number of private variants in a human exome
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7.4 years ago
User6891 ▴ 290

Hi,

I was wondering how many 'unique variants' you would find in a person's whole exome?

With unique variants I mean variants that you would only find in 1 person if you compare to let's say a group of 100 other individuals.

next-gen exome • 4.4k views
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7.4 years ago

This is a very interesting question.

Short answer: follow the Mass Genomics blog, which has a lot of interesting articles about this matter :-)

Slightly more elaborated answer: it depends on the population, as certain human populations show a lower number of singletons than expected.

For an estimate, you can check this recently published paper on the exome sequencing of 3,000 Finnish individuals. The author showed that Finns have on average 3.7 less singletons than a dataset comprising 3,000 Non-Finnish-Europeans (NFE), even though they have more low frequency variants than these. If you open Supplementary File S2 of this paper, you will find the number of variants found in the two cohorts of 3,000 samples. You have to look at the first two rows (AC=1), which correspond to the singletons. You can calculate that on average a Finnish individual has 28.99 singletons, while a Non-Finnish-European has 106.13 (summing LoF, all missense, and synonymous and dividing by 3,000 each group).

Obviously these numbers change depending on how many exomes are used for the comparison, and also on how inbred are the individuals sequenced. I am not able to tell you how many singletons you should expect for only 100 samples. Finally, note that these estimates refer to the number of "singletons", which are a slightly different concept than "private" variants in the sense you defined it (although sometimes I've found the two terms used as synonyms). Singletons are variants present in only one allele, while private variants may also be present in the two alleles but in the same individual.

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Thanks for your answer. I just want to mention that when clicking on Mass Genomics in your post, you're redirected to the GoNL NatGen. paper. I'm not sure if this is what you wanted to show me

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Thank you, it was a typo. It's fixed now.

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