A rare variant in COL11A1 is strongly associated with adult height in Chinese Han population

Changbing Shen; Xiaodong Zheng; Jing Gao; Caihong Zhu; Randy Ko; Xianfa Tang; Chao Yang; Jinfa Dou; Yan Lin; Yuyan Cheng; Lu Liu; Shuangjun Xu; Gang Chen; Xianbo Zuo; Xianyong Yin; Liangdan Sun; Yong Cui; Sen Yang; Xuejun Zhang; Fusheng Zhou

doi:10.1016/j.jgg.2016.04.002

Volume 43 Issue 9

Sep. 2016

Turn off MathJax

Article Contents

Abstract

References

Article Navigation > Journal of Genetics and Genomics > 2016 > 43(9): 549-554

PDF( 498 KB)

A rare variant in COL11A1 is strongly associated with adult height in Chinese Han population

doi: 10.1016/j.jgg.2016.04.002

Changbing Shen^{a, b, c, #},
Xiaodong Zheng^{a, b, c, #},
Jing Gao^{d, #},
Caihong Zhu^{a, b, c},
Randy Ko^e,
Xianfa Tang^{a, b, c},
Chao Yang^{a, b, c},
Jinfa Dou^{a, b, c},
Yan Lin^{a, b, c},
Yuyan Cheng^{a, b, c},
Lu Liu^{a, b, c},
Shuangjun Xu^{a, b, c},
Gang Chen^{a, b, c},
Xianbo Zuo^{a, b, c},
Xianyong Yin^f,
Liangdan Sun^{a, b, c},
Yong Cui^g,
Sen Yang^{a, b, c},
Xuejun Zhang^{a, b, c, d},
Fusheng Zhou^{a, b, c}

a
Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei 230032, China
b
The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei 230032, China
c
Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei 230032, China
d
Department of Dermatology, The Second Affiliated Hospital, Anhui Medical University, Hefei 230601, China
e
Department of Biochemistry, University of New Mexico, Albuquerque, NM 87131, USA
f
Department of Genetics, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
g
Department of Dermatology, China-Japan Friendship Hospital, Beijing 100029, China

More Information

Corresponding author: E-mail address: ayzxj@vip.sina.com (Xuejun Zhang); E-mail address: biozhoufs@163.com (Fusheng Zhou)
Received Date: 2015-12-30
Accepted Date: 2016-04-03
Rev Recd Date: 2016-03-01

Available Online: 2016-04-04

Publish Date: 2016-09-20

Abstract

Abstract

Human height is a highly heritable trait in which multiple genes are involved. Recent genome-wide association studies (GWASs) have identified that COL11A1 is an important susceptibility gene for human height. To determine whether the variants of COL11A1 are associated with adult and children height, we analyzed splicing and coding single-nucleotide variants across COL11A1 through exome-targeted sequencing and two validation stages with a total 20,426 Chinese Han samples. A total of 105 variants were identified by exome-targeted sequencing, of which 30 SNPs were located in coding region. The strongest association signal was chr1_103380393 with P value of 4.8 × 10⁻⁷. Chr1_103380393 also showed nominal significance in the validation stage (P = 1.21 × 10⁻⁶). Combined analysis of 16,738 samples strengthened the original association of chr1_103380393 with adult height (P = 3.1 × 10⁻⁸), with an increased height of 0.292sd (standard deviation) per G allele (95% CI: 0.19–0.40). There was no evidence (P = 0.843) showing that chr1_103380393 altered child height in 3688 child samples. Only the group of 12–15 years showed slight significance with P value of 0.0258. This study firstly shows that genetic variants of COL11A1 contribute to adult height in Chinese Han population but not to children height, which expand our knowledge of the genetic factors underlying height variation and the biological regulation of human height.
- Rare variant,
- Adult height,
- Chinese Han population

The first three authors contribute equally to this work.

