Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment

MOTIVATION

Analysis of mutational signatures is a powerful approach for understanding the mutagenic processes that have shaped the evolution of a cancer genome. To evaluate the mutational signatures operative in a cancer genome, one first needs to quantify their activities by estimating the number of mutations imprinted by each signature.

RESULTS

Here we present SigProfilerAssignment, a desktop and an online computational framework for assigning all types of mutational signatures to individual samples. SigProfilerAssignment is the first tool that allows both analysis of copy-number signatures and probabilistic assignment of signatures to individual somatic mutations. As its computational engine, the tool uses a custom implementation of the forward stagewise algorithm for sparse regression and nonnegative least squares for numerical optimization. Analysis of 2700 synthetic cancer genomes with and without noise demonstrates that SigProfilerAssignment outperforms four commonly used approaches for assigning mutational signatures.

AVAILABILITY AND IMPLEMENTATION

SigProfilerAssignment is available under the BSD 2-clause license at https://github.com/AlexandrovLab/SigProfilerAssignment with a web implementation at https://cancer.sanger.ac.uk/signatures/assignment/.

Defining "recklessness" in research misconduct proceedings

To find research misconduct in research that has been supported by federal funds, an institution must determine that the misconduct was committed intentionally, knowingly, or recklessly. "Intentional" and "knowing" are straightforward standards. Yet "reckless" often mystifies institutions, which struggle to assess whether a respondent's conduct should be deemed "reckless," or merely negligent. This difficulty is most pronounced when allegations are lodged against the author under whose supervision the primary research was conducted - most often, the senior and/or corresponding author of a published paper who may not have been directly involved in performing the experiments or preparing the data under scrutiny. In these situations, investigation committees and the institutional "deciding official" must assess whether the supervising scientist is guilty of research misconduct - based on the theory that their supervision of the research and development of the publication containing falsified, fabricated, or plagiarized information was reckless - even if that person did not perform the experiment or assemble the research records in question. This paper seeks to provide a framework for evaluating the circumstances in which past supervisory conduct should be deemed "reckless" and thus a basis on which a finding of research misconduct may be made.

Topography of mutational signatures in human cancer

The somatic mutations found in a cancer genome are imprinted by different mutational processes. Each process exhibits a characteristic mutational signature, which can be affected by the genome architecture. However, the interplay between mutational signatures and topographical genomic features has not been extensively explored. Here, we integrate mutations from 5,120 whole-genome-sequenced tumors from 40 cancer types with 516 topographical features from ENCODE to evaluate the effect of nucleosome occupancy, histone modifications, CTCF binding, replication timing, and transcription/replication strand asymmetries on the cancer-specific accumulation of mutations from distinct mutagenic processes. Most mutational signatures are affected by topographical features, with signatures of related etiologies being similarly affected. Certain signatures exhibit periodic behaviors or cancer-type-specific enrichments/depletions near topographical features, revealing further information about the processes that imprinted them. Our findings, disseminated via the COSMIC (Catalog of Somatic Mutations in Cancer) signatures database, provide a comprehensive online resource for exploring the interactions between mutational signatures and topographical features across human cancer.

Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator

BACKGROUND

All cancers harbor somatic mutations in their genomes. In principle, mutations affecting between one and fifty base pairs are generally classified as small mutational events. Conversely, large mutational events affect more than fifty base pairs, and, in most cases, they encompass copy-number and structural variants affecting many thousands of base pairs. Prior studies have demonstrated that examining patterns of somatic mutations can be leveraged to provide both biological and clinical insights, thus, resulting in an extensive repertoire of tools for evaluating small mutational events. Recently, classification schemas for examining large-scale mutational events have emerged and shown their utility across the spectrum of human cancers. However, there has been no computationally efficient bioinformatics tool that allows visualizing and exploring these large-scale mutational events.

RESULTS

Here, we present a new version of SigProfilerMatrixGenerator that now delivers integrated capabilities for examining large mutational events. The tool provides support for examining copy-number variants and structural variants under two previously developed classification schemas and it supports data from numerous algorithms and data modalities. SigProfilerMatrixGenerator is written in Python with an R wrapper package provided for users that prefer working in an R environment.

CONCLUSIONS

The new version of SigProfilerMatrixGenerator provides the first standardized bioinformatics tool for optimized exploration and visualization of two previously developed classification schemas for copy number and structural variants. The tool is freely available at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator with an extensive documentation at https://osf.io/s93d5/wiki/home/ .

Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment

Analysis of mutational signatures is a powerful approach for understanding the mutagenic processes that have shaped the evolution of a cancer genome. Here we present SigProfilerAssignment, a desktop and an online computational framework for assigning all types of mutational signatures to individual samples. SigProfilerAssignment is the first tool that allows both analysis of copy-number signatures and probabilistic assignment of signatures to individual somatic mutations. As its computational engine, the tool uses a custom implementation of the forward stagewise algorithm for sparse regression and nonnegative least squares for numerical optimization. Analysis of 2,700 synthetic cancer genomes with and without noise demonstrates that SigProfilerAssignment outperforms four commonly used approaches for assigning mutational signatures. SigProfilerAssignment is freely available at https://github.com/AlexandrovLab/SigProfilerAssignment with a web implementation at https://cancer.sanger.ac.uk/signatures/assignment/.

