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Genome Biology Papers on My Personal Mutanome, GBM Splicing, Gastric Cancer Transcripts

Researchers at the Cleveland Clinic, Columbia University, and other centers introduce "My personal mutanome" (MPM), a database and computational platform designed to help find clinically actionable alterations in an individual's genome, including variants related to disease risk, potential treatment targets, and anticipated drug responses. "[M]y Personal Mutanome offers a comprehensive database and powerful visualization tools that bridge the translational gap between large-scale genomic medicine studies and clinical outcomes," they write, noting that the site currently houses mutation data spanning more than 10,800 tumor exomes profiled for the Cancer Genome Atlas project, together with related protein-protein interaction, modification, functional, and clinical data. "Collectively," the authors say, MPM "offers network-based diagnosis and pharmacogenomics approaches to understand complex genotype-phenotype relationships and therapeutic responses in the clinical settings."

A University of California, San Francisco-led team takes a look at alternative splicing patterns in glioblastoma (GBM) tumors before and after treatment. Based on RNA sequencing profiles for more than three dozen primary or recurrent GBM tumors — along with RNA-seq profiles for non-malignant brain tissue samples, publicly available GBM transcriptome data, and single-cell RNA-seq profiles — the researchers searched for alternative splicing events that were specific to the recurrent adult brain tumors following standard therapy. Their results revealed a rise in alternative splicing, as well as increased expression of the splicing factor regulator SRSF5 and other genes in the recurrent GBM samples. In addition, the splicing study pointed to cell type- and tumor-specific alternative splicing events, the authors note, including potential targets for autologous T cell therapies.

Finally, investigators from the Duke-NUS Medical School, the National University of Singapore, and elsewhere present findings from a long-read RNA sequencing analysis of gastric cancer. Using a combination of long-read isoform sequencing and short-read paired-end sequencing, the team assessed transcriptome features in 10 gastric cancer cell lines, identifying more than 60,200 distinct full-length transcripts in the tumor cell lines. From that set, the authors looked at transcript isoforms in cell lines from each of the four main gastric cancer subtypes, along with transcript, splicing, and promoter use features found in the specific subtypes or cell lines. "Having observed substantial level splicing events leading to alternative promoters and previously unknown transcript isoforms," they write, "our results strongly highlight that full-length transcriptome profiling represents an under-explored area of research which may yield novel biological insights, biomarkers, and drug targets."

The Scan

Guidelines for Ancient DNA Work

More than two dozen researchers have developed new ethical guidelines for conducting ancient DNA research, which they present in Nature.

And Cleared

A UK regulator has cleared former UK Prime Minister David Cameron in concerns he should have registered as a consultant-lobbyist for his work with Illumina, according to the Financial Times.

Suit Over Allegations

The Boston Globe reports that David Sabatini, who was placed on leave from MIT after allegations of sexual harassment, is suing his accuser, the Whitehead Institute, and the institute's director.

Nature Papers on Esophageal Cancer, Origin of Modern Horses, Exome Sequencing of UK Biobank Participants

In Nature this week: genetic and environmental influences of esophageal cancer, domestic horse origin traced to Western Eurasian steppes, and more.