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- 2019-10-11 (2)
- 2019-10-11 (1)
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Keywords
Asociación genética
población
haplotipo
ancestría genética
susceptibilidad genética genetic association study
SNPs
population
haplotype
genetic ancestry
genetic susceptibility
población
haplotipo
ancestría genética
susceptibilidad genética genetic association study
SNPs
population
haplotype
genetic ancestry
genetic susceptibility
How to Cite
Criollo-Rayo, A., Bohórquez, M. E., Lott, P., Carracedo, A., Tomlinson, I., CHIBCHA, C., Carvajal, L., & Echeverry, M. (2019). Study of the relationship between genetic ancestry and colorrectal cáncer risk in Colombia. REVISTA DE LA ASOCIACION COLOMBIANA DE CIENCIAS BIOLOGICAS, 1(31), 61–72. https://doi.org/10.47499/revistaaccb.v1i31.183
Abstract
Introduction: Colorectal cancer is a public health burden in the world and Colombia. Recent genome wide association studies have identifi ed chromosomal regions associated with the disease, depicting variable risk between populations, owing to the demographic history and genetic ancestry. Objective: We aimed to study the colorectal cancer risk in Colombia provided for 20 genetic markers, by using 955 cases and 972 controls from the CHIBCHA consortium, in the context of global and local genetic ancestry.Methodology: The samples were genotyped using Axyom Affymetrix LAT and CUSTOME array in order to obtain the global genome genotypes including 20 risk SNPs. Statistical analysis was performed in PLINK (associations), ADMIXTURE (global ancestry), Elai
(local ancestry) and R language (logistic models). Results: Eleven chromosomal regions were associated with ORs ranging between 1.14-1.41 (p<0.05): 18q21.1, 19q13.11, 10p14, 14q.2.2, 20p12.3, 8q23.3, 6p21.2, 15q13.3 y 8q24.21. On average, a higher global European ancestry was associated with colorectal cancer risk (OR=3.016, IC 95%:1.162-7.894, p=0.00325). At the local chromosomal level two regions presented a signifi cant increment of European ancestry 6q23.2 (OR adjusted=1.378, CI95%: 1.202-1.580, p adjusted =4.2e-6) and 4p13 (OR adjusted=1.301, CI95%:1.137-1.489; p adjusted =0.00013). Conclusions: Genetic ancestry can be considered as a relevant factor for the colorectal cancer susceptibility in Colombia. Both Native American and European ancestry are accounting for the most part of population structure in the sample we studied, which could explain the differences for the colorectal cancer incidence between Latin American and European populations.
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26. Guan Y. (2014) Detecting Structure of Haplotypes and Local Ancestry. Genetics. 196(3): 625-642.
---------------------------------------------------------------------------------------------------
27. Bohórquez M, Sahasrabudhe R, Criollo A, Sanabria-Salas MC, Vélez A, Castro JM, et al. (2016) Clinical manifestations of colorectal cancer patients from a large multicenter study in Colombia. Medicine. 95(40): e4883.
---------------------------------------------------------------------------------------------------
28. Risch N, Merikangas k. (1999) The Future of Genetic Studies of Complex Human Diseases. Science. 273:1516-7.
---------------------------------------------------------------------------------------------------
29. Perdue DG, Haverkamp D, Perkins C, Daley CM, Provost E. (2014) Geographic variation in colorectalcancer incidence and mortality, age of onset, and stage at diagnosis among american indian and Alaska native people, 1990–2009. Am J Public Health. 104(Suppl 3): S404-S14.
---------------------------------------------------------------------------------------------------
30. Webster PC. (2012) Health in Colombia: a system in crisis. Can Med Assoc J. 184(6): E289-E90.
---------------------------------------------------------------------------------------------------
31. Moore SP, Forman D, Piñeros M, Fernández SM, Oliveira Santos M, Bray F. (2014) Cancer in indigenous people in Latin America and the Caribbean: a review. Cancer Med. 3(1):70-80.
