The HLA-net GENE[RATE] pipeline for effective HLA data analysis and its application to 145 population samples from Europe and neighbouring areas

Tissue Antigens

Volumn 83, Issue 5, 2014, Pages 307-323

  Nunes, J M ^a   Buhler, S ^a   Roessli, D ^a   Sanchez Mazas, A ^a   Andreani, M ^b   Benhamamouch, S ^c   Boldyreva, M ^d   Canossi, A ^b   Chiaroni, J ^e   Darke, C ^f   Di Cristofaro, J ^e   Dubois, V ^g   Elamin, N ^h   Eliaou, J F ⁱ   Fadhlaoui Zid, K ^j   Fischer, G F ^k   Grubic, Z ^l   Jaatinen, T ^m   Kolesar, L ⁿ   Ligeiro, D ^o   Lokki, M L ^p   Mehra, N ^q   Nicoloso, G ^b   Papaioannou Voniatis, D ^r   Papasteriades, C ^s   Piancatelli, D ^t   Poli, F ^u   Romon Alonso, I ^v   Slavcev, A ⁿ   Spiroski, M ^w   Spyropoulou Vlachou, M ^x   Sulcebe, G ^y   Suslova, T ^z   Testi, M ^b   Tiercy, J M ^aa   Toungouz Nevessignsky, M ^ab   Varnavidou Nicolaidou, A ^r   Vidan Jeras, B ^ac   more..

^a UNIVERSITY OF GENEVA   (Switzerland)

^b Laboratory of Immunogenetics and Transplant Biology IME Foundation ^*  (Switzerland)

^c UNIVERSITY OF ORAN   (Algeria)

^d INSTITUTE OF IMMUNOLOGY   (Russian Federation)

^e AIX MARSEILLE UNIVERSITY   (France)

^f Welsh Blood Service   (United Kingdom)

^g ETABLISSEMENT FRANÇAIS DU SANG   (France)

^h HANNOVER MEDICAL SCHOOL   (Germany)

ⁱ HÔPITAL SAINT ELOI   (France)

^j UNIVERSITY OF TUNIS EL MANAR   (Tunisia)

^k MEDICAL UNIVERSITY OF VIENNA   (Austria)

^l KBC Zagreb   (Croatia)

^m FINNISH RED CROSS BLOOD SERVICE   (Finland)

ⁿ INSTITUTE FOR CLINICAL AND EXPERIMENTAL MEDICINE   (Czech Republic)

^o IP   (Portugal)

^p UNIVERSITY OF HELSINKI   (Finland)

^q ALL INDIA INSTITUTE OF MEDICAL SCIENCES   (India)

^r NICOSIA GENERAL HOSPITAL   (Cyprus)

^s EVANGELISMOS HOSPITAL   (Greece)

^t INSTITUTE OF TRANSLATIONAL PHARMACOLOGY   (Italy)

^u FONDAZIONE IRCCS CA GRANDA OSPEDALE MAGGIORE POLICLINICO   (Italy)

^v HOSPITAL UNIVERSITARIO MARQUÉS DE VALDECILLA   (Spain)

^w SS CYRIL AND METHODIUS UNIVERSITY OF SKOPJE   (Macedonia)

^x General University Hospital of Athens Alexandra   (Greece)

^y UNIVERSITY HOSPITAL CENTER MOTHER TERESA   (Albania)

^z CHELYABINSK STATE UNIVERSITY   (Russian Federation)

^aa GENEVA UNIVERSITY HOSPITALS   (Switzerland)

^ab ERASME HOSPITAL   (Belgium)

^ac BLOOD TRANSFUSION CENTRE OF SLOVENIA   (Slovenia)

more..

