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Bioscience

Genomics

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Displaying 76 - 93 of 93

Standards for cell line authentication and beyond

June 14, 2016
Author(s)
Jamie L. Almeida, Kenneth D. Cole, Anne L. Plant
Different genomic technologies have been applied to cell line authentication, but only one method (short tandem repeat profiling) has been the subject of a comprehensive standard (ASN-0002). Here we discuss the power of this document, and why standards

Wide-field quantitative imaging of tissue microstructure using high-frequency structured light

June 9, 2016
Author(s)
David McClatchy III, Elizabeth Rizzo, wendy wells, Jeeseong C. Hwang, keith paulson, Brian Pogue, Stephen Kanick
Sub-diffusive structured light imaging has been shown to accurately and quantitatively map the reduced scattering coefficient and the phase function backscatter parameter in a wide-field geometry. This study shows the first the experimental imaging of

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

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

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

Evaluation of two mitochondrial DNA biomarkers for prostate cancer detection

August 17, 2015
Author(s)
Samantha D. Maragh, Steven P. Lund
BACKGROUND: A 3.4kb deletion (3.4kbΔ) in mitochondrial DNA (mtDNA) found in histologically normal prostate biopsy specimens has been reported to be a biomarker for the increased probability of prostate cancer. Increased mtDNA copy number is also reported

Quantifying and Improving Clinical-grade Coverage and Accuracy using Augmented Exome Sequencing

July 16, 2015
Author(s)
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 the

Genomic Reference Materials for Clinical Application

November 21, 2014
Author(s)
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

High-Speed Coherent Raman Fingerprint Imaging of Biological Tissues

July 20, 2014
Author(s)
Charles H. Camp, Young J. Lee, John M. Heddleston, Christopher M. Hartshorn, Angela R. Hight Walker, Jeremy N. Rich, Justin D. Lathia, Marcus T. Cicerone
We have developed a coherent Raman imaging platform using broadband coherent anti-Stokes Raman scattering (BCARS) that provides an unprecedented combination of speed, sensitivity, and spectral breadth. The system utilizes a unique configuration of laser

Guidelines for Minimum Information for Publication of Quantitative Digital PCR Experiments

April 9, 2013
Author(s)
Ross J. Haynes, Jim Huggett, Carole Foy, Vladimir Benes, Kerry Emslie, Jeremy Garson, Jan Hellemans, Mikael Kubista, Tania Nolan, Michael Pfaffl, Gregory Shipley, Jo Vandesompele, Carl Wittwer, Stephen Bustin
There is growing interest in the digital polymerase chain reaction (dPCR) as technological progress makes it a practical and increasingly affordable technology. dPCR allows the precise quantification of nucleic acid, facilitating the measurement of small

Recent Advances in Electrochemical Glyco-biosensing

April 8, 2011
Author(s)
Rebecca A. Zangmeister, Germarie Sanchez-Pomales
Biosensors based on electrochemical transduction mechanisms have recently made advances into the field of glycan analysis. These glyco-biosensor assays offer simple, rapid, sensitive and economical approaches to the measurement need for rapid glycan

Lambda exonuclease digestion of CGG trinucleotide repeats

June 7, 2009
Author(s)
Richard Conroy, Alan Koretsky, John M. Moreland
Fragile X syndrome and other trinucleotide diseases are characterized by an elongation of a repeating DNA triplet. The ensemble-averaged lambda exonuclease digestion rate of diVerent substrates, including one with an elongated FMR1 gene containing 120 CGG
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