Cost-Effectiveness of Lovotibeglogene Autotemcel (Lovo-Cel) Gene Therapy for Patients with Sickle Cell Disease and Recurrent Vaso-Occlusive Events in the United States.

BACKGROUND AND OBJECTIVE: Gene therapies for sickle cell disease (SCD) may offer meaningful benefits for patients and society. This study evaluated the cost-effectiveness of lovotibeglogene autotemcel (lovo-cel), a one-time gene therapy administered via autologous hematopoietic stem cell transplantation, compared with common care for patients in the United States (US) with SCD aged ≥ 12 years with ≥ 4 vaso-occlusive events (VOEs) in the past 24 months. METHODS: We developed a patient-level simulation model accounting for lovo-cel and SCD-related events, complications, and mortality over a lifetime time horizon. The pivotal phase 1/2 HGB-206 clinical trial (NCT02140554) served as the basis for lovo-cel efficacy and safety. Cost, quality-of-life, and other clinical data were sourced from HGB-206 data and the literature. Analyses were conducted from US societal and third-party payer perspectives. Uncertainty was assessed through probabilistic sensitivity analysis and extensive scenario analyses. RESULTS: Patients treated with lovo-cel were predicted to survive 23.84 years longer on average (standard deviation [SD], 12.80) versus common care (life expectancy, 62.24 versus 38.40 years), with associated discounted patient quality-adjusted life-year (QALY) gains of 10.20 (SD, 4.10) and direct costs avoided of $1,329,201 (SD, $1,346,446) per patient. Predicted societal benefits included discounted caregiver QALY losses avoided of 1.19 (SD, 1.38) and indirect costs avoided of $540,416 (SD, $262,353) per patient. Including lovo-cel costs ($3,282,009 [SD, $29,690] per patient) resulted in incremental cost-effectiveness ratios of $191,519 and $124,051 per QALY gained from third-party payer and societal perspectives, respectively. In scenario analyses, the predicted cost-effectiveness of lovo-cel also was sensitive to baseline age and VOE frequency and to the proportion of patients achieving and maintaining complete resolution of VOEs. CONCLUSIONS: Our analysis of lovo-cel gene therapy compared with common care for patients in the US with SCD with recurrent VOEs estimated meaningful improvements in survival, quality of life, and other clinical outcomes accompanied by increased overall costs for the health care system and for broader society. The predicted economic value of lovo-cel gene therapy was influenced by uncertainty in long-term clinical effects and by positive spillover effects on patient productivity and caregiver burden.

Going Forward: Potential Impact of Protein-Based COVID-19 Vaccination Coverage on Population Outcomes and Costs in the United States.

Policymakers in the United States (US) recommend coronavirus disease 2019 (COVID-19) vaccination with a monovalent 2023-2024 vaccine formulation based on the Omicron XBB.1.5 variant. We estimated the potential US population-level health and economic impacts of increased COVID-19 vaccine coverage that might be expected with the availability of a protein-based vaccine with simpler storage requirements in addition to messenger ribonucleic acid (mRNA) vaccines. A Markov model was developed to estimate 1-year COVID-19-related costs, cases, hospitalizations, and deaths with and without the availability of a protein-based vaccine option. The model population was stratified by age and risk status. Model inputs were sourced from published literature or derived from publicly available data. Our model estimated that a five-percentage-point increase in coverage due to the availability of a protein-based vaccine option would prevent over 500,000 cases, 66,000 hospitalizations, and 3000 COVID-19-related deaths. These clinical outcomes translated to 42,000 quality-adjusted life years (QALYs) gained and an incremental cost-effectiveness ratio of USD 16,141/QALY from a third-party payer perspective. In sensitivity analyses, outcomes were most sensitive to COVID-19 incidence and severity across age groups. The availability of a protein-based vaccine option in the US could reduce hospitalizations and deaths and is predicted to be cost-effective.

Evaluating Elements of the Care Partner Experience in Individuals Who Care for People with Alzheimer's Disease Across the Severity Spectrum.

INTRODUCTION: Non-professional care partners play an important and often evolving role in the care of persons living with Alzheimer's disease (PLWAD). We investigated two elements of the care partner experience, namely time and strain incurred by care partners providing care to PLWAD across the severity spectrum. METHODS: Data gathered from the Alzheimer's Disease Patient and Caregiver Engagement (AD PACE) What Matters Most (WMM) study series were analyzed to determine how much time care partners spent providing care to PLWAD based on where the care recipients lived. Additionally, quantitative assessments of weekly hours providing care and the strain experienced by care partners were conducted using the UsAgainstAlzheimer's A-LIST Insights Series survey, which included the Modified Caregiver Strain Index (MCSI). Finally, a targeted literature review was conducted to contextualize findings and characterize the existing literature landscape. RESULTS: Care partners in the AD PACE WMM studies (n = 139) spent significantly more hours providing care for recipients who lived with someone (mean ± standard deviation [SD], 57.3 ± 44.3 h/week) than for recipients who lived alone (26.0 ± 12.0 h/week) (P = 0.0096) or lived in assisted living/nursing home (23.6 ± 14.4 h/week) (P = 0.0002). In the A-LIST Insights Series survey, care partners provided an overall mean (± SD) 58.1 ± 53.0 h of direct care each week, with caregiving hours increasing with increasing severity of AD/AD-related dementias (AD/ADRD). Additionally, care partners for recipients with mild (n = 14), moderate (n = 111), and severe AD/ADRD (n = 91) had overall mean MCSI scores of 9.0 ± 3.8 (range 2-14), 13.3 ± 4.8 (range 4-23), and 17.5 ± 5.3 (range 4-26), respectively, with higher scores suggesting greater care partner strain. CONCLUSIONS: Persons living with AD require increasing levels of care along the spectrum of disease, and even individuals with early disease need care from partners. Early interventions that slow progression of AD and programs that improve family function may have beneficial impact on the experiences of care partners for recipients with mild, moderate, or severe AD.

