Modelling human blastocysts by reprogramming fibroblasts into iBlastoids.

Human pluripotent and trophoblast stem cells have been essential alternatives to blastocysts for understanding early human development1-4. However, these simple culture systems lack the complexity to adequately model the spatiotemporal cellular and molecular dynamics that occur during early embryonic development. Here we describe the reprogramming of fibroblasts into in vitro three-dimensional models of the human blastocyst, termed iBlastoids. Characterization of iBlastoids shows that they model the overall architecture of blastocysts, presenting an inner cell mass-like structure, with epiblast- and primitive endoderm-like cells, a blastocoel-like cavity and a trophectoderm-like outer layer of cells. Single-cell transcriptomics further confirmed the presence of epiblast-, primitive endoderm-, and trophectoderm-like cells. Moreover, iBlastoids can give rise to pluripotent and trophoblast stem cells and are capable of modelling, in vitro, several aspects of the early stage of implantation. In summary, we have developed a scalable and tractable system to model human blastocyst biology; we envision that this will facilitate the study of early human development and the effects of gene mutations and toxins during early embryogenesis, as well as aiding in the development of new therapies associated with in vitro fertilization.

Reprogramming roadmap reveals route to human induced trophoblast stem cells.

The reprogramming of human somatic cells to primed or naive induced pluripotent stem cells recapitulates the stages of early embryonic development1-6. The molecular mechanism that underpins these reprogramming processes remains largely unexplored, which impedes our understanding and limits rational improvements to reprogramming protocols. Here, to address these issues, we reconstruct molecular reprogramming trajectories of human dermal fibroblasts using single-cell transcriptomics. This revealed that reprogramming into primed and naive pluripotency follows diverging and distinct trajectories. Moreover, genome-wide analyses of accessible chromatin showed key changes in the regulatory elements of core pluripotency genes, and orchestrated global changes in chromatin accessibility over time. Integrated analysis of these datasets revealed a role for transcription factors associated with the trophectoderm lineage, and the existence of a subpopulation of cells that enter a trophectoderm-like state during reprogramming. Furthermore, this trophectoderm-like state could be captured, which enabled the derivation of induced trophoblast stem cells. Induced trophoblast stem cells are molecularly and functionally similar to trophoblast stem cells derived from human blastocysts or first-trimester placentas7. Our results provide a high-resolution roadmap for the transcription-factor-mediated reprogramming of human somatic cells, indicate a role for the trophectoderm-lineage-specific regulatory program during this process, and facilitate the direct reprogramming of somatic cells into induced trophoblast stem cells.

Dietary Fiber and Microbiota Metabolite Receptors Enhance Cognition and Alleviate Disease in the 5xFAD Mouse Model of Alzheimer's Disease.

Alzheimer's disease (AD) is a neurodegenerative disorder with poorly understood etiology. AD has several similarities with other "Western lifestyle" inflammatory diseases, where the gut microbiome and immune pathways have been associated. Previously, we and others have noted the involvement of metabolite-sensing GPCRs and their ligands, short-chain fatty acids (SCFAs), in protection of numerous Western diseases in mouse models, such as Type I diabetes and hypertension. Depletion of GPR43, GPR41, or GPR109A accelerates disease, whereas high SCFA yielding diets protect in mouse models. Here, we extended the concept that metabolite-sensing receptors and SCFAs may be a more common protective mechanism against Western diseases by studying their role in AD pathogenesis in the 5xFAD mouse model. Both male and female mice were included. Depletion of GPR41 and GPR43 accelerated cognitive decline and impaired adult hippocampal neurogenesis in 5xFAD and WT mice. Lack of fiber/SCFAs accelerated a memory deficit, whereas diets supplemented with high acetate and butyrate (HAMSAB) delayed cognitive decline in 5xFAD mice. Fiber intake impacted on microglial morphology in WT mice and microglial clustering phenotype in 5xFAD mice. Lack of fiber impaired adult hippocampal neurogenesis in both W and AD mice. Finally, maternal dietary fiber intake significantly affects offspring's cognitive functions in 5xFAD mice and microglial transcriptome in both WT and 5xFAD mice, suggesting that SCFAs may exert their effect during pregnancy and lactation. Together, metabolite-sensing GPCRs and SCFAs are essential for protection against AD, and reveal a new strategy for disease prevention.Significance Statement Alzheimer's disease (AD) is one of the most common neurodegenerative diseases; currently, there is no cure for AD. In our study, short-chain fatty acids and metabolite receptors play an important role in cognitive function and pathology in AD mouse model as well as in WT mice. SCFAs also impact on microglia transcriptome, and immune cell recruitment. Out study indicates the potential of specialized diets (supplemented with high acetate and butyrate) releasing high amounts of SCFAs to protect against disease.

