SNP-based quantitative deconvolution of biological mixtures: application to the detection of cows with subclinical mastitis by whole-genome sequencing of tank milk.

peer reviewedBiological products of importance in food (e.g., milk) and medical (e.g., donor blood-derived products) sciences often correspond to mixtures of samples contributed by multiple individuals. Identifying which individuals contributed to the mixture and in what proportions may be of interest in several circumstances. We herein present a method that allows to do this by shallow whole-genome sequencing of the DNA in mixed samples from hundreds of donors. We show the efficacy of the approach for the detection of cows with subclinical mastitis by analysis of farms' tank mixtures containing milk from as many as 500 cows

Best evidence rehabilitation for chronic pain, part 3 : low back pain

Chronic Low Back Pain (CLBP) is a major and highly prevalent health problem. Given the high number of papers available, clinicians might be overwhelmed by the evidence on CLBP management. Taking into account the scale and costs of CLBP, it is imperative that healthcare professionals have access to up-to-date, evidence-based information to assist them in treatment decision-making. Therefore, this paper provides a state-of-the-art overview of the best evidence non-invasive rehabilitation for CLBP. Taking together up-to-date evidence from systematic reviews, meta-analysis and available treatment guidelines, most physically inactive therapies should not be considered for CLBP management, except for pain neuroscience education and spinal manipulative therapy if combined with exercise therapy, with or without psychological therapy. Regarding active therapy, back schools, sensory discrimination training, proprioceptive exercises, and sling exercises should not be considered due to low-quality and/or conflicting evidence. Exercise interventions on the other hand are recommended, but while all exercise modalities appear effective compared to minimal/passive/conservative/no intervention, there is no evidence that some specific types of exercises are superior to others. Therefore, we recommend choosing exercises in line with the patient's preferences and abilities. When exercise interventions are combined with a psychological component, effects are better and maintain longer over time

Reverse genetic screen for loss-of-function mutations uncovers a frame-shifting deletion in the melanophilin gene accountable for a distinctive coat-color in Belgian Blue Cattle.

RILOUK

A Rank-Based Nonparametric Method for Mapping Quantitative Trait Loci in Outbred Half-Sib Pedigrees: Application to Milk Production in a Granddaughter Design

We describe the development of a multipoint nonparametric quantitative trait loci mapping method based on the Wilcoxon rank-sum test applicable to outbred half-sib pedigrees. The method has been evaluated on a simulated dataset and its efficiency compared with interval mapping by using regression. It was shown that the rank-based approach is slightly inferior to regression when the residual variance is homoscedastic normal; however, in three out of four other scenarios envisaged, i.e., residual variance heteroscedastic normal, homoscedastic skewed, and homoscedastic positively kurtosed, the latter outperforms the former one. Both methods were applied to a real data set analyzing the effect of bovine chromosome 6 on milk yield and composition by using a 125-cM map comprising 15 microsatellites and a granddaughter design counting 1158 Holstein-Friesian sires

arrEYE : a customized platform for high-resolution copy number analysis of coding and noncoding regions of known and candidate retinal dystrophy genes and retinal noncoding RNAs

Purpose: Our goal was to design a customized microarray, arrEYE, for high-resolution copy number variant (CNV) analysis of known and candidate genes for inherited retinal dystrophy (iRD) and retina expressed noncoding RNAs (ncRNAs). Methods: arrEYE contains probes for the full genomic region of 106 known iRD genes, including those implicated in retinitis pigmentosa (RP) (the most frequent iRD), cone rod dystrophies, macular dystrophies, and an additional 60 candidate iRD genes and 196 ncRNAs. Eight CNVs in iRD genes identified by other techniques were used as positive controls. The test cohort consisted of 57 patients with autosomal dominant, X-linked, or simplex RP. Results: In an RP patient, a novel heterozygous deletion of exons 7 and 8 of the HGSNAT gene was identified: c.634-408_820+338delins AGAATATG, p.(G1u2 I 2Glyfs*2). A known variant was found on the second allele: c.1843G>A, p.(A1a615Thr). Furthermore, we expanded the allelic spectrum of USH2A and RCBTB1 with novel CNVs. Conclusion: The arrEYE platform revealed subtle single-exon to larger CNVs in iRD genes that could be characterized at the nucleotide level, facilitated by the high resolution of the platform. We report the first CNV in HGSNAT that, combined with another mutation, leads to RP, further supporting its recently identified role in nonsyndromic iRD