Effect of subclinical endometritis and flunixin meglumine administration on pregnancy in embryo recipient beef cows

Fertility of recipient beef cows with subclinical endometritis (SCE) that did or did not receive flunixin meglumine (FM) treatment were compared following transfer of d 7 embryo. The study population comprised of 600 Angus cross cows that expressed estrus following Select-Synch + CIDR (Controlled Internal Drug Release) estrus synchronization protocol. At the time of embryo transfer, approximately 3 wk after sampling for subclinical endometritis, cows were randomly allocated either to receive FM treatment (500 mg of Banamine®; n = 300) or not (Control; n = 300). The effect of subclinical endometritis (at ≥ 1% PMN on endometrial cytology by cytobrush method) and FM treatment on pregnancy/embryo transfer (P/ET, %) were evaluated by mixed model. Of the 600 cows, 323 (53.8%) became pregnant; 55.0% (165/300) cows that received FM treatment vs. 52.7% (158/300) control cows (P > 0.1), and 55.9% (266/476) normal vs. 46.0% (57/124) subclinical endometritis cows (P < 0.05). There was a trend for treatment by subclinical endometritis for P/ET (P = 0.09). Pregnancy was recorded in 55.3% (134/242) of normal and 53.4% (31/58) of subclinical endometritis cows that received FM treatment, and in 56.4% (132/234) of normal and 39.4% (26/66) of subclinical endometritis cows that did not receive FM treatment (P = 0.09). In conclusion, subclinical endometritis in recipient beef cows resulted in lower P/ET. Though not significant in cows with subclinical endometritis, FM treatment resulted in 14.0% points more pregnancy compared with control.

Fourier transform infrared spectroscopy as a non-destructive method for analysing herbarium specimens

Dried plant specimens stored in herbaria are an untapped treasure chest of information on environmental conditions, plant evolution and change over many hundreds of years. Owing to their delicate nature and irreplaceability, there is limited access for analysis to these sensitive samples, particularly where chemical data are obtained using destructive techniques. Fourier transform infrared (FTIR) spectroscopy is a chemical analysis technique which can be applied non-destructively to understand chemical bonding information and, therefore, functional groups within the sample. This provides the potential for understanding geographical, spatial and species-specific variation in plant biochemistry. Here, we demonstrate the use of mid-FTIR microspectroscopy for the chemical analysis of Drosera rotundifolia herbarium specimens, which were collected 100 years apart from different locations. Principal component and hierarchical clustering analysis enabled differentiation between three main regions on the plant (lamina, tentacle stalk and tentacle head), and between the different specimens. Lipids and protein spectral regions were particularly sensitive differentiators of plant tissues. Differences between the different sets of specimens were smaller. This study demonstrates that relevant information can be extracted from herbarium specimens using FTIR, with little impact on the specimens. FTIR, therefore, has the potential to be a powerful tool to unlock historic information within herbaria.

Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator

Background

All cancers harbor somatic mutations in their genomes. In principle, mutations affecting between one and fifty base pairs are generally classified as small mutational events. Conversely, large mutational events affect more than fifty base pairs, and, in most cases, they encompass copy-number and structural variants affecting many thousands of base pairs. Prior studies have demonstrated that examining patterns of somatic mutations can be leveraged to provide both biological and clinical insights, thus, resulting in an extensive repertoire of tools for evaluating small mutational events. Recently, classification schemas for examining large-scale mutational events have emerged and shown their utility across the spectrum of human cancers. However, there has been no standard bioinformatics tool that allows visualizing and exploring these large-scale mutational events.

Results

Here, we present a new version of SigProfilerMatrixGenerator that now delivers integrated capabilities for examining large mutational events. The tool provides support for examining copy-number variants and structural variants under two previously developed classification schemas and it supports data from numerous algorithms and data modalities. SigProfilerMatrixGenerator is written in Python with an R wrapper package provided for users that prefer working in an R environment.

Conclusions

The new version of SigProfilerMatrixGenerator provides the first standardized bioinformatics tool for optimized exploration and visualization of two previously developed classification schemas for copy number and structural variants. The tool is freely available at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator with an extensive documentation at https://osf.io/s93d5/wiki/home/ .

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.

OP0085 CELL LINEAGE-SPECIFIC TRANSCRIPT DECONVOLUTION OF SYNOVIAL BIOPSIES FROM THE R4RA TRIAL IDENTIFIES CELL POPULATIONS ASSOCIATED WITH RESPONSE TO RITUXIMAB AND TOCILIZUMAB

Background

The R4RA trial, the first biopsy-based randomised trial in TNF-i inadequate responder patients with Rheumatoid Arthritis, showed that molecular stratification of RA synovial tissue was associated with clinical response, demonstrating that, in patients with low/absent B-cell lineage signature in synovial-tissue, tocilizumab is superior to rituximab1.

Objectives

Here, we aimed to perform cell-transcript deconvolution of pre-and post-treatment synovial biopsies from the R4RA trial.

