Quantitative weight of evidence method for combining predictions of quantitative structure-activity relationship models

A method for combining statistical-based QSAR predictions of two or more binary classification models is presented. It was assumed that all models were independent. This facilitated the combination of positive and negative predictions using a quantitative weight of evidence (qWoE) procedure based on Bayesian statistics and the additivity of the logarithms of the likelihood ratios. Previous studies combined more than one prediction but used arbitrary strengths for positive and negative predictions. In our approach, the combined models were validated by determining the sensitivity and specificity values, which are performance metrics that are a point of departure for obtaining values that measure the weight of evidence of positive and negative predictions. The developed method was experimentally applied in the prediction of Ames mutagenicity. The method achieved a similar accuracy to that of the experimental Ames test for this endpoint when the overall prediction was determined using a combination of the individual predictions of more than one model. Calculating the qWoE value would reduce the requirement for expert knowledge and decrease the subjectivity of the prediction. This method could be applied to other endpoints such as developmental toxicity and skin sensitisation with binary classification models.

Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses

Well-ordered HIV-1 envelope glycoprotein (Env) trimers are prioritized for clinical evaluation, and there is a need for an improved understanding about how elicited B cell responses evolve following immunization. To accomplish this, we prime-boosted rhesus macaques with clade C NFL trimers and identified 180 unique Ab lineages from ∼1,000 single-sorted Env-specific memory B cells. We traced all lineages in high-throughput heavy chain (HC) repertoire (Rep-seq) data generated from multiple immune compartments and time points and expressed several as monoclonal Abs (mAbs). Our results revealed broad dissemination and high levels of somatic hypermutation (SHM) of most lineages, including tier 2 virus neutralizing lineages, following boosting. SHM was highest in the Ab complementarity determining regions (CDRs) but also surprisingly high in the framework regions (FRs), especially FR3. Our results demonstrate the capacity of the immune system to affinity-mature large numbers of Env-specific B cell lineages simultaneously, supporting the use of regimens consisting of repeated boosts to improve each Ab, even those belonging to less expanded lineages.

Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.

Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.

Nationwide survey on training and device utilization during tracheal intubation in French intensive care units

Background

Intubation is a lifesaving procedure that is often performed in intensive care unit (ICU) patients, but leads to serious adverse events in 20–40% of cases. Recent trials aimed to provide guidance about which medications, devices, and modalities maximize patient safety. Videolaryngoscopes are being offered in an increasing range of options and used in broadening indications (from difficult to unremarkable intubation). The objective of this study was to describe intubation practices and device availability in French ICUs.

Materials and methods

We conducted an online nationwide survey by emailing an anonymous 26-item questionnaire to physicians in French ICUs. A single questionnaire was sent to either the head or the intubation expert at each ICU.

Results

Of 257 ICUs, 180 (70%) returned the completed questionnaire. The results showed that 43% of intubators were not fully proficient in intubation; among them, 18.8% had no intubation training or had received only basic training (lectures and observation at the bedside). Among the participating ICUs, 94.4% had a difficult intubation trolley, 74.5% an intubation protocol, 92.2% a capnography device (used routinely to check tube position in 69.3% of ICUs having the device), 91.6% a laryngeal mask, 97.2% front-of-neck access capabilities, and 76.6% a videolaryngoscope. In case of difficult intubation, 85.6% of ICUs used a bougie (154/180) and 7.8% switched to a videolaryngoscope (14/180). Use of a videolaryngoscope was reserved for difficult intubation in 84% of ICUs (154/180). Having a videolaryngoscope was significantly associated with having an intubation protocol (P = 0.043) and using capnography (P = 0.02). Airtraq^® was the most often used videolaryngoscope (39.3%), followed by McGrath^®Mac (36.9%) then by Glidescope^® (14.5%).

Conclusion

Nearly half the intubators in French ICUs are not fully proficient with OTI. Access to modern training methods such as simulation is inadequate. Most ICUs own a videolaryngoscope, but reserve it for difficult intubations.

D-dimer levels and risk of recurrence following provoked venous thromboembolism: findings from the RIETE registry

BACKGROUND

Patients with venous thromboembolism (VTE) secondary to transient risk factors may develop VTE recurrences after discontinuing anticoagulation. Identifying at-risk patients could help to guide the duration of therapy.

METHODS

We used the RIETE database to assess the prognostic value of d-dimer testing after discontinuing anticoagulation to identify patients at increased risk for recurrences. Transient risk factors were classified as major (postoperative) or minor (pregnancy, oestrogen use, immobilization or recent travel).

RESULTS

In December 2018, 1655 VTE patients with transient risk factors (major 460, minor 1195) underwent d-dimer measurements after discontinuing anticoagulation. Amongst patients with major risk factors, the recurrence rate was 5.74 (95% CI: 3.19-9.57) events per 100 patient-years in those with raised d-dimer levels and 2.68 (95% CI: 1.45-4.56) in those with normal levels. Amongst patients with minor risk factors, the rates were 7.79 (95% CI: 5.71-10.4) and 3.34 (95% CI: 2.39-4.53), respectively. Patients with major risk factors and raised d-dimer levels (n = 171) had a nonsignificantly higher rate of recurrences (hazard ratio [HR]: 2.14; 95% CI: 0.96-4.79) than those with normal levels. Patients with minor risk factors and raised d-dimer levels (n = 382) had a higher rate of recurrences (HR: 2.34; 95% CI: 1.51-3.63) than those with normal levels. On multivariate analysis, raised d-dimers (HR: 1.74; 95% CI: 1.09-2.77) were associated with an increased risk for recurrences in patients with minor risk factors, not in those with major risk factors.

CONCLUSIONS

Patients with raised d-dimer levels after discontinuing anticoagulant therapy for VTE provoked by a minor transient risk factor were at an increased risk for recurrences.

Can environmental contamination be explained by particular traits associated with patients?

BACKGROUND

Little is known about patient risk factors associated with environmental contamination.

AIM

To evaluate the rate of environmental contamination and to investigate individual risk factors.

METHODS

A prospective cohort study was conducted. Each day, five rooms occupied by patients were selected. Five critical surfaces were systematically swabbed twice a day before and after cleaning. Clinical characteristics of all patients were collected. Logisitic regression was performed to evaluate the association between environmental contamination and patients' characteristics.

FINDINGS

A total of 107 consecutive patients were included and 1052 environmental samples were performed. Nineteen (18%) patients were known previously colonized/infected with a multidrug-resistant organism (MDRO). Respectively, 723 (69%) and 112 (11%) samples grew with ≥1 and >2.5 cfu/cm² bacteria, resulting in 62 (58%) contaminated rooms. Considering positive samples with at least one pathogenic bacterium, 16 (15%) rooms were contaminated. By univariate and multivariate analysis, no variables analysed were associated with the environmental contamination. Considering contaminated rooms with >2.5 cfu/cm², three factors were protective for environmental contamination: known MDRO carriers/infected patients (odds ratio: 0.25; 95% confidence interval: 0.09-0.72; P = 0.01), patients with urinary catheter (0.19; 0.04-0.89; P = 0.03) and hospitalization in single room (0.3; 0.15-0.6; P < 0.001).

CONCLUSION

This study was conducted in a non-outbreak situation and showed a low rate of environmental contamination with pathogenic bacteria. Only 11% of environmental samples grew with >2.5 cfu/cm², and they were related to non-pathogenic bacteria. No risk factors associated with environmental contamination were identified.

Bulk and grain boundary Li-diffusion in dense LiMn2O4 pellets by means of isotope exchange and ToF-SIMS analysis

Lithium diffusion in LiMn₂O₄ pellets is studied by means of isotope exchange and Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS). A ⁶Li-enriched film deposited by Pulsed Laser Deposition (PLD) on a dense LiMn₂O₄ pellet with natural abundance of lithium isotopes is used to study the tracer diffusion of lithium. The measured profiles are analyzed by numerical models describing the ⁶Li tracer diffusion from the film into the pellet. Experiments in the Harrison type B regime of diffusion kinetics allow for the distinction and simultaneous determination of bulk and grain boundary diffusion coefficients. Changing the experimental conditions to reach Harrison type A behavior yields effective diffusion coefficients for lithium tracer diffusion in LiMn₂O₄. Activation energies for bulk and grain boundary diffusion were obtained from experiments at different temperatures. Our values are critically compared to previous studies.

Impact of palbociclib plus letrozole on patient-reported health-related quality of life: results from the PALOMA-2 trial

Background

Patient-reported outcomes are integral in benefit-risk assessments of new treatment regimens. The PALOMA-2 study provides the largest body of evidence for patient-reported health-related quality of life (QOL) for patients with metastatic breast cancer (MBC) receiving first-line endocrine-based therapy (palbociclib plus letrozole and letrozole alone).

Patients and methods

Treatment-naïve postmenopausal women with estrogen receptor-positive (ER+)/human epidermal growth factor receptor 2-negative (HER2-) MBC were randomized 2 : 1 to palbociclib plus letrozole (n = 444) or placebo plus letrozole (n = 222). Patient-reported outcomes were assessed at baseline, day 1 of cycles 2 and 3, and day 1 of every other cycle from cycle 5 using the Functional Assessment of Cancer Therapy (FACT)-Breast and EuroQOL 5 dimensions (EQ-5D) questionnaires.

