Assessment of adherence to at-home oral anti-infective therapy among paediatric patients discharged from a Quebec hospital

OBJECTIVES

Non-adherence to anti-infective therapy contributes to treatment failure and the emergence of bacterial resistance. This study aimed to assess at-home adherence, by paediatric patients, to oral anti-infective (OAI) therapy prescribed for treatment of acute infections and to explore the factors contributing to non-adherence.

METHODS

This prospective descriptive study involved French-speaking patients under 16 years of age who were discharged with one or more OAIs prescribed for home administration for a maximum of 30 days. Telephone surveys were used to assess overall adherence, which consisted of primary adherence (patient's ability to procure the medication) and secondary adherence (patient's ability to take the treatment as prescribed).

RESULTS

Overall, 51.7% (30/58) of patients were adherent to OAI therapy, with 100% primary adherence (n=69/69) and 51.7% secondary adherence (n=30/58). On average, patients took 98% of the total number of doses prescribed, and non-adherence was related mostly to not following medication administration schedules (63.3% of patients followed the exact schedule). Indeed, the adherence rate for patients taking one or two doses per day was twice the rate for patients taking more than two doses per day (81.8% vs 44.7%, p=0.043).

CONCLUSIONS

Half of the paediatric patients treated for acute infections were non-adherent to OAI therapy at home. Interventions are needed to improve this situation.

Design and Development of an Escape Game as a Knowledge Transfer Tool in Preparation for an Accreditation Visit in a Health Care Facility

Background: Knowledge transfer helps health care staff to be competent, well informed, and up to date. It also contributes to adherence to standards and best practices. Objectives: To design, implement, and evaluate an escape game based on a selection of Accreditation Canada required organizational practices (ROPs). Methods: This prospective descriptive study involved nurses and pharmacists in a health care centre. An escape game based on 6 ROPs was designed. The game was played by teams of participants in a patient room within the centre, with each game lasting 25 minutes. Participants’ satisfaction with various aspects of their experience was assessed. Results: A total of 200 people (52 teams) participated in the escape game. About half of the teams (n = 28) completed the game within the allotted time (average completion time 20 minutes, 53 seconds; standard deviation [SD] 2 minutes, 45 seconds). On average, 1.32 (SD 0.88) clues were provided to successful teams and 1.88 (SD 0.95) to unsuccessful teams. Participants were very satisfied with their experience. However, members of unsuccessful teams had significantly lower agreement that the escape game was relevant to their practice and that it was an effective method of communication. Conclusions: An escape game based on a selection of ROPs was successfully implemented as part of the hospital’s preparation for an accreditation visit. Use of an escape game as a knowledge transfer tool was appreciated by the staff.

A Descriptive Chemical Composition of Concentrated Bud Macerates through an Optimized SPE-HPLC-UV-MS2 Method-Application to Alnus glutinosa, Ribes nigrum, Rosa canina, Rosmarinus officinalis and Tilia tomentosa

Concentrated bud macerates (CBMs) are obtained from meristematic tissues such as buds and young shoots by maceration in a solvent composed of glycerin, water and ethanol (1/1/1/, v/v). Their traditional utilization in gemmotherapy has gained interest in the past years, and the knowledge of their chemical characterization can provide commercial arguments, particularly to secure their quality control. Therefore, an optimized method for phytochemical analysis including glycerol removal by a preliminary solid phase extraction (SPE) followed by compound identification using high performance liquid chromatography coupled with ultra-violet and tandem mass detectors (HPLC-UV-MS²) was developed. This method was applied on 5 CBMs obtained from Alnus glutinosa, Ribesnigrum, Rosmarinus officinalis, Rosa canina and Tilia tomentosa in order to determinate their chemical composition. Their antioxidant effects were also investigated by radical scavenging activity assays (DPPH and ORAC). Glycerol removal improved the resolution of HPLC chemical profiles and allowed us to perform TLC antioxidant screening. Our approach permitted the identification of 57 compounds distributed in eight major classes, three of them being common to all macerates including nucleosides, phenolic acids and glycosylated flavonoids. Quantification of the later class as a rutin equivalent (RE) showed a great disparity between Rosa canina macerate (809 mg RE/L), and the other ones (from 175 to 470 mg RE/L). DPPH and ORAC assays confirmed the great activity of Rosa canina (4857 and 6479 μmol TE/g of dry matter, respectively). Finally, phytochemical and antioxidant analysis of CBMs strengthened their phytomedicinal interest in the gemmotherapy field.

Revisiting the Molecular Interactions between the Tumor Protein TCTP and the Drugs Sertraline/Thioridazine

TCTP protein is a pharmacological target in cancer and TCTP inhibitors such as sertraline have been evaluated in clinical trials. The direct interaction of TCTP with the drugs sertraline and thioridazine has been reported in vitro by SPR experiments to be in the ∼30-50 μM K_d range (Amson et al. Nature Med 2012), supporting a TCTP-dependent mode of action of the drugs on tumor cells. However, the molecular details of the interaction remain elusive although they are crucial to improve the efforts of on-going medicinal chemistry. In addition, TCTP can be phosphorylated by the Plk-1 kinase, which is indicative of poor prognosis in several cancers. The impact of phosphorylation on TCTP structure/dynamics and binding with therapeutical ligands remains unexplored. Here, we combined NMR, TSA, SPR, BLI and ITC techniques to probe the molecular interactions between TCTP with the drugs sertraline and thioridazine. We reveal that drug binding is much weaker than reported with an apparent ∼mM K_d and leads to protein destabilization that obscured the analysis of the published SPR data. We further demonstrate by NMR and SAXS that TCTP S46 phosphorylation does not promote tighter interaction between TCTP and sertraline. Accordingly, we question the supported model in which sertraline and thioridazine directly interact with isolated TCTP in tumor cells and discuss alternative modes of action for the drugs in light of current literature.

