Genome Informatics

The Golden Helix Foundation has actively participated to develop a number of National/Ethnic Genetic databases and related software that record the incidence of genetic diseases and the corresponding genome variation spectrum, with clinical relevance in various populations and ethnic groups worldwide. These databases are hosted in the Golden Helix Server.

National/Ethnic genetic databases
Genetic databases are gradually assuming an increasing importance in all areas of health care. The National and Ethnic Mutation Databases are continuously updated mutation depositories, recording extensive information over the described genetic heterogeneity of an ethnic group or population. The Golden Helix Foundation has devoted a significant amount of effort to develop the Golden Helix Server, where a number of National/Ethnic Genetic databases are hosted. The Golden Helix Foundation also developed an off-the-shelf bioinformatics suite to facilitate development and curation of National/Ethnic Genetic and Mutation frequency databases. Together with the central and locus-specific databases, those resources not only enhance awareness over the various genetic disorders but also facilitate the provision of genetic services and provide useful insights into the genetic history of human populations.

In 2003, the Golden Helix Foundation has developed specialized software, namely ETHNOS that allows easy development and curation of National and Ethnic Mutation Databases. This software has enabled the development of a number of these resources in various populations, such as Greek, Cypriot, Iranian, Lebanese, Israeli, Egyptian, etc. Descriptions of several of these databases have been published in many peer-reviewed scientific journals and presented in European Human Genetics conferences.

Also, based on the same concept, FINDbase, a worldwide database to record frequencies of causative mutations and pharmacogenetic markers, has been developed. This database has been recently refurbished including many new features and functionalities.

The above projects have been mostly in the framework of collaborative research funded by the European Commission, where members of the Golden Helix Foundation participate as partners or subcontractors.

These projects have been supported by:

Related publications

  1. Patrinos GP, van Baal S, Petersen MB, Papadakis MN. (2005). The hellenic national mutation database: A prototype database for mutations leading to inherited disorders in the ellenic population. Hum Mutat, 25(4): 327-333.
  2. Patrinos GP, Brookes A (2005). DNA, disease and databases: Disastrously deficient. Trends Genet, 21(6): 333-338.
  3. 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(6): 598-599.
  4. van Baal S, Kaimakis P, Phommarinh M, Koumbi D, Cuppens H, Riccardino F, Macek M Jr, Scriver CR, Patrinos GP. (2007). FINDbase: A relational database recording frequencies of genetic defects leading to inherited disorders worldwide. Nucleic Acids Res, 35(Database issue): D690-D695.
  5. 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(10): 944-949.
  6. 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, Blcker 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, Daz 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, Mslein 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, Tpel 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(4):496-510.
  7. 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(5): 361-368.
  8. Georgitsi M, Viennas E, Gkantouna V, Christodoulopoulou E, Zagoriti Z, Tafrali C, Ntellos F, Giannakopoulou O, Boulakou A, Vlahopoulou P, Kyriacou E, Tsaknakis J, Tsakalidis A, Poulas K, Tzimas G, Patrinos GP. (2011). Population-specific documentation of pharmacogenomic markers and their allelic frequencies in FINDbase. Pharmacogenomics 12(1): 49-58.
  9. Georgitsi M, Viennas E, Gkantouna V, van Baal S, Petricoin EF, Poulas K, Tzimas G, Patrinos GP. (2011). FINDbase: A worldwide database for genetic variation allele frequencies updated. Nucleic Acids Res 39(Database issue):D926-D932.