Genetic drivers of heterogeneity in type 2 diabetes pathophysiology.

Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes1,2 and molecular mechanisms that are often specific to cell type3,4. Here, to characterize the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study data from 2,535,601 individuals (39.7% not of European ancestry), including 428,452 cases of T2D. We identify 1,289 independent association signals at genome-wide significance (P < 5 × 10-8) that map to 611 loci, of which 145 loci are, to our knowledge, previously unreported. We define eight non-overlapping clusters of T2D signals that are characterized by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type-specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial cells and enteroendocrine cells. We build cluster-specific partitioned polygenic scores5 in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care.

Computational analysis of cancer genome sequencing data.

Distilling biologically meaningful information from cancer genome sequencing data requires comprehensive identification of somatic alterations using rigorous computational methods. As the amount and complexity of sequencing data have increased, so has the number of tools for analysing them. Here, we describe the main steps involved in the bioinformatic analysis of cancer genomes, review key algorithmic developments and highlight popular tools and emerging technologies. These tools include those that identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes. We also discuss issues in experimental design, the strengths and limitations of sequencing modalities and methodological challenges for the future.

Estimating and Presenting Hazard Ratios and Absolute Risks from a Cox Model with Complex Non-linear Interactions.

Interaction analysis is a critical component of clinical and public health research and represents a key topic in precision health and medicine. In applied settings, however, interaction assessment is usually limited to the test of a product term in a regression model, and to the presentation of stratified results over levels of additional covariates. Results stratification often relies on categorizing or making linearity assumptions for continuous covariates, with substantial loss of precision and of relevant information. In time-to-event analysis, moreover, interaction assessment is often limited to the multiplicative hazard scale by inclusion of a product terms in a Cox regression model, disregarding the clinically relevant information that are captured by the absolute risk scale. In this paper we present a user-friendly procedure, based on the prediction of individual absolute risks from the Cox model, for the estimation and presentation of interactive effects on both the multiplicative and additive scale in survival analysis. We describe how to flexibly incorporate interactions with continuous covariates, which potentially operate in a non-linear fashion, we provide software material to replicate our procedure, and discuss different approaches to derive confidence intervals. The presented approach will allow clinical and public health researchers assessing complex relationships between multiple covariates as they relate to a clinical endpoint, and providing a more intuitive and precise depiction of the results in applied research papers focusing on interaction and effect stratification.

Pre- and post-treatment in flexor tendon tenolysis: An observational study.

BACKGROUND: Glide deficit of the distal flexors' tendons following primary repair in zone 1-3 are very common. Adhesions of tendons have multi factorial origins and are closely related to the healing of the affected tissues. The surgical practice used to resolve these complications is tenolysis. PURPOSE: The purpose of this study was to identify and compare the Visual Analog Scale (VAS) relate to pain and Total Active Motion (TAM) of adult patients of both sexes undergoing tenolysis surgery. The results will then be compared to existing research to confirm their significance. STUDY DESIGN: Case-series. METHODS: Retrospective data for TAM and pain VAS were extracted from the medical records for 63 patients (73 fingers) who underwent flexor tenolysis between 2017 and 2019. Data were compared pre-operatively and 3 months after surgery. All patients underwent pre- and post-surgery therapy by hand therapists. RESULTS: The sample presented very encouraging improvements, except in the VAS and active range of motion (AROM) of thumb where some patients maintained the same assessment. The fingers reported statistically significant results, whereas the thumb group did not meet significant criteria. Overall, TAM improved from 134.6° to 196.7 and VAS decreased from 2.7 to 1.2. DISCUSSION: According to the results and the data change between pre- and post-treatment, the sample demonstrated improvements in all areas examined, reporting statistically significant results for the fingers with an improvement of TAM of 62.1° with a percentage value (%TAM) of 75.6%. CONCLUSIONS: A specific treatment for this type of surgery is required for the patients so they can return to their daily and working activities. This article can be used as a starting point for further studies.

