Genome-wide association studies are likely to be conducted in large scale in the near future. In such studies, searching over hundreds of thousands of markers for the few ones that are associated with disease brings out the multiple-hypothesis testing problem in its severe form. We explore, in a two-stage design, how the use of false discovery rate (FDR) can alleviate the burden of a prohibitiv...

Recent advances of high-throughput SNP arrays such as Affymetrix’s GeneChip Human Mapping 500K array set have made it possible to genotype large samples in a fast and cheap manner. A lot of algorithms were developed to call the genotypes from SNP array. When considering the low level preprocessing of SNP array, most algorithms just borrow the techniques from the gene expression microarray. As i...

Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation and are highly adaptable to large-scale automated genotyping and population genetics studies. For nonmodel organisms, many SNP discovery projects are based on sequencing and assembly of a transcriptome and the calling of sequence variation in contigs. This paper develops a new method for avoiding intron/exon ...

This package contains functions that use logic regression as a wrapper to identify interesting combinations of binary variables and to measure the importance of these interactions. A description of the used methods is given in Schwender and Ickstadt (2006). Even though the intended purpose of this package is the identification of SNP interactions, it can also be applied to other types of binary...

the interpretation of supernumerary chromosome is important for genetic counseling and prognosis. here, we used snp array and conventional karyotyping method to identify a denovo marker chromosome originated from chromosome 22 and 11 in a newborn transferred to the neonatal intensive care unit of shahid sadoughi hospital in 2015.  clinical abnormalities identified in the newborn were dysmorphic...

UNLABELLED Understanding of human variation relevant to association studies can benefit from population comparison, especially comparing populations in the same geographical region. Variations in linkage disequilibrium patterns, in tagSNP sets, and in SNP heterozygosities among populations can be used to infer the evolutionary pattern. We present here a win32 system based Perl/Tk application fo...