Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA

Accurately calling indels with next-generation sequencing (NGS) data is critical for clinical application. The precisionFDA team collaborated with the U.S. Food and Drug Administration's (FDA's) National Center for Toxicological Research (NCTR) and successfully completed the NCTR Indel Calling from Oncopanel Sequencing Data Challenge, to evaluate the performance of indel calling pipelines. Top performers were selected based on precision, recall, and F1-score. The performance of many other pipelines was close to the top performers, which produced a top cluster of performers. The performance was significantly higher in high confidence regions and coding regions, and significantly lower in low complexity regions. Oncopanel capture and other issues may have occurred that affected the recall rate. Indels with higher variant allele frequency (VAF) may generally be called with higher confidence. Many of the indel calling pipelines had good performance. Some of them performed generally well across all three oncopanels, while others were better for a specific oncopanel. The performance of indel calling can further be improved by restricting the calls within high confidence intervals (HCIs) and coding regions, and by excluding low complexity regions (LCR) regions. Certain VAF cut-offs could be applied according to the applications.

Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project

Accurate indel calling plays an important role in precision medicine. A benchmarking indel set is essential for thoroughly evaluating the indel calling performance of bioinformatics pipelines. A reference sample with a set of known-positive variants was developed in the FDA-led Sequencing Quality Control Phase 2 (SEQC2) project, but the known indels in the known-positive set were limited. This project sought to provide an enriched set of known indels that would be more translationally relevant by focusing on additional cancer related regions. A thorough manual review process completed by 42 reviewers, two advisors, and a judging panel of three researchers significantly enriched the known indel set by an additional 516 indels. The extended benchmarking indel set has a large range of variant allele frequencies (VAFs), with 87% of them having a VAF below 20% in reference Sample A. The reference Sample A and the indel set can be used for comprehensive benchmarking of indel calling across a wider range of VAF values in the lower range. Indel length was also variable, but the majority were under 10 base pairs (bps). Most of the indels were within coding regions, with the remainder in the gene regulatory regions. Although high confidence can be derived from the robust study design and meticulous human review, this extensive indel set has not undergone orthogonal validation. The extended benchmarking indel set, along with the indels in the previously published known-positive set, was the truth set used to benchmark indel calling pipelines in a community challenge hosted on the precisionFDA platform. This benchmarking indel set and reference samples can be utilized for a comprehensive evaluation of indel calling pipelines. Additionally, the insights and solutions obtained during the manual review process can aid in improving the performance of these pipelines.

Propranolol reduces IFN-γ driven PD-L1 immunosuppression and improves anti-tumour immunity in ovarian cancer

The immune system plays an important role in controlling epithelial ovarian cancer (EOC). EOC is considered to be a "cold tumour," a tumour that has not triggered a strong response by the immune system. However, tumour infiltrating lymphocytes (TILs) and the expression of programmed cell death ligand (PD-L1) are used as prognostic indicators in EOC. Immunotherapy such as PD-(L)1 inhibitors have shown limited benefit in EOC. Since the immune system is affected by behavioural stress and the beta-adrenergic signalling pathway, this study aimed to explore the impact of propranolol (PRO), a beta-blocker, on anti-tumour immunity in both in vitro and in vivo EOC models. Noradrenaline (NA), an adrenergic agonist, did not directly regulate PD-L1 expression but PD-L1 was significantly upregulated by IFN-γ in EOC cell lines. IFN-γ also increased PD-L1 on extracellular vesicles (EVs) released by ID8 cells. PRO significantly decreased IFN-γ levels in primary immune cells activated ex vivo and showed increased viability of the CD8⁺ cell population in an EV-immune cell co-incubation. In addition, PRO reverted PD-L1 upregulation and significantly decreased IL-10 levels in an immune-cancer cell co-culture. Chronic behavioural stress increased metastasis in mice while PRO monotherapy and the combo of PRO and PD-(L)1 inhibitor significantly decreased stress-induced metastasis. The combined therapy also reduced tumour weight compared to the cancer control group and induced anti-tumour T-cell responses with significant CD8 expression in tumour tissues. In conclusion, PRO showed a modulation of the cancer immune response by decreasing IFN-γ production and, in turn, IFN-γ-mediated PD-L1 overexpression. The combined therapy of PRO and PD-(L)1 inhibitor decreased metastasis and improved anti-tumour immunity offering a promising new therapy.

Evaluation of opt-in HIV testing in the construction workplace using the socioecological framework

Background

Late diagnosis of HIV remains a challenge and the construction workforce has several risk factors for HIV. In the Test@Work programme, we delivered HIV tests embedded within a general health check to construction workers, with high uptake and acceptability. Here, we report the experiences of construction managers and health professionals involved in Test@Work and explore the suitability of construction worksites as a venue for opt-in HIV testing.

Methods

Qualitative interviews (n = 24) were conducted with construction managers who facilitated events (n = 13), and HIV/health check delivery partners (n = 11) at 21 Test@Work events held on construction sites. Interviews explored experiences of events and views towards workplace HIV testing. Event exit questionnaires (n = 107) completed by delivery partners provided qualitative data identifying facilitators and barriers to effective delivery. Thematic analysis identified themes that were mapped against a socioecological framework (individual, interpersonal, organisational, industry, public health).

Results

Delivery partners reported high engagement of construction workers with workplace HIV testing, peer-to-peer encouragement for uptake, and value for accessibility of onsite testing. HIV professionals valued the opportunity to reach an untested population, many of whom had a poor understanding of their exposure to HIV risk. Managers valued the opportunity to offer workplace health checks to employees but some identified challenges with event planning, or provision of private facilities.

Conclusions

The construction sector is complex with a largely male workforce. Providing worksite HIV testing and education to an untested population who have poor knowledge about HIV risk helped to normalise testing, increase uptake, and reduce HIV stigma. However, there are practical barriers to testing in the construction environment. This has global implications for delivery of HIV testing in construction workplace settings.

Key messages

• Delivering workplace HIV testing as part of a general health check helps to normalise HIV testing and reduce HIV-related stigma.

• Workplace testing is convenient, accessible and reaches populations at risk for HIV, but there are some barriers to implementation of rapid tests on construction sites.

Precision of the GE Lunar Total Body-Less Head Scan for the Measurement of Three-Compartment Body Composition in Athletes

INTRODUCTION

Dual energy X-ray absorptiometry (DXA) is widely used for the assessment of lean mass (LM), fat mass (FM) and bone mineral content (BMC). When observing standardised protocols, DXA has a high level of precision for the assessment of total body composition, including the head region. However, including the head region may have limited relevance in athletes and can be problematic when positioning taller athletes who exceed scan boundaries. This study investigated the precision of a new total-body-less-head (TBLH) DXA scan for three-compartment body composition measurement in athletes, with outcomes compared to the standard total-body DXA scan.

METHODS

Precision errors were calculated from two consecutive scans with re-positioning (Lunar iDXA, GE Healthcare, Madison, WI), in male and female athletes from a range of sports. TBLH precision was determined from repeat scans in 95 athletes (male n = 55; female n = 40; age: 26.0 ± 8.5 y; body mass: 81.2 ± 20.5 kg; stature: 1.77 ± 0.11 m), and standard total-body scan precision was derived from a sub-sample of 58 athletes (male n = 19; female n = 39; age: 27.6 ± 9.9 y; body mass: 69.6 ± 14.8 kg; stature: 1.72 ± 0.94 m). Data from the sub-sample were also used to compare precision error and 3-compartment body composition outcomes between the standard total-body scan and the TBLH scan.

RESULTS

TBLH precision errors [root mean squared-standard deviation, RMS-SD (coefficient of variation, %CV)] were bone mineral content (BMC): 15.6 g (0.5%), lean mass (LM): 254.3 g (0.4%) and fat mass (FM): 199.4 g (1.3%). These outcomes compared favourably to the precision errors derived from the standard total-body scan [BMC: 12.4 g (0.4%), LM: 202.2 g (0.4%), and FM: 160.8 g (1.1%)]. The TBLH scan resulted in lower BMC (-19.5%), LM (-6.6%), and FM (-4.5%) compared to the total-body scan (BMC: 2,308 vs. 2,865 g; LM: 46,954 vs. 50,276 g; FM: 15,183 vs. 15,888 g, all p<0.005). ConclusionThe TBLH scan demonstrates high in-vivo precision comparable to that of the standard total-body scan in a heterogeneous cohort of athletes. Given the impact of head exclusion on total body composition outcomes, TBLH scans should not be used interchangeably with the standard total-body scan.

Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples

Background

Clinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE) tissue or cell block cytology samples in oncology panel sequencing to identify mutations that can predict patient response to targeted therapy. To understand the technical error due to FFPE processing, a robustly characterized diploid cell line was used to create FFPE samples with four different pre-tissue processing formalin fixation times. A total of 96 FFPE sections were then distributed to different laboratories for targeted sequencing analysis by four oncopanels, and variants resulting from technical error were identified.

Results

Tissue sections that fail more frequently show low cellularity, lower than recommended library preparation DNA input, or target sequencing depth. Importantly, sections from block surfaces are more likely to show FFPE-specific errors, akin to “edge effects” seen in histology, while the inner samples display no quality degradation related to fixation time.

Conclusions

To assure reliable results, we recommend avoiding the block surface portion and restricting mutation detection to genomic regions of high confidence.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02709-8.

PLK3 amplification and tumor immune microenvironment of metastatic tumors are linked to adjuvant treatment outcomes in uterine serous cancer

Uterine serous carcinoma (USC), an aggressive variant of endometrial cancer representing approximately 10% of endometrial cancer diagnoses, accounts for ∼39% of endometrial cancer-related deaths. We examined the role of genomic alterations in advanced-stage USC associated with outcome using paired primary-metastatic tumors (n = 29) treated with adjuvant platinum and taxane chemotherapy. Comparative genomic analysis of paired primary-metastatic patient tumors included whole exome sequencing and targeted gene expression. Both PLK3 amplification and the tumor immune microenvironment (TIME) in metastatic tumors were linked to time-to-recurrence (TTR) risk without any such association observed with primary tumors. TP53 loss was significantly more frequent in metastatic tumors of platinum-resistant versus platinum-sensitive patients and was also associated with increased recurrence and mortality risk. Increased levels of chr1 breakpoints in USC metastatic versus primary tumors co-occur with PLK3 amplification. PLK3 and the TIME are potential targets for improving outcomes in USC adjuvant therapy.

Evaluating the population-level effects of oxycodone restrictions on prescription opioid utilization in Ontario

PURPOSE

To investigate the impact of restrictions on access to long acting oxycodone on prescription opioid use and opioid-related harms.

METHODS

Administrative health data from Ontario, Canada was used to measure differences in opioids dispensed and ED visits for opioid-related overdose, poisoning or substance use following provincial restrictions on access to publicly insured OxyContin (February 29, 2012) and OxyNeo (February 28, 2013). This study focused on the cohort of provincial drug insurance eligible people (people 65+ and select low-income populations) who were dispensed oxycodone prior to the restrictions. Difference-in-differences models with a propensity score matched comparison group of people who were dispensed non-oxycodone opioids were used to estimate the main effects.

RESULTS

In the six months following the delisting of OxyContin, MMEs per person per week for all opioids fell by an average of 7.5% in people dispensed oxycodone relative to the comparison group, and an average of 13.8% in chronic recipients of oxycodone. In the six months following the restrictions on OxyNeo, MMEs per person per week fell by an average of 3.1% in all people dispensed oxycodone, and 25.2% in chronic oxycodone recipients. The decline in oxycodone dispensing amongst chronic oxycodone recipients corresponded with an increase in dispensing of other opioid formulations, particularly hydromorphone and fentanyl. No important differences were observed for ED visits related to opioid poisoning, overdose, or substance use disorder.

CONCLUSIONS

Province-wide restrictions on access to long acting oxycodone had an impact on quantities of all opioids dispensed to chronic recipients of oxycodone, but small impacts on the full population of people dispensed oxycodone; the decline in use was partially offset by increases in use of other publicly-funded opioid formulations. This study suggests that policies limiting access to specific prescription opioids led to overall reductions in publicly-funded prescription opioid use, particularly in chronic oxycodone recipients, without immediate evidence of changes in opioid-related ED visits. This article is protected by copyright. All rights reserved.

Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity

Recently we reported the accuracy and reproducibility of circulating tumor DNA (ctDNA) assays using a unique set of reference materials, associated analytical framework, and suggested best practices. With the rapid adoption of ctDNA sequencing in precision oncology, it is critical to understand the analytical validity and technical limitations of this cutting-edge and medical-practice-changing technology. The SEQC2 Oncopanel Sequencing Working Group has developed a multi-site, cross-platform study design for evaluating the analytical performance of five industry-leading ctDNA assays. The study used tailor-made reference samples at various levels of input material to assess ctDNA sequencing across 12 participating clinical and research facilities. The generated dataset encompasses multiple key variables, including a broad range of mutation frequencies, sequencing coverage depth, DNA input quantity, etc. It is the most comprehensive public-facing dataset of its kind and provides valuable insights into ultra-deep ctDNA sequencing technology. Eventually the clinical utility of ctDNA assays is required and our proficiency study and corresponding dataset are needed steps towards this goal.

Measurement(s)	Somatic Mutation • spike-in quality control role
Technology Type(s)	Tumor Panel Sequencing
Factor Type(s)	Tumor Panel • DNA Library Input Quantity • Variant Allele Frequency
Sample Characteristic - Organism	Homo sapiens

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples. Above 0.5% variant allele frequency, ctDNA mutations were detected with high sensitivity, precision and reproducibility by all five assays, whereas, below this limit, detection became unreliable and varied widely between assays, especially when input material was limited. Missed mutations (false negatives) were more common than erroneous candidates (false positives), indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays. This comprehensive evaluation of the analytical performance of ctDNA assays serves to inform best practice guidelines and provides a resource for precision oncology.

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.

A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging new type of coronavirus that is responsible for the COVID-19 pandemic and the unprecedented global health emergency. Whole-genome sequencing (WGS) of SARS-CoV-2 plays a critical role in understanding the disease. Performance variation exists across SARS-CoV-2 viral WGS technologies, but there is currently no benchmarking study comparing different WGS sequencing protocols. We compared seven different SARS-CoV-2 WGS library protocols using RNA from patient nasopharyngeal swab samples under two storage conditions with low and high viral inputs. We found large differences in mappability and genome coverage, and variations in sensitivity, reproducibility, and precision of single-nucleotide variant calling across different protocols. For certain amplicon-based protocols, an appropriate primer trimming step is critical for accurate single-nucleotide variant calling. We ranked the performance of protocols based on six different metrics. Our findings offer guidance in choosing appropriate WGS protocols to characterize SARS-CoV-2 and its evolution.

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

BACKGROUND

Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing.

RESULTS

All panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden.

CONCLUSION

This comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

BACKGROUND

Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance.

RESULTS

In reference Sample A, we identify more than 40,000 variants down to 1% allele frequency with more than 25,000 variants having less than 20% allele frequency with 1653 variants in COSMIC-related genes. This is 5-100× more than existing commercially available samples. We also identify an unprecedented number of negative positions in coding regions, allowing statistical rigor in assessing limit-of-detection, sensitivity, and precision. Over 300 loci are randomly selected and independently verified via droplet digital PCR with 100% concordance. Agilent normal reference Sample B can be admixed with Sample A to create new samples with a similar number of known variants at much lower allele frequency than what exists in Sample A natively, including known variants having allele frequency of 0.02%, a range suitable for assessing liquid biopsy panels.

CONCLUSION

These new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.

Evaluation of a collaborative pharmacy service initiative for people with intellectual disabilities in residential care homes

Introduction

People with Intellectual Disabilities (ID) often have complex care needs and increased likelihood of premature death.1 The NHS has committed to improving the use of psychotropic medicines in people with ID with the Stopping the Over-Medication of People with Learning Disabilities (STOMP) programme.2 In the Wirral a cross-sector, collaborative service initiative involving community pharmacists and a specialist mental health pharmacist was developed to provide pharmaceutical care reviews for ID care home residents, which included an evaluation of the initiative.