Author keywords

Data analysis; Europe; GENE RATE ; Gene va ; HLA net; Human leukocyte antigen; North Africa; Population genetics; West Asia

Indexed keywords

HLA A ANTIGEN; HLA B ANTIGEN; HLA C ANTIGEN; HLA DPB1 ANTIGEN; HLA DQA1 ANTIGEN; HLA DQB1 ANTIGEN; HLA DRB1 ANTIGEN; HLA ANTIGEN;

ALLELE; ASIA; AUDIOVISUAL EQUIPMENT; BIOINFORMATICS; BONE MARROW TRANSPLANTATION; DATA ANALYSIS; DATA BASE; EUROPE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC VARIABILITY; GEOGRAPHIC INFORMATION SYSTEM; HAPLOTYPE; HLA SYSTEM; HLA TYPING; HUMAN; LINGUISTICS; MEDICAL ANTHROPOLOGY; NOMENCLATURE; NORTH AFRICA; PRIORITY JOURNAL; REVIEW; VALIDATION PROCESS; AFRICA; BIOLOGY; CLASSIFICATION; COMPUTER PROGRAM; DEVICES; GENETIC DATABASE; GENETIC LINKAGE; GENETICS; HISTOCOMPATIBILITY TEST; IMMUNOLOGY; PHYLOGEOGRAPHY; PROCEDURES;

AFRICA, NORTHERN; ALLELES; ASIA, WESTERN; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EUROPE; GENE FREQUENCY; GENETIC LINKAGE; GENETIC VARIATION; HAPLOTYPES; HISTOCOMPATIBILITY TESTING; HLA ANTIGENS; HUMANS; PHYLOGEOGRAPHY; SOFTWARE;

EID: 84901492011     PISSN: 00012815     EISSN: 13990039     Source Type: Journal    
DOI: 10.1111/tan.12356     Document Type: Review

References (38)

