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BMC Genomics

, 15:S3

First Online: 12 December 2014DOI: 10.1186-1471-2164-15-S10-S3

Cite this article as: Chen, CM., Sio, CP., Lu, YL. et al. BMC Genomics 2014 15Suppl 10: S3. doi:10.1186-1471-2164-15-S10-S3

Abstract

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.

KeywordsShort tandem repeat 1000 Genomes Project CODIS Next generation sequencing genetic disease orthologous gene human-unique gene List of abbreviationsSTRShort Tandem Repeat

pSTRPolymorphic STR

TLgeneTotal length of gene

TLssrTotal length of SSR

TNgeneTotal number of gene

TNpssrTotal number of polymorphism SSR

TNssrTotal number of SSR

UTRUntranslated Region

Chr-ChromChromosome

BLASTBasic Local Alignment Search Tool

MbpMega base pairs

NCBINational Center for Biotechnology Information

ENBLEnsembl

CODISCombined DNA Index System

NGSNext Generation Sequencing

BAMBinary Alignment Map

SAMSequence Alignment Map

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-15-S10-S3 contains supplementary material, which is available to authorized users.

Chien-Ming Chen, Chi-Pong Sio contributed equally to this work.

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Autor: Chien-Ming Chen - Chi-Pong Sio - Yu-Lun Lu - Hao-Teng Chang - Chin-Hwa Hu - Tun-Wen Pai

Fuente: https://link.springer.com/







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