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1.
BMC Genomics ; 25(1): 49, 2024 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-38200430

RESUMO

BACKGROUND: Cultured porcine cell lines are powerful tools for functional genomics and in vitro phenotypic testing of candidate causal variants. However, to be utilised for genomic or variant interrogation assays, the genome sequence and structure of cultured cell lines must be realised. In this work, we called variants and used read coverage in combination with within-sample allele frequency to detect potential aneuploidy in two immortalised porcine kidney epithelial (PK15) cell lines and in a pig embryonic fibroblast line. RESULTS: We compared two PK15 cultured cells samples: a new American Type Culture Collection (ATCC) sample and one that has been utilised and passaged within the laboratory for an extended period (> 10 years). Read coverage and within-sample allele frequencies showed that several chromosomes are fully or partially aneuploid in both PK15 lines, including potential trisomy of chromosome 4 and tetrasomy of chromosome 17. The older PK15 line showed evidence of additional structural variation and potentially clonal variation. By comparison, the pig embryonic fibroblast line was free from the gross aneuploidies seen in the PK15s. CONCLUSIONS: Our results show that the PK15 cell lines examined have aneuploidies and complex structural variants in their genomes. We propose that screening for aneuploidy should be considered for cell lines, and discuss implications for livestock genomics.


Assuntos
Genômica , Gado , Animais , Suínos/genética , Linhagem Celular , Aneuploidia , Cromossomos
2.
Clin Oncol (R Coll Radiol) ; 36(1): e1-e10, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-37923688

RESUMO

AIMS: New treatment options for advanced ovarian cancer have the potential to significantly change the treatment pathway in the UK. Understanding the structures and responsibilities of multidisciplinary teams/tumour boards (MDT) and regional variations will enable services to adapt more effectively to these changes. MATERIALS AND METHODS: The KNOW-OC survey was conducted in 2020 to understand the views of a selected group of 66 healthcare professionals (HCPs) involved in advanced ovarian cancer care in UK hospitals. RESULTS: The results showed that MDT involvement in the management of advanced ovarian cancer varied depending on pathway stage and line of relapse, with 98.5% of HCPs responding that the MDT was involved in decisions at initial presentation, but only 40.9% for patients with multiple relapses. The MDT was mostly responsible for determining whether the patients would undergo primary or interval cytoreductive surgery according to 75.8% of respondents, and most HCPs (80.3%) stated that tumour dissemination patterns were the most important factor influencing this decision. The most commonly assessed biomarkers at the time of the survey were CA125, gBRCA and tBRCA. Homologous recombination deficiency was viewed as the second most important factor for determining prognosis, but few centres had access to testing at the time of survey completion. The use of active surveillance was expected to decrease in favour of first-line targeted therapies. Nearly all (98.5%) HCPs agreed there is a role for secondary cytoreductive surgery for the treatment of recurrence (for carefully selected patients). CONCLUSIONS: The results highlighted UK-specific geographical variation in the views of HCPs on MDT involvement and specific practices, such as molecular biomarker testing, and the overall treatment approach. Together, these findings improve the understanding of reported clinical practice across the UK for ovarian cancer and provide insight into decision-making associated with updates to recommendations for best practice (e.g. European Society for Medical Oncology/European Society of Gynaecological Oncology consensus statements) and the introduction of new treatment options.


Assuntos
Neoplasias Ovarianas , Humanos , Feminino , Inquéritos e Questionários , Neoplasias Ovarianas/tratamento farmacológico , Carcinoma Epitelial do Ovário/terapia , Atenção à Saúde , Reino Unido
3.
Int J Parasitol Parasites Wildl ; 17: 174-184, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-35145846