The INFINITY study protocol: a retrospective cohort study on decision making and clinical impact of biomarker-driven precision oncology in routine clinical practice.

BACKGROUND: Precision oncology, defined as treatment of patients with targeted therapies matched to specific molecular alterations, has entered routine clinical practice. Particularly in patients with advanced cancer or hematologic malignancies, for whom no further standard therapies are available, this approach is increasingly applied as last resort option outside of the approved indication. However, data on patient outcomes are not systematically collected, analyzed, reported, and shared. We have initiated the INFINITY registry to provide evidence from routine clinical practice to fill this knowledge gap. METHODS: INFINITY is a retrospective, non-interventional cohort study conducted at approximately 100 sites in Germany (office-based oncologists/hematologists and hospitals). We aim to include 500 patients with advanced solid tumors or hematologic malignancies who received a non-standard targeted therapy based on potentially actionable molecular alterations or biomarkers. INFINITY aims to provide insights into the use of precision oncology in routine clinical practice within Germany. We systematically collect details on patient and disease characteristics, molecular testing, clinical decision-making, treatment, and outcome. DISCUSSION: INFINITY will provide evidence on the current biomarker landscape driving treatment decisions in routine clinical care. It will also provide insights on effectiveness of precision oncology approaches in general, and of specific drug class/alteration matches used outside their approved indications. TRIAL REGISTRATION: The study is registered at ClinicalTrials.gov, NCT04389541.

Survival after secondary liver resection in metastatic colorectal cancer: Comparing data of three prospective randomized European trials (LICC, CELIM, FIRE-3).

Metastatic colorectal cancer (mCRC) patients with liver-limited disease (LLD) have a chance of long-term survival and potential cure after hepatic metastasectomy. However, the appropriate postoperative treatment strategy is still controversial. The CELIM and FIRE-3 studies demonstrated that secondary hepatic resection significantly improved overall survival (OS). The objective of this analysis was to compare these favorable outcome data with recent results from the LICC trial investigating the antigen-specific cancer vaccine tecemotide (L-BLP25) as adjuvant therapy in mCRC patients with LLD after R0/R1 resection. Data from mCRC patients with LLD and secondary hepatic resection from each study were analyzed for efficacy outcomes based on patient characteristics, treatment and surveillance after surgery. In LICC, 40/121 (33%) patients, in CELIM 36/111 (32%) and in FIRE-3-LLD 29/133 (22%) patients were secondarily resected, respectively. Of those, 31 (77.5%) patients in LICC and all patients in CELIM were R0 resected. Median disease-free survival after resection was 8.9 months in LICC, 9.9 months in CELIM. Median OS in secondarily resected patients was 66.1 months in LICC, 53.9 months in CELIM and 56.2 months in FIRE-3-LLD. Median age was about 5 years less in LICC compared to CELIM and FIRE-3. Secondarily resected patients of LICC, CELIM and FIRE-3 showed an impressive median survival with a tendency for improved survival for patients in the LICC trial. A younger patient cohort but also more selective surgery, improved resection techniques, deep responses and a close surveillance program after surgery in the LICC trial may have had a positive impact on survival.

