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IGSR / International Genome Sample Resource

Expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups.

PanSNPdb / Pan-Asian SNP Consortium

Offers genome structural information pertaining to Asian populations in a familiar graphical comparative view. PanSNPdb offers pre-computed information of linkage disequilibrium (LD) blocks and their haplotypes on each chromosome. The comprehensive information in this database can be considered as worldwide data collection, but with special emphasis on Asian populations. The Haploview tool is also integrated into the PanSNPdb website: users can adjust the haplotype inferencing parameters in order to recalculate haplotype blocks ‘‘on-the-fly’’.

CTGA / Catalogue of Transmission Genetics in Arabs

Provides information on the occurrence of genetic disorders in the Arab populations. Information in CTGA is drawn from published research and mined hospital records. The database offers web-based basic and advanced search approaches. In either case, the final search result is a detailed HTML record that includes text-, URL- and graphic-based fields.

TPMD / Taiwan Polymorphic Marker Database

Offers experimental details and marker information allelotyped in population of Taiwan. TPMD is a shared database and resources for genotyping with microsatellite markers that reduces cost and errors of genotyping and facilitates disease gene mapping in human populations. This resource contains two major sections including the database for sharing useful microsatellite marker information and the resources for supporting consistent genotyping experiments.

Provides re-analyzed genotyping and next generation sequencing (NGS) data sets. PGG.Population permits understanding the genomic diversity and genetic ancestry of human populations. It contains a comprehensive description of the genomic diversity of over 350 population, including their genetic affinity, population structure, genetic admixture, ancestral architecture, and footprints of natural selection in their genomes.

SISu / Sequencing Initiative Suomi

Offers a way to search for data on sequence variants in Finns. SISu provides valuable summary data for researchers and clinicians as well as other people having an interest in genetics in Finland. With SISu, users can examine the attributes and appearance of different variants in Finnish cohorts and see their aggregate distribution in Finland visualized on a map. Users can search for summary data on single nucleotide variants (SNVs) and indels from exomes of over 10 000 individuals sequenced in disease-specific and population genetic studies. The SISu project is an international collaboration between multiple research groups aiming to build tools for genomic medicine. The first version of the SISu search engine was released in 2014. The project is coordinated in the Institute for Molecular Medicine Finland (FIMM) at the University of Helsinki.

Provides access to the annotations and summary statistics of The Taiwan Biobank (TWB). Taiwan View is a database that contains chromosome, position, single nucleotide polymorphism (SNP) ID, reference allele, alternative allele, counts of three genotypes, and call rate. It also provides an online query webpage for SNP information and an online genome-wide association study (GWAS) platform that allows users to upload their genotype data and perform GWASs using the Cochran–Armitage trend test.

COGR / Canadian Open Genetics Repository

A unified, open-access, clinical-grade genetic database that draws from the genetic holdings in place at clinical labs and hospitals across Canada. As clinical laboratories adopt modern genomics technologies, the need for this type of collaborative framework is increasingly important.

MFMD / Mediterranean Founder Mutation Database

A comprehensive database established to offer a web-based access to founder mutation data in Mediterranean population. The database provides an overview about the spectrum of founder mutations found in Mediterranean population to the scientific community. Furthermore, MFMD will help scientists to design more efficient diagnostic tests and provides beneficial information to understand the history and the migration events of the Mediterranean population.

ThaiMUT / Thailand Mutation and Variation database

Offers a web-based access to genetic mutation and variation information in Thai population. The mutation data cataloged in ThaiMUT database were derived from journal articles available in PubMed and local publications. In addition to collected mutation data, ThaiMUT also records genetic polymorphisms located in drug related genes. ThaiMUT could then provide useful information for clinical mutation screening services for Mendelian diseases and pharmacogenomic researches.

Cypriot National Genetic Database

An online repository of information about inherited disorders in the Cypriot population. You may search the Cypriot National Genetic Database by selecting a population, an ethnic group and finally the disorder required.

FinDis / Finnish Disease Database

Compiles information about genes for over 30 of the monogenic diseases behind the Finnish disease heritage. FinDis was first published in 2004 and recently updated by adding a current nomenclature and reference sequences. Moreover new causative variants and additional information for the sequence variants are added.

KOVA / Korean Variant Archive

Provides a whole exome sequencing (WES)-based genomic variant catalog from Korean individuals. KOVA is a database that compiles high-quality coding variant data from about 1,055 healthy Korean individuals by whole exome sequencing (WES). The database enables understanding of the Korean genome to assist with research and proper clinical treatment of Korean individuals.

