[Bioc-devel] MRD measurements in Leukemic patients using NGS data in 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 De inhoud van dit bericht is vertrouwelijk en alleen bes...{{dropped:15}} ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] MRD measurements in Leukemic patients using NGS data in r
a few thoughts: 1) look into Shearwater ( https://bioconductor.org/packages/release/bioc/html/deepSNV.html), then 2) talk to Todd Druley @ WashU, Elli Pappaemanuil @ MSKCC, Ruud & Bob @ Erasmus, the usual suspects 3) plan to validate w/ddPCR (at the absolute very least) and be aware that most MRD in leukemia is done by a combination of BCR/TCR + breakpoint PCR (lymphoid/fusion-driven) or DFN flow (myeloid + normal cyto) not saying that ML-based methods might not help, but if you've got a 30x-100x genome (or even 1000x FM1) and are trying to compete with existing standard approaches that can detect molecules at 1e-6, it'll be rough. An alternative approach (that has been used repeatedly) is to throw caution to the wind, generate primers for numerous subject-specific somatic variants, and use the ensemble to try and model MRD (speaking of ML). On the one hand, that could give the clinic a "customer for life"; on the other hand, it's not conducive to large-scale automation & deployment. As far as I know, it never got much traction, in leukemia or anywhere else. (Consider that flow cytometry is capable of detecting 1-in-10K to 1-in-a-million cells in most clinical flow labs.) Best of luck! (and if you're not already working with UMI-tagged reads, please talk to the people in #2 above; the reason most people won't go below 5% VAF is that you get thwacked by error rates at that level, and the reason most NGS-based MRD is based on UMIs is that existing PCR-based methods have 6 logs sensitivity.) --t On Thu, Mar 5, 2020 at 4:08 PM Mulder, R wrote: > 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 > > > De inhoud van dit bericht is vertrouwelijk en alleen bes...{{dropped:15}} > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] CDSB Workshop 2020: Building workflows with RStudio and Bioconductor for single cell RNA-seq analysis
Hi BioC-devel! We just made the announcement of our CDSB 2020 workshop at https://support.bioconductor.org/p/128868/ + Twitter & Facebook (both in English and Spanish). Joselyn and Rob will be among our instructors. Thank you Bioconductor Foundation for the support! Please help us spreading the word around. Also, if you have any contacts that you think might be interested in sponsoring the workshop, please let us know. At https://comunidadbioinfo.github.io/niveles-de-patrocinio/ we answer the question why should you support us? Thanks! Best, Leo Leonardo Collado Torres, Ph. D., Staff Scientist II Lieber Institute for Brain Development 855 N Wolfe St, Suite 300 Baltimore, MD 21205 Website: http://lcolladotor.github.io ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] CDSB Workshop 2020: Building workflows with RStudio and Bioconductor for single cell RNA-seq analysis
Hi, I should clarify that this workshop will be held in Cuernavaca, Morelos, Mexico during August 3rd to the 7th, 2020. Best, Leo On Thu, Mar 5, 2020 at 10:05 PM Leonardo Collado Torres wrote: > > Hi BioC-devel! > > We just made the announcement of our CDSB 2020 workshop at > https://support.bioconductor.org/p/128868/ + Twitter & Facebook (both > in English and Spanish). Joselyn and Rob will be among our > instructors. Thank you Bioconductor Foundation for the support! > > Please help us spreading the word around. Also, if you have any > contacts that you think might be interested in sponsoring the > workshop, please let us know. At > https://comunidadbioinfo.github.io/niveles-de-patrocinio/ we answer > the question why should you support us? Thanks! > > Best, > Leo > > Leonardo Collado Torres, Ph. D., Staff Scientist II > Lieber Institute for Brain Development > 855 N Wolfe St, Suite 300 > Baltimore, MD 21205 > Website: http://lcolladotor.github.io ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] [rOpenSci] Community Call: Maintaining an R Package
Hi BioC-devel, Since 2018 I've been interacting with rOpenSci's organizers. For those that don't know, rOpenSci https://ropensci.org/ is a non-profit that aims to > make scientific data retrieval reproducible. Over the past seven years we > have developed an ecosystem of open source tools, we run annual > unconferences, and review community developed software. (taken from their https://ropensci.org/about/ page) That is, they are in some ways similar to Bioconductor and that's why they want to build a bridge between the two communities. Stefanie Butland, their community manager, invited me to be a part of a community call (webinar) on the topic of Maintaining an R Package in order to bring in a little bit of the Bioconductor perspective. They have a pretty nice system where they take questions before hand through a GitHub issue page, so please feel free to chime in. I think that besides the Bioconductor side, I bring in a bit of the CDSB perspective (the work we do to help others in Mexico and Latin America). In any case, feel free to tune in to the webinar (details below) as well as share the information with anyone who might be interested. https://support.bioconductor.org/p/128869/ Best, Leo ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel