Recommendations for genetic variation data capture in developing countries to ensure a comprehensive worldwide data collection

Human Mutation

Volumn 32, Issue 1, 2011, Pages 2-9

  Patrinos, George P ^a,n   Al Aama, Jumana ^b   Al Aqeel, Aida ^c   Al Mulla, Fahd ^d   Borg, Joseph ^e   Devereux, Andrew ^f   Felice, Alex E ^e   Macrae, Finlay ^g   Marafie, Makia J ^h   Petersen, Michael B ⁱ   Qi, Ming ^j   Ramesar, Rajkumar S ^k   Zlotogora, Joel ^l   Cotton, Richard G H ^m  

^a UNIVERSITY OF PATRAS   (Greece)

^b KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

^c KING FAISAL SPECIALIST HOSPITAL AND RESEARCH CENTER   (Saudi Arabia)

^d KUWAIT UNIVERSITY   (Kuwait)

^e UNIVERSITY OF MALTA   (Malta)

^f ST MARY S HOSPITAL   (United Kingdom)

^g UNIVERSITY OF MELBOURNE   (Australia)

^h AL SABAH HOSPITAL   (Kuwait)

ⁱ Institute of Child Health   (Greece)

^j ZHEJIANG UNIVERSITY   (China)

^k UNIVERSITY OF CAPE TOWN   (South Africa)

^l MINISTRY OF HEALTH   (Israel)

^m FLOREY INSTITUTE OF NEUROSCIENCE AND MENTAL HEALTH   (Australia)

ⁿ UNIVERSITY OF MELBOURNE   (Australia)

more..

Author keywords

Developing countries; Genetic variation; National ethnic mutation databases; Populations

Indexed keywords

AFRICA; ARTICLE; DATA BASE; DEVELOPING COUNTRY; DNA POLYMORPHISM; ECONOMIC ASPECT; GENE MUTATION; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; INDIGENOUS PEOPLE; POPULATION GENETICS; PRIORITY JOURNAL;

DATA COLLECTION; DEVELOPING COUNTRIES; GENETIC VARIATION; HUMANS;

EID: 78650458147     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.21397     Document Type: Article

References (36)

