Assessing housing exposures and interventions that impact healthy cities: a systematic overview of reviews

AIM

There are direct links between housing and health. However, there is a lack of systematic reviews that bring together the evidence to outline the health impacts of exposures in housing and housing interventions. This article aims to address this gap by synthesising systematic reviews on the themes of housing exposures and interventions.

METHODS

We searched four databases: Scopus (Elsevier), PsycINFO (OvidSP), Science Citation Index and Social Science Citation Index (Web of Science Core Collection), and the Sociology Collection (Proquest). We used keywords related to 'health' and 'city*' and included all types of reviews. We extracted data into a predesigned extraction form and synthesised information narratively.

RESULTS

745 articles were identified and screened, of which 256 reviews were included and 16 (6%) related to housing. All reviews related to housing exposures found that poor housing, including crowding, coldness, dampness, mould, and indoor air pollution had a negative impact on health. Most reviews found that housing interventions such as housing refurbishment, heating, and energy efficiency interventions positively impacted health outcomes. An online toolkit was developed to disseminate and communicate this research: https://www.healthycitiescommission.org/toolkit/.

CONCLUSION

Governments have a pivotal role in addressing health issues related to housing interventions and exposures in housing. This includes interventions through building regulations following international guidance and financial assistance to encourage housing modifications that will improve health.

Choosing Midwifery - The perceptions and experiences of Black, Asian and Minority Ethnic applicants to midwifery programmes: A mixed methods study

AIM

to explore recruitment to UK midwifery programmes from the perspective of applicants from Black, Asian and Minority Ethnic (BAME) groups and describe the perceptions and experiences of the application process for these applicants and those from white backgrounds.

BACKGROUND

Midwifery in the Global North is an overwhelmingly white profession. This lack of diversity has been cited as a factor in the poorer outcomes experienced by women from non-white backgrounds. There is a need for midwifery programmes to recruit and support more ethnically and racially diverse cohorts if this situation is to be addressed. Very little is currently known about the recruitment experiences of midwifery applicants.

DESIGN

A mixed methods study comprising a survey and individual interview or focus group. The study was conducted between September 2020 and March 2021 in three universities in South East England. Participants comprised 440 applicants to midwifery programmes and 13 current or recently qualified BAME midwifery students.

FINDINGS

Although many survey findings in respect to choosing a midwifery programme were broadly similar between candidates from BAME and non-BAME backgrounds, some trends were noted. More BAME applicants cited school/college rather than family as encouraging. More BAME applicants also indicated that they would consider issues of diversity when selecting a place of study, and BAME respondents appeared less likely to consider location and university life. Survey and focus group findings combined may indicate deficits in social capital available to BAME midwifery applicants. Focus group findings in particular suggest multiple experiences of challenge and inequity at all stages of the application process, together with a perception that midwifery is a niche and white profession. Applicants value proactive support from universities and would appreciate increased diversity, opportunities for mentorship and an individualised approach to recruitment.

CONCLUSIONS

BAME applicants to midwifery can face additional challenges which have an impact on their ability to secure a place. There is a need to reposition midwifery as an inclusive and welcoming option for people from all backgrounds and to develop equitable recruitment processes that value a range of skills and life experiences.

Factors Associated With Normal Physiologic Birth for Women Who Labor In Water: A Secondary Analysis of A Prospective Observational Study

Introduction

Research to understand factors associated with normal physiologic birth (unassisted vaginal birth, spontaneous labor onset without epidural analgesia, spinal, or general anesthetic, without episiotomy) is required. Laboring and/or giving birth in water has been shown to be associated with a high proportion of physiologic birth but with little understanding of factors that may influence this outcome. This study explored factors associated with normal physiologic birth for women who labored in water.

Methods

We conducted a secondary analysis of a UK‐based prospective observational study of 8064 women at low risk of childbirth complications who labored in water. Consecutive women were recruited from birth settings in England, Scotland, and Northern Ireland. Planned place of birth, maternal characteristics, intrapartum events, and maternal and neonatal outcomes were measured. Univariable and multivariable logistic regression modelling explored factors associated with normal physiologic birth.

Results

In total, 5758 (71.4%) of women who labored in water had a normal physiologic birth. Planned birth in the community (adjusted odds ratio [aOR], 2.58; 95% CI, 2.22‐2.99) or at an alongside midwifery unit (aOR, 1.21; 95% CI, 1.04‐1.41) was positively associated with normal physiologic birth compared with planned birth in an obstetric unit. Duration of second stage (aOR, 0.66; 95% CI, 0.62‐0.70), duration in the pool [aOR, 0.93; 95% CI, 0.90‐0.96), and birth weight of the neonate (aOR, 0.74; 95% CI, 0.65‐0.85) were negatively associated with normal physiologic birth. Parity was not associated with normal physiologic birth in multivariate analyses.

Discussion

Our findings largely reflected wider research, both in and out of water. We found midwifery‐led birth settings may increase the likelihood of normal physiologic birth among healthy women who labor in water, irrespective of parity. This association supports growing evidence demonstrating the importance of planned place of birth on reducing intervention rates and adds to research on labor and birth in water.

