User:Etchevers/Notebook/Conference notes/2009/09/15: Difference between revisions
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Are they planning a system to manage the associated clinical data? Yes, idea of a project website for data entry, Brody can underwrite the administrative and other infrastructure costs. Costs for sample shipping, perhaps meetings... [http://www.cidr.jhmi.edu/ CIDR] projects are different funding mechanism than P01 or R01s. | Are they planning a system to manage the associated clinical data? Yes, idea of a project website for data entry, Brody can underwrite the administrative and other infrastructure costs. Costs for sample shipping, perhaps meetings... [http://www.cidr.jhmi.edu/ CIDR] projects are different funding mechanism than P01 or R01s. | ||
cf. [http://www.nature.com/ejhg/journal/v17/n10/full/ejhg200915a.html this recent review] on how to prioritize GWAS regions based on protein interaction maps like Ingenuity. | |||
Revision as of 05:45, 24 September 2009
 Conference and seminar notes
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Fourth day of 6th Intl Neural Tube Defects conferenceAlex Massuk - Intl Spina Bifida Genomics Consortium to detect CNVsI slept through it :-( But there is already a consortium set up, with some 30-odd investigators associated, cf the abstract. Alison and Simon are contibuting some 150-ish samples from Marcy's collection, perhaps some are better quality than others and more adapted to this analysis. Will use aCGH (what they call here "CGH array"?) and in theory can recycle the arrays up to 5x. Would need to ask Damien about this technology, or Laurence. Larry Brody and Anne Molloy - Genome-wide association studyComplementary to the CNV study lbrody at helix.nih.gov amolloy at tcd.ie Center for Inherited Disease Research http://www.cidr.jhmi.edu - lots of tools. >99.9% success in hybridization (?). Lower resolution than CGH array. Can pick up large homozygosity regions though. Omni Quad arrays - $425 per sample, expect costs of about $1.25 million and then later costs for follow-up. To collaborate, cost will be that of sample preps. Want to screen >1000 cases and controls or trios. If odds ratios 1.5-2 then only getting some info. Requirement for replication set to be established at the same time (John Gilbert thinks this is somewhat spurious, perhaps preferable to increase power by including them to begin with). Wide data release anticipated need to keep this idea when thinking of consentments for human subjects. Have 653 Irish trios, 367 English and 56049 controls (I think from the Wellcome Trust) - also have a genotyping tech and statisticians, can perform follow-up genotyping in the Brody group. Get back: detailed SNP info for your favorite gene in your favorite region. Questions about population stratification and clinical heterogeneity, or heterogeneous exposure conditions? - wants to be as inclusive as possible. Anyone with a cohort >30 is welcome. Currently will combine cranial and caudal NTDs and split out later, but study design is still being thought out. Are they planning a system to manage the associated clinical data? Yes, idea of a project website for data entry, Brody can underwrite the administrative and other infrastructure costs. Costs for sample shipping, perhaps meetings... CIDR projects are different funding mechanism than P01 or R01s. cf. this recent review on how to prioritize GWAS regions based on protein interaction maps like Ingenuity.
Kim Waller - ascertainment of NTDs by ultrasound in the Texas Birth Defects RegistryMight want to take a look at discussion of spinal bifida ascertainment on [Sept 21st]. Asserts "exencephaly" is a "precursor" to "anencephaly". This is semantics IMHO. Wide range of gestational ages in the database at which the US took place. Ontology problems for homogenous names for the same condition. 49K prenatal US exams in registry over 6 years at clinics attached to UT Medical School in Houston. 130 fetuses with NTDs. Observe confirmation of
and then says the others are missing because of medical terminations of pregnancy. Mary Seller asked if there were followups on the terminated foetuses to ascertain if the scan diagnosis was correct - as it could be another fetal pathology? are there samples sent to a pathologist and/or geneticist? apparently not.
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