Sigve Nakken (@sigven) profile picture

Sigve Nakken

@sigven

Computational scientist at Oslo University Hospital, Norway. General interest in computational cancer genomics and cancer precision medicine.

 Oslo, Norway
sigven.github.io
Joined July 2009
  • Tweets519
  • Following245
  • Followers231
Happy to release v1.0.0 of the Personal Cancer Genome Reporter (PCGR). Easier installation, updated data bundle. See more at sigven.github.io/pcgr Great collab with Peter Diakumis @UMCCR
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Sigve Nakken retweeted
Paul Gordon (@YYCist) profile picture
Paul Gordon@YYCist21 Aug 2024
GitHub update: Tamor, a Snakemake pipeline for Personal Cancer Genome Reports from FASTQ files + Dragen genome/transcriptome analysis, has been updated to work with @sigven’s 2.0 PCGR system! Now comes with working a public leukaemia data example. GitHub.com/nodrogluap/tamor
GitHub - nodrogluap/tamor: Illumina Dragen cancer genome and transcriptome analysis automation...

GitHub - nodrogluap/tamor: Illumina Dragen cancer genome and transcriptome analysis automation...

Illumina Dragen cancer genome and transcriptome analysis automation using Snakemake - nodrogluap/tamor

github.com
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Sigve Nakken retweeted
Andrew Beggs (@adbeggs) profile picture
Andrew Beggs@adbeggs9 Jul 2024
Excited to show our latest attempt at a clinically meaningful clinical cancer genome with rapid turn around (24 hours!) times using Oxford Nanopore sequencing technology for patients who need a rapid, whole genome assessment of their tumour and germline, offering them (1/n):
Image from Andrew Beggs (@adbeggs)
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The iCAN-PEDI study & @viljmaria examine personalized childhood cancer treatment using genetics, drug responses, and AI. Read more about how this research aims to enhance personalized cancer treatment ⬇️🔬 @FIMM_UH @CSCfi @ELIXIREurope elixir-finland.org/en/artifi…
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Sigve Nakken retweeted
Paul Gordon (@YYCist) profile picture
Paul Gordon@YYCist21 Jun 2023
GitHub update: 'Tamor' is a 1st try at an easy-to-use workflow for rapid Personal Cancer Genome Report (amazing work from @sigven et al.) generation using @Illumina Dragen + Snakemake (@johanneskoester) + @condaproject. Instrument files ➡️ Web report. github.com/nodrogluap/tamor
Screenshot of PCGR FlexDB Web page summarizing somatic mutation and germline susceptibility finding for a head and neck cancer case. Mutations are categorized into 4 tiers, and details of proetin changes are listed.

ALT Screenshot of PCGR FlexDB Web page summarizing somatic mutation and germline susceptibility finding for a head and neck cancer case. Mutations are categorized into 4 tiers, and details of proetin changes are listed.

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Little is known about non-coding somatic mutations in people without cancer. To learn a bit more about this class of mutations, we comprehensively profiled blood somatic mutations across ~43K individuals from the TOPMed consortium, now out @ScienceAdvances science.org/doi/10.1126/scia…

The genetic determinants of recurrent somatic mutations in 43,693 blood genomes

Somatic mutations are common in blood from healthy individuals and have germline genetic causes and health consequences.

science.org
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Sigve Nakken retweeted
James Black (@jrm_black) profile picture
James Black
@jrm_black11 Mar 2023
📢Our preprint ‘RNA allelic frequencies of somatic mutations encode substantial functional information in cancers’ is out today. Excited to tell you all about it, and our new tool, RVdriver: biorxiv.org/content/10.1101/… (1/8)
RNA allelic frequencies of somatic mutations encode substantial functional information in cancers

RNA allelic frequencies of somatic mutations encode substantial functional information in cancers

A central goal of cancer research is the identification of cancer genes that drive tumour growth and progression. Existing approaches to this problem typically leverage frequentist approaches based...