Reversing Reactivity: Stereoselective Desulfurative 1,2-trans-O-Glycosylation of Anomeric Thiosugars with Carboxylic Acids under Copper or Cobalt Catalysis

We have discovered a new mode of reactivity of 1-thiosugars in the presence of Cu(II) or Co(II) for a stereoselective O-glycosylation reaction. The process involves the use of a catalytic amount of Cu(acac)₂ or Co(acac)₂ and Ag₂CO₃ as an oxidant in α,α,α-trifluorotoluene. Moreover, this protocol turned out to have a broad scope, allowing the preparation of a wide range of complex substituted O-glycoside esters in good to excellent yields with an exclusive 1,2-trans-selectivity. The late-stage modification of pharmaceuticals by this method was also demonstrated. To obtain a closer insight into the reaction mechanism, cyclic voltammetry was performed.

Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing data

The emergence of next-generation sequencing (NGS) has revolutionized the way of reaching a genome sequence, with the promise of potentially providing a comprehensive characterization of DNA variations. Nevertheless, detecting somatic mutations is still a difficult problem, in particular when trying to identify low abundance mutations, such as subclonal mutations, tumour-derived alterations in body fluids or somatic mutations from histological normal tissue. The main challenge is to precisely distinguish between sequencing artefacts and true mutations, particularly when the latter are so rare they reach similar abundance levels as artefacts. Here, we present needlestack, a highly sensitive variant caller, which directly learns from the data the level of systematic sequencing errors to accurately call mutations. Needlestack is based on the idea that the sequencing error rate can be dynamically estimated from analysing multiple samples together. We show that the sequencing error rate varies across alterations, illustrating the need to precisely estimate it. We evaluate the performance of needlestack for various types of variations, and we show that needlestack is robust among positions and outperforms existing state-of-the-art method for low abundance mutations. Needlestack, along with its source code is freely available on the GitHub platform: https://github.com/IARCbioinfo/needlestack.

Conformité du circuit du médicament dans les unités de soins et les cliniques externes : étude observationnelle transversale au sein d’un établissement universitaire de 500 lits

RÉSUMÉContexte : En établissement de santé, le circuit du médicament est complexe, puisqu’il compte plus de 50 étapes. Pour évaluer la conformité du circuit du médicament de notre établissement, nous avons mis en place un processus annuel d’audit.Objectifs : L’objectif principal vise à décrire la conformité de certaines étapes du circuit du medicament (principalement la gestion des médicaments) aux unités de soins et dans les cliniques externes d’un centre hospitalier universitaire mère-enfant. L’objectif secondaire consiste à comparer les résultats à ceux des audits précédents.Méthodes : Il s’agit d’une étude descriptive observationnelle transversal réalisée à l’été 2018 dans les unités de soins (n = 34) et les cliniques externes (n = 28) de l’établissement. Les données ont été recueillies à partir d’une grille d’audit.Résultats : En 2018, le taux de conformité de l’ensemble des unités de soins aux critères mentionnés dans la grille d’audit variait de 32 % à 100 %. Par rapport à l’année précédente, le taux de conformité à 30 critères est demeuré inchangé et celui à quatre critères s’est détérioré. La conformité à 35 % des critères (12/34) était totale à plus de 85 %. En 2018, le taux de conformité de l’ensemble des cliniques externes aux critères mentionnés dans la grille d’audit variait de 0 % à 100 %. Le taux de conformité à un critère s’est amélioré, celui à 21 critères est demeuré inchangé et celui à deux critères s’est détérioré. La conformité à 32 % des critères (9/28) était totale à plus de 85 %. Trente-cinq recommandations ont été formulées au comité pharmacie-soins infirmiers et un rapport personnalisé a été transmis aux gestionnaires.Conclusions : Cette étude descriptive observationnelle transversale décrit le degré de conformité du circuit du médicament relatif à la gestion des médicaments, principalement dans les unités de soins et les cliniques externes. Cette démarche originale à l’initiative du Département de pharmacie a abouti à la formulation de 35 recommandations au comité pharmacie-soins infirmiers, ce qui a permis d’améliorer la sécurité du circuit du médicament dans les unités de soins et les cliniques externes. ABSTRACTBackground: In the hospital setting, the medication-use system is complex, having more than 50 steps. To assess the compliance of the study organization’s medication-use system with established criteria, an annual audit process was developed.Objectives: The primary objective was to describe the compliance of certain steps in the medication-use system (mainly medication management) in care units and outpatient clinics of a mother and child university hospital centre. The secondary objective was to compare the current results with those of previous audits.Methods:This cross-sectional descriptive observational study was carried out in summer 2018 in patient care units (n = 34) and outpatient clinics (n = 28) of the study hospital. Data were collected according to an audit matrix.Results: In 2018, the rate of compliance with audit criteria varied between 32% and 100% for the patient care units. Relative to the previous year, the compliance rate remained unchanged for 30 criteria and worsened for 4 criteria. For 35% of the criteria (12/34), compliance was greater than 85%. In 2018, the rate of compliance with audit criteria varied between 0% and 100% for the outpatient clinics. The compliance rate increased for one criterion, remained unchanged for 21 criteria, and worsened for 2 criteria. For 32% of the criteria (9/28), compliance was more than 85%. Thirty-five recommendations were made to the pharmacy and nursing care committee, and a personalized report was sent to managers.Conclusions:This cross-sectional descriptive observational study reports the degree to which the medication-use system complies with medication management criteria, mainly in patient care units and outpatients’ clinics. This original approach from the Pharmacy Department led to the formulation of 35 recommendations to the pharmacy and nursing care committee, which helped to improve the safety of the medication-use system in patient care units and outpatient clinics.

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BACKGROUND

In the hospital setting, the medication-use system is complex, having more than 50 steps. To assess the compliance of the study organization's medication-use system with established criteria, an annual audit process was developed.

