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TIARA - Total Integrated Archive of short-Read and Array


NAR Molecular Biology Database Collection entry number 1450
Dongwan Hong1, Sung-Soo Park2, Young Seok Ju1,3,4, Sheehyun Kim1,4, Jong-Yeon Shin1,2, Sujung Kim2, Saet-Byeol Yu2, Won-Chul Lee2, Seungbok Lee5, Hansoo Park6, Jong-Il Kim1,2,5 and Jeong-Sun Seo1,2,3,4,5
1Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, Korea 2Psoma Therapeutics Inc. Seoul 110-799, Korea 3Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 110-799, Korea 4Macrogen Inc., Seoul 153-801, Korea 5Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 110-799, Korea 6Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA

Database Description

The Total Integrated Archive of short-Read and Array (TIARA) accumulates raw-level personal genomic data from whole genome next-generation sequencing (NGS) and comparative genomic hybridization (CGH) arrays. Initially, it contains 36 individual genomic data sets that have been analyzed and reported by the Genomic Medicine Institute (GMI) at Seoul National University (1,2,3). TIARA improves the accuracy of detecting personal genomic variations, such as SNPs, short indels, and structural variants (SVs). TIARA supports a user-friendly genome browser, which retrieves read-depths (RDs) and log2 ratios from NGS and CGH arrays, respectively. In addition, TIARA provides information on all genomic variants and the raw data, including short reads and feature-level CGH data, through anonymous file transfer protocol (FTP).

Recent Developments

Recently, the genome browser of TIARA has the functions of displaying SNPs, indels, Read Depths (RD) with Refseq genes from high-throughput sequencing, copy number variants (CNVS) regions and log2 ratio for high-resolution CGH array. Moreover, a genome-wide map summarizing the location and allele frequency for each SNPs can be found in TIARA. In detail, massively parallel sequencing data from six Korean genomes (AK3, AK5, AK7, AK9, AK14, and AK20) were sequenced using the Illumina Genome Analyzer IIx and deposited in TIARA. In addition, genomic variants such SNPs, indels, and CNV regions and read RDs for those data were also browsed and downloaded in genome browser of TIARA.

Acknowledgements

TIARA was supported by the Korean Ministry of Knowledge Economy [grant number 0411-20100061], the Korean Ministry of Education, Science, and Technology [grant number 2010-0013662], Green Cross Therapeutics [grant number 0411-20080023]. Funding for open access charge: Korean Ministry of Education, Science, and Technology [grant number 2010-0013662]

References

1. Kim, J.I., Ju, Y.S., Park, H., Kim, S., Lee, S., Yi, J.H., Mudge, J., Miller, N.A., Hong, D., Bell, C.J. et al. (2009) A highly annotated whole-genome sequence of a Korean individual. Nature, 460, 1011-1015.

2. Ju, Y.S., Hong, D., Kim, S., Park, S.S., Lee, S., Park, H., Kim, J.I. and Seo, J.S. (2010) Reference-unbiased copy number variant analysis using CGH microarrays. Nucleic Acids Res, 38 (20):e190 (http://nar.oxfordjournals.org/content/38/20/e190).

3. Park, H., Kim, J.I., Ju, Y.S., Gokcumen, O., Mills, R.E., Kim, S., Lee, S., Suh, D., Hong, D., Kang, H.P. et al. (2010) Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat Genet, 42, 400-405.


Go to the abstract in the NAR 2011 Database Issue.
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