Dr Ben Langmead is a computational biologist and assistant professor in the Computer Science Department at Johns Hopkins University, most famous for his creation of the Bowtie and Bowtie 2 sequence alignment algorithms, used to improve sequencing alignment quality. FLG spoke to Dr Langmead about his lab, his recent work using the Stampede2 supercomputer cluster to optimise sequencing data analysis software, and the future for DNA sequencers as a whole.
Yale University researchers have discovered a potential new biomarker for identifying individuals with increased risk of prostate cancer metastasis. The findings announced that mitochondrial protein syntaphilin is vital in determining the balance between tumour cell proliferation and tumour cell invasion, and is expressed significantly at the invasive tumour edge in prostate cancer.
Gene therapy can make heart cells regenerate after a heart attack, King’s College London researchers have found. The study, published in Nature, stated that a small piece of genetic material called microRNA-199 delivered into a pig’s heart after myocardial infarction resulted in almost total cardiac recovery a month later.
Swiss scientists have found a potential new way to block metastasis, with promising results demonstrated in mice. The researchers have found a “barrier”, built by the Activin B protein and a receptor called ALK7, the combo of which prevents tumours from spreading through the body.
When the MDM2 gene acts with a specific protein found in cancer cells’ mitochondria, it can lead to cancer cell death. The study which discovered this fact, published by Mount Sinai researchers in Molecular Cell journal, could open new treatment opportunities for cancer patients in the future.
The ATDC gene has been identified as necessary for the development of pancreatic cancer. Deleting the gene in pancreatic cells led to “one of the most profound blocks of tumour formation ever observed in a well-known mice model engineered to develop pancreatic ductal adenocarcinoma”.
Two molecules which switch off CRISPR could be used to make gene editing therapies safer in the future. Harvard University’s Amit Choudhary and his colleagues said the molecules could stop CRISPR making unintended changes to DNA, potentially harming the individual.
Network algorithms can improve cancer treatment effectiveness by better determining how genes interact, researchers from the University of Sussex have found. The algorithm built by the scientists, Slant, uses current data to find patterns associated with being part of a synthetic lethal interaction.
Questions around legality, protecting privacy and ensuring quality of data in DNA sequencing all need answering, a symposium recently held at the University of Minnesota has announced. LawSeq, a $2 million project looking to solve the issue of privacy and legality in sequencing, is exploring how to ensure the legal world catches up with current science.
A new polygenic risk score tested data from 300,000 people to forecast risk of obesity. The study found that 10% of adults with the highest genetic risk were 25 times more likely to become severely obese than the 10% whose genes were most likely to keep them slim.
Genetic research is a big data problem without researchers generally having access to this “big” genomic and medical data. Not only has it been nearly impossible to access enough relevant data to support research, but analysing the data has been slow and challenging due to its sheer volume. To counter this, in recent years a number of pharmaceutical companies have announced large-scale collaborations around genomic data to uncover novel drug targets, validate existing drug pipelines, predict response, and expand therapeutics use. We discuss some of the biggest and most recent.
Front Line Genomics’ “Biodata Analysis and Management – Genome Analytics, Interoperability, and Data Life Cycle” report isn’t just an update of our old Genomic Data 101 guides: packed with new information on AI and machine learning,. data discoverability and data interoperability, it is much much more.
Genomic compression expert PetaGene has become a NetApp Alliance Partner, the company announced recently, a move set to improve performance and reduce costs for researchers using large datasets within the genomics field.
Two companies with access to data from the 100,000 Genomes Project have identified patients with previously undiscovered life-threatening kidney and neurological diseases. The companies, Alexion and BioMarin, were part of Genomic England’s Discovery Forum, which grants certain industry research proposals access to data from the project after vetting.
SOPHiA GENETICS’ Solid Tumor Solution (STS) application was recently granted a CE-IVD designation, a regulatory stamp that a product has satisfied the EU’s in vitro diagnostic device requirements. We spoke to Gioia Althoff, SOPHiA’s Senior Vice President, Genomics Business Area, about the STS application and where SOPHiA is going from here.