You searched on: Author: Marc Salit
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1. SVClassify: a method to use multiple datasets to classify candidate structural variants into true positives and false positives
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 Consorti ...
2. Benchmarks for genome sequencing
Justin M Zook, Marc L Salit
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 ...
3. Using mixtures of biological samples as genome-scale process controls
Jerod R Parsons, Patrick S Pine, Marc L Salit, Sarah A Munro, Jennifer H McDaniel
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 ...
4. svviz: a read viewer for validating structural variants
Noah Spies, Justin M Zook, Marc L Salit, Arend Sidow
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 ...
5. Quantifying and Improving Clinical-grade Coverage and Accuracy using Augmented Exome Sequencing
Justin M Zook, Anil Patwardhan, Marc L Salit, Carlos Bustamante, Euan Ashley, Michael Snyder, John West, Richard Chen
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 ...
6. Optimization of Next-Generation Sequencing Informatics Pipelines for Clinical Laboratory Practice
Justin M Zook, Amy Gargis, Lisa Kalman, Ira Lubin, Marc L Salit
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 ...
7. Best Practices for Evaluating Single Nucleotide Variant Calling Methods for Microbial Genomics
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
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 ...
8. The Use of Cause-and-Effect Analysis to Design a High Quality Nano-Cyto-Toxicology Assay
Matthias Rosslein, John T Elliott, Marc L Salit, Elijah J Petersen, Cordula Hirsch, Harald Krug, Peter Wick
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 ...
9. Genomic Reference Materials for Clinical Application
Justin M Zook, Marc L Salit
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 ...
10. Assessing technical performance in differential gene expression experiments with external spike-
in RNA control ratio mixtures
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
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 ...