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Clinical and Translational Medicine

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Open Access 01-12-2015 | Research

Human Chromosome Y and Haplogroups; introducing YDHS Database

Authors: Timo Tiirikka, Jukka S Moilanen

Published in: Clinical and Translational Medicine | Issue 1/2015

Abstract

Background

As the high throughput sequencing efforts generate more biological information, scientists from different disciplines are interpreting the polymorphisms that make us unique. In addition, there is an increasing trend in general public to research their own genealogy, find distant relatives and to know more about their biological background. Commercial vendors are providing analyses of mitochondrial and Y-chromosomal markers for such purposes. Clearly, an easy-to-use free interface to the existing data on the identified variants would be in the interest of general public and professionals less familiar with the field. Here we introduce a novel metadatabase YDHS that aims to provide such an interface for Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants.

Methods

The database uses ISOGG Y-DNA tree as the source of mutations and haplogroups and by using genomic positions of the mutations the database links them to genes and other biological entities. YDHS contains analysis tools for deeper Y-SNP analysis.

Results

YDHS addresses the shortage of Y-DNA related databases. We have tested our database using a set of different cases from literature ranging from infertility to autism. The database is at http://www.semanticgen.net/ydhs

Conclusions

Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants have not been in the scientific limelight, excluding certain specialized fields like forensics, mainly because there is not much freely available information or it is scattered in different sources. However, as we have demonstrated Y-SNPs do play a role in various cases on the haplogroup level and it is possible to create a free Y-DNA dedicated bioinformatics resource.

Krausz C, Quintana-Murci L, Forti G. Y chromosome polymorphisms in medicine. Ann Med. 2004;36:573–83.PubMedCrossRef

Ma K, Sharkey A, Kirsch S, Vogt P, Keil R, Hargreave TB, et al. Towards the molecular localization of the AZF locus - mapping of microdeletions in azoospermic men with 14 subintervals of interval-6 of the human Y-chromosome. Hum Mol Genet. 1992;1:29–33.PubMedCrossRef

Vogt PH, Edelmann A, Kirsch S, Henegariu O, Hirschmann P, Kiesewetter F, et al. Human Y chromosome azoospermia factors (AZF) mapped to different subregions in Yq11. Hum Mol Genet. 1996;5:933–43.PubMedCrossRef

Kunej T, Zorn B, Peterlin B. Y chromosome microdeletions in infertile men with cryptorchidism. Fertil Steril. 2003;79:1559–65.PubMedCrossRef

Plaseska-Karanfilska D, Noveski P, Plaseski T, Maleva I, Madjunkova S, Moneva Z. Genetic causes of male infertility. Balk J Med Genet. 2012;15:31–4.

McElreavey K, Quintana-Murci L. Y chromosome haplogroups: A correlation with testicular dysgenesis syndrome? Apmis. 2003;111:106–14.PubMedCrossRef

Rosser ZH, Zerjal T, Hurles ME, Adojaan M, Alavantic D, Amorim A, et al. Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language. Am J Hum Genet. 2000;67:1526–43.PubMedCentralPubMedCrossRef

Choi J, Koh E, Matsui F, Sugimoto K, Suzuki H, Maeda Y, et al. Study of azoospermia factor-a deletion caused by homologous recombination between the human endogenous retroviral elements and population-specific alleles in Japanese infertile males. Fertil Steril. 2008;89:1177–82.PubMedCrossRef

Repping S, Skaletsky H, Brown L, van Daalen SKM, Korver CM, Pyntikova T, et al. Polymorphism for a 1.6-Mb deletion of the human Y chromosome persists through balance between recurrent mutation and haploid selection. Nat Genet. 2003;35:247–51.PubMedCrossRef

10.

Underhill PA, Passarino G, Lin AA, Shen P, Lahr MM, Foley RA, et al. The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations. Ann Hum Genet. 2001;65:43–62.PubMedCrossRef

11.

Sato Y, Shinka T, Nakahori Y. Y chromosome haplogroup d2* lineage is associated with azoospermia in Japanese males. 2013(88):107.

12.

Paracchini S, Stuppia L, Gatta V, Palka G, Moro E, Foresta C, et al. Y-chromosomal DNA haplotypes in infertile European males carrying Y-microdeletions. J Endocrinol Invest. 2000;23:671–6.PubMedCrossRef

13.

Aston KI, Carrell DT. Emerging evidence for the role of genomic instability in male factor infertility. Syst Biol Reprod Med. 2012;58:71–80.PubMedCrossRef

14.

Gazvani MR, Wilson EDA, Richmond DH, Howard PJ, Kingsland CR, Lewis-Jones DI. Evaluation of the role of mitotic instability in karyotypically normal men with oligozoospermia. Fertil Steril. 2000;73:51–5.PubMedCrossRef

15.

