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Bioscience

Genomics

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Displaying 51 - 75 of 166

Current Explorations of Nutrition and the Gut Microbiome: A Systematic Review

September 23, 2021
Author(s)
Scott Jackson, Leigh A. Frame, Elise Costas
Background The ability to measure and describe the microbiome has led to a surge in information about the gut microbiome and its role in health and disease. The relationship between nutrition and the gut microbiome is central, as the diet is a source of

Nanopore sensing: a physical-chemical approach

September 1, 2021
Author(s)
Joseph W. Robertson, Madhav Ghimire, Joseph Reiner
Protein nanopores have emerged as an important class of sensor, for the understanding of biophysical processes, such as molecular transport across membranes, and detection and characterization of biopolymers. We trace the development of these sensors from

Challenges of Accuracy in Germline Clinical Sequencing Data

July 20, 2021
Author(s)
Justin Zook, Ryan Poplin, Mark DePristo
Physicians are increasingly using clinical sequencing tests to establish diagnoses of patients who might have genetic disorders, which means that accuracy of sequencing and interpretation are important elements in ensuring the benefits of genetic testing

Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution

June 7, 2021
Author(s)
Claire R. Peart, Christina Williams, Saurabh Pophaly, Jeremy Johnson, Ben Neely, Frances Gulland, David Adams, Bee Ng, William Cheng, Joseph Hoffman, Matthew Breen, Jochen Wolf
With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale genome

One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation

May 18, 2021
Author(s)
Stephen Lincoln, Tina Hambuch, Justin Zook, Sara Bristow, Kathryn Hatchell, Rebecca Truty, Michael Kennemer, Brian Shirts, Andrew Fellowes, Shimul Chowdhury, Eric Klee, Shazia Mahamdallie, Megan Cleveland, Peter Vallone, Yan Ding, Sheila Seal, Wasanthi DeSilva, Farol Tomson, Catherine Huang Huang, Russell Garlick, Nazneen Rahman, Marc L. Salit, Stephen Kingsmore, Matthew Ferber, Swaroop Aradhya, Robert Nussbaum
Next-generation sequencing (NGS) is widely used and cost-effective. However, depending on the specific methods used, NGS can have limitations with certain technically challenging variant types. These types are poorly represented in some validation studies

Species and population specific gene expression in blood transcriptomes of marine turtles

May 13, 2021
Author(s)
Shreya M. Banerjee, Jamie A. Stoll, Camryn D. Allen, Jennifer Lynch, Heather Harris, Lauren Kenyon, Eleanor Sterling, Eugenia Naro-Maciel, Kate McFadden, Margaret Lamont, James Benge, Jeffrey A. Seminoff, Scott Benson, Rebecca L. Lewison, Tomoharu Eguchi, T. T. Jones, Peter Dutton, George H. Balazs, Lisa M. Komoroske
Background Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms' responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can

Cautionary Note on Contamination of Reagents Used for Molecular Detection of SARS-CoV-2

May 3, 2021
Author(s)
Peter Vallone, James Huggett, Vladimir Benes, Jeremy Garson, Kathryn Harris, Mikael Kubista, Timothy McHugh, Jacob Moran-Gilad, Tania Nolan, Michael Pfaffl, Marc Salit, Greg Shipley, Jo Vandesompele
Reverse transcription (RT)-PCR, the principal diagnostic method applied in the world-wide struggle against COVID-19, is capable of detecting a single molecule of a viral genome. Correctly designed and practiced RT-PCR assays for SARS-CoV-2 should not cross

Sequence-based U.S. population data for 7 X STR loci

April 26, 2021
Author(s)
Lisa Borsuk, Carolyn R. Steffen, Kevin M. Kiesler, Peter Vallone, Katherine Gettings
The National Institute of Standards and Technology (NIST) U.S. population sample set of unrelated individuals was used to determine allele and haplotype frequencies for seven X-chromosome short tandem repeat (STR) loci in four linkage groups. DXS7132

The NIH Somatic Cell Genome Editing program

April 7, 2021
Author(s)
Samantha Maragh
The move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more