TOPMed
Overview
The Trans-Omics for Precision Medicine (TOPMed) program, sponsored by the National Institutes of Health (NIH) National Heart, Lung and Blood Institute (NHLBI), is part of a broader Precision Medicine Initiative, which aims to provide disease treatments tailored to an individual’s unique genes and environment. TOPMed contributes to this Initiative through the integration of whole-genome sequencing (WGS) and other omics (e.g., metabolic profiles, epigenomics, protein and RNA expression patterns) data with molecular, behavioral, imaging, environmental, and clinical data.
Publication
Kowalski, M.H., Qian, H., Hou, Z., Rosen, J.D., Tapia, A.L., Shan, Y., Jain, D., Argos, M., Arnett, D.K., Avery, C. and Barnes, K.C., 2019. Use of> 100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium whole genome sequences improves imputation quality and detection of rare variant associations in admixed African and Hispanic/Latino populations. PLoS genetics, 15(12), p.e1008500.
VCF extraction
We currently extract the following fields from TOPMed VCF file:
##INFO=<ID=AN,Number=1,Type=Integer,Description="Number of Alleles in Samples with Coverage">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Alternate Allele Counts in Samples with Coverage">
##INFO=<ID=AF,Number=A,Type=Float,Description="Alternate Allele Frequencies">
##INFO=<ID=Het,Number=A,Type=Integer,Description="Number of samples with heterozygous genotype calls">
##INFO=<ID=Hom,Number=A,Type=Integer,Description="Number of samples with homozygous alternate genotype calls">
Example:
chr1 10132 TOPMed_freeze_5?chr1:10,132 T C 255 SVM VRT=1;NS=62784;AN=125568;AC=32;AF=0.000254842;Het=32;Hom=0 NA:FRQ 125568:0.000254842
GRCh37 liftover
The data is not available for GRCh37 on TOPMed website. We performed a liftover from GRCh38 to GRCh37 using dbSNP ids.
Download URL
https://bravo.sph.umich.edu/freeze5/hg38/download
JSON output
"topmed":{
"allAc":20,
"allAn":125568,
"allAf":0.000159,
"allHc":0,
"failedFilter":true
}
Field | Type | Notes |
---|---|---|
allAc | int | TOPMed allele count |
allAn | int | TOPMed allele number. Non-zero integer. |
allAf | float | TOPMed allele frequency (computed by Illumina Connected Annotations) |
allHc | int | TOPMed homozygous count |
failedFilter | bool | True if this variant failed any filters |