Aim

This study aimed to determine the number and type of pharmacists’ interventions and GP recommendations in this service initiative.

Methods

Pharmacists provided pharmaceutical care reviews for ID care home residents using a framework and where applicable made interventions or recommendations to residents’ GPs or consultant psychiatrist. The framework was devised by the lead Consultant, Mental Health Trust lead pharmacist and Local Pharmaceutical Committee representatives to align with national ID priorities.1 Pharmacists were recruited via expressions of interest and direct recruitment by the mental health trust. Using anonymised, aggregated, Clinical Commissioning Group data, an Oversight Group divided all ID care homes in the locality into two groups: homes with residents with low psychotropic medicines use were primarily assigned to community pharmacists, whilst those with higher psychotropic use were assigned to the specialist mental health pharmacist. Pharmacists contacted care home managers and arranged reviews with all residents, sharing learnings in weekly reviews. Community pharmacists identified residents who would benefit from specialist mental health pharmacist review and referred them. Data collected included patient demographic details, medication history, results of assessments completed and interventions/recommendations. Following institutional ethical approval, this data was downloaded from PharmOutcomes into Microsoft Excel and personally identifiable data removed. The data underwent descriptive statistical analysis in SPSS, including frequency counting interventions by type.

Results

The pharmacists conducted reviews with 160 residents (76 by community pharmacists and 84 by the specialist mental health pharmacist) from November 2019 – May 2020, reflecting all residents in visited care homes. These residents were prescribed 1207 medicines, 74% were prescribed 5 or more medicines (i.e. polypharmacy) and 507 interventions or recommendations were made, averaging 3.3 per resident. Table 1 shows that the highest proportion (30.4%) of these were public health related, whilst changing and stopping medicines accounted for 17.9% and 12.8% respectively. The majority (63%) of interventions made by community pharmacists were public health related, whilst those made by the mental health specialist pharmacist most frequently concerned changing medicines (25%), stopping medicines (18%), and blood monitoring (13%).

Conclusion

The study findings indicate a high level of polypharmacy among the ID residents and a high number of interventions / recommendations were needed to improve care, in line with national priorities.1,2 The small scale of the study is acknowledged, and further research is warranted. However, the findings suggest that this service model may be an effective use of the respective skill sets of the pharmacists involved and suitable for wider adoption, with community pharmacists focusing on holistic care and specialist mental health making specialist medicines interventions.

References

1. University of Bristol Norah Fry Centre for Learning Disability Studies. The Learning Disability Mortality Review (LeDeR) Programme Annual Report 2018. Available at: https://www.hqip.org.uk/wp-content/uploads/2019/05/LeDeR-Annual-Report-Final-21-May-2019.pdf (last accessed 12/10/20).

2. NHS England. Stopping over medication of people with a learning disability, autism or both (STOMP). https://www.england.nhs.uk/learning-disabilities/improving-health/stomp/ (last accessed 12/10/20).

112 Outcomes and Clinical Characteristics of COVID-19 Disease in the Frail, Elderly Population of Tayside

Introduction

With advancing age, frailty, multi-morbidity and need for care, elderly patients are some of the most vulnerable to Covid-19 disease. In NHS Tayside, a dedicated Covid-19 Medicine for the Elderly (MFE) Team was formed to care for patients identified as frail and likely to benefit from comprehensive geriatric assessment.

Methods

All Covid-19 patients meeting frailty criteria1, cared for by the Covid-19 MFE Team were identified. Data on outcomes and clinical characteristics for all (140) patients admitted during the first pandemic wave (March–July 2020) was collected using electronic patient records and analysed.

Results

Patients were predominantly male (58.6%). Ages ranged from 65–99 years, with 43.6% aged ≥85 years. 82.1% had one or more of cough, fever and anosmia on admission fitting Covid-19 case definition 2. Lymphopenia was present in 92.1%. Of note, 26.5% of patients had a normal or unchanged chest x-ray report, with only 10.2% showing bilateral peripheral infiltrates. 28-day mortality was 37.1% with Covid-19 Disease listed as primary cause of death in 90.4%.

Conclusion(s)

Entering further “waves” of infection, it is vital that we understand the clinical presentation and course of Covid-19 disease in elderly patients. Our data highlights that any Covid-19 symptom, even in isolation, should raise suspicion of disease. Chest x-rays should not be used alone as a diagnostic tool. The presence of lymphopenia should raise suspicion of Covid-19 infection. In developing an understanding of how elderly patients with Covid-19 present, we can ensure early identification and initiation of appropriate infection control measures.

References

1. Healthcare Improvement Scotland. Think Frailty. 2014. http://www.healthcareimprovementscotland.org/his/idoc.ashx?docid=8abd8530-48f3-4152-bbfb-d0918b870ec9&version=-1

2. Scottish Government. Update to Coronavirus Symptoms 2020. https://www.gov.scot/news/update-to-coronavirus-symptoms

Latent-transforming growth factor beta-binding protein-2 (LTBP-2) is required for longevity but not for development of zonular fibers

Latent-transforming growth factor beta-binding protein 2 (LTBP-2) is a major component of arterial and lung tissue and of the ciliary zonule, the system of extracellular fibers that centers and suspends the lens in the eye. LTBP-2 has been implicated previously in the development of extracellular microfibrils, although its exact role remains unclear. Here, we analyzed the three-dimensional structure of the ciliary zonule in wild type mice and used a knockout model to test the contribution of LTBP-2 to zonule structure and mechanical properties. In wild types, zonular fibers had diameters of 0.5-1.0 micrometers, with an outer layer of fibrillin-1-rich microfibrils and a core of fibrillin-2-rich microfibrils. LTBP-2 was present in both layers. The absence of LTBP-2 did not affect the number of fibers, their diameters, nor their coaxial organization. However, by two months of age, LTBP-2-depleted fibers began to rupture, and by six months, a fully penetrant ectopia lentis phenotype was present, as confirmed by in vivo imaging. To determine whether the seemingly normal fibers of young mice were compromised mechanically, we compared zonule stress/strain relationships of wild type and LTBP-2-deficient mice and developed a quasi-linear viscoelastic engineering model to analyze the resulting data. In the absence of LTBP-2, the ultimate tensile strength of the zonule was reduced by about 50%, and the viscoelastic behavior of the fibers was altered significantly. We developed a harmonic oscillator model to calculate the forces generated during saccadic eye movement. Model simulations suggested that mutant fibers are prone to failure during rapid rotation of the eyeball. Together, these data indicate that LTBP-2 is necessary for the strength and longevity of zonular fibers, but not necessarily for their formation.

Enrichment and preserved functionality of multipotential stromal cells in bone marrow concentrate processed by vertical centrifugation

The concentration of bone marrow (BM) aspirate (BMA) is increasingly valued for bone and cartilage repair, particularly with the rarity and donor-variability of BM-multipotential stromal cells (BM-MSCs). The present study aimed to assess BM-MSC yield following BM concentration using a fast and compact-sized vertical centrifugation system. BMA concentrate (BMAC) was separated in a 1 min process and collected easily after an automatic discarding of plasma and red blood cells. A significant increase in CD45low CD271high cells per BMAC volume (measured using flow-cytometry) was noted (4-fold, p = 0.0001). Additionally, the vertical centrifugation system helped to enrich colony numbers (assessed by CFU-F assays) in BMAC comparably with conventional centrifugation systems, BioCUE™ and SmartPReP-2® (4.3-fold, 4.6-fold and 3-fold, respectively). Next, a functional assessment of BM-MSCs processed by vertical centrifugation was performed, and MSC viability and proliferation were not affected. Also, these BM-MSCs showed similar alkaline phosphatase and calcium levels to those of BMA-MSCs when osteogenically induced. Furthermore, glycosaminoglycans and Nile red levels in addition to the gene expression assays confirmed that there was no significant change in chondrogenic or adipogenic abilities between BMA-MSCs and BMAC-MSCs. The expression levels of selected angiogenic and immunomodulatory mediators were also similar between the two groups. Collectively, the vertical centrifugation system helped to enrich BM-MSCs effectively, while maintaining cell viability and functions. Thus, such a vertical centrifugation system for BM concentration can be valuable for various regenerative therapies.