---------------------------------------------------------------------------------------------------
32. Center for Disease Control and Prevention. (2016) Colorectal cancer rates by race and ethnicity: division of cancer prevention and control, Centers for Disease Control and Prevention. [updated 16-junio-2016]. Available from: https://http://www.cdc.gov/cancer/colorectal/statistics/race.htm.
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33. Cobb N, Paisano RE. (1998) Patterns of cancer mortality among Native Americans. Cancer. 83(11):2377-83.
---------------------------------------------------------------------------------------------------
34. Sandoval-Castaño EA. (2016) Perfi l de Salud de la Población Indígena, y Perfi l de salud de la población indígena, y medición de desigualdades en salud. Colombia 2016. Bogotá: Ministerio de Salud y Protección Social. Producto desarrollado en el marco del contrato No. 074 de 2016.
---------------------------------------------------------------------------------------------------
35. Fortini BK, Tring S, Plummer SJ, Edlund CK, Moreno V, Bresalier RS, et al. (2014) Multiple functional risk variants in a SMAD7 enhancer implicate a colorectal cancer risk haplotype. PLoS One. 9(11):e111914.
---------------------------------------------------------------------------------------------------
36. Study, C. O. G. E. N. T. (2008) Meta-analysis of genome-wide association data identifi es four new susceptibility loci for colorectal cancer. Nat Genet. 40 (12):1426-35.
---------------------------------------------------------------------------------------------------
37. Chang Y-WE, Marlin JW, Chance TW, Jakobi R. (2006) RhoA mediates cyclooxygenase-2 signaling to disrupt the formation of adherens junctions and increase cell motility. Cancer Res. 66(24):11700-8.
---------------------------------------------------------------------------------------------------
38. Okamoto H, Yasui K, Zhao C, Arii S, Inazawa J. (2003) PTK2 and EIF3S3 genes may be amplifi cation targets at 8q23-q24 and are associated with large hepatocellular carcinomas. Hepatology. 38(5):1242-9.
---------------------------------------------------------------------------------------------------
39. Liu WM, Maraia RJ, Rubin CM, Schmid CW. (1994) Alu transcripts: cytoplasmic localisation and regulation by DNA methylation. Nucleic Acids Res. 22(6):1087-95.
---------------------------------------------------------------------------------------------------
40. Zhu M, Chen X, Zhang H, Xiao N, Zhu C, He Q, et al. (2011) AluYb8 Insertion in the MUTYH Gene and risk of early-onset breast and gastric cancers in the Chinese population. Asian Pac J Cancer Prev. 12(6):1451-5.
---------------------------------------------------------------------------------------------------
41. Borun P, De Rosa M, Nedoszytko B, Walkowiak J, Plawski A. (2015) Specifi c Alu elements involved in a signifi cant percentage of copy number variations of the STK11 gene in patients with Peutz-Jeghers syndrome. Fam Cancer. 14(3):455-61.
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42. Xiao-Jie L, Ai-Mei G, Li-Juan J, Jiang X. (2015) Pseudogene in cancer: real functions and promising signature. J Med Genet. 52(1):17-24.
---------------------------------------------------------------------------------------------------
43. Lanier MH, McConnell P, Cooper JA. (2016) Cell migration and invadopodia formation require a membrane-binding domain of CARMIL2. J Biol Chem. 291(3):1076-91.
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44. Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, et al. (2011) New gene functions in megakaryopoiesis and platelet formation. Nature. 480(7376):201-208.
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45. Bai Y, Sun Y, Peng J, Liao H, Gao H, Guo Y, et al. (2014) Overexpression of secretagogin inhibits cell apoptosis and induces chemoresistance in small cell lung cancer under the regulation of miR-494. Oncotarget. 5(17):7760-75.
---------------------------------------------------------------------------------------------------
46. Fagerberg L, Hallström BM, Oksvold P, Kampf C, Djureinovic D, Odeberg J, et al. (2014) Analysis of the human tissue-specifi c expression by genome-wide integration of transcriptomics and antibody based proteomics. Proteomics. Mol Cel Prot: 13(2):397-406.
---------------------------------------------------------------------------------------------------
47. Wu M, Lu W, Santos RE, Frattini MG, Kelly TJ. (2014) Geminin inhibits a late step in the formation of human pre-replicative complexes. J Biol Chem. 289(44):30810-21.
---------------------------------------------------------------------------------------------------
48. Kushwaha PP, Rapalli KC, Kumar S. (2016) Geminin a multi task protein involved in cancer pathophysiology and developmental process: A review. Biochimie. 131:115-27.
---------------------------------------------------------------------------------------------------
49. Nishihara K, Shomori K, Tamura T, Fujioka S, Ogawa T, Ito H. (2009) Immunohistochemical expression of geminin in colorectal cancer: Implication of prognostic signifi cance. Oncol Rep. 21:1189-95.
---------------------------------------------------------------------------------------------------
50. Furushima K, Yamamoto A, Nagano T, Shibata M, Miyachi H, Abe T, et al. (2007) Mouse homologues of Shisa antagonistic to Wnt and Fgf signalings. Dev Biol. 306(2):480-92.
---------------------------------------------------------------------------------------------------
51. Chun-Chieh C, Hsuan-Yu C, Kang-Yi S, Qi-Sheng H, Bo-Shiun Y, Ching-Hsien C, et al. (2014) Shisa3 is associated with prolonged survival through promoting β-catenin degradation in lung cancer. Am J Respir Crit Care Med. 190(4):433-44.
---------------------------------------------------------------------------------------------------
52. Kim BM, Mao J, Taketo MM, Shivdasani RA. (2007) Phases of canonical Wnt signaling during the development of mouse intestinal epithelium. Gastroenterology. 33(2):529-38.
---------------------------------------------------------------------------------------------------
53. Dong W, Yao C, Teng X, Chai J, Yang X, Li B. (2016) MiR-140-3p suppressed cell growth and invasion by downregulating the expression of ATP8A1 in non-small cell lung cancer. Tumor Biol. 37(3):2973-85.
---------------------------------------------------------------------------------------------------
54. Kato U, Inadome H, Yamamoto M, Emoto K, Kobayashi T, Umeda M. (2013) Role for Phospholipid Flippase Complex of ATP8A1 and CDC50A proteins in cell migration. J Biol Chem. 288(7):4922-34.Rev.
---------------------------------------------------------------------------------------------------
2. Kriza C, Emmert M, Wahlster P, Niederländer C, Kolominsky-Rabas P. (2013) Cost of illness in colorectal cancer: An international review. Pharmacoeconomics. 31(7):577-88.
---------------------------------------------------------------------------------------------------
3. Soerjomataram I, Lortet-Tieulent J, Parkin DM, Ferlay J, Mathers C, Forman D, et al. (2012) Global burden of cancer in 2008: a systematic analysis of disability-adjusted life-years in 12 world regions. Lancet. 380(9856):1840-50.
---------------------------------------------------------------------------------------------------
4. Burt RW, Barthel JS, Dunn KB, David DS, Drelichman E, Ford JM, et al. (2010) Colorectal cancer screening. J Natl Compr Canc Netw.8(1):8-61.
---------------------------------------------------------------------------------------------------
5. Davies RJ, Miller R, Coleman N. (2005) Colorectal cancer screening: prospects for molecular stool analysis. Nat Rev Cancer. 5(3):199-209.
---------------------------------------------------------------------------------------------------
6. Costi R, Leonardi F, Zanoni D, Violi V, Roncoroni L. (2014) Palliative care and end-stage colorectal cancer management: The surgeon meets the oncologist. World J Gastroent: 20(24):7602-21.
---------------------------------------------------------------------------------------------------
7. Global Burden of Disease Cancer C. (2015) The Global Burden of Cancer 2013. JAMA oncology. 1(4):505-27.
---------------------------------------------------------------------------------------------------
8. Center MM, Jemal A, Smith RA, Ward E. (2009) Worldwide variations in colorectal cancer. CA CancerJ Clin. 59(6):366-78.