Mapping QTL influencing gastrointestinal nematode burden in Dutch Holstein-Friesian dairy cattle

BACKGROUND: Parasitic gastroenteritis caused by nematodes is only second to mastitis in terms of health costs to dairy farmers in developed countries. Sustainable control strategies complementing anthelmintics are desired, including selective breeding for enhanced resistance. RESULTS AND CONCLUSION: To quantify and characterize the genetic contribution to variation in resistance to gastro-intestinal parasites, we measured the heritability of faecal egg and larval counts in the Dutch Holstein-Friesian dairy cattle population. The heritability of faecal egg counts ranged from 7 to 21% and was generally higher than for larval counts. We performed a whole genome scan in 12 paternal half-daughter groups for a total of 768 cows, corresponding to the approximately 10% most and least infected daughters within each family (selective genotyping). Two genome-wide significant QTL were identified in an across-family analysis, respectively on chromosomes 9 and 19, coinciding with previous findings in orthologous chromosomal regions in sheep. We identified six more suggestive QTL by within-family analysis. An additional 73 informative SNPs were genotyped on chromosome 19 and the ensuing high density map used in a variance component approach to simultaneously exploit linkage and linkage disequilibrium in an initial inconclusive attempt to refine the QTL map position

Selection in action: dissecting the molecular underpinnings of the increasing muscle mass of Belgian Blue Cattle.

BACKGROUND: Belgian Blue cattle are famous for their exceptional muscular development or "double-muscling". This defining feature emerged following the fixation of a loss-of-function variant in the myostatin gene in the eighties. Since then, sustained selection has further increased muscle mass of Belgian Blue animals to a comparable extent. In the present paper, we study the genetic determinants of this second wave of muscle growth. RESULTS: A scan for selective sweeps did not reveal the recent fixation of another allele with major effect on muscularity. However, a genome-wide association study identified two genome-wide significant and three suggestive quantitative trait loci (QTL) affecting specific muscle groups and jointly explaining 8-21% of the heritability. The top two QTL are caused by presumably recent mutations on unique haplotypes that have rapidly risen in frequency in the population. While one appears on its way to fixation, the ascent of the other is compromised as the likely underlying MRC2 mutation causes crooked tail syndrome in homozygotes. Genomic prediction models indicate that the residual additive variance is largely polygenic. CONCLUSIONS: Contrary to complex traits in humans which have a near-exclusive polygenic architecture, muscle mass in beef cattle (as other production traits under directional selection), appears to be controlled by (i) a handful of recent mutations with large effect that rapidly sweep through the population, and (ii) a large number of presumably older variants with very small effects that rise slowly in the population (polygenic adaptation)

Fine-Scale Study of Meiotic Recombination in Cattle

peer reviewe

Benchmarking phasing software with a whole-genome sequenced cattle pedigree.

