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Potential relationship between single nucleotide polymorphisms used in forensic genetics and diseases or other traits in European population

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An Erratum to this article was published on 01 August 2015

Abstract

Single nucleotide polymorphisms (SNPs) are an interesting option to facilitate the analysis of highly degraded DNA by allowing the reduction of the size of the DNA amplicons. The SNPforID 52-plex panel is a clear example of the use of non-coding SNPs in forensic genetics. However, nonstop advances in studies of genetic polymorphisms are leading to the discovery of new associations between SNPs and diseases. The aim of this study was to perform a comprehensive review of the state of association between the 52 SNPs in the 52-plex panel and diseases or other traits related to their treatment, such as drug response characters. In order to achieve this goal, we have conducted a bioinformatic search for each SNP included in the panel and the SNPs in linkage disequilibrium (LD) with them in the European population (r 2 > 0.8). A total of 424 SNPs (52 in the panel and 372 in LD) were investigated in PubMed, Scopus, and dbSNP databases. Our results show that three SNPs in the SNPforID 52-plex panel (rs2107612, rs1979255, rs1463729) have been associated with diseases such as hypertension or macular degeneration, as well as drug response. Similarly, three out of the 372 SNPs in LD (rs2107614, r 2 = 0.859; rs765250, r 2 = 0.858; rs11064560, r 2 = 0,887) are also associated with various pathologies. In view of these results, we propose the need for a periodic review of the SNPs used in forensic genetics in order to keep their associations with diseases or related phenotypes updated and to evaluate their continuity in forensic panels for avoiding legal and ethical conflicts.

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References

  1. Decorte R (2010) Genetic identification in the 21st century: current status and future developments. Forensic Sci Int 201(1–3):160–4. doi:10.1016/j.forsciint.2010.02.029

    Article  CAS  PubMed  Google Scholar 

  2. Alaeddini R, Walsh SJ, Abbas A (2010) Forensic implications of genetic analyses from degraded DNA—a review. Forensic Sci Int Genet 4(3):148–57. doi:10.1016/j.fsigen.2009.09.007

    Article  CAS  PubMed  Google Scholar 

  3. Holobinko A (2012) Forensic human identification in the United States and Canada: a review of the law, admissible techniques, and the legal implications of their application in forensic cases. Forensic Sci Int 222(1-3):394.e1–13. doi:10.1016/j.forsciint.2012.06.001

    Article  Google Scholar 

  4. Budowle B, van Daal A (2008) Forensically relevant SNP classes. Biotechniques 44(5):603–8, 610. doi:10.2144/000112806

    Article  CAS  PubMed  Google Scholar 

  5. Kayser M, de Knijff P (2011) Improving human forensics through advances in genetics, genomics and molecular biology. Nat Rev Genet 12(3):179–92. doi:10.1038/nrg2952

    Article  CAS  PubMed  Google Scholar 

  6. Kidd KK, Kidd JR, Speed WC, Fang R, Furtado MR, Hyland FCL, Pakstis AJ (2012) Expanding data and resources for forensic use of SNPs in individual identification. Forensic Sci Int Genet 6(5):646–52. doi:10.1016/j.fsigen.2012.02.012

    Article  CAS  PubMed  Google Scholar 

  7. Sanchez JJ, Phillips C, Børsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27(9):1713–24

    Article  CAS  PubMed  Google Scholar 

  8. Musgrave-Brown E, Ballard D, Balogh K, Bender K, Berger B, Bogus M, Børsting C, Brion M, Fondevila M, Harrison C, Oguzturun C, Parson W, Phillips C, Proff C, Ramos-Luis E, Sanchez JJ, Sanchez-Diz P, Sobrino-Rey B, Stradmann-Bellinghausen B, Tacker C, Carracedo A, Morling N, Scheithauer R, Schneider PM, Syndercombe-Court D (2007) Forensic validation of the SNPforID 52-plex assay. Forensic Sci Int Genet 1(2):186–90. doi:10.1016/j.fsigen.2007.01.004

    Article  PubMed  Google Scholar 

  9. Ramírez-Bello J, Vargas-Alarcón G, Tovilla-Zárate C, Fragoso JM (2013) Polimorfismos de un solo nucleótido (SNP): implicaciones funcionales de los SNP reguladores (rSNP) y de los SNP-ARN estructurales (srSNP) en enfermedades complejas. Gac Med Mex 149(2):220–8

