Results 31 to 40 of about 122,799 (164)

VarScan: variant detection in massively parallel sequencing of individual and pooled samples [PDF]

Bioinformatics, 2009
Abstract Summary: Massively parallel sequencing technologies hold incredible promise for the study of DNA sequence variation, particularly the identification of variants affecting human disease. The unprecedented throughput and relatively short read lengths of Roche/454, Illumina/Solexa, and other platforms have spurred development of a ...
Daniel C, Koboldt, Ken, Chen, Todd, Wylie, David E, Larson, Michael D, McLellan, Elaine R, Mardis, George M, Weinstock, Richard K, Wilson, Li, Ding   +8 more
openaire   +2 more sources

Localization of association signal from risk and protective variants in sequencing studies

Frontiers in Genetics, 2012
Aggregating information across multiple variants in a gene or region can improve power for rare variant association testing. Power is maximized when the aggregation region contains many causal variants and few neutral variants.
Abra eBrisbin, Gregory D. Jenkins, Katarzyna eEllsworth, Liewei eWang, Brooke L. Fridley   +4 more
doaj   +1 more source

Pooled Analysis of Phosphatidylinositol 3-Kinase Pathway Variants and Risk of Prostate Cancer [PDF]

Cancer Research, 2010
Abstract The phosphatidylinositol 3-kinase (PI3K) pathway regulates various cellular processes, including cellular proliferation and intracellular trafficking, and may affect prostate carcinogenesis. Thus, we explored the association between single-nucleotide polymorphisms (SNP) in PI3K genes and prostate cancer.
Koutros, Stella, Schumacher, Fredrick R., Hayes, Richard B., Ma, Jing, Huang, Wen-Yi, Albanes, Demetrius, Canzian, Federico, Chanock, Stephen J., Crawford, E. David, Diver, W. Ryan, Feigelson, Heather Spencer, Giovanucci, Edward, Haiman, Christopher A., Henderson, Brian E., Hunter, David J., Kaaks, Rudolf, Kolonel, Laurence N., Kraft, Peter, Marchand, Loïc Le, Riboli, Elio, Siddiq, Afshan, Stampfer, Meir, Stram, Daniel O., Thomas, Gilles, Travis, Ruth C., Thun, Michael J., Yeager, Meredith, Berndt, Sonja I.   +27 more
openaire   +4 more sources

A pooled RT-PCR testing strategy for more efficient COVID-19 pandemic management

International Journal of Infectious Diseases, 2022
: Objectives: Reverse transcription polymerase chain reaction (RT-PCR) testing is indispensable in management of the coronavirus disease 2019 (COVID-19) pandemic.
Akif Ayaz, Asli Guner Ozturk Demir, Gurkan Ozturk, Mehmet Kocak   +3 more
doaj   +1 more source

dNTP pool levels modulate mutator phenotypes of error-prone DNA polymerase ε variants [PDF]

Proceedings of the National Academy of Sciences, 2015
Significance An increased rate of mutation, or “mutator phenotype,” generates genetic diversity that can accelerate cancer progression or confer resistance to chemotherapy drugs. New therapeutic strategies are needed that target mutator phenotypes directly.
Lindsey N. Williams, Lisette Marjavaara, Gary M. Knowels, Eric M. Schultz, Edward J. Fox, Andrei Chabes, Alan J. Herr   +6 more
openaire   +2 more sources

Convolutional Neural Networks: A Roundup and Benchmark of Their Pooling Layer Variants

Algorithms, 2022
One of the essential layers in most Convolutional Neural Networks (CNNs) is the pooling layer, which is placed right after the convolution layer, effectively downsampling the input and reducing the computational power required. Different pooling methods have been proposed over the years, each with its own advantages and disadvantages, rendering them a ...
Nikolaos-Ioannis Galanis, Panagiotis Vafiadis, Kostas-Gkouram Mirzaev, George A. Papakostas   +3 more
openaire   +2 more sources

Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans. [PDF]

PLoS Genetics, 2013
Whole-exome or gene targeted resequencing in hundreds to thousands of individuals has shown that the majority of genetic variants are at low frequency in human populations.
Ferran Casals, Alan Hodgkinson, Julie Hussin, Youssef Idaghdour, Vanessa Bruat, Thibault de Maillard, Jean-Christophe Grenier, Elias Gbeha, Fadi F Hamdan, Simon Girard, Jean-François Spinella, Mathieu Larivière, Virginie Saillour, Jasmine Healy, Isabel Fernández, Daniel Sinnett, Jacques L Michaud, Guy A Rouleau, Elie Haddad, Françoise Le Deist, Philip Awadalla   +20 more
doaj   +1 more source

Pan-Cancer Study on Variants of Canonical miRNA Biogenesis Pathway Components: A Pooled Analysis

Cancers, 2023
Single nucleotide polymorphisms in genes involved in microRNA processing/maturation and release may deregulate the microRNAome expression levels. We aimed to assess the relationship between miRNA machinery genetic variants and human cancer risk using integrative bioinformatics analyses to identify the role of these genes in cancer aggressiveness ...
Rami M. Elshazli, Eman A. Toraih, Mohammad H. Hussein, Emmanuelle M. Ruiz, Emad Kandil, Manal S. Fawzy   +5 more
openaire   +2 more sources

Estimating Allele Frequency from Next-Generation Sequencing of Pooled Mitochondrial DNA Samples

Frontiers in Genetics, 2011
Background: Both common and rare mitochondrial DNA (mtDNA) variants may contribute to genetic susceptibility to some complex human diseases. Next-generation sequencing of pooled mtDNA samples may represent an cost-effective approach for large-scale ...
Tao eWang, Kith ePradhan, Kenny eYe, Lee-jun eWong, Thomas E Rohan   +4 more
doaj   +1 more source

Quantitative tRNA-sequencing uncovers metazoan tissue-specific tRNA regulation

Nature Communications, 2020
The relative abundance of specific tRNA can impact protein production rate, folding, and messenger RNA stability. Here the authors describe QuantM-tRNA seq — a method to monitor tRNA abundance and sequence variants — and uncover distinctions in ...
Otis Pinkard, Sean McFarland, Thomas Sweet, Jeff Coller   +3 more
doaj   +1 more source