[Reference values in isometric strength diagnostics : Measurement of core strength values in patients with back pain]. / Referenzwerte in der isometrischen Kraftdiagnostik : Messung von Rumpfkraftwerten bei Patienten mit Rückenschmerzen.

OBJECTIVE: Isometric strength testing is known as a valid and reliable tool in the context of functional diagnostics and quality control for chronic low back pain rehabilitation, but reference values differ markedly between varied assessment devices, depending on their biomechanical lever arm framework. This study aimed to evaluate sex and age-specific isometric peak force reference values of trunk muscle functions in all dimensions using the Myoline® test device (Diers, Schlangenbad, Germany). MATERIAL AND METHODS: In a retrospective cross-sectional study, data of 678 (541 females, 137 males) age-clustered (18-35, 36-50, 51-65 years) low back pain patients (ICD-10: M54) were analyzed referring to their absolute (N) and body weight related (N/kg) isometric maximum peak forces in all spatial dimensions (flexion, extension, rotation, lateral flexion) and the corresponding ratios (M ± SD, 95% CI), accompanied by sex and age-related effect analyses (two-way ANOVA). RESULTS: Male and younger patients were significantly stronger than females and older patients (p < 0.05), but none of the ratios differed significantly between any sex or age cluster (p > 0.05). The flexion/extension ratio showed a 1:2 relation, and the rotation and lateral flexion ratios demonstrated a 1:1 relation, but all ratios varied markedly (30-50%). CONCLUSIONS: The demonstrated data represented a special norm for sex and age clustered low back pain patients assessed with the recent Myoline® test device. The markedly varying peak forces and their ratios underlined the individual diversity and heterogeneous state of functional capacities within low back pain patients.

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly.

The identification of genomic rearrangements with high sensitivity and specificity using massively parallel sequencing remains a major challenge, particularly in precision medicine and cancer research. Here, we describe a new method for detecting rearrangements, GRIDSS (Genome Rearrangement IDentification Software Suite). GRIDSS is a multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph-based assembler. By combining assembly, split read, and read pair evidence using a probabilistic scoring, GRIDSS achieves high sensitivity and specificity on simulated, cell line, and patient tumor data, recently winning SV subchallenge #5 of the ICGC-TCGA DREAM8.5 Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods while matching or exceeding their sensitivity. GRIDSS identifies nontemplate sequence insertions, microhomologies, and large imperfect homologies, estimates a quality score for each breakpoint, stratifies calls into high or low confidence, and supports multisample analysis.

Trapped-ion toolkit for studies of quantum harmonic oscillators under extreme conditions.

Many phenomena described in relativistic quantum field theory are inaccessible to direct observations, but analogue processes studied under well-defined laboratory conditions can present an alternative perspective. Recently, we demonstrated an analogy of particle creation using an intrinsically robust motional mode of two trapped atomic ions. Here, we substantially extend our classical control techniques by implementing machine-learning strategies in our platform and, consequently, increase the accessible parameter regime. As a proof of methodology, we present experimental results of multiple quenches and parametric modulation of an unprotected motional mode of a single ion, demonstrating the increased level of real-time control. In combination with previous results, we enable future experiments that may yield entanglement generation using a process in analogy to Hawking radiation. This article is part of a discussion meeting issue 'The next generation of analogue gravity experiments'.

[Effects and sustainability of knee school : 2-year results of a secondary prevention program for gonarthrosis]. / Effekte und Nachhaltigkeit des Kniekollegs : 2-Jahres-Ergebnisse eines Sekundärpräventionsprogramms bei Gonarthrose.

