scholarly journals Parent-progeny imputation from pooled samples for cost-efficient genotyping in plant breeding

2017 ◽  
Author(s):  
Frank Technow ◽  
Justin Gerke
Keyword(s):  
Plant Breeding ◽  
Large Scale ◽  
Genotyping By Sequencing ◽  
Cost Effective ◽  
Breeding Cycle ◽  
High Concordance ◽  
Estimated Breeding Values ◽  
Cost Efficient ◽  
Pooled Samples ◽  
Genotype Probabilities

AbstractThe increased usage of whole-genome selection (WGS) and other molecular evaluation methods in plant breeding relies on the ability to genotype a very large number of untested individuals in each breeding cycle. Many plant breeding programs evaluate large biparental populations of homozygous individuals derived from homozygous parent inbred lines. This structure lends itself to parent-progeny imputation, which transfers the genotype scores of the parents to progeny individuals that are genotyped for a much smaller number of loci. Here we introduce a parent-progeny imputation method that infers individual genotypes from index-free pooled samples of DNA of multiple individuals using a Hidden Markov Model (HMM). We demonstrated the method for pools of simulated maize double haploids (DH) from biparental populations, genotyped using a genotyping by sequencing (GBS) approach for 3,000 loci at 0.125xto 4xcoverage. We observed high concordance between true and imputed marker scores and the HMM produced well-calibrated genotype probabilities that correctly reflected the uncertainty of the imputed scores. Genomic estimated breeding values (GEBV) calculated from the imputed scores closely matched GEBV calculated from the true marker scores. The within-population correlation between these sets of GEBV approached 0.95 at 1xand 4xcoverage when pooling two or four individuals, respectively. Our approach can reduce the genotyping cost per individual by a factor up to the number of pooled individuals in GBS applications without the need for extra sequencing coverage, thereby enabling cost-effective large scale genotyping for applications such as WGS in plant breeding.

scholarly journals Rapid and Inexpensive Whole-Genome Genotyping-by-Sequencing for Crossover Localization and Fine-Scale Genetic Mapping

2015 ◽  
Vol 5 (3) ◽  
pp. 385-398 ◽  
Author(s):  
Beth A Rowan ◽  
Vipul Patel ◽  
Detlef Weigel ◽  
Korbinian Schneeberger
Keyword(s):  
Qtl Mapping ◽  
Large Scale ◽  
Probabilistic Method ◽  
Genotyping By Sequencing ◽  
Dna Helicase ◽  
Whole Genome ◽  
Library Preparation ◽  
Individual Genome ◽  
Trait Locus ◽  
Cost Efficient

Abstract The reshuffling of existing genetic variation during meiosis is important both during evolution and in breeding. The reassortment of genetic variants relies on the formation of crossovers (COs) between homologous chromosomes. The pattern of genome-wide CO distributions can be rapidly and precisely established by the short-read sequencing of individuals from F2 populations, which in turn are useful for quantitative trait locus (QTL) mapping. Although sequencing costs have decreased precipitously in recent years, the costs of library preparation for hundreds of individuals have remained high. To enable rapid and inexpensive CO detection and QTL mapping using low-coverage whole-genome sequencing of large mapping populations, we have developed a new method for library preparation along with Trained Individual GenomE Reconstruction, a probabilistic method for genotype and CO predictions for recombinant individuals. In an example case with hundreds of F2 individuals from two Arabidopsis thaliana accessions, we resolved most CO breakpoints to within 2 kb and reduced a major flowering time QTL to a 9-kb interval. In addition, an extended region of unusually low recombination revealed a 1.8-Mb inversion polymorphism on the long arm of chromosome 4. We observed no significant differences in the frequency and distribution of COs between F2 individuals with and without a functional copy of the DNA helicase gene RECQ4A. In summary, we present a new, cost-efficient method for large-scale, high-precision genotyping-by-sequencing.

scholarly journals Assessing hospital cost data quality in the quest for a cost-effective health care

2020 ◽  
Author(s):  
Margit Malmmose ◽  
Jogvan Pauli Lydersen
Keyword(s):  
Health Care ◽  
Decision Making ◽  
Hospital Cost ◽  
Large Scale ◽  
Indirect Costs ◽  
Cost Effective ◽  
Cost Data ◽  
Integrated Cost ◽  
Cost Efficient ◽  
Account System

Abstract Background: The objective is to examine hospital cost accounts in order to understand the foundation upon which large-scale health care decisions are based. More specifically, the aim is to add insights to accounting practices and their applicability towards a newly establish value-based agenda with a focus on patient-level cost data. Methods: We apply a cost accounting framework developed to position and understand hospital cost practices in relation to government requirements. Allocated cost account data from 2015 from all Danish hospitals were collected and analysed. Results: We find exceedingly aggregated department-level data that are not tied to patient information. We further observe variations in integrated cost centre definitions and allocation methods, as well as a melding of both overhead and indirect costs with direct costs at the department level. Additionally, we find large structural variances within hospitals. Conclusions: The findings raise concern about the cost accounts’ ability to provide valid information in health care decision-making due to a lack of transparency. Additionally, standardisation of costs stemming from hospitals with large organisational differences has significant implications on the fairness of resource allocation and decision-making at large. Thus, for hospitals to become more cost efficient, a substantially more detailed cost account system is essential.