RESUMO

The Virunga Massif mountain gorilla population has been periodically monitored since the early 1970s, with gradually increasing effort. The population declined drastically in the 1970s, but the numbers stabilized in the 1980s. Since then, the population has been steadily increasing within their limited habitat fragment that is surrounded by a dense human population. We examined fecal samples collected during the Virunga 2015-2016 surveys in monitored and unmonitored gorilla groups and quantified strongylid and tapeworm infections using egg counts per gram to determine environmental and host factors that shape these helminth infections. We showed that higher strongylid infections were present in gorilla groups with smaller size of the 500-m buffered minimum-convex polygon (MCP) of detected nest sites per gorilla group, but in higher gorilla densities and inhabiting vegetation types occurring at higher elevations with higher precipitation and lower temperatures. On the contrary, the impact of monitoring (habituation) was minor, detected in tapeworms and only when in the interaction with environmental variables and MCP area. Our results suggest that the Virunga mountain gorilla population may be partially regulated by strongylid nematodes at higher gorilla densities. New health challenges are probably emerging among mountain gorillas because of the success of conservation efforts, as manifested by significant increases in gorilla numbers in recent decades, but few possibilities for the population expansion due to limited amounts of habitat.

4.
J Dairy Sci ; 102(11): 9971-9982, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31477287

RESUMO

In this study, we compared genetic gain, genetic variation, and the efficiency of converting variation into gain under different genomic selection scenarios with truncation or optimum contribution selection in a small dairy population by simulation. Breeding programs have to maximize genetic gain but also ensure sustainability by maintaining genetic variation. Numerous studies have shown that genomic selection increases genetic gain. Although genomic selection is a well-established method, small populations still struggle with choosing the most sustainable strategy to adopt this type of selection. We developed a simulator of a dairy population and simulated a model after the Slovenian Brown Swiss population with ∼10,500 cows. We compared different truncation selection scenarios by varying (1) the method of sire selection and their use on cows or bull-dams, and (2) selection intensity and the number of years a sire is in use. Furthermore, we compared different optimum contribution selection scenarios with optimization of sire selection and their usage. We compared scenarios in terms of genetic gain, selection accuracy, generation interval, genetic and genic variance, rate of coancestry, effective population size, and conversion efficiency. The results showed that early use of genomically tested sires increased genetic gain compared with progeny testing, as expected from changes in selection accuracy and generation interval. A faster turnover of sires from year to year and higher intensity increased the genetic gain even further but increased the loss of genetic variation per year. Although maximizing intensity gave the lowest conversion efficiency, faster turnover of sires gave an intermediate conversion efficiency. The largest conversion efficiency was achieved with the simultaneous use of genomically and progeny-tested sires that were used over several years. Compared with truncation selection, optimizing sire selection and their usage increased the conversion efficiency by achieving either comparable genetic gain for a smaller loss of genetic variation or higher genetic gain for a comparable loss of genetic variation. Our results will help breeding organizations implement sustainable genomic selection.


Assuntos
Bovinos/genética , Seleção Artificial , Animais , Cruzamentos Genéticos , Indústria de Laticínios/métodos , Feminino , Testes Genéticos/veterinária , Genômica , Masculino , Modelos Genéticos , Seleção Genética
5.
Child Youth Serv Rev ; 96: 194-203, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31346300

RESUMO

Despite a need to improve community mental health services for youths, little is known about compliance with state policies created to improve the quality of services in these settings. This study examined rates, patterns, and predictors of compliance with utilization management guidelines developed by the state of Texas to support a public health policy based on empirical evidence of effective mental health services (i.e., an evidence-based policy). Compliance was defined as authorizing policy-recommended service packages, whereas policy "overrides" occurred when recommended service packages were not authorized. The study sample consisted of 688 youths from ethnically and economically diverse backgrounds. Clinics reported that forty-six percent of youths were not authorized the policy-recommended service package. Overrides were primarily based on level of intensity. Most often, authorized services were less intensive than those recommended by the state guidelines. Higher severity at intake across multiple indicators was associated with authorizing less intensive services than what the policy guidelines recommended. Future studies evaluating system-level efforts such as state mental health policies should pay close attention to levels of service intensity, and their relation to the needs of youth in community settings.

