The golden hour of sepsis: An in-depth analysis of sepsis-related maternal mortality in middle-income country Suriname

Research into fetal development and medicin

Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring

Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a mother to her child. The chromothripsis in the mothers resulted in completely balanced rearrangements involving 8-23 breakpoint junctions across three to five chromosomes. Two mothers did not show any phenotypic abnormalities, although 3-13 protein-coding genes were affected by breakpoints. Unbalanced but stable transmission of a subset of the derivative chromosomes caused apparently de novo complex copy-number changes in two children. This resulted in gene-dosage changes, which are probably responsible for the severe congenital phenotypes of these two children. In contrast, the third child, who has a severe congenital disease, harbored all three chromothripsis chromosomes from his healthy mother, but one of the chromosomes acquired de novo rearrangements leading to copy-number changes. These results show that the human genome can tolerate extreme reshuffling of chromosomal architecture, including breakage of multiple protein-coding genes, without noticeable phenotypic effects. The presence of chromothripsis in healthy individuals affects reproduction and is expected to substantially increase the risk of miscarriages, abortions, and severe congenital disease. © 2015 The American Society of Human Genetics

Partner-independent fusion gene detection by multiplexed CRISPR/Cas9 enrichment and long-read Nanopore sequencing

Fusion genes are hallmarks of various cancer types and important determinants for diagnosis, prognosis and treatment possibilities. The promiscuity of fusion genes with respect to partner choice and exact breakpoint-positions restricts their detection in the diagnostic setting, even for known and recurrent fusion gene configurations. To accurately identify these gene fusions in an unbiased manner, we developed FUDGE: a FUsion gene Detection assay from Gene Enrichment. FUDGE couples target-selected and strand-specific CRISPR/Cas9 activity for enrichment and detection of fusion gene drivers (e.g. BRAF, EWSR1, KMT2A/MLL) - without prior knowledge of fusion partner or breakpoint-location - to long-read Nanopore sequencing. FUDGE encompasses a dedicated bioinformatics approach (NanoFG) to detect fusion genes from Nanopore sequencing data. Our strategy is flexible with respect to target choice and enables multiplexed enrichment for simultaneous analysis of several genes in multiple samples in a single sequencing run. We observe on average a 508 fold on-target enrichment and identify fusion breakpoints at nucleotide resolution - all within two days. We demonstrate that FUDGE effectively identifies fusion genes in cancer cell lines, tumor samples and on whole genome amplified DNA irrespective of partner gene or breakpoint-position in 100% of cases. Furthermore, we show that FUDGE is superior to routine diagnostic methods for fusion gene detection. In summary, we have developed a rapid and versatile fusion gene detection assay, providing an unparalleled opportunity for pan-cancer detection of fusion genes in routine diagnostics

Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing

Fusion genes are hallmarks of various cancer types and important determinants for diagnosis, prognosis and treatment. Fusion gene partner choice and breakpoint-position promiscuity restricts diagnostic detection, even for known and recurrent configurations. Here, we develop FUDGE (FUsion Detection from Gene Enrichment) to accurately and impartially identify fusions. FUDGE couples target-selected and strand-specific CRISPR-Cas9 activity for fusion gene driver enrichment - without prior knowledge of fusion partner or breakpoint-location - to long read nanopore sequencing with the bioinformatics pipeline NanoFG. FUDGE has flexible target-loci choices and enables multiplexed enrichment for simultaneous analysis of several genes in multiple samples in one sequencing run. We observe on-average 665 fold breakpoint-site enrichment and identify nucleotide resolution fusion breakpoints within 2 days. The assay identifies cancer cell line and tumor sample fusions irrespective of partner gene or breakpoint-position. FUDGE is a rapid and versatile fusion detection assay for diagnostic pan-cancer fusion detection