BACKGROUND: Craftsmen and workers in the construction industry are at an increased risk of developing gonarthrosis due to their work-related burdens. In order to maintain the ability to work, occupational co-operative measures for secondary prevention can be carried out (BG Bau/Kniekolleg). The aim was to evaluate the efficacy after 2 years, depending on the degree of exercise adherence. MATERIAL AND METHODS: In a repeated measurement design (T1 before, T2 after knee school, T3 after 1 year, T4 after 2 years), 140 construction patients were assessed for their dynamic muscular strength (knee extension, 60°/s,); their quality of life (SF-36) and characteristics for gonarthrosis (WOMAC) were evaluated using analyses of variances, whereby one group trained after the knee training in the gym with instruction (Gr. 1 n = 63), one group completed a home-training program (Gr. 2 n = 38), and one group completed exercises outside of knee school (Gr.3 n = 39). RESULTS: For all parameters, significant acute efficacy and 2­year sustainability effects were observed (p ≤ 0.05, d: 0.2-0.8). There was no interaction with adherence during training after knee school (p > 0.05). CONCLUSION: Knee school has proved to be effective in the long term, leading to a critical questioning of future research, why there are no differences between guided, reduced or even missing long-term maintenance training.

Phonon Pair Creation by Inflating Quantum Fluctuations in an Ion Trap.

Quantum theory predicts intriguing dynamics during drastic changes of external conditions. We switch the trapping field of two ions sufficiently fast to tear apart quantum fluctuations, i.e., create pairs of phonons and, thereby, squeeze the ions' motional state. This process can be interpreted as an experimental analog to cosmological particle creation and is accompanied by the formation of spatial entanglement. Hence, our platform allows one to study the causal connections of squeezing, pair creation, and entanglement and might permit one to cross-fertilize between concepts in cosmology and applications of quantum information processing.

A forward genetic screen identifies a negative regulator of rapid Ca2+-dependent cell egress (MS1) in the intracellular parasite Toxoplasma gondii.

Toxoplasma gondii, like all apicomplexan parasites, uses Ca2+ signaling pathways to activate gliding motility to power tissue dissemination and host cell invasion and egress. A group of "plant-like" Ca2+-dependent protein kinases (CDPKs) transduces cytosolic Ca2+ flux into enzymatic activity, but how they function is poorly understood. To investigate how Ca2+ signaling activates egress through CDPKs, we performed a forward genetic screen to isolate gain-of-function mutants from an egress-deficient cdpk3 knockout strain. We recovered mutants that regained the ability to egress from host cells that harbored mutations in the gene Suppressor of Ca2+-dependent Egress 1 (SCE1). Global phosphoproteomic analysis showed that SCE1 deletion restored many Δcdpk3-dependent phosphorylation events to near wild-type levels. We also show that CDPK3-dependent SCE1 phosphorylation is required to relieve its suppressive activity to potentiate egress. In summary, our work has uncovered a novel component and suppressor of Ca2+-dependent cell egress during Toxoplasma lytic growth.

HYSYS: have you swapped your samples?

Motivation: The application of a genomics assay to samples from a cohort is a frequently applied experimental design in cancer genomics studies. The collection and analysis of cancer sequencing data in the clinical setting is an elaborate process that may involve consenting patients, obtaining possibly-multiple DNA samples, sequencing and analysis. Many of these steps are manual. At any stage mistakes can occur that cause a DNA sample to be labelled incorrectly. However, there is a paucity of methods in the literature to identify such swaps specifically in cancer studies. Results: Here, we introduce a simple method, HYSYS, to estimate the relatedness of samples and test for sample swaps and contamination. The test uses the concordance of homozygous SNPs between samples. The method is motivated by the observation that homozygous germline population variants rarely change in the disease and are not affected by loss of heterozygosity. Our tools include visualization and a testing framework to flag possible sample swaps. We demonstrate the utility of this approach on a small cohort. Availability and Implementation: http://github.com/PapenfussLab/HaveYouSwappedYourSamples. Contact: papenfuss@wehi.edu.au. Supplementary information: Supplementary data are available at Bioinformatics online.

Isoprenoid Quinones Resolve the Stratification of Redox Processes in a Biogeochemical Continuum from the Photic Zone to Deep Anoxic Sediments of the Black Sea.

