Osteoporosis International

, Volume 21, Issue 4, pp 579–587 | Cite as

Genome-wide copy number variation association study suggested VPS13B gene for osteoporosis in Caucasians

  • F.-Y. Deng
  • L.-J. Zhao
  • Y.-F. Pei
  • B.-Y. Sha
  • X.-G. Liu
  • H. Yan
  • L. Wang
  • T.-L. Yang
  • R. R. Recker
  • C. J. Papasian
  • H.-W. DengEmail author
Original Article



Osteoporotic fracture (OF) is a serious outcome of osteoporosis. Important risk factors for OF include reduced bone mineral density and unstable bone structure. This genome-wide copy number variation association study suggested VPS13B gene for osteoporosis in Caucasians.


Bone mineral density (BMD) and femoral neck cross-sectional geometric parameters (FNCSGPs) are under strong genetic control. DNA copy number variation (CNV) is an important source of genetic diversity for human diseases. This study aims to identify CNVs associated with BMD and FNCSGPs.


Genome-wide CNV association analyses were conducted in 1,000 unrelated Caucasian subjects for BMD at the spine, hip, femoral neck, and for three FNCSGPs —cortical thickness (CT), cross-section area (CSA), and buckling ratio (BR). BMD was measured by dual energy X-ray absorptiometry (DEXA). CT, CSA, and BR were estimated using DEXA measurements. Affymetrix 500K arrays and copy number analysis tool was used to identify CNVs.


A CNV in VPS13B gene was significantly associated with spine, hip and FN BMDs, and CT, CSA, and BR (p < 0.05). Compared to subjects with two copies of the CNV, carriers of one copy had an average of 14.6%, 12.4%, and 13.6% higher spine, hip, and FN BMD, 20.0% thicker CT, 10.6% larger CSA, and 12.4% lower BR. Thus, a decrease of the CNV consistently produced stronger bone, thereby reducing osteoporotic fracture risk.


VPS13B gene, via affecting BMD and FNCSGPs, is a novel osteoporosis risk gene.


Bone geometry Bone mineral density Copy number variation Osteoporosis 



We thank Dr. Tian-Bo Jin for help in CNV and CNVR determination. Investigators of this work were partially supported by grants from NIH (R01 AR050496-01, R21 AG027110, R01 AG026564, R21 AA015973, and P50 AR055081), the Cancer and Smoking Disease Research Bone Biology Program, and Nebraska tobacco settlement biomedical research development award, both supported by the State of Nebraska. The study also benefited from grants from National Science Foundation of China, Huo Ying Dong Education Foundation, Xi’an Jiaotong University, and the Ministry of Education of China.

Conflicts of interest


Supplementary material

198_2009_998_MOESM1_ESM.doc (48 kb)
Supplement 1 Illustration of the relationship among SNPs, CNVs, CNVRs, and CNV subregions. Briefly, CNVs detected are marked and bounded by Affymetrix 500K SNPs, and they vary not only in copy numbers but also in length, so the variant unit’s sequence coverage may differ between subjects. Along a specific chromosome, the length of each variant unit in a certain subject was determined by the corresponding sequentially located SNPs’ signal intensity changes against reference signals; a longer or shorter variant unit (involving more or less SNPs for different subjects) could be recognized and called (reported) by software CNAT; calls 1, 2, 3, 4 represent variant units for four random subjects. CNVRs represent genomic regions covering overlapping CNVs; in this study, complex CNVRs, which contains CNVs with inconsistent boundaries, were divided into several CNV subregions. Subregions defined thereby have the same conservative boundary among subjects. (DOC 47 kb)
198_2009_998_MOESM2_ESM.xls (152 kb)
Supplement 2 Information of 243 CNV subregions. A total of 243 CNV IDs were assigned. Since the exact boundaries of CNVs cannot be obtained from data produced by the Affymetrix 500K SNP genotyping platform, they are approximated by physical positions (NCBI Build 36.1, March 2006) of the probe pairs having the maximal distance within a CNV, yielding conservatively shorter defined sizes of CNVs than the actual sizes. In the sheet “CNV Subregions”, the Start and End Physical Position is for the approximate boundary probe pairs. A length of “–” means that the CNV subregion was assigned by only one Probe Set; thus, the length was undefined. “Number with CNV Loss”, “Number with Normal CNV”, and “Number with CNV Gain” are the number of individuals carrying the specific CN state among the 985 Caucasian subjects. “CNV Frequency” is the percentage of subjects who do not have a normal CNV among the Caucasian sample. “Associated Gene” shows genes overlapped with the CNV. In the sheet “Probe Sets”, we list the sequential probe sets on Affymetrix 500K SNPs arrays within the corresponding CNVs. (XLS 152 kb)
198_2009_998_MOESM3_ESM.xls (39 kb)
Supplement 3 CNV associations with BMD and FNCSGPs. All nominal significant associations (p < 0.05) between CNV and BMD or FNCSGPs across the whole genome are presented. p values less than 0.01 are italicized. (XLS 39 kb)