Results

As of 26 February 2016, the median duration of follow-up was 23 months. Baseline scores were comparable between the two treatment arms. No significant between-arm differences were observed in change from baseline in FACT-Breast Total, FACT-General Total, or EQ-5D scores. Significantly greater improvement in pain scores was observed in the palbociclib plus letrozole arm (-0.256 versus -0.098; P = 0.0183). In both arms, deterioration of FACT-Breast Total score was significantly delayed in patients without progression versus those with progression and patients with partial or complete response versus those without. No significant difference was observed in FACT-Breast and EQ-5D index scores in patients with and without neutropenia.

Conclusions

Overall, women with MBC receiving first-line endocrine therapy have a good QOL. The addition of palbociclib to letrozole maintains health-related QOL and improves pain scores in treatment-naïve postmenopausal patients with ER+/HER2- MBC compared with letrozole alone. Significantly greater delay in deterioration of health-related QOL was observed in patients without progression versus those who progressed and in patients with an objective response versus non-responders. ClinicalTrials.gov: NCT01740427 (https://clinicaltrials.gov/ct2/show/NCT01740427).

[Inflammatory myopathy following acute meningoccemia in a properdin-deficient patient: A case report]

INTRODUCTION

Myalgia is a classical sign in invasive meningococcal diseases (IMD), but severe and persistent myalgia following an IMD have never been reported to date.

CASE REPORT

A 20-year-old man presented with purpura fulminans and meningitis caused by Neisseria meningitidis serogroup Y, revealing properdin deficiency. Although meningitis symptoms improved after antibiotherapy, initial myalgia of the lower limbs increased, associated with mild rhabdomyolysis. Magnetic resonance imaging (MRI) revealed an increased STIR (Short TI inversion recovery) signal of both quadriceps muscles, without abscess. After exclusion of other causes of myopathy, a post-infectious myositis was diagnosed. A four-week course of corticosteroids led to dramatic improvement.

CONCLUSION

Post-infectious inflammatory myopathy should be suspected in case of severe and persistent myalgia associated with rhabdomyolysis following an IMD, after exclusion of pyomyositis especially. A short course of corticosteroids seems to be effective.

Situation, challenges, and SEOM recommendations for the future of undergraduate education in Oncology in Spain

PURPOSE

The Spanish Society of Medical Oncology (SEOM, for its Spanish acronym) would like to attest to the relevance of training in Oncology as part of the undergraduate education in Medicine program and issue recommendations to improve said training, with the aim of responding better to the challenges that cancer poses to our society.

MATERIALS AND METHODS

The curricula of 42 schools of medicine were reviewed with interviews with at least one teaching medical oncologist from each faculty. The qualitative and opinion analysis was completed by means of an online questionnaire targeting lecturers, resident tutors, and residents in Medical Oncology (MO), enabling the detection of needs and areas for improvement at an organizational level and in terms of skill acquisition.

RESULTS

While the number of medical schools with a specific, mandatory program in MO has grown by up to 90%, it has not been accompanied by an increase in independent programs. Instead, they largely consist of programs shared with other specialties (61% of the medical faculties). In most of the undergraduate education programs, Oncology contents are fragmented and approached from the perspective of each organ system.

CONCLUSIONS

Despite the positive evolution in recent years, the heterogeneity in Oncology contents during undergraduate education training continues to be remarkable. Cross-sectional programs with an integral vision, taught in the final years of undergraduate medical education would be desirable. Among the recommendations for improvement of training in Medical Oncology, the SEOM proposes that updated, theoretical content be incorporated and clinical practice in Medical Oncology departments be promoted.

From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability

Background

Since different types of genetic variants, from single nucleotide variants (SNVs) to large chromosomal rearrangements, underlie intellectual disability, we evaluated the use of whole-genome sequencing (WGS) rather than chromosomal microarray analysis (CMA) as a first-line genetic diagnostic test.

Methods

We analyzed three cohorts with short-read WGS: (i) a retrospective cohort with validated copy number variants (CNVs) (cohort 1, n = 68), (ii) individuals referred for monogenic multi-gene panels (cohort 2, n = 156), and (iii) 100 prospective, consecutive cases referred to our center for CMA (cohort 3). Bioinformatic tools developed include FindSV, SVDB, Rhocall, Rhoviz, and vcf2cytosure.

Results

First, we validated our structural variant (SV)-calling pipeline on cohort 1, consisting of three trisomies and 79 deletions and duplications with a median size of 850 kb (min 500 bp, max 155 Mb). All variants were detected. Second, we utilized the same pipeline in cohort 2 and analyzed with monogenic WGS panels, increasing the diagnostic yield to 8%. Next, cohort 3 was analyzed by both CMA and WGS. The WGS data was processed for large (> 10 kb) SVs genome-wide and for exonic SVs and SNVs in a panel of 887 genes linked to intellectual disability as well as genes matched to patient-specific Human Phenotype Ontology (HPO) phenotypes. This yielded a total of 25 pathogenic variants (SNVs or SVs), of which 12 were detected by CMA as well. We also applied short tandem repeat (STR) expansion detection and discovered one pathologic expansion in ATXN7. Finally, a case of Prader-Willi syndrome with uniparental disomy (UPD) was validated in the WGS data.