[The end of dialysis: the weariness to carry on]. / Médecin et patient face à l'arrêt de la dialyse : la fatigue de continuer.

Voluntary cessation of hemodialysis is a common cause of death in dialysis patients, often occurring related to an alteration in their quality of life. At the same time, psychiatric disorders such as depression or anxiety are common and often underestimated among these patients, that accentuate the suffering and complicate compliance with dialysis. In this paper some psychopathological conditions will be addressed, as well as the question of the patient's ambivalence towards dialysis and the clinical and ethical dilemma of caregivers: respect the patient's choice to stop treatment or keep them alive at all costs? A multidisciplinary approach, including palliative care, is essential to support the reflection and make balanced decisions while respecting patient autonomy.

L'arrêt volontaire de l'hémodialyse est une cause fréquente de décès chez les patients dialysés, survenant souvent en lien avec une détérioration de leur qualité de vie. Parallèlement, les conditions psychiatriques comme la dépression ou l'anxiété sont répandues et souvent sous-estimées chez ces patients, en accentuant la souffrance et en compliquant la compliance à la dialyse. Dans cet article, sont abordées certaines conditions psychopathologiques, ainsi que la question de l'ambivalence du patient face à la dialyse et le dilemme clinique et éthique des soignants: respecter le choix du patient d'arrêter le traitement ou le maintenir en vie à tout prix? Une approche pluridisciplinaire, incluant également les soins palliatifs, est essentielle pour accompagner la réflexion et prendre des décisions pondérées dans le respect de l'autonomie des patients.

[Borderline psychiatric disorder in the general hospital : specificity and clinical challenges]. / Personnalité borderline à l'hôpital général : spécificités et défis cliniques.

Borderline personality disorder (BPD) is a psychiatric condition frequently encountered at the general hospital. This article will focus on the multiple presentation of this mental illness in the aforementioned setting, such as chronic somatic disease, multiple physical complaints as well as chronic pain, all of which that could severely alter the life quality. In this context, especially if there is an unsatisfied need for reinsurance, risk taking behavior (self-harm or harming others) may arise, as well as significant rise of medical costs through multiple medical consultations, longer average lengths of stay and additional complementary examinations. Through a variety of recommendations and a better understanding of BPD, a therapeutic link can be established to facilitate management.

Le trouble de la personnalité borderline (TPB) est une condition psychopathologique fréquente à l'hôpital général. Dans cet article, nous abordons le spectre des présentations cliniques intrahospitalières, dont les pathologies somatiques chroniques, les plaintes physiques multiples et les douleurs chroniques. L'ensemble de ces conditions impactent lourdement la qualité de vie des patients atteints d'un TPB. Lorsque les besoins de réassurance ne sont pas satisfaits, peuvent apparaître des comportements auto et hétéro-agressifs, ainsi qu'une augmentation des coûts médicaux, via une hausse des consultations, des durées de séjour à l'hôpital somatique et des examens complémentaires. Grâce à diverses recommandations et à une meilleure connaissance du TPB, un lien thérapeutique facilitant la prise en charge peut être établi.

Respiratory Intensive Care Unit management and efficacy during the COVID-19 outbreak in Naples, Italy.

The World Health Organization declared the Coronavirus Diseases 2019 (COVID-19) outbreak a global pandemic on March 11, 2020. COVID-19 had an impact on over 500 million people worldwide. According to the American Thoracic Society criteria, the respiratory spectrum of this disease ranges from mild illness to severe pneumonia, with the latter occurring in a not insignificant 15% of patients. A rapid increase in the incidence of COVID-19 pneumonia cases has been observed all over the world, resulting in a saturation of the Intensive Care Unit's capacity (ICUs). Because of this impressive outbreak, the ICU beds and invasive mechanical ventilators reached their capacity. Non-invasive supportive care has become an important option for keeping respiratory conditions under control. As a result, proper healthcare resource management was required to ensure adequate patient care. Respiratory Intensive Care Units (RICUs) have become a useful resource for managing complex patients due to a shortage of ICU capacity. This highlighted the importance of RICUs, where patients with moderate to severe respiratory failure can be treated with non-invasive respiratory support rather than being admitted to the ICU. The clinical outcomes and baseline characteristics of patients admitted to the RICU of Cotugno Hospital, a tertiary referral center in Naples (Italy), from January 2021 to October 2021 are described in this report.