1. Sanchez-Mazas A, Vidan-Jeras B, Nunes JM et al. Strategies to work with HLA data in human populations for histocompatibility, clinical transplantation, epidemiology and population genetics: HLA-NET methodological recommendations. Int J Immunogenet 2012: 39: 459-76.
2. Little AM. Report of the EFI General Assembly, held during the 27th EFI Annual Meeting in Maastricht, the Netherlands. EFI Newsletter 2013: 71: 7-9.
3. Barbujani G, Ghirotto S, Tassi F. Nine things to remember about human genome diversity. Tissue Antigens 2013: 82: 155-64.
4. Nunes JM, Buhler S, Sanchez-Mazas A. NO to obsolete definitions: YES to blanks. Tissue Antigens 2014: 83: 119-20.
5. Bhopal R, Donaldson L. White, European, Western, Caucasian, or what? Inappropriate labeling in research on race, ethnicity, and health. Am J Public Health 1998: 88: 1303-7.
6. Lewis MP, Simons GF, Fennig CD. Ethnologue: Languages of the World, 17 edn. Dallas: SIL International, http://www.ethnologue.com, 2013.
7. Nunes JM. Using uniformat and GENE[RATE] to analyse data with ambiguities in population genetics. 10.6084/m9.figshare.984299.
8. Nunes JM. Tools for analysing ambiguous HLA data. Tissue Antigens 2007: 69: 203-5.
9. Nunes JM, Riccio ME, Tiercy JM, Sanchez-Mazas A. Allele frequency estimation from ambiguous data: using resampling schema in validating frequency estimates and in selective neutrality testing. Hum Biol 2011: 83: 437-47.
10. Sanchez-Mazas A, Buhler S, Nunes JM. A new HLA map of Europe: regional genetic variation and its implication for peopling history, disease-association studies and tissue transplantation. Hum Hered 2013: 76: 162-77.
11. Nunes JM, Riccio ME, Buhler S et al. Analysis of the HLA population data (AHPD) submitted to the 15th International Histocompatibility/Immunogenetics Workshop by using the GENE[RATE] computer tools accommodating ambiguous data (AHPD project report). Tissue Antigens 2010: 76: 18-30.
12. Riccio ME, Buhler S, Nunes JM et al. 16th IHIW: Analysis of HLA Population Data, with updated results for 1996 to 2012 workshop data (AHPD project report). Int J Immunogenet 2013: 40: 21-30.
13. Buhler S, Nunes JM, Nicoloso G, Tiercy J-M, Sanchez-Mazas A. The heterogeneous HLA genetic makeup of the Swiss population. PLoS One 2012: 7: e41400.
14. Menozzi P, Piazza A, Cavalli-Sforza L. Synthetic maps of human gene frequencies in Europeans. Science 1978: 201: 786-92.
15. Ryder LP, Andersen E, Svejgaard A. An HLA map of Europe. Hum Hered 1978: 28: 171-200.
16. Bodmer J, Cambon-Thomsen A, Hors J, Piazza A, Sanchez-Mazas A. Anthropology report: introduction. In: Charron D, ed. Genetic Diversity of HLA : Functional and Medical Implication: Proceedings of the 12th International Histocompatibility Workshop and Conference. Paris: EDK, 1997, 269-84.
17. Mack SJ, Tsai Y, Sanchez-Mazas A, Erlich HA. 13th International Histocompatibility Workshop Anthropology/Human Genetic Diversity Joint Report. Chapter 3: Anthropology/human genetic diversity population reports. In: Hansen JA, ed. Immunobiology of the Human MHC: Proceedings of the 13th International Histocompatibility Workshop and Conference. Seattle: IHWG Press, 2007, 580-652.
18. Buhler S, Megarbane A, Lefranc G, Tiercy JM, Sanchez-Mazas A. HLA-C molecular characterization of a Lebanese population and genetic structure of 39 populations from Europe to India-Pakistan. Tissue Antigens 2006: 68: 44-57.
19. Meyer D, Thomson G. How selection shapes variation of the human major histocompatibility complex: a review. Ann Hum Genet 2001: 65: 1-26.
20. Fernandez Viña MA, Hollenbach JA, Lyke KE et al. Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations. Philos Trans R Soc Lond B Biol Sci 2012: 367: 820-9.
21. Meyer D, Single RM, Mack SJ, Erlich HA, Thomson G. Signatures of demographic history and natural selection in the human major histocompatibility complex Loci. Genetics 2006: 173: 2121-42.
22. Sanchez-Mazas A, Fernandez-Vina MA, Middleton D et al. Immunogenetics as a tool in anthropological studies. Immunology 2011: 133: 143-64.
23. Buhler S, Sanchez-Mazas A. HLA DNA sequence variation among human populations: molecular signatures of demographic and selective events. PLoS One 2011: 6: e14643.
24. Solberg OD, Mack SJ, Lancaster AK et al. Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies. Hum Immunol 2008: 69: 443-64.
25. Sanchez-Mazas A, Lemaitre JF, Currat M. Distinct evolutionary strategies of human leucocyte antigen loci in pathogen-rich environments. Philos Trans R Soc Lond B Biol Sci 2012: 367: 830-9.
26. Currat M, Poloni ES, Sanchez-Mazas A. Human genetic differentiation across the Strait of Gibraltar. BMC Evol Biol 2010: 10: 237.
27. Epperson BK. Gustave Malecot, 1911-1998: population genetics founding father. Genetics 1999: 152: 477-84.
28. Ammerman AJ, Cavalli-Sforza LL. The Neolithic Transition and the Genetics of Populations in Europe. Princeton: Princeton University Press, 1984.
29. Barbujani G. Genetic evidence for prehistoric demographic changes in Europe. Hum Hered 2013: 76: 133-41.
30. Lao O, Lu TT, Nothnagel M et al. Correlation between genetic and geographic structure in Europe. Curr Biol 2008: 18: 1241-8.
31. Novembre J, Johnson T, Bryc K et al. Genes mirror geography within Europe. Nature 2008: 456: 98-101.
32. Tiercy JM, Claas FHJ. Impact of HLA diversity on donor selection in organ and stem cell transplantation. Hum Hered 2013: 76: 178-86.
33. Petersdorf EW. Optimal HLA matching in hematopoietic cell transplantation. Curr Opin Immunol 2008: 20: 588-93.
34. Mack SJ, Tu B, Lazaro A et al. HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies distinguish Eastern European Americans from the general European American population. Tissue Antigens 2009: 73: 17-32.
35. Mack SJ, Tu B, Yang R, Masaberg C, Ng J, Hurley CK. Human leukocyte antigen-A, -B, -C, -DRB1 allele and haplotype frequencies in Americans originating from southern Europe: contrasting patterns of population differentiation between Italian and Spanish Americans. Hum Immunol 2011: 72: 144-9.
36. Heath SC, Gut IG, Brennan P et al. Investigation of the fine structure of European populations with applications to disease association studies. Eur J Hum Genet 2008: 16: 1413-29.
37. Gonzalez-Galarza FF, Christmas S, Middleton D, Jones AR. Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acids Res 2011: 39: D913-9.
38. Robinson J, Halliwell JA, McWilliam H, Lopez R, Parham P, Marsh SGE. The IMGT/HLA database. Nucleic Acids Res 2013: 41: D1222-7.