Reference-unbiased copy number variant analysis using CGH microarrays

被引：20

作者：

Ju, Young Seok ^{[1
,2
,3
]}

Hong, Dongwan ^{[1
]}

Kim, Sheehyun ^{[1
,3
]}

Park, Sung-Soo ^{[4
]}

Kim, Sujung ^{[4
]}

Lee, Seungbok ^{[1
,5
]}

Park, Hansoo ^{[1
,6
,7
]}

Kim, Jong-Il ^{[1
,2
,4
]}

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

[3] Macrogen Inc, Seoul 153801, South Korea

[4] Psoma Therapeut 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 | 2010年 / 38卷 / 20期

关键词：

HUMAN GENOME; STRUCTURAL VARIATION; FINE-SCALE; EVOLUTION; SEQUENCE; HUMANS;

D O I：

10.1093/nar/gkq730

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：

Comparative genomic hybridization (CGH) microarrays have been used to determine copy number variations (CNVs) and their effects on complex diseases. Detection of absolute CNVs independent of genomic variants of an arbitrary reference sample has been a critical issue in CGH array experiments. Whole genome analysis using massively parallel sequencing with multiple ultra-high resolution CGH arrays provides an opportunity to catalog highly accurate genomic variants of the reference DNA (NA10851). Using information on variants, we developed a new method, the CGH array reference-free algorithm (CARA), which can determine reference-unbiased absolute CNVs from any CGH array platform. The algorithm enables the removal and rescue of false positive and false negative CNVs, respectively, which appear due to the effects of genomic variants of the reference sample in raw CGH array experiments. We found that the CARA remarkably enhanced the accuracy of CGH array in determining absolute CNVs. Our method thus provides a new approach to interpret CGH array data for personalized medicine.

引用

页数：11

共 24 条

[1] Personalized copy number and segmental duplication maps using next-generation sequencing [J].

Alkan, Can ;

Kidd, Jeffrey M. ;

Marques-Bonet, Tomas ;

Aksay, Gozde ;

Antonacci, Francesca ;

Hormozdiari, Fereydoun ;

Kitzman, Jacob O. ;

Baker, Carl ;

Malig, Maika ;

Mutlu, Onur ;

Sahinalp, S. Cenk ;

Gibbs, Richard A. ;

Eichler, Evan E. .

NATURE GENETICS, 2009, 41 (10) :1061-U29

[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] Methods and strategies for analyzing copy number variation using DNA microarrays [J].

Carter, Nigel P. .

NATURE GENETICS, 2007, 39 (Suppl 7) :S16-S21

[4] 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

[5] 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

[6] The functional impact of structural variation in humans [J].

Hurles, Matthew E. ;

Dermitzakis, Emmanouil T. ;

Tyler-Smith, Chris .

TRENDS IN GENETICS, 2008, 24 (05) :238-245

[7] 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

[8] Mapping and sequencing of structural variation from eight human genomes (Reprinted from Nature, vol 453, pg 56-64, 2008) [J].

Kidd, Jeffrey M. ;

Cooper, Gregory M. ;

Donahue, William F. ;

Hayden, Hillary S. ;

Sampas, Nick ;

Graves, Tina ;

Hansen, Nancy ;

Teague, Brian ;

Alkan, Can ;

Antonacci, Francesca ;

Haugen, Eric ;

Zerr, Troy ;

Yamada, N. Alice ;

Tsang, Peter ;

Newman, Tera L. ;

Tuzun, Eray ;

Cheng, Ze ;

Ebling, Heather M. ;

Tusneem, Nadeem ;

David, Robert ;

Gillett, Will ;

Phelps, Karen A. ;

Weaver, Molly ;

Saranga, David ;

Brand, Adrianne ;

Tao, Wei ;

Gustafson, Erik ;

McKernan, Kevin ;

Chen, Lin ;

Malig, Maika ;

Smith, Joshua D. ;

Korn, Joshua M. ;

McCarroll, Steven A. ;

Altshuler, David A. ;

Peiffer, Daniel A. ;

Dorschner, Michael ;

Stamatoyannopoulos, John ;

Schwartz, David ;

Nickerson, Deborah A. ;

Mullikin, James C. ;

Wilson, Richard K. ;

Bruhn, Laurakay ;

Olson, Maynard V. ;

Kaul, Rajinder ;

Smith, Douglas R. ;

Eichler, Evan E. .

NATURE GENETICS, 2009, :S22-S30

[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

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