Methods

A total of 164 patients underwent pre-treatment synovial biopsy (US-guided or arthroscopic) prior to randomization 1:1 to rituximab (83) or tocilizumab (81). 65 patients had a repeat biopsy at 16 weeks when clinical response was assessed using Clinical Disease Activity Index (CDAI) 50% improvement. RNA extracted from a minimum of 6 synovial samples/patient underwent RNA-sequencing and the abundance of tissue-infiltrating immune and stromal cell populations was estimated using the Microenvironment Cell Populations-counter (MCP-counter) method (Figure 1a).

Results

At baseline, while synovial semiquantitative immunohistochemistry scores did not differ between CDAI50% responders and non-responders, both for rituximab and tocilizumab, MCP-counter analysis showed significantly higher CD8 T-cells in responders to rituximab and higher macrophage-monocytes and myeloid dendritic cells (mDC) in responders to tocilizumab (Figure 1b). Moreover, when patients were classified according to MCP-counter scores, B-cell poor patients (MCP-counter B cell score <median value) showed significantly higher response rates to tocilizumab, while no difference was found in B-cell rich patients (Figure 1c). In contrast, macrophage and myeloid dendritic cell (mDC) rich individuals showed higher responses to tocilizumab (Figure 1d). Combined scores for lymphoid and myeloid cells demonstrated that patients poor in B-cells but rich in macrophages/mDC had a significantly higher response to tocilizumab (77% responders to tocilizumab vs 14% responders to rituximab, p=0.017, OR 16.48, 95%CI 1.29-1000.5) (Figure 1e). By analysing disease activity over time from baseline to week 16, we found a statistically significant interaction effect between treatments and time in B-cell poor (p=0.003), T-cell poor (p=0.022), mDC rich (p=0.029) and B-cell poor/Macrophages-mDC rich patients (p=0.006) (Figure 1f-g-h). Finally, by applying MCP-counter on matched pre-and post-treatment biopsies, rituximab-treated patients showed a significant reduction of B-cells, T-cells and monocyte/macrophages, while tocilizumab-treated patients showed a significant reduction of monocyte/macrophages, T-cells, but also neutrophils, myeloid dendritic cells and, interestingly, an increase in fibroblast signature (Figure 1i).

Conclusion

In silico deconvolution of the synovial tissue identify pre-treatment lymphoid cell lineages associated with response to rituximab and myeloid cells for tocilizumab. The longitudinal analysis of matched pre- and post-treatment synovial biopsies indicated that both medications have an effect on synovial immune cells, but tocilizumab can also affect stromal cells.

References

[1]Humby et al. Rituximab versus tocilizumab in anti-TNF inadequate responder patients with rheumatoid arthritis (R4RA): 16-week outcomes of a stratified, biopsy-driven, multicentre, open-label, phase 4 randomised controlled trial Lancet. 2021 Jan 23;397(10271):305-317. doi: 10.1016/S0140-6736(20)32341-2.

Acknowledgements

We would like to thank all patients and the R4RA recruiting centres and principal investigators http://www.r4ra-nihr.whri.qmul.ac.uk/recruiting_centres.php We would also like to acknowledge the UK National Institute of Health Research for funding the R4RA trial (grant reference: 11/100/76) and Versus Arthritis for providing infrastructure support through the Experimental Arthritis Treatment Centre (grant number: 20022).

Disclosure of Interests

None declared.

OP0109 EXPRESSION QUANTITATIVE TRAIT LOCI IN EARLY TREATMENT-NAÏVE RHEUMATOID ARTHRITIS

Background

To date more than 100 genetic loci have been associated with rheumatoid arthritis (RA), particularly in the human leukocyte antigen (HLA) region. Our understanding of the functional consequences of genetic variation in RA causality, however, is limited and it has been shown that a substantial portion of complex disease risk alleles modify gene expression in a cell-specific manner [1]. The Pathobiology of Early Arthritis Cohort (PEAC) is a longitudinal study looking at treatment-naiv̈e RA patients with genotyped data as well as both synovial and blood RNA-sequenced biopsies prior to treatment with disease modifying anti-rheumatic drugs (DMARDs).

Objectives

To explore expression quantitative trait loci (eQTL) in synovium and blood within PEAC and characterise the effects of genetic variation on gene expression measured by RNA-sequencing. A further goal was to investigate the role of these variants in RA disease severity and response variables.

Methods

Genotypes were generated by Illumina Human CoreExome-24 version 1-0 array in 118 RA patients. Single nucleotide polymorphisms (SNPs) in the HLA region were imputed using HLA-TAPAS. A candidate gene study was performed on variants within the HLA region using Plink v2.0. Synovial (n=85) and blood (n=51) RNA-sequenced samples then underwent cis-eQTL analysis (loci within ±5x105Mb of the variant) based on linear regression models with the matrixeQTL R package using PEER [2] and PCA eigenvectors as covariates. Differences in eQTL between tissues were determined using a linear interaction term.

