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NBRP Genome Information Upgrading Program Project's Progress


Focus Whole genome resequencing of the representative rat strains and development of a SNP typing kit
Principal Investigator Mikita Suyama  Kyushu University
Project Period FY2016
Overview   Rats have been used as animal models of human diseases such as cancer and hypertension. NBRP-Rat is the largest repository for the rat strains, and currently about 700 strains are registered in the repository. Among those strains, there are many rat models of immune-mediated disorders and cancers.
  This project focuses on whole genome resequencing of the representative rat strains, which include 12 strains of the representative inbred rats, one strain of the inbred rats originated from the wild populations, and seven strains of disease models derived from selective breeding. Based on the SNP information obtained by the whole genome resequencing, we will also develop a SNP typing kit that can be used for linkage analyses to detect responsible loci of diseases and for quality control of registered strains by detecting genetic contamination. This project is conducted in the collaboration with The Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, which is the NBRP Center for rat strains, and Kazusa DNA Research Institute. The genomic data obtained by this project, together with the development of a SNP typing kit based on the genomic data, will be of help to the researchers in the field of rat genetics.
Project's Progress ACI/Nkyo, BUF/Mna, DOB/Oda, DON/Kyo, F344/NSlc, F344/Stm, HER/Wkmt, KFRS4/Kyo, KHR/Kyo, LE/Stm, LEC/Tj, NER/Kyo, PVG/Seac, SDT/Jcl, TO/Hkm, W/Kyo, WKY/NCrlCrlj, WNA/Nshm, ZF, ZFDM
http://bioinfo.sls.kyushu-u.ac.jp/minako/NBRP_rat/rn5_20wgs_dp5_snv_merge.vcf http://bioinfo.sls.kyushu-u.ac.jp/minako/NBRP_rat/rn5_20wgs_dp5_indel_merge.vcf