KIR alleles harvested from 1000 genomes whole-exome data. Diversity of Human KIR

These sequences are identified from 1000 genomes reads for a project examining the polymorphism of the Killer cell Immunoglobulin-like Receptors (KIR), which are immune cell regulators involved in control of infection, cancer and implantation during pregnancy. The example shown is KIR3DL2. All of the 1000 genomes were genotyped in silico from fastq-format reads, which -following filtering- mapped uniquely to the KIR3DL2 locus. There are 46 novel alleles identified here. The bioinformatic methods are verified using standard wet-lab methods in the following publication: BMC Genomics. Apr 4;15(1):262, 2014. The reads were filtered using Bowtie, variants called using Samtools and R scripting, and visual inspections made from independent alignments created with MIRA. Reads were obtained as per the following example: samtools view -b -f2 ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/NA19240/exome_alignment/NA19240.mapped.ILLUMINA.bwa.YRI.exome.20130415.bam 19:55,228,188-55,383,188 GL000209.1 -h -o NA19240_KIR.bam Bowtie filters for positive (all3DL2) and negative (allKIRnot3DL2) filtering for KIR3DL2 specificity were generated using full-length sequences available at http://www.ebi.ac.uk/ipd/kir/align.html

本数据集的序列源自一项研究杀伤细胞免疫球蛋白样受体（Killer cell Immunoglobulin-like Receptors，KIR）多态性的项目所使用的1000基因组测序读段。KIR是一类免疫细胞调控分子，参与感染、癌症的免疫防控以及妊娠期间的胚胎着床过程。本次展示的示例为KIR3DL2基因座。
所有1000基因组样本均通过计算机模拟基因分型，从fastq格式测序读段中提取得到；经过滤后的读段可唯一比对至KIR3DL2基因座。本数据集共鉴定得到46个全新的等位基因。
本研究采用的生物信息学方法已通过标准湿实验方法验证，相关成果发表于期刊BMC Genomics（2014年4月4日，第15卷第1期，第262页）。具体分析流程如下：测序读段通过Bowtie进行过滤，变异位点的识别采用Samtools与R脚本完成，同时借助MIRA生成独立比对结果以进行可视化校验。
测序读段的获取可参照以下示例命令：
samtools view -b -f2 ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/NA19240/exome_alignment/NA19240.mapped.ILLUMINA.bwa.YRI.exome.20130415.bam 19:55,228,188-55,383,188 GL000209.1 -h -o NA19240_KIR.bam
针对KIR3DL2特异性鉴定的Bowtie过滤策略包含正向筛选（保留所有3DL2序列）与负向筛选（排除所有非3DL2的KIR序列），该策略所需的过滤参数依托于http://www.ebi.ac.uk/ipd/kir/align.html 公开的全长序列生成。