PMC:3480683 / 6001-7820 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3480683","sourcedb":"PMC","sourceid":"3480683","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3480683","text":"Genotyping\nWe obtained genotype data for single-nucleotide polymorphisms (SNPs) located in the LPL gene, including the 3' flanking region, from KoGES, which are accessible to the research community through the Korean Associated Resource project. The study protocol was approved by the Institutional Review Board of KNIH. For genotyping of the samples from the Ansung and Ansan cohorts, Affymetrix Genome-Wide Human SNP Array 5.0 (Affymetrix Inc., Santa Clara, CA, USA) was used. Affymetrix Genome-Wide Human SNP Array 6.0 (Affymetrix Inc.) was used for genotyping samples from the Seoul and Busan cohorts. The Bayesian Robust Linear Model with the Mahalanobis distance algorithm was used to determine the genotypes at each SNP of Affymetrix 5.0. The BirdSeed calling genotyping algorithm was used on Affymetrix 6.0. The SNPs were filtered if any of the following criteria was met: i) a call rate lower than 95%, ii) a minor allele frequency (MAF) lower than 0.05, or iii) significant deviation from the Hardy-Weinberg equilibrium (HWE). Significant deviation from HWE for 28 successfully genotyped SNPs was determined based on a threshold of p \u003c 0.002 (0.05/28).\nSNP imputation was performed using the IMPUTE program (https://mathgen.stats.ox.ac.uk/impute/impute.html). A reference panel from International HapMap (phase II/release 22/NCBI build 36 and dbSNP build 126) data, comprising SNPs from 90 Japanese (JPT) and Han Chinese (CHB) individuals, was used as a template for inferring untyped genotypes. Imputed SNPs that were located in the LPL gene, including the 3' flanking region, with low quality were excluded according to the following criteria: low genotype information content (information lower than 0.5), a posterior probability score lower than 0.90, a call rate lower than 0.95, and MAF lower than 0.05.","divisions":[{"label":"Title","span":{"begin":0,"end":10}}],"tracks":[]}