Methanol photo-reforming with water on pure titania for hydrogen production

The behaviour of titania for the photo-reforming of methanol with water at ambient temperature has been examined. It is shown that the reactivity is very poor, compared with metal-loaded catalysts at low methanol levels in solution, but the rate becomes much higher at high methanol levels, such that the difference from metal-loaded samples is much less. The optimum yield is with approximately a 1 : 1 methanol/water solution. The reaction also proceeds well in the gas phase. During all such catalysis, the titania becomes blue, due to light absorption increasing across the range 400-800 nm. However, this does not result in visible range activity for the photo-reforming and is due to the reduction of the material in the presence of light and the formation of anion vacancies and Ti³⁺ centres. These anion vacancies are only very slowly re-oxidized in air on P25 titania, taking days to recover the original whiteness of the oxide. The performance of anatase, rutile and the mixed phase is compared. This article is part of a discussion meeting issue 'Science to enable the circular economy'.

Understanding young peoples' and family members' views of treatment for first episode psychosis in a randomised controlled trial (MAPS)

BACKGROUND

There is limited evidence to inform treatment decision-making in adolescents experiencing first episode psychosis (FEP). In the MAPS trial (Managing Adolescent first Episode Psychosis: a feasibility Study), adolescents with FEP received either antipsychotic medication (AP), psychological intervention (PI), or both. We investigated treatment views of young people and family members across each treatment arm of MAPS.

METHODS

Thirteen adolescents participating in MAPS and eighteen family members attended in-depth audio-recorded interviews to discuss trial treatments. Interviews were analysed using inductive Thematic Analysis, identifying salient themes across these accounts.

FINDINGS

Family members in particular reported an urgent need for treatment regardless of type. Both AP and PI were broadly viewed as acceptable treatment approaches, but for differing reasons which participants weighed against a range of concerns. AP were often seen to reduce symptoms of psychosis, though participants expressed concerns about side effects. PI were viewed as interactive treatment approaches that helped improve understanding of psychosis and enhanced coping, although some found PI emotionally and cognitively challenging. Combining treatments was seen to maximise benefits, with a perceived interaction whereby AP facilitated engagement with PI.

INTERPRETATION

Acceptability of and engagement with treatments for FEP may differ between individual young people and their family/carers. In order to be able to offer fully informed choices, and determine an optimum treatment approach for young people with FEP, definitive trial evidence should be established to determine wanted and unwanted treatment impacts.

FUNDING

NIHR HTA programme (project number 15/31/04).

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.

Evaluation of the GeneQuence® DNA Hybridization Method in Conjunction with 24-Hour Enrichment Protocols for Detection of Salmonella spp. in Select Foods: Collaborative Study

A multilaboratory study was conducted to compare performance of the GeneQuence® DNA hybridization (DNAH) method incorporating new 24 h enrichment protocols and reference culture procedures for detection of Salmonella spp. in select foods. Six food types (raw ground turkey, raw ground beef, dried whole egg, milk chocolate, walnuts, and dry pet food) were tested by the DNAH method and by the culture methods of either the U.S. Department of Agriculture-Food Safety and Inspection Service (USDA-FSIS) or the U.S. Food and Drug Administration's Bacteriological Analytical Manual (FDA/BAM). Fifteen laboratories participated in the study. Four of the foods tested (raw ground turkey, dried whole egg, milk chocolate, and dry pet food), showed no statistically significant differences in performance between the DNAH method and the reference procedure as determined by Chi square analysis. Sensitivity rates for the DNAH method ranged from 92 to 100. The DNAH method, with the specific enrichment protocol evaluated, was found to be ineffective for detection of Salmonella spp. in walnuts. For raw ground beef, results from one trial showed a statistically significant difference in performance, with more positives obtained by the reference method. However, evidence suggests that the difference in the number of positives was likely due to lack of homogeneity of the test samples rather than to DNAH method performance.

A phase 1 study of the safety, reactogenicity, and immunogenicity of a Schistosoma mansoni vaccine with or without glucopyranosyl lipid A aqueous formulation (GLA-AF) in healthy adults from a non-endemic area

BACKGROUND

Schistosomiasis caused by Schistosoma mansoni (Sm) is a chronic, debilitating and potentially deadly neglected tropical disease. The licensure of a vaccine to prevent schistosomiasis would represent a major breakthrough in public health.

METHODS

The safety and immunogenicity of a candidate Sm vaccine were assessed in this phase I, double-blind, dose-escalation trial. Seventy-two healthy Sm-naïve 18-50 year olds were randomized to receive 3 doses ∼ 8 weeks apart of saline placebo, or 10 µg, 30 µg, or 100 µg of recombinant Sm-Tetraspanin-2 vaccine formulated on aluminum hydroxide adjuvant (Sm-TSP-2/Al) with or without 5 µg of glucopyranosyl lipid A aqueous formulation (GLA-AF). Clinical and serologic responses were assessed for 1 year after dose 3.

RESULTS

Vaccines were safe and well-tolerated. The most common reactions were injection site tenderness and pain, and headache and fatigue. Tenderness and pain were more frequent in groups receiving vaccine with GLA-AF than placebo (p = 0.0036 and p = 0.0014, respectively). Injection site reactions among those given Sm-TSP-2/Al with GLA-AF lasted 1.22 and 1.33 days longer than those receiving Sm-TSP-2/Al without GLA-AF or placebo (p < 0.001 for both). Dose- and adjuvant-related increases in serum IgG against Sm-TSP-2 were observed. Peak IgG levels occurred 14 days after dose 3. Seroresponse frequencies were low among recipients of Sm-TSP-2/Al without GLA-AF, but higher among subjects receiving 30 µg or 100 µg of Sm-TSP-2/Al with GLA-AF. More seroresponses were observed among those given 30 µg or 100 µg of Sm-TSP-2/Al with GLA-AF compared to placebo (p = 0.023 and p < 0.001, respectively). Seroresponse frequencies were 0%, 30%, 50%, and 89%, respectively, among those given placebo, or 10 µg, 30 µg or 100 µg of Sm-TSP-2/Al with GLA-AF, suggesting a dose-response relationship for Sm-TSP-2/Al with GLA-AF (p = 0.0001).

CONCLUSIONS

Sm-TSP-2/Al with or without GLA-AF was safe and well tolerated in a Sm-naïve population. A vaccine like the one under development may represent our best hope to eliminating this neglected tropical disease.

Abstract 4462: Sensitivity and reproducibility of onco-panel sequencing across multiple laboratories and technologies

Onco-panel sequencing targets sequencing reads to few small regions of the genome and thus is better enabled to detect of rare but clinically relevant sub-clonal mutations. Accurate diagnosis and subsequent tailoring of therapy depends on thorough characterization of tumor mutational spectra. The lack of tumor reference samples, comprehensive approaches to assessing reproducibility and detection sensitivity, and standard practice guidelines is hindering the development of onco-panel sequencing and the realization of its benefits in cancer diagnosis and treatment. As a component of the FDA-led SEQC project phase 2 (SEQC2), the Onco-panel Working Group has designed and characterized a set of reference materials. These materials were created using cell line gDNA pooling and dilution to enable such comprehensive assessments of targeted mutation detection approaches. To this end, a cross-lab evaluation of eight Pan-Cancer panels and five ctDNA liquid biopsy assays is currently underway. Each panel was tested in three independent laboratories. To further evaluate methods to boost reproducibility, synthetic spike-in controls and synthetic plasma were also incorporated into the testing samples. Contrived samples for liquid biopsy testing were prepared through enzymatic fragmentation and size selection to mimic cell-free DNA. The onco-panels tested represent two target enrichment approaches (amplicon based and capture based) and sequencing technologies (multiple Illumina platforms and Ion Torrent). Of note, the liquid biopsy assays employ various molecular barcoding techniques to improve their detection sensitivity of rare mutations. Extensive lab QC data has been collected along with sequencing data. Performance measures have been devised to evaluate reproducibility and sensitivity of the variant/mutation calling results that are produced by the panel providers. Meta-analysis of performance measures will then be conducted for cross panel comparison. This comprehensive study will yield insights into factors underpinning sensitivity and reproducibility of onco-panel sequencing. Quantitative performance metrics and actionable data analysis recommendations will be presented to the targeted sequencing panel community.

