Mapping structural variants to rare disease genes using long-read whole genome sequencing and trait-relevant polygenic scores

Recent studies have revealed the pervasive landscape of rare structural variants (rSVs) present in human genomes. rSVs can have extreme effects on the expression of proximal genes and, in a rare disease context, have been implicated in patient cases where no diagnostic single nucleotide variant (SNV) was found. Approaches for integrating rSVs to date have focused on targeted approaches in known Mendelian rare disease genes. This approach is intractable for rare diseases with many causal loci or patients with complex, multi-phenotype syndromes. We hypothesized that integrating trait-relevant polygenic scores (PGS) would provide a substantial reduction in the number of candidate disease genes in which to assess rSV effects. We further implemented a method for ranking PGS genes to define a set of core/key genes where a rSV has the potential to exert relatively larger effects on disease risk. Among a subset of patients enrolled in the Genomic Answers for Kids (GA4K) rare disease program (N=497), we used PacBio HiFi long-read whole genome sequencing (lrWGS) to identify rSVs intersecting genes in trait-relevant PGSs. Illustrating our approach in Autism (N=54 cases), we identified 1,827 deletions, 158 duplications, 619 insertions, and 14 inversions overlapping putative core/key PGS genes. Additionally, by integrating genomic constraint annotations from gnomAD, we observed that rare duplications overlapping putative core/key PGS genes were frequently in higher constraint regions compared to controls (P = 2×10-04). This difference was not observed in the lowest-ranked gene set (P = 0.18). Overall, our study provides a framework for the annotation of long-read rSVs from lrWGS data and prioritization of disease-linked genomic regions for downstream functional validation of rSV impacts. To enable reuse by other researchers, we have made SV allele frequencies and gene associations freely available.

Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics

The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of "local" when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.

Implementation of Practical Surface SARS-CoV-2 Surveillance in School Settings

Surface sampling for SARS-CoV-2 RNA detection has shown considerable promise to detect exposure of built environments to infected individuals shedding virus who would not otherwise be detected. Here, we compare two popular sampling media (VTM and SDS) and two popular workflows (Thermo and PerkinElmer) for implementation of a surface sampling program suitable for environmental monitoring in public schools. We find that the SDS/Thermo pipeline shows superior sensitivity and specificity, but that the VTM/PerkinElmer pipeline is still sufficient to support surface surveillance in any indoor setting with stable cohorts of occupants (e.g., schools, prisons, group homes, etc.) and may be used to leverage existing investments in infrastructure. IMPORTANCE The ongoing COVID-19 pandemic has claimed the lives of over 5 million people worldwide. Due to high density occupancy of indoor spaces for prolonged periods of time, schools are often of concern for transmission, leading to widespread school closings to combat pandemic spread when cases rise. Since pediatric clinical testing is expensive and difficult from a consent perspective, we have deployed surface sampling in SASEA (Safer at School Early Alert), which allows for detection of SARS-CoV-2 from surfaces within a classroom. In this previous work, we developed a high-throughput method which requires robotic automation and specific reagents that are often not available for public health laboratories such as the San Diego County Public Health Laboratory (SDPHL). Therefore, we benchmarked our method (Thermo pipeline) against SDPHL's (PerkinElmer) more widely used method for the detection and prediction of SARS-CoV-2 exposure. While our method shows superior sensitivity (false-negative rate of 9% versus 27% for SDPHL), the SDPHL pipeline is sufficient to support surface surveillance in indoor settings. These findings are important since they show that existing investments in infrastructure can be leveraged to slow the spread of SARS-CoV-2 not in just the classroom but also in prisons, nursing homes, and other high-risk, indoor settings.

Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School Settings

A promising approach to help students safely return to in person learning is through the application of sentinel cards for accurate high resolution environmental monitoring of SARS-CoV-2 traces indoors. Because SARS-CoV-2 RNA can persist for up to a week on several indoor surface materials, there is a need for increased temporal resolution to determine whether consecutive surface positives arise from new infection events or continue to report past events. Cleaning sentinel cards after sampling would provide the needed resolution but might interfere with assay performance. We tested the effect of three cleaning solutions (BZK wipes, Wet Wipes, RNase Away) at three different viral loads: "high" (4 × 104 GE/mL), "medium" (1 × 104 GE/mL), and "low" (2.5 × 103 GE/mL). RNase Away, chosen as a positive control, was the most effective cleaning solution on all three viral loads. Wet Wipes were found to be more effective than BZK wipes in the medium viral load condition. The low viral load condition was easily reset with all three cleaning solutions. These findings will enable temporal SARS-CoV-2 monitoring in indoor environments where transmission risk of the virus is high and the need to avoid individual-level sampling for privacy or compliance reasons exists. IMPORTANCE Because SARS-CoV-2, the virus that causes COVID-19, persists on surfaces, testing swabs taken from surfaces is useful as a monitoring tool. This approach is especially valuable in school settings, where there are cost and privacy concerns that are eliminated by taking a single sample from a classroom. However, the virus persists for days to weeks on surface samples, so it is impossible to tell whether positive detection events on consecutive days are a persistent signal or new infectious cases and therefore whether the positive individuals have been successfully removed from the classroom. We compare several methods for cleaning "sentinel cards" to show that this approach can be used to identify new SARS-CoV-2 signals day to day. The results are important for determining how to monitor classrooms and other indoor environments for SARS-CoV-2 virus.

Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases^1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing^4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

Emerging SARS-CoV-2 variants of concern were detected early and multiple cases of virus spread not captured by clinical genomic surveillance were identified using high-resolution wastewater and clinical sequencing.

SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp

Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions and to test whether our past observations linking SARS-CoV-2 abundance to Rothia sp. in hospitals also hold in a residential setting, we performed a detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences (to assess the bacterial community at each location), and to the Cq value of the contemporaneous clinical test. Our results showed that the highest SARS-CoV-2 load in this setting is on touched surfaces, such as light switches and faucets, but a detectable signal was present in many untouched surfaces (e.g., floors) that may be more relevant in settings, such as schools where mask-wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association. IMPORTANCE Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g., touching a light switch) or indirectly (e.g., by droplets or aerosols settling). We found the highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g., in schools, where students did not touch the light switches and also wore masks such that they had no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.

Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp

Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work has demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces such as Halloween candy, and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions, and to test whether our past observations linking SARS-CoV-2 abundance to Rothia spp. in hospitals also hold in a residential setting, we performed detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences to assess the bacterial community at each location and to the Cq value of the contemporaneous clinical test. Our results show that the highest SARS-CoV-2 load in this setting is on touched surfaces such as light switches and faucets, but detectable signal is present in many non-touched surfaces that may be more relevant in settings such as schools where mask wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association.

IMPORTANCE

Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g. touching a light switch) or indirectly (e.g. by droplets or aerosols settling). We found highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g. in schools, where students do not touch the light switches and also wear masks so they have no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.

SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp

Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work has demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces such as Halloween candy, and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions, and to test whether our past observations linking SARS-CoV-2 abundance to Rothia spp. in hospitals also hold in a residential setting, we performed detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences to assess the bacterial community at each location and to the Cq value of the contemporaneous clinical test. Our results show that the highest SARS-CoV-2 load in this setting is on touched surfaces such as light switches and faucets, but detectable signal is present in many non-touched surfaces that may be more relevant in settings such as schools where mask wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association.

IMPORTANCE

Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g. touching a light switch) or indirectly (e.g. by droplets or aerosols settling). We found highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g. in schools, where students do not touch the light switches and also wear masks so they have no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.

Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence

Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with COVID-19 and inform appropriate infection mitigation responses. Research groups have reported detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on surfaces days or weeks after the virus has been deposited, making it difficult to estimate when an infected individual may have shed virus onto a SARS-CoV-2 positive surface, which in turn complicates the process of establishing effective quarantine measures. In this study, we determined that reverse transcription-quantitative polymerase chain reaction (RT-qPCR) detection of viral RNA from heat-inactivated particles experiences minimal decay over seven days of monitoring on eight out of nine surfaces tested. The properties of the studied surfaces result in RT-qPCR signatures that can be segregated into two material categories, rough and smooth, where smooth surfaces have a lower limit of detection. RT-qPCR signal intensity (average quantification cycle (Cq)) can be correlated to surface viral load using only one linear regression model per material category. The same experiment was performed with infectious viral particles on one surface from each category, with essentially identical results. The stability of RT-qPCR viral signal demonstrates the need to clean monitored surfaces after sampling to establish temporal resolution. Additionally, these findings can be used to minimize the number of materials and time points tested and allow for the use of heat-inactivated viral particles when optimizing environmental monitoring methods.