Results

The candidate gene study determined several amino acids around HLA-DRB1 acting as markers for seropositivity, which replicated findings by Raychaudhuri et. al. [3]. Using eQTL analysis, around 33,000 synovial SNPs were found with genome-wide significance (p ≤ 5x10-8) and around 29,000 in blood. This corresponded to 279 unique significant genes in synovium and 417 in blood (Figure 1). There were 100 genes common to both synovium and blood, including PSORS1C3, HLA-DRB9 and ERAP2, which have known associations with autoimmune diseases and inflammatory arthritis. Notably, 92 genes showed significantly different patterns of QTL expression between synovial tissue and blood (p ≤ 5x10-8). eQTL data also confirmed the triad of genetic variants significantly driving tissue gene expression of HLA-DPB2, while both HLA-DPB2 SNPs and HLA-DPB2 RNA-sequencing synovial expression correlated highly with erythrocyte sedimentation rate (ESR).

Figure 1.

Manhattan plots for cis-expression quantitative trait loci (eQTL) analysis performed on 85 synovial samples (top) and 51 blood samples (middle). Tissue interaction eQTL (bottom) show significant differences between tissues (p ≤ 5x10-8).

Conclusion

The high significance of genes in the HLA region in both tissues is in-keeping with the strong association between HLA and susceptibility to RA, as well as other autoimmune diseases. Most notably variants linked to HLA-DPB2 synovial expression were found to be a marker for disease severity through ESR association. Additionally, the significant differences between eQTL in blood and synovium highlight the need to explore functional consequences of genetic associations in the diseased tissue directly.

References

[1]Thalayasingam et. al. (2018). CD4+ and B lymphocyte expression quantitative traits at rheumatoid arthritis risk loci in patients with untreated early arthritis: implications for causal gene identification. Arthritis & Rheumatology, 70(3), 361-370.

[2]Stegle et al. (2012). Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nature protocols, 7(3), 500-507.

[3]Raychaudhuri et al. (2012). Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Nature genetics, 44(3), 291-296.

Disclosure of Interests

None declared

OP0012 INTERFERON-α MEDIATED THERAPEUTIC RESISTANCE IN EARLY RA IMPLICATES EPIGENETIC REPROGRAMMING

Background

An interferon gene signature (IGS) is present in approximately 50% of early, treatment naive rheumatoid arthritis (eRA) patients. We previously demonstrated it negatively impacts on initial disease outcomes.

Objectives

To 1) reproduce previous findings demonstrating the harmful effects of the IGS on early RA clinical outcomes, 2) identify which IFN class is responsible for the IGS and 3) seek evidence that IFN-α exposure contributes to harmful epigenetic footprint at disease onset.

Methods

In a large multicentre inception cohort (n=190) of eRA patients (RA-MAP TACERA) whole blood transcriptome, IGS (MxA, IFI44L, OAS1, ISG15, IFI6) and circulating interferons (IFN)-α, -β, -γ and -λ was examined at baseline and 6 months in conjunction with disease activity and clinical characteristics. A separate eRA cohort of paired methylome and transcriptome from CD4 T and CD19 B cells (n=41 for each) was used to explore any epigenetic influence of the IGS.

Results

The baseline IGS reproducibly and significantly negatively impacts on 6-month clinical outcomes. In the high IGS cohort there was increased DAS-28 (p=0.025) and reduced probability of achieving a good EULAR response (p=0.034) at 6-months. In addition, the IGS in eRA is shown for the first time to predominantly reflect raised circulating IFN-α protein, not other classes of IFN and examination of whole blood upstream nucleic acid sensors expression suggest a RNA trigger. Both the IGS and IFN-α significantly fell in parallel at 6 months (p<0.0001), whereas other classes of IFN remained statistically static. There was a significant association with IFN-α and RF titre but not ACPA. Comparison of CD4 T and CD19 B cells between IGS high and low eRA patients demonstrated differentially methylated CPG sites and altered transcript expression of disease relevant genes e.g. PARP9, STAT1, EPTSI1 which was similarly, and persistently, altered 6 months in the separate TACERA cohort. Differentially methylated CPGs implicated altered transcription factor binding in B cells (GATA3, ETSI, NFATC2, EZH2) and T cells (p300, HIF1α) which cumulatively suggested IFN-α induced epigenetic changes promoting increased, and sustained, lymphocyte activation, proliferation and loss of anergy in the IGS high cohort.

Conclusion

We validate that the IGS is a robust prognostic biomarker in eRA predicting poor therapeutic response. Its persistent harmful effects may be driven via epigenetic modifications. These data have relevance for other IFN-α states, such as COVID-19, but also provide a rationale for the initial therapeutic targeting of IFN-α signalling, such as with JAKi, at disease onset in stratified eRA subsets.

References

nil

Acknowledgements

JDI is a National Institute for Health Research (NIHR) Senior Investigator. The authors acknowledge the support of TACERA Principal Investigators from all contributing NHS sites and the members of the TACERA Study Steering and Data Monitoring Committee. Additional acknowledgements include patient volunteers and administrative support from Ben Hargreaves. Newcastle researchers received infrastructural support via the Versus Arthritis Research into Inflammatory Arthritis Centre (Ref 22072), funding from The Medical Research Council; Academy of Medical Sciences; British Society of Rheumatology; The Wellcome Trust; JGW Patterson Foundation; Immune-Mediated Inflammatory Disease Biobank in the UK (IMID-Bio-UK), ANR and RTCure. This work was supported by the NIHR Newcastle Biomedical Research Centre at Newcastle Hospitals Foundation Trust and Newcastle University; views expressed are the authors’ and not necessarily those of the National Health Service, the National Institute of Health Research or the Department of Health.