People get ready! A new generation of Alzheimer's therapies may require new ways to deliver and pay for healthcare.

The development of disease-modifying therapies (DMTs) for Alzheimer's disease (AD) has progressed over the last decade, and the first-ever therapies with potential to slow the progression of disease are approved in the United States. AD DMTs could provide life-changing opportunities for people living with this disease, as well as for their caregivers. They could also ease some of the immense societal and economic burden of dementia. However, AD DMTs also come with major challenges due to the large unmet medical need, high prevalence of AD, new costs related to diagnosis, treatment and monitoring, and uncertainty in the therapies' actual clinical value. This perspective article discusses, from the broad perspective of various health systems and stakeholders, how we can overcome these challenges and improve society's readiness for AD DMTs. We propose that innovative payment models such as performance-based payments, in combination with learning healthcare systems, could be the way forward to enable timely patient access to treatments, improve accuracy of cost-effectiveness evaluations and overcome budgetary barriers. Other important considerations include the need for identification of key drivers of patient value, the relevance of different economic perspectives (i.e. healthcare vs. societal) and ethical questions in terms of treatment eligibility criteria.

Using residual regressions to quantify and map signal leakage in genomic prediction.

BACKGROUND: Most genomic prediction applications in animal breeding use genotypes with tens of thousands of single nucleotide polymorphisms (SNPs). However, modern sequencing technologies and imputation algorithms can generate ultra-high-density genotypes (including millions of SNPs) at an affordable cost. Empirical studies have not produced clear evidence that using ultra-high-density genotypes can significantly improve prediction accuracy. However, (whole-genome) prediction accuracy is not very informative about the ability of a model to capture the genetic signals from specific genomic regions. To address this problem, we propose a simple methodology that detects chromosome regions for which a specific model (e.g., single-step genomic best linear unbiased prediction (ssGBLUP)) may fail to fully capture the genetic signal present in such segments-a phenomenon that we refer to as signal leakage. We propose to detect regions with evidence of signal leakage by testing the association of residuals from a pedigree or a genomic model with SNP genotypes. We discuss how this approach can be used to map regions with signals that are poorly captured by a model and to identify strategies to fix those problems (e.g., using a different prior or increasing marker density). Finally, we explored the proposed approach to scan for signal leakage of different models (pedigree-based, ssGBLUP, and various Bayesian models) applied to growth-related phenotypes (average daily gain and backfat thickness) in pigs. RESULTS: We report widespread evidence of signal leakage for pedigree-based models. Including a percentage of animals with SNP data in ssGBLUP reduced the extent of signal leakage. However, local peaks of missed signals remained in some regions, even when all animals were genotyped. Using variable selection priors solves leakage points that are caused by excessive shrinkage of marker effects. Nevertheless, these models still miss signals in some regions due to low linkage disequilibrium between the SNPs on the array used and causal variants. Thus, we discuss how such problems could be addressed by adding sequence SNPs from those regions to the prediction model. CONCLUSIONS: Residual single-marker regression analysis is a simple approach that can be used to detect regional genomic signals that are poorly captured by a model and to indicate ways to fix such problems.

Using pre-selected variants from large-scale whole-genome sequence data for single-step genomic predictions in pigs.

BACKGROUND: Whole-genome sequence (WGS) data harbor causative variants that may not be present in standard single nucleotide polymorphism (SNP) chip data. The objective of this study was to investigate the impact of using preselected variants from WGS for single-step genomic predictions in maternal and terminal pig lines with up to 1.8k sequenced and 104k sequence imputed animals per line. METHODS: Two maternal and four terminal lines were investigated for eight and seven traits, respectively. The number of sequenced animals ranged from 1365 to 1491 for the maternal lines and 381 to 1865 for the terminal lines. Imputation to sequence occurred within each line for 66k to 76k animals for the maternal lines and 29k to 104k animals for the terminal lines. Two preselected SNP sets were generated based on a genome-wide association study (GWAS). Top40k included the SNPs with the lowest p-value in each of the 40k genomic windows, and ChipPlusSign included significant variants integrated into the porcine SNP chip used for routine genotyping. We compared the performance of single-step genomic predictions between using preselected SNP sets assuming equal or different variances and the standard porcine SNP chip. RESULTS: In the maternal lines, ChipPlusSign and Top40k showed an average increase in accuracy of 0.6 and 4.9%, respectively, compared to the regular porcine SNP chip. The greatest increase was obtained with Top40k, particularly for fertility traits, for which the initial accuracy based on the standard SNP chip was low. However, in the terminal lines, Top40k resulted in an average loss of accuracy of 1%. ChipPlusSign provided a positive, although small, gain in accuracy (0.9%). Assigning different variances for the SNPs slightly improved accuracies when using variances obtained from BayesR. However, increases were inconsistent across the lines and traits. CONCLUSIONS: The benefit of using sequence data depends on the line, the size of the genotyped population, and how the WGS variants are preselected. When WGS data are available on hundreds of thousands of animals, using sequence data presents an advantage but this remains limited in pigs.