The Effect of PCSK9 (Proprotein Convertase Subtilisin/Kexin Type 9) Inhibition on the Risk of Venous Thromboembolism.

BACKGROUND: The relationship between cholesterol levels and risk of venous thromboembolism (VTE) is uncertain. We set out to determine the effect of PCSK9 (proprotein convertase subtilisin/kexin type 9) inhibition on the risk of VTE, explore potential mechanisms, and examine the efficacy in subgroups with clinically and genetically defined risk. METHODS: We performed a post hoc analysis of the FOURIER trial (Further Cardiovascular Outcomes Research With PCSK9 Inhibition in Subjects With Elevated Risk) testing whether evolocumab reduces the risk of VTE events (deep venous thrombosis or pulmonary embolism). Data from FOURIER and ODYSSEY OUTCOMES (Evaluation of Cardiovascular Outcomes After an Acute Coronary Syndrome During Treatment with Alirocumab) were then combined in a meta-analysis to assess the class effect of PCSK9 inhibition on the risk of VTE. We also analyzed baseline lipids in FOURIER to investigate potential mechanisms explaining the reduction in VTE with evolocumab. Last, an exploratory genetic analysis was performed in FOURIER to determine whether a VTE polygenic risk score could identify high-risk patients who would derive the greatest VTE reduction from evolocumab. RESULTS: In FOURIER, the hazard ratio (HR) for VTE with evolocumab was 0.71 (95% CI, 0.50-1.00; P=0.05), with no effect in the 1st year (HR, 0.96 [95% CI, 0.57-1.62]) but a 46% reduction (HR, 0.54 [95% CI, 0.33-0.88]; P=0.014) beyond 1 year. A meta-analysis of FOURIER and ODYSSEY OUTCOMES demonstrated a 31% relative risk reduction in VTE with PCSK9 inhibition (HR, 0.69 [95% CI, 0.53-0.90]; P=0.007). There was no relation between baseline low-density lipoprotein cholesterol levels and magnitude of VTE risk reduction. In contrast, in patients with higher baseline lipoprotein(a) (Lp[a]) levels, evolocumab reduced Lp(a) by 33 nmol/L and risk of VTE by 48% (HR, 0.52 [95% CI, 0.30-0.89]; P=0.017), whereas, in patients with lower baseline Lp(a) levels, evolocumab reduced Lp(a) by only 7 nmol/L and had no effect on VTE risk (Pinteraction 0.087 for HR; Pheterogeneity 0.037 for absolute risk reduction). Modeled as a continuous variable, there was a significant interaction between baseline Lp(a) concentration and magnitude of VTE risk reduction (Pinteraction=0.04). A polygenic risk score identified patients who were at >2-fold increased risk for VTE and who derived greater relative (Pinteraction=0.04) and absolute VTE reduction (Pheterogeneity=0.009) in comparison with those without high genetic risk. CONCLUSIONS: PCSK9 inhibition significantly reduces the risk of VTE. Lp(a) reduction may be an important mediator of this effect, a finding of particular interest given the ongoing development of potent Lp(a) inhibitors.

Organizational aspects of pediatric anesthesia and surgery between two waves of Covid-19.

