Indian genetic disease database

Published online 30 October 2010 Nucleic Acids Research, 2011, Vol. 39, Database issue D933–D938 doi:10.1093/nar/gkq1025 Indian genetic disease database Sanchari Pradhan1, Mainak Sengupta2, Anirban Dutta1, Kausik Bhattacharyya2, Sumit K. Bag1, Chitra Dutta1 and Kunal Ray2,* 1 Structural Biology and Bioinformatics Division and 2Molecular and Human Genetics Division, Indian Institute of Chemical Biology (a unit of CSIR), Kolkata, India Received August 14, 2010; Revised October 6, 2010; Accepted October 10, 2010 ABSTRACT INTRODUCTION Indians, representing about one-sixth of the world population, consist of several thousands of endogamous groups with strong potential for excess of recessive diseases. However, no database is available on Indian population with comprehensive information on the diseases common in the country. To address this issue, we present Indian Genetic Disease Database (IGDD) release 1.0 (http://www .igdd.iicb.res.in)—an integrated and curated repository of growing number of mutation data on common genetic diseases afflicting the Indian populations. Currently the database covers 52 diseases with information on 5760 individuals carrying the mutant alleles of causal genes. Information on locus heterogeneity, type of mutation, clinical and biochemical data, geographical location and common mutations are furnished based on published literature. The database is currently designed to work best with Internet Explorer 8 (optimal resolution 1440  900) and it can be searched based on disease of interest, causal gene, type of mutation and geographical location of the patients or carriers. Provisions have been made for deposition of new data and logistics for regular updation of the database. The IGDD web portal, planned to be made freely available, contains user-friendly interfaces and is expected to be highly useful to the geneticists, clinicians, biologists and patient support groups of various genetic diseases. The load of genetic diseases varies widely between different populations depending on its structure, reproductive practices and other factors. Control and management of the genetic disorders depend on identification of the variants in the genome that are causally linked with the disease. The spectrum of such variants, i.e. mutations, is different in different population groups. Remarkable progress has been made towards capturing the genomic variation in the context of genetic diseases with the advancement of DNA sequencing technologies, the capacity to handle large amount of data by building databases and faster dissemination of information through the worldwide web. It is, therefore, not surprising that the initial modest beginning of Mendelian Inheritance of Man (MIM) transformed later to Online MIM (OMIM). Currently, the most expanded version of database specifically cataloging the mutations relating genetic diseases across globe is Human Gene Mutation Database (HGMD). In addition, special interest groups generated ‘locus specific databases’ (LSDBs) and lately ‘national and ethnic mutation databases’ (NEMDBs) have also emerged containing mutational data for specific countries (Table 1). Such endeavor enormously boosts the efforts related to diagnosis of genetic diseases, detection of carriers for disease management and control and genetic counseling to mitigate the suffering of the affected families. However, no such database on genetic diseases exists for India, a country inhabited by more than a billion people and predicted to have a high load of recessive disorders in the population. The evolutionary history of primitive Indian ethnic groups and migration from Africa, middle-east and west Asia, southern China and south-east Asia has added to the *To whom correspondence should be addressed. Tel: +91 33 2483 1984; Fax: +91 33 2473 5197/+91 33 2472 3967; Email: , Present address: Sumit K. Bag, National Botanical Research Institute, Lucknow, India. The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors. ß The Author(s) 2010. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. NA: Not applicable; INR: Information not retrievable. a Currently available/accessible online; Singapore Human Mutation and Polymorphism Database is not included since the variants listed in the database are not distinctly categorized into ‘mutations’ or ‘polymorphisms’. b Not specified whether total or unique mutations. c Database records only unique mutations. d Patient-specific record of IGDD includes personal data (e.g. age, sex, ethnicity, geographical location, etc.) and clinical and bio-chemical data. Yes (1) No Yes (2) Yes (3) Yes (2) Yes (4) Yes (5) Yes (6) No Yes (7) No Yes (8) This report 2002 September 2003 August 2006 June 2006 August 2006 July 2010 January 2006 February 2010 April 2006 August 2008 January2006 June 2009 August 2010 No Yes No No No No No No No Yes No Yes Yes No No No No No No No No No No No No Yesd INR 415 85 221 74 904 60 229 68 518 57 1226 780 1362b 466 1478 3179 2614 2581 880 INR 68c 589 57c 3553 6647 5.30 68.69 1.05 10.68 68.69 7.60 0.02 28.56 7.78 66.40 71.51 NA 1180.16 Finnish Disease Database (Finland) Iranian Human Mutation Database (Iran) The Cypriot National Mutation Frequency Database (Cyprus) The Hellenic National Mutation Database (Greece) The Iranian National Mutation Frequency Database (Iran) The Israeli National Genetic Database (Israel) The Lebanese National Mutation Frequency Database (Lebanon) The Moroccan Human Mutation Database (Morocco) The Serbian National Mutation Frequency Database (Serbia) Thailand Human Mutation and Variation database (Thailand) Turkish Human Mutation Database (Turkey) FINDbase worldwide (92 populations) Indian Genetic Disease Database (India) INR INR INR INR INR INR INR INR INR INR INR INR 5760 35 98 19 14 8 330 6 138 6 119 2 32 52 Unique mutations Patients/ carriers studied Country population (in millions) Databases Table 1. IGDD compared to existinga NEMDBs (National and Ethnic Mutation Databases) Diseases Total mutations recorded Patientspecific records Summary statistics provided Launched/ last updated Published D934 Nucleic Acids Research, 2011, Vol. 39, Database issue genetic diversity of the country (9). However, religion, language and geographical location of habitat serve as barriers to random mating in the Indian population. Inbreeding is practiced in some geographical regions of India (population-inbreeding coefficient: 0.00 to 0.20) (10). Thus, the overall heterogeneity of population along with the underlying endogamy makes India, a unique case of importance with respect to a high prevalence of genetic diseases and mutation (...truncated)