TY - GEN
T1 - Definition and analysis of SNP-free regions of current genome wide association study databases
AU - Qiu, Rang
AU - Wu, Min
AU - Liu, Chunyu
AU - Jiang, Hang
AU - Fu, Lingyun
PY - 2010
Y1 - 2010
N2 - Single Nucleotide Polymorphism (SNP) is the important part in genome wide association study (GWAS). We investigated the SNPs that are not genotyped directly or indirectly by the current GWAS, and genomic regions associated with these unassayed SNPs. Through analysis of HapMap CEU (European Caucasian), CHB (Han Chinese), JPT (Japanese) and YRI (Yoruba African) data, we identified the NGS SNP-free regions and the NGS common SNP-free regions (minor allele frequency (MAF) > = 0.05), We also calculated the number and the size of the NGS SNP-free regions and the NGS common SNP- free regions, where they have been reported so far, in different populations. In the analysis of NGS SNP-free regions and NGS common SNP-free regions, we found they have the character of independence. The distributions of the NGS SNP-free regions and NGS common SNP-free regions have the character of imbalance. The GWAS genotyping platforms could be further upgraded to include more SNPs to ensure true whole genome coverage.
AB - Single Nucleotide Polymorphism (SNP) is the important part in genome wide association study (GWAS). We investigated the SNPs that are not genotyped directly or indirectly by the current GWAS, and genomic regions associated with these unassayed SNPs. Through analysis of HapMap CEU (European Caucasian), CHB (Han Chinese), JPT (Japanese) and YRI (Yoruba African) data, we identified the NGS SNP-free regions and the NGS common SNP-free regions (minor allele frequency (MAF) > = 0.05), We also calculated the number and the size of the NGS SNP-free regions and the NGS common SNP- free regions, where they have been reported so far, in different populations. In the analysis of NGS SNP-free regions and NGS common SNP-free regions, we found they have the character of independence. The distributions of the NGS SNP-free regions and NGS common SNP-free regions have the character of imbalance. The GWAS genotyping platforms could be further upgraded to include more SNPs to ensure true whole genome coverage.
KW - Common SNP-free regions
KW - GWAS
KW - SNP
KW - SNP-free regions
UR - https://www.scopus.com/pages/publications/78650618687
U2 - 10.1109/BICTA.2010.5645123
DO - 10.1109/BICTA.2010.5645123
M3 - Conference contribution
SN - 9781424464388
T3 - Proceedings 2010 IEEE 5th International Conference on Bio-Inspired Computing: Theories and Applications, BIC-TA 2010
SP - 1018
EP - 1022
BT - Proceedings 2010 IEEE 5th International Conference on Bio-Inspired Computing
T2 - 2010 IEEE 5th International Conference on Bio-Inspired Computing: Theories and Applications, BIC-TA 2010
Y2 - 23 September 2010 through 26 September 2010
ER -