Arthur Dondi

LongSom: a #bioinformatics workflow for detecting de novo SNVs, CNAs, #cancer gene fusions to reconstruct tumor clonal heterogeneity. Shows that with @PacBio long-read single-cell RNA-Seq you can reconstruct clones and find clinically relevant SNVs in each clone. Nice work @ArthurDondi ! biorxiv.org/content/10.110…

Our TRGT paper published today in Nature Biotech! nature.com/articles/s4158… Tandem Repeat Genotyping Tool (TRGT) is a new method for genotyping tandem repeats in @PacBio HiFi long reads. We used some nice algorithmic strategies to improve genotyping accuracy.

@zevkronenberg @labfranz Oh my bad. I'm pretty sure it will find them, and even more! I recently used github.com/TrinityCTAT/CT… and found even more fusions, some expressed in >20 cells

@ArthurDondi @labfranz pbfusion is stand-alone and developed independent of the cupcake ecosystem. Anyway v. curious if we recover the interesting events you find :-).

Delighted to present our full-length scRNA-seq study on ovarian cancer patients, in collaboration with the University Hospital Basel @labfranz ! nature.com/articles/s4146… Can we simultaneously detect isoform-level gene expression, mutations and gene fusions in cancer cells? 1/

@zevkronenberg @labfranz I used fusion_finder from cupcake circa 2020, which I believe is the ancestor of pbfusion?

@ArthurDondi @labfranz Very nice article, I'd be really curious to see if pbfusion finds the fusions you've highlighted. google.com/url?sa=t&rct=j…

With the recent cost-reductions, we envision the technology to be broadly used in oncology and to enter the clinic in the near future: the ability to detect genetic and non-genetic sources of heterogeneity in cancer subclones using only one data modality is just too good! 16/

In conclusion, we showed that, using long-reads scRNA-seq, one can capture both isoform-level gene expression and genomic mutations/fusions, thus getting closer to same-cell genotype-phenotype linkage. 15/