  10. Kayser M, Schneider PM (2009) DNA-based prediction of human externally visible characteristics in forensics: motivations, scientific challenges, and ethical considerations. Forensic Sci Int Genet 3(3):154–61. doi:10.1016/j.fsigen.2009.01.012

    Article  CAS  PubMed  Google Scholar 

  11. Prinz M, Carracedo A, Mayr WR, Morling N, Parsons TJ, Sajantila A, Scheithauer R, Schmitter H, Schneider PM, International Society for Forensic Genetics (2007) DNA Commission of the International Society for Forensic Genetics (ISFG): recommendations regarding the role of forensic genetics for disaster victim identification (DVI). Forensic Sci Int Genet 1(1):3–12. doi:10.1016/j.fsigen.2006.10.003

    Article  CAS  PubMed  Google Scholar 

  12. International Declaration on Human Genetic Data, UNESCO’s 32nd General Conference, 16 October 2003. Universal Declaration on the Human Genome and Human Rights

  13. 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA (2010) A map of human genome variation from population-scale sequencing. Nature 467(7319):1061–73. doi:10.1038/nature09534

    Article  Google Scholar 

  14. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D (2002) The structure of haplotype blocks in the human genome. Science 296(5576):2225–9

    Article  CAS  PubMed  Google Scholar 

  15. Newhouse S, Farrall M, Wallace C, Hoti M, Burke B, Howard P, Onipinla A, Lee K, Shaw-Hawkins S, Dobson R, Brown M, Samani NJ, Dominiczak AF, Connell JM, Lathrop GM, Kooner J, Chambers J, Elliott P, Clarke R, Collins R, Laan M, Org E, Juhanson P, Veldre G, Viigimaa M, Eyheramendy S, Cappuccio FP, Ji C, Iacone R, Strazzullo P, Kumari M, Marmot M, Brunner E, Caulfield M, Munroe PB (2009) Polymorphisms in the WNK1 gene are associated with blood pressure variation and urinary potassium excretion. PLoS One 4(4):e5003. doi:10.1371/journal.pone.0005003

    Article  PubMed Central  PubMed  Google Scholar 

  16. Turner ST, Schwartz GL, Chapman AB, Boerwinkle E (2005) WNK1 kinase polymorphism and blood pressure response to a thiazide diuretic. Hypertension 46(4):758–65

    Article  CAS  PubMed  Google Scholar 

  17. Lambrechts D, Moisse M, Delmar P, Miles DW, Leighl N, Escudier B, Van Cutsem E, Bansal AT, Carmeliet P, Scherer SJ, de Haas S, Pallaud C (2014) Genetic markers of bevacizumab-induced hypertension. Angiogenesis 17(3):685–94. doi:10.1007/s10456-014-9424-7

    CAS  PubMed  Google Scholar 

  18. Wilson FH, Disse-Nicodeme S, Choate KA, Ishikawa K, Nelson-Williams C, Desitter I, Gunel M, Milford DV, Lipkin GW, Achard JM, Feely MP, Dussol B, Berland Y, Unwin RJ, Mayan H, Simon DB, Farfel Z, Jeunemaitre X, Lifton RP (2001) Human hypertension caused by mutations in WNK kinases. Science 293(5532):1107–12

    Article  CAS  PubMed  Google Scholar 

  19. El Shamieh S, Visvikis-Siest S (2012) Genetic biomarkers of hypertension and future challenges integrating epigenomics. Clin Chim Acta 414:259–65. doi:10.1016/j.cca.2012.09.018

    Article  PubMed  Google Scholar 

  20. Saltz LB, Clarke S, Díaz-Rubio E, Scheithauer W, Figer A, Wong R, Koski S, Lichinitser M, Yang TS, Rivera F, Couture F, Sirzén F, Cassidy J (2008) Bevacizumab in combination with oxaliplatin-based chemotherapy as first-line therapy in metastatic colorectal cancer: a randomized phase III study. J Clin Oncol 26(12):2013–9. doi:10.1200/JCO.2007.14.9930