6.
Anim Genet ; 49(4): 303-311, 2018 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-29974966

RESUMO

The dog is a valuable model species for the genetic analysis of complex traits, and the use of genotype imputation in dogs will be an important tool for future studies. It is of particular interest to analyse the effect of factors like single nucleotide polymorphism (SNP) density of genotyping arrays and relatedness between dogs on imputation accuracy due to the acknowledged genetic and pedigree structure of dog breeds. In this study, we simulated different genotyping strategies based on data from 1179 Labrador Retriever dogs. The study involved 5826 SNPs on chromosome 1 representing the high density (HighD) array; the low-density (LowD) array was simulated by masking different proportions of SNPs on the HighD array. The correlations between true and imputed genotypes for a realistic masking level of 87.5% ranged from 0.92 to 0.97, depending on the scenario used. A correlation of 0.92 was found for a likely scenario (10% of dogs genotyped using HighD, 87.5% of HighD SNPs masked in the LowD array), which indicates that genotype imputation in Labrador Retrievers can be a valuable tool to reduce experimental costs while increasing sample size. Furthermore, we show that genotype imputation can be performed successfully even without pedigree information and with low relatedness between dogs in the reference and validation sets. Based on these results, the impact of genotype imputation was evaluated in a genome-wide association analysis and genomic prediction in Labrador Retrievers.


Assuntos
Genótipo , Polimorfismo de Nucleotídeo Único , Animais , Cruzamento , Cães , Feminino , Estudos de Associação Genética/veterinária , Genômica , Masculino , Análise de Sequência com Séries de Oligonucleotídeos/veterinária , Linhagem
7.
Diabet Med ; 2018 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-29766565

RESUMO

AIM: To evaluate the impact of severe hypoglycaemia on NHS resources and overall glycaemic control in adults with Type 1 diabetes. METHODS: An observational, retrospective study of adults (aged ≥ 18 years) with Type 1 diabetes reporting one or more episodes of severe hypoglycaemia during the preceding 24 months in 10 NHS hospital diabetes centres in England and Wales. The primary outcome was healthcare resource utilization associated with severe hypoglycaemia. Secondary outcomes included demographic and clinical characteristics, diabetes control and pathway of care. RESULTS: Some 140 episodes of severe hypoglycaemia were reported by 85 people during the 2-year observation period. Ambulances were called in 99 of 140 (71%) episodes and Accident and Emergency attendance occurred in 26 of 140 (19%) episodes, whereas 29 of 140 (21%) episode required no immediate help from healthcare providers. Participants attended a median of 5 (range 0-58) diabetes clinic consultations during the observation period; 13% (70 of 552) of all consultations were severe hypoglycaemia-related. Of the HbA1c measurements recorded closest prior to severe hypoglycaemia (n = 119), only 7 of 119 measurements were < 48 mmol/mol (< 6.5%) and mean HbA1c was 70 (sd 19) mmol/mol (8.5%, sd 1.7%). Some 119 changes to diabetes treatment were recorded during the observation period (median/person 0;, range 0-11), of which 52 of 119 changes (44%) followed severe hypoglycaemic events. CONCLUSIONS: We observed a high level of ambulance service intervention but surprisingly low levels of hypoglycaemia follow-up, therapy change and specialist intervention in people self-reporting severe hypoglycaemia. These results suggest there may be important gaps in care pathways for people with Type 1 diabetes self-reporting severe hypoglycaemia.

8.
Orbit ; 36(3): 159-169, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-28296512

RESUMO

This article aims to provide baseline data and highlight any major deficiencies in the current level of care provided for adult patients with thyroid eye disease (TED). We undertook a prospective, nonrandomized cross-sectional multicenter observational study. During a 3-month period June-August 2014, consecutive adult patients with TED who presented to nominated specialist eye clinics in the United Kingdom, completed a standardized questionnaire. Main outcome measures were: demographics, time from diagnosis to referral to tertiary centre, time from referral to review in specialist eye clinic, management of thyroid dysfunction, radioiodine and provision of steroid prophylaxis, smoking, and TED classification. 91 patients (mean age 47.88 years) were included. Female-to-male ratio was 6:1. Mean time since first symptoms of TED = 27.92 (73.71) months; from first visit to any doctor with symptoms to diagnosis = 9.37 (26.03) months; from hyperthyroidism diagnosis to euthyroidism 12.45 (16.81) months. First, 13% had received radioiodine. All those with active TED received prophylactic steroids. Seven patients who received radioiodine and did not have TED at the time went on to develop it. Then, 60% patients were current or ex-smokers. 63% current smokers had been offered smoking cessation advice. 65% patients had active TED; 4% had sight-threatening TED. A large proportion of patients (54%) were unaware of their thyroid status. Not enough patients are being provided with smoking cessation advice and information on the impact of smoking on TED and control of thyroid function.


