optimum solution.

KW - Linkage analysis

KW - Mean allele sharing tests

KW - SIBPAL

UR - http://www.scopus.com/inward/record.url?scp=33646849471&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33646849471&partnerID=8YFLogxK

M3 - Article

C2 - 17049024

AN - SCOPUS:33646849471

VL - 5

JO - Statistical Applications in Genetics and Molecular Biology

JF - Statistical Applications in Genetics and Molecular Biology

SN - 1544-6115

IS - 1

M1 - 13

ER -