Thursday, September 16, 2010

IGVBrowser Publication

I would like to share the link of IGVBrowser publication -“IGVBrowser–a genomic variation resource from diverse Indian populations” available at http://database.oxfordjournals.org/content/2010/baq022.full
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IGVBrowser updation : CNV data of 26 Indian Populations will be added soon !!!!!!!!

Tuesday, June 29, 2010

We are Not Alone .....

Next Era : In "Metagenomics" - Human Microbiome
A beautiful story - "the tale of our other genome" by Liping Zhao

This unravels the intersting Facts:
Some 1.5 kilograms of bacteria colonize the human gut, with others inhabiting the external and internal surfaces of the body.

Infact, only 10% of the total number of cells in the human body consists of human cells,with the rest coming from symbiotic bacterial cell.

It is estimated that the human gut microbiome contains around 1,000 bacterial species

Qin et al. used next-generation sequencing technology — which in a single run can generate millions of short DNA reads — to create a catalogue of 3.3 million genes from 124 Euro-
pean faecal samples collected as part of the MetaHIT project.

The International Human Microbiome Consortium aims to generate a reference set of 1,000
microbial genomes.

I think Diversity of Indian Microbiome will also be a intersting study...,

Wednesday, June 2, 2010

BUzz Word : Synthetic Genomics and its applications All about it

Some one says: “God Loses Monopoly or open source community) known as evolution"

Anothony Forster, a molecular biologist at Vanderbilt University in Nashville, Tennessee and other emphasize that the work of Venter didn't truly create synthetic life form because the genome was put in to an already exsisting cell.

News : Synthetic Genome Brings New Life to Bacterium a very precise description what actually happens -- hurdles and achievement.
Paper in Science : Creation of a Bacterial Cell controlled by a chemically synthesized Genome : Broad and Complete view of story.

Research on Small Genomes - Implication for Synthetic Biology -- A review article : Its helps me to visualize Synthetic Genomics for future, Few points points from paper which helps us to understand the applications of Synthetic Biology --
>>>>>Endosymbionts with synthetic genomes for clinical use fordelivery of drugs to humans and animals.
>>>>>From genome sequence to synthesis to phenotype -- Next gen sequencing provide opportunities to sequence whole genomes of bacterias that cannot be cultured in laboratory. Comparative genomics of such unculturable organisms will provide information about the combination and flux of genes in different environments and generate hypothesis about how the genomic diversity is in the phenotypic diversity of the community as whole.
>>>>>Probiotics : Bacteria used in food products as probiotics.

Rest, Synthetic Genomics a company working on idea tells about its application for:
energy – Fuels and Chemicals: http://www.syntheticgenomics.com/what/renewablefuels.html
Explore it for much more

Sunday, May 16, 2010

Wednesday, May 5, 2010

open source softwares for Everyone......

This post of mine is motivated by one of the  paragraph in Nature review by Anthony Brookes -- Genotype-Phenotype databases: challenges and solutions for the post-genomic era. Contribution of the scientific community in open source softwares makes life of a researcher very relaxing....... less effort, better ouputs. Genomic researchers, clinician, gene-specialised researchers how they visualize the data in mind, they can now easily visualize it on Desktops........ From some people's perspective, there is no science in developing and using the softwares, its really like looking life in just 1-dimension,  always see your life from different angles and always change the themes, Monotonous attiude makes anyone dull...., May be you can get an idea, which your brain never sensed before, when you can see the data from all prospectives- Genomics, Proteomics .....etc, then one can realise all the "OMICS" are just interrelated. If u cant visualize what you have, there is no sense..... Thanks to GMOD Project, LOVD community etc who believe that science is not for money, its for making science more easier, more friendly and more useful...........

Thursday, April 29, 2010

Manuscripts where Indian Genome Variation Consortium is an author

1.Indian Genome Variation Consortium. The Indian Genome Variation database (IGVdb): a project overview. Hum Genet. 2005 Oct;118(1):1-11. Epub 2005 Aug 25.Review. PubMed PMID: 16133172.

2.Mahajan A, Chavali S, Ghosh S, Kabra M, Chowdhury MR; Indian Genome Variation Consortium, Bharadwaj D. Allelic heterogeneity of molecular events in human coagulation factor IX in Asian Indians. Mutation in brief #965. Online. Hum Mutat. 2007 May;28(5):526. PubMed PMID: 17397055.

3. Gupta A, Maulik M, Nasipuri P, Chattopadhyay I, Das SK, Gangopadhyay PK; Indian Genome Variation Consortium, Ray K. Molecular diagnosis of Wilson disease using prevalent mutations and informative single-nucleotide polymorphism markers. Clin Chem. 2007 Sep;53(9):1601-8. Epub 2007 Jul 18. PubMed PMID: 17634212.

4.Biswas A, Maulik M, Das SK; Indian Genome Variation Consortium, Ray K, Ray J. Parkin polymorphisms: risk for Parkinson's disease in Indian population. Clin Genet. 2007 Nov;72(5):484-6. PubMed PMID: 17935510.