    Article  CAS  PubMed  Google Scholar 

  21. Escudier B, Pluzanska A, Koralewski P, Ravaud A, Bracarda S, Szczylik C, Chevreau C, Filipek M, Melichar B, Bajetta E, Gorbunova V, Bay JO, Bodrogi I, Jagiello-Gruszfeld A, Moore N, AVOREN Trial investigators (2007) Bevacizumab plus interferon alfa-2a for treatment of metastatic renal cell carcinoma: a randomised, double-blind phase III trial. Lancet 370(9605):2103–11

    Article  PubMed  Google Scholar 

  22. Frey MK, Olvera N, Bogomolniy F, Dao F, Borsu L, Konner JA, Rizvi NA, Barakat RR, Dickler MN, Levine DA (2008) WNK1 haplotypes and bevacizumab induced hypertension. J Clin Oncol 26(15 Suppl):11003

    Google Scholar 

  23. Strunnikova NV, Maminishkis A, Barb JJ, Wang F, Zhi C, Sergeev Y, Chen W, Edwards AO, Stambolian D, Abecasis G, Swaroop A, Munson PJ, Miller SS (2010) Transcriptome analysis and molecular signature of human retinal pigment epithelium. Hum Mol Genet 19(12):2468–86. doi:10.1093/hmg/ddq129

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  24. Parmeggiani F, Sorrentino FS, Romano MR, Costagliola C, Semeraro F, Incorvaia C, D’Angelo S, Perri P, De Nadai K, Bonomo Roversi E, Franceschelli P, Sebastiani A, Rubini M (2013) Mechanism of inflammation in age-related macular degeneration: an up-to-date on genetic landmarks. Mediators Inflamm 2013:435607. doi:10.1155/2013/435607

    Article  PubMed Central  PubMed  Google Scholar 

  25. Fritsche LG, Chen W, Schu M et al (2013) Seven new loci associated with age-related macular degeneration. Nat Genet 45(4):433-9, 439e1-2. doi:10.1038/ng.2578

    Article  Google Scholar 

  26. Chen W, Stambolian D, Edwards AO, Branham KE, Othman M, Jakobsdottir J, Tosakulwong N, Pericak-Vance MA, Campochiaro PA, Klein ML, Tan PL, Conley YP, Kanda A, Kopplin L et al (2010) Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration. Proc Natl Acad Sci U S A 107(16):7401–6. doi:10.1073/pnas.0912702107

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Craddock N, Owen MJ, O’Donovan MC (2006) The catechol-O-methyl transferase (COMT) gene as a candidate for psychiatric phenotypes: evidence and lessons. Mol Psychiatry 11(5):446–58

    Article  CAS  PubMed  Google Scholar 

  28. Xing C, Torres-Caban M, Wang T, Lu Q, Xing G, Elston RC (2007) Linkage studies of catechol-O-methyltransferase (COMT) and dopamine-beta-hydroxylase (DBH) cDNA expression levels. BMC Proc Suppl 1:S95

    Article  Google Scholar 

  29. Cheung VG, Spielman RS (2009) Genetics of human gene expression: mapping DNA variants that influence gene expression. Nat Rev Genet 10(9):595–604. doi:10.1038/nrg2630

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Liu XQ, Greenwood CM, Wang KS, Paterson AD (2005) A genome scan for parent-of-origin linkage effects in alcoholism. BMC Genet 30;6(Suppl 1):S160

    Article  Google Scholar 

  31. Morozova TV, Goldman D, Mackay TFC, Anholt RRH (2012) The genetic basis of alcoholism: multiple phenotypes, many genes, complex networks. Genome Biol 13(2):239. doi:10.1186/gb-2012-13-2-239

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  32. Luo X, Kranzler HR, Zuo L, Wang S, Blumberg HP, Gelernter J (2005) CHRM2 gene predisposes to alcohol dependence, drug dependence and affective disorders: results from an extended case-control structured association study. Hum Mol Genet 14:2421–2434

    Article  CAS  PubMed  Google Scholar 

  33. Agrawal A, Edenberg HJ, Foroud T, Bierut LJ, Dunne G, Hinrichs AL, Nurnberger JI, Crowe R, Kuperman S, Schuckit MA, Begleiter H, Porjesz B, Dick DM (2006) Association of GABRA2 with drug dependence in the collaborative study of the genetics of alcoholism sample. Behav Genet 36:640–650

