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
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
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:
- 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")
- 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")
Download the software