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Bioscience

Genomics

Search Publications

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  • Published Date
Displaying 51 - 75 of 93

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures.

March 13, 2020
Author(s)
Nathanael Olson, Senthil Kumar, Stephanie Hao, Winston Timp, Marc L. Salit, O Colin Stine, Hector Corrada Bravo
Background: There are a variety of bioinformatic pipelines and downstream analysis methods for analyzing 16S rRNA marker-gene surveys. However, appropriate assessment datasets and metrics are needed as there is limited guidance to decide between available

genomeview - an extensible python-based genomics visualization engine

June 26, 2019
Author(s)
Noah Spies, Justin Zook, Marc L. Salit, Arend Sidow
Visual inspection and analysis is integral to quality control, hypothesis generation, methods development and validation of genomic data. The richness and complexity of genomic data necessitates customized visualizations highlighting specific features of

High-coverage, long-read sequencing of Chinese trio reference samples

June 14, 2019
Author(s)
Justin M. Zook, Nathanael D. Olson, Marc L. Salit, Aaron Wenger, Chunlin Xiao, Robert Sebra
Genome In a Bottle (GIAB) is a consortium hosted by the National Institute of Standards and Technology whose primary objective is the development and characterization of human genomic reference materials. The consortium includes representatives from

Development and Interlaboratory Evaluation of a NIST Reference Material RM 8366 for EGFR and MET Gene Copy Number Measurements

May 21, 2019
Author(s)
Hua-Jun He, Biswajit Das, Megan H. Cleveland, Chen Li, Corinne Camalier, Liang-Chu Liu, Kara L. Norman, Andrew Fellowes, Christopher McEvoy, Steven P. Lund, Jamie L. Almeida, Carolyn R. Steffen, Chris Karlovich, P. M. Williams, Kenneth D. Cole
The National Institute Standard and Technology (NIST) Reference Material RM 8366 was developed to improve the quality of gene copy measurements of EGFR (epidermal growth factor receptor) and MET (proto-oncogene, receptor tyrosine kinase), important targets

Multi-Laboratory Assessment of a New Reference Material for Quality Assurance of Cell-Free Tumor DNA Measurements

May 2, 2019
Author(s)
Hua-Jun He, Erica V. Stein, Yves Konigshofer, Thomas Forbes, Farol L. Tomson, Russell Garlick, Emiko Yamada, Tony Godfrey, Toshiya Abe, Koji Tamura, Michael Borges, Michael Goggins, Sandra Elmore, Margaret L. Gulley, Jessica L. Larson, Lando Ringel, Brian C. Haynes, Corinne Camalier, Chris Karlovich, Biswajit Das, P. M. Williams, Aaron Garnett, Anders Stahlberg, Stefan Filges, Lynn Sorbara, Mathew R. Young, Sudhir Srivastava, Kenneth D. Cole
We conducted a multi-laboratory assessment to determine the suitability of a new commercially- available reference material with 40 cancer variants in a background of wild-type DNA at four different variant allele fractions (VAF): 2%, 0.5%, 0.125%, and 0 %

An open resource for accurately benchmarking small variant and reference calls

April 1, 2019
Author(s)
Justin M. Zook, Jennifer H. McDaniel, Marc L. Salit, Nathanael D. Olson, Justin M. Wagner
Benchmark small variant calls are required for developing, optimizing and assessing the performance of sequencing and bioinformatics methods. Here, as part of the Genome in a Bottle (GIAB) Consortium, we apply a reproducible, cloud-based pipeline to

Best practices for benchmarking germline small-variant calls in human genomes

March 11, 2019
Author(s)
Justin M. Zook, Marc L. Salit
Standardized benchmarking approaches are required to assess the accuracy of variants called from sequence data. Although variant- calling tools and the metrics used to assess their performance continue to improve, important challenges remain. Here, as part

CrowdVariant: a crowdsourcing approach to curate copy number variants

January 6, 2019
Author(s)
Justin M. Zook, Marc L. Salit, Peyton Greenside, Ryan Poplin, Mark DePristo, Madeleine Cule
Copy number variants (CNVs) are an important type of genetic variation and play a causal role in many diseases. However, they are also notoriously difficult to identify accurately from next-generation sequencing (NGS) data. For larger CNVs, genotyping

Aflatoxin-guanine DNA Adducts and Oxidatively-induced DNA Damage in Aflatoxin-treated Mice in vivo as Measured by Liquid Chromatography-Tandem Mass Spectrometry with Isotope-dilution

December 11, 2018
Author(s)
Erdem Coskun, Pawel Jaruga, Vladimir Vartanian, Onur Erdem, Patricia Egner, John D. Groopman, R. S. Lloyd, Miral M. Dizdar
Dietary exposure to aflatoxin (AFB1) is a significant reason for the incidence of hepatocellular carcinomas globally. AFB1-exposure leads to the formation of AFB1-N7-guanine (AFB1-N7-Gua) and two diastereomers of 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4

Conference Report: Representing Ethnic Diversity for Precision Medicine

August 23, 2018
Author(s)
Justin M. Zook, Luke Hickey, Benedict Paten, Robert Sebra, Valerie Schneider
There is a pressing need to better represent ethnic diversity with genomic resources — and to do so in a way that maximizes utility for people working with the Genome Reference Consortium’s human reference genome. That was the theme of a panel discussion

Tools for annotation and comparison of structural variation

October 3, 2017
Author(s)
Justin M. Zook, Fritz Sedlazeck, Andi Dhroso, Justin Paschall
The impact of structural variants (SVs) on a variety of organisms and diseases like cancer has become increasingly evident. Methods for SV detection when studying genomic differences across cells, individuals or populations are being actively developed

Using metagenomic methods to detect organismal contaminants in microbial materials.

September 12, 2017
Author(s)
Nathanael D. Olson, Justin M. Zook, Jayne B. Morrow, Nancy J. Lin
High sensitivity methods as next generation sequencing and PCR are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive enough and require

Exposure to Engineered Nanomaterials: Impact on DNA Repair Pathways

July 13, 2017
Author(s)
Neenu Singh, Bryant C. Nelson, Leona D. Scanlan, Erdem Coskun, Pawel Jaruga, Shareen Doak
Some engineered nanomaterials (ENMs) may have the potential to cause damage to the genetic material in living systems. The mechanistic machinery functioning at the cellular/molecular level, in the form of DNA repair processes, has evolved to help

Development and Characterization of Reference Materials for Genetic Testing

November 1, 2016
Author(s)
Justin M. Zook, Marc L. Salit, Lisa V. Kalman, Mickey Williams, Vivekananda Datta, Jin-Yeong Han
Characterized reference materials (RM) are needed for test development and validation, quality control procedures and proficiency testing to assure the quality of clinical laboratory tests. In this article, we review the development and characterization of
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