Results 11 to 20 of about 122,799 (164)

Exodus: sequencing-based pipeline for quantification of pooled variants

Bioinformatics, 2022
AbstractSummaryNext-Generation Sequencing is widely used as a tool for identifying and quantifying microorganisms pooled together in either natural or designed samples. However, a prominent obstacle is achieving correct quantification when the pooled microbes are genetically related.
Ilya Vainberg-Slutskin, Noga Kowalsman, Yael Silberberg, Tal Cohen, Jenia Gold, Edith Kario, Iddo Weiner, Inbar Gahali-Sass, Sharon Kredo-Russo, Naomi B Zak, Merav Bassan   +10 more
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Evaluation of pooled association tests for rare variant identification [PDF]

BMC Proceedings, 2011
Abstract Genome-wide association studies have successfully identified many common variants associated with complex human diseases. However, a large portion of the remaining heritability cannot be explained by these common variants. Exploring rare variants associated with diseases is now catching more attention.
Lin, Wan-Yu, Zhang, Boshao, Yi, Nengjun, Gao, Guimin, Liu, Nianjun   +4 more
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Quantification of rare allelic variants from pooled genomic DNA [PDF]

Nature Methods, 2009
We report a targeted, cost-effective method to quantify rare single-nucleotide polymorphisms from pooled human genomic DNA using second-generation sequencing. We pooled DNA from 1,111 individuals and targeted four genes to identify rare germline variants.
Druley, Todd E, Vallania, Francesco LM, Wegner, Daniel J, Varley, Katherine E, Knowles, Olivia L, Bonds, Jacqueline A, Robison, Sarah W, Doniger, Scott W, Hamvas, Aaron, Cole, F. Sessions, Fay, Justin C, Mitra, Robi D   +11 more
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Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis [PDF]

Genome Biology, 2011
AbstractSequencing targeted DNA regions in large samples is necessary to discover the full spectrum of rare variants. We report an effective Illumina sequencing strategy utilizing pooled samples with novel quality (Srfim) and filtering (SERVIC 4 E) algorithms.
Niranjan, Tejasvi S, Adamczyk, Abby, Bravo, Héctor Corrada, Taub, Margaret A, Wheelan, Sarah J, Irizarry, Rafael, Wang, Tao   +6 more
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Next Generation Sequencing of Pooled Samples: Guideline for Variants’ Filtering [PDF]

Scientific Reports, 2016
AbstractSequencing large number of individuals, which is often needed for population genetics studies, is still economically challenging despite falling costs of Next Generation Sequencing (NGS). Pool-seq is an alternative cost- and time-effective option in which DNA from several individuals is pooled for sequencing. However, pooling of DNA creates new
Anand Santosh, Anand Santosh, Anand Santosh, Mangano Eleonora, Barizzone Nadia, Barizzone Nadia, Bordoni Roberta, Sorosina Melissa, Clarelli Ferdinando, Corrado Lucia, Corrado Lucia, Boneschi Filippo Martinelli, Boneschi Filippo Martinelli, D'Alfonso Sandra, D'Alfonso Sandra, De Bellis Gianluca   +15 more
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High-throughput, image-based screening of pooled genetic-variant libraries [PDF]

Nature Methods, 2017
We report a high-throughput screening method that allows diverse genotypes and corresponding phenotypes to be imaged in individual cells. We achieve genotyping by introducing barcoded genetic variants into cells as pooled libraries and reading the barcodes out using massively multiplexed fluorescence in situ hybridization.
George Emanuel, Jeffrey R Moffitt, Xiaowei Zhuang   +2 more
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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER [PDF]

Journal of Visualized Experiments, 2012
As DNA sequencing technology has markedly advanced in recent years(2), it has become increasingly evident that the amount of genetic variation between any two individuals is greater than previously thought(3). In contrast, array-based genotyping has failed to identify a significant contribution of common sequence variants to the phenotypic variability ...
Vallania, Francesco, Ramos, Enrique, Cresci, Sharon, Mitra, Robi D., Druley, Todd E.   +4 more
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Evaluation of variant detection software for pooled next-generation sequence data [PDF]

BMC Bioinformatics, 2015
Despite the tremendous drop in the cost of nucleotide sequencing in recent years, many research projects still utilize sequencing of pools containing multiple samples for the detection of sequence variants as a cost saving measure. Various software tools exist to analyze these pooled sequence data, yet little has been reported on the relative accuracy ...
Huang, Howard W., Mullikin, James C., Hansen, Nancy F.   +2 more
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Comparison of similarity-based tests and pooling strategies for rare variants [PDF]

BMC Genomics, 2013
As several rare genomic variants have been shown to affect common phenotypes, rare variants association analysis has received considerable attention. Several efficient association tests using genotype and phenotype similarity measures have been proposed in the literature.
Zakharov, S, Salim, A, Thalamuthu, A
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Resequencing of pooled DNA for detecting disease associations with rare variants [PDF]

Genetic Epidemiology, 2010
AbstractA combination of common and rare variants is thought to contribute to genetic susceptibility to complex diseases. Recently, next‐generation sequencers have greatly lowered sequencing costs, providing an opportunity to identify rare disease variants in large genetic epidemiology studies.
Tao, Wang, Chang-Yun, Lin, Thomas E, Rohan, Kenny, Ye   +3 more
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