Genome-wide Survey of Runs of Homozygosity Identifies Recessive Loci for Bone Mineral Density in Caucasian and Chinese Populations

Journal of Bone and Mineral Research

Volumn 30, Issue 11, 2015, Pages 2119-2126

  Yang, Tie Lin ^a   Guo, Yan ^a   Zhang, Ji Gang ^b   Xu, Chao ^b   Tian, Qing ^b   Deng, Hong Wen ^a  

^a XI'AN JIAOTONG UNIVERSITY   (China)

^b TULANE UNIVERSITY   (United States)

Author keywords

ASSOCIATION; BMD; FRACTURES; ROHs

Indexed keywords

MESSENGER RNA;

ADULT; AGED; ARTICLE; BONE DENSITY; CAUCASIAN; CHINESE; CONTROLLED STUDY; COPY NUMBER VARIATION; EAST ASIAN; FEMALE; FRAGILITY FRACTURE; GENE LOCUS; GENETIC ASSOCIATION; HIP FRACTURE; HOMOZYGOSITY; HUMAN; LYMPHOBLAST; MAJOR CLINICAL STUDY; MALE; MIDDLE AGED; QUANTITATIVE TRAIT LOCUS; RECESSIVE GENE; RUN OF HOMOZYGOSITY; SINGLE NUCLEOTIDE POLYMORPHISM; ASIAN CONTINENTAL ANCESTRY GROUP; GENETIC PREDISPOSITION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HOMOZYGOTE; MOLECULAR GENETICS;

AGED; ASIAN CONTINENTAL ANCESTRY GROUP; BONE DENSITY; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENES, RECESSIVE; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HIP FRACTURES; HOMOZYGOTE; HUMANS; MALE; MIDDLE AGED; MOLECULAR SEQUENCE ANNOTATION; OSTEOPOROTIC FRACTURES; QUANTITATIVE TRAIT LOCI;

EID: 84945442164     PISSN: 08840431     EISSN: 15234681     Source Type: Journal    
DOI: 10.1002/jbmr.2558     Document Type: Article

References (50)

