TY  - JOUR
AU  - Choi, Sungkyoung
AU  - Lee, Sungyoung
AU  - Cichon, Sven
AU  - Nöthen, Markus M
AU  - Lange, Christoph
AU  - Park, Taesung
AU  - Won, Sungho
TI  - FARVAT: a family-based rare variant association test.
JO  - Bioinformatics
VL  - 30
IS  - 22
SN  - 1460-2059
CY  - Oxford
PB  - Oxford Univ. Press
M1  - DZNE-2020-03954
SP  - 3197-3205
PY  - 2014
AB  - Individuals in each family are genetically more homogeneous than unrelated individuals, and family-based designs are often recommended for the analysis of rare variants. However, despite the importance of family-based samples analysis, few statistical methods for rare variant association analysis are available.In this report, we propose a FAmily-based Rare Variant Association Test (FARVAT). FARVAT is based on the quasi-likelihood of whole families, and is statistically and computationally efficient for the extended families. FARVAT assumed that families were ascertained with the disease status of family members, and incorporation of the estimated genetic relationship matrix to the proposed method provided robustness under the presence of the population substructure. Depending on the choice of working matrix, our method could be a burden test or a variance component test, and could be extended to the SKAT-O-type statistic. FARVAT was implemented in C++, and application of the proposed method to schizophrenia data and simulated data for GAW17 illustrated its practical importance.The software calculates various statistics for the analysis of related samples, and it is freely downloadable from http://healthstats.snu.ac.kr/software/farvat.won1@snu.ac.kr or tspark@stats.snu.ac.krsupplementary data are available at Bioinformatics online.
KW  - Family
KW  - Genetic Association Studies: methods
KW  - Genetic Variation
KW  - Humans
KW  - Schizophrenia: genetics
KW  - Software
LB  - PUB:(DE-HGF)16
C6  - pmid:25075118
DO  - DOI:10.1093/bioinformatics/btu496
UR  - https://pub.dzne.de/record/137632
ER  -