BACKGROUND: The initial wave of the Covid-19 pandemic has hit Italy, and Lombardy in particular, with violence, forcing to reshape all hospitals' activities; this happened even in pediatric hospitals, although the young population seemed initially spared from the disease. "Vittore Buzzi" Children's Hospital, which is a pediatric/maternal hospital located in Milan (Lombardy Region), had to stop elective procedures-with the exception of urgent/emergent ones-between February and May 2020 to leave space and resources to adults' care. We describe the challenges of reshaping the hospital's identity and structure, and restarting pediatric surgery and anesthesia, from May on, in the most hit area of the world, with the purpose to avoid and contain infections. Both patients and caregivers admitted to hospital have been tested for Sars-CoV-2 in every case. METHODS: Observational cohort study via review of clinical charts of patients undergoing surgery between 16th May and 30th September 2020, together with SARS-CoV -2 RT-PCR testing outcomes, and comparison to same period surgeries in 2019. RESULTS: An increase of approximately 70% in pediatric surgeries (OR 1.68 [1.33-2.13], P < .001) and a higher increase in the number of surgeries were reported (OR 1.75 (1.43-2.15), P < .001). Considering only urgent procedures, a significant difference in the distribution of the type of surgery was observed (Chi-squared P-value < .001). Sars-CoV-2-positive patients have been 0.8% of total number; 14% of these was discovered through caregiver's positivity. CONCLUSION: We describe our pathway for safe pediatric surgery and anesthesia and the importance of testing both patient and caregiver.

Very low-depth whole-genome sequencing in complex trait association studies.

MOTIVATION: Very low-depth sequencing has been proposed as a cost-effective approach to capture low-frequency and rare variation in complex trait association studies. However, a full characterization of the genotype quality and association power for very low-depth sequencing designs is still lacking. RESULTS: We perform cohort-wide whole-genome sequencing (WGS) at low depth in 1239 individuals (990 at 1× depth and 249 at 4× depth) from an isolated population, and establish a robust pipeline for calling and imputing very low-depth WGS genotypes from standard bioinformatics tools. Using genotyping chip, whole-exome sequencing (75× depth) and high-depth (22×) WGS data in the same samples, we examine in detail the sensitivity of this approach, and show that imputed 1× WGS recapitulates 95.2% of variants found by imputed GWAS with an average minor allele concordance of 97% for common and low-frequency variants. In our study, 1× further allowed the discovery of 140 844 true low-frequency variants with 73% genotype concordance when compared to high-depth WGS data. Finally, using association results for 57 quantitative traits, we show that very low-depth WGS is an efficient alternative to imputed GWAS chip designs, allowing the discovery of up to twice as many true association signals than the classical imputed GWAS design. AVAILABILITY AND IMPLEMENTATION: The HELIC genotype and WGS datasets have been deposited to the European Genome-phenome Archive (https://www.ebi.ac.uk/ega/home): EGAD00010000518; EGAD00010000522; EGAD00010000610; EGAD00001001636, EGAD00001001637. The peakplotter software is available at https://github.com/wtsi-team144/peakplotter, the transformPhenotype app can be downloaded at https://github.com/wtsi-team144/transformPhenotype. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Severe depletion of peripheral blood dendritic cell subsets in obstructive sleep apnea patients: A new link with cancer?

Recent evidence suggests that alterations of the immune responses are associated with the inflammatory nature of obstructive sleep apnea (OSA) and of its related co-morbidities. In this scenario, we asked whether circulating dendritic cell (DC) subsets may be possible players as their role has not yet been detailed. The frequency distribution of peripheral blood myeloid (mDC1 and mDC2) and plasmacytoid (p) DCs was investigated by mean of multi-parametric flow cytometry in 45 OSA patients (mean age: 53 yrs; M = 29) at the time of the first diagnosis and compared to 30 age- and sex-matched healthy controls. Oxidative burst (OB) and serum levels of tumor necrosis factor (TNF)-α, (interleukin) (IL)-6, interferon (INF)-γ, IL-2, IL-4, IL-10 and vascular endothelial growth factor (VEGF) were also analyzed. All subsets of circulating DCs were significantly depleted in OSA patients as compared to healthy subjects (p < 0.01, in all instances), with mDC2 and pDC subtypes being more severely compromised. These findings were co-existing with higher levels of OB along with an increased expression of IL-6, IL-10, TNF-α, IFN-γ, and VEGF (p < 0.005 in all instances). In particular, IL6 levels were significantly higher (p = 0.013) in severe OSA patients (apnea/hypopnea index >30) and were inversely correlated with both mDC2 (r = -0.802, p < 0.007) and pDC (r = -0.317, p = 0.04) subsets. We first provide evidence for a constitutive reduction of all circulating DC subsets in OSA patients. Perturbation of DCs coexists with an inflammatory milieu and is negatively correlated with the expression of IL-6, which is actually recognized as a pivotal inhibitor of DC maturation. Future studies exploring the contribution of DCs in the pathogenesis of OSA and of its complications should be encouraged.