1. Cooper C, Campion G, Melton LJ, 3rd,. Hip fractures in the elderly: a world-wide projection. Osteoporos Int. 1992; 2 (6): 285-9.
2. Gullberg B, Johnell O, Kanis JA., World-wide projections for hip fracture. Osteoporos Int. 1997; 7 (5): 407-13.
3. Johnell O, Kanis JA, Oden A, Johansson H, De Laet C, Delmas P, et al., Predictive value of BMD for hip and other fractures. J Bone Miner Res. 2005; 20 (7): 1185-94.
4. Peacock M, Turner CH, Econs MJ, Foroud T., Genetics of osteoporosis. Endocr Rev. 2002; 23 (3): 303 -26.
5. Michaelsson K, Melhus H, Ferm H, Ahlbom A, Pedersen NL., Genetic liability to fractures in the elderly. Arch Intern Med. 2005; 165 (16): 1825-30.
6. Estrada K, Styrkarsdottir U, Evangelou E, Hsu YH, Duncan EL, Ntzani EE, et al., Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. Nat Genet. 2012; 44 (5): 491-501.
7. Guo Y, Tan LJ, Lei SF, Yang TL, Chen XD, Zhang F, et al., Genome-wide association study identifies ALDH7A1 as a novel susceptibility gene for osteoporosis. PLoS Genet. 2010; 6 (1): e1000806.
8. Guo Y, Zhang LS, Yang TL, Tian Q, Xiong DH, Pei YF, et al., IL21R and PTH may underlie variation of femoral neck bone mineral density as revealed by a genome-wide association study. J Bone Miner Res. 2010; 25 (5): 1042-8.
9. Richards JB, Zheng HF, Spector TD., Genetics of osteoporosis from genome-wide association studies: advances and challenges. Nat Rev Genet. 2012; 13 (8): 576-88.
10. Rivadeneira F, Styrkarsdottir U, Estrada K, Halldorsson BV, Hsu YH, Richards JB, et al., Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. Nat Genet. 2009; 41 (11): 1199-206.
11. Styrkarsdottir U, Halldorsson BV, Gretarsdottir S, Gudbjartsson DF, Walters GB, Ingvarsson T, et al., Multiple genetic loci for bone mineral density and fractures. N Engl J Med. 2008; 358 (22): 2355-65.
12. Styrkarsdottir U, Halldorsson BV, Gretarsdottir S, Gudbjartsson DF, Walters GB, Ingvarsson T, et al., New sequence variants associated with bone mineral density. Nat Genet. 2009; 41 (1): 15-7.
13. Zhang L, Choi HJ, Estrada K, Leo PJ, Li J, Pei YF, et al., Multistage genome-wide association meta-analyses identified two new loci for bone mineral density. Hum Mol Genet. 2014; 23 (7): 1923-33.
14. Li LH, Ho SF, Chen CH, Wei CY, Wong WC, Li LY, et al., Long contiguous stretches of homozygosity in the human genome. Hum Mutat. 2006; 27 (11): 1115-21.
15. Ku CS, Naidoo N, Teo SM, Pawitan Y., Regions of homozygosity and their impact on complex diseases and traits. Hum Genet. 2011; 129 (1): 1-15.
16. Gamsiz ED, Viscidi EW, Frederick AM, Nagpal S, Sanders SJ, Murtha MT, et al., Intellectual disability is associated with increased runs of homozygosity in simplex autism. Am J Hum Genet. 2013; 93 (1): 103-9.
17. Ghani M, Sato C, Lee JH, Reitz C, Moreno D, Mayeux R, et al., Evidence of recessive Alzheimer disease loci in a Caribbean Hispanic data set: genome-wide survey of runs of homozygosity. JAMA Neurol. 2013; 70 (10): 1261-7.
18. Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan TV, Kane JM, et al., Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci U S.A. 2007; 104 (50): 19942-7.
19. Lin PI, Kuo PH, Chen CH, Wu JY, Gau SS, Wu YY, et al., Runs of homozygosity associated with speech delay in autism in a taiwanese han population: evidence for the recessive model. PLoS One. 2013; 8 (8): e72056.
20. Wang C, Xu Z, Jin G, Hu Z, Dai J, Ma H, et al., Genome-wide analysis of runs of homozygosity identifies new susceptibility regions of lung cancer in Han Chinese. J Biomed Res. 2013; 27 (3): 208-14.
21. Yang TL, Guo Y, Zhang LS, Tian Q, Yan H, Papasian CJ, et al., Runs of homozygosity identify a recessive locus 12q21.31 for human adult height. J Clin Endocrinol Metab. 2010; 95 (8): 3777-82.
22. Agueda L, Bustamante M, Jurado S, Garcia-Giralt N, Ciria M, Salo G, et al., A haplotype-based analysis of the LRP5 gene in relation to osteoporosis phenotypes in Spanish postmenopausal women. J Bone Miner Res. 2008; 23 (12): 1954-63.
23. Jin HS, Kim BY, Kim J, Hong KW, Jung SY, Lee YS, et al., Association between the SPRY1 gene polymorphism and obesity-related traits and osteoporosis in Korean women. Mol Genet Metab. 2013; 108 (1): 95-101.
24. Velazquez-Cruz R, Garcia-Ortiz H, Castillejos-Lopez M, Quiterio M, Valdes-Flores M, Orozco L, et al., WNT3A gene polymorphisms are associated with bone mineral density variation in postmenopausal mestizo women of an urban Mexican population: findings of a pathway-based high-density single nucleotide screening. Age (Dordr). 2014; 36 (3): 9635.