Wallerand H, Chabannes E, Bittard H. Idiopathic male infertility and androgen receptors. Prog Urol. 2001;11:610–20.PubMed

16.

Jarvi K, Chitayat D. The genetics you never knew: A genetics primer. Urol Clin North Am. 2008;35:243.PubMedCrossRef

17.

Walsh TJ. Male reproductive health and prostate cancer risk. Curr Opin Urol. 2011;21:506–13.PubMedCentralPubMedCrossRef

18.

Jangravi Z, Alikhani M, Arefnezhad B, Tabar MS, Taleahmad S, Karamzadeh R, et al. A Fresh Look at the Male-specific Region of the Human Y Chromosome. J Proteome Res. 2013;12:6–22.PubMedCrossRef

19.

Sandberg AA. Chromosomal abnormalities and related events in prostate cancer. Hum Pathol. 1992;23:368–80.PubMedCrossRef

20.

Dasari VK, Goharderakhshan RZ, Perinchery G, Li L-C, Tanaka Y, Alonzo J, et al. Expression analysis of Y chromosome genes in human prostate cancer. J Urol. 2001;165:1335–41.PubMedCrossRef

21.

Lau Y-FC, Zhang J. Expression analysis of thirty one Y chromosome genes in human prostate cancer. Mol Carcinog. 2000;27:308–21.PubMedCrossRef

22.

Vergnaud G, Page DC, Simmler MC, Brown L, Rouyer F, Noel B, et al. A deletion map of the human Y-chromosome based on DNA hybridization. Am J Hum Genet. 1986;38:109–24.PubMedCentralPubMed

23.

Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature. 2003;423:825–37.PubMedCrossRef

24.

Vijayakumar S, Hall DC, Reveles XT, Troyer DA, Thompson IM, Garcia D, et al. Detection of Recurrent Copy Number Loss at Yp11.2 Involving TSPY Gene Cluster in Prostate Cancer Using Array-Based Comparative Genomic Hybridization. Cancer Res. 2006;66:4055–64.PubMedCrossRef

25.

Chen MW, Vacherot F, de la Taille A, Gil-Diez-de-Medina S, Shen RQ, Friedman RA, et al. The emergence of protocadherin-PC expression during the acquisition of apoptosis-resistance by prostate cancer cells. Oncogene. 2002;21:7861–71.PubMedCrossRef

26.

Blanco P, Shlumukova M, Sargent CA, Jobling MA, Affara N, Hurles ME. Divergent outcomes of intrachromosomal recombination on the human Y chromosome: male infertility and recurrent polymorphism. J Med Genet. 2000;37:752–8.PubMedCentralPubMedCrossRef

27.

Terry S, Queires L, Gil-Diez-de-Medina S, Chen M-W, de la Taille A, Allory Y, et al. Protocadherin-PC promotes androgen-independent prostate cancer cell growth. Prostate. 2006;66:1100–13.PubMedCentralPubMedCrossRef

28.

Lindstrom S, Adami HO, Adolfsson J, Wiklund F. Y Chromosome Haplotypes and Prostate Cancer in Sweden. Clin Cancer Res. 2008;14:6712–6.PubMedCrossRef

29.

Nargesi MM, Ismail P, Razack AHA, Pasalar P, Nazemi A, Oshkoor SA, et al. Linkage between Prostate Cancer Occurrence and Y-Chromosomal DYS Loci in Malaysian Subjects. Asian Pac J Cancer Prev. 2011;12:1265–8.PubMed

30.

Wang ZM, Parikh H, Jia JP, Myers T, Yeager M, Jacobs KB, et al. Y chromosome haplogroups and prostate cancer in populations of European and Ashkenazi Jewish ancestry. Hum Genet. 2012;131:1173–85.PubMedCentralPubMedCrossRef

31.

Hildenbrand R, Schröder W, Brude E, Schepler A, König R, Stutte HJ, et al. Detection of TSPY protein in a unilateral microscopic gonadoblastoma of a Turner mosaic patient with a Y-derived marker chromosome. J Pathol. 1999;189:623–6.PubMedCrossRef

32.

Kersemaekers A-MF, Honecker F, Stoop H, Cools M, Molier M, Wolffenbuttel K, et al. Identification of germ cells at risk for neoplastic transformation in gonadoblastoma: An immunohistochemical study for OCT3/4 and TSPY. Hum Pathol. 2005;36:512–21.PubMedCrossRef

33.

Page DC. Hypothesis - a Y-chromosomal gene causes gonadoblastoma in dysgenetic gonads. Development. 1987;101:151–5.PubMed

34.