Irreversible Electroporation For Hepatocellular Carcinoma: Longer-Term Outcomes At A Single Centre

BACKGROUND AND AIMS

Irreversible electroporation (IRE) is a non-thermal ablation technique for unresectable hepatocellular carcinoma (HCC) not amenable to standard thermal ablation. The aim of this study was to report our longer-term outcomes using this treatment modality.

METHOD

We identified all patients at our institution who underwent IRE for HCC between December 2008 and October 2019 as recommended after multi-disciplinary team review. Demographic, clinical, tumour response and survival data up until 1 March, 2020 were analysed. The primary outcome was local recurrence-free survival (LRFS) in patients who had a complete response (CR). Secondary outcomes included CR rates, procedure-related complications and the incidence of death or liver transplantation.

RESULTS

A total of 23 patients (78% males, median age 65.2 years) received IRE therapy to 33 HCC lesions during the study period with the median tumour size being 2.0 cm (range 1.0-5.0 cm). Twenty-nine (87.9%) lesions were successfully ablated after one (n = 26) or two (n = 3) procedures. The median follow-up time for these lesions was 20.4 months. The median overall LRFS was 34.5 (95% CI 24.8 -) months with a 6- and 12-month LRFS of 87.9% (95% CI 75.8-100) and 83.6% (95% CI 70.2-99.7), respectively. Tumours < 2 cm had a 12-month LRFS of 100% (95% CI 100-100).

CONCLUSION

IRE appears to be an efficacious local ablative method for early stage HCC not amenable to standard ablative techniques, with very good CR rates and longer-term LRFS, particularly for smaller lesions. Further studies comparing this technique to more widely accepted ablative methods such as radiofrequency and microwave ablation are warranted.

Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study

BACKGROUND

This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery.

METHODS

This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery.

RESULTS

A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498).

CONCLUSION

There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.

Abstract P1-13-02: Real world outcomes of adjuvant FECD, ddACT and ACT for the treatment of early stage breast cancer - A multicenter retrospective analysis

Background: Adjuvant chemotherapy combining anthracyclines and taxanes for early stage breast cancer (ESBC) have demonstrated disease-free survival (DFS) and overall survival (OS) benefits. Among the 3rd generation regimens, 2 options have been favoured: FEC-Docetaxel (FECD) and AC-Paclitaxel (ACT). ACT may be delivered with dose-dense (ddACT) or weekly taxane scheduling (ddACWT), compared to traditional every 3-weekly (q3ACT) scheduling. Despite literature supporting both FECD and (dd)ACT regimens in the management of ESBC, no direct prospective trial has evaluated their comparative effectiveness.

Methods: A retrospective review of the BC Cancer Breast Cancer Outcomes Unit (BCOU) and the Alberta Health Services (AHS) databases was performed to identify patients with HER2 negative, stage 1-3 ESBC, who received adjuvant chemotherapy between 2007-2014. The primary endpoint was OS and the secondary endpoint was RFS, defined as freedom from local (invasive), regional or distant recurrence or breast cancer death. Outcome comparisons were made between FECD, ddACT/ddACWT and q3ACT using the Kaplan Meier method. Treatment arms were compared using a log-rank test for univariate analysis. A multivariate analysis was also conducted for OS comprising age, stage, grade, receptor status and type of chemotherapy received (FECD vs combined ACT group).

