What is New

Asian Genomes Browser in beta

posted Apr 24, 2012, 11:44 PM by Vinod Scaria   [ updated Apr 24, 2012, 11:44 PM ]

The Asian Genomes Browser integrating variation information from all published Asian Genomes is now in beta testing. We hope to incorporate more datasets for personal genomes from other Asian countries that are currently ongoing. We hope to integrate other post-genomic annotation datasets and computational methods for functional annotation of variations to provide a comprehensive resource towards understanding biological significance of the variations and a starting point towards understanding similarities, differences and provide a baseline dataset towards addressing biological questions like disease predisposition and phenomena like natural seletion. 

Please feel free to suggest a resource that we would have missed to Dr. Vinod Scaria vinods[at]igib.in

Indian Genome Published

posted Apr 24, 2012, 11:39 PM by Vinod Scaria

Abstract

Whole genome sequencing of personal genomes has revealed a large repertoire of genomic variations and has provided a rich template for identification of common and rare variants in genomes in addition to understanding the genetic basis of diseases. The widespread application of personal genome sequencing in clinical settings for predictive and preventive medicine has been limited due to the lack of comprehensive computational analysis pipelines. We have used next-generation sequencing technology to sequence the whole genome of a self-declared healthy male of Indian origin. We have generated around 28X of the reference human genome with over 99% coverage. Analysis revealed over 3 million single nucleotide variations and about 490,000 small insertion–deletion events including several novel variants. Using this dataset as a template, we designed a comprehensive computational analysis pipeline for the systematic analysis and annotation of functionally relevant variants in the genome. This study follows a systematic and intuitive data analysis workflow to annotate genome variations and its potential functional effects. Moreover, we integrate predictive analysis of pharmacogenomic traits with emphasis on drugs for which pharmacogenomic testing has been recommended. This study thus provides the template for genome-scale analysis of personal genomes for personalized medicine.

Citation: 
Patowary A, Purkanti R, Singh M, Chauhan RK, Bhartiya D, Dwivedi OP, Chauhan G, Bharadwaj D, Sivasubbu S, Scaria V.
Systematic analysis and functional annotation of variations in the genome of an Indian individual.
Hum Mutat. 2012 Mar 27. doi: 10.1002/humu.22091. [Epub ahead of print]

Datasets:
Variation Data at the Asian Genome Browser  [Asian Genome  Browser] 


OpenPGx at FAOBMB 2011

posted Sep 5, 2011, 1:37 AM by Vinod Scaria   [ updated Sep 5, 2011, 1:45 AM ]

OpenPGx will be part of the presentation entitled "Comparative Personal genomics: Annotating and Comparing Complete Human genomes" at the Asian Genomes session at the FAOBMB Annual meeting 

2011 Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) Conference
Theme: Creativity and Innovation in Life Science Research, Enterprise and Education
5 – 7 October 2011
Level 4, Matrix Building, Biopolis, Singapore

OpenPGx Annotation Manual ver 0.5 beta

posted Aug 19, 2011, 3:01 AM by Vinod Scaria   [ updated Aug 19, 2011, 3:51 AM ]

We are happy to release the OpenPGx Annotation Manual ver 0.5 beta.
The Manual outlines the OpenPGx Annotation Interface and describes in simple terms how to go about annotating Pharmacogenomics datasets and literature evidence.

The manual is stuill in beta and we would be keen to have your sugegstions/comments on the same.This manual would not have been possible without the dedication and support from Mr Gaurav Kandoi and Dr. Yasha Hasija from the Delhi Technological University.

Please feel free to contact vinods@igib.in with your comments and suggestions.



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