[Bioc-devel] MRD measurements in Leukemic patients using NGS data in r

[Mulder, R]

Hi,


I was wondering if anyone could help me with a script and support for the above mentioned goal.

For this I have several BAM files for which I want to determine de nucleotide count per region of interest. The latter could be several hotspot mutation sites. I would like to get an overall overview of all the BAM files. Next I want to use these counts to determine for any new BAM file if the count for a particular genomic position is higher than the allowable range, hence could indicate if a mutation is present. For this I would like to use the modified Thompson Tau test. I think machine learning could be used for this. So, why do I want to do all this? Well, normal NGS pipelines only deal with variants at a frequency of 5%. Mutatios below this frequency are often missed. To know if a mutation is present below this level, you showed dive into the alignment and most often manually investigate the base calls. I know that this races some questions regarding call qualities, but then again our conventional assays have actually confirmed some of these low mutations. In addition, NGS can be used to determine the presence of low frequent mutation which is of great importance for determining the measurable residual disease after treatment.


I am new to r and bioconductor so I would be very thankful if someone could help me in my mission to setting up a script for this purpose.


Thanks,


Rene Mulder

Laboratory Medicine

University Medical Center Groningen

The Netherlands

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