A genome-wide association study for loin depth and muscle pH in pigs from intensely selected purebred lines.

BACKGROUND: Genome-wide association studies (GWAS) aim at identifying genomic regions involved in phenotype expression, but identifying causative variants is difficult. Pig Combined Annotation Dependent Depletion (pCADD) scores provide a measure of the predicted consequences of genetic variants. Incorporating pCADD into the GWAS pipeline may help their identification. Our objective was to identify genomic regions associated with loin depth and muscle pH, and identify regions of interest for fine-mapping and further experimental work. Genotypes for ~ 40,000 single nucleotide morphisms (SNPs) were used to perform GWAS for these two traits, using de-regressed breeding values (dEBV) for 329,964 pigs from four commercial lines. Imputed sequence data was used to identify SNPs in strong ([Formula: see text] 0.80) linkage disequilibrium with lead GWAS SNPs with the highest pCADD scores. RESULTS: Fifteen distinct regions were associated with loin depth and one with loin pH at genome-wide significance. Regions on chromosomes 1, 2, 5, 7, and 16, explained between 0.06 and 3.55% of the additive genetic variance and were strongly associated with loin depth. Only a small part of the additive genetic variance in muscle pH was attributed to SNPs. The results of our pCADD analysis suggests that high-scoring pCADD variants are enriched for missense mutations. Two close but distinct regions on SSC1 were associated with loin depth, and pCADD identified the previously identified missense variant within the MC4R gene for one of the lines. For loin pH, pCADD identified a synonymous variant in the RNF25 gene (SSC15) as the most likely candidate for the muscle pH association. The missense mutation in the PRKAG3 gene known to affect glycogen content was not prioritised by pCADD for loin pH. CONCLUSIONS: For loin depth, we identified several strong candidate regions for further statistical fine-mapping that are supported in the literature, and two novel regions. For loin muscle pH, we identified one previously identified associated region. We found mixed evidence for the utility of pCADD as an extension of heuristic fine-mapping. The next step is to perform more sophisticated fine-mapping and expression quantitative trait loci (eQTL) analysis, and then interrogate candidate variants in vitro by perturbation-CRISPR assays.

Multi-line ssGBLUP evaluation using preselected markers from whole-genome sequence data in pigs.

Genomic evaluations in pigs could benefit from using multi-line data along with whole-genome sequencing (WGS) if the data are large enough to represent the variability across populations. The objective of this study was to investigate strategies to combine large-scale data from different terminal pig lines in a multi-line genomic evaluation (MLE) through single-step GBLUP (ssGBLUP) models while including variants preselected from whole-genome sequence (WGS) data. We investigated single-line and multi-line evaluations for five traits recorded in three terminal lines. The number of sequenced animals in each line ranged from 731 to 1,865, with 60k to 104k imputed to WGS. Unknown parent groups (UPG) and metafounders (MF) were explored to account for genetic differences among the lines and improve the compatibility between pedigree and genomic relationships in the MLE. Sequence variants were preselected based on multi-line genome-wide association studies (GWAS) or linkage disequilibrium (LD) pruning. These preselected variant sets were used for ssGBLUP predictions without and with weights from BayesR, and the performances were compared to that of a commercial porcine single-nucleotide polymorphisms (SNP) chip. Using UPG and MF in MLE showed small to no gain in prediction accuracy (up to 0.02), depending on the lines and traits, compared to the single-line genomic evaluation (SLE). Likewise, adding selected variants from the GWAS to the commercial SNP chip resulted in a maximum increase of 0.02 in the prediction accuracy, only for average daily feed intake in the most numerous lines. In addition, no benefits were observed when using preselected sequence variants in multi-line genomic predictions. Weights from BayesR did not help improve the performance of ssGBLUP. This study revealed limited benefits of using preselected whole-genome sequence variants for multi-line genomic predictions, even when tens of thousands of animals had imputed sequence data. Correctly accounting for line differences with UPG or MF in MLE is essential to obtain predictions similar to SLE; however, the only observed benefit of an MLE is to have comparable predictions across lines. Further investigation into the amount of data and novel methods to preselect whole-genome causative variants in combined populations would be of significant interest.