The stratified water column of the Black Sea serves as a model ecosystem for studying the interactions of microorganisms with major biogeochemical cycles. Here, we provide detailed analysis of isoprenoid quinones to study microbial redox processes in the ocean. In a continuum from the photic zone through the chemocline into deep anoxic sediments of the southern Black Sea, diagnostic quinones and inorganic geochemical parameters indicate niche segregation between redox processes and corresponding shifts in microbial community composition. Quinones specific for oxygenic photosynthesis and aerobic respiration dominate oxic waters, while quinones associated with thaumarchaeal ammonia oxidation and bacterial methanotrophy, respectively, dominate a narrow interval in suboxic waters. Quinone distributions indicate highest metabolic diversity within the anoxic zone, with anoxygenic photosynthesis being a major process in its photic layer. In the dark anoxic layer, quinone profiles indicate the occurrence of bacterial sulfur and nitrogen cycling, archaeal methanogenesis, and archaeal methanotrophy. Multiple novel ubiquinone isomers, possibly originating from unidentified intra-aerobic anaerobes, occur in this zone. The respiration modes found in the anoxic zone continue into shallow subsurface sediments, but quinone abundances rapidly decrease within the upper 50 cm below the sea floor, reflecting the transition to lower energy availability. In the deep subseafloor sediments, quinone distributions and geochemical profiles indicate archaeal methanogenesis/methanotrophy and potentially bacterial fermentative metabolisms. We observed that sedimentary quinone distributions track lithology, which supports prior hypotheses that deep biosphere community composition and metabolisms are determined by environmental conditions during sediment deposition.IMPORTANCE Microorganisms play crucial roles in global biogeochemical cycles, yet we have only a fragmentary understanding of the diversity of microorganisms and their metabolisms, as the majority remains uncultured. Thus, culture-independent approaches are critical for determining microbial diversity and active metabolic processes. In order to resolve the stratification of microbial communities in the Black Sea, we comprehensively analyzed redox process-specific isoprenoid quinone biomarkers in a unique continuous record from the photic zone through the chemocline into anoxic subsurface sediments. We describe an unprecedented quinone diversity that allowed us to detect distinct biogeochemical processes, including oxygenic photosynthesis, archaeal ammonia oxidation, aerobic methanotrophy, and anoxygenic photosynthesis in defined geochemical zones.

Spinal posture changes using dynamic rasterstereography during the modified Matthiass test discriminate between postural weak and strong healthy children (10-14 years): a pilot study.

The aim of this pilot study was to investigate whether the clinical Matthiass test can be objectified by means of dynamic rasterstereography in children. We aimed at discriminating between postural weak and strong children. Dynamic rasterstereography was used to capture sagittal spinal posture changes during the modified Matthiass test (mMT). Primary outcomes were spinal posture changes (trunk inclination, kyphotic and lordotic angles) during the test. Two-step cluster analysis was run jointly on the three primary outcomes. Data of 101 healthy children (10-14 years, 46% girls) were assessed. Cluster analysis identified two groups of participants with significantly different postural performance levels during the mMT (low vs. high performers). Low performers showed a higher increase in backward lean, as well as kyphosis and lordosis (4°-5°, respectively) when compared to high performers. The two performance groups were age-, BMI-, and activity-matched.Conclusion: This pilot study established preliminary normative data on spinal posture changes during the Matthiass test (high performers) and provided corresponding cutoff values for postural weakness (low performers). These results could provide a basis for future longitudinal and interventional studies targeting long-term consequences of childhood postural weakness and the prevention of back pain. What is Known: • The prevalence of postural insufficiencies in children is high. • No consensus exists about the postural assessment in children. • A common clinical test to identify postural insufficiency is the Matthiass test yet criticized for its subjective assessment. What is New: • This pilot study objectified the modified Matthiass test by rasterstereography and statistically identified two groups of healthy children with different postural performance levels. • It established preliminary normative data on spinal posture changes and provided corresponding cutoff values for postural weakness.