Results: A total of 4047 patients met inclusion criteria, including 2685 FECD, 1259 ddACT and 103 ACT. Median age was 53 (24-77) in the FECD group vs 52 (26-68) in the ddACT/ddACWT group and 58 (43-78) in the q3ACT group. The majority had stage 2 disease, 51.3%, 53.5% and 50.5% in the FECD, ddACT/ddACWT and q3ACT groups, respectively. Most were HR+, 84.5% in the FECD group vs 66.9% in both the ddACT/ddACWT and q3ACT groups. In the FECD group, 42.8% had a grade 2 tumour and 48.2% a grade 3 tumour vs 35.4% and 56.4% in the ddACT/ddACWT group and 35.0% and 58.3% in the q3ACT group. Lymphovascular invasion (LVI) was present in 40.7% of patients who received FECD vs 39.7% for ddACT/ddACWT and 26.2% for ACT. 5-year OS, for the FECD group was 90.3% (95%CI 89.1,91.4) vs 87.0% (95%CI 84.3,89.2) for the ddACT/ddACWT and 84.9% (95%CI 75.5,90.8) for the q3ACT groups, p=0.0907. 5-year RFS was 85.5% (95%CI 84.0-86.8) with FECD vs 84.4% (95% 81.9,86.6) for ddACT/ddACWT and 87.7% (95%CI 79.2,92.8) with q3ACT,p=0.4200. In multivariate analysis: age, stage and grade were significantly associated with OS whereas type of chemotherapy received (FECD vs ACT) was not (p=0.165). Finally, OS rates were compared across provinces and no significant differences were identified, 87.0% vs 88.0% (p=0.6294). Subgroup analyses by receptor type, comparing HR+ and TNBC are ongoing.

Conclusions: The use of FECD as compared to ACT based chemotherapy did not reveal significant differences in OS or RFS in this population-based study. Further, chemotherapy regimen was not associated with differences in overall survival, as compared to other well recognized prognostic factors. While the results were obtained from a retrospective analysis, conclusive prospective data is lacking. These results may therefore reassure physicians and patients alike on a comparable efficacy of these regimens in a real-life setting.

Citation Format: LeVasseur N, Veitch Z, Diocee RM, Gondara L, Cheung W, Khan O, Cossetti R, Gelmon KA, King K, Lupichuk S, Chia SK, Tang P, Simmons C. Real world outcomes of adjuvant FECD, ddACT and ACT for the treatment of early stage breast cancer - A multicenter retrospective analysis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-13-02.

Abstract P4-11-01: Effects of high anxiety scores on surgical and overall treatment plan in breast cancer patients treated with neoadjuvant therapy

Introduction:

Anxiety is a common symptom in patients with newly diagnosed cancer. Patients with high levels of anxiety have been shown to choose more invasive surgeries in various cancer settings. Rates of contralateral prophylactic mastectomy in the adjuvant setting remain high, despite offering no survival advantage. In the neoadjuvant setting, patients have more time for decisions regarding final surgery. If anxiety is playing a role in their decisions, this could be addressed while on neoadjuvant therapy (NAT). However, the impact of anxiety at initial diagnosis on surgical decision making in this setting has not yet been studied.

Methods:

Data collected from a prospective institutional database of breast cancer patients treated with NAT at the British Columbia Cancer Agency (BCCA) were utilized to identify all patients. Information was extracted from this database with regards to patient and tumour characteristics, initial surgical plan, and final surgery performed. This was cross referenced with patient self-reported anxiety, which was extracted from the Edmonton Symptom Assessment System (ESAS) and the Psychosocial Screen for Cancer (PSSCAN) forms administered at initial consultation. Patients were assigned a score of 0 to 3 based on their answers to the ESAS anxiety scale and the PSSCAN anxiety questions, and whether or not they had any concerns related to their care. Patients were excluded if they had bilateral breast cancer, BRCA mutation or referral to the Hereditary Cancer Program, did not receive NAT or undergo breast surgery, or did not complete the forms. Fisher's exact tests were applied for statistical analysis.

Results:

From 2012-2016, 361 potential patients were identified for this study. A total of 203 patients met eligibility criteria. 93 patients (46%) had low anxiety (score 0 or 1) and 110 patients (54%) had high anxiety (score 2 or 3). Patients with high self-reported anxiety at initial consultation were significantly more likely to undergo bilateral mastectomy for unilateral disease and mastectomy for breast conserving surgery (BCS) eligible disease than those with low self-reported anxiety at initial consultation (37.3% VS 18.3%; p=0.003). No significant differences in treatment times (time interval between biopsy to chemotherapy, chemotherapy to surgery, and surgery to radiation) or investigations were identified when comparing high and low anxiety patients.

