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Search Publications by: Justin Zook (Fed)

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Displaying 26 - 50 of 72

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

A crowdsourced set of curated structural variants for the human genome

June 19, 2020
Author(s)
Lesley M. Chapman, Noah Spies, Patrick Pai, Andrew Carroll, Marc L. Salit, Justin M. Zook
A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs) is more

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

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

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

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

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

Genome-wide reconstruction of complex structural variants using read clouds

July 17, 2017
Author(s)
Noah Spies, Ziming Weng, Alex Bishara, Jennifer H. McDaniel, David N. Catoe, Justin M. Zook, Marc L. Salit, Robert B. West, Serafim Batzoglou, Arend Sidow
Recently developed methods that utilize partitioning of long genomic DNA fragments, and barcoding of shorter fragments derived from them, have succeeded in retaining long-range information in short sequencing reads. These so-called read cloud approaches

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

Extensive sequencing of seven human genomes to characterize benchmark reference materials

June 7, 2016
Author(s)
Justin M. Zook, Jennifer H. McDaniel, David N. Catoe, Lindsay Harris, Marc L. Salit
The Genome in a Bottle Consortium hosted by the National Institute of Standards and Technology, (NIST), is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. Here, we describe a

A Roadmap for Regulatory Science Research for Next Generation Sequencing Informatics

April 20, 2016
Author(s)
Justin M. Zook, Marc L. Salit, Russ B. Altman, Arend Sidow, Rachel Goldfeder, Euan Ashley, Elizabeth Mansfield
The Precision Medicine Initiative (PMI) is a national effort in the United States “to enable a new era of medicine through research, technology, and policies that empower patients, researchers, and providers to work together toward development of

PEPR: Pipeline for Evaluating Prokaryotic References

April 1, 2016
Author(s)
Nathanael D. Olson, Justin M. Zook, Daniel V. Samarov, Scott A. Jackson, Marc L. Salit
The rapid adoption of microbial whole genome sequencing in public health, clinical testing, and forensic labo-ratories requires the use of validated and well characterized measurement processes. Reference materials thatare well characterized and
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