Safety and passivation of faecal contamination in waste

Absorbent hygiene wastes like nappies and incontinence pads are ubiquitous in municipal and healthcare waste streams around the world as they are convenient products used in child-care and adult incontinence management. Absorbent Hygiene Product (AHP) manufacturing is resource-intensive as the products are required to be of the highest value as they are in almost-constant contact with sensitive body parts. The potential for recovering such valuable resources such as cellulose-based fibres and super-absorbent polymers for reuse in non-food sectors like the construction and wastewater industries has been considered in this study. Appropriate decontamination via chemical methods have been examined using AHPs contaminated with human-associated bacteria.

Findings suggest that for simulated AHP wastes inoculated with 108–109 CFU g-1 of human-associated bacteria like Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis, and Streptococcus pyogenes, a 1:1 ratio of 0.5% calcium hypochlorite/AHP waste is adequate to inactivate the bacteria particularly when combined with an inorganic salt for at least 60 min. Specifically, 4 to 5 log10 reductions were observed. Following such disinfection, material storage and temperatures above 25ºC minimise incidences of microbial regrowth. The disinfection protocol was not found to adversely affect the AHP quality. Overall, such findings suggest that AHP recycling is a potential alternative to current AHP waste disposal practices like incineration (with or without energy recovery) and landfilling.

Antibiotic usage in chronic rhinosinusitis: analysis of national primary care electronic health records

BACKGROUND

The aim of this study was to analyse rates of antibiotic usage in chronic rhinosinusitis (CRS) in primary care in England and Wales and to identify trends in the choice of antibiotics prescribed.

METHODS

We used linked data from primary care EHRs, with diagnoses coded using the Read terminology (Clinical Practice Research Datalink) from consenting general practices, with (2) hospital care administrative records (Hospital Episode Statistics, HES recorded using ICD-10).

RESULTS

From the total of 88,317 cases of CRS identified, 40,462 (46%) had an antibiotic prescription within 5 days of their first CRS diagnosis. Of patients receiving a first line antibiotic within 5 days of CRS diagnosis, over 80%, in each CRS group, received a subsequent prescription for an antibiotic. Within 5 years of diagnosis, 9% are estimated to have had 5 or more antibiotics within 5 days of a CRS-related consultation. With data spanning almost 20 years, it was possible to discern trends in antibiotics prescriptions, with a clear increasing trend towards macrolide and tetracycline prescribing evident.

CONCLUSIONS

While antibiotics may have been prescribed for acute exacerbations, we have found high rates of repeated antibiotic prescription in some patients with CRS in primary care. There is a need for stronger evidence on the role of antibiotics in CRS management.

Risk of mortality and cardiovascular events following macrolide prescription in chronic rhinosinusitis patients: a cohort study using linked primary care electronic health records

BACKGROUND

Macrolide antibiotics have demonstrated important anti-inflammatory and immunomodulatory properties in chronic rhinosinusitis (CRS) patients. However, reports of increased risks of cardiovascular events have led to safety concerns. We investigated the risk of all-cause and cardiac death, and cardiovascular outcomes, associated with macrolide use.

METHODOLOGY

Observational cohort (1997-2016) using linked data from the Clinical Practice Research Datalink, Hospital Episodes Statistics, and the Office for National Statistics. Patients aged 16-80 years with CRS prescribed a macrolide antibiotic or penicillin were included, comparing prescriptions for macrolide antibiotics to penicillin. Outcomes were all-cause mortality, cardiac death, myocardial infarction, stroke, diagnosis of peripheral vascular disease, and cardiac arrhythmia.

RESULTS

Analysis included 320,798 prescriptions received by 66,331 patients. There were 3,251 deaths, 815 due to cardiovascular causes, 925 incident myocardial infarctions, 859 strokes, 637 diagnoses of peripheral vascular disease, and 1,436 cardiac arrhythmias. A non-statistically significant trend towards increased risk of myocardial infarction during the first 30 days following macrolide prescription was observed. No statistically significant short- or long-term risks were observed for macrolide prescription. No significant risks were identified for clarithromycin in particular.

CONCLUSIONS

Although not statistically significant, our best estimates suggest an increased short-term risk of myocardial infarction in patients with CRS following macrolide prescription, supporting previous observational evidence. However, confounding by indication remains a possible explanation for this apparent increased risk. We found no evidence of longer term increased risks.

Offensive waste valorisation in the UK: Assessment of the potentials for absorbent hygiene product (AHP) recycling

Offensive human waste refers to non-hazardous waste that contains body fluids from non-infectious humans, comprised of post-consumer Absorbent Hygiene Products (AHPs), swabs, dressings, bedding, gloves, and other materials. While this waste category requires more stringent handling, storage and disposal measures than general waste, its non-hazardous nature suggests that there are opportunities for waste valorisation. An inventory of 200 offensive human waste bags collected from various healthcare institutions in South-Eastern England show that about 76% of the waste is comprised of AHPs, most of which are adult incontinence pads and child nappies. Mixed plastics comprised of predominantly HDPE represent 9% of the waste. To evaluate the potentials for offensive human waste valorisation, small-scale separation tests involving artificially-soiled nappies and associated mixed plastic packaging wastes have been performed. Findings suggest that about 50% of the total superabsorbent polymer is recoverable from fluff pulp fractions, recoveries of which are unaffected by the presence of ionic species typically present in human waste. On the other hand, recovery of mixed plastic packaging is more challenging. Overall, however, findings suggest that viable AHP recycling is possible if recyclate materials are targeted towards non-food related markets outlets such as the construction and land remediation sectors.

