Identification of conserved and polymorphic STRs for personal genomes

BMC Genomics

Research

Tun-Wen Pai¹  Yu-Lun Lu¹  Chien-Ming Chen¹  Chi-Pong Sio¹  Hao-Teng Chang²  Chin-Hwa Hu³ 

[1] Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan;Graduate Institute of Molecular System Biomedicine, China Medical University, Taichung, Taiwan;Institute of Biosciences and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan;

关键词: Short tandem repeat;    1000 Genomes Project;    CODIS;    Next generation sequencing;    genetic disease;    orthologous gene;    human-unique gene;   

DOI  :  10.1186/1471-2164-15-S10-S3

来源: Springer

【 摘 要 】

BackgroundShort tandem repeats (STRs) are abundant in human genomes. Numerous STRs have been shown to be associated with genetic diseases and gene regulatory functions, and have been selected as genetic markers for evolutionary and forensic analyses. High-throughput next generation sequencers have fostered new cutting-edge computing techniques for genome-scale analyses, and cross-genome comparisons have facilitated the efficient identification of polymorphic STR markers for various applications.ResultsAn automated and efficient system for detecting human polymorphic STRs at the genome scale is proposed in this study. Assembled contigs from next generation sequencing data were aligned and calibrated according to selected reference sequences. To verify identified polymorphic STRs, human genomes from the 1000 Genomes Project were employed for comprehensive analyses, and STR markers from the Combined DNA Index System (CODIS) and disease-related STR motifs were also applied as cases for evaluation. In addition, we analyzed STR variations for highly conserved homologous genes and human-unique genes. In total 477 polymorphic STRs were identified from 492 human-unique genes, among which 26 STRs were retrieved and clustered into three different groups for efficient comparison.ConclusionsWe have developed an online system that efficiently identifies polymorphic STRs and provides novel distinguishable STR biomarkers for different levels of specificity. Candidate polymorphic STRs within a personal genome could be easily retrieved and compared to the constructed STR profile through query keywords, gene names, or assembled contigs.

【 授权许可】

Unknown   
© Chen et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.