Assuntos
Oftalmopatia de Graves/terapia , Acessibilidade aos Serviços de Saúde/estatística & dados numéricos , Auditoria Administrativa , Satisfação do Paciente/estatística & dados numéricos , Adulto , Idoso , Idoso de 80 Anos ou mais , Estudos Transversais , Feminino , Glucocorticoides/administração & dosagem , Oftalmopatia de Graves/epidemiologia , Oftalmopatia de Graves/psicologia , Humanos , Radioisótopos do Iodo/administração & dosagem , Masculino , Pessoa de Meia-Idade , Estudos Prospectivos , Inquéritos e Questionários , Reino Unido , Adulto Jovem
10.
Biomaterials ; 118: 16-26, 2017 02.
Artigo em Inglês | MEDLINE | ID: mdl-27940380

RESUMO

Biomimetic materials that target the immune system and generate an anti-tumor responses hold promise in augmenting cancer immunotherapy. These synthetic materials can be engineered and optimized for their biodegradability, physical parameters such as shape and size, and controlled release of immune-modulators. As these new platforms enter the playing field, it is imperative to understand their interaction with existing immunotherapies since single-targeted approaches have limited efficacy. Here, we investigate the synergy between a PLGA-based artificial antigen presenting cell (aAPC) and a checkpoint blockade molecule, anti-PD1 monoclonal antibody (mAb). The combination of antigen-specific aAPC-based activation and anti-PD-1 mAb checkpoint blockade induced the greatest IFN-γ secretion by CD8+ T cells in vitro. Combination treatment also acted synergistically in an in vivo murine melanoma model to result in delayed tumor growth and extended survival, while either treatment alone had no effect. This was shown mechanistically to be due to decreased PD-1 expression and increased antigen-specific proliferation of CD8+ T cells within the tumor microenvironment and spleen. Thus, biomaterial-based therapy can synergize with other immunotherapies and motivates the translation of biomimetic combinatorial treatments.


Assuntos
Anticorpos Monoclonais/uso terapêutico , Células Apresentadoras de Antígenos/imunologia , Células Artificiais/imunologia , Materiais Biomiméticos/uso terapêutico , Melanoma/imunologia , Melanoma/terapia , Implantes Absorvíveis , Animais , Anticorpos Monoclonais/imunologia , Linhagem Celular Tumoral , Implantes de Medicamento/administração & dosagem , Sinergismo Farmacológico , Ácido Láctico/química , Melanoma/patologia , Camundongos , Camundongos Endogâmicos C57BL , Ácido Poliglicólico/química , Copolímero de Ácido Poliláctico e Ácido Poliglicólico , Resultado do Tratamento
12.
Nat Prod Rep ; 33(6): 761-800, 2016 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-26911790

RESUMO

Covering: up to the end of 2015.Peptides are naturally occurring compounds that play an important role in all living systems and are responsible for a range of essential functions. Peptide receptors have been implicated in disease states such as oncology, metabolic disorders and cardiovascular disease. Therefore, natural peptides have been exploited as diagnostic and therapeutic agents due to the unique target specificity for their endogenous receptors. This review discusses a variety of natural peptides highlighting their discovery, endogenous receptors, as well as their derivatization to create molecular imaging agents, with an emphasis on the design of radiolabelled peptides. This review also highlights methods for discovering new and novel peptides when knowledge of specific targets and endogenous ligands are not available.


