Embedded Files
Post date: Jun 26, 2014 1:35:39 AM
Access Phone Number: 1-800-501-8979
International Access Phone Number: +1 3032489662
7-Digit Access Code: 5250856#
International COPD Genetics Consortium (ICGC)
Genetic Analysis Working Group
Conference call agenda: July 1, 2014
A. Status of first genetic analysis
a. Completed analyses: COPDGene, B58C, ECLIPSE, NETT/NAS, GenKOLS, Lung Health (lung function).
CHARGE/SPIROMETA (Wilk et al AJRCCM) meta-analysis results now available -- however the results from each cohort are not. Need to be able to exclude the cohhorts that are being re-analyzed -- will see if we can obtain individual study results.
b. Pending analyses: Lifelines, COPACETIC (Marike)
c. Committed analyses: Lovelace, KARE3, SPIROMICS
SPIROMICS genetic data is now clean (Gene Bleecker) - analyzing phenotypes.
d. Additional potential cohorts, not included:
Salford will be completing enrollment, genotyping in ?next 12 months - exome chip?
e. Barriers to sharing data: none identified.
Discussed focus on current analysis is GWAS of existing cohorts -- case control and lung function, to be completed in the next 6 months.
B. Analytic issues
a. Case / control definitions: issues as outlined above.
i. Feasibility of re-analysis
ii. Meta-analytic techniques
b. Matching controls to case-heavy or case-only datasets
Will be necessary to given that there are many case-only or case-heavy cohorts.
Many challenges in trying to do this -- will need to further explore and determine time frame.
c. Other technical issues
i. Dosage versus best guess genotypes: dosage
ii. Harmonizing different imputation datasets: CHARGE / SPIROMETA are HapMap, so will likely will lose many SNPs that do not overlap.
Yohan Bosse brought up the lung eQTL dataset -- great resource for investigating upcoming associations.
C. Organizational Issues
a. Conference calls: Marike and Michael will work on trying to identify a reasonable time, probably monthly
b. Subgroup structure: e.g. analytic, writing groups: probably not necessary at this time.
c. Website and upload usability / effectiveness: no issues identified.
Discussed having a master spreadsheet (similar to Subtyping-Project documents) for phenotypes and available genetic data. Will work with Pete Castaldi to try to do this. Consider sharing on Basecamp for COPDGene investigators.
d. Mechanism for proposing other genetic analysis projects: Michael will investigate. Discussed potential for exome chip / rare variant analyses.
e. Grant funding: Michael's R21 not funded - likely reapply this fall.
Report abuse