On the call –Sarah, Margie, Nick, Barbara, Alejandro, Paul, Jason, Derrek, Neda, Josh, Sudha,
Lenore Launer
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Arfan and Charlie could not be on call due to prior commitment but reviewed and sent
around an analysis plan prior to call. Reinhold could not be on call.
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Summary: Details of conversation are given further below:
CHARGE and ENGIMA will each run GWAS of 3 phenotypes:
1) ICV
2) Total Brain Volume
3) HV
Sample: Caucasian only at this phaseAll available in CHARGE and ENIGMA including additional samples since Nat Gen
papers to be included in discovery.
Use studies with HV and DNA alone for replication.
Exclusions:
ICV: None
TBV: One analysis using same criteria as previously, another excluding stroke and
dementia and ‘other neuro’- brain tumor, major head injury, craniectomy etc. Not
excluding psychiatric illness such as depression, schiz, alcohol abuse.
HV: One analysis excluding dementia (persons with MCI will not be excluded) and
another including everyone.
Platform: GWAS data imputed to latest release of 1000 G Phase 1 v3 , (March/April
2012)- ENIGMA will let us know their parameters as they complete QC, using only
Caucasian panel- details below; timeline: October 12
Covariates:
Age, Sex, study site and familial relationships + age2 and ageX sex interaction + 1st 4
principal components (done in ENIGMA) + in ENIGMA alone (dummy covariate for
scanner). It was felt that in CHARGE this was taken care of by study site.
Models to run:
1) ICV with above covariates
2) ICV with height as additional covariate(ENIGMA will check if all sites can do that,
may be self-reported height recorded at time of MRI which is okay)
3) Total brain (does not matter if posterior fossa was included or not, use what
study has)
4) Total brain adjusted for ICV as well
5) HV- mean of both sides (no adjustment for ICV)
6) HV –mean of both sides, adjusted for ICV
Upload: Without filters, filter at meta-analysis. Perform meta-analysis at two sites to be
able to cross-check and verify.
Leads: Sarah and Alejandro, Arfan and Josh
Authorship: alternate across two cohorts
Timeline: next call in about 3 weeks, Jason/Derek will send Doodle, October for initial
analysis
Introduction
 Paul – Lets all look at Arfan’s protocol, are there any comments?
 Sudha – The idea here is to start our collaboration by doing a pooled Meta Analysis
of ICV, Brain Volume and Hippocampal volume across both studies (CHARGE and
ENIGMA) using 1000 genomes imputation.
 Paul – collaboration so far has been very successful, additionally Arfan and Charlie
looked up more CHARGE hits in ENIGMA and that is promising
http://enigma.loni.ucla.edu/enigma-vis/
Imputation
 Paul – Sarah where are ENIGMA sites with imputation to 1000G?
o Sarah - People should all have it finished by the next week or 2
 ENIGMA has been using the most recent version, while CHARGE has
used the older version (Oct 2010)
o Josh – CHS is close to completing imputation with latest version but will not
have it next week, all core CHARGE sites have or are imputing. Time line to be
determined for ASPS, 3C and TASCOG-likely ok by Oct.
 Sarah – changed a couple things in the imputation protocol
o Removed everything that wasn’t a doubleton or higher
o GIANT has done the same thing
o 13-14 million usable SNV (autosomal) for Caucasians (out of ~42 million
overall)
o 23 million available online, 10 singletons in European template that were
removed
o The number depends on whether we are using the European or all template.
o Also doing X
 Launer – what do we use for replication
 Paul – since the first ENIGMA, more sites have joined to do the second phase of
analysis which includes all subcortical structures and we can add more sites than
were initially in ENIGMA
 Sudha– ideally we can include everyone with 1000G imputation for the discovery
sample
o For replication we can look in samples with phenotype data and DNA but no
GWAS or 1000G imputation
 Josh - don’t know what it will be like to combine 1000G data across releases but we
did do that in the past- no final decision on this yet
 Sudha– smaller studies may be delayed on imputation, so about 2000 to 3000
samples
o If we wait till end of Oct, everyone should have imputation, but not if we
want to get started by September
o Josh – do not see a real need to rush as anyone with the phenotype in the
world is pretty much part of these 2 consortiums
o Sarah – it is worth waiting till October
 Barbara – how many do we need for replication
o Sudha– it will not be clear, ideally we want about the same sample size as the
discovery but that will not be possible
MAF Threshold
 Sudha– it may be sites upload everything and then we decide
Diseases in populations  Sudha– what do we do about people with dementia, MCI and psychiatric disorders?
o Paul - Phenotypes measured differently – ICV ex
 Fairly routine step in ENIGMA was to have sites exclude people with
disease
o Sudha– excluded many people with dementia, included MCI, since not all
studies had the same threshold for determining MCI
o Would it be feasible to ask ENIGMA sites to remove AD
 Sarah yes, we can ask it should be ok
o Jason - ENIGMA was done with only healthy and also with everyone
 Results were similar
 Pvals lower in larger sample
Tests and covariates
 Sudha– some studies have a measure of ICV and some others don’t
o CHARGE ran BV controlling for ICV, ENIGMA did not
o Jason – HV was done controlling for ICV,
 Sudha– why was this done for HV and not TBV? CHARGE went back
and forth decided not to for HV because it could introduce noise
 Jason – we did this a lot of ways, same effect size was given for each
analyses
o Sudha– need to decide on that between the 2 consortiums on ICV adjustment
for HV and TBV
 Age may be an issue, with younger persons ICV adjsutment is less
important perhaps
 We have a lot of older people so TBV/ICV was preferred as a measure
of atrophy
o Jason we are running with and without ICV
 Also age, sex, ageXsex, age^2, dummy variables for scanning
differences, 4 MDS
o CHARGE has site variable which takes care of scanning differences
 Derrek - ENIGMA2 doesn’t have BV
o Sarah it wasn’t less interesting, just less powerful in ENIGMA1, as some sites
did not have it.
o We can try to get other sites to get it
o Derrek we only have to ask new sites
 Jason – we are following up ENIGMA2 with additional tests including L/R Average,
and separate M/F for analyses, would CHARGE be interested in this?
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o Sudha may be interested, will think about it
Josh – what’s the logic? MF tests would be ½ the sample
Sudha– there is some interest in laterality
Pay penalties with all these multiple tests
Paul - sex difference exploration was pushed by one site in ENIGMA
Barbara – are we doing with or without controlling for ICV
Sudha– We have done ICV controlling for height…
o Jason ENIGMA does not have height
o Height SNPS come up as top SNPS in ICV analyses
o Height strongly correlated with ICV
Margie- can we ask sites for height?
Paul lets not commit to it at the moment but lets ask
Authorship
 Paul – authorship, basically combine starred authors from CHARGE and ENIGMA
with Sarah and Alejandro leading from ENIGMA
Ethnicity
 Sudha– should we use Caucasians only?
o Paul - there may be a political issue if we tell people we do not want their
data
o Sudha: African American cohorts do have phenotypes in the same way, can
use for replication, exploration at lociConclusions
 Paul - Another call in a month or so before then encourage people for Oct finish date
for imputations
 Josh if sites are quick with imputation we can use that to decide what thresholds to
use