Important positional information was obtained in all cohorts. Remarkably, 7% of the analyzed cases harbored complex structural variants, as exemplified by a ring chromosome and two duplications found to be an insertional translocation and part of a cryptic unbalanced translocation, respectively.

Conclusion

The overall diagnostic rate of 27% was more than doubled compared to clinical microarray (12%). Using WGS, we detected a wide range of SVs with high accuracy. Since the WGS data also allowed for analysis of SNVs, UPD, and STRs, it represents a powerful comprehensive genetic test in a clinical diagnostic laboratory setting.

Randomised phase III trial of vinflunine plus capecitabine versus capecitabine alone in patients with advanced breast cancer previously treated with an anthracycline and resistant to taxane

Background

Capecitabine is an approved standard therapy for anthracycline- and taxane-pretreated locally advanced or metastatic breast cancer (BC). Vinflunine has demonstrated single-agent activity in phase II studies in this setting and activity and tolerability when combined with capecitabine. We compared the combination of vinflunine plus capecitabine (VC) with single-agent capecitabine.

Patients and methods

Patients with locally recurrent/metastatic BC previously treated or resistant to an anthracycline and resistant to taxane therapy were randomly assigned to either vinflunine (280 mg/m2, day 1) plus oral capecitabine [825 mg/m2 twice daily (b.i.d.), days 1-14] every 3 weeks (q3w) or single-agent oral capecitabine (1250 mg/m2 b.i.d., days 1-14) q3w. The primary end point was progression-free survival (PFS) assessed by an independent review committee. The study had 90% power to detect a 30% improvement in PFS.

Results

Overall, 770 patients were randomised. PFS was significantly longer with VC than with capecitabine alone [hazard ratio, 0.84, 95% confidence interval (CI), 0.71-0.99; log-rank P = 0.043; median 5.6 versus 4.3 months, respectively]. Median overall survival was 13.9 versus 11.7 months with VC versus capecitabine alone, respectively (hazard ratio, 0.98; 95% CI, 0.83-1.15; log-rank P = 0.77). No difference in quality of life was observed between the two treatment arms. The most common adverse events (NCI CTCAE version 3.0) in the combination arm were haematological and gastrointestinal. Grade 4 neutropenia was more frequent with VC (12% versus 1% with capecitabine alone); febrile neutropenia occurred in 2% versus 0.5%, respectively. Hand-foot syndrome was less frequent with VC (grade 3: 4% versus 19% for capecitabine alone). Peripheral neuropathy was uncommon in both arms (grade 3: 1% versus 0.3%).

Conclusions

Vinflunine combined with capecitabine demonstrated a modest improvement in PFS and an acceptable safety profile compared with capecitabine alone in patients with anthracycline- and taxane-pretreated locally recurrent/metastatic BC.

ClinicalTrials.gov

NCT01095003.

Influence of permafrost, rock and ice glaciers on chemistry of high-elevation ponds (NW Italian Alps)

Permafrost degradation, rock-glacier thawing, and glacier retreat are influencing surface water quality at high elevations. However, there is a lack of knowledge on the dominant geochemical reactions occurring in different cryospheric conditions and how these reactions change during the ice-free season. In the Col d'Olen area (LTER site, NW Italian Alps), four ponds with similar sizes, located in basins with different cryospheric features (glacier, permafrost, rock glacier, none of these), are present in a geographically limited area. All ponds were sampled weekly in 2015 and partially in 2014. Major ions, selected trace elements, and biotic parameters (dissolved organic carbon-DOC, fluorescence index-FI, and nitrate) are examined to evidence the effect of different cryospheric features on water characteristics. Where cryospheric conditions occur chemical weathering is more intensive, with strong seasonal increase of major ions. Sulphide oxidation dominates in glacier and permafrost lying on acid rocks, probably driven by enhanced weathering of freshly exposed rocks in subglacial environment and recently deglaciated areas, and active layer thickness increase. Differently, carbonation dominates for the rock glacier lying on ultramafic rocks. There, high Ni concentrations originate from dissolution of Mg-bearing rocks in the landform. In all settings, pH neutralisation occurs because of the presence of secondary carbonate lithology and ultramafic rocks. Nitrate highest concentrations and changes occur in cryospheric settings while DOC and FI do not show strong differences and seasonal variations. The establishment of more frequent monitoring for water quality in high-elevated surface waters is necessary to provide greater statistical power to detect changes on longer time scales.

Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System

Rock glaciers (RG) are assumed to influence the biogeochemistry of downstream ecosystems because of the high ratio of rock:water in those systems, but no studies have considered the effects of a RG inflow on the microbial ecology of sediments in a downstream pond. An alpine RG-pond system, located in the NW Italian Alps has been chosen as a model, and Bacteria and Archaea 16S rRNA genes abundance, distribution and diversity have been assessed by qPCR and Illumina sequencing, coupled with geochemical analyses on sediments collected along a distance gradient from the RG inflow. RG surface material and neighbouring soil have been included in the analysis to better elucidate relationships among different habitats.Our results showed that different habitats harboured different, well-separated microbial assemblages. Across the pond, the main variations in community composition (e.g. Thaumarchaeota and Cyanobacteria relative abundance) and porewater geochemistry (pH, DOC, TDN and NH₄⁺) were not directly linked to RG proximity, but to differences in water depth. Some microbial markers potentially linked to the presence of meltwater inputs from the RG have been recognised, although the RG seems to have a greater influence on the pond microbial communities due to its contribution in terms of sedimentary material.

Abaloparatide for risk reduction of nonvertebral and vertebral fractures in postmenopausal women with osteoporosis: a network meta-analysis

This network meta-analysis assessed the efficacy of abaloparatide versus other treatment options to reduce the risk of fractures in women with postmenopausal osteoporosis. The analysis indicates that abaloparatide reduces the risk of fractures in women with postmenopausal osteoporosis versus placebo and compared with other treatment options.

INTRODUCTION

This network meta-analysis (NMA) assessed the relative efficacy of abaloparatide versus other treatments to reduce the risk of fractures in women with postmenopausal osteoporosis (PMO).

METHODS

PubMed®, Embase®, and the Cochrane Central Register of Controlled Trials were searched for randomized controlled trials published before December 20, 2017, that included women with PMO who were eligible to receive interventions for primary or secondary fracture prevention. The NMA was conducted by fracture site (vertebral [VF], nonvertebral [NVF], and wrist), with the relative risk (RR) of fracture versus placebo the main clinical endpoint. The NMA used fixed-effects and random-effects approaches.

RESULTS

A total of 4978 articles were screened, of which 22 were included in the analysis. Compared with other treatments, abaloparatide demonstrated the greatest treatment effect relative to placebo in the VF network (RR = 0.13; 95% credible interval [CrI] 0.04-0.34), the NVF network (RR = 0.50; 95% CrI 0.28-0.85), and the wrist fracture network (RR = 0.39; CrI 0.15-0.90). Treatment ranking showed that abaloparatide had the highest estimated probability of preventing fractures in each of the networks (79% for VF, 70% for NVF, and 53% for wrist fracture) compared with other treatments. Individual networks demonstrated a good level of agreement with direct trial evidence and direct pair-wise comparisons.

CONCLUSIONS

This NMA indicates that abaloparatide reduces the RR of VF, NVF, and wrist fracture in women with PMO with or without prior fracture versus placebo, compared with other treatment options. Limitations include that adverse events and drug costs were not considered, and that generalizability is limited to the trial populations and endpoints included in the NMA.

Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

Background

Full RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification agreement between RNA-Seq and a digital multiplexed gene expression platform, and the subtype call after running the PAM50 assay in a series of breast cancer patients classified as triple negative by IHC/FISH. The goal of this study is to analyze the concordance between both expression platforms overall, and for calling PAM50 triple negative breast cancer intrinsic subtypes in particular.

Results

The analyses were performed in paraffin-embedded tissues from 96 patients recruited in a multicenter, prospective, non-randomized neoadjuvant triple negative breast cancer trial (NCT01560663). Pre-treatment core biopsies were obtained following clinical practice guidelines and conserved as FFPE for further RNA extraction. PAM50 was performed on both digital multiplexed gene expression and RNA-Seq platforms. Subtype assignment was based on the nearest centroid classification following this procedure for both platforms and it was concordant on 96% of the cases (N = 96). In four cases, digital multiplexed gene expression analysis and RNA-Seq were discordant. The Spearman correlation to each of the centroids and the risk of recurrence were above 0.89 in both platforms while the agreement on Proliferation Score reached up to 0.97. In addition, 82% of the individual PAM50 genes showed a correlation coefficient > 0.80.

Conclusions

In our analysis, the subtype calling in most of the samples was concordant in both platforms and the potential discordances had reduced clinical implications in terms of prognosis. If speed and cost are the main driving forces then the preferred technique is the digital multiplexed platform, while if whole genome patterns and subtype are the driving forces, then RNA-Seq is the preferred method.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5849-0) contains supplementary material, which is available to authorized users.