Efficient ways to combine data from broiler and layer chickens to account for sequential genomic selection.

In broiler breeding, superior individuals for growth become parents and are later evaluated for reproduction in an independent evaluation; however, ignoring broiler data can produce inaccurate and biased predictions. This research aimed to determine the most accurate, unbiased, and time-efficient approach for jointly evaluating reproductive and broiler traits. The data comprised a pedigree with 577K birds, 146K genotypes, phenotypes for three reproductive (egg production [EP], fertility [FE], hatch of fertile eggs [HF]; 9K each), and four broiler traits (body weight [BW], breast meat percent [BP], fat percent [FP], residual feed intake [RF]; up to 467K). Broiler data were added sequentially to assess the impact on the quality of predictions for reproductive traits. The baseline scenario (RE) included pedigrees, genotypes, and phenotypes for reproductive traits of selected animals; in RE2, we added their broiler phenotypes; in RE_BR, broiler phenotypes of nonselected animals, and in RE_BR_GE, their genotypes. We computed accuracy, bias, and dispersion of predictions for hens from the last two breeding cycles and their sires. We tested three core definitions for the algorithm of proven and young to find the most time-efficient approach: two random cores with 7K and 12K animals and one with 19K animals, containing parents and young animals. From RE to RE_BR_GE, changes in accuracy were null or minimal for EP (0.51 in hens, 0.59 in roosters) and HF (0.47 in hens, 0.49 in roosters); for FE in hens (roosters), it changed from 0.4 (0.49) to 0.47 (0.53). In hens (roosters), bias (additive SD units) decreased from 0.69 (0.7) to 0.04 (0.05) for EP, 1.48 (1.44) to 0.11 (0.03) for FE, and 1.06 (0.96) to 0.09 (0.02) for HF. Dispersion remained stable in hens (roosters) at ~0.93 (~1.03) for EP, and it improved from 0.57 (0.72) to 0.87 (1.0) for FE and from 0.8 (0.79) to 0.88 (0.87) for HF. Ignoring broiler data deteriorated the predictions' quality. The impact was significant for the low heritability trait (0.02; FE); bias (up to 1.5) and dispersion (as low as 0.57) were farther from the ideal value, and accuracy losses were up to 17.5%. Accuracy was maintained in traits with moderate heritability (~0.3; EP and HF), and bias and dispersion were less substantial. Adding information from the broiler phase maximized accuracy and unbiased predictions. The most time-efficient approach is a random core with 7K animals in the algorithm for proven and young.

In breeding programs with sequential selection, the estimation of breeding values becomes biased and inaccurate if the information from the past selection is ignored. We investigated the impact of incorporating broiler data (traits for past selection) into the evaluation of broiler reproductive traits. Including all the information increased the computing demands; therefore, we tested three core definitions for the algorithm for proven and young to determine the most accurate, unbiased, and time-efficient approach for jointly evaluating broiler and reproductive traits. When we ignored broiler data, the estimated breeding values for reproductive traits were biased (up to ~1.5 additive standard deviations). For low heritability traits, accuracy was reduced by up to 17.5%, and breeding values were overestimated (dispersion ~ 0.6). In contrast, incorporating broiler data eliminated bias and overestimation; and it maximized accuracy. A random core definition for the algorithm for proven and young with a number of animals equal to the number of the largest eigenvalues explaining 99% of the variation in the genomic relationship matrix is the most time-efficient, keeping accurate and unbiased predictions in the joint evaluation of broiler and reproductive traits.

Cost-Effectiveness of Respiratory Syncytial Virus Preventive Interventions in Children: A Model Comparison Study.

OBJECTIVES: Model-based cost-effectiveness analyses on maternal vaccine (MV) and monoclonal antibody (mAb) interventions against respiratory syncytial virus (RSV) use context-specific data and produce varied results. Through model comparison, we aim to characterize RSV cost-effectiveness models and examine drivers for their outputs. METHODS: We compared 3 static and 2 dynamic models using a common input parameter set for a hypothetical birth cohort of 100 000 infants. Year-round and seasonal programs were evaluated for MV and mAb interventions, using available evidence during the study period (eg, phase III MV and phase IIb mAb efficacy). RESULTS: Three static models estimated comparable medically attended (MA) cases averted versus no intervention (MV, 1019-1073; mAb, 5075-5487), with the year-round MV directly saving ∼€1 million medical and €0.3 million nonmedical costs, while gaining 4 to 5 discounted quality-adjusted life years (QALYs) annually in <1-year-olds, and mAb resulting in €4 million medical and €1.5 million nonmedical cost savings, and 21 to 25 discounted QALYs gained. In contrast, both dynamic models estimated fewer MA cases averted (MV, 402-752; mAb, 3362-4622); one showed an age shift of RSV cases, whereas the other one reported many non-MA symptomatic cases averted, especially by MV (2014). These differences can be explained by model types, assumptions on non-MA burden, and interventions' effectiveness over time. CONCLUSIONS: Our static and dynamic models produced overall similar hospitalization and death estimates, but also important differences, especially in non-MA cases averted. Despite the small QALY decrement per non-MA case, their larger number makes them influential for the costs per QALY gained of RSV interventions.

