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Search Publications by: Justin Zook (Fed)

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Displaying 26 - 50 of 131

The complete sequence of a human genome

March 31, 2022
Author(s)
Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Jennifer McDaniel, Nathanael David Olson, Justin Wagner, Justin Zook, Evan Eichler, Karen Miga, Adam Phillippy
Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T)

Curated variation benchmarks for challenging medically relevant autosomal genes

February 7, 2022
Author(s)
Justin Wagner, Nathanael David Olson, Lindsay Harris, Jennifer McDaniel, Fritz Sedlazeck, Chen-Shan Chin, Justin Zook
The repetitive nature and complexity of some medically relevant genes poses a challenge for their accurate analysis in a clinical setting. The Genome in a Bottle Consortium has provided variant benchmark sets, but these exclude nearly 400 medically

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

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

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