Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes OPEN

By limiting sequencing to those sequences transcribed as mRNA, whole exome sequencing is a costefficient technique often used in disease-association studies. We developed two target enrichment designs based on the recently released annotation of the canine genome: the exome-plus design and the exome-CDS design. The exome-plus design combines the exons of the CanFam 3.1 Ensembl annotation, more recently discovered protein-coding exons and a variety of non-coding RNA regions (microRNAs, long non-coding RNAs and antisense transcripts), leading to a total size of ≈152 Mb. The exome-CDS was designed as a subset of the exome-plus by omitting all 3' and 5' untranslated regions. This reduced the size of the exome-CDS to ≈71 Mb. To test the capturing performance, four exome-plus captures were sequenced on a NextSeq 500 with each capture containing four precapture pooled, barcoded samples. At an average sequencing depth of 68.3x, 80% of the regions and well over 90% of the targeted base pairs were completely covered at least 5 times with high reproducibility. Based on the performance of the exome-plus, we estimated the performance of the exome-CDS. Overall, these designs provide flexible solutions for a variety of research questions and are likely to be reliable tools in disease studies. In 2014, the first report detailing the design and performance of a whole exome sequencing (WES) enrichment assay for the dog was published by our group 1 . Aiming to selectively sequence all the regions that are transcribed to mRNA, WES is a reliable tool used to identify disease-causing or predisposing mutations at a fraction of the price of whole genome sequencing (WGS) studies. A limitation of WES is that it is based on our current knowledge of the annotation of the genome and that many disease causing mutations are likely to fall outside protein-coding regions. With new information becoming available, updates and extensions are required. Recently, an improved annotation for the dog genome has been published and new data on non-protein coding genes has been obtained 2 . Based on this data, two new target enrichment designs for dogs, called the exome-plus and the exome-CDS, were developed. The exome-plus offers the most comprehensive design. The exome-CDS is a subset of the exome-plus, focusing on the coding DNA sequences (CDS) by excluding the 3′ and 5′ untranslated regions (UTRs). Thes

Correlation analysis for energy losses, waiting times and durations of type I edge-localized modes in the Joint European Torus

Several important ELM control techniques are in large part motivated by the empirically observed inverse relationship between average ELM energy loss and ELM frequency in a plasma. However, to ensure a reliable effect on the energy released by the ELMs, it is important that this relation is verified for individual ELM events. Therefore, in this work the relation between ELM energy loss (W-ELM) and waiting time (Delta t(ELM)) is investigated for individual ELMs in a set of ITER-like wall plasmas in JET. A comparison is made with the results from a set of carbon-wall and nitrogen-seeded ITER-like wall JET plasmas. It is found that the correlation between W-ELM and Delta t(ELM) for individual ELMs varies from strongly positive to zero. Furthermore, the effect of the extended collapse phase often accompanying ELMs from unseeded JET ILW plasmas and referred to as the slow transport event (STE) is studied on the distribution of ELM durations, and on the correlation between W-ELM and Delta t(ELM). A high correlation between W-ELM and Delta t(ELM), comparable to CW plasmas is only found in nitrogen-seeded ILW plasmas. Finally, a regression analysis is performed using plasma engineering parameters as predictors for determining the region of the plasma operational space with a high correlation between W-ELM and Delta t(ELM)

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes

By limiting sequencing to those sequences transcribed as mRNA, whole exome sequencing is a cost-efficient technique often used in disease-association studies. We developed two target enrichment designs based on the recently released annotation of the canine genome: the exome-plus design and the exome-CDS design. The exome-plus design combines the exons of the CanFam 3.1 Ensembl annotation, more recently discovered protein-coding exons and a variety of non-coding RNA regions (microRNAs, long non-coding RNAs and antisense transcripts), leading to a total size of approximate to 152 Mb. The exome-CDS was designed as a subset of the exome-plus by omitting all 3' and 5' untranslated regions. This reduced the size of the exome-CDS to approximate to 71 Mb. To test the capturing performance, four exome-plus captures were sequenced on a NextSeq 500 with each capture containing four pre-capture pooled, barcoded samples. At an average sequencing depth of 68.3x, 80% of the regions and well over 90% of the targeted base pairs were completely covered at least 5 times with high reproducibility. Based on the performance of the exome-plus, we estimated the performance of the exome-CDS. Overall, these designs provide flexible solutions for a variety of research questions and are likely to be reliable tools in disease studies

Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes

By limiting sequencing to those sequences transcribed as mRNA, whole exome sequencing is a cost-efficient technique often used in disease-association studies. We developed two target enrichment designs based on the recently released annotation of the canine genome: the exome-plus design and the exome-CDS design. The exome-plus design combines the exons of the CanFam 3.1 Ensembl annotation, more recently discovered protein-coding exons and a variety of non-coding RNA regions (microRNAs, long non-coding RNAs and antisense transcripts), leading to a total size of approximate to 152 Mb. The exome-CDS was designed as a subset of the exome-plus by omitting all 3' and 5' untranslated regions. This reduced the size of the exome-CDS to approximate to 71 Mb. To test the capturing performance, four exome-plus captures were sequenced on a NextSeq 500 with each capture containing four pre-capture pooled, barcoded samples. At an average sequencing depth of 68.3x, 80% of the regions and well over 90% of the targeted base pairs were completely covered at least 5 times with high reproducibility. Based on the performance of the exome-plus, we estimated the performance of the exome-CDS. Overall, these designs provide flexible solutions for a variety of research questions and are likely to be reliable tools in disease studies

The prevalence of nine genetic disorders in a dog population from Belgium, the Netherlands and Germany.

The objective of this study was to screen a dog population from Belgium, the Netherlands and Germany for the presence of mutant alleles associated with hip dysplasia (HD), degenerative myelopathy (DM), exercise-induced collapse (EIC), neuronal ceroid lipofuscinosis 4A (NCL), centronuclear myopathy (HMLR), mucopolysaccharidosis VII (MPS VII), myotonia congenita (MG), gangliosidosis (GM1) and muscular dystrophy (Duchenne type) (GRMD). Blood samples (K3EDTA) were collected for genotyping with Kompetitive Allele Specific PCR (n = 476). Allele and genotype frequencies were calculated in those breeds with at least 12 samples (n = 8). Hardy-Weinberg equilibrium was tested. Genetic variation was identified for 4 out of 9 disorders: mutant alleles were found in 49, 15, 3 and 2 breeds for HD, DM, EIC and NCL respectively. Additionally, mutant alleles were identified in crossbreeds for both HD and EIC. For HD, DM, EIC and NCL mutant alleles were newly discovered in 43, 13, 2 and 1 breed(s), respectively. In 9, 2 and 1 breed(s) for DM, EIC and NCL respectively, the mutant allele was detected, but the respective disorder has not been reported in those breeds. For 5 disorders (HMLR, MPS VII, MG, GM1, GRMD), the mutant allele could not be identified in our population. For the other 4 disorders (HD, DM, EIC, NCL), prevalence of associated mutant alleles seems strongly breed dependent. Surprisingly, mutant alleles were found in many breeds where the disorder has not been reported to date

Towards a typology of specific language impairment

Contains fulltext : 54578.pdf (publisher's version ) (Closed access)Background - The population of children with specific language impairments (SLI) is heterogeneous. The present study was conducted to examine this heterogeneity more closely, by identifying and describing subgroups within the population of children with SLI in the Netherlands. Method - A broad battery of language tests and language-related cognitive tests were administered to 147 six-year-old and 136 eight-year-old children with SLI. Results - Factor analyses revealed 4 factors indicating 4 distinctive linguistic domains for both age samples: 1) lexical-semantic abilities, 2) auditory conceptualization, 3) verbal sequential memory and 4) speech production. These empirical findings were further validated by the positive correlations found between the language factors and the judgments of teachers and speech therapists. Finally, a cluster analysis revealed 4 distinct clusters of SLI children for each sample with specific language profiles based on the 4 factors. Results were nearly the same for both age samples. Conclusions - The language problems that emerged from the two samples of children with SLI could be described as falling into four types. Based on these language types, four subgroups of children with SLI could be distinguished, each with a specific profile. Some subgroups had severe problems on one specific type of language problem; others had severe problems in more than one type of language problem when compared to the other subgroups of the same age sample. The different profiles may indicate that a more dynamic approach is needed in intervention, considering the presence of both compensating and restricting factors within each child with SLI.14 p

Breed and samples per breed tested.

a<p> = not specified whether English or Welsh Springer Spaniel.</p