OBJECTIVES

The primary objective was to describe the compliance of certain steps in the medication-use system (mainly medication management) in care units and outpatient clinics of a mother and child university hospital centre. The secondary objective was to compare the current results with those of previous audits.

METHODS

This cross-sectional descriptive observational study was carried out in summer 2018 in patient care units (n = 34) and outpatient clinics (n = 28) of the study hospital. Data were collected according to an audit matrix.

RESULTS

In 2018, the rate of compliance with audit criteria varied between 32% and 100% for the patient care units. Relative to the previous year, the compliance rate remained unchanged for 30 criteria and worsened for 4 criteria. For 35% of the criteria (12/34), compliance was greater than 85%. In 2018, the rate of compliance with audit criteria varied between 0% and 100% for the outpatient clinics. The compliance rate increased for one criterion, remained unchanged for 21 criteria, and worsened for 2 criteria. For 32% of the criteria (9/28), compliance was more than 85%. Thirty-five recommendations were made to the pharmacy and nursing care committee, and a personalized report was sent to managers.

CONCLUSIONS

This cross-sectional descriptive observational study reports the degree to which the medication-use system complies with medication management criteria, mainly in patient care units and outpatients' clinics. This original approach from the Pharmacy Department led to the formulation of 35 recommendations to the pharmacy and nursing care committee, which helped to improve the safety of the medication-use system in patient care units and outpatient clinics.

Utilisation des jeux d’évasion en santé : une revue de littérature

RÉSUMÉContexte : Il existe différentes stratégies pédagogiques permettant l’apprentissage, tant en milieu universitaire qu’en milieu professionnel. Parmi toutes ces stratégies, on note l’émergence de simulation ayant recours au concept de jeu d’évasion.Objectif : L’objectif était de recenser les modalités entourant l’utilisation, la conception et la réalisation de jeux d’évasion dans le domaine de la santé.Sources des données : Les recherches sur Pubmed, Embase et CINAHL ont été effectuées jusqu’au 3 décembre 2018. Sélection des études : Toutes les études portant sur la conception ou la réalisation de jeux d’évasion dans le domaine de la santé, en anglais et en français, ont été incluses. Extraction des données : Le pays, la population cible, la conception, la réalisation, la méthode d’évaluation et les résultats ont été extraits.Synthèse des données : Sept résumés de communication affichée et neuf articles ont été inclus. Douze jeux d’évasion ont été réalisés aux États-Unis. Ils sont utilisés en médecine (n = 5), en pharmacie (n = 4), en sciences infirmières (n = 4) ainsi que dans d’autres disciplines (n = 3), principalement dans un cadre pédagogique universitaire (n = 12) mais aussi professionnel (n = 4). Leurs objectifs visaient à améliorer les connaissances (n = 8), à augmenter l’intérêt et la motivation des participants pour un sujet précis (n = 2) et à améliorer la cohésion et la communication dans une équipe (n = 2). Dix des jeux d’évasion décrits dans les articles étaient basés sur un scénario orienté vers la clinique. Dix équipes ont réalisé un débriefing avec les participants, une équipe n’en a pas fait et cinq articles ne mentionnaient pas cette information.Conclusion : Il existe peu de données entourant l’utilisation de jeux d’évasion en santé. Il est trop tôt pour juger de l’efficacité de cette approche. Toutefois, l’intérêt grandissant justifie l’instauration d’une veille documentaire pour suivre l’évolution et mieux comprendre la place de ce type de stratégie dans l’apprentissage en santé.ABSTRACTBackground: Many different teaching strategies are used to promote learning in an academic or professional environment. Among these can be noted the emergence of simulation, based on the concept of escape games.Objective: To identify methodologies relating to the use, design, and implementation of escape games in health care.Data Sources: The Pubmed, Embase, and CINAHL databases were searched up to December 3, 2018.Study Selection: All studies focusing on the design or development of escape games in the health care field (published in English or French) were included.Data Extraction: For each study, the country, target population, design, development, method of evaluation, and results were extracted for analysis.Data Synthesis: Seven poster abstracts and 9 published articles were included. Twelve escape games were developed in the United States. They were used in medicine (n = 5), pharmacy (n = 4), nursing (n = 4) and other fields (n = 3), mainly within academic teaching contexts (n = 12) but also in professional settings (n = 4). Their goals were to improve knowledge (n = 8), to increase participants’ interest and motivation regarding a specific topic (n = 2), and to improve cohesion and commu-nication within a team (n = 2). Ten of the escape games described in the articles were based on a clinical scenario. Ten of the research teams held debriefings with participants, and one did not; 5 articles did not report information about debriefing.Conclusions: Few data exist concerning the use of escape games in the health care setting, and it is too early to judge the efficiency of this approach to learning. However, growing interest justifies systematic monitoring of the literature to follow the evolution of such strategies and to better understand their place in health care education.

Utilisation des jeux d’évasion en santé : une revue de littérature

BACKGROUND

Many different teaching strategies are used to promote learning in an academic or professional environment. Among these can be noted the emergence of simulation, based on the concept of escape games.

OBJECTIVE

To identify methodologies relating to the use, design, and implementation of escape games in health care.

DATA SOURCES

The Pubmed, Embase, and CINAHL databases were searched up to December 3, 2018.

STUDY SELECTION

All studies focusing on the design or development of escape games in the health care field (published in English or French) were included.

DATA EXTRACTION

For each study, the country, target population, design, development, method of evaluation, and results were extracted for analysis.

DATA SYNTHESIS

Seven poster abstracts and 9 published articles were included. Twelve escape games were developed in the United States. They were used in medicine (n = 5), pharmacy (n = 4), nursing (n = 4) and other fields (n = 3), mainly within academic teaching contexts (n = 12) but also in professional settings (n = 4). Their goals were to improve knowledge (n = 8), to increase participants' interest and motivation regarding a specific topic (n = 2), and to improve cohesion and communication within a team (n = 2). Ten of the escape games described in the articles were based on a clinical scenario. Ten of the research teams held debriefings with participants, and one did not; 5 articles did not report information about debriefing.

