Abstract
The Total Integrated Archive of short-Read and Array (TIARA; http://tiara.gmi.ac.kr) database stores and integrates human genome data generated from multiple technologies including next-generation sequencing and high-resolution comparative genomic hybridization array. The TIARA genome browser is a powerful tool for the analysis of personal genomic information by exploring genomic variants such as SNPs, indels and structural variants simultaneously. As of September 2012, the TIARA database provides raw data and variant information for 13 sequenced whole genomes, 16 sequenced transcriptomes and 33 high resolution array assays. Sequencing reads are available at a depth of ∼30× for whole genomes and 50× for transcriptomes. Information on genomic variants includes a total of ∼9.56 million SNPs, 23 025 of which are non-synonymous SNPs, and ∼1.19 million indels. In this update, by adding high coverage sequencing of additional human individuals, the TIARA genome database now provides an extensive record of rare variants in humans. Following TIARA’s fundamentally integrative approach, new transcriptome sequencing data are matched with whole-genome sequencing data in the genome browser. Users can here observe, for example, the expression levels of human genes with allele-specific quantification. Improvements to the TIARA genome browser include the intuitive display of new complex and large-scale data sets.
Highlights
Next-generation sequencing technology has been used extensively in biological and clinical research, revealing information on a wide spectrum of human genomic variation, and generating a concomitantly tremendous amount of raw data. This increase in accumulated sequencing data is expected to improve the precision of human genome analysis, and widespread disease-specific and cancer genome sequencing contributes a great effort towards improved diagnosis and therapy
The short reads generated by human genome and transcriptome sequencing were previously aligned on human genome reference NCBI Build 36.3 using the Genomic Short-read Nucleotide Alignment Program (GSNAP) short-read alignment tool [20], and human genome variants such as Single Nucleotide Polymorphisms (SNPs), short indels and Structural
The raw data from these experiments have been deposited to the Total Integrated Archive of short-Read and Array (TIARA) genome database, as well as variants such as SNPs, short indels and Copy Number Variations (CNVs), detected from the data
Summary
Next-generation sequencing technology has been used extensively in biological and clinical research, revealing information on a wide spectrum of human genomic variation, and generating a concomitantly tremendous amount of raw data. This increase in accumulated sequencing data is expected to improve the precision of human genome analysis, and widespread disease-specific and cancer genome sequencing contributes a great effort towards improved diagnosis and therapy.
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