Clinical considerations of the role of palbociclib in the management of advanced breast cancer patients with and without visceral metastases

Background

This report assesses the efficacy and safety of palbociclib plus endocrine therapy (ET) in women with hormone receptor-positive, human epidermal growth factor receptor 2-negative advanced breast cancer (ABC) with or without visceral metastases.

Patients and methods

Pre- and postmenopausal women with disease progression following prior ET (PALOMA-3; N = 521) and postmenopausal women untreated for ABC (PALOMA-2; N = 666) were randomized 2 : 1 to ET (fulvestrant or letrozole, respectively) plus palbociclib or placebo. Progression-free survival (PFS), safety, and patient-reported quality of life (QoL) were evaluated by prior treatment and visceral involvement.

Results

Visceral metastases incidence was higher in patients with prior resistance to ET (58.3%, PALOMA-3) than in patients naive to ET in the ABC setting (48.6%, PALOMA-2). In patients with prior resistance to ET and visceral metastases, median PFS (mPFS) was 9.2 months with palbociclib plus fulvestrant versus 3.4 months with placebo plus fulvestrant [hazard ratio (HR), 0.47; 95% confidence interval (CI), 0.35–0.61], and objective response rate (ORR) was 28.0% versus 6.7%, respectively. In patients with nonvisceral metastases, mPFS was 16.6 versus 7.3 months, HR 0.53; 95% CI 0.36–0.77. In patients with visceral disease and naive to ET in the advanced disease setting, mPFS was 19.3 months with palbociclib plus letrozole versus 12.9 months with placebo plus letrozole (HR 0.63; 95% CI 0.47–0.85); ORR was 55.1% versus 40.0%; in patients with nonvisceral disease, mPFS was not reached with palbociclib plus letrozole versus 16.8 months with placebo plus letrozole (HR 0.50; 95% CI 0.36–0.70). In patients with prior resistance to ET with visceral metastases, palbociclib plus fulvestrant significantly delayed deterioration of QoL versus placebo plus fulvestrant, whereas patient-reported QoL was maintained with palbociclib plus letrozole in patients naive to endocrine-based therapy for ABC.

Conclusions

Palbociclib plus ET prolonged mPFS in patients with visceral metastases, increased ORRs, and in patients previously treated for ABC, delayed QoL deterioration, presenting a standard treatment option among patients with visceral metastases amenable to endocrine-based therapy.

Clinical trial registration

NCT01942135, NCT01740427

High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis

Next generation sequencing (NGS) of immunoglobulin (Ig) repertoires (Rep-seq) enables examination of the adaptive immune system at an unprecedented level. Applications include studies of expressed repertoires, gene usage, somatic hypermutation levels, Ig lineage tracing and identification of genetic variation within the Ig loci through inference methods. All these applications require starting libraries that allow the generation of sequence data with low error rate and optimal representation of the expressed repertoire. Here, we provide detailed protocols for the production of libraries suitable for human Ig germline gene inference and Ig repertoire studies. Various parameters used in the process were tested in order to demonstrate factors that are critical to obtain high quality libraries. We demonstrate an improved 5'RACE technique that reduces the length constraints of Illumina MiSeq based Rep-seq analysis but allows for the acquisition of sequences upstream of Ig V genes, useful for primer design. We then describe a 5' multiplex method for library preparation, which yields full length V(D)J sequences suitable for genotype identification and novel gene inference. We provide comprehensive sets of primers targeting IGHV, IGKV, and IGLV genes. Using the optimized protocol, we produced IgM, IgG, IgK, and IgL libraries and analyzed them using the germline inference tool IgDiscover to identify expressed germline V alleles. This process additionally uncovered three IGHV, one IGKV, and six IGLV novel alleles in a single individual, which are absent from the IMGT reference database, highlighting the need for further study of Ig genetic variation. The library generation protocols presented here enable a robust means of analyzing expressed Ig repertoires, identifying novel alleles and producing individualized germline gene databases from humans.

First Measurement of Charm Production in its Fixed-Target Configuration at the LHC

The first measurement of heavy-flavor production by the LHCb experiment in its fixed-target mode is presented. The production of J/ψ and D^{0} mesons is studied with beams of protons of different energies colliding with gaseous targets of helium and argon with nucleon-nucleon center-of-mass energies of sqrt[s_{NN}]=86.6 and 110.4 GeV, respectively. The J/ψ and D^{0} production cross sections in pHe collisions in the rapidity range [2, 4.6] are found to be σ_{J/ψ}=652±33(stat)±42(syst)   nb/nucleon and σ_{D^{0}}=80.8±2.4(stat)±6.3(syst)  μb/nucleon, where the first uncertainty is statistical and the second is systematic. No evidence for a substantial intrinsic charm content of the nucleon is observed in the large Bjorken-x region.