Disclosure of Interests

Faye Cooles Speakers bureau: Astrazeneca: December 2021, Jessica Tarn: None declared, Dennis Lendrem: None declared, Najib Naamane: None declared, Alice Lin: None declared, Ben Millar: None declared, Nicola Maney: None declared, Nishanthi Thalayasingam: None declared, Vincent Bondet: None declared, Darragh Duffy: None declared, Michael Barnes: None declared, Graham Smith: None declared, Sandra Ng: None declared, David Watson: None declared, Rafael Henkin: None declared, Andrew Cope: None declared, Louise Reynard: None declared, Arthur Pratt: None declared, RA-MAP Consortium: None declared, John Isaacs Speakers bureau: speaker/consulting fees from AbbVie, Gilead, Roche and UCB., Grant/research support from: JDI discloses research grants from Pfizer, Janssen and GSK.

Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA

Clustered somatic mutations are common in cancer genomes and previous analyses reveal several types of clustered single-base substitutions, which include doublet- and multi-base substitutions1-5, diffuse hypermutation termed omikli6, and longer strand-coordinated events termed kataegis3,7-9. Here we provide a comprehensive characterization of clustered substitutions and clustered small insertions and deletions (indels) across 2,583 whole-genome-sequenced cancers from 30 types of cancer10. Clustered mutations were highly enriched in driver genes and associated with differential gene expression and changes in overall survival. Several distinct mutational processes gave rise to clustered indels, including signatures that were enriched in tobacco smokers and homologous-recombination-deficient cancers. Doublet-base substitutions were caused by at least 12 mutational processes, whereas most multi-base substitutions were generated by either tobacco smoking or exposure to ultraviolet light. Omikli events, which have previously been attributed to APOBEC3 activity6, accounted for a large proportion of clustered substitutions; however, only 16.2% of omikli matched APOBEC3 patterns. Kataegis was generated by multiple mutational processes, and 76.1% of all kataegic events exhibited mutational patterns that are associated with the activation-induced deaminase (AID) and APOBEC3 family of deaminases. Co-occurrence of APOBEC3 kataegis and extrachromosomal DNA (ecDNA), termed kyklonas (Greek for cyclone), was found in 31% of samples with ecDNA. Multiple distinct kyklonic events were observed on most mutated ecDNA. ecDNA containing known cancer genes exhibited both positive selection and kyklonic hypermutation. Our results reveal the diversity of clustered mutational processes in human cancer and the role of APOBEC3 in recurrently mutating and fuelling the evolution of ecDNA.

Applying Civil Rights Law to Clinical Research: Title VI's Equal Access Mandate

Title VI of the Civil Rights Act of 1964 and its implementing regulations prohibit federally-funded educational institutions and healthcare centers from engaging in disparate impact discrimination "on the ground of race, color, or national origin" in all of their operations.

Cookstove Emissions and Performance Evaluation Using a New ISO Protocol and Comparison of Results with Previous Test Protocols

In 2018, the International Organization for Standardization (ISO) 19867-1 "Harmonized laboratory test protocols" were released for establishing improved quality and comparability for data on cookstove air pollutant emissions, efficiency, safety, and durability. This is the first study that compares emissions [carbon dioxide, carbon monoxide, total hydrocarbons, methane, nitrogen oxides, fine particulate matter (PM_2.5), organic carbon, elemental carbon, and ultrafine particles] and efficiency data between the ISO protocol and the Water Boiling Test (WBT). The study examines six stove/fuel combinations [liquefied petroleum gas (LPG), pellet, wood fan, wood rocket, three stone fire, and charcoal] tested in the same US EPA laboratory. Evaluation of the ISO protocol shows improvements over previous test protocols and that results are relatively consistent with former WBT data in terms of tier ratings for emissions and efficiency, as defined by the ISO 19867-3 "Voluntary Performance Targets." Most stove types remain similarly ranked using ISO and WBT protocols, except charcoal and LPG are in higher PM_2.5 tiers with the ISO protocol. Additionally, emissions data including polycyclic aromatic hydrocarbons are utilized to compare between the ISO and Firepower Sweep Test (FST) protocols. Compared to the FST, the ISO protocol results in generally higher PM_2.5 tier ratings.

Ethical and Practical Concerns about IRB Restrictions on the Use of Research Data

In response to researcher noncompliance with ethical and regulatory provisions governing research with humans, protocol deviations, and unanticipated problems with research, institutional review boards (IRBs) or institutions sometimes impose restrictions on the use of research data, although specific cases in which this happens are unlikely to be known publicly. We review IRB policies at top research institutions in the United States about restrictions on the use of research data and describe potential reasons for restricting the use of such data in the context of ensuring compliance with human subjects research standards. We also discuss ethical considerations related to restricting the use of research data and argue that IRBs have limited regulatory authority to take such actions. Finally, we offer recommendations regarding decision-making about restricting the use of research data and call for additional guidance in this area.