biorxiv.org
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GBC today announces the first set of Global Core Biodata Resources (GCBRs) - a collection of 37 data resources whose long-term funding and sustainability is critical to the global research endeavour in life sciences and biomedicine. See globalbiodata.org/global-bio… #opendata
Image from GlobalBiodata (@globalbiodata)
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Our latest paper with #mutationalanalysis, #signalingproteinprofiling and #cancerdrugsensitivityscreening in #multiplemyeloma cell lines is now out in @FrontOncology! @Mariase55115145 @SigridSkanland @TorilHol @KristineMisund @sigven @MezaZepeda frontiersin.org/articles/10.…
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Sigve Nakken retweeted
Khrono (@AvisenKhrono) profile picture
Khrono@AvisenKhrono19 May 2022
— Edvard og jeg er ikke kjent for å sutre, vi sutrer heller ikke nå, vi er sjokkerte og redde for framtida. Dette er et varsku, sier nobelprisvinner May-Britt Moser etter de varslede kuttene i Forskningsrådet. khrono.no/nobelprisvinnerne-…
Nobelprisvinnerne roper varsku om forskningskutt. — Vi er sjokkerte

Nobelprisvinnerne roper varsku om forskningskutt. — Vi er sjokkerte

— Edvard og jeg er ikke kjent for å sutre, vi sutrer heller ikke nå, vi er sjokkerte og redde for framtida. Dette er et varsku, sier hjerneforsker May-Britt Moser.

khrono.no
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Feasibility of clinical whole genome and transcriptome sequencing (WGTS) in oncology. A 🧵 on our latest study published in Nature Communications today:rdcu.be/cNOyQ
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Accompanying release of the Cancer Predisposition Sequencing Reporter (CPSR), v1.0.0. sigven.github.io/cpsr. CPSR provides a detailed and flexible report of cancer-predisposing germline variants on a per-patient basis.
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We all agree the status quo is unsustainable. Here are 1,000 words on how we could get the role of Open Source maintainer to graduate to a real, properly paid profession. The thing is, companies need it as much as maintainers do. blog.filippo.io/professional…
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After a multi-year effort from so many brilliant people involved in this project, I am excited to share our work published today in @NatureBiotech. @JOlweus @Irenegr5 @Oslounivsykehus @UniOslo nature.com/articles/s41587-0…
T cells targeted to TdT kill leukemic lymphoblasts while sparing normal lymphocytes

T cells targeted to TdT kill leukemic lymphoblasts while sparing normal lymphocytes

Nature Biotechnology - Engineered T cells kill leukemic cells with little off-target toxicity.

nature.com
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Interrogate and prioritise your gene list for cancer relevance with github.com/sigven/oncoEnrich…. New release out (1.0.6), including regulatory and ligand-receptor interactions. R package and web access (oncotools.elixir.no) @Wesche_Lab @ultanmcd @CanCell_UiO
GitHub - sigven/oncoEnrichR: Explore the cancer relevance of your gene list

GitHub - sigven/oncoEnrichR: Explore the cancer relevance of your gene list

Explore the cancer relevance of your gene list. Contribute to sigven/oncoEnrichR development by creating an account on GitHub.

github.com
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Detecting expressed cancer somatic mutations from single-cell RNA sequencing data biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Tumor mutational burden (TMB) has emerged as a tissue-agnostic predictive biomarker for immunotherapy. Empirical variability exists across panel assays. The TMB Consortium investigated factors contributing to variability in this #OpenAccess paper annalsofoncology.org/article…
Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the...

Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the...

Tumor mutational burden (TMB) measurements aid in identifying patients who are likely to benefit from immunotherapy; however, there is empirical variability across panel assays and factors contribu...

annalsofoncology.org
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We're excited to share a preprint of our new paper for calling somatic mutations from tumor RNA-seq without a matched-normal sample, and its application for estimating tumor mutational burden. #Cancer #Genomics #immunotherapy. biorxiv.org/content/10.1101/…
Estimating tumor mutational burden from RNA-sequencing without a matched-normal sample

Estimating tumor mutational burden from RNA-sequencing without a matched-normal sample

Detection of somatic point mutations using patients sequencing data has many clinical applications, including the identification of cancer driver genes, detection of mutational signatures, and...

biorxiv.org
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Limited evolution of the actionable metastatic cancer genome under therapeutic pressure @NatureMedicine doi.org/10.1038/s41591-021-0…

Limited evolution of the actionable metastatic cancer genome under therapeutic pressure

Nature Medicine - Whole-genome sequencing of metastatic biopsies longitudinally sampled during the course of anticancer treatment reveals that the actionable metastatic cancer genome remains...

nature.com
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