Assuntos
Produtos Biológicos/química , Imagem Molecular/métodos , Peptídeos/química , Produtos Biológicos/farmacologia , Desenho de Fármacos , Humanos , Ligantes , Sondas Moleculares , Estrutura Molecular , Peptídeos/farmacologia , Receptores de Peptídeos
13.
Deep Sea Res 2 Top Stud Oceanogr ; 103: 277-287, 2014 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-25076815

RESUMO

Development of forecasting systems for harmful algal blooms (HABs) has been a long-standing research and management goal. Significant progress has been made in the Gulf of Maine, where seasonal bloom forecasts are now being issued annually using Alexandrium fundyense cyst abundance maps and a population dynamics model developed for that organism. Thus far, these forecasts have used terms such as "significant", "moderately large" or "moderate" to convey the extent of forecasted paralytic shellfish poisoning (PSP) outbreaks. In this study, historical shellfish harvesting closure data along the coast of the Gulf of Maine were used to derive a series of bloom severity levels that are analogous to those used to define major storms like hurricanes or tornados. Thirty-four years of PSP-related shellfish closure data for Maine, Massachusetts and New Hampshire were collected and mapped to depict the extent of coastline closure in each year. Due to fractal considerations, different methods were explored for measuring length of coastline closed. Ultimately, a simple procedure was developed using arbitrary straight-line segments to represent specific sections of the coastline. This method was consistently applied to each year's PSP toxicity closure map to calculate the total length of coastline closed. Maps were then clustered together statistically to yield distinct groups of years with similar characteristics. A series of categories or levels was defined ("Level 1: Limited", "Level 2: Moderate", and "Level 3: Extensive") each with an associated range of expected coastline closed, which can now be used instead of vague descriptors in future forecasts. This will provide scientifically consistent and simply defined information to the public as well as resource managers who make decisions on the basis of the forecasts.

14.
Animal ; 8(11): 1743-53, 2014 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-25045914

RESUMO

In livestock, many studies have reported the results of imputation to 50k single nucleotide polymorphism (SNP) genotypes for animals that are genotyped with low-density SNP panels. The objective of this paper is to review different measures of correctness of imputation, and to evaluate their utility depending on the purpose of the imputed genotypes. Across studies, imputation accuracy, computed as the correlation between true and imputed genotypes, and imputation error rates, that counts the number of incorrectly imputed alleles, are commonly used measures of imputation correctness. Based on the nature of both measures and results reported in the literature, imputation accuracy appears to be a more useful measure of the correctness of imputation than imputation error rates, because imputation accuracy does not depend on minor allele frequency (MAF), whereas imputation error rate depends on MAF. Therefore imputation accuracy can be better compared across loci with different MAF. Imputation accuracy depends on the ability of identifying the correct haplotype of a SNP, but many other factors have been identified as well, including the number of genotyped immediate ancestors, the number of animals with genotypes at the high-density panel, the SNP density on the low- and high-density panel, the MAF of the imputed SNP and whether imputed SNP are located at the end of a chromosome or not. Some of these factors directly contribute to the linkage disequilibrium between imputed SNP and SNP on the low-density panel. When imputation accuracy is assessed as a predictor for the accuracy of subsequent genomic prediction, we recommend that: (1) individual-specific imputation accuracies should be used that are computed after centring and scaling both true and imputed genotypes; and (2) imputation of gene dosage is preferred over imputation of the most likely genotype, as this increases accuracy and reduces bias of the imputed genotypes and the subsequent genomic predictions.


Assuntos
Genoma , Genômica/métodos , Genótipo , Gado/genética , Polimorfismo de Nucleotídeo Único , Animais , Cruzamento , Frequência do Gene , Haplótipos
15.
Chem Sci ; 5(6): 2503-2516, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24976945