CONCLUSIONS

Few data exist concerning the use of escape games in the health care setting, and it is too early to judge the efficiency of this approach to learning. However, growing interest justifies systematic monitoring of the literature to follow the evolution of such strategies and to better understand their place in health care education.

Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids

The worldwide incidence of pulmonary carcinoids is increasing, but little is known about their molecular characteristics. Through machine learning and multi-omics factor analysis, we compare and contrast the genomic profiles of 116 pulmonary carcinoids (including 35 atypical), 75 large-cell neuroendocrine carcinomas (LCNEC), and 66 small-cell lung cancers. Here we report that the integrative analyses on 257 lung neuroendocrine neoplasms stratify atypical carcinoids into two prognostic groups with a 10-year overall survival of 88% and 27%, respectively. We identify therapeutically relevant molecular groups of pulmonary carcinoids, suggesting DLL3 and the immune system as candidate therapeutic targets; we confirm the value of OTP expression levels for the prognosis and diagnosis of these diseases, and we unveil the group of supra-carcinoids. This group comprises samples with carcinoid-like morphology yet the molecular and clinical features of the deadly LCNEC, further supporting the previously proposed molecular link between the low- and high-grade lung neuroendocrine neoplasms.

Genetic subtypes of large cell neuroendocrine carcinoma (LCNEC) to predict response to chemotherapy

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Background: To treat LCNEC with non-small cell lung carcinoma type chemotherapy (NSCLC-ct, i.e. gemcitabine/taxanes or pemetrexed) or small cell lung carcinoma type (SCLC-ct, i.e. platinum-etoposide) is subject of debate. Molecular studies have identified two mutually exclusive subtypes in LCNEC, the co-mutated TP53 and RB1and the STK11/ KEAP1 (predominantly RB1 wildtype(wt)) group. We investigated if overall survival (OS) and progression free survival (PFS) correlates with targeted next-generation sequencing (TNGS) results in LCNEC treated with NSCLC-ct or SCLC-ct. Methods: For this population based retrospective cohort study all diagnoses of stage IV ct treated high grade neuroendocrine carcinomas (NEC, not being SCLC) were retrieved from the Netherlands Cancer Registry and Pathology Registry (PALGA) (2003-2012). Panel-consensus pathology revision of original tumor slides was performed on (N = 230) and TNGS for genes TP53, RB1, STK11 and KEAP1 analyzed with a multi-sample variant caller (Needlestack). Results: LCNEC was consensus diagnosed in 146/230 and 77 passed quality control for TNGS. Mean coverage was 2832x, a mutation(mt) in TP53 was present in 87%, RB1mt in 46%, STK11mt in 13% and KEAP1mt in 18% of sequenced LCNEC. RB1 was co-altered with TP53 in 94% of LCNEC; mutually exclusive to STK11mt (100%) but not KEAP1mt (57%). NSCLC-ct or SCLC-ct was specified in 92% of patients and RB1wt LCNEC treated with NSCLC-ct (n = 22) showed a trend to better OS compared to SCLC-ct (n = 13) (8.5 months (95% confidence interval (CI): [6.3-10.6]) vs. 5.8 [5.5-6.1] months, p = 0.055). Due to reported resistance in NECs we analyzed NSCLC-ct without pemetrexed-ct; OS was significantly longer for NSCLC-ct (n = 15) compared to SCLC-ct (9.6 [7.7-11.6] vs. 5.8 [5.5-6.1] months, p = 0.026). PFS of RB1wt NSCLC-ct treated patients was significantly longer than SCLC-ct (p = 0.044), without pemetrexed (p = 0.018). In patients with RB1mt LCNEC OS/PFS was not significantly different for NSCLC-ct vs. SCLC-ct. Conclusions: In LCNEC with RB1wt, NSCLC-ct correlates with a more favorable outcome compared to SCLC-ct. However, RB1mt LCNEC treated with NSCLC-ct do similarly worse as SCLC-ct. Prospective studies should be initiated.

Immuno-related polymorphisms and cervical cancer risk: The IARC multicentric case-control study

A small proportion of women who are exposed to infection with human-papillomavirus (HPV) develop cervical cancer (CC). Genetic factors may affect the risk of progression from HPV infection to cervical precancer and cancer. We used samples from the International Agency for Research on Cancer (IARC) multicentric case-control study to evaluate the association of selected genetic variants with CC. Overall, 790 CC cases and 717 controls from Algeria, Morocco, India and Thailand were included. Cervical exfoliated cells were obtained from control women and cervical exfoliated cells or biopsy specimens from cases. HPV-positivity was determined using a general primer GP5+/6+ mediated PCR. Unconditional logistic regression was used to estimate odds ratios (OR) and corresponding 95% confidence intervals (CI) of host genotypes with CC risk, using the homozygous wild type genotype as the referent category and adjusting by age and study centre. The association of polymorphisms with the risk of high-risk HPV-positivity among controls was also evaluated. A statistically significant association was observed between single nucleotide polymorphism (SNP) CHR6 rs2844511 and CC risk: the OR for carriers of the GA or GG genotypes was 0.70 (95% CI: 0.43-1.14) and 0.61 (95% CI: 0.38-0.98), respectively, relative to carriers of AA genotype (p-value for trend 0.03). We also observed associations of borderline significance with the TIPARP rs2665390 polymorphism, which was previously found to be associated with ovarian and breast cancer, and with the EXOC1 rs13117307 polymorphism, which has been linked to cervical cancer in a large study in a Chinese population. We confirmed the association between CC and the rs2844511 polymorphism previously identified in a GWAS study in a Swedish population. The major histocompatibility region of chromosome 6, or perhaps other SNPs in linkage disequilibrium, may be involved in CC onset.

