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

被引：15

作者：

Hong, Dongwan ^{[1
]}

Park, Sung-Soo ^{[2
]}

Ju, Young Seok ^{[1
,3
,4
]}

Kim, Sheehyun ^{[1
,4
]}

Shin, Jong-Yeon ^{[1
,2
]}

Kim, Sujung ^{[2
]}

Yu, Saet-Byeol ^{[2
]}

Lee, Won-Chul ^{[2
]}

Lee, Seungbok ^{[5
]}

Park, Hansoo ^{[6
,7
]}

Kim, Jong-Il ^{[1
,2
,5
]}

Seo, Jeong-Sun ^{[1
,2
,3
,4
,5
]}

机构：

[1] Seoul Natl Univ, Med Res Ctr, Genom Med Inst, Seoul 110799, South Korea

[2] Psoma Therapeut Inc, Seoul 110799, South Korea

[3] Seoul Natl Univ, Coll Med, Dept Biochem & Mol Biol, Seoul 110799, South Korea

[4] Macrogen Inc, Seoul 153801, South Korea

[5] Seoul Natl Univ, Grad Sch, Dept Biomed Sci, Seoul 110799, South Korea

[6] Brigham & Womens Hosp, Dept Pathol, Boston, MA 02115 USA

[7] Harvard Univ, Sch Med, Boston, MA 02115 USA

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

关键词：

COPY-NUMBER; STRUCTURAL VARIATION; VARIANTS; SEQUENCE; BROWSER; SCALE; READ;

D O I：

10.1093/nar/gkq1101

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 At present, 36 individual genomes have been archived and may be displayed in the database.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.

引用

页码：D883 / D888

页数：6

共 26 条

[1] The HuRef Browser: a web resource for individual human genomics [J].

Axelrod, Nelson ;

Lin, Yuan ;

Ng, Pauline C. ;

Stockwell, Timothy B. ;

Crabtree, Jonathan ;

Huang, Jiaqi ;

Kirkness, Ewen ;

Strausberg, Robert L. ;

Frazier, Marvin E. ;

Venter, J. Craig ;

Kravitz, Saul ;

Levy, Samuel .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D1018-D1024

[2] Accurate whole human genome sequencing using reversible terminator chemistry [J].

Bentley, David R. ;

Balasubramanian, Shankar ;

Swerdlow, Harold P. ;

Smith, Geoffrey P. ;

Milton, John ;

Brown, Clive G. ;

Hall, Kevin P. ;

Evers, Dirk J. ;

Barnes, Colin L. ;

Bignell, Helen R. ;

Boutell, Jonathan M. ;

Bryant, Jason ;

Carter, Richard J. ;

Cheetham, R. Keira ;

Cox, Anthony J. ;

Ellis, Darren J. ;

Flatbush, Michael R. ;

Gormley, Niall A. ;

Humphray, Sean J. ;

Irving, Leslie J. ;

Karbelashvili, Mirian S. ;

Kirk, Scott M. ;

Li, Heng ;

Liu, Xiaohai ;

Maisinger, Klaus S. ;

Murray, Lisa J. ;

Obradovic, Bojan ;

Ost, Tobias ;

Parkinson, Michael L. ;

Pratt, Mark R. ;

Rasolonjatovo, Isabelle M. J. ;

Reed, Mark T. ;

Rigatti, Roberto ;

Rodighiero, Chiara ;

Ross, Mark T. ;

Sabot, Andrea ;

Sankar, Subramanian V. ;

Scally, Aylwyn ;

Schroth, Gary P. ;

Smith, Mark E. ;

Smith, Vincent P. ;

Spiridou, Anastassia ;

Torrance, Peta E. ;

Tzonev, Svilen S. ;

Vermaas, Eric H. ;

Walter, Klaudia ;

Wu, Xiaolin ;

Zhang, Lu ;

Alam, Mohammed D. ;

Anastasi, Carole .

NATURE, 2008, 456 (7218) :53-59

[3] High-resolution mapping of copy-number alterations with massively parallel sequencing [J].

Chiang, Derek Y. ;

Getz, Gad ;

Jaffe, David B. ;

O'Kelly, Michael J. T. ;

Zhao, Xiaojun ;

Carter, Scott L. ;

Russ, Carsten ;

Nusbaum, Chad ;

Meyerson, Matthew ;

Lander, Eric S. .

NATURE METHODS, 2009, 6 (01) :99-103

[4] Origins and functional impact of copy number variation in the human genome [J].

Conrad, Donald F. ;

Pinto, Dalila ;

Redon, Richard ;

Feuk, Lars ;

Gokcumen, Omer ;

Zhang, Yujun ;

Aerts, Jan ;

Andrews, T. Daniel ;

Barnes, Chris ;

Campbell, Peter ;

Fitzgerald, Tomas ;

Hu, Min ;

Ihm, Chun Hwa ;

Kristiansson, Kati ;

MacArthur, Daniel G. ;

MacDonald, Jeffrey R. ;

Onyiah, Ifejinelo ;

Pang, Andy Wing Chun ;

Robson, Sam ;

Stirrups, Kathy ;

Valsesia, Armand ;

Walter, Klaudia ;

Wei, John ;

Tyler-Smith, Chris ;

Carter, Nigel P. ;

Lee, Charles ;

Scherer, Stephen W. ;

Hurles, Matthew E. .

