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Efficient and cost effective population resequencing by pooling and in-solution hybridization.

ABSTRACT: High-throughput sequencing of targeted genomic loci in large populations is an effective approach for evaluating the contribution of rare variants to disease risk. We evaluated the feasibility of using in-solution hybridization-based target capture on pooled DNA samples to enable cost-efficient population sequencing studies. For this, we performed pooled sequencing of 100 HapMap samples across ? 600 kb of DNA sequence using the Illumina GAIIx. Using our accurate variant calling method for pooled sequence data, we were able to not only identify single nucleotide variants with a low false discovery rate (<1%) but also accurately detect short insertion/deletion variants. In addition, with sufficient coverage per individual in each pool (30-fold) we detected 97.2% of the total variants and 93.6% of variants below 5% in frequency. Finally, allele frequencies for single nucleotide variants (SNVs) estimated from the pooled data and the HapMap genotype data were tightly correlated (correlation coefficient >? =? 0.995).

SUBMITTER: Bansal V

PROVIDER: S-EPMC3068187 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature

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Efficient and cost effective population resequencing by pooling and in-solution hybridization.

Bansal Vikas V Tewhey Ryan R Leproust Emily M EM Schork Nicholas J NJ

PloS one 20110330 3

High-throughput sequencing of targeted genomic loci in large populations is an effective approach for evaluating the contribution of rare variants to disease risk. We evaluated the feasibility of using in-solution hybridization-based target capture on pooled DNA samples to enable cost-efficient population sequencing studies. For this, we performed pooled sequencing of 100 HapMap samples across ∼ 600 kb of DNA sequence using the Illumina GAIIx. Using our accurate variant calling method for pooled ...[more]

PMID: 21479135

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Project description:BackgroundA key epidemiologic feature of schistosomiasis is its focal distribution, which has important implications for the spatial targeting of preventive chemotherapy programs. We evaluated the diagnostic accuracy of a urine pooling strategy using a point-of-care circulating cathodic antigen (POC-CCA) cassette test for detection of Schistosoma mansoni, and employed simulation modeling to test the classification accuracy and efficiency of this strategy in determining where preventive chemotherapy is needed in low-endemicity settings.MethodologyWe performed a cross-sectional study involving 114 children aged 6-15 years in six neighborhoods in Azaguié Ahoua, south Côte d'Ivoire to characterize the sensitivity and specificity of the POC-CCA cassette test with urine samples that were tested individually and in pools of 4, 8, and 12. We used a Bayesian latent class model to estimate test characteristics for individual POC-CCA and quadruplicate Kato-Katz thick smears on stool samples. We then developed a microsimulation model and used lot quality assurance sampling to test the performance, number of tests, and total cost per school for each pooled testing strategy to predict the binary need for school-based preventive chemotherapy using a 10% prevalence threshold for treatment.Principal findingsThe sensitivity of the urine pooling strategy for S. mansoni diagnosis using pool sizes of 4, 8, and 12 was 85.9%, 79.5%, and 65.4%, respectively, when POC-CCA trace results were considered positive, and 61.5%, 47.4%, and 30.8% when POC-CCA trace results were considered negative. The modeled specificity ranged from 94.0-97.7% for the urine pooling strategies (when POC-CCA trace results were considered negative). The urine pooling strategy, regardless of the pool size, gave comparable and often superior classification performance to stool microscopy for the same number of tests. The urine pooling strategy with a pool size of 4 reduced the number of tests and total cost compared to classical stool microscopy.Conclusions/significanceThis study introduces a method for rapid and efficient S. mansoni prevalence estimation through examining pooled urine samples with POC-CCA as an alternative to widely used stool microscopy.

Project description:The morphology-controlled synthesis of nanostructured photocatalysts by an environmentally friendly and low-cost method provides a feasible way to realize practical applications of photocatalysts. Herein, Bi2WO6 (BWO) nanophotocatalysts with mulberry shape, sheet-like, and round-cake morphologies have been successfully synthesized through a highly facile solvothermal process by simply adjusting the solvothermal temperature or utilizing selective addition of ethylene glycol as an orientation agent without using strong acids and bases and/or hazardous chemicals. The ratio of ethylene glycol and glacial acetic acid can affect the morphology and oxygen vacancy content of BWO, thereby influencing the photocatalytic performance. The photocatalytic activity of the as-prepared samples was evaluated by degradation of rhodamine B (RhB) and tetracycline under visible-light irradiation. The results indicated that all the BWO samples exhibited morphology-associated photocatalytic activity, and the sheet-like structure of BWO obtained via solvothermal treatment at 120 °C with ethylene glycol and glacial acetic acid ratio of 1:3 achieved the maximum specific surface area and possessed abundant oxygen vacancies, exhibiting outstanding photocatalytic activity for degradation of RhB and tetracycline. The degradation rate of RhB reached 100% within 20 min. To the best of our knowledge, this value is one of the most remarkable values for pristine BWO photocatalysts. Radical capture experiments demonstrated that hydroxyl radicals (·OH) play major roles compared with electrons (e−) and holes (h+) in the photocatalytic degradation process. A possible mechanism for the photocatalytic degradation of pollutants was proposed to better understand the reaction process. We believe that the more economical, efficient and greener methodology can provide guidance to develop highly efficient photocatalysts with favourable morphology and structure. Supplementary Information The online version contains supplementary material available at 10.1007/s10854-022-09654-z.

Dataset Information

Efficient and cost effective population resequencing by pooling and in-solution hybridization.

Publications

Efficient and cost effective population resequencing by pooling and in-solution hybridization.

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