    Article  PubMed  Google Scholar 

  34. Lind PA, Macgregor S, Vink JM, Pergadia ML, Hansell NK, de Moor MH, Smit AB, Hottenga JJ, Richter MM, Heath AC, Martin NG, Willemsen G, de Geus EJ, Vogelzangs N, Penninx BW, Whitfield JB, Montgomery GW, Boomsma DI, Madden PA (2010) A genome-wide association study of nicotine and alcohol dependence in Australian and Dutch populations. Twin Res Hum Genet 13(1):10–29. doi:10.1375/twin.13.1.10

    Article  PubMed Central  PubMed  Google Scholar 

  35. Bierut LJ, Agrawal A, Bucholz KK, Doheny KF, Laurie C, Pugh E, Fisher S, Fox L, Howells W, Bertelsen S, Hinrichs AL, Almasy L, Breslau N, Culverhouse RC, Dick DM, Edenberg HJ, Foroud T, Grucza RA, Hatsukami D, Hesselbrock V, Johnson EO, Kramer J, Krueger RF, Kuperman S, Lynskey M, Mann K, Neuman RJ, Nöthen MM, Nurnberger JI Jr, Porjesz B et al (2010) A genome- wide association study of alcohol dependence. Proc Natl Acad Sci U S A 16;107(11):5082–7. doi:10.1073/pnas.0911109107

    Article  Google Scholar 

  36. Song J, Koller DL, Foroud T, Carr K, Zhao J, Rice J, Nurnberger JI Jr, Begleiter H, Porjesz B, Smith TL, Schuckit MA, Edenberg HJ (2003) Association of GABA(A) receptors and alcohol dependence and the effects of genetic imprinting. Am J Med Genet B Neuropsychiatr Genet 117B(1):39–45

    Article  PubMed  Google Scholar 

  37. Kong A, Steinthorsdottir V, Masson G, Thorleifsson G, Sulem P et al (2009) Parental origin of sequence variants associated with complex diseases. Nature 462(7275):868–74. doi:10.1038/nature08625

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  38. Dong C, Li WD, Geller F, Lei L, Li D, Gorlova OY, Hebebrand J, Amos CI, Nicholls RD, Price RA (2005) Possible genomic imprinting of three human obesity-related genetic loci. Am J Hum Genet 76(3):427–37

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  39. Roy-Gagnon MH, Mathias RA, Wilson AF (2005) Application of the regression of offspring on mid-parent method to detect associations between single-nucleotide polymorphisms and the beta 2 electroencephalogram phenotype in the COGA data. BMC Genet 6(Suppl 1):S56

    Article  PubMed Central  PubMed  Google Scholar 

  40. Porjesz B, Begleiter H, Wang K, Almasy L, Chorlian DB, Stimus AT, Kuperman S, O’Connor SJ, Rohrbaugh J, Bauer LO, Edenberg HJ, Goate A, Rice JP, Reich T (2002) Linkage and linkage disequilibrium mapping of ERP and EEG phenotypes. Biol Psychol 61:229–48 (b)

    Article  PubMed  Google Scholar 

  41. Edenberg HJ, Dick DM, Xuei X, Tian H, Almasy L, Bauer LO, Crowe RR, Goate A, Hesselbrock V, Jones K, Kwon J, Li TK, Nurnberger JI Jr, O’Connor SJ, Reich T, Rice J, Schuckit MA, Porjesz B, Foroud T, Begleiter H (2004) Variations in GABRA2, encoding the alpha 2 subunit of the GABA(A) receptor, are associated with alcohol dependence and with brain oscillations. Am J Hum Genet 74:705–14

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  42. Cai J, Hao CG, Luo DH, Du L, Zhang XY (2014) Association between single nucleotide polymorphisms in Wnk1 gene and ischemic stroke in Chinese Han population. Zhejiang Da Xue Xue Bao Yi Xue Ban 43(1):43–50

    CAS  PubMed  Google Scholar 

  43. Suarez BK, Duan J, Sanders AR, Hinrichs AL, Jin CH, Hou C, Buccola NG, Hale N, Weilbaecher AN, Nertney DA, Olincy A, Green S, Schaffer AW, Smith CJ, Hannah DE, Rice JP, Cox NJ, Martinez M, Mowry BJ, Amin F, Silverman JM, Black DW, Byerley WF, Crowe RR, Freedman R, Cloninger CR, Levinson DF, Gejman PV (2006) Genomewide linkage scan of 409 European-ancestry and African American families with schizophrenia: suggestive evidence of linkage at 8p23.3-p21.2 and 11p13.1-q14.1 in the combined sample. Am J Hum Genet 78(2):315–33

