Frequently Asked Questions

General

• How should I cite discoveries made using the Macaque Capture and Whole Exome Database (mCED)?

  Please cite our paper available here.

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

  The current database does not have phenotype data available.

• Can I get access to individual-level genotype data from Macaque Database?

  Macaque Database contains individual-level genotype data for each variant. You can check genotype data in each variant page.

• What are the restrictions on data usage?

  The data presented here are released for the broader research community's benefit. You are welcome to freely download and explore the data. We encourage utilization and publication of frequency data for specific targeted sets of variants, such as analyzing candidate causal variants found in rare disease patients. However, we request refraining from publishing global (genome-wide) analyses of this data or large gene sets until after our capture and exome data papers are published, which is anticipated in 2025.

Technical details

• What genome build is the Macaque Database data based on?

  All data are based on Mmul_10/rhemac10, GRCh37/hg19 and GRCh38/hg38

• How are the variants annotated?

  The variants in the rhesus macaque genome (Mmul_10) were annotated using the Variant Effect Predictor (VEP) in release 101. This annotation was conducted based on merged Ensembl and RefSeq gene models specific to Mmul_10.
  The rhesus macaque variants in Mmul_10 coordinates were also converted to the human genome hg19 assembly using the UCSC Genome Browser program liftOver. The variants in hg19 coordinates were subsequently annotated with ANNOVAR (v. 07/17/2017) and dbNSFP (v.3.5a, including SIFT, PolyPhen-2, etc.) based on the hg19 gene model.

• What colony/cohorts are represented in the Macaque database data?

  Colony/Cohort	Samples
  Cayo: Caribbean Primate Research Center	186
  CNPRC: California National Primate Research Center	983
  NEPRC: New England Primate Research Center	205
  ONPRC: Oregon National Primate Research Center	134
  SNPRC: Southwest National Primate Research Center	116
  TNPRC: Tulane National Primate Research Center	66
  WNPRC: Wisconsin National Primate Research Center	580
  YNPRC: Emory National Primate Research Center	199
  Total	2,469