TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology

High-throughput genomic technologies have been used to explore personal human genomes for the past few years. Although the integration of technologies is important for high-accuracy detection of personal genomic variations, no databases have been prepared to systematically archive genomes and to facilitate the comparison of personal genomic data sets prepared using a variety of experimental platforms. We describe here the Total Integrated Archive of Short-Read and Array (TIARA; http://tiara.gmi.ac.kr) database, which contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). At present, 36 individual genomes have been archived and may be displayed in the database. TIARA supports a user-friendly genome browser, which retrieves read-depths (RDs) and log2 ratios from NGS and CGH arrays, respectively. In addition, this database provides information on all genomic variants and the raw data, including short reads and feature-level CGH data, through anonymous file transfer protocol. More personal genomes will be archived as more individuals are analyzed by NGS or CGH array. TIARA provides a new approach to the accurate interpretation of personal genomes for genome research

Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing

Copy number variants (CNVs) account for the majority of human genomic diversity in terms of base coverage. Here, we have developed and applied a new method to combine high-resolution array comparative genomic hybridization (CGH) data with whole-genome DNA sequencing data to obtain a comprehensive catalog of common CNVs in Asian individuals. The genomes of 30 individuals from three Asian populations (Korean, Chinese and Japanese) were interrogated with an ultra-high-resolution array CGH platform containing 24 million probes. Whole-genome sequencing data from a reference genome (NA10851, with 28.3x coverage) and two Asian genomes (AK1, with 27.8x coverage and AK2, with 32.0x coverage) were used to transform the relative copy number information obtained from array CGH experiments into absolute copy number values. We discovered 5,177 CNVs, of which 3,547 were putative Asian-specific CNVs. These common CNVs in Asian populations will be a useful resource for subsequent genetic studies in these populations, and the new method of calling absolute CNVs will be essential for applying CNV data to personalized medicine.Conrad DF, 2010, NATURE, V464, P704, DOI 10.1038/nature08516Kim JI, 2009, NATURE, V460, P1011, DOI 10.1038/nature08211Horowitz RE, 2008, NEW ENGL J MED, V359, P2393Shiffman D, 2008, PLOS ONE, V3, DOI 10.1371/journal.pone.0002895Kidd JM, 2008, NATURE, V453, P56, DOI 10.1038/nature06862Perry GH, 2008, AM J HUM GENET, V82, P685, DOI 10.1016/j.ajhg.2007.12.010Graham DSC, 2008, GENES IMMUN, V9, P93, DOI 10.1038/sj.gene.6364453Lohmueller KE, 2008, NATURE, V451, P994, DOI 10.1038/nature06611Korbel JO, 2007, SCIENCE, V318, P420, DOI 10.1126/science.1149504Hossain P, 2007, NEW ENGL J MED, V356, P213Larson MG, 2007, BMC MED GENET, V8, DOI 10.1186/1471-2350-8-S1-S5Redon R, 2006, NATURE, V444, P444, DOI 10.1038/nature05329Jee SH, 2006, NEW ENGL J MED, V355, P779Aitman TJ, 2006, NATURE, V439, P851, DOI 10.1038/nature04489Conrad DF, 2006, NAT GENET, V38, P75, DOI 10.1038/ng1697Wang YH, 2005, J LAB CLIN MED, V146, P321, DOI 10.1016/j.lab.2005.07.007Lindner I, 2005, MOL NUTR FOOD RES, V49, P972, DOI 10.1002/mnfr.200500087Tuzun E, 2005, NAT GENET, V37, P727, DOI 10.1038/ng1562Lee JW, 2005, ONCOGENE, V24, P1477, DOI 10.1038/sj.onc.1208304Iafrate AJ, 2004, NAT GENET, V36, P949, DOI 10.1038/ng1416Samuels Y, 2004, SCIENCE, V304, P554, DOI 10.1126/science.1096502Burchard EG, 2003, NEW ENGL J MED, V348, P1170COLIN Y, 1991, BLOOD, V78, P27474