BioProject

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. More...

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 Less...