Corrigendum: Guaranteed Income and Financial Treatment Trial (GIFT Trial or GIFTT): a 12-month, randomized controlled trial to compare the effectiveness of monthly unconditional cash transfers to treatment as usual in reducing financial toxicity in people with cancer who have low incomes.

[This corrects the article DOI: 10.3389/fpsyg.2023.

Corrigendum: Guaranteed Income and Financial Treatment (G.I.F.T.): a 12-month, randomized controlled trial to compare the effectiveness of monthly unconditional cash transfers to treatment as usual in reducing financial toxicity in people with cancer who have low incomes.

[This corrects the article DOI: 10.3389/fpsyg.2023.

CLARITY: a Shiny app for interactive visualisation of the bovine physical-genetic map.

The arrangement of markers on the genome can be defined in either physical or linkage terms. While a physical map represents the inter-marker distances in base pairs, a genetic (or linkage) map pictures the recombination rate between pairs of markers. High-resolution genetic maps are key elements for genomic research, such as fine-mapping of quantitative trait loci, but they are also needed for creating and updating chromosome-level assemblies of whole-genome sequences.

Relationship between milk urea content and important milk traits in Holstein cattle.

Breeding cattle with low nitrogen emissions has been proposed as a countermeasure against eutrophication due to dairy production. Milk urea content (MU) could potentially serve as a new readily measured indicator trait for nitrogen emissions by cows. Therefore, we estimated genetic parameters related to MU and its relationship with other milk traits.

Evidence of rare misassemblies in the bovine reference genome revealed by population genetic metrics.

Creation of the bovine reference assembly paved the way to develop the high-throughput genotyping arrays of the single nucleotide polymorphisms (SNPs) based on the available map coordinates that facilitated major advances in gene mapping and selection programs. The assembly flaws, however, may cause false results in the downstream gene mapping studies. The most recent bovine reference genome (ARS-UCD1.

A Fitted Sparse-Group Lasso for Genome-Based Evaluations.

In life sciences, high-throughput techniques typically lead to high-dimensional data and often the number of covariates is much larger than the number of observations. This inherently comes with multicollinearity challenging a statistical analysis in a linear regression framework. Penalization methods such as the lasso, ridge regression, the group lasso, and convex combinations thereof, which introduce additional conditions on regression variables, have proven themselves effective.

Analysis of Autozygosity Using Whole-Genome Sequence Data of Full-Sib Families in Pikeperch ().

Pikeperch () has emerged as a high value species to the aquaculture industry. However, its farming techniques are at an early stage and its production is often performed without a selective breeding program, potentially leading to high levels of inbreeding. In this study, we identified and characterized autozygosity based on genome-wide runs of homozygosity (ROH) on a sample of parental and offspring individuals, determined effective population size ( ), and assessed relatedness among parental individuals.

National and State Trends in autistic Adult Supplemental Security Income Awardees: 2005-2019.

This paper used Social Security Administration program data from 2005 to 2019 to examine national- and state-level changes in the number of new adult supplemental security income (SSI) awardees on the autism spectrum relative to awardees with intellectual disability and other mental health disorders. We identified three main findings: the number of autistic awards increased between 2005 and 2019 when awards for all other mental health disorders declined; roughly nine out of every 10 autistic adult awardees were between ages 18-25 years; there was variation in the growth of autistic awards across states. These findings support the need to consider geographic and age differences in SSI program participation among autistic adults and determine the underlying causes.

Grouping of genomic markers in populations with family structure.

Background: Linkage and linkage disequilibrium (LD) between genome regions cause dependencies among genomic markers. Due to family stratification in populations with non-random mating in livestock or crop, the standard measures of population LD such as [Formula: see text] may be biased. Grouping of markers according to their interdependence needs to account for the actual population structure in order to allow proper inference in genome-based evaluations.

An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale.

Pikeperch (Sander lucioperca) is a fish species with growing economic significance in the aquaculture industry. However, successful positioning of pikeperch in large-scale aquaculture requires advances in our understanding of its genome organization. In this study, an ultra-high density linkage map for pikeperch comprising 24 linkage groups and 1,023,625 single nucleotide polymorphisms markers was constructed after genotyping whole-genome sequencing data from 11 broodstock and 363 progeny, belonging to 6 full-sib families.

Male recombination map of the autosomal genome in German Holstein.

Background: Recombination is a process by which chromosomes are broken and recombine to generate new combinations of alleles, therefore playing a major role in shaping genome variation. Recombination frequencies ([Formula: see text]) between markers are used to construct genetic maps, which have important implications in genomic studies. Here, we report a recombination map for 44,696 autosomal single nucleotide polymorphisms (SNPs) according to the coordinates of the most recent bovine reference assembly.

Seagull: lasso, group lasso and sparse-group lasso regularization for linear regression models via proximal gradient descent.

