Dr. Kevin M. Boehm et al. published the paper Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer in Nature Cancer. In it they assemble a multimodal dataset of 444 patients with primarily late-stage high-grade serous ovarian cancer and discover quantitative features, such as tumor nuclear size on staining with...Read More

Dr. Benjamin Greenbaum co authored the paper, “Neoantigen quality predicts immunoediting in survivors of pancreatic cancer” along with Marta Łuksza et al. in the journal Nature .  In it they investigate how 70 human pancreatic cancers evolved over 10 years. They find that, despite having more time to accumulate mutations, rare long-term survivors of pancreatic...Read More

Dr. Elli Papaemmanuil co authored the paper, “Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers” along with N. Shukla et al. in the journal Nature Communications.  In it they explore how the utility of cancer whole genome and transcriptome sequencing (cWGTS) in oncology is increasingly recognized. However, implementation of cWGTS...Read More

Dr. Benjamin Greenbaum co authored the paper “Fundamental immune–oncogenicity trade-offs define driver mutation fitness” along with David Hoyos et al. in the journal Nature. In it, they propose a unified theoretical ‘free fitness’ framework that parsimoniously integrates multimodal genomic, epigenetic, transcriptomic and proteomic data into a biophysical model of the rate-limiting processes underlying the fitness advantage...Read More

Dr. Nikolaus Schultz co authored the paper, “Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients“, along with Nguyen et al. in the journal Cell. In it, they assembled MSK-MET, a pan-cancer cohort of over 25,000 patients with metastatic diseases. By analyzing genomic and clinical data from this cohort, they identified associations...Read More

Dr. Sohrab Shah’s paper led by Salehi, et al. details their study where 42,000 genomes were generated from multi-year time-series single-cell whole-genome sequencing of breast epithelium and primary triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), revealing the nature of CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy. Using a new Wright–Fisher population genetics model to...Read More

Dr. Elli Papaemmanuil‘s paper led by Bolton, et al. followed a large cohort (25K) of solid tumor patients retrospective including longitudinal samples from 525 individuals. They show how different oncologic therapies and other environmental stressors promotes the expansion of hematopoietic stem/progenitor cells bearing specific mutations. The group then went on to show what mutational features...Read More

Dr. Elli Papaemmanuil‘s large international study on myelodysplastic syndrome and acute myeloid leukemia revealed the impact of TP53 gene mutations on blood cancer severity. 25 centers from 12 different countries contributed clinical data for over 4,000 patients. Dr. Elsa Bernard, first author on the paper and a postdoc in Dr. Papaemmanuil’s lab, presenting the results...Read More

Research from Computational Oncology reports on the pervasive presence and function of composite mutations: two or more mutations to the same gene. They describe the myriad ways that these mutations interact to promote the development and progression of cancer. Dr. Ed Reznik explains more about his lab’s recent paper on his Twitter. Dr. Barry Taylor...Read More

We have moved into our new facility at 321 East 61st Street where we have consolidated cross departmental and cross center computational groups, resulting in MSK’s brand new computational campus.  Computational Pathology, Radiology Informatics, Clinical Bioinformatics, Center for Molecular Oncology, Computational Sciences, High Performance Computing, and others are an integrated unit at the new Joy...Read More