Dental anomalies as a possible clue of 1p36 deletion syndrome due to germline mosaicism: a case report.

BACKGROUND: Monosomy 1p36 is the most common terminal deletion syndrome with an autosomal dominant pattern of inheritance. This syndrome is defined by an extremely wide spectrum of characteristics; however, developmental delay and intellectual disability of various degree are present in all patients and about the 90% of patients have a severe intellectual disability. Dental agenesis or other dental anomalies have not been described in previous reports. CASE PRESENTATION: We report the case of two little sisters born from healthy and non-consanguineous parents, presenting with dental anomalies and one of them with epilepsy, dilated cardiomyopathy with left-ventricular non-compaction, strabismus, history of poor growth, hypotonia and mild language delay. Patients were evaluated in several departments (genetic, child neuropsychiatric, cardiology, odontostomatology, ophthalmology, otorhinolaryngology) of Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy. They underwent investigations such as electrocardiogram, echocardiogram, dental orthopantomography X-Ray and Computed Tomography, electroencephalograms, abdomen ultrasound, blood tests, IQ tests, genetic analysis. They both have an Intelligence Quotient greater than 70 and a negative neurologic exam. Each sister carries the same 1p36 deletion of about 2.3 Mb. Genetic analysis of the parents' blood samples (Single Nucleotide Polymorphism- array, karyotype and Fluorescent In Situ Hybridization) did not reveal any deletion, translocation or inversion and confirmed the paternity. A third sib of the probands does not carry the 1p36 deletion or other quantitative alterations. CONCLUSION: This report describes a new trait linked to monosomy 1p36, namely a mild intellectual outcome associated with significant dental anomalies. Our finding suggests that 1p36 deletion syndrome may present with a mild cognitive impairment or even with a normal intellectual development: this is very important for the genetic counselling, especially in a prenatal setting. Moreover, we report the third study with recurrent 1p36 deletion syndrome in two siblings, likely due to germline mosaicism. Finally, we believe that the dental anomalies should be investigated in 1p36 deletion syndrome and that the spectrum of the condition could be broader than we assume.

COVID-19 in a Patient with ß-Thalassemia Major and Severe Pulmonary Arterial Hypertension.

We here report the successful recovery from coronavirus disease-19 (COVID-19) pneumonia in a patient with ß-thalassemia major (ß-TM) and severe pulmonary arterial hypertension (PAH), focusing on the patient's comorbidities, therapeutic course and drug interaction.

Different presentation of pulmonary parenchymal disruption in COVID-19 pneumonia. Case series of Sub-Intensive Care Unit in Naples, Italy.

The coronavirus disease 2019 (COVID-19) is a recent pandemic that affected more than 5 million people worldwide. Chest high resolution computed tomography (HRCT) is an essential tool in diagnosis and management of the disease. Pulmonary parenchymal opacity is a typical sign of the disease, but not the only one. Pneumothorax, pneumomediastinum, bronchiectasis and cysts are probably underrated complications of COVID-19 that can worsen prognosis, in terms of prolonged hospitalization and need of oxygen therapy. In our single center case series, we outline four different manifestations of pneumothorax, pneumomediastinum and cysts in hospitalized patients with COVID-19 pneumonia.

