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Contains fulltext : 230111.pdf (publisher's version ) (Open Access)

Accurate discovery of somatic variants is of central importance in cancer research. However, count statistics on discovered somatic insertions and deletions (indels) indicate that large amounts of discoveries are missed because of the quantification of uncertainties related to gap and alignment ambiguities, twilight zone indels, cancer heterogeneity, sample purity, sampling, and strand bias. We provide a unifying statistical model whose dependency structures enable accurate quantification of all inherent uncertainties in short time. Consequently, false discovery rate (FDR) in somatic indel discovery can now be controlled at utmost accuracy, increasing the amount of true discoveries while safely suppressing the FDR.

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Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.

Item does not contain fulltext, AIM: To assess development of reaching and head stability in infants at very high risk (VHR-infants) of cerebral palsy (CP) who did and did not develop CP. METHOD: This explorative longitudinal study assessed the kinematics of reaching and head sway in sitting in 37 VHR-infants (18 CP) one to four times between 4.7 months and 22.6 months corrected age. Developmental trajectories were calculated using linear mixed effect models. Motor function was evaluated with the Infant Motor Profile (IMP) around 13 months corrected age. RESULTS: Throughout infancy, VHR-infants with CP had a worse reaching quality than infants without CP, reflected for example by more movement units (factor 1.52, 95% CI 1.16-1.99) and smaller transport movement units (factor 1.86, 95% CI 1.20-2.90). Total head sway of infants with and without CP was similar, but infants with CP used more head movement units to achieve stability. The rate of developmental change in infants with and without CP was similar. Around 13 months, head control and reaching quality were interrelated; both were associated with IMP-scores. INTERPRETATION: Infants with CP showed a worse kinematic reaching quality and head stability throughout infancy from early age onwards than VHR-infants without CP, implying that kinematically they do not grow into a deficit, but exhibit deficits from early infancy on. WHAT THIS PAPER ADDS: Reaching quality improves throughout infancy in all infants at high risk (VHR-infants). Infants with cerebral palsy (CP) show a worse reaching quality than VHR-infants without CP. Infants with CP achieve head stability differently from infants without CP. Infants with CP exhibit kinematic reaching problems from early age onwards.

Item does not contain fulltext, BACKGROUND: Following our clinical observation of tonic responses in response to the knee jerk in infants at very high risk for cerebral palsy (VHR infants), we systematically studied tonic responses, clonus, and reflex irradiation. We questioned (i) whether these responses occurred more often in VHR infants than in typically developing (TD) infants, and (ii) whether they were associated with abnormal general movement quality. METHODS: Twenty-four VHR and 26 TD infants were assessed around 3 mo corrected age. Surface electromyograms of leg, trunk, neck, and arm muscles were recorded while eliciting the knee jerk. All assessments were video-recorded. RESULTS: VHR infants more often than TD infants showed tonic responses in the ipsilateral quadriceps and hamstring (Mann-Whitney U; P = 0.0005 and P = 0.0009), clonus (Chi-square; P = 0.0005) and phasic responses in the contralateral quadriceps and hamstring (Mann-Whitney U; P = 0.002 and P = 0.0003, respectively). Widespread reflex irradiation occurred in VHR and TD infants. Definitely abnormal general movements and stiff movements were associated with tonic responses (Mann-Whitney U; P = 0.0005, P = 0.007, respectively) and clonus (Mann-Whitney U; P = 0.003 and P = 0.0005) in the ipsilateral quadriceps. CONCLUSION: Similar to clonus, tonic responses may be regarded as a marker of a loss of supraspinal control. Reflex irradiation primarily is a neurodevelopmental phenomenon of early ontogeny.

Contains fulltext : 165777.pdf (publisher's version ) (Closed access), AIM: Having observed slow pupillary light responses (PLRs) in infants at high risk of cerebral palsy, we retrospectively evaluated whether these were associated with specific brain lesions or unfavourable outcomes. METHODS: We carried out neurological examinations on 30 infants at very high risk of cerebral palsy five times until the corrected age of 21 months, classifying each PLR assessment as normal or slow. The predominant reaction during development was determined for each infant. Neonatal brain scans were classified based on the type of brain lesion. Developmental outcome was evaluated at 21 months of corrected age with a neurological examination, the Bayley Scales of Infant Development Second Edition and the Infant Motor Profile. RESULTS: Of the 30 infants, 16 developed cerebral palsy. Predominantly slow PLRs were observed in eight infants and were associated with periventricular leukomalacia (p = 0.007), cerebral palsy (p = 0.039), bilateral cerebral palsy (p = 0.001), poorer quality of motor behaviour (p < 0.0005) and poorer cognitive outcome (p = 0.045). CONCLUSION: This explorative study suggested that predominantly slow PLR in infants at high risk of cerebral palsy were associated with periventricular leukomalacia and poorer developmental outcome. Slow PLR might be an expression of white matter damage, resulting in dysfunction of the complex cortico-subcortical circuitries.

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals.

This study deals with the question how an insect parasitoid can maximize its fitness through adaptation of its reproductive behaviour. It concentrates on the behaviour of a parasitoid after it has encountered a host. Optimal exploitation of individual hosts is emphasized rather than a maximization of the number of parasitized hosts.In Chapter I the topic of optimization of behaviour is introduced in relation to the study of insect parasitoids. The choice of the experimental animals is explained and behavioural alternatives of the parasitoid are discussed. In this study the number of granddaughters is taken as a measure of fitness.The chalcidoid wasp Colpoclypeus florus (Hym., Eulophidae) is a gregarious ectoparasitoid of larvae of at least 32 species of leafrollers (Lep., Tortricidae; Table 2.1). Host plants are predominantly trees and shrubs. The parasitoid has a west palearctic distribution (Fig. 2.1) and is rare in natural or semi-natural habitats. However, C. florus can be found in abundance in intensively cultivated habitats. In the Netherlands they are found especially in apple orchards, during outbreaks of the summer fruit tortrix moth, Adoxophyes orana . Efforts to control A. orana with mass releases of the parasitoid had not been successful. However, the parasitoid is considered as promising by those working on integrated control and more biological information was required.In Chapter 2 the parasitization behaviour, development and phenology of the parasitoid is described. The experimental host ( A. orana ), general techniques and conditions are also described. Field experiments were carried out in an experimental apple orchard. Unlike many internal and external parasitoids, C. florus has the unusual habit of ovipositing beside instead of on or in the host. This offers the opportunity to manipulate the eggs and hosts separately. In addition, the number of hosts parasitized by an individual in the field is low, about 2-3 hosts per female, and the time taken