Effects of neratinib on health-related quality of life in women with HER2-positive early-stage breast cancer: longitudinal analyses from the randomized phase III ExteNET trial

BACKGROUND

We report longitudinal health-related quality-of-life (HRQoL) data from the international, randomized, double-blind, placebo-controlled phase III ExteNET study, which demonstrated an invasive disease-free survival benefit of extended adjuvant therapy with neratinib over placebo in human epidermal growth factor receptor-2-positive early-stage breast cancer.

PATIENTS AND METHODS

Women (N  = 2840) with early-stage HER2-positive breast cancer who had completed trastuzumab-based adjuvant therapy were randomly assigned to neratinib 240  mg/day or placebo for 12  months. HRQoL was an exploratory end point. Patients completed the Functional Assessment of Cancer Therapy-Breast (FACT-B) and EuroQol 5-Dimensions (EQ-5D) questionnaires at baseline and months 1, 3, 6, 9, and 12. Changes from baseline were compared using analysis of covariance with no imputation for missing values. Sensitivity analyses used alternative methods. Changes in HRQoL scores were regarded as clinically meaningful if they exceeded previously reported important differences (IDs).

RESULTS

Of the 2840 patients (intention-to-treat population), 2407 patients were evaluable for FACT-B (neratinib, N  = 1171; placebo, N  = 1236) and 2427 patients for EQ-5D (neratinib, N  = 1186; placebo, N  = 1241). Questionnaire completion rates exceeded 85%. Neratinib was associated with a decrease in global HRQoL scores at month 1 compared with placebo (adjusted mean differences: FACT-B total, -2.9 points; EQ-5D index, -0.02), after which between-group differences diminished at later time-points. Except for the FACT-B physical well-being (PWB) subscale at month 1; all between-group differences were less than reported IDs. The FACT-B breast cancer-specific subscale showed small improvements with neratinib at months 3-9, but all were less than IDs. Sensitivity analyses exploring missing data did not change the results.

CONCLUSIONS

Extended adjuvant neratinib was associated with a transient, reversible decrease in HRQoL during the first month of treatment, possibly linked to treatment-related diarrhea. With the exception of the PWB subscale at month 1, all neratinib-related HRQoL changes did not reach clinically meaningful thresholds. ClinicalTrials.gov: NCT00878709.

[Hereditary diffuse gastric cancer : case serie of 8 patients from a single family and literature review]

Hereditary diffuse gastric cancer is a form of gastric cancer associated, in about 40 % of cases, with a germline mutation of the CDH1 gene. The management of patients with a pathogenic mutation of this gene is based on total prophylactic gastrectomy because, until proven otherwise, endoscopic monitoring is insufficient. We report a series of eight patients with pathogenic CDH1 mutation who underwent total prophylactic gastrectomy in our centre.

Abstract P6-18-16: Ribociclib (RIBO) + letrozole (LET) in older patients with hormone receptor-positive (HR+), human epidermal growth factor receptor-2–negative (HER2–) advanced breast cancer (ABC): Preliminary subgroup results from the phase 3b CompLEEment-1 trial

Background: The cyclin-dependent kinase (CDK)4/6 inhibitor RIBO is approved in combination with an aromatase inhibitor (AI) for HR+, HER2– ABC in postmenopausal women with no prior therapy for ABC, based on the MONALEESA-2 trial (Hortobagyi et al. NEJM 2016). Although a high proportion of patients with HR+, HER2– ABC are &gt;65 years of age, older patients are often under-represented in clinical trials. Furthermore, treatment decisions may be complicated by comorbidities, functional status, and concurrent medications. Here, we report early safety results for patients ≥65 years of age enrolled in CompLEEment-1, an open-label, phase 3b trial evaluating RIBO+LET as first-line endocrine-based therapy in an expanded patient population.

Methods: Patients with HR+, HER2– ABC, ≤1 line of prior chemotherapy (CT), and no prior endocrine therapy for ABC received RIBO (600 mg/day, 3 weeks on/1 week off) + LET (2.5 mg/day); men and premenopausal women received concomitant goserelin (3.6-mg subcutaneous implant every 28 days). The primary outcome was safety and tolerability. A pre-planned interim analysis was conducted ˜15 months after first patient first visit.