Citation Format: Joshua Xu, Binsheng Gong, Wendell Jones, Don Johann, Onco-panel Working Group of the Sequencing QualityControl Phase 2 (SEQC2) Consortium. Sensitivity and reproducibility of onco-panel sequencing across multiple laboratories and technologies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4462.

CBP/p300 Drives the Differentiation of Regulatory T Cells through Transcriptional and Non-Transcriptional Mechanisms

Regulatory T cells (Treg) are immunosuppressive and negatively impact response to cancer immunotherapies. CREB-binding protein (CBP) and p300 are closely related acetyltransferases and transcriptional coactivators. Here, we evaluate the mechanisms by which CBP/p300 regulate Treg differentiation and the consequences of CBP/p300 loss-of-function mutations in follicular lymphoma. Transcriptional and epigenetic profiling identified a cascade of transcription factors essential for Treg differentiation. Mass spectrometry analysis showed that CBP/p300 acetylates prostacyclin synthase, which regulates Treg differentiation by altering proinflammatory cytokine secretion by T and B cells. Reduced Treg presence in tissues harboring CBP/p300 loss-of-function mutations was observed in follicular lymphoma. Our findings provide novel insights into the regulation of Treg differentiation by CBP/p300, with potential clinical implications on alteration of the immune landscape. SIGNIFICANCE: This study provides insights into the dynamic role of CBP/p300 in the differentiation of Tregs, with potential clinical implications in the alteration of the immune landscape in follicular lymphoma.

Immunotherapy clinical trials suggest predictive immune-related biomarkers are tissue specific

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Background: RNA-based immune landscape signatures (RILS) portray the breadth of immune and stromal cell activity in the tumor microenvironment (TME). Their predictive and prognostic capability for patients with solid tumors and treated with various therapies has been reported. Methods: Single and multi-variable survival analysis, multi-variable linear models, publicly available data on clinical trials NCT00796445, NCT01621490, NCT02108652. Results: Using publicly available data, RILS were compared to each other and to tumor mutational burden (TMB) to determine their relative ability to identify responders/non-responders and estimate patient survival in a series of immunotherapy clinical trials. These immunotherapy trials include patients treated with a PD1 inhibitor, PD-L1 inhibitor or MAGE-A3 tumor antigen combined with immunostimulant (MAGE-A3). Although no single RILS/TMB biomarker emerged as a clear indicator of immunotherapy response and survival for all cases, there were certain immune-related signatures that recurred as significant (p < .05) or had near-significance (p < .10) related to a specific cancer or therapy. Immune signatures for T cell trafficking, ratios of PD1 to PD-L1 expression, cytotoxic lymphocytes and B cells were consistently predictive and prognostic in melanoma patients treated with the PD1 inhibitor, nivolumab or MAGE-A3. However, while these same signatures were not predictive/prognostic in bladder and kidney/ureter cancer patients treated with the PD-L1 inhibitor, atezolizumab, biomarkers significantly associated with outcome included TMB, TGFB1, and the ratio of T cell trafficking to M2 tumor associated macrophage activity. Since TMB and various immune signatures generally worked better together than individually in predicting outcome, there is potential for utilization of a combination of biomarkers and immune signatures in the design of effective immunotherapy clinical trials. Conclusions: In summary, our results suggest effective immunotherapy trials may require tissue-specific biomarker development. Further, a combination of immune signatures and biomarkers such as TMB shows markedly increased utility compared to single factor such as TMB, PD-1 or PD-L1 expression alone.

Deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles

The National Cancer Institute conducted the Biospecimen Pre-analytical Variables (BPV) study to determine the effects of formalin fixation and delay to fixation (DTF) on the analysis of nucleic acids. By performing whole transcriptome sequencing and small RNA profiling on matched snap-frozen and FFPE specimens exposed to different delays to fixation, this study aimed to determine acceptable delays to fixation and proper workflow for accurate and reliable Next-Generation Sequencing (NGS) analysis of FFPE specimens. In comparison to snap-freezing, formalin fixation changed the relative proportions of intronic/exonic/untranslated RNA captured by RNA-seq for most genes. The effects of DTF on NGS analysis were negligible. In 80% of specimens, a subset of RNAs was found to differ between snap-frozen and FFPE specimens in a consistent manner across tissue groups; this subset was unaffected in the remaining 20% of specimens. In contrast, miRNA expression was generally stable across various formalin fixation protocols, but displayed increased variability following a 12 h delay to fixation.

Identical and Nonidentical Twins: Risk and Factors Involved in Development of Islet Autoimmunity and Type 1 Diabetes

OBJECTIVE

There are variable reports of risk of concordance for progression to islet autoantibodies and type 1 diabetes in identical twins after one twin is diagnosed. We examined development of positive autoantibodies and type 1 diabetes and the effects of genetic factors and common environment on autoantibody positivity in identical twins, nonidentical twins, and full siblings.

RESEARCH DESIGN AND METHODS

Subjects from the TrialNet Pathway to Prevention Study (N = 48,026) were screened from 2004 to 2015 for islet autoantibodies (GAD antibody [GADA], insulinoma-associated antigen 2 [IA-2A], and autoantibodies against insulin [IAA]). Of these subjects, 17,226 (157 identical twins, 283 nonidentical twins, and 16,786 full siblings) were followed for autoantibody positivity or type 1 diabetes for a median of 2.1 years.

RESULTS

At screening, identical twins were more likely to have positive GADA, IA-2A, and IAA than nonidentical twins or full siblings (all P < 0.0001). Younger age, male sex, and genetic factors were significant factors for expression of IA-2A, IAA, one or more positive autoantibodies, and two or more positive autoantibodies (all P ≤ 0.03). Initially autoantibody-positive identical twins had a 69% risk of diabetes by 3 years compared with 1.5% for initially autoantibody-negative identical twins. In nonidentical twins, type 1 diabetes risk by 3 years was 72% for initially multiple autoantibody-positive, 13% for single autoantibody-positive, and 0% for initially autoantibody-negative nonidentical twins. Full siblings had a 3-year type 1 diabetes risk of 47% for multiple autoantibody-positive, 12% for single autoantibody-positive, and 0.5% for initially autoantibody-negative subjects.

CONCLUSIONS

Risk of type 1 diabetes at 3 years is high for initially multiple and single autoantibody-positive identical twins and multiple autoantibody-positive nonidentical twins. Genetic predisposition, age, and male sex are significant risk factors for development of positive autoantibodies in twins.

Targeted deletion of fibrillin-1 in the mouse eye results in ectopia lentis and other ocular phenotypes associated with Marfan syndrome

Fibrillin is an evolutionarily ancient protein that lends elasticity and resiliency to a variety of tissues. In humans, mutations in fibrillin-1 cause Marfan and related syndromes, conditions in which the eye is often severely affected. To gain insights into the ocular sequelae of Marfan syndrome, we targeted Fbn1 in mouse lens or non-pigmented ciliary epithelium (NPCE). Conditional knockout of Fbn1 in NPCE, but not lens, profoundly affected the ciliary zonule, the system of fibrillin-rich fibers that centers the lens in the eye. The tensile strength of the fibrillin-depleted zonule was reduced substantially, due to a shift toward production of smaller caliber fibers. By 3 months, zonular fibers invariably ruptured and mice developed ectopia lentis, a hallmark of Marfan syndrome. At later stages, untethered lenses lost their polarity and developed cataracts, and the length and volume of mutant eyes increased. This model thus captures key aspects of Marfan-related syndromes, providing insights into the role of fibrillin-1 in eye development and disease.

Summary: Targeted knockout of Fbn1 in the ciliary epithelium of the mouse eye undermines the structural and biomechanical integrity of the ciliary zonule and results in an ectopia lentis phenotype.