Anxiety level and type of surgery performedType of SurgeryAnxiety Level  Low (n=93)High (n=110) Bilateral Mastectomy and Mastectomy for BCS eligible disease17 (18.3%)41 (37.3%) BCS and Mastectomy for non-BCS eligible disease76 (81.7%)69 (62.7%)    p = 0.0031

Conclusion:

High anxiety scores lead to a 19% increase in bilateral mastectomies in patients without bilateral disease and mastectomies in patients eligible for BCS compared to patients with low anxiety (p = 0.003). These findings suggest that self-reported anxiety levels can inform and assist physicians to identify patients who are more likely to undergo aggressive surgery and may need further counselling and support services. Future work should examine the effects of counselling intervention in patients with high anxiety on surgical decisions.

Citation Format: Li H, Cheung W, Myers P, McKevitt E, Willemsma K, Deruchie Tan A, Chia S, Simmons C. Effects of high anxiety scores on surgical and overall treatment plan in breast cancer patients treated with neoadjuvant therapy [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-11-01.

Evaluation of Epoetin Alpha (rHuEPO) and Darbepoetin Alpha (DARB) on Human Burst-colony Formation (BFU-E) in Culture

The erythropoietic effect of recombinant human erythropoietin, epoetin alpha (rHuEPO), in promoting the growth of erythroid burst-forming units (BFU-E) was compared with darbepoetin alpha (DARB), a rHuEPO analogue obtained by site-directed mutagenesis. Human bone marrow cells derived from healthy donors were cultured with different concentrations of rHuEPO or DARB for 12-21 days and BFU-E were counted using an inverted microscope. The EC50 of rHuEPO was about 10-fold lower than DARB and the size of the colonies was significantly larger in rHuEPO-containing cultures using comparable concentrations. The maximum number of colonies obtained in some rHuEPO-containing cultures was also higher than for DARB. The number of colonies in DARB-containing cultures was increased, in part, by the addition of low concentrations of rHuEPO, but not by DARB, even at high concentrations. We conclude that DARB is not as effective as rHuEPO in supporting the in vitro growth of human BFU-E.

Recent trends in breast, cervical, and colorectal cancer screening test utilization in Canada, using self-reported data from 2008 and 2012

In Canada, self-reported data from the Canadian Community Health Survey 2008 and 2012 provide an opportunity to examine overall utilization of breast, cervical, and colorectal cancer screening tests for both programmatic and opportunistic screening. Among women 50-74 years of age, utilization of screening mammography was stable (62.0% in 2008 and 63.0% in 2012). Pap test utilization for women 25-69 years of age remained high and stable across Canada in 2008 and 2012 (78.9% in 2012). The percentage of individuals 50-74 years of age who reporting having at least 1 fecal test within the preceding 2 years increased in 2012 (to 23.0% from 16.9% in 2008), but remains low. Stable rates of screening mammography utilization (about 30%) were reported in 2008 and 2012 among women 40-49 years of age, a group for which population-based screening is not recommended. Although declining over time, cervical cancer screening rates were high for women less than 25 years of age (for whom screening is not recommended). Interestingly, an increased percentage of women 70-74 years of age reported having a Pap test. In 2012, a smaller percentage of women 50-69 years of age reported having no screening test (5.9% vs. 8.5% in 2008), and more women reported having the three types of cancer screening tests (19.0% vs. 13.2%). Efforts to encourage use of screening within the recommended average-risk age groups are needed, and education for stakeholders about the possible harms of screening outside those age groups has to continue.

Odontogenic facial swelling of unknown origin

BACKGROUND

Current radiography techniques have limitations in detecting subtle odontogenic anomalies or defects that can lead to dentoalveolar and facial infections. This report examines the application of micro-CT imaging on two extracted teeth to enable detailed visualization of subtle odontogenic defects that had given rise to facial swelling.

METHODS

Two extracted non-carious mandibular left primary canine teeth (73) associated with odontogenic infections were selected from two patients, and an intact contralateral tooth (83) from one of the patients was used as a control. All three teeth were subjected to three-dimensional micro-CT imaging at a resolution of 20 μm.