Lau Y-FC. Gonadoblastoma, Testicular and Prostate Cancers, and the TSPY Gene. Am J Hum Genet. 1999;64:921–7.PubMedCentralPubMedCrossRef

35.

Salo P, Kääriäinen H, Petrovic V, Peltomäki P, Page DC, de la Chapelle A. Molecular mapping of the putative gonadoblastoma locus on the Y chromosome. Genes Chromosomes Cancer. 1995;14:210–4.PubMedCrossRef

36.

Schocken DD, Arrieta MI, Leaverton PE, Ross EA. Prevalence and mortality rate of congestive heart failure in the United States. J Am Coll Cardiol. 1992;20:301–6.PubMedCrossRef

37.

Heidecker B, Lamirault G, Kasper EK, Wittstein IS, Champion HC, Breton E, et al. The gene expression profile of patients with new-onset heart failure reveals important gender-specific differences. Eur Heart J. 2010;31:1188–96.PubMedCentralPubMedCrossRef

38.

Russo P, Siani A, Miller MA, Karanam S, Esposito T, Gianfrancesco F, et al. Genetic variants of Y chromosome are associated with a protective lipid profile in black men. Arterioscler Thromb Vasc Biol. 2008;28:1569–74.PubMedCrossRef

39.

Charchar FJ, Bloomer LDS, Barnes TA, Cowley MJ, Nelson CP, Wang YZ, et al. Inheritance of coronary artery disease in men: an analysis of the role of the Y chromosome. Lancet. 2012;379:915–22.PubMedCentralPubMedCrossRef

40.

Chen XH, Rodriguez S, Hawe E, Talmud PJ, Miller GJ, Underhill P, et al. Evidence of admixture from haplotyping in an epidemiological study of UK Caucasian males: Implications for association analyses. Hum Hered. 2004;57:142–55.PubMedCrossRef

41.

Miles JH, Hillman RE. Value of a clinical morphology examination in autism. Am J Med Genet. 2000;91:245–53.PubMedCrossRef

42.

Baron-Cohen S, Lombardo MV, Auyeung B, Ashwin E, Chakrabarti B, Knickmeyer R. Why Are Autism Spectrum Conditions More Prevalent in Males? Plos Biol [Internet]. 2011 Jun;9. Available from: ://WOS:000292191200008

43.

Serajee FJ, Mahbubul Huq AHM. Association of Y Chromosome Haplotypes With Autism. J Child Neurol. 2009;24:1258–61.PubMedCrossRef

44.

Mariner R, Jackson AW, Levitas A, Hagerman RJ, Braden M, McBogg PM, et al. Autism, mental retardation, and chromosomal abnormalities. J Autism Dev Disord. 1986;16:425–40.PubMedCrossRef

45.

Tartaglia N, Davis S, Hench A, Nitnishakavi S, Beauregard R, Reynolds A, et al. A new look at XXYY syndrome: Medical and psychological features. Am J Med Genet A. 2008;146A:1509–22.PubMedCentralPubMedCrossRef

46.

Jamain S, Quach H, Quintana-Murci L, Betancur C, Philippe A, Gillberg C, et al. Y chromosome haplogroups in autistic subjects. Mol Psychiatry. 2002;7:217–9.PubMedCentralPubMedCrossRef

47.

Lappalainen T, Laitinen V, Salmela E, Andersen P, Huoponen K, Savontaus ML, et al. Migration waves to the Baltic Sea region. Ann Hum Genet. 2008;72(Pt 3):337–48.PubMedCrossRef

48.

McKusick VA. On the X chromosome of man. Q Rev Biol. 1962;37(2):69–175.PubMedCrossRef

49.

Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Graves T, Fulton RS, Dugan S, Ding Y, Buhay CJ, Kremitzki C, Wang Q, Shen H, Holder M, Villasana D, Nazareth LV, Cree A, Courtney L, Veizer J, Kotkiewicz H, Cho TJ, Koutseva N, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. Nature 483(7387):82–6

Title: Human Chromosome Y and Haplogroups; introducing YDHS Database
Authors: Timo Tiirikka
Jukka S Moilanen
Publication date: 01-12-2015
Publisher: Springer Berlin Heidelberg
Published in: Clinical and Translational Medicine / Issue 1/2015
Electronic ISSN: 2001-1326
DOI: https://doi.org/10.1186/s40169-015-0060-7

Keynote webinar | Spotlight on medication adherence

Springer Medicine

Human Chromosome Y and Haplogroups; introducing YDHS Database

Abstract

Background

Methods

Results

Conclusions

Keynote webinar | Spotlight on medication adherence

Springer Medicine

Abstract

Background

Methods

Results

Conclusions

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