Advanced Genomics and Bioinformatics Research Center, The Scientific and Technological Research Council of Turkey (TUBITAK-BILGEM), 41470 Gebze, Kocaeli, Turkey and Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Abdullah Gul University, 38039 Kayseri, Turkey.
Bioinformatics. 2014 Feb 1;30(3):445-7. doi: 10.1093/bioinformatics/btt686. Epub 2013 Dec 3.
In consanguineous families, as a result of inheriting the same genomic segments through both parents, the individuals have stretches of their genomes that are homozygous. This situation leads to the prevalence of recessive diseases among the members of these families. Homozygosity mapping is based on this observation, and in consanguineous families, several recessive disease genes have been discovered with the help of this technique. The researchers typically use single nucleotide polymorphism arrays to determine the homozygous regions and then search for the disease gene by sequencing the genes within this candidate disease loci. Recently, the advent of next-generation sequencing enables the concurrent identification of homozygous regions and the detection of mutations relevant for diagnosis, using data from a single sequencing experiment. In this respect, we have developed a novel tool that identifies homozygous regions using deep sequence data. Using *.vcf (variant call format) files as an input file, our program identifies the majority of homozygous regions found by microarray single nucleotide polymorphism genotype data.
HomSI software is freely available at www.igbam.bilgem.tubitak.gov.tr/softwares/HomSI, with an online manual.
在血缘家庭中，由于父母双方都遗传了相同的基因组片段，个体的基因组中有一部分是纯合子。这种情况导致这些家庭的成员中隐性疾病的流行。同型性定位映射就是基于这一观察结果，在血缘家庭中，借助这种技术已经发现了几个隐性疾病基因。研究人员通常使用单核苷酸多态性微阵列来确定纯合子区域，然后通过对候选疾病基因座内的基因进行测序来寻找疾病基因。最近，新一代测序技术的出现使得通过单个测序实验同时识别纯合子区域和检测与诊断相关的突变成为可能。在这方面，我们开发了一种新的工具，该工具使用深度测序数据识别纯合子区域。我们的程序使用 *.vcf（变体调用格式）文件作为输入文件，可识别微阵列单核苷酸多态性基因型数据中发现的大多数纯合子区域。
HomSI 软件可在 www.igbam.bilgem.tubitak.gov.tr/softwares/HomSI 上免费获得，并附有在线手册。