Reducing Redundant Anaerobic Therapy Through Spaced Education and Antimicrobial Stewardship Interventions

BACKGROUND

Decreasing the use of redundant anaerobic therapy is a key target for antimicrobial stewardship. Education techniques that optimize knowledge retention could be an important component of reducing these regimens.

METHODS

We implemented a quality improvement project that incorporated spaced education to reduce the use of redundant anaerobic therapy. The initial interventions (November through December 2015) included education in a hospital-wide newsletter and review of redundant anaerobic regimens by the antimicrobial stewardship program. A spaced education module was then developed with the gastroenterology (GI) service, which had a relatively high rate of redundant anaerobic therapy use. Ten questions with teaching points were delivered to GI physicians at spaced intervals over 2 to 4 weeks (February through March 2016). Knowledge scores were compared at initial and final question presentation using generalized estimating equations. Interrupted time-series analysis was used to compare the rates of redundant-metronidazole-days per 1000 patient-days among patients in the patients admitted to the GI service and those in the non-GI group before and after the intervention.

RESULTS

Of 66 GI physicians, 56 (85%) participated in the spaced education activity. After the intervention, their knowledge scores on all the questions improved, and their mean knowledge score increased from 57% to 86% (P < .001). Nearly all (91%) of the participants were very or generally satisfied with the activity. In the GI group, the rate of redundant-metronidazole-days decreased from 26.2 to 13.0 per 1000 patient-days (relative risk [RR], 0.45 [95% confidence interval (CI), 0.27-0.73]; P = .001). This rate in the non-GI group also decreased from 5.47 to 2.18 per 1000 patient-days (RR, 0.47 [95% CI, 0.36-0.60]; P < .001) after our interventions.

CONCLUSIONS

Spaced education is an effective approach for teaching antimicrobial stewardship topics. Focused provider education was associated with a sustained reduction in the use of redundant anaerobic therapy.

Perceptions of Physician Order Entry: Results of a Cross-Site Qualitative Study

Objective: To identify perspectives of success factors for implementing computerized physician order entry (POE) in the inpatient setting.

Design: Qualitative study by a multidisciplinary team using data from observation, focus groups, and both formal and informal interviews. Data were analyzed using a grounded approach to develop a taxonomy of patterns and themes from the transcripts and field notes.

Results: A taxonomy of ten high level themes was developed, including 1) separating POE from other processes, 2) terms, concepts, and connotations, 3) context, 4) tradeoffs, 5) conflicts and contradictions, 6) collaboration and trust, 7) leaders and bridgers, 8) the organization of information, 9) the ongoing nature of implementation, and 10) temporal concerns.

Conclusion: The identified success factors indicate that POE implementation is an iterative and difficult process, but informants perceive it is worth the effort.

PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS

BACKGROUND

The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk as high as those associated with rare BRCA2 mutations. We aimed to estimate the relative risks associated with specific rare variants in PALB2, CHEK2 and ATM via a multicentre case-control study.

METHODS

We genotyped 10 rare mutations using the custom iCOGS array: PALB2 c.1592delT, c.2816T>G and c.3113G>A, CHEK2 c.349A>G, c.538C>T, c.715G>A, c.1036C>T, c.1312G>T, and c.1343T>G and ATM c.7271T>G. We assessed associations with breast cancer risk (42 671 cases and 42 164 controls), as well as prostate (22 301 cases and 22 320 controls) and ovarian (14 542 cases and 23 491 controls) cancer risk, for each variant.

RESULTS

For European women, strong evidence of association with breast cancer risk was observed for PALB2 c.1592delT OR 3.44 (95% CI 1.39 to 8.52, p=7.1×10-5), PALB2 c.3113G>A OR 4.21 (95% CI 1.84 to 9.60, p=6.9×10-8) and ATM c.7271T>G OR 11.0 (95% CI 1.42 to 85.7, p=0.0012). We also found evidence of association with breast cancer risk for three variants in CHEK2, c.349A>G OR 2.26 (95% CI 1.29 to 3.95), c.1036C>T OR 5.06 (95% CI 1.09 to 23.5) and c.538C>T OR 1.33 (95% CI 1.05 to 1.67) (p≤0.017). Evidence for prostate cancer risk was observed for CHEK2 c.1343T>G OR 3.03 (95% CI 1.53 to 6.03, p=0.0006) for African men and CHEK2 c.1312G>T OR 2.21 (95% CI 1.06 to 4.63, p=0.030) for European men. No evidence of association with ovarian cancer was found for any of these variants.

CONCLUSIONS

This report adds to accumulating evidence that at least some variants in these genes are associated with an increased risk of breast cancer that is clinically important.