VCGDB / Virtual Chinese Genome Database

Supports real-time high-performance searches using a web search engine and a genome browser. VCGDB is a dynamic genome database of the Chinese population based on whole-genome sequencing (WGS) of 194 individuals. This resource offers a strategy for processing large amounts of genomic data and is a robust database for genomics and disease-related studies in the Chinese population.

JG-SNP / Japanese Single Nucleotide Polymorphism for Geriatric Research

Collects information about genetic polymorphisms topic. JG-SNP is an online resource that informs about allele frequencies of single nucleotide polymorphisms (SNPs) of candidate genes and associations between SNPs and geriatric diseases. It provides an explanation on the significance of genetic polymorphisms and brief explanations on each geriatric disease. Comparison can be made between researchers’ data on SNPs of the candidate genes to obtain the allele frequencies in the elderly population.

HGVD / Human Genetic Variation Database

A reference database of genetic variations in the Japanese population. We collected exomic sequencing data of 1208 Japanese individuals from five institutes and a data set of common variants determined by Illumina’s BeadArray technology from 3248 individuals of Japanese cohorts. Although several sequencing projects are going on for the East Asian population including Japanese for East Asian-specific genetic diversity information, our data sets currently provide the largest catalog of genetic diversity on the protein coding regions in the Japanese population. We centralized these data sets into a newly developed public database—human genetic variation database (HGVD). HGDV will serve as a useful resource sharing system, which will be required for research in genetic profiling in the future as well as for the development of genetic tests to screen for clinically relevant variants in personal genomes.

Thai CNV database

A reference CNV database for Thais. Thai CNV database contains CNVs from 3,017 unrelated Thai individuals whose high-resolution Illumina SNP array-derived GWAS data were previously published. These subjects consisted of patients with infectious diseases namely tuberculosis, leprosy, and HIV/AIDS, patients with Thyrotoxic Hypokalemic Periodic Paralysis (THPP), and patients with Hb E/β-thalassemia.

Provides allele and genotype frequency data generated in the Indian Genome Variation Consortium (IGVC) project. The database harbors 4,229 SNPs from more than 900 candidate genes in contrasting Indian populations. Analysis shows that most of the markers are from genic regions. Further, a large fraction of genes are implicated in cardiovascular, metabolic, cancer and immune system-related diseases. Thus, the IGVC data provide a basal level variation data in Indian population to study genetic diseases and pharmacology.

Amish, Mennonite, and Hutterite Genetic Disorders Database

Assists in research and diagnosis of genetic conditions in Anabaptist groups. The Amish, Mennonite, and Hutterite Genetic Disorders Database focuses on single-gene Mendelian disorders and the specific mutations that have been reported. To navigate the database, user can search by disorder, mutation, clinical signs, symptoms, and can input either the OMIM number or the name of disorder, and is directed to the corresponding page.

iJGVD / Integrative Japanese Genome Variation Database

Provides allele frequency data for more than 4 000 000 autosomal single nucleotide variants (SNVs). iJGVD contains SNV alleles, genomic positions based on the GRCh37/hg19 coordinates, allele frequencies, the corresponding dbSNP IDs, P values for the Hardy–Weinberg equilibrium test, gene annotations and so on. It provides functions to explore the region surrounding an SNV based on chromosome coordinates. The database can be requested with gene symbol, rsSNP ID, or genomic position.

MyHVPDb / Malaysian Node of the Human Variome Project database

A specialized database was developed to store and manage the data based on genetic variations which also associated with health and disease of Malaysian ethnic groups. MyHVPDb provides only information about the genetic variations and mutations found in the Malays. In the near future, it will expand for the other Malaysian ethnics as well. The data sets are specified based on diseases or genetic mutation types which have three main subcategories: single nucleotide polymorphism (SNP), copy number variation (CNV) followed by the mutations which code for the common diseases among Malaysians.

A database which hosts whole-genome variant frequencies for 1000 Swedish individuals generated within the SweGen project. SweGen is intended to be used as a resource for the research community and clinical genetics laboratories. Individual positions in the genome can be viewed using the Data Beacon or ExAC Browser. Please note that the 1000 individuals included in the SweGen project represent a cross-section of the Swedish population and that no disease information has been used for the selection. The frequency data may therefore include genetic variants that are associated with, or causative of, disease.