Genome-wide association analyses identify new susceptibility loci for oral cavity and pharyngeal cancer

We conducted a genome-wide association study of oral cavity and pharyngeal cancer in 6,034 cases and 6,585 controls from Europe, North America and South America. We detected eight significantly associated loci (P < 5 × 10-8), seven of which are new for these cancer sites. Oral and pharyngeal cancers combined were associated with loci at 6p21.32 (rs3828805, HLA-DQB1), 10q26.13 (rs201982221, LHPP) and 11p15.4 (rs1453414, OR52N2-TRIM5). Oral cancer was associated with two new regions, 2p23.3 (rs6547741, GPN1) and 9q34.12 (rs928674, LAMC3), and with known cancer-related loci-9p21.3 (rs8181047, CDKN2B-AS1) and 5p15.33 (rs10462706, CLPTM1L). Oropharyngeal cancer associations were limited to the human leukocyte antigen (HLA) region, and classical HLA allele imputation showed a protective association with the class II haplotype HLA-DRB1*1301-HLA-DQA1*0103-HLA-DQB1*0603 (odds ratio (OR) = 0.59, P = 2.7 × 10-9). Stratified analyses on a subgroup of oropharyngeal cases with information available on human papillomavirus (HPV) status indicated that this association was considerably stronger in HPV-positive (OR = 0.23, P = 1.6 × 10-6) than in HPV-negative (OR = 0.75, P = 0.16) cancers.

A rare truncating BRCA2 variant and genetic susceptibility to upper aerodigestive tract cancer

Deleterious BRCA2 genetic variants markedly increase risk of developing breast cancer. A rare truncating BRCA2 genetic variant, rs11571833 (K3326X), has been associated with a 2.5-fold risk of lung squamous cell carcinoma but only a modest 26% increase in breast cancer risk. We analyzed the association between BRCA2 SNP rs11571833 and upper aerodigestive tract (UADT) cancer risk with multivariable unconditional logistic regression adjusted by sex and combinations of study and country for 5942 UADT squamous cell carcinoma case patients and 8086 control patients from nine different studies. All statistical tests were two-sided. rs11571833 was associated with UADT cancers (odds ratio = 2.53, 95% confidence interval = 1.89 to 3.38, P = 3x10(-10)) and was present in European, Latin American, and Indian populations but extremely rare in Japanese populations. The association appeared more apparent in smokers (current or former) compared with never smokers (P het = .026). A robust association between a truncating BRCA2 variant and UADT cancer risk suggests that treatment strategies orientated towards BRCA2 mutations may warrant further investigation in UADT tumors.

A systematic investigation of the contribution of genetic variation within the MHC region to HPV seropositivity

High-risk mucosal types of human papillomavirus (HPV) cause anogenital and oropharyngeal cancers, whereas cutaneous types (e.g. HPV8 and 77) are suspected to be involved in non-melanoma skin cancer. The antibody response to HPVs is a key determinant of protective immunity, but not all infected individuals seroconvert. Genetic variability of the host may have large impact on seroconversion. A previous genome-wide association study (GWAS) has identified a susceptibility locus (rs41270488) for HPV8 seropositivity within the major histocompatibility complex (MHC) region. To further study this locus, we imputed alleles at classical leukocyte antigen (HLA) loci using HLA*IMP:02 with a reference panel from the HapMap Project and the 1958 Birth Cohort, and conducted an integrated analysis among 4811 central European subjects to assess the contribution of classical HLA alleles and gene copy number variation (CNV) at the hypervariable DRB locus within the MHC region to HPV seropositivity at both the individual HPV type level and the phylogenetic species level. Our study provides evidence that the association noted between rs41270488 and HPV8 seropositivity is driven by two independent variants, namely DQB1*0301 [odds ratio (OR) = 1.51, 95% confidence interval (CI) = 1.36-1.68, P = 1.0 × 10(-14)] and DRB1*1101 (OR = 1.89, 95%CI = 1.57-2.28, P = 1.5 × 10(-11)) within the HLA class II region. Additionally, we identified two correlated alleles DRB1*0701 (OR = 1.67, 95%CI = 1.41-1.98, P = 2.6 × 10(-9)) and DQA1*0201 (OR = 1.67, 95%CI = 1.38-1.93, P = 1.7 × 10(-8)), to be associated with HPV77 seropositivity. Comparable results were observed through imputation using SNP2HLA with another reference panel from the Type 1 diabetes Genetics Consortium. This study provides support for an important role of HLA class II alleles in antibody response to HPV infection.

The 12p13.33/RAD52 locus and genetic susceptibility to squamous cell cancers of upper aerodigestive tract

Genetic variants located within the 12p13.33/RAD52 locus have been associated with lung squamous cell carcinoma (LUSC). Here, within 5,947 UADT cancers and 7,789 controls from 9 different studies, we found rs10849605, a common intronic variant in RAD52, to be also associated with upper aerodigestive tract (UADT) squamous cell carcinoma cases (OR = 1.09, 95% CI: 1.04-1.15, p = 6x10(-4)). We additionally identified rs10849605 as a RAD52 cis-eQTL inUADT(p = 1x10(-3)) and LUSC (p = 9x10(-4)) tumours, with the UADT/LUSC risk allele correlated with increased RAD52 expression levels. The 12p13.33 locus, encompassing rs10849605/RAD52, was identified as a significant somatic focal copy number amplification in UADT(n = 374, q-value = 0.075) and LUSC (n = 464, q-value = 0.007) tumors and correlated with higher RAD52 tumor expression levels (p = 6x10(-48) and p = 3x10(-29) in UADT and LUSC, respectively). In combination, these results implicate increased RAD52 expression in both genetic susceptibility and tumorigenesis of UADT and LUSC tumors.

Genetic variants in nicotine addiction and alcohol metabolism genes, oral cancer risk and the propensity to smoke and drink alcohol: a replication study in India

BACKGROUND

Genetic variants in nicotinic acetylcholine receptor and alcohol metabolism genes have been associated with propensity to smoke tobacco and drink alcohol, respectively, and also implicated in genetic susceptibility to head and neck cancer. In addition to smoking and alcohol, tobacco chewing is an important oral cancer risk factor in India. It is not known if these genetic variants influence propensity or oral cancer susceptibility in the context of this distinct etiology.