HOXA4/HOXB3 gene expression signature as a biomarker of recurrence in patients with high-grade serous ovarian cancer following primary cytoreductive surgery and first-line adjuvant chemotherapy

OBJECTIVES

Aberrant homeobox (HOX) gene expression is reported in high-grade serous ovarian carcinoma (HGSOC), however, its prognostic significance remains unclear.

METHODS

HOX genes associated with progression-free survival (PFS) in a discovery cohort of primary HGSOC samples with RNA sequencing data, and those previously reported to be associated with clinical outcomes, were selected for qPCR testing in an independent training cohort of primary HGSOC samples (n=71). A prognostic model for PFS was developed using univariate and multivariate Cox regression. Patients were stratified into risk groups that optimized the test statistic. The model was tested in an independent HGSOC cohort from The Cancer Genome Atlas (TCGA) (n=320). The effect of selected HOX genes on drug sensitivity and reactive oxygen species (ROS) accumulation was examined in vitro.

RESULTS

Of 23 HOX genes tested in the training cohort, HOXA4 (HR=1.20, 95% CI=1.07-1.34, P=0.002) and HOXB3 (HR=1.09, 95% CI=1.01-1.17, P=0.027) overexpression were significantly associated with shorter PFS in multivariate analysis. Based on the optimal cutoff of the HOXA4/HOXB3 risk score, median PFS was 16.9months (95% CI=14.6-21.2months) and not reached (>80months) for patients with high and low risk scores, respectively (HR=8.89, 95% CI=2.09-37.74, P<0.001). In TCGA, the HOXA4/HOXB3 risk score was significantly associated with disease-free survival (HR=1.44, 95% CI=1.00-2.09, P=0.048). HOXA4 or HOXB3 overexpression in ovarian cancer cells decreased sensitivity to cisplatin and attenuated the generation of cisplatin-induced ROS (P<0.05).

CONCLUSIONS

HOXA4/HOXB3 gene expression-based risk score may be useful for prognostic risk stratification and warrants prospective validation in HGSOC patients.

Abstract 1307: Effect of tumor purity on somatic mutation detection using next-generation sequencing technology: A benchmarking study

Next generation sequencing (NGS) is becoming an essential tool for clinical cancer care. Whole genome sequencing (WGS), whole exome sequencing (WES), and targeted gene sequencing (TGS) have emerged as important tools and are critical for advancing precision oncology to meaningfully impact patient lives. To enable this goal, we must first thoroughly characterize the complexities of using NGS to identify somatic mutations in samples with tumor heterogeneity and variable tissue sample purity.

Here, we applied both experiment and in silico approaches to determine the effects of tumor heterogeneity on somatic mutation detection. First, we systematically investigated somatic mutation events in paired cell lines (breast carcinoma and matched normal) using a myriad of NGS platforms and protocols. Then, we applied machine learning algorithms to define high confidence mutation calls with datasets from the combination of all platforms and pipelines. Finally, we performed whole genome sequencing from tumor DNA samples titrated with matched normal cells to create a gradient of tumor purities from 100%, 75%, 50%, 20%, 10%, 5%, and 0%. We also created a series of in silico mixes by pooling reads from tumor and normal cell lines at respective ratios.

With somatic variation “ground truth” established by multiple orthogonal sequencing platforms and multiple analysis tools, we evaluated performance of individual software tools for tumor purity assessment and for mutation detection. Our experimental design allowed us to systematically evaluate accuracy, specificity and sensitivity of mutation detection across a range of tumor purities, as well as conduct a head-to-head comparison of in silico approaches versus experimental approaches.

This comprehensive study will help to clarify our understanding of experimental and analytical challenges that arise when confronted with tumor heterogeneity in patient care clinical decisions. In addition, data generated in this study will be used as a benchmark resource for the community to develop and improve tools to meet clinical challenges.

Citation Format: Wendell Jones, Wenming Xiao, Somatic Mutation Working Group, SEQC2 Consortium. Effect of tumor purity on somatic mutation detection using next-generation sequencing technology: A benchmarking study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1307.

Abstract 2250: Tumor mutational burden: Guidelines for derivation and robustness of measurement

Tumor mutational burden (TMB) is defined as the number of somatic mutations per Mb of the genome and is used to represent accumulation of somatic mutations over the life of the tumor. Recent evidence has shown that high TMB scores are associated with improved response to immune therapies across multiple indications. However, the derivation of this score is not well characterized, nor is this score universally performed across laboratories.

Here we describe our methodology for calculating TMB, which considers an estimation of true germline mutations, the efficacy of different somatic callers, and the identification of regions within a capture panel that most reliably contribute to robust TMB scoring. To accomplish this, we only include positions that fall within high confidence regions of the genome as defined by NIST GIAB datasets HG001-HG005 v3.3.2. The high confidence regions encompass 88% of the exome.

Somatic variant calling is performed utilizing the tumor and normal samples using only positions where there is sufficient depth of coverage in both samples. Any remaining germline variants are excluded, leaving only somatic variants in the targeted, high-confidence regions for the final TMB calculation. TMB calculations utilizing high-confidence regions reduce the contribution of false positive variants in the mutational burden estimate.

We have compared TMB scores using this approach to those provided from evaluating somatic calls from TCGA, where matched tumor/normal pairs exist. In addition, we introduce a method to determine the effect on TMB scores when in silico determination of germline variants is used to derive somatic calls when matching normal samples are not available.

Defining the robustness of this score across and criteria for its derivation will help better position defining analytical range and future utility across indications and NGS panels

Citation Format: Natalie Mola, Matthew Schu, Suzy Stiegelmeyer, Wendell Jones, Victor J. Weigman. Tumor mutational burden: Guidelines for derivation and robustness of measurement [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2250.

Abstract LB-380: TMB calling in absence of matched normal: Learning germline behavior

In most standard cases, mutational burden is derived from samples where mutational calling is performed in tumor and matched normal specimens. While this is ideal to get a true sense of tumor-derived mutations, it creates limitations due to cost of extra sequencing or in many trials, unavailable for genomic profiling. Without this normal material, there are increased difficulties of eliciting the accurate somatic mutation calls away from natural variation. This is even further complicated by the fact that different tumor types have different spectra of mutations so a method built on an individual indication have risks of overfitting. We present here the results of our investigations of machine learning to build reliable germline variant estimates appropriate for use in calculating burden. In this draft, we examine two tumor mutation classification methods based on our latest TMB tool: random forest and neural network across multiple indications in TCGA. We compare calls made by these methods against burden scores that we have generated from our own paired tumor/normal method (sister submission) to determine accuracy. Using sampled tumor results from each indication, different models were built across both random forest and neural networks, showing accuracy in some indications, up to 98%. Looking to work to create and indication-independent classifier, validation results show we can reach an average of 89% accuracy where training is built across all indications. In all cases, cross validation was performed to prove the consistency of the classification method and test the algorithm on our latest tumor only data set against what was generated from paired results.

Citation Format: Yiqing Tian, Wendell Jones, Natalie Mola, Victor J. Weigman. TMB calling in absence of matched normal: Learning germline behavior [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-380.