  1. 1.
    Ray NF, Chan JK, Thamer M, Melton LJ 3rd (1997) Medical expenditures for the treatment of osteoporotic fractures in the United States in 1995: report from the National Osteoporosis Foundation. J Bone Miner Res 12:24–35CrossRefPubMedGoogle Scholar
  2. 2.
    Cummings SR, Black D (1995) Bone mass measurements and risk of fracture in Caucasian women: a review of findings from prospective studies. Am J Med 98:24S–28SCrossRefPubMedGoogle Scholar
  3. 3.
    Liu YJ, Shen H, Xiao P, Xiong DH, Li LH, Recker RR, Deng HW (2006) Molecular genetic studies of gene identification for osteoporosis: a 2004 update. J Bone Miner Res 21:1511–1535CrossRefPubMedGoogle Scholar
  4. 4.
    Cauley JA, Thompson DE, Ensrud KC, Scott JC, Black D (2000) Risk of mortality following clinical fractures. Osteoporos Int 11:556–561CrossRefPubMedGoogle Scholar
  5. 5.
    Fleurence RL, Iglesias CP, Torgerson DJ (2006) Economic evaluations of interventions for the prevention and treatment of osteoporosis: a structured review of the literature. Osteoporos Int 17:29–40CrossRefPubMedGoogle Scholar
  6. 6.
    Wehren LE, Magaziner J (2003) Hip fracture: risk factors and outcomes. Curr Osteoporos Rep 1:78–85CrossRefPubMedGoogle Scholar
  7. 7.
    Cheng XG, Lowet G, Boonen S, Nicholson PH, Brys P, Nijs J, Dequeker J (1997) Assessment of the strength of proximal femur in vitro: relationship to femoral bone mineral density and femoral geometry. Bone 20:213–218CrossRefPubMedGoogle Scholar
  8. 8.
    Ammann P, Rizzoli R (2003) Bone strength and its determinants. Osteoporos Int 14(Suppl 3):S13–S18PubMedGoogle Scholar
  9. 9.
    Pulkkinen P, Partanen J, Jalovaara P, Jamsa T (2004) Combination of bone mineral density and upper femur geometry improves the prediction of hip fracture. Osteoporos Int 15:274–280CrossRefPubMedGoogle Scholar
  10. 10.
    Shen H, Long JR, Xiong DH, Liu YJ, Liu YZ, Xiao P, Zhao LJ, Dvornyk V, Zhang YY, Rocha-Sanchez S, Liu PY, Li JL, Deng HW (2005) Mapping quantitative trait loci for cross-sectional geometry at the femoral neck. J Bone Miner Res 20:1973–1982CrossRefPubMedGoogle Scholar
  11. 11.
    Slemenda CW, Turner CH, Peacock M, Christian JC, Sorbel J, Hui SL, Johnston CC (1996) The genetics of proximal femur geometry, distribution of bone mass and bone mineral density. Osteoporos Int 6:178–182CrossRefPubMedGoogle Scholar
  12. 12.
    Demissie S, Dupuis J, Cupples LA, Beck TJ, Kiel DP, Karasik D (2007) Proximal hip geometry is linked to several chromosomal regions: genome-wide linkage results from the Framingham Osteoporosis Study. Bone 40:743–750CrossRefPubMedGoogle Scholar
  13. 13.
    Moffett SP, Zmuda JM, Oakley JI, Beck TJ, Cauley JA, Stone KL, Lui LY, Ensrud KE, Hillier TA, Hochberg MC, Morin P, Peltz G, Greene D, Cummings SR (2005) Tumor necrosis factor-alpha polymorphism, bone strength phenotypes, and the risk of fracture in older women. J Clin Endocrinol Metab 90:3491–3497CrossRefPubMedGoogle Scholar
  14. 14.
    Rivadeneira F, Houwing-Duistermaat JJ, Beck TJ, Janssen JA, Hofman A, Pols HA, Van Duijn CM, Uitterlinden AG (2004) The influence of an insulin-like growth factor I gene promoter polymorphism on hip bone geometry and the risk of nonvertebral fracture in the elderly: the Rotterdam Study. J Bone Miner Res 19:1280–1290CrossRefPubMedGoogle Scholar
  15. 15.
    Feuk L, Carson AR, Scherer SW (2006) Structural variation in the human genome. Nat Rev Genet 7:85–97CrossRefPubMedGoogle Scholar
  16. 16.
    Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME (2006) Global variation in copy number in the human genome. Nature 444:444–454CrossRefPubMedGoogle Scholar
  17. 17.
    Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavare S, Deloukas P, Hurles ME, Dermitzakis ET (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315:848–853CrossRefPubMedGoogle Scholar