METHODS

We examined 639 oral and pharyngeal cancer cases and 791 controls from two case-control studies conducted in India. We investigated six variants known to influence nicotine addiction or alcohol metabolism, including rs16969968 (CHRNA5), rs578776 (CHRNA3), rs1229984 (ADH1B), rs698 (ADH1C), rs1573496 (ADH7), and rs4767364 (ALDH2).

RESULTS

The CHRN variants were associated with the number of chewing events per day, including in those who chewed tobacco but never smoked (P =  0.003, P =  0.01 for rs16969968 and rs578776 respectively). Presence of the variant allele contributed to approximately 13% difference in chewing frequency compared to non-carriers. While no association was observed between rs16969968 and oral cancer risk (OR =  1.01, 95% CI =  0.83- 1.22), rs578776 was modestly associated with a 16% decreased risk of oral cancer (OR =  0.84, 95% CI =  0.72- 0.98). There was little evidence for association between polymorphisms in genes encoding alcohol metabolism and oral cancer in this population.

CONCLUSION

The association between rs16969968 and number of chewing events implies that the effect on smoking propensity conferred by this gene variant extends to the use of smokeless tobacco.

Association between TP53 R249S mutation and polymorphisms in TP53 intron 1 in hepatocellular carcinoma

Over 100 single nucleotide polymorphisms (SNP) are validated in the TP53 tumor suppressor gene. They define haplotypes, which may differ in their activities. Therefore, mutation in cancer may occur at different rates depending upon haplotypes. However, these associations may be masked by differences in mutations types and causes of mutagenesis. We have analyzed the associations between 19 SNPs spanning the TP53 locus and a single specific aflatoxin-induced TP53 mutation (R249S) in 85 in hepatocellular carcinoma cases and 132 controls from Thailand. An association with R249S mutation (P = 0.007) was observed for a combination of two SNPs (rs17882227 and rs8064946) in a linkage disequilibrium block extending from upstream of exon 1 to the first half of intron 1. This domain contains two coding sequences overlapping with TP53 (WRAP53 and Hp53int1) suggesting that sequences in TP53 intron 1 encode transcripts that may modulate R249S mutation rate in HCC.

Genome-wide association study of HPV seropositivity

High-risk α mucosal types of human papillomavirus (HPV) cause anogenital and oropharyngeal cancers, whereas β cutaneous HPV types (e.g. HPV8) have been implicated in non-melanoma skin cancer. Although antibodies against the capsid protein L1 of HPV are considered as markers of cumulative exposure, not all infected persons seroconvert. To identify common genetic variants that influence HPV seroconversion, we performed a two-stage genome-wide association study. Genome-wide genotyping of 316 015 single nucleotide polymorphisms was carried out using the Illumina HumanHap300 BeadChip in 4811 subjects from a central European case-control study of lung, head and neck and kidney cancer that had serology data available on 13 HPV types. Only one association met genome-wide significance criteria, namely that between HPV8 seropositivity and rs9357152 [odds ratio (OR) = 1.37, 95% confidence interval (CI) = 1.24-1.50 for the minor allele G; P=1.2 × 10(-10)], a common genetic variant (minor allele frequency=0.33) located within the major histocompatibility complex (MHC) II region at 6p21.32. This association was subsequently replicated in an independent set of 2344 subjects from a Latin American case-control study of head and neck cancer (OR=1.35, 95% CI=1.18-1.56, P=2.2 × 10(-5)), yielding P=1.3 × 10(-14) in the combined analysis (P-heterogeneity=0.87). No heterogeneity was noted by cancer status (controls/lung cancer cases/head and neck cancer cases/kidney cancer cases). This study provides a proof of principle that genetic variation plays a role in antibody reactivity to HPV infection.

Genetic polymorphisms in 15q25 and 19q13 loci, cotinine levels, and risk of lung cancer in EPIC

BACKGROUNDS

Multiple polymorphisms affecting smoking behavior have been identified through genome-wide association studies. Circulating levels of the nicotine metabolite cotinine is a marker of recent smoking exposure. Hence, genetic variants influencing smoking behavior are expected to be associated with cotinine levels.

METHODS

We conducted an analysis in a lung cancer case-control study nested within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. We investigated the effects of single-nucleotide polymorphisms (SNP) previously associated with smoking behavior on (i) circulating cotinine and (ii) lung cancer risk. A total of 894 cases and 1,805 controls were analyzed for cotinine and genotyped for 10 polymorphisms on 7p14, 8p11, 10q23, 15q25, and 19q13.

RESULTS

Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CHRNA3 on 15q25, rs16969968 and rs578776, were associated with cotinine (P = 0.001 and 0.03, respectively) in current smokers and with lung cancer risk (P < 0.001 and P = 0.001, respectively). Two 19q13 variants, rs7937 and rs4105144, were associated with increased cotinine (P = 0.003 and P < 0.001, respectively) but decreased lung cancer risk (P = 0.01 for both, after adjusting for cotinine). Variants in 7p14, 8p11, and 10q23 were not associated with cotinine or lung cancer risk.

CONCLUSIONS

15q25 and 19q13 SNPs were associated with circulating cotinine. The directions of association for 15q25 variants with cotinine were in accordance with that expected of lung cancer risk, whereas SNPs on 19q13 displayed contrasting associations of cotinine and lung cancer that require further investigation.

IMPACT

This study is the largest to date investigating the effects of polymorphisms affecting smoking behavior on lung cancer risk using circulating cotinine measures as proxies for recent smoking behavior.