Cost-effectiveness models for Alzheimer's disease and related dementias: IPECAD modeling workshop cross-comparison challenge.

INTRODUCTION: The credibility of model-based economic evaluations of Alzheimer's disease (AD) interventions is central to appropriate decision-making in a policy context. We report on the International PharmacoEconomic Collaboration on Alzheimer's Disease (IPECAD) Modeling Workshop Challenge. METHODS: Two common benchmark scenarios, for the hypothetical treatment of AD mild cognitive impairment (MCI) and mild dementia, were developed jointly by 29 participants. Model outcomes were summarized, and cross-comparisons were discussed during a structured workshop. RESULTS: A broad concordance was established among participants. Mean 10-year restricted survival and time in MCI in the control group ranged across 10 MCI models from 6.7 to 9.5 years and 3.4 to 5.6 years, respectively; and across 4 mild dementia models from 5.4 to 7.9 years (survival) and 1.5 to 4.2 years (mild dementia). DISCUSSION: The model comparison increased our understanding of methods, data used, and disease progression. We established a collaboration framework to assess cost-effectiveness outcomes, an important step toward transparent and credible AD models.

Optimisation of the core subset for the APY approximation of genomic relationships.

BACKGROUND: By entering the era of mega-scale genomics, we are facing many computational issues with standard genomic evaluation models due to their dense data structure and cubic computational complexity. Several scalable approaches have been proposed to address this challenge, such as the Algorithm for Proven and Young (APY). In APY, genotyped animals are partitioned into core and non-core subsets, which induces a sparser inverse of the genomic relationship matrix. This partitioning is often done at random. While APY is a good approximation of the full model, random partitioning can make results unstable, possibly affecting accuracy or even reranking animals. Here we present a stable optimisation of the core subset by choosing animals with the most informative genotype data. METHODS: We derived a novel algorithm for optimising the core subset based on a conditional genomic relationship matrix or a conditional single nucleotide polymorphism (SNP) genotype matrix. We compared the accuracy of genomic predictions with different core subsets for simulated and real pig data sets. The core subsets were constructed (1) at random, (2) based on the diagonal of the genomic relationship matrix, (3) at random with weights from (2), or (4) based on the novel conditional algorithm. To understand the different core subset constructions, we visualise the population structure of the genotyped animals with linear Principal Component Analysis and non-linear Uniform Manifold Approximation and Projection. RESULTS: All core subset constructions performed equally well when the number of core animals captured most of the variation in the genomic relationships, both in simulated and real data sets. When the number of core animals was not sufficiently large, there was substantial variability in the results with the random construction but no variability with the conditional construction. Visualisation of the population structure and chosen core animals showed that the conditional construction spreads core animals across the whole domain of genotyped animals in a repeatable manner. CONCLUSIONS: Our results confirm that the size of the core subset in APY is critical. Furthermore, the results show that the core subset can be optimised with the conditional algorithm that achieves an optimal and repeatable spread of core animals across the domain of genotyped animals.

Evaluation of emerging NASH therapies: the impact of treatment efficacy profiles on long-term health outcomes.

Aim: Evaluations of nonalcoholic steatohepatitis (NASH) treatments require predicting lifetime outcomes from short-term clinical trials. Materials & methods: A Markov model with NASH fibrosis stages F0-F3, NASH resolution, compensated cirrhosis (F4/CC), and liver-related complication (LRC) states was developed using literature-based standard of care (SoC) data. Hypothetical efficacy profiles were defined affecting resolution (100%-increase), fibrosis improvement (100% increase), or fibrosis worsening (50% decrease). Results: For the SoC, 10-year LRC rates increased with baseline fibrosis stage (F1: 3.0%; F2: 9.8%; F3: 27.2%; F4/CC: 64.9%). The fibrosis worsening profile reduced predicted 10-year LRC rates (F1: 1.9%; F2: 6.5%; F3: 19.1%; F4/CC: 55.0%) more than the resolution and fibrosis improvement profiles (F1: 2.6%/2.6%; F2: 8.5%/8.3%; F3: 23.3%/23.0%; F4/CC: NA/59.0%). Scenario analyses considered alternative SoC progression, treatment efficacy and treatment-stopping rules. Conclusion: Potential NASH efficacy profiles have differing impacts on predicted long-term outcomes, providing insights for future stakeholders.

Many new treatments are being investigated for nonalcoholic steatohepatitis (NASH), a progressive and life-threatening disease often resulting in liver fibrosis (scarring) and advanced liver disease. The clinical value of these treatments and whether they are good value for money will depend on their ability to reduce the risk of advanced liver disease and subsequent liver transplantation. We developed a disease progression model which tracks survival and quality of life for two identical groups of NASH patients over their lifetimes. One group received a new hypothetical treatment for NASH while the other received current standard care. We used the model to estimate the potential health benefits of different hypothetical treatments for NASH. Our results suggest that treatments slowing fibrosis worsening may lead to greater long-term health benefits than treatments that improve NASH or improve existing fibrosis. These findings may provide insights to researchers involved in the development of new treatments for NASH.