FullText(HTML)

References(20)

References

[1]	Annunen, S., Korkko, J., Czarny, M. et al. Am. J. Hum. Genet., 65 (1999),pp. 974-983
[2]	Du, M., Auer, P.L., Jiao, S. et al. Whole-exome imputation of sequence variants identified two novel alleles associated with adult body height in African Americans Hum. Mol. Genet., 23 (2014),pp. 6607-6615
[3]	Hao, Y., Liu, X., Lu, X. et al. Genome-wide association study in Han Chinese identifies three novel loci for human height Hum. Genet., 132 (2013),pp. 681-689
[4]	Keene, D.R., Oxford, J.T., Morris, N.P. Ultrastructural localization of collagen types II, IX, and XI in the growth plate of human rib and fetal bovine epiphyseal cartilage: type XI collagen is restricted to thin fibrils J. Histochem. Cytochem, 43 (1995),pp. 967-979
[5]	Kimura, T., Kobayashi, T., Munkhbat, B. et al. Genome-wide association analysis with selective genotyping identifies candidate loci for adult height at 8q21.13 and 15q22.33-q23 in Mongolians Hum. Genet., 123 (2008),pp. 655-660
[6]	Lango Allen, H., Estrada, K., Lettre, G. et al. Hundreds of variants clustered in genomic loci and biological pathways affect human height Nature, 467 (2010),pp. 832-838
[7]	Lanktree, M.B., Guo, Y., Murtaza, M. et al. Meta-analysis of dense genecentric association studies reveals common and uncommon variants associated with height Am. J. Hum. Genet., 88 (2011),pp. 6-18
[8]	Li, Y., Lacerda, D.A., Warman, M.L. et al. Cell, 80 (1995),pp. 423-430
[9]	Liu, J.Z., Medland, S.E., Wright, M.J. et al. Genome-wide association study of height and body mass index in Australian twin families Twin Res. Hum. Genet., 13 (2010),pp. 179-193
[10]	Macgregor, S., Cornes, B.K., Martin, N.G. et al. Bias, precision and heritability of self-reported and clinically measured height in Australian twins Hum. Genet., 120 (2006),pp. 571-580
[11]	Perola, M. Genome-wide association approaches for identifying loci for human height genes Best Pract. Res. Clin. Endocrinol. Metab., 25 (2011),pp. 19-23
[12]	Raine, E.V., Dodd, A.W., Reynard, L.N. et al. BMC Musculoskelet. Disord., 14 (2013),pp. 1471-2474
[13]	Richards, A.J., McNinch, A., Whittaker, J. et al. Eur. J. Hum. Genet., 20 (2012),pp. 552-558
[14]	Sanna, S., Jackson, A.U., Nagaraja, R. et al. Common variants in the GDF5-UQCC region are associated with variation in human height Nat. Genet., 40 (2008),pp. 198-203
[15]	Snead, M.P., Yates, J.R. Clinical and molecular genetics of Stickler syndrome J. Med. Genet., 36 (1999),pp. 353-359
[16]	Tang, H., Jin, X., Li, Y. et al. A large-scale screen for coding variants predisposing to psoriasis Nat. Genet., 46 (2014),pp. 45-50
[17]	Tetens, J., Widmann, P., Kuhn, C. et al. Anim. Genet., 44 (2013),pp. 467-471
[18]	Weedon, M.N., Frayling, T.M. Reaching new heights: insights into the genetics of human stature Trends Genet., 24 (2008),pp. 595-603
[19]	Weedon, M.N., Lettre, G., Freathy, R.M. et al. Nat. Genet., 39 (2007),pp. 1245-1250
[20]	Wood, A.R., Esko, T., Yang, J. et al. Defining the role of common variation in the genomic and biological architecture of adult human height Nat. Genet., 46 (2014),pp. 1173-1186