International Lung Cancer Consortium: coordinated association study of 10 potential lung cancer susceptibility variants

BACKGROUND

Analysis of candidate genes in individual studies has had only limited success in identifying particular gene variants that are conclusively associated with lung cancer risk. In the International Lung Cancer Consortium (ILCCO), we conducted a coordinated genotyping study of 10 common variants selected because of their prior evidence of an association with lung cancer. These variants belonged to candidate genes from different cancer-related pathways including inflammation (IL1B), folate metabolism (MTHFR), regulatory function (AKAP9 and CAMKK1), cell adhesion (SEZL6) and apoptosis (FAS, FASL, TP53, TP53BP1 and BAT3).

METHODS

Genotype data from 15 ILCCO case-control studies were available for a total of 8431 lung cancer cases and 11 072 controls of European descent and Asian ethnic groups. Unconditional logistic regression was used to model the association between each variant and lung cancer risk.

RESULTS

Only the association between a non-synonymous variant of TP53BP1 (rs560191) and lung cancer risk was significant (OR = 0.91, P = 0.002). This association was more striking for squamous cell carcinoma (OR = 0.86, P = 6 x 10(-4)). No heterogeneity by center, ethnicity, smoking status, age group or sex was observed. In order to confirm this association, we included results for this variant from a set of independent studies (9966 cases/11,722 controls) and we reported similar results. When combining all these studies together, we reported an overall OR = 0.93 (0.89-0.97) (P = 0.001). This association was significant only for squamous cell carcinoma [OR = 0.89 (0.85-0.95), P = 1 x 10(-4)].

CONCLUSION

This study suggests that rs560191 is associated to lung cancer risk and further highlights the value of consortia in replicating or refuting published genetic associations.

Obesity and cancer: Mendelian randomization approach utilizing the FTO genotype

BACKGROUND

Obesity is a risk factor for several cancers although appears to have an inverse association with cancers strongly related to tobacco. Studying obesity is difficult due to numerous biases and confounding.

METHODS

To avoid these biases we used a Mendelian randomization approach incorporating an analysis of variants in the FTO gene that are strongly associated with BMI levels among 7000 subjects from a study of lung, kidney and upper-aerodigestive cancer.

RESULTS

The FTO A allele which is linked with increased BMI was associated with a decreased risk of lung cancer (allelic odds ratio (OR) = 0.92, 95% confidence interval (CI) 0.84-1.00). It was also associated with a weak increased risk of kidney cancer, which was more apparent before the age of 50 (OR = 1.44, CI 1.09-1.90).

CONCLUSION

Our results highlight the potential for genetic variation to act as an unconfounded marker of environmentally modifiable factors, and offer the potential to obtain estimates of the causal effect of obesity. However, far larger sample sizes than studied here will be required to undertake this with precision.

Polymorphisms in genes of nucleotide and base excision repair: risk and prognosis of colorectal cancer

OBJECTIVES

We have undertaken a comprehensive study of common polymorphisms in genes of DNA repair, exploring both the risk of developing colorectal cancer and the prognosis of patients.

METHODS

Subjects from a case-control study (377 cases and 329 controls) designed to assess gene-environment interactions were genotyped by use of an oligonucleotide microarray and the arrayed primer extension technique. Twenty-eight single nucleotide polymorphisms in 15 DNA repair genes were included. The candidate genes belong to different DNA repair pathways: base excision repair (OGG1, LIG3, APEX, POLB, XRCC1, PCNA, and MUTYH), nucleotide excision repair (ERCC1, ERCC2, ERCC4, and ERCC5), double-strand breaks repair (XRCC2, XRCC3, and XRCC9), and reversion repair (MGMT) genes.

RESULTS

Polymorphism OGG1 S326C was associated with an increased risk of colorectal cancer [odds ratio (OR), 2.3; 95% confidence interval (95% CI), 1.1-5.0], the risk being higher in younger individuals. A haplotype of ERCC1 was associated with increased risk (OR, 2.3; 95% CI, 1.0-5.3). POLB P242R was also associated with decreased risk (OR, 0.23; 95% CI, 0.05-0.99), although the number of variant allele carriers was low. In the univariate analysis, adjusted for age, sex, and Dukes' stage, three polymorphisms were significantly associated with better prognosis: XRCC1 R399Q [hazard ratio (HR), 0.38; 95% CI, 0.17-0.85], XRCC3 T141M (HR, 0.66; 95% CI, 0.45-0.97), and MGMT L84F (HR, 0.14; 95% CI, 0.02-0.99). ERCC1 19007T>C was associated with worse prognosis (HR, 1.51; 95% CI, 1.01-2.27). In a multivariate analysis, only XRCC1 R399Q and ERCC1 19007T>C remained significant. These associations were stronger among patients receiving adjuvant chemotherapy.

CONCLUSIONS

Although the overall effect of DNA repair genes in colorectal cancer etiology seems limited, their influence in the response to chemotherapy and prognosis may be more relevant. This knowledge may help to clarify the utility of specific adjuvant treatments according to the individual genetic background.

A comprehensive analysis of phase I and phase II metabolism gene polymorphisms and risk of colorectal cancer

OBJECTIVES

Sporadic colorectal cancer (CRC) is considered a multifactorial disease where multiple exposures interact with the individual genetic background resulting in risk modulation. We performed an association study aimed to investigate the role of single nucleotide polymorphisms (SNPs) within genes of phase I (CYP1A1, CYP1A2, CYP1B1, CYP2A6, CYP2D6, CYP2E1, CYP2C9, CYP2C19, CYP3A4, ADH2, EPHX1) and phase II of the xenobiotic metabolism (ALDH2, COMT, GSTA2, GSTA4, GSTM1, GSTM3, GSTP1, GSTT2, MTHFR, NAT1, NAT2, NQO1, MnSOD2, SULT1A1, TPMT).

METHODS

We genotyped 377 cases and 326 controls, by use of an oligonucleotide micro-array and the arrayed primer extension technique (APEX).