Evaluation of Control Strategies for Porcine Reproductive and Respiratory Syndrome (PRRS) in Swine Breeding Herds Using a Discrete Event Agent-Based Model

The objective of this study was to develop a discrete event agent-based stochastic model to explore the likelihood of the occurrence of porcine reproductive and respiratory syndrome (PRRS) outbreaks in swine herds with different PRRS control measures in place. The control measures evaluated included vaccination with a modified-live attenuated vaccine and live-virus inoculation of gilts, and both were compared to a baseline scenario where no control measures were in place. A typical North American 1,000-sow farrow-to-wean swine herd was used as a model, with production and disease parameters estimated from the literature and expert opinion. The model constructed herein was not only able to capture individual animal heterogeneity in immunity to and shedding of the PRRS virus, but also the dynamic animal flow and contact structure typical in such herds under field conditions. The model outcomes included maximum number of females infected per simulation, and time at which that happened and the incidence of infected weaned piglets during the first year of challenge-virus introduction. Results showed that the baseline scenario produced a larger percentage of simulations resulting in outbreaks compared to the control scenarios, and interestingly some of the outbreaks occurred over long periods after virus introduction. The live-virus inoculation scenario showed promising results, with fewer simulations resulting in outbreaks than the other scenarios, but the negative impacts of maintaining a PRRS-positive population should be considered. Finally, under the assumptions of the current model, neither of the control strategies prevented the infection from spreading to the piglet population, which highlights the importance of maintaining internal biosecurity practices at the farrowing room level.

Contralateral Hypoplastic Venous Draining Sinuses Are Associated with Elevated Intracranial Pressure in Unilateral Cerebral Sinovenous Thrombosis

Variations in cerebral venous development can influence the ability to regulate drainage. In cerebral sinovenous thrombosis, these variations can be associated with elevated intracranial pressure. We present a series of pediatric patients with unilateral cerebral sinovenous thrombosis and investigate whether the contralateral venous sinus size increases the risk of developing elevated intracranial pressure. Patients diagnosed with a unilateral cerebral sinovenous thrombosis were identified by querying our institutional radiology data base. The difference in the occurrence of elevated intracranial pressure in patients with cerebral sinovenous thrombosis with and without hypoplastic venous sinuses was studied. Twelve cases of unilateral cerebral sinovenous thrombosis met the inclusion criteria and had sufficient images. Six patients had hypoplastic contralateral venous sinuses. The presence of hypoplastic contralateral venous sinus in the setting of thrombosis of a dominant sinus was associated with elevation of intracranial pressure (83% versus 0%, P = .015). Patients with cerebral sinovenous thrombosis and contralateral hypoplastic venous sinuses are at higher risk of developing elevated ICP and may benefit from screening with an ophthalmologic examination.

Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus

BACKGROUND

Multiple recent genome-wide association studies (GWAS) have identified a single nucleotide polymorphism (SNP), rs10771399, at 12p11 that is associated with breast cancer risk.

METHOD

We performed a fine-scale mapping study of a 700 kb region including 441 genotyped and more than 1300 imputed genetic variants in 48,155 cases and 43,612 controls of European descent, 6269 cases and 6624 controls of East Asian descent and 1116 cases and 932 controls of African descent in the Breast Cancer Association Consortium (BCAC; http://bcac.ccge.medschl.cam.ac.uk/ ), and in 15,252 BRCA1 mutation carriers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Stepwise regression analyses were performed to identify independent association signals. Data from the Encyclopedia of DNA Elements project (ENCODE) and the Cancer Genome Atlas (TCGA) were used for functional annotation.

RESULTS

Analysis of data from European descendants found evidence for four independent association signals at 12p11, represented by rs7297051 (odds ratio (OR) = 1.09, 95 % confidence interval (CI) = 1.06-1.12; P = 3 × 10(-9)), rs805510 (OR = 1.08, 95 % CI = 1.04-1.12, P = 2 × 10(-5)), and rs1871152 (OR = 1.04, 95 % CI = 1.02-1.06; P = 2 × 10(-4)) identified in the general populations, and rs113824616 (P = 7 × 10(-5)) identified in the meta-analysis of BCAC ER-negative cases and BRCA1 mutation carriers. SNPs rs7297051, rs805510 and rs113824616 were also associated with breast cancer risk at P < 0.05 in East Asians, but none of the associations were statistically significant in African descendants. Multiple candidate functional variants are located in putative enhancer sequences. Chromatin interaction data suggested that PTHLH was the likely target gene of these enhancers. Of the six variants with the strongest evidence of potential functionality, rs11049453 was statistically significantly associated with the expression of PTHLH and its nearby gene CCDC91 at P < 0.05.

CONCLUSION

This study identified four independent association signals at 12p11 and revealed potentially functional variants, providing additional insights into the underlying biological mechanism(s) for the association observed between variants at 12p11 and breast cancer risk.

Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer

Common variants in 94 loci have been associated with breast cancer including 15 loci with genome-wide significant associations (P<5 × 10(-8)) with oestrogen receptor (ER)-negative breast cancer and BRCA1-associated breast cancer risk. In this study, to identify new ER-negative susceptibility loci, we performed a meta-analysis of 11 genome-wide association studies (GWAS) consisting of 4,939 ER-negative cases and 14,352 controls, combined with 7,333 ER-negative cases and 42,468 controls and 15,252 BRCA1 mutation carriers genotyped on the iCOGS array. We identify four previously unidentified loci including two loci at 13q22 near KLF5, a 2p23.2 locus near WDR43 and a 2q33 locus near PPIL3 that display genome-wide significant associations with ER-negative breast cancer. In addition, 19 known breast cancer risk loci have genome-wide significant associations and 40 had moderate associations (P<0.05) with ER-negative disease. Using functional and eQTL studies we implicate TRMT61B and WDR43 at 2p23.2 and PPIL3 at 2q33 in ER-negative breast cancer aetiology. All ER-negative loci combined account for ∼11% of familial relative risk for ER-negative disease and may contribute to improved ER-negative and BRCA1 breast cancer risk prediction.

Network, cluster and risk factor analyses for porcine reproductive and respiratory syndrome using data from swine sites participating in a disease control program

The objectives of this study were to describe networks of Ontario swine sites and their service providers (including trucking, feed, semen, gilt and boar companies); to categorize swine sites into clusters based on site-level centrality measures, and to investigate risk factors for porcine reproductive and respiratory syndrome (PRRS) using information gathered from the above-mentioned analyses. All 816 sites included in the current study were enrolled in the PRRS area regional control and elimination projects in Ontario. Demographics, biosecurity and network data were collected using a standardized questionnaire and PRRS status was determined on the basis of available diagnostic tests and assessment by site veterinarians. Two-mode networks were transformed into one-mode dichotomized networks. Cluster and risk factor analyses were conducted separately for breeding and growing pig sites. In addition to the clusters obtained from cluster analyses, other explanatory variables of interest included: production type, type of animal flow, use of a shower facility, and number of neighboring swine sites within 3km. Unadjusted univariable analyses were followed by two types of adjusted models (adjusted for production systems): a generalizing estimation equation model (GEE) and a generalized linear mixed model (GLMM). Results showed that the gilt network was the most fragmented network, followed by the boar and truck networks. Considering all networks simultaneously, approximately 94% of all swine sites were indirectly connected. Unadjusted risk factor analyses showed significant associations between almost all predictors of interest and PRRS positivity, but these disappeared once production system was taken into consideration. Finally, the vast majority of the variation on PRRS status was explained by production system according to GLMM, which shows the highly correlated nature of the data, and raises the point that interventions at this level could potentially have high impact in PRRS status change and/or maintenance.

Descriptive analysis and spatial epidemiology of porcine reproductive and respiratory syndrome (PRRS) for swine sites participating in area regional control and elimination programs from 3 regions of Ontario

The objectives of this study were to describe demographics, basic biosecurity practices, ownership structure, and prevalence of porcine reproductive and respiratory syndrome (PRRS) in swine sites located in 3 regions in Ontario, and investigate the presence of spatial clustering and clusters of PRRS positive sites in the 3 regions. A total of 370 swine sites were enrolled in Area Regional Control and Elimination projects in Niagara, Watford, and Perth from 2010 to 2013. Demographics, biosecurity, and site ownership data were collected using a standardized questionnaire and site locations were obtained from an industry organization. Status was assigned on the basis of available diagnostic tests and/or assessment by site veterinarians. Spatial dependence was investigated using the D-function, the spatial scan statistic test and the spatial relative risk method. Results showed that the use of strict all-in all-out (AIAO) pig flow and shower before entry are uncommon biosecurity practices in swine sites, but a larger proportion of sites reported having a Danish entry. The prevalence of PRRS in the 3 regions ranged from 17% to 48% and localized high and low risk clusters were detected. Sites enrolled in the PRRS control projects were characterized by membership in multiple and overlapping ownership structures and networks, which complicates the way the results of monitoring and disease management measures are communicated to the target population.

Abstract 1924: Genes associated with histopathologic features of triple negative breast tumors predict molecular subtypes

Distinct subtypes of triple negative (TN) breast cancer have currently been identified by tumor expression profiling and are thought to be influenced by the tumor microenvironment. However, little is known about the relationship between distinguishing histopathologic features of TN tumors, which reflect aspects of both tumor behavior and tumor microenvironment, and molecular TN subtypes. We analyzed whole genome expression profiles of 593 TN tumors from the Triple Negative Breast Cancer Consortium (TNBCC) using the Illumina Whole Genome DASL array. Histopathologic review of mitotic index, grade, trabecular pattern, growth pattern, involution, presence of ductal carcinoma in situ, and degree of lymphoid infiltrate, necrosis, fibrosis, and lobulitis was completed for 310 of these tumors. Clusters were identified both agnostically and using genes associated with these histopathologic features, and subtypes were evaluated for enriched pathways and associations with histopathologic features. Agnostic clustering identified four stable clusters which represented a basal-like (BL) signature, a luminal signature with overexpression of androgen receptor and targets, an immune signature, and a stromal (STR) signature. Overall, the TN tumors tended to have little or no necrosis (91%), high grade (88%), a high mitotic index (80%), fibrosis (77%), an epicentric growth pattern (62%), incomplete lobular involution (55%), trabecular structures (37%), lymphocytic infiltration (25%), adjacent ductal carcinoma in situ (24%), and variable amounts of lobulitis. Using a combined total of 2,776 unique probes individually associated with the ten histopathologic features measured, we identified six distinct TN subtypes, with an additional BL and STR signature compared to the four agnostic subtypes. Our findings suggest that histopathologic features that reflect heterogeneity in tumor cell structure and behavior as well as the tumor microenvironment, particularly the presence of lymphocytic infiltrate, are critical for TN subtype identification. Further work is needed to validate these signatures and to better understand the immunologic pathways associated with each subtype.