Results: Of the first 1,008 patients enrolled who completed 56 days of follow-up or discontinued before the data cut-off date, 377 were ≥65 years of age. Of these, 157 (41.6%) were 65-&lt;70 years, 107 (28.4%) were 70-&lt;75 years, and 113 (30%) were ≥75 years. The majority of patients (94.4%) had an Eastern Cooperative Oncology Group performance status ≤1; 33.2% presented with stage IV disease at diagnosis; 9 patients were male. The most common sites of metastasis were bone (70.0%), lung (44.8%), and lymph nodes (29.7%). The most common all-grade adverse events (AEs) were neutropenia (58.4%), nausea (31.8%), and fatigue (24.1%). The most common grade 3/4 AEs were neutropenia (37.7%) and alanine aminotransferase increase (4.2%). QT prolongation events were mild (majority grade 1/2) and occurred in 6.1% of patients (0.5% grade 3/4). Dose reduction or interruption due to AEs occurred in 54.5% of patients; 6.9% of patients had AEs leading to treatment discontinuation. In the overall patient population, the most frequent grade 3/4 AEs were neutropenia (42.8%), leukopenia (3.4%), and increased alanine aminotransferase (2.9%); QT prolongation occurred in 5.4% of patients (0.5% grade 3/4).

Conclusions: Initial safety results from CompLEEment-1, from the first 56 days of follow-up, demonstrate the tolerability of RIBO+LET in older patients, consistent with the overall patient population. NCT02941926.

Citation Format: Ring A, Borstnar S, Ferreira A, Azim HA, Cottu P, Lu J, Martin M, Zamagni C, Beck JT, Zhou K, Wu J, Menon L, De Laurentiis M. Ribociclib (RIBO) + letrozole (LET) in older patients with hormone receptor-positive (HR+), human epidermal growth factor receptor-2–negative (HER2–) advanced breast cancer (ABC): Preliminary subgroup results from the phase 3b CompLEEment-1 trial [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-18-16.

Abstract P2-07-05: A clinical calculator to predict disease outcomes in women with hormone receptor-positive advanced stage breast cancer treated with first-line endocrine therapy

Purpose: Endocrine based therapy is an effective strategy to manage hormone receptor-positive, human epidermal growth factor receptor 2-negative (HR+/HER2-) advanced breast cancer (ABC). However, nearly all patients exhibit/develop either de novo or acquired resistance. While prognostic biomarkers of endocrine responsiveness are well established for the adjuvant treatment in ER+ breast cancer, less is known regarding prognostic and predictive biomarkers of response in the first line ABC setting. We sought to develop a clinical calculator based on clinical criteria for predicting progression-free survival (PFS) and overall survival (OS) of women with HR+/HER2- ABC who will be receiving endocrine monotherapy as first-line treatment for ABC.

Methods: The development of the clinical calculator will be based on data from modern clinical trials in women with HR+/HER2- ABC. The studies to be included in the final analyses are given in Table 1. The control arm data from trials1-6 will form the training dataset (N = 1,223) and be used to construct the clinical prediction models. Variables considered include age, race, ECOG status, disease measurability, body mass index, disease-free interval, number of metastatic sites, locations of metastatic sites, prior endocrine therapy, and prior chemotherapy. Missing values will be imputed using single imputation with all variables included in the imputation model. For continuous variables, restricted cubic splines will be used to determine if non-linear effects may be more appropriate. The Lasso regression will be used as a variable selection technique to reduce the dimensionality of covariates; initially all pairwise interactions will be included in the model. Following Lasso regression, the multivariable Cox proportional hazards models will be constructed for PFS and OS including only variables retained in Lasso. The final model will be internally validated for discrimination and calibration using 10-fold cross-validation. External validation will be performed using control arm data from EGF 30008 (N = 536).

Results: To date, control arm data from four trials (trials 1-4) have been received. The preliminary results presented here are based on pooled data from C40503 and LEA, for which data elements have been harmonized. Models for predicting PFS and OS have good calibration and are associated with bias-corrected C-indices of 0.61 and 0.65, respectively. These models will be updated using pooled data from trials 1-6.

Conclusions: Our preliminary data demonstrate that clinical calculators based on baseline clinical factors can provide accurate prediction of PFS and OS in patients with HR+/HER2- ABC treated with first-line ET. If validated, these tools may be used for risk stratification in future clinical trials and to identify patients who may require more or less aggressive therapy.

Table 1:Studies to be includedTrial NumberTrial NameTrial PISample Size in Control Arm1C40503Maura Dickler152 (letrozole)2LEAMiguel Martin179 (letrozole)3FACTJonas Bergh188 (anastrozole)4FALCONJohn Robertson194 (anastrozole)5S0226Rita Mehta345 (anastrozole)6MONARCH 3Matthew Goetz165 (nonsteroidal AI)7EGF 30008Stephen Johnston536 (letrozole)

Citation Format: Polley M-YC, Dickler MN, Johnston S, Goetz MP, de la Haba J, Loibl S, Mehta RS, Bergh J, Roberston J, Barlow W, Liu H, Tenner K, Martin M. A clinical calculator to predict disease outcomes in women with hormone receptor-positive advanced stage breast cancer treated with first-line endocrine therapy [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-07-05.