Demystifying Schrems II for the cross-border transfer of clinical research data

The Courts of Justice of the European Union (CJEU) held in its July 2020 Schrems II decision that, in order for entities in other countries to import personal data from the European Economic Area (EEA), the importer must be able to provide data protections 'essentially equivalent' to those the EEA offers under its General Data Protection Regulation. The CJEU expressed particular concern that United States' national security intelligence gathering laws prevent U.S.-based entities from providing such protections. This decision has sharply limited the sharing of clinical research data from the EEA to the United States. After describing the pertinent aspects of the Schrems II decision, this article evaluates U.S. national security intelligence gathering frameworks, including Section 702 of the Foreign Intelligence Surveillance Act and Executive Order 12333. The article then leverages recent draft guidance from the European Data Protection Board to explain how entities may be able to adopt widely used contractual and technical measures, such as data pseudonymization, to provide 'essentially equivalent' protections in the clinical research context.

P35: BODY COMPOSITION: ASSOCIATION WITH OPERATIVE AND ONCOLOGIC OUTCOMES IN THE MODERN MANAGEMENT OF RETROPERITONEAL SARCOMA – RESULTS OF A FEASIBILITY STUDY

Introduction

Sarcopenia and obesity in cancer may confer negative outcomes, but their prevalence and impact on modern regimens for retroperitoneal sarcoma (RPS) have not been systematically studied. Sarcopaenia and obesity measurements by computed tomography (CT) measurements at L3 may be confounded by the disease process itself. The aim of this study is to determine feasibility in providing the prevalence of sarcopenia and visceral obesity in the management of RPS to assess their potential impact on operative and oncologic outcomes.

Method

Consecutive sample patients undergoing treatment for RPS from our database were retrospectively studied. Total, subcutaneous and visceral fat areas (VFA), myosteatosis, skeletal muscle index (SMI) lean body mass and fat mass were determined at diagnosis by CT. Sarcopenia will be defined by CT at L3 as SMI &lt;52.4 cm2/m2 for males and SMI &lt;38.5 cm2/m2 for females, and visceral obesity as VFA &gt;163.8cm2 for men and &gt;80.1cm2 for women.

Result

40 consecutive patients, 21 [52.5%] female, 56.7±15.1 years, were studied. The most common histologic types were leiomyosarcoma (8 [20.0%]), dedifferentiated liposarcoma (7 [17.5%]), well differentiated liposarcoma (7 [17.5%]), myxoid liposarcoma (4 [10.0%]). Mean±SD body composition measures were: lean body mass, 50.4±12.0 kg; total fat mass, 27.2±8.6 kg; visceral fat area, 148.5±120.2 cm2; subcutaneous fat area, 222.2±20.4 cm2; myosteatosis, 8.9±7.3 cm2.

Conclusion

Assessment of body composition among patients with RPS is feasible. Analysis to identify the prevalence and significance of sarcopenia and visceral obesity and its relationship to operative and oncologic outcomes is ongoing.

Take-home message

Assessment of body composition in RPS is feasible and its effect on outcomes is under investigation

A commercial treatment planning system with a hybrid dose calculation algorithm for synchrotron radiotherapy trials

Synchrotron Radiotherapy (SyncRT) is a preclinical radiation treatment which delivers synchrotron x-rays to cancer targets. SyncRT allows for novel treatments such as Microbeam Radiotherapy, which has been shown to have exceptional healthy tissue sparing capabilities while maintaining good tumour control. Veterinary trials in SyncRT are anticipated to take place in the near future at the Australian Synchrotron's Imaging and Medical Beamline (IMBL). However, before veterinary trials can commence, a computerised treatment planning system (TPS) is required, which can quickly and accurately calculate the synchrotron x-ray dose through patient CT images. Furthermore, SyncRT TPS's must be familiar and intuitive to radiotherapy planners in order to alleviate necessary training and reduce user error. We have paired an accurate and fast Monte Carlo (MC) based SyncRT dose calculation algorithm with Eclipse^TM, the most widely implemented commercial TPS in the clinic. Using Eclipse^TM, we have performed preliminary SyncRT trials on dog cadavers at the IMBL, and verified calculated doses against dosimetric measurement to within 5% for heterogeneous tissue-equivalent phantoms. We have also performed a validation of the TPS against a full MC simulation for constructed heterogeneous phantoms in Eclipse^TM, and showed good agreement for a range of water-like tissues to within 5%-8%. Our custom Eclipse^TM TPS for SyncRT is ready to perform live veterinary trials at the IMBL.

Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator

BACKGROUND

Performing a statistical test requires a null hypothesis. In cancer genomics, a key challenge is the fast generation of accurate somatic mutational landscapes that can be used as a realistic null hypothesis for making biological discoveries.

RESULTS

Here we present SigProfilerSimulator, a powerful tool that is capable of simulating the mutational landscapes of thousands of cancer genomes at different resolutions within seconds. Applying SigProfilerSimulator to 2144 whole-genome sequenced cancers reveals: (i) that most doublet base substitutions are not due to two adjacent single base substitutions but likely occur as single genomic events; (ii) that an extended sequencing context of ± 2 bp is required to more completely capture the patterns of substitution mutational signatures in human cancer; (iii) information on false-positive discovery rate of commonly used bioinformatics tools for detecting driver genes.

