Obesity is a risk factor for cancer, but whether obesity is linked to specific genomic subtypes of cancer is unknown. We examined the relationship between obesity and tumor genotype in two clinicogenomic corpora. Obesity was associated with specific driver mutations in lung adenocarcinoma, endometrial carcinoma and cancers of unknown primaries, independent of clinical covariates, demographic...Read More

The digitization of health records and growing availability of tumour DNA sequencing provide an opportunity to study the determinants of cancer outcomes with unprecedented richness. Patient data are often stored in unstructured text and siloed datasets. Here we combine natural language processing annotations1,2 with structured medication, patient-reported demographic, tumour registry and tumour genomic data from 24,950...Read More

Dr. Adam Weiner published the paper Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data. The study explores how dysregulated DNA replication is a cause and a consequence of aneuploidy in cancer, yet the interplay between copy number alterations (CNAs), replication timing (RT) and cell cycle dynamics remain understudied in aneuploid tumors. We...Read More

Dr. Nicholas Ceglia et al. published the paper Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector. A scalable framework for dimensionality reduction, GeneVector identifies transcriptional programs and classifies cell types. You can read the paper in Nature Communications here.Read More

Dr. Elli Papaemmanuil et al. published the paper Clonal evolution during metastatic spread in high-risk neuroblastoma. Patients with high-risk neuroblastoma generally present with widely metastatic disease and often relapse despite intensive therapy. As most studies to date focused on diagnosis-relapse pairs, our understanding of the genetic and clonal dynamics of metastatic spread and disease progression...Read More

Dr. Benjamin Greenbaum et al. published the paper Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer. Pancreatic ductal adenocarcinoma (PDAC) is lethal in 88% of patients, yet harbours mutation-derived T cell neoantigens that are suitable for vaccines. Here in a phase I trial of adjuvant autogene cevumeran, an individualized neoantigen vaccine based on uridine mRNA–lipoplex...Read More

Genetics and anatomy sculpt immune-cell partners of ovarian cancer was recently published in Nature. The most common type of ovarian cancer, called high-grade serous ovarian cancer (HGSOC), is challenging from a therapeutic perspective. By the time most individuals are diagnosed with this type of tumour, it has already spread (metastasized) from the primary site to...Read More

Dr. Sohrab Shah et al. published the paper Ovarian cancer mutational processes drive site-specific immune evasion in Nature. High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability patterned by distinct mutational processes, tumour heterogeneity and intraperitoneal spread. Immunotherapies have had limited efficacy in HGSOC, highlighting an unmet need to assess how mutational...Read More

Dr. Sohrab Shah et al. published the paper Single-cell genomic variation induced by mutational processes in cancer in Nature. How cell-to-cell copy number alterations that underpin genomic instability in human cancers drive genomic and phenotypic variation, and consequently the evolution of cancer, remains understudied. Here, by applying scaled single-cell whole-genome sequencing to wild-type, TP53-deficient and TP53-deficient;BRCA1-deficient or TP53-deficient;BRCA2-deficient...Read More

Dr. Elli Papaemmanuil et al. published the paper Unified classification and risk-stratification in Acute Myeloid Leukemia in Nature Communications. In it they use use comprehensive molecular profiling data from 3,653 patients to characterize and validate 16 molecular classes describing 100% of AML patients. Each class represents diverse biological AML subgroups, and is associated with distinct...Read More