ATRIUM: Testing Untyped SNPs in Case-Control Association Studies with Related Individuals

Version 1.0 October 22, 2009
Copyright(C) Zuoheng Wang and Mary Sara McPeek


ATRIUM is a C++ program that performs case-control association testing between a binary trait and an untyped SNP, based on genotype data from multiple typed SNPs that are in linkage disequilibrium with the untyped SNP, where information on the joint distribution of typed and untyped SNPs is obtained from an external reference panel. A special feature of ATRIUM is that both related and unrelated individuals can be included in the case-control sample. The user specifies a set of untyped SNPs on which external reference panel information is available, and the ATRIUM program computes a test statistic for association with each untyped SNP in the set. This test is suitable for case-control analysis in any outbred sample with related and/or unrelated individuals, including large pedigrees, provided that the relationships are known.

The main reference for this program is Wang Z. and McPeek M. S. ATRIUM: Testing Untyped SNPs in Case-Control Association Studies with Related Individuals (2009) American Journal of Human Genetics 85:667-678. The ATRIUM program can be considered an extension, to testing untyped SNPs, of the IQLS program for haplotype testing. The original IQLS method is described in Wang Z. and McPeek M. S. An Incomplete-Data Quasi-likelihood Approach to Haplotype-Based Genetic Association Studies on Related Individuals (2009) Journal of the American Statistical Association 104: 1251-1260.

Note: Two of the input files needed for ATRIUM (the IBD coefficient file and the multilocus LD database file) can be obtained by running the following two pieces of software:

  1. The IdCoefs software by Mark Abney, which computes condensed identity coefficients for pairs of individuals within each family. The output of IdCoefs can be directly used as input to ATRIUM (called the "IBD coefficient input file")

  2. The tuna_db program of the TUNA package by William Wen and Dan Nicolae. The tuna_db program constructs multi-locus databases for untyped SNPs based on reference panel information. The output of tuna_db can be directly used as input to ATRIUM (called the "multilocus LD database input file")



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