Spinal postural changes during the modified Matthiass test in healthy children : Interday and interrater reliability of dynamic rasterstereographic measurements.

OBJECTIVE: The Matthiass test serves to identify postural insufficiencies by evaluating the sagittal posture but this subjective assessment may be responsible for different reports on the prevalence of postural insufficiencies in children. Previously, rasterstereography was used to objectify this clinical test. Until now, the coupling of the Matthiass test with rasterstereography has not yet been applied to children and the reliability is unknown; therefore, the objective of our study was to provide interday and interrater reliability of rasterstereographic measurements during dynamic (modified Matthiass test) and static trials (only interday) in healthy children. METHODS: Trunk inclination, kyphotic, and lordotic angles were measured using rasterstereography during static and dynamic trials (modified Matthiass test: 90° shoulder flexion, hand-held load, 5% of body weight). Intraclass correlation coefficients (ICC) were calculated using a two-way mixed model (absolute agreement, average measure). RESULTS: In this study 21 healthy children were assessed (age range 10-12 years). Dynamic rasterstereographic measurements showed fair to good interday and interrater reliability (ICC 0.46-0.70) and static measurements good to excellent interday reliability (ICC 0.63-0.91). CONCLUSION: Dynamic rasterstereography during the modified Matthiass test furnishes reliable data serving to objectify spinal changes of healthy children and detect postural insufficiencies. Additional efforts are needed to investigate how the early detection of postural insufficiencies can help to prevent back pain in children, adolescents and adults.

CLOVE: classification of genomic fusions into structural variation events.

BACKGROUND: A precise understanding of structural variants (SVs) in DNA is important in the study of cancer and population diversity. Many methods have been designed to identify SVs from DNA sequencing data. However, the problem remains challenging because existing approaches suffer from low sensitivity, precision, and positional accuracy. Furthermore, many existing tools only identify breakpoints, and so not collect related breakpoints and classify them as a particular type of SV. Due to the rapidly increasing usage of high throughput sequencing technologies in this area, there is an urgent need for algorithms that can accurately classify complex genomic rearrangements (involving more than one breakpoint or fusion). RESULTS: We present CLOVE, an algorithm for integrating the results of multiple breakpoint or SV callers and classifying the results as a particular SV. CLOVE is based on a graph data structure that is created from the breakpoint information. The algorithm looks for patterns in the graph that are characteristic of more complex rearrangement types. CLOVE is able to integrate the results of multiple callers, producing a consensus call. CONCLUSIONS: We demonstrate using simulated and real data that re-classified SV calls produced by CLOVE improve on the raw call set of existing SV algorithms, particularly in terms of accuracy. CLOVE is freely available from http://www.github.com/PapenfussLab .

2,6-Bis(diazaboryl)pyridine: A Superbasic Sterically Demanding Pyridine Ligand.

Herein a convenient one-pot route to a sterically demanding superbasic pyridine is presented. Functionalization of the 2- and 6-positions with the strongly σ-donating boryl-groups shifts the calculated gas phase basicity of the pyridine nitrogen atom to 1012 kJ mol-1 , which outperforms the "proton sponge" 1,8-bis(dimethylamino)naphthalene (996 kJ mol-1 ). The diazaboryl groups are oriented orthogonally to the pyridine ring and do not block the N-position, which resembles the geometry of commonly used N-heterocyclic carbenes. This allows the substituted pyridine to be used as a neutral N-donor ligand in coordination chemistry that is demonstrated herein with the Lewis adducts of haloboranes. Contrary to NHCs, which can form extraordinarily stable adducts, the pyridine ligand is intended to act as a weaker-coordinating alternative and could allow for alternative ligand chemistry.

Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment.

