title: SEQ Mapper: A DNA sequence searching tool for massively parallel sequencing data.
abstract: The development of massively parallel sequencing (MPS) has increased greatly the scale of DNA sequencing. The analysis of massive data-files from single MPS analysis can be a major challenge if examining the data for potential polymorphic loci. To aid in the analysis of both short tandem repeat (STR) and single nucleotide polymorphisms (SNP), we have designed a new program called SEQ Mapper to search for genetic polymorphisms within a large number of reads generated by MPS. This new program has been designed to perform sequence mapping between reference data and generated reads. As a proof-of-concept, sequences derived from the allelic ladders of five STR loci and data from the amelogenin locus were used as reference data sets. Detecting and recording the polymorphic nature of each STR loci was performed using four levels of search criteria: the entire STR locus spanning the two primers; the STR region plus the two primer sequences; the STR region only; and the two primers only. All the genotypes of 5 STR loci and the amelogenin gene were identified correctly using SEQ Mapper when compared to results obtained from capillary electrophoresis based on 10 test samples in this study. SEQ Mapper is a useful tool to detect STR or SNP alleles generated by MPS in both clinical medicine and forensic genetics.
authors: Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei 10051, Taiwan, ROC. Electronic address: jimlee@ntu.edu.tw.
authors: James Chun-I
authors: JC
authors: Lee
authors: Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei 10051, Taiwan, ROC.
authors: Bill
authors: B
authors: Tseng
authors: Laboratory of Cancer Genomic Medicine, LIHPAO Life Science. CO., Ltd., 8F Med Sci & Tech Bldg, No 201, Sec 2 Shipai Rd, Taipei 11217, Taiwan, ROC. Electronic address: steven.chang@llsc.com.tw.
authors: Liang-Kai
authors: LK
authors: Chang
authors: School of Biological Sciences, Flinders University, Adelaide 5001, Australia. Electronic address: adrian.linacre@flinders.edu.au.
authors: Adrian
authors: A
authors: Linacre
mesh_terms: D000483:Alleles; D053523:Amelogenin / Q000235:genetics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D018895:Microsatellite Repeats; D060885:Multiplex Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D012984:Software
chemical_list: D053523:Amelogenin
keywords: Bioinformatics; Forensic science; Massively parallel sequencing; Next generation sequencing; SNP; STR