RESULTS

N-acetyl-transferase 1 'rapid' phenotype and CYP1A2 -164C>A carriers were associated with increased risk of CRC, confirming data reported in previous studies. Interestingly, homozygotes for allele 48G within CYP1B1, a variant with an increased activity towards several substrates including sex hormones, were at increased risk (OR=2.81, 95% CI 1.32-5.99). Moreover, CYP1A1 SNPs T461N and -1738A>C were associated with a reduced risk of cancer (OR=0.52; 95% CI 0.31-0.88 and OR=0.69, 95% CI 0.50-0.94 for carriers, respectively).

CONCLUSIONS

The present data suggest a role for CYP1B1 and CYP1A1 as new candidate genes in the etiology of CRC and confirm the carcinogenic role of aromatic amines metabolism for colorectum.

Polymorphisms of the Dopamine Receptor Gene DRD2 and Colorectal Cancer Risk

Sporadic colorectal cancer is considered a multifactorial disease in which multiple exposures interact with the individual genetic background resulting in risk modulation. Recent experimental data suggest a role of dopamine and dopamine receptors in the control of proliferation of the cells of colon and gastrointestinal tract. To investigate whether polymorphisms within dopamine receptors genes could have a role in modulating the risk of sporadic colorectal cancer, we did a case-control association study and genotyped 370 cases and 327 controls for seven single-nucleotide polymorphisms (SNP) of DRD2 (-141Cdel, 957T>C, TaqIB, TaqIA, 1412A>G, S311C, and 3208G>T) by a microarray-based technique. Three SNPs within DRD2 were associated with colorectal cancer, with a maximum odds ratio of 2.28 (95% confidence interval, 1.38-3.76) for carriers of the functional SNP -141Cdel. The haplotype which includes -141Cdel, together with the variants 957C and 1412G, shows an odds ratio of 2.86 (95% confidence interval, 1.58-5.18), as compared with the most frequent haplotype. The SNPs within DRD2 associated with colorectal cancer are known to be related to reduced levels of D2 dopamine receptor. Thus, our data point to a possible role of dopamine receptor DRD2 in modulating the risk of colorectal cancer. Future studies on dopamine receptor-mediated signal transduction may provide new insight into the mechanisms of colorectal cancer and suggest new therapeutic strategies.

Generation of a DNA microarray for determination of E6 natural variants of human papillomavirus type 16

Infection with high-risk types of human papillomavirus (HPV) is necessary for the development of cervical cancer. However, the majority of the HPV infections are efficiently cleared by the immune system and only a minority persist and induce the development of malignant lesions. Several studies provided evidence that intratype genetic variations are implicated in determining the clinical outcome of HPV infections. In this study, we describe a DNA chip based on arrayed primer extension (APEX) for the analysis of the natural variants of HPV16, the most frequently detected type in cervical cancer world-wide. We show that HPV16 E6 variants are detected efficiently by APEX. In addition, APEX is a valid assay for the simultaneous detection of different HPV16 variants. Thus, it could be used for clinical studies aiming to analyse multiple infections with different HPV16 subtypes. Finally, since APEX combines the advantages of dideoxy DNA sequencing with the high-throughput potential of the microarray, it is suitable for the simultaneous analysis of a number of variable regions of HPV16 genome in large-scale studies.

A TP53 polymorphism is associated with increased risk of colorectal cancer and with reduced levels of TP53 mRNA

We undertook a case-control study to examine the possible associations of the TP53 variants Arg > Pro at codon 72 and p53PIN3, a 16 bp insertion/duplication in intron 3, with the risk of colorectal cancer (CRC). The p53PIN3 A2 allele (16 bp duplication) was associated with an increased risk (OR 1.55, 95% CI 1.10-2.18, P = 0.012), of the same order of magnitude as that observed in previous studies for other types of cancer. The Pro72 allele was weakly associated with CRC (OR = 1.34, 95% CI 0.98-1.84, P = 0.066). The possible functional role of p53PIN3 was investigated by examining the TP53 mRNA transcripts in 15 lymphoblastoid cell lines with different genotypes. The possibility that the insertion/deletion could lead to alternatively spliced mRNAs was excluded. However, we found reduced levels of TP53 mRNA associated with the A2 allele. In conclusion, the epidemiological study suggests a role for p53PIN3 in tumorigenesis, supported by the in vitro characterization of this variant.

Evaluation of a microarray for genotyping polymorphisms related to xenobiotic metabolism and DNA repair

We present an oligonucleotide microarray (“MetaboChip”) based on the arrayed primer extension (APEX) technique, allowing genotyping of single nucleotide polymorphisms (SNPs) in genes of interest for cancer susceptibility and pharmacogenetics. APEX consists of a sequencing reaction primed by an oligonucleotide anchored with its 5′ end to a glass slide and terminating one nucleotide before the polymorphic site. The extension with one fluorescently labeled dideoxynucleotide complementary to the template reveals the polymorphism. Ninety-three SNPs in 42 genes were selected among those resequenced in the context of the SNP500 project, using a set of 102 reference DNA samples from the Coriell Biorepository. Selected SNPs belong to the following genes: ADH1B, ALDH2, APEX, CDKN2A, COMT, CYP1A1, CYP1A2, CYP1B1, CYP2A6, CYP2C19, CYP2C9, CYP2E1, CYP3A4, DRD2, DRD4, EPHX1, ERCC1, ERCC2, ERCC4, ERCC5, GRPR, GSTA4, GSTM3, GSTP1, GSTT2, LIG3, MDM2, MGMT, MPO, NAT1, NAT2, NQO1, OGG1, PCNA, POLB, SLC6A3, SOD2, TP53, XRCC1, XRCC2, XRCC3, and XRCC9. We assessed the performance of APEX by comparing the results obtained with MetaboChip against those reported by the SNP500. Among 88 SNPs that yielded signals, 6 showed less than 99% of concordance, whereas 82 performed accurately, showing that APEX is a reliable and sensitive genotyping method.