The distribution of respiratory quinone electron carriers among cultivated organisms provides clues on both the taxonomy of their producers and the redox processes these are mediating. Our study of the quinone inventories of 25 archaeal species belonging to the phyla Eury-, Cren- and Thaumarchaeota facilitates their use as chemotaxonomic markers for ecologically important archaeal clades. Saturated and monounsaturated menaquinones with six isoprenoid units forming the alkyl chain may serve as chemotaxonomic markers for Thaumarchaeota. Other diagnostic biomarkers are thiophene-bearing quinones for Sulfolobales and methanophenazines as functional quinone analogues of the Methanosarcinales. The ubiquity of saturated menaquinones in the Archaea in comparison to Bacteria suggests that these compounds may represent an ancestral and diagnostic feature of the Archaea. Overlap between quinone compositions of distinct thermophilic and halophilic archaea and bacteria may indicate lateral gene transfer. The biomarker potential of thaumarchaeal quinones was exemplarily demonstrated on a water column profile of the Black Sea. Both, thaumarchaeal quinones and membrane lipids showed similar distributions with maxima at the chemocline. Quinone distributions indicate that Thaumarchaeota dominate respiratory activity at a narrow interval in the chemocline, while they contribute only 9% to the microbial biomass at this depth, as determined by membrane lipid analysis.

Capecitabine in the routine first-line treatment of elderly patients with advanced colorectal cancer--results from a non-interventional observation study.

BACKGROUND: The purpose of this observational study was to evaluate feasibility, efficacy results and toxicity observations of capecitabine in routine first line treatment of patients with metastatic colorectal cancer, with particular regard of elderly patients (>75 years of age). METHODS: Patients with colorectal cancer receiving capecitabine as part of their first-line treatment were recorded until detection of disease progression or up to a maximum of 12 cycles on standardized evaluation forms. Additional information on long-term outcomes, progression-free survival, and overall survival were retrieved at two follow-up time points. Obtained data were analyzed with regard to age up to 75 and >75 years of age. There were no specific requirements for patient selection and conduct of therapy, corresponding to the non-interventional nature of the study. RESULTS: In total, 1249 evaluable patients were enrolled in Germany. The median age of the study population was 74 years (range: 21-99). Capecitabine-based combination was administered in 56% of patients in the overall population. The median treatment duration was about 5 months. Severe toxicities occurred rarely without any difference regarding age groups. The most common hematological toxicity was anemia. Gastrointestinal side effects and hand-food-syndrome (HFS) were the most frequent non-hematologic toxicities. Overall response rate (ORR) was significantly higher in the patient group <=75 years compared to patients >75 years of age (38 vs. 32%, p=0.019). Median progression free survival (PFS 9.7 vs. 8.2 months, p=0.00021) and overall survival (OS 31.0 vs. 22.6 months, p<0.0001) was decreased in elderly patients. CONCLUSION: Efficacy and tolerability of capecitabine treatment either as single drug or in various combination regimens, as proven in randomized studies, could be confirmed in a clinical routine setting. Patients older than 75 years may derive a relevant benefit by first line capecitabine-based treatment with good tolerability.

Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads.

MOTIVATION: Methods for detecting somatic genome rearrangements in tumours using next-generation sequencing are vital in cancer genomics. Available algorithms use one or more sources of evidence, such as read depth, paired-end reads or split reads to predict structural variants. However, the problem remains challenging due to the significant computational burden and high false-positive or false-negative rates. RESULTS: In this article, we present Socrates (SOft Clip re-alignment To idEntify Structural variants), a highly efficient and effective method for detecting genomic rearrangements in tumours that uses only split-read data. Socrates has single-nucleotide resolution, identifies micro-homologies and untemplated sequence at break points, has high sensitivity and high specificity and takes advantage of parallelism for efficient use of resources. We demonstrate using simulated and real data that Socrates performs well compared with a number of existing structural variant detection tools. AVAILABILITY AND IMPLEMENTATION: Socrates is released as open source and available from http://bioinf.wehi.edu.au/socrates CONTACT: papenfuss@wehi.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.