U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

Search Publications by: Marc L. Salit (Assoc)

Search Title, Abstract, Conference, Citation, Keyword or Author
Displaying 1 - 25 of 64

Variant calling and benchmarking in an era of complete human genome sequences

April 14, 2023
Author(s)
Nathanael David Olson, Justin Wagner, Nathan Dwarshuis, Karen Miga, Marc L. Salit, Justin Zook
Genetic variant calling from DNA sequencing has enabled understanding of germline variation in hundreds of thousands of humans. Sequencing technologies and variant-calling methods have advanced rapidly, routinely providing reliable variant calls in most of

Benchmarking challenging small variants with linked and long reads

May 11, 2022
Author(s)
Justin Wagner, Nathanael David Olson, Lindsay Harris, Marc L. Salit, Fritz Sedlazeck, Chunlin Xiao, Justin Zook
Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines and develop variant calling and sequencing methods. Here we use accurate linked and long reads to expand benchmarks in 7 samples to include difficult-to-map

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

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

March 13, 2020
Author(s)
Nathanael David 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

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

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

Measurements of translation initiation from all 64 codons in E. coli

February 21, 2017
Author(s)
Ariel H. Hecht, Jeff E. Glasgow, Paul Jaschke, Lukmaan Bawazer, Matthew S. Munson, Jennifer R. Cochran, Drew Endy, Marc L. Salit
Our understanding of translation represents a cornerstone of molecular biology and underpins our capacity to engineer living matter. For decades, the codon AUG and a few near-cognates (GUG, UUG) have been exclusively considered as “start codons” for

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

Toward Achieving Harmonization in a Nano-cytotoxicity Assay Measurement through an Interlaboratory Comparison Study

September 29, 2016
Author(s)
John T. Elliott, Matthias Roesslein, Nam W. Song, Blaza Toman, Agnieszka Kinsner-Ovaskainen, Rawiwan Maniratanachote, Marc L. Salit, Elijah J. Petersen, Fatima Sequeira, Jieun Lee, Francois Rossi, Cordula Hirsch, Harald Krug, Wongsakorn Suchaoin, Peter Wick
Design and development of reliable cell-based nanotoxicology assays is important for ranking of potential hazardous engineered nanomaterials. Challenges to producing a reliable assay protocol include working with nanoparticle dispersions and living cell

Roles of Nanofiber Scaffold Structure and Chemistry in Directing Human Bone Marrow Stromal Cell Response

August 22, 2016
Author(s)
Sumona Sarkar, Bryan A. Baker, Desu Chen, Patrick S. Pine, Jennifer H. McDaniel, Marc L. Salit, Wolfgang Losert, Carl G. Simon Jr., Joy P. Dunkers
Nanofiber technology has emerged as a promising tool to recapitulate the native extracellular matrix structure; however the properties of nanofibers governing cell-material interactions are still largely undetermined. In this study we have systematically

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

Clinical Implications of Technical Performance in Medical Genome Sequencing

March 2, 2016
Author(s)
Justin M. Zook, James Priest, Rachel Goldfeder, Megan Grove, Daryl Waggott, Matthew Wheeler, Euan Ashley, Marc L. Salit
As next-generation sequencing is becoming routinely applied to clinical care, the predictive characteristics and limitations of whole exome and whole genome sequencing need to be well-understood. The Genome in a Bottle Consortium has recently published a

Evaluation of microbial qPCR workflows using engineered Saccharomyces cerevisiae

January 24, 2016
Author(s)
Sandra M. Da Silva, Lindsay Harris, Nathanael David Olson, Steven Lund, Autumn S. Downey, Zvi Kelman, Marc L. Salit, Jayne D. Morrow
Aims: We describe the development and interlaboratory study of modified Saccharomyces cerevisiae as a candidate material to evaluate a full detection workflow including DNA extraction and quantitative polymerase chain reaction (qPCR). Methods and results

SVClassify: a method to use multiple datasets to classify candidate structural variants into true positives and false positives

January 16, 2016
Author(s)
Justin M. Zook, Hemang M. Parikh, Desu Chen, Hariharan K. Iyer, Marc L. Salit, Wolfgang Losert
The human genome contains variants ranging in size from small single nucleotide polymorphisms (SNPs) to large structural variants (SVs). While high-quality benchmark small variant calls have recently been developed by the Genome in a Bottle Consortium, no