Scientific Reports: Gene Updater: a web tool that autocorrects and updates for Excel misidentified gene names. “…we developed a web tool with Streamlit that can convert old gene names and dates back into the new gene names recommended by [HUGO Gene Nomenclature Committee]. The web app is named Gene Updater, which is open source…”
Bloomberg: Scientists discover gene that increases risk of dying from Covid – Times of India. “Polish scientists have discovered a gene that they say more than doubles the risk of falling severely ill with, or even dying from Covid-19. The health ministry in Warsaw expects the discovery to help identify people who are most at risk from the disease, which has already killed more than 100,000 people in Poland alone. It also plans to include genetic tests when it screens patients for potential Covid-19 infections as soon as the end of June.”
EurekAlert: New tool facilitates inclusion of people of diverse ancestry in large genetics studies. “Genome-wide association studies (GWAS) have typically excluded diverse and minority individuals in the search for gene variants that confer risk of disease. Researchers at Massachusetts General Hospital (MGH), the Broad Institute of MIT and Harvard, and other institutions around the world have now developed a free-access software package called Tractor that increases the discovery power of genomics in understudied populations. A study of Tractor’s performance and accuracy was published in Nature Genetics.”
EurekAlert: Historical bias overlooks genes related to COVID-19. “A historical bias — which has long dictated which human genes are studied — is now affecting how biomedical researchers study COVID-19, according to new Northwestern University research. Although biomedical researchers know that many overlooked human genes play a role in COVID-19, they currently do not study them. Instead, researchers that study COVID-19 continue to focus on human genes that have already been heavily investigated independent of coronaviruses.”
The Verge: Scientists rename human genes to stop Microsoft Excel from misreading them as dates. “There are tens of thousands of genes in the human genome: minuscule twists of DNA and RNA that combine to express all of the traits and characteristics that make each of us unique. Each gene is given a name and alphanumeric code, known as a symbol, which scientists use to coordinate research. But over the past year or so, some 27 human genes have been renamed, all because Microsoft Excel kept misreading their symbols as dates.”
Medical Xpress: Hundreds of UCLA students publish encyclopedia of 1,000 genes linked to organ development. “A team of 245 UCLA undergraduates and 31 high school students has published an encyclopedia of more than 1,000 genes, including 421 genes whose functions were previously unknown. The research was conducted in fruit flies, and the genes the researchers describe in the analysis may be associated with the development of the brain, eye, lymph gland and wings.” Loved the soccer analogy.
News Medical: Genome reference database can help predict disease-linked gene variants more accurately. “Most diseases have a genetic component. To better understand disease, researchers led by the Garvan Institute of Medical Research are analysing genetic information to determine what keeps us healthy. In a world first, the team has compiled a genome reference database of thousands of healthy older Australians, which has the potential to predict disease-linked gene variants more accurately than has been previously possible.”
Spectrum News: New database catalogs variants in autism genes. “VariCarta catalogs variants from more than 13,000 autistic people. So far, it has identified and corrected for 16,832 variants that have been reported in multiple studies. The team continually adds studies to the database.”
EurekAlert: New database enhances genomics research collaboration. “The MaveDB database is a repository for data from experiments – called multiplex assays of variant effect (MAVEs) – that systematically measure the impact of thousands of individual sequence variants on a gene’s function. These experiments can provide valuable information about how proteins produced by that gene function, how variants in that gene may contribute to disease, and how to engineer synthetic versions of naturally occurring proteins that are more effective than the original protein.”
National Cancer Institute: BRCA Exchange aggregates data on thousands of BRCA variants to inform understanding of cancer risk. “A global resource that includes data on thousands of inherited variants in the BRCA1 and BRCA2 genes is available to the public. The BRCA Exchange was created through the BRCA Challenge, a long-term demonstration project initiated by the Global Alliance for Genomics and Health (GA4GH) to enhance sharing of BRCA1 and BRCA2 data. The resource, available through a website and a new smartphone appExit Disclaimer, allows clinicians to review expert classifications of variants in these major cancer predisposition genes as part of their individual assessment of complex questions related to cancer prevention, screening, and intervention for high-risk patients.”
TechCrunch: Mammoth Biosciences launches a CRISPR-powered search engine for disease detection. “Most people tend to think of CRISPR as a groundbreaking gene-editing technology that can hunt down and snip away bits of DNA, like the cut and paste function on a keyboard. While many research projects tend to emphasize the potential of that process in replacing target bits of genetic material, for Mammoth Biosciences, the search function is the real game changer.”
Phys.org: New gene catalog of ocean microbiome reveals surprises . “Microbes dominate the planet, especially the ocean, and help support the entire marine food web. In a recent report published in Nature Microbiology, University of Hawai’i at Mānoa (UHM) oceanography professor Ed DeLong and his team report the largest single-site microbiome gene catalog constructed to date.”
Microsoft is being blamed for errors in gene studies. “Microsoft’s Excel has been blamed for errors in academic papers on genomics. Researchers trying to raise awareness of the issue claim that the spreadsheet software automatically converts the names of certain genes into dates.” I wonder if Gnumeric does this? It is my spreadsheet of choice.
This looks terrific! A new Chrome plugin attempts to easily draw connections between items in PubMed. “Every day, more than 3,000 new abstracts are uploaded to PubMed, the main biomedical literature reference database. Even in a researcher’s narrowly-defined field, it is impossible to stay on top of the ever-evolving webs of interconnections between these papers. For example, a new gene is described – might it be relevant to a researcher’s specialty? It could take many painstaking hours of searching to discover the answer. Now a new tool developed in the A.C. Tan lab at the University of Colorado Cancer Center and described today in the journal Bioinformatics helps researchers make these connections. The free tool, HiPub, is available for download as plugin for the Chrome web browser.”
A new Web site hopes to aggregate information on people with very rare genetic disorders. “The site, called MyGene2, went live in March and now has more than 100 profiles posted by families, researchers and clinicians — with more added daily. It’s one of the first advanced, searchable platforms that makes it easy to share clinical and scientific information about genetic mutations that may underlie unknown conditions.”
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