Question

We Found A Gene Involved In A Genetic Disease. Now, What Is The Todo List ?

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13.7 years ago

Pierre Lindenbaum 164k

Hi,

Our paper describing how NOTCH2 is involved in a genetic disease has just been published (waves) . We mapped five mutations on the gene.

I've just updated the articles in wikipedia (here and here) and I wonder if I should update some other databases.

Omim : Can I update an article ? Should I suggest a correction ?
Genbank/Protein: should I add/suggest some new annotations. How ? (to an already existing protein ? or should I submit the new truncated sequences ?)
anything else ? another database ?

Thanks

Pierre

sequence database annotation • 5.0k views

ADD COMMENT • link updated 13.3 years ago by Malachi Griffith 20k • written 13.7 years ago by Pierre Lindenbaum 164k

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Before you do any updating, make sure you celebrate appropriately!

ADD REPLY • link 13.7 years ago by Aaronquinlan 12k

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Nice! Since I happen to be proud of the new Gene Wiki Twitter feed, I was happy to see your WP edits flow by earlier today! (http://twitter.com/#!/search?q=%23NOTCH2)

ADD REPLY • link updated 5.2 years ago by Ram 44k • written 13.7 years ago by Andrew Su 4.9k

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One of the few success stories of autosomal dominant exome sequencing that I have seen. Congrats!

ADD REPLY • link 13.7 years ago by jvijai ★ 1.2k

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This question is now featured in http://www.slideshare.net/lindenb/notch2-backstage

ADD REPLY • link updated 5.2 years ago by Ram 44k • written 13.7 years ago by Pierre Lindenbaum 164k

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I would take a week of really deserved holidays

ADD REPLY • link 13.5 years ago by Flow ★ 1.6k

score 8 · Answer 1 · 2011-03-07

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13.7 years ago

David Quigley 11k

File a GeneRIF with the NCBI Gene database. You submit your own brief blurb so that when people search for your gene, it plays an advertisement for your paper... ahem, I mean, it informs them of your finding. Note that the RIF has to be different from the title of your paper.

ADD COMMENT • link 13.7 years ago by David Quigley 11k

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Thanks, filling a GeneRIF was the easiest thing to do among all the (good) answers.

ADD REPLY • link 13.7 years ago by Pierre Lindenbaum 164k

score 4 · Answer 2 · 2011-03-07

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13.7 years ago

Bert Overduin ★ 3.7k

I would also consider the following databases:

UniProtKB: http://www.uniprot.org/update

WikiGenes: http://www.wikigenes.org/e/gene/e/4853.html

ADD COMMENT • link 13.7 years ago by Bert Overduin ★ 3.7k

score 4 · Answer 3 · 2011-03-08

Congratulations! Your finding is not just about new gene variants but also about their relation to disease. For that Omim is certainly a good start, but there are different data sources for genotype-phenotype relationships now being developed. For instance by the human variome program. You might want to ask the gen2phen community at gen2phen.org for the best places to submit that information.

score 3 · Answer 4 · 2011-03-07

Any sequence data (genomic DNA, mRNAs, protein, etc.) you generated can certainly be submitted to NCBI, especially if those 5 variants are newly reported in the paper. Those entries can link to your PubMed ID in one of the annotation fields. OMIM is culled from literature and so you cannot edit those pages. I once tried to suggest a change, but they are busy folks there... NCBI's PopSet may be of interest depending on the nature of the populations you used to find the variants and the disease association.

If the disease pathway, not NOTCH2 itself, is in KEGG or Reactome, talk to those folks and send them a pdf of the paper to help them along. Suggest how NOTCH2 might be included in that disease pathway. Speaking of disease pathways, the people at MGI (Jackson Labs, mouse) and RGD (rat genome database) might be interested in your new disease annotation for Notch2/NOTCH2.

I like David's GenRIF idea - do that!

Can you add new GO (gene ontology) terms to NOTCH2? If so, see www.geneontology.org to learn how to update the GO annotation for this gene.

score 3 · Answer 5 · 2011-03-07

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13.7 years ago

Mary 11k

Congrats!

A couple of thoughts:

1) Maybe offer to do an article for GHR: http://ghr.nlm.nih.gov/

2) Is there a research test available? Maybe also GeneTests?

ADD COMMENT • link 13.7 years ago by Mary 11k

score 2 · Answer 6 · 2012-02-04

Related to the other databases part of your question. When novel gene mutations are found to be associated with a disease, it is of great value to the community for the mutations to be entered in the appropriate public variant/mutation databases. If the disease in question is Cancer, then COSMIC would be the place to go. For other diseases, one might consider: HGMD, GWAS Central, dbVar or dbSNP.

COSMIC - operates under the premise that all cancers are a result of DNA sequence abnormalities that confer a growth advantage to cells that harbor them. COSMIC is designed for the storage and visualization of such mutations identified as somatic in human cancers.

dbVar/dbSNP - A structural variant is defined by dbVar as a region of DNA involved in an inversion, translocation, insertion, or deletion. Although it accepts variants of any size, dbVar recommends that variants smaller than 50 bp be submitted to dbSNP and those larger than 50 bp to dbVar.

GWAS Central (formally HGVBASE) - The primary purpose of GWAS Central is to facilitate genotype-phenotype association analyses that explore how single nucleotide polymorphisms (SNPs) and other common sequence variations may influence phenotypes such as common disease risk and drug response differences.

HGMD - The Human Gene Mutation Database is an attempt to compile and organize observations of gene mutations responsible for inherited human diseases. Somatic mutations and mutations in the mitochondrial genome are excluded from the database

These definitions are snippets from the upcoming updated edition of the Bioinformatics Dictionary. Current edition is here.