Abstract 4050: Immune microenvironment characteristics of primary tumor predict long-term disease-free survival in high-grade serous ovarian cancer (HGSOC)

Epithelial ovarian cancer is a heterogeneous disease with HGSOC being the most common subtype and &gt;70% of women are diagnosed at an advanced stage of the disease. Standard of care involving primary cytoreductive surgery followed by first-line adjuvant platinum/taxane based chemotherapy can lead to a favorable response in 80% of the patients, but the rate of recurrence is &gt;70%. Patient outcome in serous ovarian cancer has been associated with presence of intra-tumoral T cells and an “immunoreactive” subtype. Further, chemotherapy can also affect the immune microenvironment in serous ovarian cancer. We hypothesized that in patients with HGSOC who have long-term disease-free survival the primary tumors harbor a more active adaptive immune cell response. To identify genes associated with immune activity we performed Pan-Cancer immunome analysis (Nature Methods 12, 453-457, 2015) of 4446 RNA-Seq tumor samples balanced for tissue and cancer subtypes, from The Cancer Genome Atlas (TCGA). This analysis yielded several highly correlated gene clusters. After mean-centering by gene and hierarchically clustering both genes and samples, gene-cancer type interactions as well as immunogenic tissue-independent characteristics in the clustered expression profile was observed. We identified a highly-correlated primary cluster of 57 genes associated with cytotoxic lymphocyte activity, referred to as the Cytotoxic Lymphocyte Immune Signature (CLIS). This signature was tested for association with disease-free survival (DFS) in a patient cohort (N=48) that received surgical cytoreduction of tumor followed by adjuvant platinum-taxane chemotherapy and was stratified in three risk-groups: a) Platinum-Resistant, median disease-free interval (MDFI) 0 months (range 0-12 months); b) Platinum-Sensitive, MDFI 15 months (range 13-30 months) and (c) Exceptional-Responders, MDFI &gt;80 months (range 66 - &gt;144 months). RNA isolated from frozen primary tumors was depleted of ribosomal RNA and sequenced using the Illumina TruSeq stranded Total Gold protocol yielding &gt;50M 100 bp paired-end sequences per specimen. In this patient cohort CLIS was distinct in &gt;66% of exceptional-responders compared to &lt;25% in platinum-resistant patients and 44% of platinum-sensitive patients. Using Cox proportional hazards regression, CLIS (p=0.0031), as well as M1 macrophage (p=0.020) and B-cell (p=0.028) signatures were independently associated with DFS after accounting for age and stage. This novel association between CLIS, M1 macrophage and B-cell signature in DFS was replicated independently in HGSOC patient datasets from TCGA, N=164 (p &lt; 0.05) and another (JNCI 106: dju249, 2014) HGSOC patient cohort, N=174 (p &lt; 0.05). In summary, primary tumors in exceptional responders with HGSOC harbor a distinct gene profile/immune microenvironment for optimal treatment efficacy.

Citation Format: Wendell Jones, Mahrukh Ganapathi, Chad Michener, Ram N. Ganapathi. Immune microenvironment characteristics of primary tumor predict long-term disease-free survival in high-grade serous ovarian cancer (HGSOC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4050.

Applicability of Precision Medicine Approaches to Managing Hypertension in Rural Populations

As part of the Heart Healthy Lenoir Project, we developed a practice level intervention to improve blood pressure control. The goal of this study was: (i) to determine if single nucleotide polymorphisms (SNPs) that associate with blood pressure variation, identified in large studies, are applicable to blood pressure control in subjects from a rural population; (ii) to measure the association of these SNPs with subjects' responsiveness to the hypertension intervention; and (iii) to identify other SNPs that may help understand patient-specific responses to an intervention. We used a combination of candidate SNPs and genome-wide analyses to test associations with either baseline systolic blood pressure (SBP) or change in systolic blood pressure one year after the intervention in two genetically defined ancestral groups: African Americans (AA) and Caucasian Americans (CAU). Of the 48 candidate SNPs, 13 SNPs associated with baseline SBP in our study; however, one candidate SNP, rs592582, also associated with a change in SBP after one year. Using our study data, we identified 4 and 15 additional loci that associated with a change in SBP in the AA and CAU groups, respectively. Our analysis of gene-age interactions identified genotypes associated with SBP improvement within different age groups of our populations. Moreover, our integrative analysis identified AQP4-AS1 and PADI2 as genes whose expression levels may contribute to the pleiotropy of complex traits involved in cardiovascular health and blood pressure regulation in response to an intervention targeting hypertension. In conclusion, the identification of SNPs associated with the success of a hypertension treatment intervention suggests that genetic factors in combination with age may contribute to an individual's success in lowering SBP. If these findings prove to be applicable to other populations, the use of this genetic variation in making patient-specific interventions may help providers with making decisions to improve patient outcomes. Further investigation is required to determine the role of this genetic variance with respect to the management of hypertension such that more precise treatment recommendations may be made in the future as part of personalized medicine.

An agenda for 21st century neurodevelopmental medicine: lessons from autism

The future of neurodevelopmental medicine has the potential of situating child neurology at the forefront of a broad-based public health effort to optimize neurodevelopmental outcomes of children born with high-prevalence and diverse genetic, pre- and peri-natal, and environmental burdens compromising early brain development and leading to lifetime disabilities. Building on advancements in developmental social neuroscience and in implementation science, this shift is already occurring in the case of emblematic neurodevelopmental disorders such as autism. Capitalizing on early neuroplasticity and on quantification of trajectories of social-communicative development, new technologies are emerging for high-throughput and cost-effective diagnosis and for community-viable delivery of powerful treatments, in seamless integration across previously fragmented systems of healthcare delivery. These solutions could be deployed in the case of other groups of children at greater risk for autism and communication delays, such as those born extremely premature or with congenital heart disease. The galvanizing concept in this aspirational future is a public health focus on promoting optimal conditions for early brain development, not unlike current campaigns promoting pre-natal care, nutrition or vaccination.

Enzyme Replacement Therapy Ameliorates Multiple Symptoms of Murine Homocystinuria

Classical homocystinuria (HCU) is the most common inherited disorder of sulfur amino acid metabolism caused by deficiency in cystathionine beta-synthase (CBS) activity and characterized by severe elevation of homocysteine in blood and tissues. Treatment with dietary methionine restriction is not optimal, and poor compliance leads to serious complications. We developed an enzyme replacement therapy (ERT) and studied its efficacy in a severe form of HCU in mouse (the I278T model). Treatment was initiated before or after the onset of clinical symptoms in an effort to prevent or reverse the phenotype. ERT substantially reduced and sustained plasma homocysteine concentration at around 100 μM and normalized plasma cysteine for up to 9 months of treatment. Biochemical balance was also restored in the liver, kidney, and brain. Furthermore, ERT corrected liver glucose and lipid metabolism. The treatment prevented or reversed facial alopecia, fragile and lean phenotype, and low bone mass. In addition, structurally defective ciliary zonules in the eyes of I278T mice contained low density and/or broken fibers, while administration of ERT from birth partially rescued the ocular phenotype. In conclusion, ERT maintained an improved metabolic pattern and ameliorated many of the clinical complications in the I278T mouse model of HCU.

Abstract 5708: HOXA4 and HOXB3 gene expression signature as a biomarker of tumor recurrence in patients with high-grade serous ovarian cancer (HGSOC) following primary cytoreductive surgery and first-line adjuvant chemotherapy

Background: Aberrant HOX gene expression has been observed in various malignancies; however, their role as a biomarker for recurrence in patients with HGSOC is unknown. We tested the hypothesis that a HOX gene signature is a biomarker for disease-free survival (DFS) in HGSOC patients following primary cytoreductive surgery and adjuvant platinum-based chemotherapy. Methods: A panel of HOX genes associated with DFS in a discovery cohort of 19 HGSOC patients with available RNA-Seq data, and/or previously reported as associated with survival endpoints in the literature, were selected for testing by qPCR using the Fluidigm platform in an independent training cohort of primary tumors from 73 HGSOC patients. Cox proportional hazards model was used to identify HOX genes significantly associated with DFS. A prognostic gene signature was developed based on the combined linear predictor from the final multivariable Cox model. Patients were stratified into risk groups using the optimal cutoff of the linear predictor risk score, whereby the optimal cutoff was defined as the value that maximized the log-rank test statistic. Risk group stratification was further tested for association with DFS in a larger HGSOC dataset (N=414) with similar clinical characteristics from The Cancer Genome Atlas (TCGA). The role of the identified HOX genes in influencing drug sensitivity was examined by overexpressing these genes in a HGSOC cell line, PEO1. Results: Of 23 HOX genes selected for testing in the training cohort, overexpression of HOXA4 (HR=1.21, 95% CI=1.08-1.35, P=0.001) and HOXB3 (HR=1.09, 95% CI=1.02-1.17, P=0.016) were significantly associated with decreased DFS in multivariate analysis. The median DFS in patients with a HOXA4/HOXB3 risk score ≤ the optimal cutoff was &gt; 80 months (not yet reached), whereas the median DFS in patients with a HOXA4/HOXB3 risk score &gt; the optimal cutoff was 16.9 months (HR=7.85, 95% CI=4.19-14.69, P&lt;0.001). The HOXA4/HOXB3 risk score remained significantly associated with DFS in the HGSOC dataset from the TCGA (P=0.02). In vitro studies demonstrated that PEO1 cells overexpressing either HOXA4 or HOXB3 were significantly (P&lt;0.05) more resistant to cisplatin and carboplatin, but not to paclitaxel, as compared to empty vector transfected cells. Conclusion: The HOXA4/HOXB3 risk score was significantly associated with DFS in a training cohort of HGSOC patients, and remained significantly associated in a larger independent HGSOC dataset from the TCGA. Further, in vitro studies suggest that HOXA4 and HOXB3 overexpression is associated with platinum resistance. Thus, overexpression of HOXA4 and HOXB3 in primary HGSOC may serve as a potential biomarker for recurrence and the risk score model developed warrants prospective validation in HGSOC patients.