[Psychogenic polydipsia†: a (still) unknown psychosomatic entity]. / Polydipsie psychogène†: une entité somato-psychiatrique (encore) méconnue.

Psychogenic polydipsia, as well referred to as «â€…potomania ¼, is a clinical entity that can be found in psychiatric as well as in physical care settings. Its diagnosis is based on the detection of an excessive fluid intake along with a polyuria, after excluding any potential somatic cause of this clinical presentation. Given the different somatic complications and care complexity, early detection and multidisciplinary interventions are necessary. This article offers a literature review on this topic.

La polydipsie psychogène, également dénommée «â€…potomanie ¼, est une entité clinique que l'on rencontre en milieu psychiatrique, ainsi qu'en milieu somatique. Son diagnostic se base sur la détection d'une consommation excessive d'eau et d'une polyurie, après exclusion de toute cause somatique pouvant être à l'origine du tableau clinique. Vu les diverses complications somatiques et la complexité de la prise en charge, la nécessité de la détection précoce et d'une approche pluridisciplinaire est primordiale. Cet article propose une revue de la littérature scientifique sur ce sujet.

A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments.

We present our assessment of tertiary structure predictions for hard targets in Critical Assessment of Structure Prediction round 13 (CASP13). The analysis includes (a) assignment and discussion of best models through scores-aided visual inspection of models for each evaluation unit (EU); (b) ranking of predictors resulting from this evaluation and from global scores; and (c) evaluation of progress, state of the art, and current limitations of protein structure prediction. We witness a sizable improvement in tertiary structure prediction building on the progress observed from CASP11 to CASP12, with (a) top models reaching backbone RMSD <3 å for several EUs of size <150 residues, contributed by many groups; (b) at least one model that roughly captures global topology for all EUs, probably unprecedented in this track of CASP; and (c) even quite good models for full, unsplit targets. Better structure predictions are brought about mainly by improved residue-residue contact predictions, and since this CASP also by distance predictions, achieved through state-of-the-art machine learning methods which also progressed to work with slightly shallower alignments compared to CASP12. As we reach a new realm of tertiary structure prediction quality, new directions are proposed and explored for future CASPs: (a) dropping splitting into EUs, (b) rethinking difficulty metrics probably in terms of contact and distance predictions, (c) assessing also side chains for models of high backbone accuracy, and (d) assessing residue-wise and possibly residue-residue quality estimates.

Prevalence and phenotype of the c.1529C>T SPG7 variant in adult-onset cerebellar ataxia in Italy.

BACKGROUND AND PURPOSE: Hereditary ataxias are heterogeneous groups of neurodegenerative disorders, characterized by cerebellar syndromes associated with dysarthria, oculomotor and corticospinal signs, neuropathy and cognitive impairment. Recent reports have suggested mutations in the SPG7 gene, causing the most common form of autosomal recessive spastic paraplegia (MIM#607259), as a main cause of ataxias. The majority of described patients were homozygotes or compound heterozygotes for the c.1529C>T (p.Ala510Val) change. We screened a cohort of 895 Italian patients with ataxia for p.Ala510Val in order to define the prevalence and genotype-phenotype correlation of this variant. METHODS: We set up a rapid assay for c.1529C>T using restriction enzyme analysis after polymerase chain reaction amplification. We confirmed the diagnosis with Sanger sequencing. RESULTS: We identified eight homozygotes and 13 compound heterozygotes, including two novel variants affecting splicing. Mutated patients showed a pure cerebellar ataxia at onset, evolving in mild spastic ataxia (alternatively) associated with dysarthria (~80% of patients), urinary urgency (~30%) and pyramidal signs (~70%). Comparing homozygotes and compound heterozygotes, we noted a difference in age at onset and Scale for the Assessment and Rating of Ataxia score between the two groups, supporting an earlier and more severe phenotype in compound heterozygotes versus homozygotes. CONCLUSIONS: The SPG7 c.1529C>T (p.Ala510Val) mutants accounted for 2.3% of cerebellar ataxia cases in Italy, suggesting that this variant should be considered as a priority test in the presence of late-onset pure ataxia. Moreover, the heterozygous/homozygous genotype appeared to predict the onset of clinical manifestation and disease progression.