CONCLUSIONS

SigProfilerSimulator's breadth of features allows one to construct a tailored null hypothesis and use it for evaluating the accuracy of other bioinformatics tools or for downstream statistical analysis for biological discoveries. SigProfilerSimulator is freely available at https://github.com/AlexandrovLab/SigProfilerSimulator with an extensive documentation at https://osf.io/usxjz/wiki/home/ .

A Monte Carlo model of synchrotron radiotherapy shows good agreement with experimental dosimetry measurements: Data from the imaging and medical beamline at the Australian Synchrotron

Experimental measurement of Synchrotron Radiotherapy (SyncRT) doses is challenging, especially for Microbeam Radiotherapy (MRT), which is characterised by very high dynamic ranges with spatial resolutions on the micrometer scale. Monte Carlo (MC) simulation is considered a gold standard for accurate dose calculation in radiotherapy, and is therefore routinely relied upon to produce verification data. We present a MC model for Australian Synchrotron's Imaging and Medical Beamline (IMBL), which is capable of generating accurate dosimetry data to inform and/or verify SyncRT experiments. Our MC model showed excellent agreement with dosimetric measurement for Synchrotron Broadbeam Radiotherapy (SBBR). Our MC model is also the first to achieve validation for MRT, using two methods of dosimetry, to within clinical tolerances of 5% for a 20×20 mm² field size, except for surface measurements at 5 mm depth, which remained to within good agreement of 7.5%. Our experimental methodology has allowed us to control measurement uncertainties for MRT doses to within 5-6%, which has also not been previously achieved, and provides a confidence which until now has been lacking in MRT validation studies. The MC model is suitable for SyncRT dose calculation of clinically relevant field sizes at the IMBL, and can be extended to include medical beamlines at other Synchrotron facilities as well. The presented MC model will be used as a validation tool for treatment planning dose calculation algorithms, and is an important step towards veterinary SyncRT trials at the Australian Synchrotron.

Key considerations and challenges in the application of social-network research for environmental decision making

Attempts to better understand the social context in which conservation and environmental decisions are made has led to increased interest in human social networks. To improve the use of social-network analysis in conservation, we reviewed recent studies in the literature in which such methods were applied. In our review, we looked for problems in research design and analysis that limit the utility of network analysis. Nineteen of 55 articles published from January 2016 to June 2019 exhibited at least 1 of the following problems: application of analytical methods inadequate or sensitive to incomplete network data; application of statistical approaches that ignore dependency in the network; or lack of connection between the theoretical base, research question, and choice of analytical techniques. By drawing attention to these specific areas of concern and highlighting research frontiers and challenges, including causality, network dynamics, and new approaches, we responded to calls for increasing the rigorous application of social science in conservation.

0665 Bilateral Hypoglossal Nerve Stimulation for Treatment of Obstructive Sleep Apnea

Introduction

Hypoglossal Nerve Stimulation (HGNS) decreases obstructive sleep apnea (OSA) severity by contracting the tongue and decreasing upper airway collapsibility. This study assessed the safety and effectiveness of a new implantable device that delivers bilateral HGNS: the Genio™ system.

Methods

The BLAST OSA study (BiLAteral Hypoglossal Nerve Stimulation for Treatment of Obstructive Sleep Apnea), was a prospective, open-label, non-randomized, single arm treatment study conducted at eight centres in three countries (Australia, France, UK). Primary outcomes were the incidence of device-related Serious Adverse Events (SAEs) and change in the Apnea-Hypopnea Index (AHI). The secondary outcome was change in the 4% Oxygen Desaturation Index (ODI). Additional outcomes included measures of sleepiness, quality of life, snoring, and device use. Participants were eligible if: 21-75 years old; BMI ≤ 32 kg/m2; obstructive AHI 20-60 events/hr and combined central and mixed AHI &lt; 10 events/hr; no positional OSA; no Complete Concentric Collapse of the soft palate during Drug Induced Sleep Endoscopy; and failed to tolerate or accept Positive Airway Pressure treatments.

Results

27 participants were implanted (63% male, aged 55.9±12.0 years, BMI 27.4±3.0 kg/m2). 22 completed the protocol. At 6 months, AHI decreased from 23.7±12.2 to 12.9±10.1 events/hr [p&lt;0.001]; and ODI decreased from 19.1±11.2 to 9.8±6.9 events/hr [p&lt;0.001]. Daytime sleepiness (ESS, p=0.011) and sleep-related quality of life (FOSQ-10, p=0.016) both significantly improved. 91% of participants reported using their device &gt;5 days per week, and 77% used it &gt;5 hours per night. The number of bed partners reporting disruptive snoring decreased from 96% to 35%. No device-related SAE occurred.

Conclusion

In a targeted population of individuals with moderate-to-severe OSA, the Genio system reduced OSA severity and sleepiness, improved quality of life, and was associated with high adherence and an acceptable safety profile.

Support

This study trial was funded by Nyxoah S.A. This trial was registered with ClinicalTrials.gov, number NCT03048604.