RESUMO

Biometals such as zinc, iron, copper and calcium play key roles in diverse physiological processes in the brain, but can be toxic in excess. A hallmark of neurodegeneration is a failure of homeostatic mechanisms controlling the concentration and distribution of these elements, resulting in overload, deficiency or mislocalization. A major roadblock to understanding the impact of altered biometal homeostasis in neurodegenerative disease is the lack of rapid, specific and sensitive techniques capable of providing quantitative subcellular information on biometal homeostasis in situ. Recent advances in X-ray fluorescence detectors have provided an opportunity to rapidly measure biometal content at subcellular resolution in cell populations using X-ray Fluorescence Microscopy (XFM). We applied this approach to investigate subcellular biometal homeostasis in a cerebellar cell line isolated from a natural mouse model of a childhood neurodegenerative disorder, the CLN6 form of neuronal ceroid lipofuscinosis, commonly known as Batten disease. Despite no global changes to whole cell concentrations of zinc or calcium, XFM revealed significant subcellular mislocalization of these important biological second messengers in cerebellar Cln6nclf (CbCln6nclf ) cells. XFM revealed that nuclear-to-cytoplasmic trafficking of zinc was severely perturbed in diseased cells and the subcellular distribution of calcium was drastically altered in CbCln6nclf cells. Subtle differences in the zinc K-edge X-ray Absorption Near Edge Structure (XANES) spectra of control and CbCln6nclf cells suggested that impaired zinc homeostasis may be associated with an altered ligand set in CbCln6nclf cells. Importantly, a zinc-complex, ZnII(atsm), restored the nuclear-to-cytoplasmic zinc ratios in CbCln6nclf cells via nuclear zinc delivery, and restored the relationship between subcellular zinc and calcium levels to that observed in healthy control cells. ZnII(atsm) treatment also resulted in a reduction in the number of calcium-rich puncta observed in CbCln6nclf cells. This study highlights the complementarities of bulk and single cell analysis of metal content for understanding disease states. We demonstrate the utility and broad applicability of XFM for subcellular analysis of perturbed biometal metabolism and mechanism of action studies for novel therapeutics to target neurodegeneration.

16.
Deep Sea Res 2 Top Stud Oceanogr ; 103: 264-276, 2014 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-24948849

RESUMO

A major goal in harmful algal bloom (HAB) research has been to identify mechanisms underlying interannual variability in bloom magnitude and impact. Here the focus is on variability in Alexandrium fundyense blooms and paralytic shellfish poisoning (PSP) toxicity in Maine, USA, over 34 years (1978 - 2011). The Maine coastline was divided into two regions -eastern and western Maine, and within those two regions, three measures of PSP toxicity (the percent of stations showing detectable toxicity over the year, the cumulative amount of toxicity per station measured in all shellfish (mussel) samples during that year, and the duration of measurable toxicity) were examined for each year in the time series. These metrics were combined into a simple HAB Index that provides a single measure of annual toxin severity across each region. The three toxin metrics, as well as the HAB Index that integrates them, reveal significant variability in overall toxicity between individual years as well as long-term, decadal patterns or regimes. Based on different conceptual models of the system, we considered three trend formulations to characterize the long-term patterns in the Index - a three-phase (mean-shift) model, a linear two-phase model, and a pulse-decline model. The first represents a "regime shift" or multiple equilibria formulation as might occur with alternating periods of sustained high and low cyst abundance or favorable and unfavorable growth conditions, the second depicts a scenario of more gradual transitions in cyst abundance or growth conditions of vegetative cells, and the third characterizes a "sawtooth" pattern in which upward shifts in toxicity are associated with major cyst recruitment events, followed by a gradual but continuous decline until the next pulse. The fitted models were compared using both residual sum of squares and Akaike's Information Criterion. There were some differences between model fits, but none consistently gave a better fit than the others. This statistical underpinning can guide efforts to identify physical and/or biological mechanisms underlying the patterns revealed by the HAB Index. Although A. fundyense cyst survey data (limited to 9 years) do not span the entire interval of the shellfish toxicity records, this analysis leads us to hypothesize that major changes in the abundance of A. fundyense cysts may be a primary factor contributing to the decadal trends in shellfish toxicity in this region. The HAB Index approach taken here is simple but represents a novel and potentially useful tool for resource managers in many areas of the world subject to toxic HABs.

17.
Heredity (Edinb) ; 112(1): 48-60, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-23572121

RESUMO

Genomic selection (GS) has been implemented in animal and plant species, and is regarded as a useful tool for accelerating genetic gains. Varying levels of genomic prediction accuracy have been obtained in plants, depending on the prediction problem assessed and on several other factors, such as trait heritability, the relationship between the individuals to be predicted and those used to train the models for prediction, number of markers, sample size and genotype × environment interaction (GE). The main objective of this article is to describe the results of genomic prediction in International Maize and Wheat Improvement Center's (CIMMYT's) maize and wheat breeding programs, from the initial assessment of the predictive ability of different models using pedigree and marker information to the present, when methods for implementing GS in practical global maize and wheat breeding programs are being studied and investigated. Results show that pedigree (population structure) accounts for a sizeable proportion of the prediction accuracy when a global population is the prediction problem to be assessed. However, when the prediction uses unrelated populations to train the prediction equations, prediction accuracy becomes negligible. When genomic prediction includes modeling GE, an increase in prediction accuracy can be achieved by borrowing information from correlated environments. Several questions on how to incorporate GS into CIMMYT's maize and wheat programs remain unanswered and subject to further investigation, for example, prediction within and between related bi-parental crosses. Further research on the quantification of breeding value components for GS in plant breeding populations is required.


