CNVbase: Batch identification of novel and rare copy number variations based on multi-ethnic population data

Cheng Zhang^{1, 2, 3},
Jianqi Lu^{4, 5},
Haiyi Lou⁶,
Renqian Du⁷,
Shuhua Xu^{8, 9},
Yiping Shen^{10, 11, 12},
Feng Zhang^{13, 14
, ,},
Li Jin^{16
, ,}

1.
Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200438, China
2.
Key Laboratory of Reproduction Regulation of NPFPC, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China
3.
Departments of Laboratory Medicine and Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
4.
Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200438, China
5.
Key Laboratory of Reproduction Regulation of NPFPC, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China
6.
Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
7.
Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200438, China
8.
Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
9.
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
10.
Departments of Laboratory Medicine and Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
11.
Department of Genetic Metabolism, Children's Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
12.
Department of Medical Genetics, Shanghai Children's Medical Center, Shanghai 200127, China
13.
Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200438, China
14.
Key Laboratory of Reproduction Regulation of NPFPC, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China
16.
Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200438, China

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Corresponding author: E-mail address: zhangfeng@fudan.edu.cn (Feng Zhang); E-mail address: lijin@fudan.edu.cn (Li Jin)

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[1]	Abecasis, G.R., Auton, A., Brooks, L.D. et al. An integrated map of genetic variation from 1,092 human genomes Nature, 491 (2012),pp. 56-65
[2]	Alkan, C., Coe, B.P., Eichler, E.E. Genome structural variation discovery and genotyping Nat. Rev. Genet., 12 (2011),pp. 363-376
[3]	Campbell, C.D., Sampas, N., Tsalenko, A. et al. Population-genetic properties of differentiated human copy-number polymorphisms Am. J. Hum. Genet., 88 (2011),pp. 317-332
[4]	Conrad, D.F., Pinto, D., Redon, R. et al. Origins and functional impact of copy number variation in the human genome Nature, 464 (2010),pp. 704-712
[5]	Iafrate, A.J., Feuk, L., Rivera, M.N. et al. Detection of large-scale variation in the human genome Nat. Genet., 36 (2004),pp. 949-951
[6]	Itsara, A., Cooper, G.M., Baker, C. et al. Population analysis of large copy number variants and hotspots of human genetic disease Am. J. Hum. Genet., 84 (2009),pp. 148-161
[7]	Kim, J.H., Hu, H.J., Chung, Y.J. Web-based database and viewer of East Asian copy number variations Genomics Inf., 10 (2012),pp. 65-67
[8]	Lou, H., Li, S., Yang, Y. et al. A map of copy number variations in Chinese populations PLoS One, 6 (2011),p. e27341
[9]	Lupski, J.R. Structural variation in the human genome N. Engl. J. Med., 356 (2007),pp. 1169-1171
[10]	MacDonald, J.R., Ziman, R., Yuen, R.K. et al. The Database of Genomic Variants: a curated collection of structural variation in the human genome Nucleic Acids Res., 42 (2014),pp. 986-992
[11]	Ogasawara, O., Mashima, J., Kodama, Y. et al. DDBJ new system and service refactoring Nucleic Acids Res., 41 (2013),pp. 25-29
[12]	Park, H., Kim, J.I., Ju, Y.S. et al. Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing Nat. Genet., 42 (2010),pp. 400-405
[13]	Perry, G.H., Ben-Dor, A., Tsalenko, A. et al. The fine-scale and complex architecture of human copy-number variation Am. J. Hum. Genet., 82 (2008),pp. 685-695
[14]	Redon, R., Ishikawa, S., Fitch, K.R. et al. Global variation in copy number in the human genome Nature, 444 (2006),pp. 444-454
[15]	Ruangrit, U., Srikummool, M., Assawamakin, A. et al. Thailand mutation and variation database (ThaiMUT) Hum. Mutat., 29 (2008),pp. 68-75
[16]	Sebat, J., Lakshmi, B., Troge, J. et al. Large-scale copy number polymorphism in the human genome Science, 305 (2004),pp. 525-528
[17]	Sudmant, P.H., Rausch, T., Gardner, E.J. et al. An integrated map of structural variation in 2,504 human genomes Nature, 526 (2015),pp. 75-81
[18]	Tan, E.C., Loh, M., Chuon, D. et al. Singapore Human Mutation/Polymorphism Database: a country-specific database for mutations and polymorphisms in inherited disorders and candidate gene association studies Hum. Mutat., 27 (2006),pp. 232-235
[19]	Wu, N., Ming, X., Xiao, J. et al. N. Engl. J. Med., 372 (2015),pp. 341-350
[20]	Zhang, F., Gu, W., Hurles, M.E. et al. Copy number variation in human health, disease and evolution Annu. Rev. Genomics Hum. Genet., 10 (2009),pp. 451-481

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doi: 10.1016/j.jgg.2017.07.001

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CNVbase: Batch identification of novel and rare copy number variations based on multi-ethnic population data

Corresponding author: E-mail address: zhangfeng@fudan.edu.cn (Feng Zhang); E-mail address: lijin@fudan.edu.cn (Li Jin)

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doi: 10.1016/j.jgg.2017.07.001

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CNVbase: Batch identification of novel and rare copy number variations based on multi-ethnic population data

Corresponding author: E-mail address: zhangfeng@fudan.edu.cn (Feng Zhang); E-mail address: lijin@fudan.edu.cn (Li Jin)

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