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Find video protocols related to scientific articles indexed in Pubmed.
The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data.
Nucleic Acids Res.
PUBLISHED: 10-28-2014
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Rapid development of next generation sequencing technology has enabled the identification of genomic alterations from short sequencing reads. There are a number of software pipelines available for calling single nucleotide variants from genomic DNA but, no comprehensive pipelines to identify, annotate and prioritize expressed SNVs (eSNVs) from non-directional paired-end RNA-Seq data. We have developed the eSNV-Detect, a novel computational system, which utilizes data from multiple aligners to call, even at low read depths, and rank variants from RNA-Seq. Multi-platform comparisons with the eSNV-Detect variant candidates were performed. The method was first applied to RNA-Seq from a lymphoblastoid cell-line, achieving 99.7% precision and 91.0% sensitivity in the expressed SNPs for the matching HumanOmni2.5 BeadChip data. Comparison of RNA-Seq eSNV candidates from 25 ER+ breast tumors from The Cancer Genome Atlas (TCGA) project with whole exome coding data showed 90.6-96.8% precision and 91.6-95.7% sensitivity. Contrasting single-cell mRNA-Seq variants with matching traditional multicellular RNA-Seq data for the MD-MB231 breast cancer cell-line delineated variant heterogeneity among the single-cells. Further, Sanger sequencing validation was performed for an ER+ breast tumor with paired normal adjacent tissue validating 29 out of 31 candidate eSNVs. The source code and user manuals of the eSNV-Detect pipeline for Sun Grid Engine and virtual machine are available at http://bioinformaticstools.mayo.edu/research/esnv-detect/.
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Integrated Fluidic Circuits (IFCs) for digital PCR.
Methods Mol. Biol.
PUBLISHED: 01-19-2013
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The Fluidigm Digital Array IFC is a nanofluidic biochip where digital PCR reactions can be performed with isolated individual DNA template molecules. This chip is part of a family of integrated fluidic circuits (IFC) and contains a network of fluid lines, NanoFlex™ valves and chambers. NanoFlex™ valves are made of an elastomeric material that deflects under pressure to create a tight seal and are used to regulate the flow of liquids in the IFC. Digital Arrays have enabled a different approach to digital PCR, by partitioning DNA molecules instead of diluting them. Single DNA molecules are randomly distributed into nanoliter volume reaction chambers and then PCR amplified in the presence of a fluorophore-containing probe. Positive fluorescent signal indicates the presence of a DNA molecule in a reaction chamber, while negative chambers are blank. IFC technology enables the delivery of very precise volumes of solutions in a simple, fast procedure, utilizing a minimum of sample and assay reagents. The development of the IFC technology and the Digital Array chip has revolutionized the field of biology, and has been utilized in gene copy number studies, absolute quantitation (molecule counting) of genomic DNA and cDNA, rare mutation detection, and digital haplotyping.
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Association between maximal skin dose and breast brachytherapy outcome: a proposal for more rigorous dosimetric constraints.
Int. J. Radiat. Oncol. Biol. Phys.
PUBLISHED: 02-09-2011
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Multiple investigations have used the skin distance as a surrogate for the skin dose and have shown that distances <6 mm have been associated with late toxicity after MammoSite brachytherapy. No publications have yet described the relationship between the actual maximal skin dose and the outcome. The present study analyzed the maximal skin dose delivered and the occurrence of late toxicity in a large cohort of patients with prolonged follow-up.
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Extending and evaluating a warfarin dosing algorithm that includes CYP4F2 and pooled rare variants of CYP2C9.
Pharmacogenet. Genomics
PUBLISHED: 05-06-2010
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Warfarin dosing remains challenging because of its narrow therapeutic window and large variability in dose response. We sought to analyze new factors involved in its dosing and to evaluate eight dosing algorithms, including two developed by the International Warfarin Pharmacogenetics Consortium (IWPC).
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Experimental generation of SNP haplotype signatures in patients with sickle cell anaemia.