Leveraging low-density crossbred genotypes to offset crossbred phenotypes and their impact on purebred predictions.

The objectives of this study were to 1) investigate the predictability and bias of genomic breeding values (GEBV) of purebred (PB) sires for CB performance when CB genotypes imputed from a low-density panel are available, 2) assess if the availability of those CB genotypes can be used to partially offset CB phenotypic recording, and 3) investigate the impact of including imputed CB genotypes in genomic analyses when using the algorithm for proven and young (APY). Two pig populations with up to 207,375 PB and 32,893 CB phenotypic records per trait and 138,026 PB and 32,893 CB genotypes were evaluated. PB sires were genotyped for a 50K panel, whereas CB animals were genotyped for a low-density panel of 600 SNP and imputed to 50K. The predictability and bias of GEBV of PB sires for backfat thickness (BFX) and average daily gain recorded (ADGX) recorded on CB animals were assessed when CB genotypes were available or not in the analyses. In the first set of analyses, direct inverses of the genomic relationship matrix (G) were used with phenotypic datasets truncated at different time points. In the next step, we evaluated the APY algorithm with core compositions differing in the CB genotype contributions. After that, the performance of core compositions was compared with an analysis using a random PB core from a purely PB genomic set. The number of rounds to convergence was recorded for all APY analyses. With the direct inverse of G in the first set of analyses, adding CB genotypes imputed from a low-density panel (600 SNP) did not improve predictability or reduce the bias of PB sires' GEBV for CB performance, even for sires with fewer CB progeny phenotypes in the analysis. That indicates that the inclusion of CB genotypes primarily used for inferring pedigree in commercial farms is of no benefit to offset CB phenotyping. When CB genotypes were incorporated into APY, a random core composition or a core with no CB genotypes reduced bias and the number of rounds to convergence but did not affect predictability. Still, a PB random core composition from a genomic set with only PB genotypes resulted in the highest predictability and the smallest number of rounds to convergence, although bias increased. Genotyping CB individuals for low-density panels is a valuable identification tool for linking CB phenotypes to pedigree; however, the inclusion of those CB genotypes imputed from a low-density panel (600 SNP) might not benefit genomic predictions for PB individuals or offset CB phenotyping for the evaluated CB performance traits. Further studies will help understand the usefulness of those imputed CB genotypes for traits with lower PB-CB genetic correlations and traits not recorded in the PB environment, such as mortality and disease traits.

Crossbred (CB) genotypes primarily used for inferring pedigree in commercial farms can be potentially used for genomic prediction and partially offset CB phenotyping. We investigated the predictability and bias of genomic breeding values (GEBV) of purebred (PB) sires for CB performance when CB genotypes are available, assessed if the availability of those CB genotypes can be used to partially offset CB phenotypic recording, and investigated the impact of including CB genotypes in genomic analyses when using the algorithm for proven and young (APY). The predictability and bias of GEBV of PB sires for two CB traits were assessed when CB genotypes were available or not in the analyses. Later, the performance of different APY core compositions accounting for CB genotypes was compared with a random core from a purely PB genomic set. Adding CB genotypes did not improve predictability or reduce the bias of PB sires' GEBV for CB performance, indicating that the inclusion of CB genotypes imputed from a low-density (600 SNP) panel is of no benefit to offset CB phenotyping. With APY, a random core composition from a genomic set with only PB genotypes resulted in the highest predictability and the smallest number of rounds to convergence, although bias increased.

Genomic prediction with whole-genome sequence data in intensely selected pig lines.

BACKGROUND: Early simulations indicated that whole-genome sequence data (WGS) could improve the accuracy of genomic predictions within and across breeds. However, empirical results have been ambiguous so far. Large datasets that capture most of the genomic diversity in a population must be assembled so that allele substitution effects are estimated with high accuracy. The objectives of this study were to use a large pig dataset from seven intensely selected lines to assess the benefits of using WGS for genomic prediction compared to using commercial marker arrays and to identify scenarios in which WGS provides the largest advantage. METHODS: We sequenced 6931 individuals from seven commercial pig lines with different numerical sizes. Genotypes of 32.8 million variants were imputed for 396,100 individuals (17,224 to 104,661 per line). We used BayesR to perform genomic prediction for eight complex traits. Genomic predictions were performed using either data from a standard marker array or variants preselected from WGS based on association tests. RESULTS: The accuracies of genomic predictions based on preselected WGS variants were not robust across traits and lines and the improvements in prediction accuracy that we achieved so far with WGS compared to standard marker arrays were generally small. The most favourable results for WGS were obtained when the largest training sets were available and standard marker arrays were augmented with preselected variants with statistically significant associations to the trait. With this method and training sets of around 80k individuals, the accuracy of within-line genomic predictions was on average improved by 0.025. With multi-line training sets, improvements of 0.04 compared to marker arrays could be expected. CONCLUSIONS: Our results showed that WGS has limited potential to improve the accuracy of genomic predictions compared to marker arrays in intensely selected pig lines. Thus, although we expect that larger improvements in accuracy from the use of WGS are possible with a combination of larger training sets and optimised pipelines for generating and analysing such datasets, the use of WGS in the current implementations of genomic prediction should be carefully evaluated against the cost of large-scale WGS data on a case-by-case basis.

