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Notes for Lyonnet-Vekemans lab meeting
Sabina’s paper is accepted but need to answer reviewers on a couple of details (see further on).
Michel - Susan Lindsay: Marie Curie fellowship has dropped the idea. A few conference calls. Now Tom Roop in there. Proof that can set up network – furnish tissues to Niels, ask for from Susan – redo a paper together, eg. paper with Strachan, applications. Expression is good for genome-wide association – which are the important genes in that area? Vs tissue. Have followed up with this with e-mail to Susan cc: Niels, Asli, Michel, Marie-Laure Sobrier on Friday. Suggested LHX slide transfer HDBR to us, we provide HDBR if they need, both of us give Asli if she can use anything, and we could give ChIP’d material to Asli/Niels for Illumina sequencing.
Talk about HIS of miRNA on human tissues. Alexandra showed up later, but one doesn't prevent the other as I tried to explain to Stanislas.
Anne-Sophie – consortium data on RET for association-liaison; sibpairs also. All linkage data not explained by one single SNP but probably a haplotype with other SNPs implicated aside from the 16 known. Combination test, uses also a software LAMP from Abecassis – get same results with different software? No linkage probably to 3’ SNPs. Will present in meeting as well as a paper that Michel asked her to interpret.
Anna wants to resequence over 100kb on a hi-thruput sequencer. How to enrich a locus? All private companies are on the problem. Probable solution will come out in near future – must be cheaper than whole genome sequencing. Still talking with Wincker at Genoscope.
Agnes: puces Nimblegen on atresie oesophage and Feingolds. Nothing yet. Small deletions (1kb) around MYCN trying to confirm by PCR. Found in a few patients but not CNV known. Has not yet confirmed, I suggested eventually check SOX-binding sites in these areas? Agnes says that they have lots of TF-binding sites. Could possibly do ChIP for SOX2 on it. One patient with apparent Feingold has a truncating exon in another gene, she's working on it. 6 is in X-linked RM. This patient has finger anomalies, retard, atresie oesophage…
Renaud (M1 stage) – family with 3 generations prognathe (DNA)- 4th also clinically. Linkage study? Probably dominant with some modifying genes. Sent to Affymatrix platform for SNP analysis 250K. Linked to chirg maxillofacial for tissues. Surgeon checked out the radios so measurements are indeed correlated to prognathism.
With Sabina looking at *more* minimal promoter of SOX9 instead of one used already in paper (to check efficacy of 1MB upstream element in repressing MSX1 expression), transfecting in mesenchymal primary arch mouse cells, culture at 30ºC if want undifferentiated, will differentiate at 37ºC. Need the more minimal promoter because the negative control wasn’t that negative. Stan had to redo tableau clinique. qPCR on the ChIP was required as well.
Candice: 2 HIS en cours – LHX3/4 on C20 inner ear. Explained rationale. Also MKS6 hyb – probably worked.
Affymetrix platform for SNPs – other projects: Loic mort subite de nourisson; Alexandra families (see below); Poste vert – Moroccan families will go on but what they have clinically I don't know; atresie oesophage possible prevue…; Malfo anorectale et teratoma family with Celia in future once has checked HLXB9 sequence.. Interface for MERLIN which is more user-friendly on Paris-Descartes. Can also extract CNV info using genotyping console. Get p/w and username once project is launched with the Affy platform Christine and Astrid, whom I met yesterday (christine.bole at inserm.fr and astrid.cariou) I gave them responsibility and the doc about our 1/2 Agilent Bioanalyzer.
Anna: 1M SNPs on chip raw results for Tri-21 HSCR patients; 18 French trios with a few Italian, American etc.. Helped by bioinfo here Patrick Nietscke. Focus only on chr 21? Can see any CNV in these – some work involved – in two trios there are “some” in terminal part of chromosome; known if transmitted from father or mother? If transmitted more often by mother than father, take as basis of hypothesis to proceed in identifying any additional copies >3. Lead eventually to overexpression of intervening region, but that didn’t work out. Overexpn of genes/elements in these CNV? These flank RUNX1, could there be regulatory elements in CNV that affect RUNX1 expression?
Laetitia, blonde doctor in M1 Santé, will start 4th year medicine (like Daina who will go into M1 génétique next year in science): Exons of ALK on NB patients some exons 16-29 sequenced. Stagiaire sequencing other exons (12-13)
Sophie: covering article criticisms. All set by end of week, article is published.
Stanislas/Michel: project d’equipe for (independent) AERES – will do the visit, but the INSERM will use these results – can get some ideas from the European project (ChIP/SAGE). Discuss this with Anne-Sophie to analyze the usefulness of the bioinfo/biostat parts of the project.
Alexandra: project with families of atresia of biliary canals, work with Anne-Sophie to assist in stats. 20 trios all Polynesians/Maori. Also a family with hepatocarcinomas/blastomas in tour de genome SNP on site. Other project: Existence of regulation of mitochondrial function by miRNAs via the nucleus? Some arguments in favor – eg. proteins involved in the actual silencing of messages as translated, present at mitochondria. Being cautious. Lastly, screen of all diseases – some where locus/gene known but the locus clone orphans. Looking for miRNAs physically localized in regions, like we did for NCC genes. Or, link to 3’ UTR variations in target genes in these loci for post-translational regulation. Current examples: Tourette syndrome – fixation of site miRNA in 3’ site of gene. Her tools validate this. Spastic paraplegia for a mitochondrial protein. Hemochromatose: HFE gene also has miRNA regulation but via a coding variant. Other proof of concept – cholestasis (B7 gene). Want to also examine with mucoviscidose CFTR mutations – why expressivity so variable?
Later discussion with Alexandra about giving her list of hNCC SAGE tags. The “known” miRNAs none of the tags are present in hNCC or NT databases when I do the query on Access – but based on what paper SAGE-miRNA? How old is it? What is the other list in my Access database? Also crossed OMIM-mapped genes to disease loci, separated known loci that now the gene is ID’d but it is expressed in hNCC, from the relatively few loci without a known gene, kept the list of hNCC-expressed genes in that interval +1Mb. Thought to ask if known miRNA’s in those intervals or regulating those genes.
Jeanne will have another M2 surgeon; Tania has asked for more students M2 (Emmanuelle will be leaving for a PhD-financed position, Sophie A has left to become a teacher, Geraldine has moved south and Catherine transferred back to cytogenetics); Alexandra would like to recruit an M2 doctor on Friedreich ataxia and has some money to do that with. And M2 Alexis has got his money to come work with tissues that Celia and Sabine will take out of freezer or continue to place in freezer.
Mathieu “guest star!” is living off of RMI and trying to write up a couple of other papers. Microdissection laser paper is nearly accepted at RNA (journal), has finished some last RT-PCRs to show can amplify even little-expressed genes besides actin and GAPDH, thanks to Sophie. Comparisons with Curie – will submit to Genome Biology or BMC Genetics (C. Ducraene) and third paper: with Pasteur bioinformatics people on plugin they developed to link to KEGG pathways. Followup with EMBL/EBI positions. I sent him some suggestions culled from bioinfo people on FriendFeed.