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Health

Precision medicine

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Displaying 51 - 75 of 106

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

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

Reference standards for accurate validation and optimization of assays that determine integrated Lentiviral vector copy number in transduced cells

July 11, 2021
Author(s)
Barbara S. Paugh, Lajos Baranyi, Andre Roy, Hua-Jun He, Lindsay Harris, Kenneth Cole, Caroline Raimund, Patricia S. Langan, Moria Artlip, Srikanta Jana, Rimas J. Orentas, Sheng Lin-Gibson, Winfried Krueger, Boro Dropuli?
Lentiviral vectors (LV) have emerged as a robust technology for therapeutic gene delivery into human cells as advanced medicinal products. As these products are increasingly commercialized, there are concomitant demands for their characterization to ensure

Portable bioluminescent platform for in vivo monitoring of biological processes in non-transgenic animals

May 11, 2021
Author(s)
Aleksey Yevtodiyenko, Arkadiy Bazhin, Pavlo Khodakivskyi, Aurelien Godinat, Gyslain Budin, Marina Kunchulia, Giorgio Pietramaggiori, Sandra Scherer, Elena Goun, Sergey Polyakov, George P. Eppeldauer
Bioluminescent imaging (BLI) is one of the most powerful and widely used preclinical imaging modalities. However, the current technology relies on the use of transgenic luciferase-expressing cells and animals and therefore can only be applied to a limited

Characterization of extracellular vesicles and artificial nanoparticles with four orthogonal single-particle analysis platforms

April 6, 2021
Author(s)
Emily Mallick, Tanina Arab, Yiyao Huang, Liang Dong, Zhaohao Liao, Zezhou Zhao, Barbara Smith, Norman J. Haughey, Kenneth Pienta, Barbara Slusher, Patrick Tarwater, Juan Pablo Tosar, Angela M. Zivkovic, Wyatt Vreeland, Michael E. Paulaitis, Kenneth W. Witwer
We compared four orthogonal technologies for sizing, counting, and phenotyping of extracellular vesicles (EVs) and synthetic particles. The platforms were: single-particle interferometric reflectance imaging sensing (SP-IRIS) with fluorescence

Accelerating Innovation and Commercialization Through Standardization of Microfluidic-Based Medical Devices

January 5, 2021
Author(s)
Darwin R. Reyes-Hernandez, Henne van Heeren, Suvajyoti Guha, Luke Herbertson, Alexios P. Tzannis, Jens Ducr?e, Hugo Bissig, Holger Becker
The microfluidics industry has grown steadily over the last 5 years worldwide, with the market for microfluidic medical devices experiencing a compound growth rate of 18%. The number of submissions to regulatory agencies such as the U.S. Food & Drug

Chromosome-scale, haplotype-resolved assembly of human genomes

December 7, 2020
Author(s)
Justin Zook, Shilpa Garg, Heng Li
Haplotype-resolved or phased genome assembly provides a complete picture of genomes and their complex genetic variations. However, current algorithms for phased assembly either do not generate chromosome-scale phasing or require pedigree information, which

A Diploid Assembly-based Benchmark for Variants in The Major Histocompatibility Complex

September 22, 2020
Author(s)
Justin M. Zook, Justin M. Wagner, Chen-Shan Chin, Qiandong Zeng, Alexander Dilthey, Tobias Marschall, Mikko Rautiainen, Erik Garrison, Shilpa Garg
Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct accurate, phased de novo assemblies. We focus on a medically important, highly variable, 5

High-Resolution Biochemical Activity Measurements with Commercial Transistors

September 1, 2020
Author(s)
Seulki Cho, Son T. Le, Curt A. Richter, Arvind Balijepalli
We demonstrate that single-gated, commercially-sourced, field-effect transistors (FETs) operated with a lock- in amplifier (LIA) under closed-loop control can achieve an average pH resolution of 9x10^-4. This performance represents an 8-fold improvement

A robust benchmark for detection of germline large deletions and insertions

June 15, 2020
Author(s)
Justin Zook, Nathanael David Olson, Marc Salit, Fritz Sedlazeck
New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a

Assembly and annotation of an Ashkenazi human reference genome

June 2, 2020
Author(s)
Justin M. Zook, Justin M. Wagner, Nathanael D. Olson, Steven L. Salzberg, Alaina Shumate, Aleksey V. Zimin, Daniela Puiu, Mihaela Pertea, Marc Salit
Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very small sample of the human population. There is a

T1 Mapping Performance and Measurement Stability: Results from the Multi-National T1MES (T1 Mapping and ECV Standardization) Phantom Program

May 7, 2020
Author(s)
Gabriella Captur, Abhiyan Bandari, Ye Yang, Richard James, Giulia Benedetti, Camilla Torlasco, Lewis Ricketts, Redha Boubertakh, Katy Keenan, Ruediger Bruehl, Bernd Itterman, Nasri Fatih, John Greenwood, Leonie Paulis, Chris Lawton, Chiara Bucciarelli-Ducci, Hildo Lamb, Richard Steeds, Steve Leung, Colin Berry, Sinitsyn Valentin, Andrew Flett, Charlotte de Lange, Francesco DeCobelli, Magalie Viallon, Pierre Croisille, David Higgins, Andreas Greiser, Wenjie Peng, Christian Hamilton-Craig, Wendy Strugnell, Tom Dresselaers, Andrea Barison, Dana Dawson, Andrew Taylor, Francois-Pierre Mongeon, Sven Plein, Daniel Messroghli, Mouaz Al-Mallah, Stuart Grieve, Massimo Lombardi, Jihye Jang, Michael Salerno, Nish Chaturvedi, Peter Kellman, David Bluemke, Reza Nezafat, Peter Gatehouse, James C. Moon

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

May 4, 2020
Author(s)
Justin M. Zook, Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E. Olsen, Miten Jain, Benedict Paten
De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable rapid human genome assembly, we present Shasta, a de novo long-read assembler, and

Mass Spectral Library of Acylcarnitines Derived from Human Urine

April 8, 2020
Author(s)
Xinjian Yan, Sanford Markey, Ramesh Marupaka, Qian Dong, Brian T. Cooper, Yuri Mirokhin, William E. Wallace, Stephen Stein
We describe the creation of a mass spectral library of acylcarnitines and conjugated acylcarnitines from the LC–MS/MS analysis of six NIST urine reference materials. To recognize acylcarnitines, we conducted in-depth analyses of fragmentation patterns of
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