25. Yang TL, Chen XD, Guo Y, Lei SF, Wang JT, Zhou Q, et al., Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis. Am J Hum Genet. 2008; 83 (6): 663-74.
26. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al., PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81 (3): 559-75.
27. Yang TL, Guo Y, Shen H, Li J, Glessner JT, Qiu C, et al., Copy number variation on chromosome 10q26.3 for obesity identified by a genome-wide study. J Clin Endocrinol Metab. 2013; 98 (1): E191-5.
28. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D., Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006; 38 (8): 904-9.
29. Yoav B, Yosef H., Controlling the false dicovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B. 1995; 57 (1): 289-300.
30. Lange C, DeMeo DL, Laird NM., Power and design considerations for a general class of family-based association tests: quantitative traits. Am J Hum Genet. 2002; 71 (6): 1330-41.
31. Smemo S, Tena JJ, Kim KH, Gamazon ER, Sakabe NJ, Gomez-Marin C, et al., Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature. 2014; 507 (7492): 371-5.
32. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, et al., Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 2007; 315 (5813): 848-53.
33. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, et al., Population genomics of human gene expression. Nat Genet. 2007; 39 (10): 1217-24.
34. Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, et al., ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 2013; 41 (Database issue): D56-63.
35. Noma K, Allis CD, Grewal SI., Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science. 2001; 293 (5532): 1150-5.
36. Ernst J, Kellis M., Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010; 28 (8): 817-25.
37. McWhirter RE, Thomson RJ, Marthick JR, Rumbold AR, Brown MA, Taylor-Thomson D, et al., Runs of homozygosity and a cluster of vulvar cancer in young Australian Aboriginal women. Gynecol Oncol. 2014; 133 (3): 421-6.
38. Fujikawa Y, Quinn JM, Sabokbar A, McGee JO, Athanasou NA., The human osteoclast precursor circulates in the monocyte fraction. Endocrinology. 1996; 137 (9): 4058-60.
39. Purton LE, Lee MY, Torok-Storb B., Normal human peripheral blood mononuclear cells mobilized with granulocyte colony-stimulating factor have increased osteoclastogenic potential compared to nonmobilized blood. Blood. 1996; 87 (5): 1802-8.
40. Pacifici R., Estrogen, cytokines, and pathogenesis of postmenopausal osteoporosis. J Bone Miner Res. 1996; 11 (8): 1043-51.
41. Nishimura Y, Takiguchi S, Yoshioka K, Nakabeppu Y, Itoh K., Silencing of SNX1 by siRNA stimulates the ligand-induced endocytosis of EGFR and increases EGFR phosphorylation in gefitinib-resistant human lung cancer cell lines. Int J Oncol. 2012; 41 (4): 1520-30.
42. Kurten RC, Cadena DL, Gill GN., Enhanced degradation of EGF receptors by a sorting nexin, SNX1. Science. 1996; 272 (5264): 1008-10.
43. Zhang X, Tamasi J, Lu X, Zhu J, Chen H, Tian X, et al., Epidermal growth factor receptor plays an anabolic role in bone metabolism in vivo. J Bone Miner Res. 2011; 26 (5): 1022-34.
44. Buck L, Axel R., A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell. 1991; 65 (1): 175-87.
45. Maione L, Benadjaoud S, Eloit C, Sinisi AA, Colao A, Chanson P, et al., Computed tomography of the anterior skull base in Kallmann syndrome reveals specific ethmoid bone abnormalities associated with olfactory bulb defects. J Clin Endocrinol Metab. 2013; 98 (3): E537-46.
46. Abe E, Marians RC, Yu W, Wu XB, Ando T, Li Y, et al., TSH is a negative regulator of skeletal remodeling. Cell. 2003; 115 (2): 151-62.
47. Sun L, Vukicevic S, Baliram R, Yang G, Sendak R, McPherson J, et al., Intermittent recombinant TSH injections prevent ovariectomy-induced bone loss. Proc Natl Acad Sci U S.A. 2008; 105 (11): 4289-94.
48. Baliram R, Sun L, Cao J, Li J, Latif R, Huber AK, et al., Hyperthyroid-associated osteoporosis is exacerbated by the loss of TSH signaling. J Clin Invest. 2012; 122 (10): 3737-41.
49. Thakkinstian A, D'Este C, Eisman J, Nguyen T, Attia J., Meta-analysis of molecular association studies: vitamin D receptor gene polymorphisms and BMD as a case study. J Bone Miner Res. 2004; 19 (3): 419-28.
50. Purcell S, Cherny SS, Sham PC,. Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics. 2003; 19 (1): 149-50.