We have 50 bladder cancer germline samples. One of the researchers we collaborate with has retired, and we cannot get metadata. Therefore, we are unsure whether these 50 samples came from 50 individuals or from 30 individuals. Is there any way to determine this?
thank you in advance.
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written
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Lee •
1 answer
If you have enough SNVs, you can try SMaSH, which attempts to computationally identify samples that are derived from the same individual. The program takes VCF as input. Here's an excerpt from the GitHub page:
Sample swaps are a real concern in high throughput sequencing studies. SMaSH helps detect such sample swaps by integrating the information from over 6000 carefully selected single nucleotide polymorphism (SNP) sites from across the human genome to identify which samples in a group of sequencing data sets are derived from the same human individual. Importantly, SMaSH is able to verify sample identity between different data types, such as RNA-Seq, exome, and MethylCap-Seq data.
use somalier https://github.com/brentp/somalier it accepts vcf as input
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You could say that it's highly possible that two samples came from the same individual if almost all of their high quality SNVs match. Back when I was performing such forensics, we had to caveat these as identical genotypes, as they could be from identical twins for all you know, and this was with a subset of SNVs picked from across the genome where 99% of the subset (or something like that) matched.