PLoS ONE
PUBLISHED: 05-04-2010
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Sickle cell anemia is caused by a single type of mutation, a homozygous A?T substitution in the ß globin gene. Clinical severity is diverse, partially due to additional, disease-modifying genetic factors. We are studying one such modifier locus, HMIP (HBS1L-MYB intergenic polymorphism, chromosome 6q23.3). Working with a genetically admixed patient population, we have encountered the necessity to generate haplotype signatures of genetic markers to label genomic fragments with distinct genealogical origin at this locus. With the goal to generate haplotype signatures from patients experimentally, we have investigated the suitability of an existing nanofluidic assay platform to perform phase alignment with single-nucleotide polymorphism alleles.
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Results of a rural school-based peer-led intervention for youth: goals for health.
J Sch Health
PUBLISHED: 03-19-2010
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School-based interventions are critical for enhancing the health of youth. The Goals for Health (GFH) school-based project was a goal-setting and life-skills intervention conducted in rural areas to increase self-efficacy, knowledge, and positive behaviors related to healthy eating. The intervention was peer-led with high school students teaching health and life skills to sixth-grade students. The purpose of this study was to examine the impact of the GFH school-based program on healthy eating outcomes related to self-efficacy, attitudes, knowledge, and behavior, and to examine the impact of quality of program implementation on the above outcomes.
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Quantifying EGFR alterations in the lung cancer genome with nanofluidic digital PCR arrays.
Clin. Chem.
PUBLISHED: 03-05-2010
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The EGFR [epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)] gene is known to harbor genomic alterations in advanced lung cancer involving gene amplification and kinase mutations that predict the clinical response to EGFR-targeted inhibitors. Methods for detecting such molecular changes in lung cancer tumors are desirable.
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Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution.
Methods
PUBLISHED: 01-11-2010
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This paper assesses the quantitative resolution of qPCR using copy number variation (CNV) as a paradigm. An error model is developed for real-time qPCR data showing how the precision of CNV determination varies with the number of replicates. Using samples with varying numbers of X chromosomes, experimental data demonstrates that real-time qPCR can readily distinguish four copes from five copies, which corresponds to a 1.25-fold difference in relative quantity. Digital PCR is considered as an alternative form of qPCR. For digital PCR, an error model is shown that relates the precision of CNV determination to the number of reaction chambers. The quantitative capability of digital PCR is illustrated with an experiment distinguishing four and five copies of the human gene MRGPRX1. For either real-time qPCR or digital PCR, practical application of these models to achieve enhanced quantitative resolution requires use of a high throughput PCR platform that can simultaneously perform thousands of reactions. Comparing the two methods, real-time qPCR has the advantage of throughput and digital PCR has the advantage of simplicity in terms of the assumptions made for data analysis.
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SNP genotyping by the 5-nuclease reaction: advances in high-throughput genotyping with nonmodel organisms.
Methods Mol. Biol.
PUBLISHED: 09-22-2009
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Population genetics studies play an increasingly important role in the management and conservation of nonmodel organisms. Unlike studies with model organisms, a typical population genetics study of a nonmodel organism may be conducted by analyzing thousands or hundreds of thousands of individuals for several dozen single nucleotide polymorphisms (SNPs). The use of robust, robotically mediated TaqMan reactions provides substantial advantages in these types of studies. We describe the methods and laboratory setup for analyzing a sustained high throughput of SNP assays in routine university or natural resource agency laboratories with a handful of thermal cyclers. Agencies sustain rates of nearly 150,000 assays per week using uniplex reactions with the Applied Biosystems 7900HT Fast Real-Time PCR System (AB 7900HT). We further describe the medium-density array run on the BioMark from Fluidigm, which increases this rate to over 500,000 assays per week by multiplexing 96 samples for 96 SNPs.
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High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays.
BMC Genomics
PUBLISHED: 07-08-2009
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Single nucleotide polymorphisms (SNPs) have emerged as the genetic marker of choice for mapping disease loci and candidate gene association studies, because of their high density and relatively even distribution in the human genomes. There is a need for systems allowing medium multiplexing (ten to hundreds of SNPs) with high throughput, which can efficiently and cost-effectively generate genotypes for a very large sample set (thousands of individuals). Methods that are flexible, fast, accurate and cost-effective are urgently needed. This is also important for those who work on high throughput genotyping in non-model systems where off-the-shelf assays are not available and a flexible platform is needed.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.