  18. 18.
    Aitman TJ, Dong R, Vyse TJ, Norsworthy PJ, Johnson MD, Smith J, Mangion J, Roberton-Lowe C, Marshall AJ, Petretto E, Hodges MD, Bhangal G, Patel SG, Sheehan-Rooney K, Duda M, Cook PR, Evans DJ, Domin J, Flint J, Boyle JJ, Pusey CD, Cook HT (2006) Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 439:851–855CrossRefPubMedGoogle Scholar
  19. 19.
    Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, Nibbs RJ, Freedman BI, Quinones MP, Bamshad MJ, Murthy KK, Rovin BH, Bradley W, Clark RA, Anderson SA, O’Connell RJ, Agan BK, Ahuja SS, Bologna R, Sen L, Dolan MJ, Ahuja SK (2005) The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science (New York NY) 307:1434–1440Google Scholar
  20. 20.
    Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R, Lee YH, Hicks J, Spence SJ, Lee AT, Puura K, Lehtimaki T, Ledbetter D, Gregersen PK, Bregman J, Sutcliffe JS, Jobanputra V, Chung W, Warburton D, King MC, Skuse D, Geschwind DH, Gilliam TC, Ye K, Wigler M (2007) Strong association of de novo copy number mutations with autism. Science (New York NY) 316:445–449Google Scholar
  21. 21.
    Yang TL, Chen XD, Guo Y, Lei SF, Wang JT, Zhou Q, Pan F, Chen Y, Zhang ZX, Dong SS, Xu XH, Yan H, Liu X, Qiu C, Zhu XZ, Chen T, Li M, Zhang H, Zhang L, Drees BM, Hamilton JJ, Papasian CJ, Recker RR, Song XP, Cheng J, Deng HW (2008) Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis. Am J Hum Genet 83:663–674CrossRefPubMedGoogle Scholar
  22. 22.
    Duan Y, Beck TJ, Wang XF, Seeman E (2003) Structural and biomechanical basis of sexual dimorphism in femoral neck fragility has its origins in growth and aging. J Bone Miner Res 18:1766–1774CrossRefPubMedGoogle Scholar
  23. 23.
    Beck TJ (2003) Measuring the structural strength of bones with dual-energy X-ray absorptiometry: principles, technical limitations, and future possibilities. Osteoporos Int 14:S81–S88CrossRefPubMedGoogle Scholar
  24. 24.
    Rabbee N, Speed TP (2006) A genotype calling algorithm for Affymetrix SNP arrays. Bioinformatics 22:7–12CrossRefPubMedGoogle Scholar
  25. 25.
    Di X, Matsuzaki H, Webster TA, Hubbell E, Liu G, Dong S, Bartell D, Huang J, Chiles R, Yang G, Shen MM, Kulp D, Kennedy GC, Mei R, Jones KW, Cawley S (2005) Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays. Bioinformatics 21:1958–1963CrossRefPubMedGoogle Scholar
  26. 26.
    Sun X, Lei SF, Deng FY, Wu S, Papacian C, Hamilton J, Recker RR, Deng HW (2006) Genetic and environmental correlations between bone geometric parameters and body compositions. Calcif Tissue Int 79:43–49CrossRefPubMedGoogle Scholar
  27. 27.
    Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  28. 28.
    Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55:997–1004CrossRefPubMedGoogle Scholar
  29. 29.
    Filardi S, Zebaze RM, Duan Y, Edmonds J, Beck T, Seeman E (2004) Femoral neck fragility in women has its structural and biomechanical basis established by periosteal modeling during growth and endocortical remodeling during aging. Osteoporos Int 15:103–107CrossRefPubMedGoogle Scholar
  30. 30.
    Beck TJ, Stone KL, Oreskovic TL, Hochberg MC, Nevitt MC, Genant HK, Cummings SR (2001) Effects of current and discontinued estrogen replacement therapy on hip structural geometry: the study of osteoporotic fractures. J Bone Miner Res 16:2103–2110CrossRefPubMedGoogle Scholar
  31. 31.
    Beck TJ, Oreskovic TL, Stone KL, Ruff CB, Ensrud K, Nevitt MC, Genant HK, Cummings SR (2001) Structural adaptation to changing skeletal load in the progression toward hip fragility: the study of osteoporotic fractures. J Bone Miner Res 16:1108–1119CrossRefPubMedGoogle Scholar
  32. 32.
    Velayos-Baeza A, Vettori A, Copley RR, Dobson-Stone C, Monaco AP (2004) Analysis of the human VPS13 gene family. Genomics 84:536–549CrossRefPubMedGoogle Scholar