Rare and population-specific functional variation across pig lines.

BACKGROUND: It is expected that functional, mainly missense and loss-of-function (LOF), and regulatory variants are responsible for most phenotypic differences between breeds and genetic lines of livestock species that have undergone diverse selection histories. However, there is still limited knowledge about the existing missense and LOF variation in commercial livestock populations, in particular regarding population-specific variation and how it can affect applications such as across-breed genomic prediction. METHODS: We re-sequenced the whole genome of 7848 individuals from nine commercial pig lines (average sequencing coverage: 4.1×) and imputed whole-genome genotypes for 440,610 pedigree-related individuals. The called variants were categorized according to predicted functional annotation (from LOF to intergenic) and prevalence level (number of lines in which the variant segregated; from private to widespread). Variants in each category were examined in terms of their distribution along the genome, alternative allele frequency, per-site Wright's fixation index (FST), individual load, and association to production traits. RESULTS: Of the 46 million called variants, 28% were private (called in only one line) and 21% were widespread (called in all nine lines). Genomic regions with a low recombination rate were enriched with private variants. Low-prevalence variants (called in one or a few lines only) were enriched for lower allele frequencies, lower FST, and putatively functional and regulatory roles (including LOF and deleterious missense variants). On average, individuals carried fewer private deleterious missense alleles than expected compared to alleles with other predicted consequences. Only a small subset of the low-prevalence variants had intermediate allele frequencies and explained small fractions of phenotypic variance (up to 3.2%) of production traits. The significant low-prevalence variants had higher per-site FST than the non-significant ones. These associated low-prevalence variants were tagged by other more widespread variants in high linkage disequilibrium, including intergenic variants. CONCLUSIONS: Most low-prevalence variants have low minor allele frequencies and only a small subset of low-prevalence variants contributed detectable fractions of phenotypic variance of production traits. Accounting for low-prevalence variants is therefore unlikely to noticeably benefit across-breed analyses, such as the prediction of genomic breeding values in a population using reference populations of a different genetic background.

What might have happened: the impact of interrupting entry of innovative drugs on disease outcomes in the United States.

INTRODUCTION: The study estimated the extent to which drug innovations over the past 30 years may have improved outcomes for six diseases. AREAS COVERED: We analyzed six diseases (ischemic heart disease, lung cancer, breast cancer, human immunodeficiency virus [HIV] infection, type 2 diabetes mellitus, and rheumatoid arthritis [RA]) with significant mortality or morbidity for which there have been major drug innovations over the past 30 years. We used U.S. data from the Global Burden of Disease (GBD) database and a patient registry to perform counterfactual time-series analyses predicting the improved health outcomes that may have been associated with major drug innovations. For 5 conditions using data from the GBD study, years of life lost per individual with the condition could have been higher by 17.1% (breast cancer) to 660.6% (HIV infection) in 2017 had the major drug innovations not been introduced. For RA, using patient registry data, patients' functional status could have been 11.5% worse had biological therapies not been introduced. EXPERT OPINION: Policies targeting drug prices should be broadened to consider the price and value of all health-care services. The societal importance of the pharmaceutical industry's ability to respond rapidly to emerging diseases should be recognized.

Comparative Effectiveness and Cost-Effectiveness of Natalizumab and Fingolimod in Patients with Inadequate Response to Disease-Modifying Therapies in Relapsing-Remitting Multiple Sclerosis in the United Kingdom.

BACKGROUND: Patients with highly active relapsing-remitting multiple sclerosis inadequately responding to first-line therapies (interferon-based therapies, glatiramer acetate, dimethyl fumarate, and teriflunomide, known collectively as "BRACETD") often switch to natalizumab or fingolimod. OBJECTIVE: The aim was to estimate the comparative effectiveness of switching to natalizumab or fingolimod or within BRACETD using real-world data and to evaluate the cost-effectiveness of switching to natalizumab versus fingolimod using a United Kingdom (UK) third-party payer perspective. METHODS: Real-world data were obtained from MSBase for patients relapsing on BRACETD in the year before switching to natalizumab or fingolimod or within BRACETD. Three-way-multinomial-propensity-score-matched cohorts were identified, and comparisons between treatment groups were conducted for annualised relapse rate (ARR) and 6-month-confirmed disability worsening (CDW6M) and improvement (CDI6M). Results were applied in a cost-effectiveness model over a lifetime horizon using a published Markov structure with health states based on the Expanded Disability Status Scale. Other model parameters were obtained from the UK MS Survey 2015, published literature, and publicly available UK sources. RESULTS: The MSBase analysis found a significant reduction in ARR (rate ratio [RR] = 0.64; 95% confidence interval [CI] 0.57-0.72; p < 0.001) and an increase in CDI6M (hazard ratio [HR] = 1.67; 95% CI 1.30-2.15; p < 0.001) for switching to natalizumab compared with BRACETD. For switching to fingolimod, the reduction in ARR (RR = 0.91; 95% CI 0.81-1.03; p = 0.133) and increase in CDI6M (HR = 1.30; 95% CI 0.99-1.72; p = 0.058) compared with BRACETD were not significant. Switching to natalizumab was associated with a significant reduction in ARR (RR = 0.70; 95% CI 0.62-0.79; p < 0.001) and an increase in CDI6M (HR = 1.28; 95% CI 1.01-1.62; p = 0.040) compared to switching to fingolimod. No evidence of difference in CDW6M was found between treatment groups. Natalizumab dominated (higher quality-adjusted life-years [QALYs] and lower costs) fingolimod in the base-case cost-effectiveness analysis (0.453 higher QALYs and £20,843 lower costs per patient). Results were consistent across sensitivity analyses. CONCLUSIONS: This novel real-world analysis suggests a clinical benefit for therapy escalation to natalizumab versus fingolimod based on comparative effectiveness results, translating to higher QALYs and lower costs for UK patients inadequately responding to BRACETD.

