Frequently Asked Questions

• How should I cite discoveries made using ExAC data?

  We anticipate the publication of a flagship paper describing this data set in early 2015. Until that is published, please cite: Exome Aggregation Consortium (ExAC), Cambridge, MA (URL: http://exac.broadinstitute.org) [date (month, year) accessed].

• I have identified a rare variant in ExAC that I believe is associated with a specific clinical phenotype. What phenotype data are available for these individuals?

  Many of the individuals who have contributed data to ExAC were not fully consented for phenotype data sharing, and unfortunately at this time we are typically unable to provide any information about the clinical status of variant carriers. We have made every effort to exclude individuals with severe pediatric diseases from the ExAC data set, and certainly do not expect our data set to be enriched for such individuals, but we typically cannot rule out the possibility that some of our participants do actually suffer from your disease of interest. 
  
  In the future it may be possible to obtain phenotype data for a subset of ExAC samples. If you are interested in using such data in your studies, please email us.

• What genome build is the ExAC data based on?

  All data are based on GRCh37/hg19

• What version of dbSNP was used to annotate variants?

  dbSNP 135. The browser supports RSIDs up to dbSNP 141, but these are not included in the VCF.

• What version of Gencode was used to annotate variants?

  Version 19 (annotated with VEP version 77).

• Why does the browser seem to disagree with the ExAC VCF at this multiallelic site?

  Due to the limitations of the VCF format, multi-allelic variants are put together on one VCF line. This inevitably adds complexity to otherwise simple variants, and thus when parsing onto the browser, we apply a minimal representation script. For instance, a variant whose REF is GC and ALT alleles are TC,G - the first ALT allele is actually a SNP and will be represented in the browser as G->T.

• What are the restrictions on data usage?

  All data here are released under a Fort Lauderdale Agreement for the benefit of the wider biomedical community. You can freely download and search the data, and use it for publications focused on specific sets of variants (for instance, assessing the frequency of a set of candidate causal variants observed in a collection of rare disease patients). However, we ask that you not publish global (genome-wide) analyses of these data until after the ExAC flagship paper has been published, estimated to be in early 2015. If you’re uncertain which category your analyses fall into, please email us. The data are available under the ODC Open Database License (ODbL) (summary available here): you are free to share and modify the ExAC data so long as you attribute any public use of the database, or works produced from the database; keep the resulting data-sets open; and offer your shared or adapted version of the dataset under the same ODbL license.

• Are all the individuals in the Exome Variant Server included?

  No. We were not given permission from dbGaP to include individuals from several of the cohorts included in the NHLBI's Exome Sequencing Project. As a result, genuine rare variants that are present in the EVS may not be observed in ExAC.

• What populations are represented in the ExAC data?

  Population	Male Samples	Female Samples	Total
  African/African American (AFR)	1,888	3,315	5,203
  Latino (AMR)	2,254	3,535	5,789
  East Asian (EAS)	2,016	2,311	4,327
  Finnish (FIN)	2,084	1,223	3,307
  Non-Finnish European (NFE)	18,740	14,630	33,370
  South Asian (SAS)	6,387	1,869	8,256
  Other (OTH)	275	179	454
  Total	33,644	27,062	60,706

• What cohorts are represented in the ExAC data?

  Consortium/Cohort	Samples
  1000 Genomes	1,851
  Bulgarian Trios	461
  GoT2D	2,502
  Inflammatory Bowel Disease	1,675
  Myocardial Infarction Genetics Consortium	14,622
  NHLBI-GO Exome Sequencing Project (ESP)	3,936
  National Institute of Mental Health (NIMH) Controls	364
  SIGMA-T2D	3,845
  Sequencing in Suomi (SISu)	948
  Swedish Schizophrenia & Bipolar Studies	12,119
  T2D-GENES	8,980
  Schizophrenia Trios from Taiwan	1,505
  The Cancer Genome Atlas (TCGA)	7,601
  Tourette Syndrome Association International Consortium for Genomics (TSAICG)	297
  Total	60,706