TMC-SNPdb / Tata Memorial Centre-SNP database

A database of ‘normal’ germline variants derived from Indian (nonEuropean Caucasian population). TMC-SNPdb is the first open source, flexible, upgradable, and freely available single nucleotide polymorphism (SNP) database, not yet included in the public databases with predominant Caucasian representations. Beyond cancer somatic analyses, we anticipate utility of the TMC-SNPdb in several Mendelian germline diseases. This database is flexible to accommodate the need for customization by allowing inclusion of similar datasets from additional individuals.

CAAPA / Consortium on Asthma among African-ancestry Populations in the Americas

Hosts whole genome sequences available on 883 individuals from 19 case-control studies of asthma. CAAPA uses these data to summarize the genomic contributions to individuals of African ancestry. The original selection criteria were (i) self-reported African ancestry; (ii) a physician’s diagnosis of asthma for cases or a negative history of asthma symptoms and asthma medication usage for controls. Recruitment sites included 9 cities in the US (Atlanta, Baltimore/Washington, Chicago, Detroit, Nashville, New York City, San Francisco, Jackson, MS, and Winston-Salem NC), 4 populations in the Caribbean (Barbados, Dominican Republic, Jamaica, and Puerto Rico), 4 in Central/South America (Brazil, Honduras, and 2 in Colombia) and 2 populations representing West Africa (Nigeria and Gabon), from which most ancestral founders of the African diaspora originated.

Provides access to single nucleotide polymorphism (SNP) data for Korean population. KoVariome is a comprehensive database of genomic variations and corresponding metadata, constructed based on whole genome sequencing (WGS) data from 50 unrelated Korean individuals who responded to questionnaires detailing body characteristics, habits, allergies, family histories, and physical conditions related to 19 disease classes. It was used to predict candidate loci, inheritance patterns, and genetic risk for several diseases. The database can be useful for biomedical researchers and health practitioners.

Turkish Human Mutation Database

Provides a database about human mutations of the turkish population.

KRGDB / Korean Reference Genome DB

Aims to furnish users with a comprehensive map of the Korean genomic variants. KRGDB is a genome variants database that contains information from about 622 healthy individuals. It can be useful for studying disease association and population genetics.

HLD / The Human Life-Table Database

Consists of a collection of population life tables for a multitude of countries covering several years. HLD is an online database that provides information about the evolution of human mortality by providing a quantitative life-table description of mortality patterns. It also supplies information on calculation techniques as well as on ways of publishing mortality data used in different countries in different times.

ThaiSNPdb / Thailand SNP database

Determines Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs) in Thai population by using 5th generation Affymetrix SNP genotyping array, each array contains approximately 500,000 known SNP genotyping positions. ThaiSNPdb allows easy browsing and comparisons of genetic polymorphism data from Thai populations as well as others, which were retrieved from several public variation databases including NCBI dbSNP, HapMap3, JSNP and Database of Genomic Variant (DGV).

HVDB / Human Variation Database

Stores information about human mutation data. HVDB contains several types of information such as structural variations and repeat variations with statistical genetics analysis results. It supplies different ways of browsing: by disease name, gene name, or chromosome. It also offers overview of single-nucleotide polymorphism (SNP) density or summary of all diseases.

[email protected]

A public database of ethnically variant single-nucleotide polymorphisms (ESNPs) with annotation information that currently contains 100 736 ESNPs from 10 138 genes. The [email protected] database can be queried using gene symbols, RefSeq mRNA IDs, dbSNP rs numbers and lists containing multiple genes.

Provides access to information about sequence polymorphism. Polymorphix is a database, dedicated to within-species sequence polymorphism, that organizes GenBank/EMBL sequences into within-species sequence ‘families’, using both nucleotide similarity and bibliographic criteria. It contains more than 200 million bases, 200 000 sequences and 18 000 bibliographic references and allows simple or elaborate queries on EMBL/GenBank fields (species names, keywords, etc.), and a blast-assisted selection of families.

KGVDB / Korean Genomic Variant Database

Provides multi-class CNV regions and well-tagged SNP information. The data were obtained from 4694 individuals using two different genotyping platforms and publicly available CNV data. The major features of KGVDB that are different from others include the following: (i) polymorphic CNV regions identified under strict quality controls and manual curation; (ii) CNV information from Korean populations to supplement currently biased ethnic information; (iii) large dataset of CNVs tagged with SNPs from 4694 individuals using two different genotyping platforms (SNP array and CGH array); (iv) rich information on tagging SNPs, including frequencies in HapMap populations; and (v) copy number states of the reference sample using log2 ratios from two kinds of CGH data and the depth of coverage from whole-genome sequencing data. The large dataset of KGVDB will provide a rich public resource for the study of CNV and SNP.