NATURE, 2010, 464 (7289) :704-712

[5] Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays [J].

Drmanac, Radoje ;

Sparks, Andrew B. ;

Callow, Matthew J. ;

Halpern, Aaron L. ;

Burns, Norman L. ;

Kermani, Bahram G. ;

Carnevali, Paolo ;

Nazarenko, Igor ;

Nilsen, Geoffrey B. ;

Yeung, George ;

Dahl, Fredrik ;

Fernandez, Andres ;

Staker, Bryan ;

Pant, Krishna P. ;

Baccash, Jonathan ;

Borcherding, Adam P. ;

Brownley, Anushka ;

Cedeno, Ryan ;

Chen, Linsu ;

Chernikoff, Dan ;

Cheung, Alex ;

Chirita, Razvan ;

Curson, Benjamin ;

Ebert, Jessica C. ;

Hacker, Coleen R. ;

Hartlage, Robert ;

Hauser, Brian ;

Huang, Steve ;

Jiang, Yuan ;

Karpinchyk, Vitali ;

Koenig, Mark ;

Kong, Calvin ;

Landers, Tom ;

Le, Catherine ;

Liu, Jia ;

McBride, Celeste E. ;

Morenzoni, Matt ;

Morey, Robert E. ;

Mutch, Karl ;

Perazich, Helena ;

Perry, Kimberly ;

Peters, Brock A. ;

Peterson, Joe ;

Pethiyagoda, Charit L. ;

Pothuraju, Kaliprasad ;

Richter, Claudia ;

Rosenbaum, Abraham M. ;

Roy, Shaunak ;

Shafto, Jay ;

Sharanhovich, Uladzislau .

SCIENCE, 2010, 327 (5961) :78-81

[6] Detection of large-scale variation in the human genome [J].

Iafrate, AJ ;

Feuk, L ;

Rivera, MN ;

Listewnik, ML ;

Donahoe, PK ;

Qi, Y ;

Scherer, SW ;

Lee, C .

NATURE GENETICS, 2004, 36 (09) :949-951

[7] Reference-unbiased copy number variant analysis using CGH microarrays [J].

Ju, Young Seok ;

Hong, Dongwan ;

Kim, Sheehyun ;

Park, Sung-Soo ;

Kim, Sujung ;

Lee, Seungbok ;

Park, Hansoo ;

Kim, Jong-Il ;

Seo, Jeong-Sun .

NUCLEIC ACIDS RESEARCH, 2010, 38 (20) :e190

[8] Ensembl Genomes: Extending Ensembl across the taxonomic space [J].

Kersey, P. J. ;

Lawson, D. ;

Birney, E. ;

Derwent, P. S. ;

Haimel, M. ;

Herrero, J. ;

Keenan, S. ;

Kerhornou, A. ;

Koscielny, G. ;

Kaehaeri, A. ;

Kinsella, R. J. ;

Kulesha, E. ;

Maheswari, U. ;

Megy, K. ;

Nuhn, M. ;

Proctor, G. ;

Staines, D. ;

Valentin, F. ;

Vilella, A. J. ;

Yates, A. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D563-D569

[9] A highly annotated whole-genome sequence of a Korean individual [J].

Kim, Jong-Il ;

Ju, Young Seok ;

Park, Hansoo ;

Kim, Sheehyun ;

Lee, Seonwook ;

Yi, Jae-Hyuk ;

Mudge, Joann ;

Miller, Neil A. ;

Hong, Dongwan ;

Bell, Callum J. ;

Kim, Hye-Sun ;

Chung, In-Soon ;

Lee, Woo-Chung ;

Lee, Ji-Sun ;

Seo, Seung-Hyun ;

Yun, Ji-Young ;

Woo, Hyun Nyun ;

Lee, Heewook ;

Suh, Dongwhan ;

Lee, Seungbok ;

Kim, Hyun-Jin ;

Yavartanoo, Maryam ;

Kwak, Minhye ;

Zheng, Ying ;

Lee, Mi Kyeong ;

Park, Hyunjun ;

Kim, Jeong Yeon ;

Gokcumen, Omer ;

Mills, Ryan E. ;

Zaranek, Alexander Wait ;

Thakuria, Joseph ;

Wu, Xiaodi ;

Kim, Ryan W. ;

Huntley, Jim J. ;

Luo, Shujun ;

Schroth, Gary P. ;

Wu, Thomas D. ;

Kim, HyeRan ;

Yang, Kap-Seok ;

Park, Woong-Yang ;

Kim, Hyungtae ;

Church, George M. ;

Lee, Charles ;

Kingsmore, Stephen F. ;

Seo, Jeong-Sun .

NATURE, 2009, 460 (7258) :1011-U96

[10]

Korbel JO, 2007, SCIENCE, V318, P420, DOI 10.1126/science.1149504

← 1 2 3 →