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  44. Enomoto H, Noguchi E, Iijima S, Takahashi T, Hayakawa K, Ito M, Kano T, Aoki T, Suzuki Y, Koga M, Tamari M, Shiohara T, Otsuka F, Arinami T (2007) Single nucleotide polymorphism-based genome-wide linkage analysis in Japanese atopic dermatitis families. BMC Dermatol 7:5

    Article  PubMed Central  PubMed  Google Scholar 

  45. Shi J, Hattori E, Zou H, Badner JA, Christian SL, Gershon ES, Liu C (2007) No evidence for association between 19 cholinergic genes and bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 144B(6):715–23

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  46. Kathiresan S, Manning AK, Demissie S, D’Agostino RB, Surti A, Guiducci C, Gianniny L, Burtt NP, Melander O, Orho-Melander M, Arnett DK, Peloso GM, Ordovas JM, Cupples LA (2007) A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. BMC Med Genet 8(Suppl 1):S17

    Article  PubMed Central  PubMed  Google Scholar 

  47. Benjamin EJ, Dupuis J, Larson MG, Lunetta KL, Booth SL, Govindaraju DR, Kathiresan S, Keaney JF Jr, Keyes MJ, Lin JP, Meigs JB, Robins SJ, Rong J, Schnabel R, Vita JA, Wang TJ, Wilson PW, Wolf PA, Vasan RS (2007) Genome-wide association with select biomarker traits in the Framingham Heart Study. BMC Med Genet 8(Suppl 1):S11

    Article  PubMed Central  PubMed  Google Scholar 

  48. Taupitz J (2000) The conflict of understanding the genetic make-up of man and his knowledge of it. Forensic Sci Int 11;113(1-3):477–82

    Article  Google Scholar 

  49. Nguyen KD, Pihur V, Ganesh SK, Rakha A, Cooper RS, Hunt SC, Freedman BI, Coresh J, Kao WH, Morrison AC, Boerwinkle E, Ehret GB, Chakravarti A (2013) Effects of rare and common blood pressure gene variants on essential hypertension: results from the family blood pressure program, CLUE, and atherosclerosis risk in communities studies. Circ Res 112(2):318–26. doi:10.1161/CIRCRESAHA.112.276725

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  50. National Center for Biotechnology Information, NCBI (2015) dbSNP short genetics variation. http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs = 765250. Accessed 7 February 2015

  51. Cho MK, Sankar P (2004) Forensic genetics and ethical, legal and social implications beyond the clinic. Nat Genet 36(11 Suppl):S8–12

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  52. Mascalzoni D, Hicks A, Pramstaller P, Wjst M (2008) Informed consent in the genomics era. PLoS Med 16;5(9):e192. doi:10.1371/journal.pmed.0050192

    Article  Google Scholar 

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Acknowledgments

This project was supported by RETICS (RD12/0036/0060), UPV/EHU (UFI 11/35), and the Basque Government (IT661-13, S-PE12UN060). ELL was supported by a postdoctoral grant from the Basque Government (Programa Posdoctoral de Perfeccionamiento de Personal Investigador doctor, Departamento de Educación, Política Lingüística y Cultura del Gobierno Vasco).

Conflict of interest

The authors reported no potential conflicts of interest.

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Authors and Affiliations

  1. Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Odontology, University of the Basque Country (UPV/EHU), Leioa, Spain

    Maria Pombar-Gomez, Elixabet Lopez-Lopez, Idoia Martin-Guerrero & Africa Garcia-Orad Carles

  2. BioCruces Health Research Institute, Bilbao, Spain

    Africa Garcia-Orad Carles

  3. BIOMICs Research Group, Centro de Investigación “Lascaray” Ikergunea, University of the Basque Country (UPV/EHU), Avda. Miguel de Unamuno 3, 01006, Vitoria-Gasteiz, Spain

    Marian M. de Pancorbo

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Pombar-Gomez, M., Lopez-Lopez, E., Martin-Guerrero, I. et al. Potential relationship between single nucleotide polymorphisms used in forensic genetics and diseases or other traits in European population. Int J Legal Med 129, 435–443 (2015). https://doi.org/10.1007/s00414-015-1165-7

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