Original Paper

Enhanced Pedigree Error Detection
Lei Sun^a,d, Kenneth Wilder^a,b, Mary Sara McPeek^a,c

Departments of
^aStatistics,
^bMathematics, and
^cHuman Genetics, University of Chicago, Chicago, Ill., USA;
^dPresent affiiliation: Department of Public Health Sciences, University of Toronto, and Hospital for Sick Children, Toronto, Canada

Address of Corresponding Author

Hum Hered 2002;54:99-110 (DOI: 10.1159/000067666)

  Key Words

• Markov chain
• Hidden Markov model
• Likelihood ratio test
• Pedigree error
• Misspecified relationship
• Relationship estimation
• Software
• PREST
• ALTERTEST

  Abstract

Accurate information on the relationships among individuals in a study is critical for valid linkage analysis. We extend the MLLR, EIBD, AIBS and IBS tests for detection of misspecified relationships to a broader range of relative pairs, and we improve the two-stage screening procedure for analyzing large data sets. We have developed software, PREST, which calculates the test statistics and performs the corresponding hypothesis tests for relationship misclassification in general outbred pedigrees. When a potential pedigree error is detected, our companion program, ALTERTEST, can be used to determine which relationships are compatible with the genotype data. Both programs are now freely available on the web.

Copyright © 2003 S. Karger AG, Basel

  Author Contacts

Lei Sun
Department of Public Health Sciences, University of Toronto
12 Queen's Park Crescent West
Toronto, ON M5S 1A8 (Canada)
Tel. +1 416 978 7519, Fax +1 416 978 8299, E-Mail lei.sun@utoronto.ca

  Article Information

Received: Received: December 12, 2001
Revision received: October 4, 2002
Accepted: October 7, 2002
Number of Figures : 1, Number of Tables : 6, Number of References : 21