Relative Articles

[1]	Weiwei Chen, Wenjun Wang, Liang Yong, Qi Zhen, Yafen Yu, Huiyao Ge, Yiwen Mao, Lu Cao, Ruixue Zhang, Xia Hu, Zhuo Li, Yirui Wang, Wencheng Fan, Qiongqiong Xu, Hui Zhang, Shirui Chen, Jing Wu, Liangdan Sun. Genome-wide meta-analysis identifies ten new psoriasis susceptibility loci in the Chinese population[J]. Journal of Genetics and Genomics, 2022, 49(2): 177-180. doi: 10.1016/j.jgg.2021.10.001
[2]	Bao Li, Liang Yong, Yafen Yu, Yanqin Yu, Qi Zhen, Huiyao Ge, Yiwen Mao, Weiwei Chen, Yanxia Yu, Yirui Wang, Zhuo Li, Wencheng Fan, Chang Zhang, Xia Hu, Ruixue Zhang, Lu Cao, Hao Liu, Zhuan Bian, Miao He, Liangdan Sun. Genome-wide analyses of nonsyndromic cleft lip with or without palate identify 20 new risk loci in the Chinese Han population[J]. Journal of Genetics and Genomics, 2022, 49(9): 903-905. doi: 10.1016/j.jgg.2022.02.004
[3]	Yin Huang, Dan Li, Lu Qiao, Yu Liu, Qianqian Peng, Sijie Wu, Manfei Zhang, Yajun Yang, Jingze Tan, Shuhua Xu, Li Jin, Sijia Wang, Kun Tang, Stefan Grünewald. A genome-wide association study of facial morphology identifies novel genetic loci in Han Chinese[J]. Journal of Genetics and Genomics, 2021, 48(3): 198-207. doi: 10.1016/j.jgg.2020.10.004
[4]	Meng Hao, Weilin Pu, Yi Li, Shaoqing Wen, Chang Sun, Yanyun Ma, Hongxiang Zheng, Xingdong Chen, Jingze Tan, Guoqing Zhang, Menghan Zhang, Shuhua Xu, Yi Wang, Hui Li, Jiucun Wang, Li Jin. The HuaBiao project: whole-exome sequencing of 5000 Han Chinese individuals[J]. Journal of Genetics and Genomics, 2021, 48(11): 1032-1035. doi: 10.1016/j.jgg.2021.07.013
[5]	Weihua Shou, Chenhui Zhang, Jinxiu Shi, Hong Wu, Wei Huang. Fine genetic mapping of the chromosome 11q23.3 region in a Han Chinese population: insights into the apolipoprotein genes underlying the blood lipid-lipoprotein variances[J]. Journal of Genetics and Genomics, 2020, 47(12): 756-769. doi: 10.1016/j.jgg.2020.11.010
[6]	Kaiqin Li, Yifan Li, Junyang Wang, Yongxia Huo, Di Huang, Shiwu Li, Jiewei Liu, Xiaoyan Li, Rong Liu, Xiaogang Chen, Yong-Gang Yao, Ceshi Chen, Xiao Xiao, Ming Li, Xiong-Jian Luo. A functional missense variant in ITIH3 affects protein expression and neurodevelopment and confers schizophrenia risk in the Han Chinese population[J]. Journal of Genetics and Genomics, 2020, 47(5): 233-248. doi: 10.1016/j.jgg.2020.04.001
[7]	Cheng Zhang, Jianqi Lu, Haiyi Lou, Renqian Du, Shuhua Xu, Yiping Shen, Feng Zhang, Li Jin. CNVbase: Batch identification of novel and rare copy number variations based on multi-ethnic population data[J]. Journal of Genetics and Genomics, 2017, 44(7): 367-370. doi: 10.1016/j.jgg.2017.07.001
[8]	Wen Zhang, Jinsong Tang, A-Mei Zhang, Min-Sheng Peng, Hai-Bing Xie, Liwen Tan, Lin Xu, Ya-Ping Zhang, Xiaogang Chen, Yong-Gang Yao. A Matrilineal Genetic Legacy from the Last Glacial Maximum Confers Susceptibility to Schizophrenia in Han Chinese[J]. Journal of Genetics and Genomics, 2014, 41(7): 397-407. doi: 10.1016/j.jgg.2014.05.004
[9]	Ping Fang, Jin-Fei Lin, Hong-Chao Pan, Yan-Qin Shen, Melitta Schachner. A Surgery Protocol for Adult Zebrafish Spinal Cord Injury[J]. Journal of Genetics and Genomics, 2012, 39(9): 481-487. doi: 10.1016/j.jgg.2012.07.010
[10]	Hou-Feng Zheng, Martin Ladouceur, Celia M.T. Greenwood, J. Brent Richards. Effect of Genome-Wide Genotyping and Reference Panels on Rare Variants Imputation[J]. Journal of Genetics and Genomics, 2012, 39(10): 545-550. doi: 10.1016/j.jgg.2012.07.002