Citation Format: Jai N. Patel, Katherine Miller, James Symanowski, Jalid Sehouli, Chad Michener, Ioana Braicu, Darla Destephanis, Ashley P. Sutker, Eric J. Norris, David Tait, Wendell Jones, Qing Zhang, Chad Livasy, Charles Biscotti, Ram N. Ganapathi, Mahrukh K. Ganapathi. HOXA4 and HOXB3 gene expression signature as a biomarker of tumor recurrence in patients with high-grade serous ovarian cancer (HGSOC) following primary cytoreductive surgery and first-line adjuvant chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5708. doi:10.1158/1538-7445.AM2017-5708

PdZn catalysts for CO2 hydrogenation to methanol using chemical vapour impregnation (CVI)

The formation of PdZn bimetallic alloys on ZnO, TiO₂ and Al₂O₃ supports was investigated, together with the effect of alloy formation on the CO₂ hydrogenation reaction. The chemical vapour impregnation (CVI) method produced PdZn nanoparticles with diameters of 3–6 nm. X-ray photoelectron spectroscopy and X-ray diffraction revealed the changes in the structure of the PdZn alloy that help stabilise formate intermediates during methanol synthesis. PdZn supported on TiO₂ exhibits high methanol productivity of 1730 mmol kg_cat⁻¹ h⁻¹ that is associated with the high dispersion of the supported PdZn alloy.

Editor's Highlight: Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded Samples

Use of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-sequencing offers a promising way to address this problem. Here, we evaluated transcriptomic dose responses using RNA-sequencing in paired FFPE and frozen (FROZ) samples from 2 archival studies in mice, one <2 years old and the other >20 years old. Experimental treatments included 3 different doses of di(2-ethylhexyl)phthalate or dichloroacetic acid for the recently archived and older studies, respectively. Total RNA was ribo-depleted and sequenced using the Illumina HiSeq platform. In the recently archived study, FFPE samples had 35% lower total counts compared to FROZ samples but high concordance in fold-change values of differentially expressed genes (DEGs) (r²  =0.99), highly enriched pathways (90% overlap with FROZ), and benchmark dose estimates for preselected target genes (<5% difference vs FROZ). In contrast, older FFPE samples had markedly lower total counts (3% of FROZ) and poor concordance in global DEGs and pathways. However, counts from FFPE and FROZ samples still positively correlated (r² = 0.84 across all transcripts) and showed comparable dose responses for more highly expressed target genes. These findings highlight potential applications and issues in using RNA-sequencing data from FFPE samples. Recently archived FFPE samples were highly similar to FROZ samples in sequencing quality metrics, DEG profiles, and dose-response parameters, while further methods development is needed for older lower-quality FFPE samples. This work should help advance the use of archival resources in chemical safety and translational science.

Designing an information interface to support sharing of information in cancer care

This paper describes the design, implementation and testing of a functional prototype interface which enables primary healthcare teams to access the information system supporting clinical oncology specialists in South Wales, UK. A lack of information sharing has been recognized for some time as a barrier to improving the primary care of cancer patients. This extension to the existing ISCO information system will allow sharing of information about patient management at all levels of cancer patient support (general practitioners, hospital-based clinicians and palliative care teams). The application was designed to allow general practitioners to gain access to the existing system. This will give all healthcare professionals interested in a cancer patient's care the advantage of accessing detailed multiple providers' electronic casenotes in almost real time, thus improving communication of information within a care team. However, no attempt was made to include the much bigger issue of patients and their families or carers in the scope of the project at this stage, as this is an area requiring separate investigation. The pilot also enables general practitioners to determine the information they require and the information they need to be able to communicate with the cancer specialists.

Abstract 5276: Impact of duplicate removal on low frequency NGS somatic variant calling

Cancer genomic profiles created by analysis of targeted Next Generation Sequencing (NGS) panels is emerging as a powerful tool for making informed clinical decisions. Of the critical informatics challenges to address, accurate mutation calls and allele frequency estimations after accounting for PCR-mediated artifacts are debated. The process of sample preparation for NGS sequencing involves amplification by PCR. While PCR is relatively error-free, mistakes early in DNA synthesis can be compounded, driving detection of spurious mutations and having an adverse impact on clinical reporting. Previous reports have addressed the utility of detecting and removing PCR duplicate reads in Mendelian applications but have rarely examined its use with targeted NGS panels.

We performed deduplication with 3 widely used tools (Samtools, Samblaster, and Picard) to understand sensitivity to call low frequency alleles and any impact on false positive/negative rates. Furthermore, we evaluated effects of duplicate removal on targeted panels of varying sizes and effects of sample matrices using replicates of 7 verified reference samples with several digitally confirmed alleles with frequencies ranging from 1-5%.

It is not practical to perform deduplication on PCR-enriched panels, therefore, we assessed 3 different hybrid enrichment panels of varying size (387kb, 1.3Mb, and 54Mb). Deduplication by Picard resulted in a greater decrease in the mean depth for the smaller panels (32-59%) compared to Exome (15%), showing that higher molecular diversity lowers duplication rates. Uniformity (percent of ROI with depth within 20% of the mean depth) improved 6-18% after deduplication for the smaller panels, but only 1% for the Exome.

Independent of panel size, about 32% of the total reads were marked as duplicates, reducing the power to call low frequency variants by 18%. Importantly, after added sequencing 95-96% of onco-specific variants were detected post-deduplication with a lower limit of detection of 3% compared to 2.5% pre-removal. For low-quality DNA samples we find no benefit in added sequencing for any panel. We also generally observed higher sensitivity (0% to 10% for SNV and -3% to 3% for indels) post deduplication.

Molecular diversity also varies by sample type. Intact DNA show higher molecular diversity and lower duplication rates than degraded FFPE samples. We profiled mixed-quality FFPE samples (n = 85), good-quality fresh frozen samples (n = 3), and NA12878 (n = 1) on our smallest panel and noted duplication rates of 64±14%, 40±5% and 30% respectively. On average, deduplication cut the number of SNV calls by 17.4%, with the FFPE samples affected the most (2-88%).

From our analysis we recommend performing deduplication during analysis of targeted panels. While we observed the most benefit for smaller panels with low uniformity, improved variant sensitivity was seen regardless of panel size. During experimental design, we advise a worksheet to guide deduplication decisions.

Citation Format: Jeran Stratford, Gunjan Hariani, Jeff Jasper, Chad Brown, Wendell Jones, Victor J. Weigman. Impact of duplicate removal on low frequency NGS somatic variant calling. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5276.

H2 production by the photocatalytic reforming of cellulose and raw biomass using Ni, Pd, Pt and Au on titania

Here, we report a method for sustainable hydrogen production using sunlight and biomass. It is shown that cellulose can be photoreformed to produce hydrogen, even in solid form, by use of metal-loaded titania photocatalysts. The experiments performed verified that the process is enabled by initial hydrolysis via glucose, which itself is shown to be efficiently converted to produce hydrogen by photocatalysis. Importantly, it is shown that not only precious metals such as Pt, Pd and Au can be used as the metal component, but also much more economic and less environmentally damaging Ni is effective. Even more importantly, we show for the first time, to the best our knowledge, that fescue grass as raw biomass can be effective for hydrogen production without significant pre-treatment. This provides additional benefits for the efficiency of biomass hydrogen production, because fewer processing steps for the raw material are required than in the production of purer forms of cellulose, for example.