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Displaying 1 - 6 of 6

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

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

Reference standards for accurate validation and optimization of assays that determine integrated Lentiviral vector copy number in transduced cells

July 11, 2021
Author(s)
Barbara S. Paugh, Lajos Baranyi, Andre Roy, Hua-Jun He, Lindsay Harris, Kenneth D. Cole, Caroline Raimund, Patricia S. Langan, Moria Artlip, Srikanta Jana, Rimas J. Orentas, Sheng Lin-Gibson, Winfried Krueger, Boro Dropuli?
Lentiviral vectors (LV) have emerged as a robust technology for therapeutic gene delivery into human cells as advanced medicinal products. As these products are increasingly commercialized, there are concomitant demands for their characterization to ensure

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

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