[11]	Zhao Wu, Hui Li, Lingjun Rao, Lixiazi He, Lei Bao, Jing Liao, Chun Cui, Zhenyu Zuo, Qiao Li, Huimin Dai, Lei Qian, Qing Tian, Lei Xiao, Xiaojun Tan. Derivation and characterization of human embryonic stem cell lines from the Chinese population[J]. Journal of Genetics and Genomics, 2011, 38(1): 13-20. doi: 10.1016/j.jcg.2010.12.006
[12]	Yueying Li, Jing He, Fengchao Wang, Zhenyu Ju, Sheng Liu, Yu Zhang, Zhaohui Kou, Yanfeng Liu, Tao Cheng, Shaorong Gao. Differentiation of embryonic stem cells in adult bone marrow[J]. Journal of Genetics and Genomics, 2010, 37(7): 431-439. doi: 10.1016/S1673-8527(09)60062-X
[13]	Xi Li, Lijun Tan, Xiaogang Liu, Shufeng Lei, Tielin Yang, Xiangding Chen, Fang Zhang, Yue Fang, Yan Guo, Liang Zhang, Han Yan, Feng Pan, Zhixin Zhang, Yumei Peng, Qi Zhou, Lina He, Xuezhen Zhu, Jing Cheng, Lishu Zhang, Yaozhong Liu, Qing Tian, Hongwen Deng. A genome wide association study between copy number variation (CNV) and human height in Chinese population[J]. Journal of Genetics and Genomics, 2010, 37(12): 779-785. doi: 10.1016/S1673-8527(09)60095-3
[14]	Yabing Wang, Di Zhang, Yun Liu, Yifeng Yang, Teng Zhao, Jie Xu, Sheng Li, Zuofeng Zhang, Guoyin Feng, Lin He, He Xu. Association study of the single nucleotide polymorphisms in adiponectin-associated genes with type 2 diabetes in Han Chinese[J]. Journal of Genetics and Genomics, 2009, 36(7): 417-423. doi: 10.1016/S1673-8527(08)60131-9
[15]	Yu Ding, Yongyan Li, Junyan You, Li Yang, Bobei Chen, Jianxin Lu, Min-Xin Guan. Mitochondrial tRNAGlu A14693G variant may modulate the phenotypic manifestation of deafness-associated 12S rRNA A1555G mutation in a Han Chinese family[J]. Journal of Genetics and Genomics, 2009, 36(4): 241-250. doi: 10.1016/S1673-8527(08)60111-3
[16]	Guixiang Zhang, Weisheng Chen, Ming Xue, Zhigang Wang, Hong Chang, Xu Han, Xinjun Liao, Donglei Wang. Analysis of genetic diversity and population structure of Chinese yak breeds (Bos grunniens) using microsatellite markers[J]. Journal of Genetics and Genomics, 2008, 35(4): 233-238. doi: 10.1016/S1673-8527(08)60032-6
[17]	Yumei Chang, Liqun Liang, Haitao Ma, Jianguo He, Xiaowen Sun. Microsatellite analysis of genetic diversity and population structure of Chinese mitten crab (Eriocheir sinensis)[J]. Journal of Genetics and Genomics, 2008, 35(3): 171-176. doi: 10.1016/S1673-8527(08)60023-5
[18]	Kunpu Zhang, Jichun Tian, Liang Zhao, Shanshan Wang. Mapping QTLs with epistatic effects and QTL × environment interactions for plant height using a doubled haploid population in cultivated wheat[J]. Journal of Genetics and Genomics, 2008, 35(2): 119-127. doi: 10.1016/S1673-8527(08)60017-X
[19]	Hongyi Li, Shu Meng, Zheng Chen, Haifei Li, Minlian Du, Huamei Ma, Haiyun Wei, Honglei Duan, Hui Zheng, Qing Wenren, Xinming Song. Molecular Genetic Diagnostics of Prader-Willi Syndrome: a Validation of Linkage Analysis for the Chinese Population[J]. Journal of Genetics and Genomics, 2007, 34(10): 885-891. doi: 10.1016/S1673-8527(07)60100-3
[20]	Zhaohe Yuan, Yanlei Yin, Jianlu Qu, Liqin Zhu, Yun Li. Population Genetic Diversity in Chinese Pomegranate (Punica granatum L.) Cultivars Revealed by Fluorescent-AFLP Markers[J]. Journal of Genetics and Genomics, 2007, 34(12): 1061-1071. doi: 10.1016/S1673-8527(07)60121-0