---------------------------------------------------------------------------------------------------
9. Bray F, Piñeros M. (2016) Cancer patterns, trends and projections in Latin America and the Caribbean: a global context. Salud Pub Mex. 58(2):104-17.
---------------------------------------------------------------------------------------------------
10. Curado MP, de Souza DLB. (2014) Cancer Burden in Latin America and the Caribbean. Ann Glob Health. 80(5):370-7.
---------------------------------------------------------------------------------------------------
11. Arnold M, Sierra MS, Laversanne M, Soerjomataram I, Jemal A, Bray F. (2016) Global patterns and trends in colorectal cancer incidence and mortality. Gut. 66(4): 683-91.
---------------------------------------------------------------------------------------------------
12. Piñeros M, Gamboa O, Hernández-Suárez G, Pardo C, Bray F. (2013) Patterns and trends in cancer mortality in Colombia 1984–2008. Cancer Epidemiol. 37(3):233-9.
---------------------------------------------------------------------------------------------------
13. Ramírez R, Agredo RA. (2012) El sedentarismo es un factor predictor de hipertrigliceridemia, obesidad central y sobrepeso. Rev Colomb Cardiol. 19:75-9.
---------------------------------------------------------------------------------------------------
14. Peters U, Bien S, Zubair N. (2015) Genetic Architecture of Colorectal Cancer. Gut. 64(10):1623-36.
---------------------------------------------------------------------------------------------------
15. Jobling M, Hollox E, Hurles M, Kivisild T, Tyler-Smith C. (2014) Human evolutionary genetics. 2 ed. New York-USA: Garland Science, Taylor & Francis Group, LLC. 670 p
---------------------------------------------------------------------------------------------------.
16. Shriner D. (2013) Overview of Admixture Mapping. Current protocols in human genetics / editorial board, Jonathan L Haines [et al]. CHAPTER: Unit1.23-Unit1.
---------------------------------------------------------------------------------------------------
17. Browning SR, Grinde K, Plantinga A, Gogarten SM, Stilp AM, Kaplan RC, et al. (2016) Local Ancestry Inference in a Large US-Based Hispanic/Latino Study: Hispanic Community Health Study/Study of Latinos (HCHS/SOL). G3 (Bethesda). 6(6):1525-34.
---------------------------------------------------------------------------------------------------
18. Sofer T, Baier LJ, Browning SR, Thornton TA, Talavera GA, Wassertheil-Smoller S, et al. (2017) Admixture mapping in the Hispanic Community Health Study/Study of Latinos reveals regions of genetic associations with blood pressure traits. PLoS One. 12(11): e0188400.
---------------------------------------------------------------------------------------------------
19. Galanter JM, Gignoux CR, Torgerson DG, Roth LA, Eng C, Oh SS, et al. (2014) GWAS and admixture mapping identify different asthma-associated loci in Latinos: The GALA II Study. J allergy clin immunol. 134(2):295-305.
---------------------------------------------------------------------------------------------------
20. Fejerman L, Chen GK, Eng C, Huntsman S, Hu D, Williams A, et al. Admixture Mapping Identifies a Locus on 6q25 Associated with breast cancer risk in US Latinas. Hum Mol Genet. 2012.
---------------------------------------------------------------------------------------------------
21. Criollo-Rayo AA, Bohorquez M, Prieto R, Howarth K, Culma C, Carracedo A, et al. (2018) Native American gene continuity to the modern admixed population from the Colombian Andes: Implication for biomedical, population and forensic studies. Forensic Sci Int Genet. 36: e1-e7.
---------------------------------------------------------------------------------------------------
22. Anderson C, Pettersson F, Clarke G, Cardon L, Morris A, Zondervan K. (2010) Data quality control in genetic case-control association studies. Nat Protocols. 5(9):1564-73.
---------------------------------------------------------------------------------------------------
23. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, et al. (2007) PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. Am J Hum Genet.81(3):559-75.
---------------------------------------------------------------------------------------------------
24. R Core Team. (2014) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.
---------------------------------------------------------------------------------------------------
25. Price AL, Zaitlen NA, Reich D, Patterson N. (2010) New approaches to population stratifi cation in genome-wide association studies. Nat rev Genet. 11(7):459-63.