Citation Format: Kristen Purrington, Daniel Visscher, Drakoulis Yannoukakos, Jane Carpenter, Heli Nevanlinna, Arto Mannerma, Xianshu Wang, Graham Giles, Wei Zheng, Angela Cox, Hiltrud Brauch, Ute Hamann, Diana Eccles, Celine M. Vachon, Fergus J. Couch. Genes associated with histopathologic features of triple negative breast tumors predict molecular subtypes. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1924. doi:10.1158/1538-7445.AM2015-1924

Prediction of breast cancer risk based on profiling with common genetic variants

BACKGROUND

Data for multiple common susceptibility alleles for breast cancer may be combined to identify women at different levels of breast cancer risk. Such stratification could guide preventive and screening strategies. However, empirical evidence for genetic risk stratification is lacking.

METHODS

We investigated the value of using 77 breast cancer-associated single nucleotide polymorphisms (SNPs) for risk stratification, in a study of 33 673 breast cancer cases and 33 381 control women of European origin. We tested all possible pair-wise multiplicative interactions and constructed a 77-SNP polygenic risk score (PRS) for breast cancer overall and by estrogen receptor (ER) status. Absolute risks of breast cancer by PRS were derived from relative risk estimates and UK incidence and mortality rates.

RESULTS

There was no strong evidence for departure from a multiplicative model for any SNP pair. Women in the highest 1% of the PRS had a three-fold increased risk of developing breast cancer compared with women in the middle quintile (odds ratio [OR] = 3.36, 95% confidence interval [CI] = 2.95 to 3.83). The ORs for ER-positive and ER-negative disease were 3.73 (95% CI = 3.24 to 4.30) and 2.80 (95% CI = 2.26 to 3.46), respectively. Lifetime risk of breast cancer for women in the lowest and highest quintiles of the PRS were 5.2% and 16.6% for a woman without family history, and 8.6% and 24.4% for a woman with a first-degree family history of breast cancer.

CONCLUSIONS

The PRS stratifies breast cancer risk in women both with and without a family history of breast cancer. The observed level of risk discrimination could inform targeted screening and prevention strategies. Further discrimination may be achievable through combining the PRS with lifestyle/environmental factors, although these were not considered in this report.

Investigation of the Occurrence of Porcine Reproductive and Respiratory Virus in Swine Herds Participating in an Area Regional Control and Elimination Project in Ontario, Canada

The main goal of this study was to investigate the occurrence of porcine reproductive and respiratory syndrome virus (PRRSV)-specific genotypes in swine sites in Ontario (Canada) using molecular, spatial and network data from a porcine reproductive and respiratory syndrome (PRRS) regional control project. For each site, location, animal movement service provider (truck companies), PRRSV status and sequencing data of the open reading frame 5 (ORF5) were obtained. Three-kilometre buffers were created to evaluate neighbourhood characteristics for each site. Social network analysis was conducted on swine sites and trucking companies to assemble the network and define network components. Three different PRRSV genotypes were used as outcomes for statistical analysis based on the region's phylogenetic tree of the ORF5. Multivariable exact logistic regression was conducted to investigate the association between being positive for a specific genotype and two main exposures of interest: (i) having at least one neighbour within three km also positive for the same genotype outside the production system and (ii) having at least one positive site for the same genotype in the same truck network component outside the production system. Results showed that the importance of area spread and truck network on PRRSV occurrence differed according to genotype. Additionally, the Ontario PRRS database appears suitable for conducting regional disease investigations. Finally, the use of relatively new tools available for network, spatial and molecular analysis could be useful in investigation, control and prevention of endemic infectious diseases in animal populations.

Refined histopathological predictors of BRCA1 and BRCA2 mutation status: a large-scale analysis of breast cancer characteristics from the BCAC, CIMBA, and ENIGMA consortia

INTRODUCTION

The distribution of histopathological features of invasive breast tumors in BRCA1 or BRCA2 germline mutation carriers differs from that of individuals with no known mutation. Histopathological features thus have utility for mutation prediction, including statistical modeling to assess pathogenicity of BRCA1 or BRCA2 variants of uncertain clinical significance. We analyzed large pathology datasets accrued by the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) and the Breast Cancer Association Consortium (BCAC) to reassess histopathological predictors of BRCA1 and BRCA2 mutation status, and provide robust likelihood ratio (LR) estimates for statistical modeling.

METHODS

Selection criteria for study/center inclusion were estrogen receptor (ER) status or grade data available for invasive breast cancer diagnosed younger than 70 years. The dataset included 4,477 BRCA1 mutation carriers, 2,565 BRCA2 mutation carriers, and 47,565 BCAC breast cancer cases. Country-stratified estimates of the likelihood of mutation status by histopathological markers were derived using a Mantel-Haenszel approach.