peer reviewed[en] BACKGROUND: Accurate haplotype reconstruction is required in many applications in quantitative and population genomics. Different phasing methods are available but their accuracy must be evaluated for samples with different properties (population structure, marker density, etc.). We herein took advantage of whole-genome sequence data available for a Holstein cattle pedigree containing 264 individuals, including 98 trios, to evaluate several population-based phasing methods. This data represents a typical example of a livestock population, with low effective population size, high levels of relatedness and long-range linkage disequilibrium. RESULTS: After stringent filtering of our sequence data, we evaluated several population-based phasing programs including one or more versions of AlphaPhase, ShapeIT, Beagle, Eagle and FImpute. To that end we used 98 individuals having both parents sequenced for validation. Their haplotypes reconstructed based on Mendelian segregation rules were considered the gold standard to assess the performance of population-based methods in two scenarios. In the first one, only these 98 individuals were phased, while in the second one, all the 264 sequenced individuals were phased simultaneously, ignoring the pedigree relationships. We assessed phasing accuracy based on switch error counts (SEC) and rates (SER), lengths of correctly phased haplotypes and the probability that there is no phasing error between a pair of SNPs as a function of their distance. For most evaluated metrics or scenarios, the best software was either ShapeIT4.1 or Beagle5.2, both methods resulting in particularly high phasing accuracies. For instance, ShapeIT4.1 achieved a median SEC of 50 per individual and a mean haplotype block length of 24.1 Mb (scenario 2). These statistics are remarkable since the methods were evaluated with a map of 8,400,000 SNPs, and this corresponds to only one switch error every 40,000 phased informative markers. When more relatives were included in the data (scenario 2), FImpute3.0 reconstructed extremely long segments without errors. CONCLUSIONS: We report extremely high phasing accuracies in a typical livestock sample. ShapeIT4.1 and Beagle5.2 proved to be the most accurate, particularly for phasing long segments and in the first scenario. Nevertheless, most tools achieved high accuracy at short distances and would be suitable for applications requiring only local haplotypes

Development of a bioinformatic tool for the treatment of WGS data for dermatophytes typing and characterization: Focus on squalene epoxidase mutations and terbinafine resistance.

peer reviewedObjectives: The present work aims to use the Whole Genome Sequencing (WGS) as a tool to characterize dermatophytes strains. Data generated by WGS are analyzed by using a bioinformatic tool called “WGS typer” and several markers are highlighted, such as genes implicated in resistance to antifungals or genes linked with high virulence in dermatophytes. The tool will also permit to analyze dermatophytes following their genetic diversity and provide similarity dendrograms. The present work focus on squalene epoxidase (SQLE) gene characterization among T. rubrum and T. indotineae strains by the WGS typer. Material and methods: 15 strains of T. rubrum (7 resistant to terbinafine and 8 susceptible) and 19 strains of T. indotineae (8 resistant to terbinafine and 11 susceptible) from a multicenter study, previously characterized by Eucast E.Def.11.0 method (Arendrup et al., 2020) were used for SQLE characterization by WGS.WGS has been performed by the GIGA genomics platform using the Illumina technology. The WGS Typer is a commercial bioinformatics tool developed by Hedera-22 (http://www.hedera22.com) and licensed to the Department of Clinical Microbiology of the University of Liège. This tool enables high-throughput typing of pathogen isolates based on raw sequencing data and a collection of relevant markers (single genes, gene variants, gene clusters, MLST). The analysis reports the presence/absence of targeted markers or genotypes from a sequence homology search against the assembled sequencing data according to a set of sequence identity/coverage thresholds. Results: We evaluated the ability of the tool to detect mutations in the SQLE gene that are responsible for terbinafine resistance in dermatophytes. Seven T. rubrum showed a resistant profile to terbinafine (MIC values >0.25µg/µl) with the microdilution method. Among these, four shared the F397L mutation on SQLE, one was wearing L393F mutation while two other shared the L393S mutation. All these mutations were efficiently highlighted by the WGS typer. Among the eight strains presenting a MIC value under 0.25µg/µl, no mutation was found on SQLE gene. Regarding T. indotineae, 8 strains were previously characterized to be resistant to terbinafine with the microdilution method (MIC values >0,25µg/µl). Among them, the WGS typer detected seven strains with the mutation F397L and one strain with the mutation L393F on the SQLE gene. Among the eleven strains presenting a MIC value under 0.25µg/µl by microdilution, no mutation was found on SQLE. The study was completed with genetic similarity comparisons and dendrogram creation. No clear separation into clusters was observed between resistant/susceptible strains neither in the T. rubrum group nor in the T. indotineae group. T. rubrum and T. indotineae species were well separated into two distinct clusters. Conclusion: We present here a valuable and innovative tool for the analysis of dermatophytes. The tool permits to easily and accurately detect mutations on the SQLE gene responsible for terbinafine resistance. A dendrogram of similarity based on WGS data can also be generated