Arthur Dondi

PhD Candidate @ETH Zurich, Computational Biology Group
Transcriptomics, Single-Cell & Oncology
Cats, mediterranean lifestyle & long-reads sequencing fan account

[Liz Tseng @Magdoll]

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 !

https://t.co/Lh6UA2efQ3

[Dr Harriet Dashnow @hdashnow]

Our TRGT paper published today in Nature Biotech!
https://t.co/tOY6Ac7DkA
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.

[Arthur Dondi @ArthurDondi]

@zevkronenberg @labfranz Oh my bad. I'm pretty sure it will find them, and even more! I recently used https://t.co/ealiw6N4LN and found even more fusions, some expressed in >20 cells

[Arthur Dondi @ArthurDondi]

Delighted to present our full-length scRNA-seq study on ovarian cancer patients, in collaboration with the University Hospital Basel @labfranz ! https://t.co/I7LnLDd2gr

Can we simultaneously detect isoform-level gene expression, mutations and gene fusions in cancer cells? 1/

[Arthur Dondi @ArthurDondi]

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

[Arthur Dondi @ArthurDondi]

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/

[Arthur Dondi @ArthurDondi]

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/