scholarly journals Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao

2018 ◽  
Author(s):  
Jaime A. Osorio-Guarín ◽  
Corey R. Quackenbush ◽  
Omar E. Cornejo
Keyword(s):  
Large Scale ◽  
Demographic History ◽  
Genotyping By Sequencing ◽  
Cost Effective ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Reduced Representation ◽  
Reduced Representation Library

AbstractAs the source of chocolate, cacao has become one of the most important crops in the world. The identification of molecular markers to understand the demographic history, genetic diversity and population structure plays a pivotal role in cacao breeding programs. Here, we report the use of a modified genotyping-by-sequencing (GBS) approach for large-scale single nucleotide polymorphism (SNP) discovery and allele ancestry mapping. We identified 12,357 bi-allelic SNPs after filtering, of which, 7,009 variants were ancestry informative. The GBS approach proved to be rapid, cost-effective, and highly informative for ancestry assignment in this species.

A Review of Various Nanostructures to Enhance the Efficiency of Solar-Photon-Conversions

2015 ◽  
pp. 277-312
Author(s):  
S. A. Akhoon ◽  
S. Rubab ◽  
M. A. Shah
Keyword(s):  
Solar Cells ◽  
Energy Harvesting ◽  
Solar Energy ◽  
Alternative Energy ◽  
Large Scale ◽  
Cost Effective ◽  
Energy Utilization ◽  
Electron Collection ◽  
Solar Hydrogen Production ◽  
Cost Efficient

The problem of dwindling energy can be attributed to the rapidly increasing worldwide energy demand, leading to an urgent need for alternative energy-harvesting technologies to sustain the economic growth by maintaining our appetite for energy. Among them, solar-energy-harvesting is most promising, and the huge demand for clean, cost-effective, and cost-efficient energy can be met by solar energy. The large-scale solar energy utilization has not become practical because of the high cost and inadequate efficiencies of the current solar-energy-conversions. Nanotechnology offers tools to develop cost-effective and cost-efficient technologies for solar-energy conversions. Nanostructures, such as nanowires, nanopillars, nanodomes, nanorods, quatumdots, nanoparticles, etc., facilitate photon absorption, electron transport, and electron collection properties of the solar-energy-conversion devices. This review specifically summarizes the contribution of the nanotechnology to photovoltaics, dye-sensitive solar cells, quantum-dot-sensitized solar cells, and solar hydrogen production devices.

scholarly journals A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding

2016 ◽  
Vol 3 (1) ◽  
pp. 150565 ◽  
Author(s):  
Salla Vartia ◽  
José L. Villanueva-Cañas ◽  
John Finarelli ◽  
Edward D. Farrell ◽  
Patrick C. Collins ◽  
...  
Keyword(s):  
Large Scale ◽  
Genotyping By Sequencing ◽  
Cost Effective ◽  
Universal Primers ◽  
Microsatellite Data ◽  
Experimental Conditions ◽  
Genetic Studies ◽  
Scale Population ◽  
Novel Method ◽  
Generation Sequencing

This study examines the potential of next-generation sequencing based ‘genotyping-by-sequencing’ (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.

scholarly journals Fully Screen Printed Stretchable Electrochromic Displays

2021 ◽  
Author(s):  
Ulrika Linderhed ◽  
Ioannis Petsagkourakis ◽  
Peter Andersson Ersman ◽  
Valerio Beni ◽  
Klas Tybrandt
Keyword(s):  
Internet Of Things ◽  
Large Scale ◽  
Low Cost ◽  
Cost Effective ◽  
The Internet ◽  
Wearable Electronics ◽  
Efficient Manner ◽  
Cost Efficient ◽  
The Internet Of Things ◽  
Screen Printed

Abstract The advent of the Internet of Things and the growing interest in continuous monitoring by wearables have created a need for conformable and stretchable displays. Electrochromic displays (ECDs) are receiving attention as a cost-effective solution for many simple applications. However, stretchable ECDs have yet to be produced in a robust, large scale and cost-efficient manner. Here we develop a process for making fully screen printed stretchable ECDs. By evaluating commercially available inks with respect to electromechanical properties, including electrochromic PEDOT:PSS inks, our process can be directly applied in the manufacturing of stretchable organic electronic devices. The manufactured ECDs retained colour contrast with useful switching times at static strains up to 50 % and strain cycling up to 30 % strain. To further demonstrate the applicability of the technology, double-digit 7-segment ECDs were produced, which could conform to curved surfaces and be mounted onto stretchable fabrics while remaining fully functional. Based on their simplicity, robustness and processability, we believe that low cost printed stretchable ECDs can be easily scaled up and will find many applications within the rapidly growing markets of wearable electronics and the Internet of Things.