RESULTS

ER-positive phenotype negatively predicted BRCA1 mutation status, irrespective of grade (LRs from 0.08 to 0.90). ER-negative grade 3 histopathology was more predictive of positive BRCA1 mutation status in women 50 years or older (LR = 4.13 (3.70 to 4.62)) versus younger than 50 years (LR = 3.16 (2.96 to 3.37)). For BRCA2, ER-positive grade 3 phenotype modestly predicted positive mutation status irrespective of age (LR = 1.7-fold), whereas ER-negative grade 3 features modestly predicted positive mutation status at 50 years or older (LR = 1.54 (1.27 to 1.88)). Triple-negative tumor status was highly predictive of BRCA1 mutation status for women younger than 50 years (LR = 3.73 (3.43 to 4.05)) and 50 years or older (LR = 4.41 (3.86 to 5.04)), and modestly predictive of positive BRCA2 mutation status in women 50 years or older (LR = 1.79 (1.42 to 2.24)).

CONCLUSIONS

These results refine likelihood-ratio estimates for predicting BRCA1 and BRCA2 mutation status by using commonly measured histopathological features. Age at diagnosis is an important variable for most analyses, and grade is more informative than ER status for BRCA2 mutation carrier prediction. The estimates will improve BRCA1 and BRCA2 variant classification and inform patient mutation testing and clinical management.

Genetic variation in mitotic regulatory pathway genes is associated with breast tumor grade

Mitotic index is an important component of histologic grade and has an etiologic role in breast tumorigenesis. Several small candidate gene studies have reported associations between variation in mitotic genes and breast cancer risk. We measured associations between 2156 single nucleotide polymorphisms (SNPs) from 194 mitotic genes and breast cancer risk, overall and by histologic grade, in the Breast Cancer Association Consortium (BCAC) iCOGS study (n = 39 067 cases; n = 42 106 controls). SNPs in TACC2 [rs17550038: odds ratio (OR) = 1.24, 95% confidence interval (CI) 1.16-1.33, P = 4.2 × 10(-10)) and EIF3H (rs799890: OR = 1.07, 95% CI 1.04-1.11, P = 8.7 × 10(-6)) were significantly associated with risk of low-grade breast cancer. The TACC2 signal was retained (rs17550038: OR = 1.15, 95% CI 1.07-1.23, P = 7.9 × 10(-5)) after adjustment for breast cancer risk SNPs in the nearby FGFR2 gene, suggesting that TACC2 is a novel, independent genome-wide significant genetic risk locus for low-grade breast cancer. While no SNPs were individually associated with high-grade disease, a pathway-level gene set analysis showed that variation across the 194 mitotic genes was associated with high-grade breast cancer risk (P = 2.1 × 10(-3)). These observations will provide insight into the contribution of mitotic defects to histological grade and the etiology of breast cancer.

A framework for biobank sustainability

Each year funding agencies and academic institutions spend millions of dollars and euros on biobanking. All funding providers assume that after initial investments biobanks should be able to operate sustainably. However the topic of sustainability is challenging for the discipline of biobanking for several major reasons: the diversity in the biobanking landscape, the different purposes of biobanks, the fact that biobanks are dissimilar to other research infrastructures and the absence of universally understood or applicable value metrics for funders and other stakeholders. In this article our aim is to delineate a framework to allow more effective discussion and action around approaches for improving biobank sustainability. The term sustainability is often used to mean fiscally self-sustaining, but this restricted definition is not sufficient for biobanking. Instead we propose that biobank sustainability should be considered within a framework of three dimensions - financial, operational, and social. In each dimension, areas of focus or elements are identified that may allow different types of biobanks to distinguish and evaluate the relevance, likelihood, and impact of each element, as well as the risks to the biobank of failure to address them. Examples of practical solutions, tools and strategies to address biobank sustainability are also discussed.

Abstract 3266: Expression quantitative trait locus analysis of triple negative breast cancer

Recent studies have shown that associations between common genetic variation and gene expression in breast tumors provide insight into the functional mechanisms underlying breast cancer risk loci. However, the relationship between genetic variation, gene expression, and risk of triple negative (TN) breast cancer remains largely unexplored. We performed a genome-wide expression quantitative trait locus (eQTL) analysis of TN breast cancer using 668 formalin-fixed paraffin embedded TN tumors from the Triple Negative Breast Cancer Consortium (TNBCC) to identify novel genes relevant to TN breast cancer risk and to further explore the biology underlying known TN risk loci. Cis-eQTLs were defined as correlations between single nucleotide polymorphisms (SNP) and expression of genes within 1Mb, and trans-eQTLs were defined as the remainder of all SNP-gene correlations. In a genome-wide analysis, we identified 68,012 cis-eQTLs, representing correlations between 42,193 SNPs and 2,092 genes that were significant at a 10% false discovery rate (FDR). We also identified 70 trans-eQTLs across two unique genes at the same FDR threshold. Five cis-eQTLs involved SNPs previously associated with TN breast cancer risk (p&lt;5.0x10-5) in 3,700 TN cases and 4,700 controls from the TNBCC. Three of these, located on chromosomes 5p (cis-eQTL p=4.8x10-34; risk p=1.1x10-7), 7p (cis-eQTL p=6.1x10-10; risk p=1.3x10-7), and 17q (cis-eQTL p=1.8x10-15; risk p=2.9x10-7), have previously been reported in public databases of normal tissue. The remaining two TN breast cancer cis-eQTLs, located on chromosomes 8q (cis-eQTL p=6.3x10-6, risk p=8.3x10-6) and 14q (cis-eQTL p=3.1x10-6, risk p=1.2x10-5), have not been reported as eQTLs in other tissues. In addition, 12 of 25 known TN breast cancer risk loci (PEX14, MDM4, 2q31.1, ESR1, 11q13.1, 11q24.3, 12p13.1, PTHLH, NTN4, 12q24, 19p13.1, MLK1), contained at least one significant cis-eQTL. In summary, we have identified five cis-eQTLs that may identify novel risk loci for TN breast cancer.