Clinical and economic outcomes associated with respiratory syncytial virus vaccination in older adults in the United States.

BACKGROUND: Respiratory syncytial virus (RSV) is an important cause of lower respiratory infections and hospitalizations among older adults. We aimed to estimate the potential clinical benefits and economic value of RSV vaccination of older adults in the United States (US). METHODS: We developed an economic model using a decision-tree framework to capture outcomes associated with RSV infections in US adults aged ≥ 60 years occurring during one RSV season for a hypothetical vaccine versus no vaccine. Two co-base-case epidemiology sources were selected from a targeted review of the US literature: a landmark study capturing all RSV infections and a contemporary study reporting medically attended RSV that also distinguishes mild from moderate-to-severe disease. Both base-case analyses used recent data on mortality risk in the year after RSV hospitalizations. Direct medical costs and quality-adjusted life-years (QALYs) lost per case were obtained from the literature and publicly available sources. Model outcomes included the population-level clinical and economic RSV disease burden among older adults, potential vaccine-avoidable disease burden, and the potential value-based price of a vaccine from a third-party payer perspective. RESULTS: Our two base-case analyses estimated that a vaccine with 50% efficacy and coverage matching that of influenza vaccination would prevent 43,700-81,500 RSV hospitalizations and 8,000-14,900 RSV-attributable deaths per RSV season, resulting in 1,800-3,900 fewer QALYs lost and avoiding $557-$1,024 million. Value-based prices for the co-base-case analyses were $152-$299 per vaccination at a willingness to pay of $100,000/QALY gained. Sensitivity analyses found that the economic value of vaccination was most sensitive to RSV incidence and increased posthospitalization mortality risks. CONCLUSIONS: Despite variability and gaps in the epidemiology literature, this study highlights the potential value of RSV vaccination for older adults in the US. Our analysis provides contemporary estimates of the population-level RSV disease burden and insights into the economic value drivers for RSV vaccination.

Predicted Lifetime Health Outcomes for Aducanumab in Patients with Early Alzheimer's Disease.

INTRODUCTION: Alzheimer's disease (AD) is a chronic and progressive neurodegenerative disease that places a substantial burden on patients and caregivers. Aducanumab is the first AD therapy approved by the US Food and Drug Administration to reduce a defining pathophysiological feature of the disease, brain amyloid plaques. In the phase 3 clinical trial EMERGE (NCT02484547), aducanumab reduced clinical decline in patients with mild cognitive impairment (MCI) due to AD and mild AD dementia and confirmed amyloid pathology. METHODS: We used a Markov modeling approach to predict the long-term clinical benefits of aducanumab for patients with early AD based on EMERGE efficacy data. In the model, patients could transition between AD severity levels (MCI due to AD; mild, moderate, and severe AD dementia) and care settings (community vs. institution) or transition to death. The intervention was aducanumab added to standard of care (SOC), and the comparator was SOC alone. Data sources for base-case and scenario analyses included EMERGE, published National Alzheimer's Coordinating Center analyses, and other published literature. RESULTS: Per patient over a lifetime horizon, aducanumab treatment corresponded to 0.65 incremental patient quality-adjusted life-years (QALYs) and 0.09 fewer caregiver QALYs lost compared with patients treated with SOC. Aducanumab treatment translated to a lower lifetime probability of transitioning to AD dementia, a lower lifetime probability of transitioning to institutionalization (25.2% vs. 29.4%), delays in the median time to transition to AD dementia (7.50 vs. 4.92 years from MCI to moderate AD dementia or worse), and an incremental median time in the community of 1.32 years compared with SOC. CONCLUSION: The model predicted long-term benefits of aducanumab treatment in patients with MCI due to AD and mild AD dementia and their caregivers. The predicted outcomes provide a foundation for healthcare decision-makers and policymakers to understand the potential clinical and socioeconomic value of aducanumab.