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1 - 2 of 2 results

Big data scientist National institute of Plant Gneome Reseaech (NIPGR)

Research Interests Gene fusion detection in Plants Fusion transcripts (i.e., chimeric RNAs) resulting from gene fusions are well known in case of human. But, in plants, this phenomenon is not yet explored. We are planning to discover the fusion transcripts/gene fusions in different type of plants by using RNA-Seq datasets. Further, we are planning to understand the mechanism of gene fusion formation and significance of fusions in plants. Whole genome and transcriptome sequencing data analysis of Plants In this era of Next Generation Sequencing (NGS), there is huge amount of sequencing data available in the public domain. Any novel finding from these available datasets is major challenge for a computational biologist. We are interested in the analysis of whole genome and transcriptome sequencing data of different plants to fetch out the useful information from those datasets, with the help of bioinformatics tools. Currently, we are planning to study the gene clusters of secondary metabolite pathways in different plants. Development of webservers, databases and computational pipelines for plant research Development of database is necessary to compile and share the information with scientific community. We are dedicated to develop useful databases and webserver for plant research. Another area of interest is to develop automated pipelines and tools for the analysis of high throughput genomics data, generated by NGS technologies. Professional & Academic Background Staff Scientist II (May 2017- present): National Institute of Plant Genome Research (NIPGR), New Delhi, India Postdoctoral Research Associate (2015-2017): University Of Virginia, Charlottesville, VA, USA Research Scientist (2014-2015): Sir Ganga Ram Hospital, New Delhi, India PhD Bioinformatics (2009-2014): Bioinformatics Centre, Institute of Microbial Technology (IMTECH), Chandigarh under Jawaharlal Nehru University (JNU), New Delhi, India M.Sc. Life Sciences (2007-2009): Jawaharlal Nehru University (JNU), New Delhi, India B.Sc. Biotechnology (2004-2007): Jamia Millia Islamia (JMI), New Delhi, India Awards and Fellowships Junior and Senior Research Fellowship (2009-2014): Council of Scientific and Industrial Research (CSIR), New Delhi, India GATE (Graduate Aptitude Test in Engineering): Qualified in years 2008 and 2009 Scientific Contributions/ Recognitions Associate editor: Journal of Translational Medicine. Editorial Board Member of Journal: Theoretical Biology and Medical Modelling. Reviewer: PloS One, BMC Genomics, BMC Bioinformatics, BMC Biology, BMC Biotechnology, Frontiers in Physiology and several other journals. Web Resources/ Databases (Developed/ Contributed) A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer (http://www.imtech.res.in/raghava/cancertope/) GenomeABC: A webserver for benchmarking of genome assemblers. (http://crdd.osdd.net/raghava/genomeabc/). Genomics web portal page. (http://crdd.osdd.net/raghava/genomesrs/). Map/Alignment module of CancerDr: Cancer Drug Resistance Database. (http://crdd.osdd.net/raghava/cancerdr/). Short reads and contigs alignment module of PCMDB: Pancreatic cancer methylation database. (http://crdd.osdd.net/raghava/pcmdb/). Burkholderia sp. SJ98 database. (http://crdd.osdd.net/raghava/genomesrs/burkholderia/). Rhodococcus imtechensis RKJ300 database. (http://crdd.osdd.net/raghava/genomesrs/rkj300/). Genotrick: A pipeline for whole genome assembly and annotation of Genomes (http://crdd.osdd.net/raghava/genomesrs/genotrick/) Development of Debian packages in OSDDlinux: A Customized Operating System for Drug Discovery. (http://osddlinux.osdd.net/). A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. (http://crdd.osdd.net/raghava/mtbveb/).

FusionFinder comrad

Mahantesh Biradar

‎Graduate PhD researcher focusing on Cardiovascular Epidemiology & Social Media Enthusiast Research Stash

I'm a Graduate PhD researcher in the area of Biomedical Science and focussing on the Pharmacogenomics/Pharmacogenomics of Diabetes and related complications

National/ethnic variation databases | Genome annotation

Many general and locus specific mutation disease databases have been established (Ruangrit et al., 2008; Tan et al., 2006; Kleanthous et al., 2006; Teebi et al., 2002). It is also well known that different ethnic backgrounds may have different disease-causing mutation(s) and variation(s). Therefore, population specific databases are beneficial not only for future surveys, but also for those conducting studies in the etiology of genetic disorders and distribution of the mutations. Source text: Halim-Fikri et al., 2015.

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DNA sequence databases

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