Background: Statistical analyses of biological problems in life sciences often lead to high-dimensional linear models. To solve the corresponding system of equations, penalization approaches are often the methods of choice. They are especially useful in case of multicollinearity, which appears if the number of explanatory variables exceeds the number of observations or for some biological reason.

Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout () Breeding Strains by Using Next-Generation Sequencing.

Selective breeding can significantly improve the establishment of sustainable and profitable aquaculture fish farming. For rainbow trout (), one of the main aquaculture coldwater species in Europe, a variety of selected hatchery strains are commercially available. In this study, we investigated the genetic variation between the local Born strain, selected for survival, and the commercially available Silver Steelhead strain, selected for growth.

Design of experiments for fine-mapping quantitative trait loci in livestock populations.

Background: Single nucleotide polymorphisms (SNPs) which capture a significant impact on a trait can be identified with genome-wide association studies. High linkage disequilibrium (LD) among SNPs makes it difficult to identify causative variants correctly. Thus, often target regions instead of single SNPs are reported.

The First Highly Contiguous Genome Assembly of Pikeperch (), an Emerging Aquaculture Species in Europe.

The pikeperch () is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process.

Genetic Contribution to Variation in Blood Calcium, Phosphorus, and Alkaline Phosphatase Activity in Pigs.

Blood values of calcium (Ca), inorganic phosphorus (IP), and alkaline phosphatase activity (ALP) are valuable indicators for mineral status and bone mineralization. The mineral homeostasis is maintained by absorption, retention, and excretion processes employing a number of known and unknown sensing and regulating factors with implications on immunity. Due to the high inter-individual variation of Ca and P levels in the blood of pigs and to clarify molecular contributions to this variation, the genetics of hematological traits related to the Ca and P balance were investigated in a German Landrace population, integrating both single-locus and multi-locus genome-wide association study (GWAS) approaches.

An approximate Bayesian significance test for genomic evaluations.

Genomic information can be used to study the genetic architecture of some trait. Not only the size of the genetic effect captured by molecular markers and their position on the genome but also the mode of inheritance, which might be additive or dominant, and the presence of interactions are interesting parameters. When searching for interacting loci, estimating the effect size and determining the significant marker pairs increases the computational burden in terms of speed and memory allocation dramatically.

Estimation of Recombination Rate and Maternal Linkage Disequilibrium in Half-Sibs.

A livestock population can be characterized by different population genetic parameters, such as linkage disequilibrium and recombination rate between pairs of genetic markers. The population structure, which may be caused by family stratification, has an influence on the estimates of these parameters. An expectation maximization algorithm has been proposed for estimating these parameters in half-sibs without phasing the progeny.

On Estimation of Genome Composition in Genetically Admixed Individuals Using Constrained Genomic Regression.

Quantifying the population stratification in genotype samples has become a standard procedure for data manipulation before conducting genome wide association studies, as well as for tracing patterns of migration in humans and animals, and for inference about extinct founder populations. The most widely used approach capable of providing biologically interpretable results is a likelihood formulation which allows for estimation of founder genome proportions and founder allele frequency conditional on the observed genotypes. However, if founder allele frequencies are known and samples are dominated by admixed genotypes this approach may lead to biased inference.

Alcohol use among Hispanic college students along the US/Mexico border.

Background: The trend of alcohol use among college students has been shown to vary by ethnicity and has been linked to acculturation among Hispanics. Consistent findings indicate that males consume alcohol more frequently and in greater quantities compared to females.

Objectives: This study investigated the drinking habits of Hispanic college students living in the border region of South Texas.

Covariance Between Genotypic Effects and its Use for Genomic Inference in Half-Sib Families.

In livestock, current statistical approaches utilize extensive molecular data, e.g., single nucleotide polymorphisms (SNPs), to improve the genetic evaluation of individuals.

Genomic additive and dominance variance of milk performance traits.

Milk performance traits are likely influenced by both additive and non-additive (e.g. dominance) genetic effects.

Expression variation of the porcine ADRB2 has a complex genetic background.

Porcine adrenergic receptor beta 2 (ADRB2) gene exhibits differential allelic expression in skeletal muscle, and its genetic variation has been associated with muscle pH. Exploring the molecular-genetic background of expression variation for porcine ADRB2 will provide insight into the mechanisms driving its regulatory divergence and may also contribute to unraveling the genetic basis of muscle-related traits in pigs. In the present study, we therefore examined haplotype effects on the expression of porcine ADRB2 in four tissues: longissimus dorsi muscle, liver, subcutaneous fat, and spleen.

Integrating milk metabolite profile information for the prediction of traditional milk traits based on SNP information for Holstein cows.

In this study the benefit of metabolome level analysis for the prediction of genetic value of three traditional milk traits was investigated. Our proposed approach consists of three steps: First, milk metabolite profiles are used to predict three traditional milk traits of 1,305 Holstein cows. Two regression methods, both enabling variable selection, are applied to identify important milk metabolites in this step.