Discover and read the best of Twitter Threads about #tcga

Most recents (8)

I am thrilled to announce that our work on In silico saturation mutagenesis of cancer genes is finally out @Nature. We propose a method inspired in evo biology to identify driver mutations in cancer genes. Here’s #tweetorial to sketch our results
Although we have a good knowledge of the genes that cause cancer upon mutations, most mutations in such genes are of uncertain significance. Classifying these variants in cancer genes is key to understand the mechanisms of tumorigenesis and advance precision medicine of cancer.
One approach to bridge this gap is saturation mutagenesis (aka saturation genome editing), an amazing endeavour, at the moment done for a few cancer genes (e.g. TP53, PIK3CA, PTEN, BRCA1, Ras domain) in specific experimental systems.
Read 25 tweets
Delighted to share our new study… introducing PhasED-Seq out today @NatureBiotech.
A fantastic collaboration from @StanfordMedicine led by Dave_Kurtz & Joanne Soo with @max_diehn to help transform #cancer interception & monitoring by improving #LiquidBiopsy #ctDNA detection of #MRD.
For many cancers & nearly all currently available techniques, the impressive KM plots of #ctDNA #MRD immediately after definitive Rx w/ curative-intent unfortunately still miss ~50% of all events which occur in the MRD-negative subset, thus having modest NPV.
Read 21 tweets
I’m excited to share our new paper in @NatureComms, just about 11 months after we first shared it on bioRxiv. So thankful for the great help from Guowei Huang and supervision from @benbfly and @dechen_lin.… Tweetorial follows… [1/10]
When cancer biologists think about CpG Island genes, we typically think about promoter DNA methylation and transcriptional silencing. In our new analysis of pan-cancer TCGA data, we challenge this perception by systematically analyzing changes in this large class of genes. [2/10] Image
Polycomb Repressive Complex 2 binding predisposes CGI genes to methylation and silencing. But in addition to 2,521 PRC2+CGI genes with DNA hypermethylation, we found 1,543 were *upregulated* relative to normal. Their promoters had increased chromatin accessibility & H3K27ac.[3/10 Image
Read 10 tweets
We are excited to announce our paper in @NatureGenet uncovering a role for minor introns in clonal hematopoietic disorders, Noonan Syndrome, and a diverse number of cancers. A collaboration between our lab (@sloan_kettering) and @bradleybio (@fredhutch):…
2.Most eukaryotes have 2 splicing machineries: the major & minor spliceosome. The minor spliceosome recognizes <0.5% of the introns in the human genome. Since their discovery, biological roles for minor introns have been enigmatic.
3.In work co-led by @DaichiInoue5, Jacob Polaski, and @TaylorJ_MD we identify that deletion of the minor spliceosome regulatory protein ZRSR2, frequently mutated in MDS and AML, enhances hematopoietic stem cell self-renewal.
Read 10 tweets
We are really excited to share our @biorxivpreprint on "In silico saturation mutagenesis of cancer genes". Here’s a #tweetorial to briefly summarize our findings…
Tumors are known to follow an evolutionary process whereby somatic variants can contribute to cancer development. The study of the traces of positive selection of tumorigenic mutations at the level of genes has yielded a compendium of cancer driver genes (
But not all mutations reported in cancer genes are tumorigenic. Our knowledge of how selection acts at the level of individual mutations is still limited, so we aimed to explore ways for identifying all potential driver mutations in driver genes, even if we did not observe them.
Read 26 tweets
Our new work showing "Ancestrally duplicated conserved noncoding element suggests dual regulatory roles of HOTAIR in cis and trans" is out in @iScience_CP cc @UCPHAndersenLab @ferencmueller @BorisLenhard @pundhir_sachin @GroupLenhard @LabMueller 1/N…
Two conserved noncoding elements (CNEs) overlap HOTAIR and its paralog on HOXD cluster. 2/N Image
Paralogous CNEs are embedded in mature noncoding transcripts. #ENCODE #GTEx #FANTOM5 Image
Read 8 tweets
Very happy to announce a major IntOGen update. This new version contains a comprehensive and reliable compendium of cancer genes and their mutational features across 61 tumour types, obtained by analysing 26,955 cancer genomes Thread 👇
How does intOGen identify cancer genes?

Briefly, intOGen runs six complementary driver discovery methods that analyze the pattern of mutations per gene and cohort and combines their output to produce a compendium of driver genes and a repository of their mutational features
How did you collect genomic data from >26,000 tumors?

We manually downloaded, processed and annotated tumor genomic data from different sources, such as @cbioportal #PedcBioPortal @icgc_dcc #TCGA #PCAWG @HartwigMedical #TARGET @StJude and others. 190 cohorts in total👇
Read 9 tweets
We identified for the first time a selection of three cancer driver mutations (P53, KRAS and VHL) during CRISPR-Cas9 gene editing and chart a comprehensive gene-wise editing risk map in our new work out today. This series summarizes it 1/X…
Recent reports in @NatureMedicine suggested that CRISPR-Cas9 gene editing induces a p53-dependent DNA damage response in primary cells, which may select for cells with oncogenic p53 mutations. These CRISPR-induced possible changes needs a systematic and thorough testing. 2/X Image
Leveraging computational and experimental techniques we asked whether CRISPR gene editing may select for other oncogenic mutations and if yes, which genes editing could severely induce this selection. 3/X Image
Read 10 tweets

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