A systematic analysis of oncogenic gene fusions in primary colon cancer

Genomic rearrangements that give rise to oncogenic gene fusions can offer actionable targets for cancer therapy. Here we present a systematic analysis of oncogenic gene fusions among a clinically well-characterized, prospectively collected set of 278 primary colon cancers spanning diverse tumor stages and clinical outcomes. Gene fusions and somatic genetic variations were identified in fresh frozen clinical specimens by Illumina RNA-sequencing, the STAR fusion gene detection pipeline, and GATK RNA-seq variant calling. We considered gene fusions to be pathogenically relevant when recurrent, producing divergent gene expression (outlier analysis), or as functionally important (e.g., kinase fusions). Overall, 2.5% of all specimens were defined as harboring a relevant gene fusion (kinase fusions 1.8%). Novel configurations of BRAF, NTRK3, and RET gene fusions resulting from chromosomal translocations were identified. An R-spondin fusion was found in only one tumor (0.35%), much less than an earlier reported frequency of 10% in colorectal cancers. We also found a novel fusion involving USP9X-ERAS formed by chromothripsis and leading to high expression of ERAS, a constitutively active RAS protein normally expressed only in embryonic stem cells. This USP9X–ERAS fusion appeared highly oncogenic on the basis of its ability to activate AKT signaling. Oncogenic fusions were identified only in lymph node–negative tumors that lacked BRAF or KRAS mutations. In summary, we identified several novel oncogenic gene fusions in colorectal cancer that may drive malignant development and offer new targets for personalized therapy

Characteristics of de novo structural changes in the human genome

Small insertions and deletions (indels) and large structural variations (SVs) are major contributors to human genetic diversity and disease. However, mutation rates and characteristics of de novo indels and SVs in the general population have remained largely unexplored. We report 332 validated de novo structural changes identified in whole genomes of 250 families, including complex indels, retrotransposon insertions, and interchromosomal events. These data indicate a mutation rate of 2.94 indels (120 bp) and 0.16 SVs (>20 bp) per generation. De novo structural changes affect on average 4.1 kbp of genomic sequence and 29 coding bases per generation, which is 91 and 52 times more nucleotides than de novo substitutions, respectively. This contrasts with the equal genomic footprint of inherited SVs and substitutions. An excess of structural changes originated on paternal haplotypes. Additionally, we observed a nonuniform distribution of de novo SVs across offspring. These results reveal the importance of different mutational mechanisms to changes in human genome structure across generations

Clinical characteristics of women captured by extending the definition of severe postpartum haemorrhage with 'refractoriness to treatment': a cohort study

Background: The absence of a uniform and clinically relevant definition of severe postpartum haemorrhage hampers comparative studies and optimization of clinical management. The concept of persistent postpartum haemorrhage, based on refractoriness to initial first-line treatment, was proposed as an alternative to common definitions that are either based on estimations of blood loss or transfused units of packed red blood cells (RBC). We compared characteristics and outcomes of women with severe postpartum haemorrhage captured by these three types of definitions. Methods: In this large retrospective cohort study in 61 hospitals in the Netherlands we included 1391 consecutive women with postpartum haemorrhage who received either ≥4 units of RBC or a multicomponent transfusion. Clinical characteristics and outcomes of women with severe postpartum haemorrhage defined as persistent postpartum haemorrhage were compared to definitions based on estimated blood loss or transfused units of RBC within 24 h following birth. Adverse maternal outcome was a composite of maternal mortality, hysterectomy, arterial embolisation and intensive care unit admission. Results: One thousand two hundred sixty out of 1391 women (90.6%) with postpartum haemorrhage fulfilled the definition of persistent postpartum haemorrhage. The majority, 820/1260 (65.1%), fulfilled this definition within 1 h following birth, compared to 819/1391 (58.7%) applying the definition of ≥1 L blood loss and 37/845 (4.4%) applying the definition of ≥4 units of RBC. The definition persistent postpartum haemorrhage captured 430/471 adverse maternal outcomes (91.3%), compared to 471/471 (100%) for ≥1 L blood loss and 383/471 (81.3%) for ≥4 units of RBC. Persistent postpartum haemorrhage did not capture all adverse outcomes because of missing data on timing of initial, first-line treatment. Conclusion: The definition persistent postpartum haemo

De staat van de huisartsenzorg: beschrijving van de stand van zaken in de huisartsenzorg en voorstel van een serie toezichtindicatoren voor de huisartsenzorg.

