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You searched on: Author: Marc Salit

Displaying records 1 to 10 of 40 records.
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1. SVClassify: a method to use multiple datasets to classify candidate structural variants into true positives and false positives
Published: 1/16/2016
Authors: Justin M Zook, Hemang M. Parikh, Desu Chen, Hariharan K Iyer, Marc L Salit, Wolfgang Losert
Abstract: 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 Consorti ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=918034

2. Benchmarks for genome sequencing
Published: 9/23/2015
Authors: Justin M Zook, Marc L Salit
Abstract: In this issue, Griffith et al. present one of the most comprehensive genome-sequence data sets to date from a patient with myeloid leukemia, including sequencing of normal tissue, primary cancer, and a relapse. Their raw data from a variety of sequen ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=919330

3. Using mixtures of biological samples as genome-scale process controls
Published: 9/17/2015
Authors: Jerod R Parsons, Patrick S Pine, Marc L Salit, Sarah A Munro, Jennifer H McDaniel
Abstract: Background: Genome-scale ,-omicsŠ measurements are challenging to benchmark, due to the enormous number of individual measurands. Mixtures of previously-characterized samples can be used to benchmark repeat performance using mixture proportions ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=917386

4. svviz: a read viewer for validating structural variants
Published: 8/18/2015
Authors: Noah Spies, Justin M Zook, Marc L Salit, Arend Sidow
Abstract: We present svviz, a sequencing read visualizer for structural variants (SVs) that sorts and displays only reads relevant to a candidate SV. This is accomplished by searching input bam(s) for potentially relevant reads, realigning them against the i ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=918148

5. Quantifying and Improving Clinical-grade Coverage and Accuracy using Augmented Exome Sequencing
Published: 7/16/2015
Authors: Justin M Zook, Anil Patwardhan, Marc L Salit, Carlos Bustamante, Euan Ashley, Michael Snyder, John West, Richard Chen
Abstract: Exome sequencing is increasingly used for the clinical evaluation of genetic disease, yet accuracy and coverage in medically interpretable parts of the genome remains under-characterized. We evaluate recently developed exome sequencing platforms in t ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=917740

6. Optimization of Next-Generation Sequencing Informatics Pipelines for Clinical Laboratory Practice
Published: 7/8/2015
Authors: Justin M Zook, Amy Gargis, Lisa Kalman, Ira Lubin, Marc L Salit
Abstract: We direct your readers' attention to the principles and guidelines (see Supplementary Guidelines) developed by the Next-generation Sequencing: Standardization of Clinical Testing II (Nex-StoCT II) informatics workgroup, which was convened by the Cent ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=916037

7. Best Practices for Evaluating Single Nucleotide Variant Calling Methods for Microbial Genomics
Published: 7/7/2015
Authors: Nathanael D Olson, Steven P Lund, Rebecca Colman, Jeffery T. Foster, Jason W. Sahl, James M. Schupp, Paul Keim, Jayne B Morrow, Marc L Salit, Justin M Zook
Abstract: Innovations in sequencing technologies have allowed biologists to make incredible advances in understanding biological systems. As experience grows, researchers increasingly recognize that analyzing the wealth of data provided by these new sequen ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=918229

8. The Use of Cause-and-Effect Analysis to Design a High Quality Nano-Cyto-Toxicology Assay
Published: 12/4/2014
Authors: Matthias Rosslein, John T Elliott, Marc L Salit, Elijah J Petersen, Cordula Hirsch, Harald Krug, Peter Wick
Abstract: An important consideration in developing standards and regulations that govern the production and use of commercial nanoscale materials is the development of robust and reliable measurements to assess potential biological effects of these nanomat ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=916357

9. Genomic Reference Materials for Clinical Application
Published: 11/21/2014
Authors: Justin M Zook, Marc L Salit
Abstract: Reference Materials are well-characterized, homogeneous, and stable samples that can be used to understand measurement performance. The Genome in a Bottle Consortium is developing whole human genome DNA Reference Materials from large batches of DNA ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=913928

10. Assessing technical performance in differential gene expression experiments with external spike- in RNA control ratio mixtures
Published: 9/25/2014
Authors: Sarah A Munro, Steven P Lund, Patrick S Pine, Hans Binder, Djork-Arne Clevert, Ana Conesa, Joaquin Dopazo, Mario Fasold, Sepp Hochreiter, Huixao Hong, Nederah Jafari, David P Kreil, Pawel P Labaj, Yang Liao, Simon Lin, Christopher E Mason, Javier Santoyo, Steven J Schrodi, Leming Shi, Wei Shi, Gordon K Smyth, Nancy Stralis-Pavese, Zhenqiang Su, Charles Wang, Jian Wang, Joshua Xu, Zhan Ye, Yong Yang, Ying Yu, Paul Zumbo, Marc L Salit
Abstract: There is a critical need for standard approaches to assess, report and compare the technical performance of genome-scale differential gene expression experiments. Here we assess technical performance with a proposed standard ,dashboard‰ of metric ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=913876



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