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IRBW2009 workshop presentation Axton
Posted Mon, 08/06/2009 - 11:27 by
Gudmundur A Thorisson
Brief decription of this document
Myles Axton of Nature NY - Contributor Recognition
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Contributor recognition
Myles Axton Editor, Nature Genetics IRBW2009 14 May 2009
Consolidate contributor roles as unitary tags
Communicating our metadata to popular sites
broad-sense human variome project
Study phase 1) Collect rare clinical mutations from rare hereditary diseases into 700 locus-specific databases. 3) Re-sequence genes for rare variants associated with common diseases. 2) Associate common variants with common diseases via the HapMap and and whole genome association studies. Needs Harmonize software, ontologies, formats and criteria. Add to public databases. “The legacy data framework”. Collect, publish and credit. “The track repository tsunami”. Replicate associations and find causal variants. Develop minimal report and public deposition criteria. “The candidate approach delusion”.
Time for a divorce of human and machine
Yeager et al. Nature Genetics 39, 645-649; 2007
The failure of Fort Lauderdale
Kuroki et al. Nature Genetics 38, 158-167; 2006
Accession codes. GenBank/DDBJ/EMBL: AY692036, <http://www.ncbi.nlm.nih.gov/sites/entrez?term=AY692036&cmd=Search&db=nuccore&QueryKey=1> AY692037, BS000531–BS000572, BS000574–BS000581, BS000583, BS000585, BS000587–BS000682. See Supplementary Table 1 for a full list of the clone names and accession numbers.
In addition, the following as yet unpublished BACs, listed in Supplementary Table 5, were generated and deposited in GenBank by R.K. Wilson (Washington University School of Medicine) and D.C. Page (Whitehead Institute AC142320, <http://www.ncbi.nlm.nih.gov/sites/entrez?term=AC142320&cmd=Search&db=nuccore&QueryKey=4> AC144378, AC145769, AC145782, AC146011, AC146175, AC146245, AC146268, AC147117, AC147148, AC147343, AC147657, AC147670 and AC151848. URLs. Manually annotated HSAY genes, http://vega.sanger.ac.uk/Homo_sapiens/; NCBI, http://www.ncbi.nlm.nih.gov/; NCBI BLAST, http://www.ncbi.nlm.nih.gov/BLAST/; RIKEN-Genomic Sciences Center, http://stt.gsc.riken.jp/. Note: Supplementary information is available on the Nature Genetics website.
Microattribution
• Journals provide citation links from paper to paper. Quantitative citation provides a rough measure of immediate usefulness. • Database accessions should be traceable to their original source. Citations to database accessions in peer reviewed papers and database entries should be counted and the cumulative count made prominently public. • Microcitation provides incentive for collaborative genome annotation and a more accurate picture of individual and group research activity. • Microattribution can be extended to web traffic analysis (not here).
µψ
It is clear that accessions mandated by the journal predominate, but ideally, all publicly deposited resources should be fully cited by authors, and properly logged and counted by the journals.
http://blogs.nature.com/ng/freeassociation/2007/02/duk
NCBI and EBI have some quantitative attribution
http://www.ncbi.nlm.nih.gov/sites/varvu?gene=7249
Peer review for genetic variants by locus
• Editor commissions annotation of a locus between set genome coordinates. Submitters of annotations to NCBI/EBI qualify as authors.
• Author group led by locus-specific database (LSDB) expert evaluates published and database evidence for a phenotypic effect of each variant in the locus. • Editor coordinates comments of user community and assigned expert peer referees. Web editor formats author annotations as a table of parameter lists. • Publication with digital object identifier (DOI) of the definitive set of annotations and links. • Publication in new human variome journal or participating journals (HuGENet model) of a synopsis of the locus (PubMed ID).
Essential parameters describe a genetic variant
Locus Variant type Genomic Reference transcript Predicted protein Consensus ID Map to Genome Build Publications Cited PMID of publications: OMIM MIM Allele variation Individual phenotype Population frequency = TSC2 = SNP = g.10119C>G = c.465C>G = p.Y155* = rs45444196 = 36.2 = 2 = 10205261, 17304050 = MIM191100 = MIM191100.000n = phs000025.v2.p1 = rs45444196#Diversity
>gnl|dbSNP|ss71651017|allelePos=101|len=201|taxid=9606|alleles='C/G'|mol=Genomic TCTTCTTTAA GGTCATCAAG GATTACCCTT CCAACGAAGA CCTTCACGAA AGGCTGGAGG TTTTCAAGGC CCTCACAGAC AATGGGAGAC ACATCACCTA S TTGGAGGAAG AGCTGGGTGG GTGCCACCTT GGGTTGGAGG TTTCTCTGGC CTTGACGATC AAGTGTAACC TGGATGGGAA GGACCTGGGG CTGGGGAGGG Submitter Handle of lab: email: lab: name: institution:
TSC2DB s.povey@ucl.ac.uk Galton Laboratory Sue Povey University College London
Supplementary table 1 of a variome review
seq=ss71651017, allele=G, pheno=phs25.v2.p1, sub=TSC2DB.S_Povey, freq=1 seq=ss1234, allele=A, pheno=0, sub=Illumina, probeset=Hap550, freq=1500
URL/URI points via indexing parameter (ssID) to NCBI or EBI database. Commissioning journal and participating database can use to display quantitative microcitation of each ssID and submitter. Parameter passing (Open URL/ CrossRef) allows transmission to third party site or microattribution proxy site.
Links to commercial assays and clinical tests
No compulsion without incentive
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© 2009
GEN2PHEN Project
.
The
GEN2PHEN Knowledge Centre
has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013)
under grant agreement number 200754 - the GEN2PHEN project.