RESULTS

Tooth 73 from the first case displayed dentine pores (channels) that established communication between the pulp chamber and the exposed dentine surface. In comparison, tooth 73 from the second case had a major vertical crack extending from the external enamel surface into the pulp chamber. The control tooth did not display any anomalies or major cracks.

CONCLUSIONS

The scope of micro-CT imaging can be extended from current in vitro applications to establish post-extraction diagnosis of subtle odontogenic defects, in a manner similar to deriving histopathological diagnoses in extracted teeth. Ongoing technological advancements hold the promise for more widespread translatory applications.

25 year survival outcomes for squamous cell carcinomas of the head and neck: population-based outcomes from a Canadian province

OBJECTIVES

Long term outcomes of patients with head and neck cancer (HNC) are rarely reported, but of potential benefit to clinicians and researchers. Squamous cell carcinomas (SCC) of the head and neck represent a heterogeneous group of cancers. The purpose of this population based study is to describe primary site specific, long term outcomes of HNC.

METHODS

All patients from a Canadian province diagnosed between 1986 and 1990 with SCC of the oral cavity, pharynx, and larynx were identified. Chart review and patient data were abstracted through the provincial cancer registry database. Survival analysis was performed with Kaplan Meier methods, while differences in survival between groups were assessed with log-rank tests. Multivariable analysis was performed using Cox-regression.

RESULTS

1657 patients were analyzed during the study period. Almost half (50.9%) of the cases were advanced stage (stage III IV) at presentation. Two, 5, 15 & 25year overall survival (OS) and HNC specific survival for all the patients were 64%, 46%, 21%, 11% and 74%, 63%, 53% & 49%, respectively. OS and HNC-specific mortality were statistically inferior among men, older age at diagnosis, advanced stages of disease, and was primary cancer site specific, with worse survival in oropharyngeal & hypopharyngeal sites, p<0.001.

CONCLUSIONS

Survival rates vary by primary HNC site, and the overall survival & HNC specific survival differ over this long follow up assessment. Head and neck cancer specific death is most common in the first five years, and is subsequently dominated by competing causes of mortality. These results are useful as a reference tool for clinicians, researchers, and trainees.

New chart review data validate administrative data-based indicator for guideline-recommended treatment of locally advanced non-small-cell lung cancer and shed light on reasons for non-referral and non-treatment

The 2012 Cancer System Performance Report is the 4th annual report on the Canadian cancer control system produced by the System Performance initiative at the Canadian Partnership Against Cancer, in collaboration with its provincial and national partners. [...]

Irreversible electroporation for unresectable hepatocellular carcinoma: initial experience and review of safety and outcomes

The aims of this study were to evaluate the safety, feasibility and tumour response of _irreversible electroporation, a non-thermal ablation technique, for the treatment of unresectable hepatocellular carcinoma. The endpoints were safety and local treatment efficacy. Patients with unresectable tumours and tumours not amenable for radiofrequency _ablation because of their vicinity to organs vulnerable to thermal damage such as the bowel or because they were close to large blood vessels that would limit efficacy of ablation due to the heat sink effect were treated with irreversible electroporation using percutaneous _ultrasound and/or computed tomography guided electrode placement between November 2008 and _December 2009. Early, late, minor and major complications were recorded. Tumour response was determined on triphasic helical computed tomography follow-up at one month, then every three months post-procedure. Eleven patients received IRE therapy to 18 HCC lesions (Mean diameter 2.44 ± 0.99 cm; range 1.0-6.1 cm) with five patients having more than one treated HCC. Mean follow-up was 18 months (range 14-24 months). Six patients required repeat treatments for local residual or recurrent disease; two of these also had IRE for distant intrahepatic recurrence. No serious complications were observed despite seven lesions lying adjacent to important structures or organs. Four patients developed transient urinary retention and seven developed transient local post-procedure pain. After IRE therapy, 13 (72%) lesions were completely ablated with 93% success for lesions ≤ 3 cm (13/14). The local recurrence-free period was 18 ± 4 months and the distance recurrence free period was 14 ± 6 months. These preliminary results suggest that IRE is a safe and feasible technique for local ablation of HCC, particularly for lesions less than 3 cm. No major complications were encountered during this study even for tumours close to essential structures or organs.