Citation Format: Kristen S. Purrington, Drakoulis Yannoukakos, Jane Carpenter, Heli Nevanlinna, Angela Cox, Gianluca Severi, Christine Ambrosone, Amanda Ewart Toland, Andrew K. Godwin, Hiltrud Brauch, Peter A. Fasching, Penelope Miron, Jenny Chang-Claude, Nicholas G. Martin, Grant W. Montgomery, Vessela Kristensen, Hoda Anton-Culver, Paul Goodfellow, Janet E. Olson, Hugues Sicotte, Naresh Prodduturi, Daniel W. Visscher, Jeanette E. Eckel-Passow, S. Keith Anderson, Seth Slettedahl, Curtis Olswold, Xianshu Wang, V. Shane Pankratz, Susan Slager, Wei Zheng, Arto Mannermaa, Ute Hamann, Diana M. Eccles, Celine M. Vachon, Fergus J. Couch. Expression quantitative trait locus analysis of triple negative breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3266. doi:10.1158/1538-7445.AM2014-3266

Genome-wide association study identifies 25 known breast cancer susceptibility loci as risk factors for triple-negative breast cancer

Triple-negative (TN) breast cancer is an aggressive subtype of breast cancer associated with a unique set of epidemiologic and genetic risk factors. We conducted a two-stage genome-wide association study of TN breast cancer (stage 1: 1529 TN cases, 3399 controls; stage 2: 2148 cases, 1309 controls) to identify loci that influence TN breast cancer risk. Variants in the 19p13.1 and PTHLH loci showed genome-wide significant associations (P < 5 × 10(-) (8)) in stage 1 and 2 combined. Results also suggested a substantial enrichment of significantly associated variants among the single nucleotide polymorphisms (SNPs) analyzed in stage 2. Variants from 25 of 74 known breast cancer susceptibility loci were also associated with risk of TN breast cancer (P < 0.05). Associations with TN breast cancer were confirmed for 10 loci (LGR6, MDM4, CASP8, 2q35, 2p24.1, TERT-rs10069690, ESR1, TOX3, 19p13.1, RALY), and we identified associations with TN breast cancer for 15 additional breast cancer loci (P < 0.05: PEX14, 2q24.1, 2q31.1, ADAM29, EBF1, TCF7L2, 11q13.1, 11q24.3, 12p13.1, PTHLH, NTN4, 12q24, BRCA2, RAD51L1-rs2588809, MKL1). Further, two SNPs independent of previously reported signals in ESR1 [rs12525163 odds ratio (OR) = 1.15, P = 4.9 × 10(-) (4)] and 19p13.1 (rs1864112 OR = 0.84, P = 1.8 × 10(-) (9)) were associated with TN breast cancer. A polygenic risk score (PRS) for TN breast cancer based on known breast cancer risk variants showed a 4-fold difference in risk between the highest and lowest PRS quintiles (OR = 4.03, 95% confidence interval 3.46-4.70, P = 4.8 × 10(-) (69)). This translates to an absolute risk for TN breast cancer ranging from 0.8% to 3.4%, suggesting that genetic variation may be used for TN breast cancer risk prediction.

Forehead reflectance photoplethysmography to monitor heart rate: preliminary results from neonatal patients

Around 5%-10% of newborn babies require some form of resuscitation at birth and heart rate (HR) is the best guide of efficacy. We report the development and first trial of a device that continuously monitors neonatal HR, with a view to deployment in the delivery room to guide newborn resuscitation. The device uses forehead reflectance photoplethysmography (PPG) with modulated light and lock-in detection. Forehead fixation has numerous advantages including ease of sensor placement, whilst perfusion at the forehead is better maintained in comparison to the extremities. Green light (525 nm) was used, in preference to the more usual red or infrared wavelengths, to optimize the amplitude of the pulsatile signal. Experimental results are presented showing simultaneous PPG and electrocardiogram (ECG) HRs from babies (n = 77), gestational age 26-42 weeks, on a neonatal intensive care unit. In babies ⩾32 weeks gestation, the median reliability was 97.7% at ±10 bpm and the limits of agreement (LOA) between PPG and ECG were +8.39 bpm and -8.39 bpm. In babies <32 weeks gestation, the median reliability was 94.8% at ±10 bpm and the LOA were +11.53 bpm and -12.01 bpm. Clinical evaluation during newborn deliveries is now underway.