A Review of Various Nanostructures to Enhance the Efficiency of Solar-Photon-Conversions

2017 ◽  
pp. 197-225
Author(s):  
S. A. Akhoon ◽  
S. Rubab ◽  
M. A. Shah
Keyword(s):  
Solar Cells ◽  
Energy Harvesting ◽  
Solar Energy ◽  
Alternative Energy ◽  
Large Scale ◽  
Cost Effective ◽  
Energy Utilization ◽  
Electron Collection ◽  
Solar Hydrogen Production ◽  
Cost Efficient

The problem of dwindling energy can be attributed to the rapidly increasing worldwide energy demand, leading to an urgent need for alternative energy-harvesting technologies to sustain the economic growth by maintaining our appetite for energy. Among them, solar-energy-harvesting is most promising, and the huge demand for clean, cost-effective, and cost-efficient energy can be met by solar energy. The large-scale solar energy utilization has not become practical because of the high cost and inadequate efficiencies of the current solar-energy-conversions. Nanotechnology offers tools to develop cost-effective and cost-efficient technologies for solar-energy conversions. Nanostructures, such as nanowires, nanopillars, nanodomes, nanorods, quatumdots, nanoparticles, etc., facilitate photon absorption, electron transport, and electron collection properties of the solar-energy-conversion devices. This review specifically summarizes the contribution of the nanotechnology to photovoltaics, dye-sensitive solar cells, quantum-dot-sensitized solar cells, and solar hydrogen production devices.

scholarly journals Gamma models for estimating the odds ratio for a skewed biomarker measured in pools and subject to errors

Biostatistics ◽  
2019 ◽  
Author(s):  
Dane R Van Domelen ◽  
Emily M Mitchell ◽  
Neil J Perkins ◽  
Enrique F Schisterman ◽  
Amita K Manatunga ◽  
...  
Keyword(s):  
Odds Ratio ◽  
Adjusted Odds Ratio ◽  
Lower Cost ◽  
Cost Effective ◽  
Ratio Estimation ◽  
Statistical Efficiency ◽  
Function Model ◽  
Processing Error ◽  
Wide Range ◽  
Pooled Samples

SUMMARYMeasuring a biomarker in pooled samples from multiple cases or controls can lead to cost-effective estimation of a covariate-adjusted odds ratio, particularly for expensive assays. But pooled measurements may be affected by assay-related measurement error (ME) and/or pooling-related processing error (PE), which can induce bias if ignored. Building on recently developed methods for a normal biomarker subject to additive errors, we present two related estimators for a right-skewed biomarker subject to multiplicative errors: one based on logistic regression and the other based on a Gamma discriminant function model. Applied to a reproductive health dataset with a right-skewed cytokine measured in pools of size 1 and 2, both methods suggest no association with spontaneous abortion. The fitted models indicate little ME but fairly severe PE, the latter of which is much too large to ignore. Simulations mimicking these data with a non-unity odds ratio confirm validity of the estimators and illustrate how PE can detract from pooling-related gains in statistical efficiency. These methods address a key issue associated with the homogeneous pools study design and should facilitate valid odds ratio estimation at a lower cost in a wide range of scenarios.

Efficient Schedule of Energy-Constrained UAV Using Crowdsourced Buses in Last-Mile Parcel Delivery

2021 ◽  
Vol 5 (1) ◽  
pp. 1-23
Author(s):  
Yan Pan ◽  
Shining Li ◽  
Qianwu Chen ◽  
Nan Zhang ◽  
Tao Cheng ◽  
...  
Keyword(s):  
Traffic Congestion ◽  
Large Scale ◽  
Load Capacity ◽  
Scheduling Algorithm ◽  
Cost Effective ◽  
Promising Alternative ◽  
Logistics Industry ◽  
Last Mile ◽  
Delivery Scheduling ◽  
Schedule Approach

Stimulated by the dramatical service demand in the logistics industry, logistics trucks employed in last-mile parcel delivery bring critical public concerns, such as heavy cost burden, traffic congestion and air pollution. Unmanned Aerial Vehicles (UAVs) are a promising alternative tool in last-mile delivery, which is however limited by insufficient flight range and load capacity. This paper presents an innovative energy-limited logistics UAV schedule approach using crowdsourced buses. Specifically, when one UAV delivers a parcel, it first lands on a crowdsourced social bus to parcel destination, gets recharged by the wireless recharger deployed on the bus, and then flies from the bus to the parcel destination. This novel approach not only increases the delivery range and load capacity of battery-limited UAVs, but is also much more cost-effective and environment-friendly than traditional methods. New challenges therefore emerge as the buses with spatiotemporal mobility become the bottleneck during delivery. By landing on buses, an Energy-Neutral Flight Principle and a delivery scheduling algorithm are proposed for the UAVs. Using the Energy-Neutral Flight Principle, each UAV can plan a flying path without depleting energy given buses with uncertain velocities. Besides, the delivery scheduling algorithm optimizes the delivery time and number of delivered parcels given warehouse location, logistics UAVs, parcel locations and buses. Comprehensive evaluations using a large-scale bus dataset demonstrate the superiority of the innovative logistics UAV schedule approach.

Sign in / Sign up

Export Citation Format

Share Document