1. Al Aqeel AI. 2007. Islamic ethical framework for research into and prevention of genetic diseases. Nat Genet 39:1293-1298.
2. Anonymous 2008. Human variome microattribution reviews. Nat Genet 40:1.
3. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E, Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59.
4. Bhan A, Singh JA, Upshur RE, Singer PA, Daar AS. 2007. Grand challenges in global health: engaging civil society organizations in biomedical research in developing countries. PLoS Med 4:e272.
5. Cotton RG, Al Aqeel AI, Al-Mulla F, Carrera P, Claustres M, Ekong R, Hyland VJ, Marafie MJ, Paalman MH, Patrinos GP, Qi M, Ramesar RS, Scott RJ, Sijmons RH, Sobrido MJ, Vihinen M. 2009. Capturing all disease causing mutations for clinical and research use: towards an effortless system for the human variome project. Genet Med 11:843-849.
6. Cotton RG, Appelbe W, Auerbach AD, Becker K, Bodmer W, Boone DJ, Boulyjenkov V, Brahmachari S, Brody L, Brookes A, Brown AF, Byers P, Cantu JM, Cassiman JJ, Claustres M, Concannon P, Cotton RG, den Dunnen JT, Flicek P, Gibbs R, Hall J, Hasler J, Katz M, Kwok PY, Laradi S, Lindblom A, Maglott D, Marsh S, Masimirembwa CM, Minoshima S, de Ramirez HZ, Scriver CR, Sherry S, Shimizu N, Shimizu N, Stein L, Tadmouri GO, Taylor G, Watson M. 2007. Recommendations of the 2006 Human Variome Project meeting. Nat Genet 39:433-436.
7. Fokkema IF, den Dunnen JT, Taschner PE. 2005. LOVD: easy creation of a locus-specific sequence variation database using an "LSDB-in-a-box" approach. Hum Mutat 26:63-68.
8. Georgiou I, Makis A, Chaidos A, Bouba I, Hatzi E, Kranas V, Zilidis C, Bourantas KL. 2003. Distribution and frequency of beta-thalassemia mutations in northwestern and central Greece. Eur J Haematol 70:75-78.
9. Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR. 2005. Whole-genome patterns of common DNA variation in three human populations. Science 307:1072-1079.
10. Hoffman R. 2008. A wiki for the life sciences where authorship matters. Nat Genet 40:1047-1051.
11. Indian Genome Variation Consortium 2005. The Indian Genome Variation database (IGVdb): a project overview. Hum Genet 118:1-11.
12. Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Díaz C, Dobrowolski S, Dos Santos MR, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, Hancock JM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SG, Matsubara Y, Messiaen LM, Mölslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AM, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, Yoo HS. 2009. Planning the Human Variome Project. The Spain report. Hum Mutat 30:496-510.
13. Kleanthous M, Patsalis PC, Drousiotou A, Motazacker M, Christodoulou K, Cariolou M, Baysal E, Khrizi K, Pourfarzad F, Moghimi B, van Baal S, Deltas CC, Najmabadi S, Patrinos GP. 2006. The Cypriot and Iranian National Mutation databases. Hum Mutat 27:598-599.
14. Lederer CW, Basak AN, Aydinok Y, Christou S, El-Beshlawy A, Eleftheriou A, Fattoum S, Felice AE, Fibach E, Galanello R, Gambari R, Gavrila L, Giordano PC, Grosveld F, Hassapopoulou H, Hladka E, Kanavakis E, Locatelli F, Old J, Patrinos GP, Romeo G, Taher A, Traeger-Synodinos J, Vassiliou P, Villegas A, Voskaridou E, Wajcman H, Zafeiropoulos A, Kleanthous M. 2009. An electronic infrastructure for research and treatment of the thalassemias and other hemoglobinopathies: the Euro-mediterranean ITHANET project. Hemoglobin 33:163-176.
15. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Berman J, Rogers YH, Frazier ME, Scherer SW, Strausberg FL, Venter JC. 2007. The diploid genome sequence of an individual human. PLoS Biol 5:e254.
16. Mégarbané A, Chouery E, van Baal S, Patrinos GP. 2006. The Lebanese National Mutation frequency databases. Eur J Hum Genet 14(Suppl. 1):365.
17. Metspalu A. 2002. Estonian Genome Project-before the take-off and take-off. Bioinformatics 18(Suppl. 2):S152.
18. Nelson MR, Bryc K, King KS, Indap A, Boyko AR, Novembre J, Briley LP, Maruyama Y, Waterworth DM, Waeber G, Vollenweider P, Oksenberg JR, Hauser SL, Sitrnadel HA, Kooner JS, Chambers JC, Jones B, Mooser V, Bustamanta CD, Roses AD, Burns DK, Ehm MG, Lia EH. 2008. The population reference sample, POPRES: a resource for population, disease, and pharmacological genetics research. Am J Hum Genet 83:347-358.
19. Papachatzopoulou A, Vantarakis A, Kourakli A, Stavrou E, Frangou E, Patrinos GP, Athanassiadou A. 2010. Documentation of the incidence of beta-thalassemia and HBB mutation frequencies in South-Western Greece. Hemoglobin 34:333-342.
20. Patrinos GP. 2006. National/Ethnic mutation databases: recording populations' genography. Hum Mutat 27:879-887.
21. Patrinos GP, Brookes AJ. 2005. DNA, diseases and databases: disastrously deficient. Trends Genet 21:333-338.
22. Patrinos G, Petricoin E. 2009. A new scientific journal linked to a genetic database: towards a novel publication modality. Hum Genomics Proteomics 1:e597478.
23. Patrinos GP, Giardine B, Riemer C, Miller W, Chui DH, Anagnou NP, Wajcman H, Hardison RC. 2004. Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies. Nucleic Acids Res 32:D537-D541.
24. Patrinos GP, van Baal S, Petersen MB, Papadakis MN. 2005. The Hellenic National Mutation database: a prototype database for inherited disorders in the Hellenic population. Hum Mutat, 25:327-333.
25. Povey S, Al Aqeel AI, Barash CI, Cambon-Thomsen A, Dalgleish R, den Dunnen JT, Firth HV, Greenblatt M, Parker M, Patrinos GP, Savige J, Sobrido MJ, Cotton RG. 2010. Practical Guidelines addressing ethical issues pertaining to the curation of human Locus specific variation databases (LSDBs). Hum Mutat 31:1179-1184.
26. Saadallah AA, Rashed MS. 2007. Newborn screening: experiences in the Middle East and North Africa. J Inherit Metab Dis 30:482-489.
27. Samara M, Chiotoglou I, Kalamaras A, Likousi S, Chassanidis C, Vagena A, Vagenas C, Eftichiadis E, Vamvakopoulos N, Patrinos GP, Kollia P. 2007. Large-scale population genetic analysis for hemoglobinopathies reveals different mutation spectra in central Greece compared to the rest of the country. Am J Hematol 82:634-636.
28. Singer PA, Daar AS. 2001. Harnessing genomics and biotechnology to improve global health equity. Science 294:87-89.
29. Tadmouri GO, Al Ali MT, Al-Haj Ali S, Al Khaja N. 2006. CTGA: the database for genetic disorders in Arab populations. Nucleic Acids Res 34:D602-D606.
30. van Baal S, Kaimakis P, Phommarinh M, Koumbi D, Cuppens H, Riccardino F, Macek Jr M, Scriver CR, Patrinos GP. 2007. FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide. Nucleic Acids Res 35:D690-D695.
31. van Baal S, Zlotogora J, Lagoumintzis G, Gkantouna V, Tzimas I, Poulas K, Tsakalidis A, Romeo G, Patrinos GP. 2010. ETHNOS: A versatile electronic tool for the development and curation of National Genetic databases. Hum Genomics 4:361-368.
32. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, FanW, Zhang J, Li J, Guo Y, Feng B, Li H, Lu Y, Feng X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, Ma L, Li G, Yang Z, Zhang G, Liu D, Lu Z, Li N, Guo G, Zhang J, Ye J, Fang L, Hao Q, Chen Q, Liang Y, Su Y, San A, Ping C, Yang S, Chen F, Li L, Zhou K, Zheng H, Ren Y, Yang L, Gao Y, Yang G, Li Z, Feng X, Kristiansen K, Wong GK, Nielsen R, Durbin R, Bolund L, Zhang X, Li S, Yang M, Wang J. 2008. The diploid genome sequence of an Asian individual. Nature 456:60-65.
33. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Marqulies M, Weinstock GM, Gibbs RA, Rothberg GM. 2008. The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872-876.
34. Wong ML, Chia KS, Wee S, Chia SE, Lee J, Koh WP, Shen HM, Thumboo J, Sofjan D. 2004. Concerns over participation in genetic research among Malay-Muslims, Chinese and Indians in Singapore: a focus group study. Community Genet 7:44-54.
35. Zlotogora J, van Baal S, Patrinos GP. 2007. Documentation of inherited disorders and mutation frequencies in the different religious communities in Israel in the Israeli National Genetic Database. Hum Mutat 28:944-949.
36. Zlotogora J, van Baal S, Patrinos GP. 2009. The Israeli National Genetic Database. IMAJ 6:373-375.