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In this two-part series, we’ll give you a look at some of the tools, teams, and resources built by Broad Institute scientists to support the large-scale cancer sequencing project known as The Cancer Genome Atlas (TCGA).
Cells use a complex network of connections to make a constant array of decisions about their surrounding environment: Is it time to grow? Is it time to change into a different type of cell? When a cellular component or connection is missing or defective, disease takes hold.
This spring, artists, designers, computational biologists, and software engineers gathered in the Broad Institute auditorium for three days of talks, posters, and tutorials on the cutting-edge field of visualization in biology.
Two teams – including one from the Broad Institute, Dana-Farber Cancer Institute, and the University of Pittsburgh School of Medicine – report surprising discoveries about head and neck cancer biology in back-to-back papers published in Science.
When researchers from the Broad Institute and the Department of Human Genetics at Harvard University set about the task of pinpointing ancestral diversity in African Americans, the first tool they used for the job was the HapMix software engine. HapMix is a software tool that helps researchers infer the ancestry of extremely small bits of DNA.
Today, the cancer samples we have been following will go from tangible pieces of tissue to something a bit more abstract: invisible strands of pure DNA. In the process, the samples will be whirled and spun through laboratory machinery, incubated over night, and washed repeatedly with different chemical substances. The final product of all of this will be large droplets of clear liquid at the bottom of tiny, plastic Eppendorf tubes.
Back in May, we told you on the blog about Trinity, a suite of tools that assembles transcripts, or bits of RNA that have been copied from a cell’s genome, into a “transcriptome,” even without a reference genome handy.
The liver is a critical and intriguing organ, and our understanding of it continues to evolve to this day. As reported in a paper published earlier this week in Proceedings of the National Academy of Sciences, Broad and MIT researchers teamed up to put artificial liver tissue to the test (read the news story here and Project Spotlight here).
Just yesterday, a new paper from the Project Achilles team appeared online in the Proceedings of the National Academy of Sciences. Researchers examined over 100 tumors, including 25 ovarian cancer tumors in search of genes and mutations fostering cancer growth. The team found that nearly one-fifth of the ovarian tumors harbored mutations in the PAX8 gene.
Last week on the Broad website, we told you about a new approach to detect and verify biomarkers, using the search for signals of heart attack as a test case. In this study, the team of scientists from the Broad Institute and Massachusetts General Hospital looked for proteins in the blood that are released when heart cells are injured and that can be detected quickly after the attack.