---------------------------------------------------------------------------------------------------
26. Guan Y. (2014) Detecting Structure of Haplotypes and Local Ancestry. Genetics. 196(3): 625-642.
---------------------------------------------------------------------------------------------------
27. Bohórquez M, Sahasrabudhe R, Criollo A, Sanabria-Salas MC, Vélez A, Castro JM, et al. (2016) Clinical manifestations of colorectal cancer patients from a large multicenter study in Colombia. Medicine. 95(40): e4883.
---------------------------------------------------------------------------------------------------
28. Risch N, Merikangas k. (1999) The Future of Genetic Studies of Complex Human Diseases. Science. 273:1516-7.
---------------------------------------------------------------------------------------------------
29. Perdue DG, Haverkamp D, Perkins C, Daley CM, Provost E. (2014) Geographic variation in colorectalcancer incidence and mortality, age of onset, and stage at diagnosis among american indian and Alaska native people, 1990–2009. Am J Public Health. 104(Suppl 3): S404-S14.
---------------------------------------------------------------------------------------------------
30. Webster PC. (2012) Health in Colombia: a system in crisis. Can Med Assoc J. 184(6): E289-E90.
---------------------------------------------------------------------------------------------------
31. Moore SP, Forman D, Piñeros M, Fernández SM, Oliveira Santos M, Bray F. (2014) Cancer in indigenous people in Latin America and the Caribbean: a review. Cancer Med. 3(1):70-80.
---------------------------------------------------------------------------------------------------
32. Center for Disease Control and Prevention. (2016) Colorectal cancer rates by race and ethnicity: division of cancer prevention and control, Centers for Disease Control and Prevention. [updated 16-junio-2016]. Available from: https://http://www.cdc.gov/cancer/colorectal/statistics/race.htm.
---------------------------------------------------------------------------------------------------
33. Cobb N, Paisano RE. (1998) Patterns of cancer mortality among Native Americans. Cancer. 83(11):2377-83.
---------------------------------------------------------------------------------------------------
34. Sandoval-Castaño EA. (2016) Perfi l de Salud de la Población Indígena, y Perfi l de salud de la población indígena, y medición de desigualdades en salud. Colombia 2016. Bogotá: Ministerio de Salud y Protección Social. Producto desarrollado en el marco del contrato No. 074 de 2016.
---------------------------------------------------------------------------------------------------
35. Fortini BK, Tring S, Plummer SJ, Edlund CK, Moreno V, Bresalier RS, et al. (2014) Multiple functional risk variants in a SMAD7 enhancer implicate a colorectal cancer risk haplotype. PLoS One. 9(11):e111914.
---------------------------------------------------------------------------------------------------
36. Study, C. O. G. E. N. T. (2008) Meta-analysis of genome-wide association data identifi es four new susceptibility loci for colorectal cancer. Nat Genet. 40 (12):1426-35.
---------------------------------------------------------------------------------------------------
37. Chang Y-WE, Marlin JW, Chance TW, Jakobi R. (2006) RhoA mediates cyclooxygenase-2 signaling to disrupt the formation of adherens junctions and increase cell motility. Cancer Res. 66(24):11700-8.
---------------------------------------------------------------------------------------------------
38. Okamoto H, Yasui K, Zhao C, Arii S, Inazawa J. (2003) PTK2 and EIF3S3 genes may be amplifi cation targets at 8q23-q24 and are associated with large hepatocellular carcinomas. Hepatology. 38(5):1242-9.
---------------------------------------------------------------------------------------------------
39. Liu WM, Maraia RJ, Rubin CM, Schmid CW. (1994) Alu transcripts: cytoplasmic localisation and regulation by DNA methylation. Nucleic Acids Res. 22(6):1087-95.
---------------------------------------------------------------------------------------------------
40. Zhu M, Chen X, Zhang H, Xiao N, Zhu C, He Q, et al. (2011) AluYb8 Insertion in the MUTYH Gene and risk of early-onset breast and gastric cancers in the Chinese population. Asian Pac J Cancer Prev. 12(6):1451-5.
