1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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6.7 years ago
Vivek ★ 2.5k

Is there any documented information on how many of the ESP/1000 genomes samples were included in the ExAC data release? I was under the impression that all samples were included but when I'm trying to annotate a few SNPs I can see some discordance in the allele frequencies.

For example I see this Exonic SNP with 0.119 allele frequency in 1000 genomes Phase 3 dataset but this cannot be found in ExAC data

5    131705587    rs13180043    C    T    100    PASS    AF=0.11901

Another example, present in both ESP & 1000 genomes but not in ExAC

1    156108976    rs7339    G    C    .    PASS    DBSNP=dbSNP_52;EA_AC=246,2936;AA_AC=561,823;TAC=807,3759;

1    156108976    rs7339    G    C    100    PASS    AF=0.185304;

I'd like to know preferably what kind of overlap exists between these 3 population sets and if possible what kind of capture regions were used for ExAC data.

1000genomes ESP 1000 genomes ExAC EVS • 4.0k views
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Is there any source to your assumption that all 1000g/ESP samples were included in ExAC? The About page speaks of an analysis from scratch, which would imply that the results are independent of 1000g or ESP.

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Even if they did variant calling from the scratch if you include a sample set, you expect to see a SNP with high enough allele frequency in the population.

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That makes sense. I guess you could always email them for specific details or check if they have a preprint that you could read.

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6.7 years ago
rbagnall ★ 1.7k

Neither of the variants are in the called regions.

5	131701132	131701341	-	hsa-mir-3936
5	131705614	131706109	+	SLC22A5|ice_target_65179


1	156108820	156108949	+	LMNA|ice_target_14401
1	156109511	156109680	+	LMNA|ice_target_14402

See here for the full bed file of called regions:

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Thank you! This is what I was looking for. They don't have this for the latest release (0.2) but I guess its safe to assume it would be the same.