Als elke huisartspraktijk een door het NIVEL en de WOK (Centre for Quality of Care Research) ontwikkelde lijst invult, kan de Inspectie voor de Gezondheidszorg (IGZ) beter beoordelen welke praktijken voor een bezoek van een inspecteur in aanmerking komen. Op de lijst staan aspecten van de huisartsenzorg die kwantitatief gemeten kunnen worden (risico- of kwaliteits-indicatoren) en die informatie geven over de kwaliteit van de zorg. Het doel van het onderzoek was om het toezicht door de Inspectie op de Nederlandse huisartsen te verbeteren. De Inspectie wil gerichter toezicht houden, want er zijn veel huisartsen en weinig inspecteurs. Bij inspectie op basis van toeval krijgt elke huisarts gemiddeld één keer in de 50 jaar een inspecteur op bezoek. Met de lijst van kwaliteits-indicatoren kan niet worden vastgesteld wat een goede huisartsenpraktijk is en wat niet, de lijst heeft alleen een signalerende functie. Ook het Ministerie van VWS en het Nederlands Huisartsen Genootschap (NHG) zijn overigens bezig met het ontwikkelen van kwaliteits-indicatoren om de kwaliteit van individuele huisartsen en/of huisartsenpraktijken onderling te kunnen vergelijken worden. Op die lijst staan onder andere de volgende zaken: het percentage patiënten dat binnen maximaal twee tot drie werkdagen na aanvraag een consult met de huisarts heeft, het aandeel huisbezoeken per 1000 ingeschreven patiënten, het percentage patiënten dat na het consult tevreden is over de informatie die de huisarts gegeven heeft, het aantal verwijzingen (naar bijvoorbeeld de fysiotherapeut of de medisch specialist) per 1000 patiënten, het aantal voorschriften antibiotica per 1000 ingeschreven patiënten, het percentage patiënten met suikerziekte in de praktijk, het percentage patiënten van 65 jaar en ouder die een griepvaccinatie hebben gehad. NIVEL heeft de checklist ontwikkeld in samenwerking met de WOK (Centre for quality of care research) in opdracht van de Inspectie voor de Gezondheidszorg (IGZ). De gemiddelde huisarts is een goede huisarts Het NIVEL heeft de ontwikkelde checklist met kwaliteits-indicatoren vervolgens gebruikt om de praktijken te beoordelen van huisartsen die hebben meegedaan aan de Nationale Studie van ziekten en verrichtingen in de huisartspraktijk (NS2). Hieruit blijkt dat de meeste Nederlandse huisartsen goed toegankelijk zijn, terughoudend zijn met het voorschrijven van antibiotica en met verwijzen, goed scoren op preventie (griepvaccinatie en screening op baarmoederhalskanker) en de Wet op de Geneeskundige Behandelingsovereenkomst (WGBO) goed naleven. Er zijn echter wel (soms aanzienlijke) verschillen tussen huisartsen onderling. Deze verschillen houden in het algemeen geen verband met specifieke, zichtbare kenmerken zoals het werken in een solopraktijk of in deeltijd. Daarom was het niet mogelijk een profiel van een slechte huisarts op te stellen. Ook is het niet zo dat huisartsen die op één indicator slecht scoren dat ook op andere indicatoren doen. Deels worden de verschillen tussen huisartsen verklaard door verschillen in hun patiëntpopulaties. Zo leggen huisartsen met relatief veel ouderen in hun praktijk meer huisbezoeken af en ook stellen zij vaker dan gemiddeld de diagnose suikerziekte, hoge bloeddruk of verhoogd cholesterol. Methode Bij het onderzoek is onder andere gebruik gemaakt van de Tweede Nationale Studie (NS2), een omvangrijke studie naar ziekten en verrichtingen in de huisartspraktijk die in opdracht van het Ministerie van Volksgezondheid, Welzijn en Sport (VWS) is uitgevoerd door het NIVEL in samenwerking met het RIVM. Voor het onderzoek zijn gegevens verzameld uit 104 huisartspraktijken die deel uitmaken van het Landelijk Informatie Netwerk Huisartsenzorg (LINH.