  33. 33.
    Kolehmainen J, Black GC, Saarinen A, Chandler K, Clayton-Smith J, Traskelin AL, Perveen R, Kivitie-Kallio S, Norio R, Warburg M, Fryns JP, de la Chapelle A, Lehesjoki AE (2003) Cohen syndrome is caused by mutations in a novel gene, COH1, encoding a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport. Am J Hum Genet 72:1359–1369CrossRefPubMedGoogle Scholar
  34. 34.
    Bugiani M, Gyftodimou Y, Tsimpouka P, Lamantea E, Katzaki E, d’Adamo P, Nakou S, Georgoudi N, Grigoriadou M, Tsina E, Kabolis N, Milani D, Pandelia E, Kokotas H, Gasparini P, Giannoulia-Karantana A, Renieri A, Zeviani M, Petersen MB (2008) Cohen syndrome resulting from a novel large intragenic COH1 deletion segregating in an isolated Greek island population. Am J Med Genet 146A:2221–2226CrossRefPubMedGoogle Scholar
  35. 35.
    Kivitie-Kallio S, Norio R (2001) Cohen syndrome: essential features, natural history, and heterogeneity. Am J Med Genet 102:125–135CrossRefPubMedGoogle Scholar
  36. 36.
    Alaluusua S, Kivitie-Kallio S, Wolf J, Haavio ML, Asikainen S, Pirinen S (1997) Periodontal findings in Cohen syndrome with chronic neutropenia. J Periodontol 68:473–478PubMedGoogle Scholar
  37. 37.
    Hennies HC, Rauch A, Seifert W, Schumi C, Moser E, Al-Taji E, Tariverdian G, Chrzanowska KH, Krajewska-Walasek M, Rajab A, Giugliani R, Neumann TE, Eckl KM, Karbasiyan M, Reis A, Horn D (2004) Allelic heterogeneity in the COH1 gene explains clinical variability in Cohen syndrome. Am J Hum Genet 75:138–145CrossRefPubMedGoogle Scholar
  38. 38.
    Katzaki E, Pescucci C, Uliana V, Papa FT, Ariani F, Meloni I, Priolo M, Selicorni A, Milani D, Fischetto R, Celle ME, Grasso R, Dallapiccola B, Brancati F, Bordignon M, Tenconi R, Federico A, Mari F, Renieri A, Longo I (2007) Clinical and molecular characterization of Italian patients affected by Cohen syndrome. J Hum Genet 52:1011–1017CrossRefPubMedGoogle Scholar
  39. 39.
    Kolehmainen J, Wilkinson R, Lehesjoki AE, Chandler K, Kivitie-Kallio S, Clayton-Smith J, Traskelin AL, Waris L, Saarinen A, Khan J, Gross-Tsur V, Traboulsi EI, Warburg M, Fryns JP, Norio R, Black GC, Manson FD (2004) Delineation of Cohen syndrome following a large-scale genotype-phenotype screen. Am J Hum Genet 75:122–127CrossRefPubMedGoogle Scholar
  40. 40.
    Mochida GH, Rajab A, Eyaid W, Lu A, Al-Nouri D, Kosaki K, Noruzinia M, Sarda P, Ishihara J, Bodell A, Apse K, Walsh CA (2004) Broader geographical spectrum of Cohen syndrome due to COH1 mutations. J Med Genet 41:e87CrossRefPubMedGoogle Scholar
  41. 41.
    Seifert W, Holder-Espinasse M, Spranger S, Hoeltzenbein M, Rossier E, Dollfus H, Lacombe D, Verloes A, Chrzanowska KH, Maegawa GH, Chitayat D, Kotzot D, Huhle D, Meinecke P, Albrecht B, Mathijssen I, Leheup B, Raile K, Hennies HC, Horn D (2006) Mutational spectrum of COH1 and clinical heterogeneity in Cohen syndrome. J Med Genet 43:e22CrossRefPubMedGoogle Scholar

Copyright information

© International Osteoporosis Foundation and National Osteoporosis Foundation 2009

Authors and Affiliations

  • F.-Y. Deng
    • 1
  • L.-J. Zhao
    • 2
  • Y.-F. Pei
    • 1
    • 3
  • B.-Y. Sha
    • 4
  • X.-G. Liu
    • 3
  • H. Yan
    • 3
  • L. Wang
    • 3
  • T.-L. Yang
    • 1
  • R. R. Recker
    • 2
  • C. J. Papasian
    • 1
  • H.-W. Deng
    • 1
    • 3
    • 4
    Email author
  1. 1.School of MedicineUniversity of Missouri—Kansas CityKansas CityUSA
  2. 2.Osteoporosis Research CenterCreighton UniversityOmahaUSA
  3. 3.The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and TechnologyXi’an Jiaotong UniversityXi’an, ShannxiPeople’s Republic of China
  4. 4.Laboratory of Molecular and Statistical Genetics, College of Life SciencesHunan Normal UniversityHunanPeople’s Republic of China

Personalised recommendations