Assuntos
Interação Gene-Ambiente , Característica Quantitativa Herdável , Triticum/genética , Zea mays/genética , Genética Populacional , Genoma de Planta , Genótipo , Modelos Genéticos , Fenótipo , Seleção Genética
19.
J Anim Breed Genet ; 130(4): 259-69, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23855628

RESUMO

Long-range phasing and haplotype library imputation methodologies are accurate and efficient methods to provide haplotype information that could be used in prediction of breeding value or phenotype. Modelling long haplotypes as independent effects in genomic prediction would be inefficient due to the many effects that need to be estimated and phasing errors, even if relatively low in frequency, exacerbate this problem. One approach to overcome this is to use similarity between haplotypes to model covariance of genomic effects by region or of animal breeding values. We developed a simple method to do this and tested impact on genomic prediction by simulation. Results show that the diagonal and off-diagonal elements of a genomic relationship matrix constructed using the haplotype similarity method had higher correlations with the true relationship between pairs of individuals than genomic relationship matrices built using unphased genotypes or assumed unrelated haplotypes. However, the prediction accuracy of such haplotype-based prediction methods was not higher than those based on unphased genotype information.


Assuntos
Genômica/métodos , Haplótipos , Modelos Genéticos , Animais , Inteligência Artificial , Cruzamento , Fenótipo , Fatores de Tempo
20.
J Anim Sci ; 91(8): 3583-92, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23736050

RESUMO

Genomic selection can be implemented in pig breeding at a reduced cost using genotype imputation. Accuracy of imputation and the impact on resulting genomic breeding values (gEBV) was investigated. High-density genotype data was available for 4,763 animals from a single pig line. Three low-density genotype panels were constructed with SNP densities of 450 (L450), 3,071 (L3k) and 5,963 (L6k). Accuracy of imputation was determined using 184 test individuals with no genotyped descendants in the data but with parents and grandparents genotyped using the Illumina PorcineSNP60 Beadchip. Alternative genotyping scenarios were created in which parents, grandparents, and individuals that were not direct ancestors of test animals (Other) were genotyped at high density (S1), grandparents were not genotyped (S2), dams and granddams were not genotyped (S3), and dams and granddams were genotyped at low density (S4). Four additional scenarios were created by excluding Other animal genotypes. Test individuals were always genotyped at low density. Imputation was performed with AlphaImpute. Genomic breeding values were calculated using the single-step genomic evaluation. Test animals were evaluated for the information retained in the gEBV, calculated as the correlation between gEBV using imputed genotypes and gEBV using true genotypes. Accuracy of imputation was high for all scenarios but decreased with fewer SNP on the low-density panel (0.995 to 0.965 for S1) and with reduced genotyping of ancestors, where the largest changes were for L450 (0.965 in S1 to 0.914 in S3). Exclusion of genotypes for Other animals resulted in only small accuracy decreases. Imputation accuracy was not consistent across the genome. Information retained in the gEBV was related to genotyping scenario and thus to imputation accuracy. Reducing the number of SNP on the low-density panel reduced the information retained in the gEBV, with the largest decrease observed from L3k to L450. Excluding Other animal genotypes had little impact on imputation accuracy but caused large decreases in the information retained in the gEBV. These results indicate that accuracy of gEBV from imputed genotypes depends on the level of genotyping in close relatives and the size of the genotyped dataset. Fewer high-density genotyped individuals are needed to obtain accurate imputation than are needed to obtain accurate gEBV. Strategies to optimize development of low-density panels can improve both imputation and gEBV accuracy.


Assuntos
Cruzamento , Genômica , Seleção Genética , Suínos/genética , Agricultura/economia , Animais , Cruzamento/economia , Análise Custo-Benefício , Genótipo
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