Protein partitioning driven by excluded-volume interactions in an aqueous nonionic micellar-gel system

The separation and purification of biomolecules in aqueous media driven by excluded-volume interactions is a well-established concept. In this article we propose a new separations method, based on excluded-volume principles, consisting of an aqueous micellar—gel system (AMGS). Specifically, an outer aqueous phase containing cylindrically shaped micelles of the nonionic surfactant n-decyl tetra (ethylene oxide) (C10E4) is physically separated from an inner aqueous phase defined by the interior volume of gel beads, from which the micelles are completely excluded because of their shape and size. In the AMGS, the concentration of the micelles outside the gel beads is sufficiently high that the volume excluded to a biomolecule in the solution external to the gel beads is much larger than that within the gel beads. Accordingly, when biomolecules are introduced into the AMGS, they partition preferentially into the gel-bead phase, according to their sizes, as a result of the greater effect of the excluded-volume interactions with the C10E4 micelles present in the aqueous phase outside the gel beads. The new AMGS is more versatile and adaptable than the conventional two-phase aqueous C10E4 micellar system because the micelle volume fraction is independent of the temperature and because the effects of entrainment are eliminated. After demonstrating the experimental feasibility of creating the new AMGS, the three proteins myoglobin, ovalbumin, and BSA-FITC, and the enzyme G6PD, were partitioned in the AMGS and their partitioning behavior was found to follow the experimental excluded-volume trends dictated by the interactions of the biomolecules with the C10E4 micelles. Specifically, the measured partition coefficients of the four biomolecules into the micellar phase were found to be less than unity and to decrease with increasing biomolecule size. A theoretical description of the partitioning behavior of the biomolecules in the new AMGS was formulated, based on excluded-volume considerations, and the predicted biomolecule partition coefficients were found to compare favorably with those measured for the four biomolecules studied

Colloidal interactions in liquid CO2 - A dry-cleaning perspective

Liquid CO2 is a viable alternative for the toxic and environmentally harmful solvents traditionally used in dry-cleaning industry. Although liquid CO2 dry-cleaning is being applied already at a commercial scale, it is still a relatively young technique which poses many challenges. The focus of this review is on the causes of the existing problems and directions to solve them. After presenting an overview of the state-of-the-art, we analyze the detergency challenges from the fundamentals of colloid and interface science. The properties of liquid CO2 such as dielectric constant, density, Hamaker constant, refractive index, viscosity and surface tension are presented and in the subsequent chapters their effects on CO2 dry-cleaning operation are delineated. We show, based on theory, that the van der Waals forces between a model soil (silica) and model fabric (cellulose) through liquid CO2 are much stronger compared to those across water or the traditional dry-cleaning solvent PERC (perchloroethylene). Prevention of soil particle redeposition in liquid CO2 by electrostatic stabilization is challenging and the possibility of using electrolytes having large anionic parts is discussed. Furthermore, the role of different additives used in dry-cleaning, such as water, alcohol and surfactants, is reviewed. Water is not only used as an aid to remove polar soils, but also enhances adhesion between fabric and soil by forming capillary bridges. Its role as a minor component in liquid CO2 is complex as it depends on many factors, such as the chemical nature of fabrics and soil, and also on the state of water itself, whether present as molecular solution in liquid CO2 or phase separated droplets. The phenomena of wicking and wetting in liquid CO2 systems are predicted from the Washburn–Lucas equation for fabrics of various surface energies and pore sizes. It is shown that nearly complete wetting is desirable for good detergency. The effect of mechanical action and fluid dynamic conditions on dry-cleaning is analyzed theoretically. From this it follows that in liquid CO2 an order of magnitude higher Reynold's number is required to exceed the binding forces between fabric and soil as opposed to PERC or water, mainly due to the strong van der Waals forces and the low viscosity of CO2 at dry-cleaning operational conditions