Genomics

UCI-led study uses plankton genomes as global biosensors of ocean ecosystem stress

Irvine, Calif., April 15, 2021 — By analyzing gains and losses in the genes of phytoplankton samples collected in all major ocean regions, researchers at the University of California, Irvine have created the most nuanced and high-resolution map yet to show where these photosynthetic organisms either thrive or are forced to adapt to limited quantities of key nutrients, nitrogen, phosphorus and iron.

Researchers Identify RNA Editing Events that Impact Gene Expression and Phenotype

Combining computational mining of big data with experimental testing in the lab, researchers at Children’s Hospital of Philadelphia (CHOP) have identified RNA editing events that influence gene expression and, in turn, the phenotypic manifestation of that expression. In analyzing so-called A-to-I RNA editing, in which the adenosine of an RNA molecule is chemically modified into an inosine, the researchers describe how a single nucleotide change by RNA editing can have large downstream effects. The findings were published today in Genome Biology.

Genomic Data Commons provides unprecedented cancer data resource

The National Cancer Institute’s Genomic Data Commons (GDC), launched in 2016 by then-Vice President Joseph Biden and hosted at the University of Chicago, has become one of the largest and most widely used resources in cancer genomics, with more than 3.3 petabytes of data from more than 65 projects and over 84,000 anonymized patient cases, serving more than 50,000 unique users each month.

CHOP Researchers Find NTRK Fusions More Common than Expected in Pediatric Tumors

In a large study of pediatric cancer patients, researchers from Children’s Hospital of Philadelphia (CHOP) have analyzed the frequency, fusion partners, and clinical outcome of neurotrophic tyrosine receptor kinase (NTRK) fusions, which are clinical biomarkers that identify patients suitable for treatment with FDA-approved TRK inhibitors. The researchers found that NTRK fusions are more common in pediatric tumors and also involve a wider range of tumors than adult cancers, information that could help prioritize screening for NTRK fusions in pediatric cancer patients who might benefit from treatment with TRK inhibitors.

Making sense of a universe of corn genetics

A new study details the latest efforts to predict traits in corn based on genomics and data analytics. The data management technique could help to “turbo charge” the seemingly endless amount of genetic stocks contained in the world’s seed banks, leading to faster and more efficient development of new crop varieties.

Testing Wastewater for COVID-19

UNLV researcher Edwin Oh and colleagues have implemented wastewater surveillance programs to screen samples for the presence of COVID-19 and to extract the RNA from the SARS-COV-2 virus to find targets that make vaccines more effective.

CHOP Researchers Reverse Severe Lymphatic Disorder in Patient with Noonan Syndrome by Targeting Genetic Pathway

Researchers at Children’s Hospital of Philadelphia (CHOP) have resolved a severe lymphatic disorder in a girl with Noonan Syndrome that had led to upper gastrointestinal bleeding, fluid collection around the lungs, and numerous surgeries that had been unable to resolve her symptoms. By identifying a genetic mutation along a pathway related to lymphatic vessel development and function, the research team was able to target the pathway using an existing drug they had used in a previous case to remodel a patient’s lymphatic system.

CHOP Genomic Study Reveals Role for Hypothalamus in Inflammatory Bowel Disease

Using sophisticated 3D genomic mapping and integrating with public data resulting from genome-wide association studies (GWAS), researchers at Children’s Hospital of Philadelphia (CHOP) have found significant genetic correlations between inflammatory bowel disease (IBD) and stress and depression. The researchers went on to implicate new genes involved in IBD risk that are enriched in both derived hypothalamic neurons, from a part of the brain that has a vital role in controlling stress and depression, and organoids derived from colon cells, a region more commonly studied in the context of IBD.

New Computational Model by CHOP Researchers Identifies Noncoding Mutations Across Five Pediatric Cancers

Researchers at Children’s Hospital of Philadelphia (CHOP) have developed a new computational algorithm that has, for the first time, identified a spectrum of mutations in the noncoding portion of the human genome across five major pediatric cancers. The study, which was published today in Science Advances, used the algorithm to analyze more than 500 pediatric cancer patients’ mutations and gene expression profiles to develop a comprehensive list of potentially cancer-causing mutations.