November - 2017

DNA Ghost:

This note based blog covers bioinformatics and cancer genomics

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Identify vector integration site in a efficient way

Identify vector integration site in a efficient way

Assuming we suspect that a retrovirus or artificial vector integrated into human genome, how can we find out the exact chromosome location of the integration using NGS based method? First we need have our vector containing sample sequenced. If we have an estimation of where the integration sites are, we can go with targeted sequencing that only focuses on the region of interest. However, In most cases we don't have this knowledge in advance and have to sequence entire human g

Some implications behind SNP statistics

Some implications behind SNP statistics

Note that the statistics we are going to talk about only applies to germline mutation, not somatic mutation. Once we called a list of SNPs. it is routine that we get some statistics out of them. These statistics commonly include: Transition / Transversion (Ti / Tv) ratio As figure above, Ti / Tv ratio should be around 0.5 by pure chance. However, this ratio turns out to be much higher in reality because of: 1) Tautomeric shifts. 2) Transition tends to be silent mutation which

Could PCR duplicates actually come from different cells?

Could PCR duplicates actually come from different cells?

Earlier I started a discussion regarding Duplicates issue in NGS. I later had some further thoughts about this topic and would like to mention it here. It is maybe trivial, but still interesting to think about it. In the early article I mentioned the source of PCR duplicates and the reason we want to remove them before calling variants. For paired end reads, they are considered to be PCR duplicates if these paired reads align to exact the same chromosome position like depicte

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