---------------------------------------------------------------------------------------------------
41. Borun P, De Rosa M, Nedoszytko B, Walkowiak J, Plawski A. (2015) Specifi c Alu elements involved in a signifi cant percentage of copy number variations of the STK11 gene in patients with Peutz-Jeghers syndrome. Fam Cancer. 14(3):455-61.
---------------------------------------------------------------------------------------------------
42. Xiao-Jie L, Ai-Mei G, Li-Juan J, Jiang X. (2015) Pseudogene in cancer: real functions and promising signature. J Med Genet. 52(1):17-24.
---------------------------------------------------------------------------------------------------
43. Lanier MH, McConnell P, Cooper JA. (2016) Cell migration and invadopodia formation require a membrane-binding domain of CARMIL2. J Biol Chem. 291(3):1076-91.
---------------------------------------------------------------------------------------------------
44. Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, et al. (2011) New gene functions in megakaryopoiesis and platelet formation. Nature. 480(7376):201-208.
---------------------------------------------------------------------------------------------------
45. Bai Y, Sun Y, Peng J, Liao H, Gao H, Guo Y, et al. (2014) Overexpression of secretagogin inhibits cell apoptosis and induces chemoresistance in small cell lung cancer under the regulation of miR-494. Oncotarget. 5(17):7760-75.
---------------------------------------------------------------------------------------------------
46. Fagerberg L, Hallström BM, Oksvold P, Kampf C, Djureinovic D, Odeberg J, et al. (2014) Analysis of the human tissue-specifi c expression by genome-wide integration of transcriptomics and antibody based proteomics. Proteomics. Mol Cel Prot: 13(2):397-406.
---------------------------------------------------------------------------------------------------
47. Wu M, Lu W, Santos RE, Frattini MG, Kelly TJ. (2014) Geminin inhibits a late step in the formation of human pre-replicative complexes. J Biol Chem. 289(44):30810-21.
---------------------------------------------------------------------------------------------------
48. Kushwaha PP, Rapalli KC, Kumar S. (2016) Geminin a multi task protein involved in cancer pathophysiology and developmental process: A review. Biochimie. 131:115-27.
---------------------------------------------------------------------------------------------------
49. Nishihara K, Shomori K, Tamura T, Fujioka S, Ogawa T, Ito H. (2009) Immunohistochemical expression of geminin in colorectal cancer: Implication of prognostic signifi cance. Oncol Rep. 21:1189-95.
---------------------------------------------------------------------------------------------------
50. Furushima K, Yamamoto A, Nagano T, Shibata M, Miyachi H, Abe T, et al. (2007) Mouse homologues of Shisa antagonistic to Wnt and Fgf signalings. Dev Biol. 306(2):480-92.
---------------------------------------------------------------------------------------------------
51. Chun-Chieh C, Hsuan-Yu C, Kang-Yi S, Qi-Sheng H, Bo-Shiun Y, Ching-Hsien C, et al. (2014) Shisa3 is associated with prolonged survival through promoting β-catenin degradation in lung cancer. Am J Respir Crit Care Med. 190(4):433-44.
---------------------------------------------------------------------------------------------------
52. Kim BM, Mao J, Taketo MM, Shivdasani RA. (2007) Phases of canonical Wnt signaling during the development of mouse intestinal epithelium. Gastroenterology. 33(2):529-38.
---------------------------------------------------------------------------------------------------
53. Dong W, Yao C, Teng X, Chai J, Yang X, Li B. (2016) MiR-140-3p suppressed cell growth and invasion by downregulating the expression of ATP8A1 in non-small cell lung cancer. Tumor Biol. 37(3):2973-85.
---------------------------------------------------------------------------------------------------
54. Kato U, Inadome H, Yamamoto M, Emoto K, Kobayashi T, Umeda M. (2013) Role for Phospholipid Flippase Complex of ATP8A1 and CDC50A proteins in cell migration. J Biol Chem. 288(7):4922-34.Rev.
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