Identification of SSR Polymorphisms for Human Genomes

• Main Authors: Sio, Chi-Pong, 蕭志邦
• Other Authors: Pai, Tun-Wen
• Format: Others
• Language: en_US
• Published: 2014
• Online Access: http://ndltd.ncl.edu.tw/handle/bumanq

碩士 === 國立臺灣海洋大學 === 資訊工程學系 === 101 === Simple Sequence Repeats (SSRs) are abundant in human genomes. Due to highly polymorphic characteristics among various species and strains, SSRs become popular biomarkers for evolutionary biology and genetic studies. Several SSRs have been experimentally proved with essential relationship for gene regulation, and abnormal repeat patterns or numbers of these functional SSRs might cause lethal diseases. High-throughput next generation sequencers foster new cutting-edge computing techniques for genomics analysis, and cross-genomes comparisons provide efficient examination on polymorphic characteristics of SSR biomarkers. An automatic and efficient system for detecting polymorphic SSRs at genomic scales was proposed in this study without manually curated and examining works. The workflow accepted multiple NGS sequencing datasets and started with assembly by de novo or reference mapping approaches. The consensus sequences were obtained from previously assembled contigs, and calibrated coordinates in each individual contig were aligned according to the selected reference sequences. To verify retrieved polymorphic SSRs, human genomes from the 1000 Genomes Project were employed as the testing sequence datasets, and the SSR biomarkers from Combined DNA Index System (CODIS) and disease-related SSR motifs were applied as the testing targets. In addition, we analyzed SSR variations for highly conserved homologous genes and human-unique genes, and performed statistical analysis for all polymorphic SSRs within human chromosomes. The results have shown that the proposed method could efficiently identify those experimentally verified polymorphic SSRs as well as novel distinguishable SSR biomarkers for individuals, families, and races at different levels of specificity.