5.Saha A, Mukherjee S, Maulik M, Chandak GR; Indian Genome Variation Consortium, Ray K. Evaluation of genetic markers linked to hemophilia A locus: an Indian experience. Haematologica. 2007 Dec;92(12):1725-6..

6.Sinha S, Mishra SK, Sharma S, Patibandla PK, Mallick PK, Sharma SK, Mohanty S, Pati SS, Mishra SK, Ramteke BK, Bhatt R, Joshi H, Dash AP, Ahuja RC, Awasthi S;Indian Genome Variation Consortium, Venkatesh V, Habib S. Polymorphisms of TNF-enhancer and gene for FcgammaRIIa correlate with the severity of falciparum malaria in the ethnically diverse Indian population. Malar J. 2008 Jan 14;7:13.

7.Indian Genome Variation Consortium. Genetic landscape of the people of India: a canvas for disease gene exploration. J Genet. 2008 Apr;87(1):3-20.

8.Prasher B, Negi S, Aggarwal S, Mandal AK, Sethi TP, Deshmukh SR, Purohit SG, Sengupta S, Khanna S, Mohammad F, Garg G, Brahmachari SK; Indian Genome Variation Consortium, Mukerji M. Whole genome expression and biochemical correlates of extreme constitutional types defined in Ayurveda. J Transl Med. 2008 Sep 9;6:48.

9.Sinha S, Qidwai T, Kanchan K, Anand P, Jha GN, Pati SS, Mohanty S, Mishra SK, Tyagi PK, Sharma SK; Indian Genome Variation Consortium, Venkatesh V, Habib S. Variations in host genes encoding adhesion molecules and susceptibility to falciparum malaria in India. Malar J. 2008 Dec 4;7:250.

10.Bahl S, Ahmed I; Indian Genome Variation Consortium, Mukerji M. Utilizinglinkage disequilibrium information from Indian Genome Variation Database for mapping mutations: SCA12 case study. J Genet. 2009 Apr;88(1):55-60.

11.Sinha S, Arya V, Agarwal S; Indian Genome Variation Consortium, Habib S. Genetic differentiation of populations residing in areas of high malaria endemicity in India. J Genet. 2009 Apr;88(1):77-80. PubMed PMID: 19417547.

12.HUGO Pan-Asian SNP Consortium, Abdulla MA, Ahmed I, Assawamakin A, Bhak J, Brahmachari SK, Calacal GC, Chaurasia A, Chen CH, Chen J, Chen YT, Chu J, Cutiongco-de la Paz EM, De Ungria MC, Delfin FC, Edo J, Fuchareon S, Ghang H, Gojobori T, Han J, Ho SF, Hoh BP, Huang W, Inoko H, Jha P, Jinam TA, Jin L, Jung J, Kangwanpong D, Kampuansai J, Kennedy GC, Khurana P, Kim HL, Kim K, Kim S, Kim WY, Kimm K, Kimura R, Koike T, Kulawonganunchai S, Kumar V, Lai PS, Lee JY, LeeS, Liu ET, Majumder PP, Mandapati KK, Marzuki S, Mitchell W, Mukerji M, Naritomi K, Ngamphiw C, Niikawa N, Nishida N, Oh B, Oh S, Ohashi J, Oka A, Ong R, Padilla CD, Palittapongarnpim P, Perdigon HB, Phipps ME, Png E, Sakaki Y, Salvador JM,Sandraling Y, Scaria V, Seielstad M, Sidek MR, Sinha A, Srikummool M, Sudoyo H, Sugano S, Suryadi H, Suzuki Y, Tabbada KA, Tan A, Tokunaga K, Tongsima S, Villamor LP, Wang E, Wang Y, Wang H, Wu JY, Xiao H, Xu S, Yang JO, Shugart YY, Yoo HS, Yuan W, Zhao G, Zilfalil BA; Indian Genome Variation Consortium. Mapping human genetic diversity in Asia. Science. 2009 Dec 11;326(5959):1541-5.

13.Kumar J, Garg G, Kumar A, Sundaramoorthy E, Sanapala KR, Ghosh S, Karthikeyan G, Ramakrishnan L; Indian Genome Variation Consortium, Sengupta S. Single nucleotide polymorphisms in homocysteine metabolism pathway genes: association of CHDH A119C and MTHFR C677T with hyperhomocysteinemia. Circ Cardiovasc Genet. 2009 Dec;2(6):599-606. Epub 2009 Sep 5.

Sunday, April 18, 2010

More about IGVBrowser

IGVBrowser hosts Indian Genome variation(IGV)  data of IGV-Consortium, IGV Project has been constructed in phased manner where :
Phase I: 404 SNPs from 55 Indian populations.
Phase II: 3824 SNPs from 24 Indian Populations.
Affy 50K: ~50,000 SNPs (after quality check) from 26 Indian populations.

It provides comparison of informative markers from Indian populations with other world Populations and variation data is linked with annotation from different databases like Entrez gene, DGV, UCSC etc.

Track