Assessment of data-assisted prediction by inclusion of crosslinking/mass-spectrometry and small angle X-ray scattering data in the 12th Critical Assessment of protein Structure Prediction experiment.

Integrative modeling approaches attempt to combine experiments and computation to derive structure-function relationships in complex molecular assemblies. Despite their importance for the advancement of life sciences, benchmarking of existing methodologies is rather poor. The 12th round of the Critical Assessment of protein Structure Prediction (CASP) offered a unique niche to benchmark data and methods from two kinds of experiments often used in integrative modeling, namely residue-residue contacts obtained through crosslinking/mass-spectrometry (CLMS), and small-angle X-ray scattering (SAXS) experiments. Upon assessment of the models submitted by predictors for 3 targets assisted by CLMS data and 11 targets by SAXS data, we observed no significant improvement when compared to the best data-blind models, although most predictors did improve relative to their own data-blind predictions. Only for target Tx892 of the CLMS-assisted category and for target Ts947 of the SAXS-assisted category, there was a net, albeit mild, improvement relative to the best data-blind predictions. We discuss here possible reasons for the relatively poor success, which point rather to inconsistencies in the data sources rather than in the methods, to which a few groups were less sensitive. We conclude with suggestions that could improve the potential of data integration in future CASP rounds in terms of experimental data production, methods development, data management and prediction assessment.

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods.

We present our assessment of CASP12 modeling efforts for targets with no obvious templates of high sequence/structure similarity in the PDB, that is for evaluation units of the free modeling (FM) and free modeling/template-based modeling (FM/TBM) categories. Models were clustered and ranked using the Global Distance Test-Total Score and 5 additional metrics developed in previous CASP rounds, producing short lists of models that were subject to visual inspection in comparison to the target structures. The whole procedure was implemented as a web app that facilitates model selection and visual inspection, and could become useful to facilitate and standardize future assessments. We describe cases of (1) targets with remarkably good predictions, (2) targets whose models captured some global shape and topology features, and (3) targets for which models fail to capture even coarse features. We note that despite this CASP being among the most challenging ones, a measurable improvement of the top predictions is apparent, that we attribute to the emergence of accurate contact prediction methods and the increased number of available sequences. We also briefly discuss current limitations in tertiary structure prediction exemplified by CASP12 targets. Overall, the Baker, Zhang, and Lee manual groups and servers were identified as the top global performing groups.

Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics.

For assessment purposes, CASP targets are split into evaluation units. We herein present the official definition of CASP12 evaluation units (EUs) and their classification into difficulty categories. Each target can be evaluated as one EU (the whole target) or/and several EUs (separate structural domains or groups of structural domains). The specific scenario for a target split is determined by the domain organization of available templates, the difference in server performance on separate domains versus combination of the domains, and visual inspection. In the end, 71 targets were split into 96 EUs. Classification of the EUs into difficulty categories was done semi-automatically with the assistance of metrics provided by the Prediction Center. These metrics account for sequence and structural similarities of the EUs to potential structural templates from the Protein Data Bank, and for the baseline performance of automated server predictions. The metrics readily separate the 96 EUs into 38 EUs that should be straightforward for template-based modeling (TBM) and 39 that are expected to be hard for homology modeling and are thus left for free modeling (FM). The remaining 19 borderline evaluation units were dubbed FM/TBM, and were inspected case by case. The article also overviews structural and evolutionary features of selected targets relevant to our accompanying article presenting the assessment of FM and FM/TBM predictions, and overviews structural features of the hardest evaluation units from the FM category. We finally suggest improvements for the EU definition and classification procedures.