From Genetics to Genomics: Facing the Liability Implications in Clinical Care

Health care is transitioning from genetics to genomics, in which single-gene testing for diagnosis is being replaced by multi-gene panels, genome-wide sequencing, and other multi-genic tests for disease diagnosis, prediction, prognosis, and treatment. This health care transition is spurring a new set of increased or novel liability risks for health care providers and test laboratories. This article describes this transition in both medical care and liability, and addresses 11 areas of potential increased or novel liability risk, offering recommendations to both health care and legal actors to address and manage those liability risks.

Visual Immunoprecipitate Assay (VIP) for Listeria monocytogenes and Related Listeria Species Detection in Selected Foods: Collaborative Study

Six foods representing a variety of food products were analyzed by the Assurance Listeria polyclonal enzyme immunoassay (EIA) and by either the Bacteriological Analytical Manual or the U.S. Department of Agriculture culture method for detecting Listeria monocytogenes and related Listeria species. Samples of each food type, at each inoculation level, were analyzed simultaneously by both methods. A total of 19 laboratories representing federal government agencies and private industry in the United States and Canada participated. Food types were inoculated with Listeria species including L. monocytogenes, with the exception of 3 lots of green beans, which were naturally contaminated. During this study, 1764 samples and controls were analyzed and confirmed, of which 492 were positive and 947 were negative by both methods. There were 159 samples that were positive by culture method but negative by the EIA and 188 that were negative by culture method but positive by EIA. Twenty-two samples were negative by EIA and by culture method but confirmed positive when Assurance selective enrichment broths were subcultured to selective agar. The Assurance polyclonal EIA for detecting L. monocytogenes and related Listeria species in foods has been adopted first action by AOAC INTERNATIONAL.

Assurance Polyclonal Enzyme Immunoassay for Detection of Listeria monocytogenes and Related Listeria Species in Selected Foods: Collaborative Study

Six foods representing a variety of food products were analyzed by the Assurance Listeria polyclonal enzyme immunoassay (EIA) and by either the Bacteriological Analytical Manual or the U.S. Department of Agriculture culture method for detecting Listeria monocytogenes and related Listeria species. Samples of each food type, at each inoculation level, were analyzed simultaneously by both methods. A total of 19 laboratories representing federal government agencies and private industry in the United States and Canada participated. Food types were inoculated with Listeria species including L. monocytogenes, with the exception of 3 lots of green beans, which were naturally contaminated. During this study, 1764 samples and controls were analyzed and confirmed, of which 492 were positive and 947 were negative by both methods. There were 159 samples that were positive by culture method but negative by the EIA and 188 that were negative by culture method but positive by EIA. Twenty-two samples were negative by EIA and by culture method but confirmed positive when Assurance selective enrichment broths were subcultured to selective agar. The Assurance polyclonal EIA for detecting L. monocytogenes and related Listeria species in foods has been adopted first action by AOAC INTERNATIONAL.

Toward Improving Practices for Submission of Diagnostic Tissue Blocks for National Cancer Institute Clinical Trials

OBJECTIVES

The National Cancer Institute (NCI) National Clinical Trials Network performs phase II and III clinical trials, which increasingly rely on the submission of diagnostic formalin-fixed, paraffin-embedded tissue blocks for biomarker assessment. Simultaneously, advances in precision oncology require that clinical centers maintain diagnostic specimens for ancillary, standard-of-care diagnostics. This has caused tissue blocks to become a limited resource for advancing the NCI clinical trial enterprise and the practice of modern molecular pathology.

METHODS

The NCI convened a 1-day workshop of multidisciplined experts to discuss barriers and strategic solutions to facilitate diagnostic block submission for clinical trial science, from the perspective of patient advocates, legal experts, pathologists, and clinical oncologists.

RESULTS

The expert views and opinions were carefully noted and reported.

CONCLUSIONS

Recommendations were proposed to reduce institutional barriers and to assist organizations in developing clear policies regarding diagnostic block submission for clinical trials.

Acceptability and feasibility of recruiting women to collect a self-administered vaginal swab at a pharmacy clinic for sexually transmissible infection screening

Willingness to self-collect vaginal swabs at a pharmacy clinic is of interest as a venue to increase sexually transmissible infections (STIs) screening for chlamydia, gonorrhoea and trichomonas. Women self-collected vaginal swabs at the pharmacy, completed questionnaires and received STI results within 2 h. Women with STIs were offered free treatment. A total of 313 of 777 (40.3%) women consented and prevalence for any STI was 3.9%. Questionnaires demonstrated acceptability for self-collection at the pharmacy, with 63% (95% CI 57.3-68) and 32.3% (95% CI 27.4-37.8) indicating they 'strongly agreed' or 'agreed' that they felt comfortable with pharmacy collection, respectively. Self-collected vaginal swabs for STI testing for women who were at a pharmacy were feasible and acceptable to women.

P959 Handheld echocardiography in a real world scenario: concordances compared to standard echo reports

Background

Handheld echocardiography devices(HH) arise as a common tool in clinical examination and screening for various cardiovascular disorders. Despite of it, studies with this method are small, with unselected patients and limited scope of diagnostic comparison.

Purpose

Assess the usefulness of the new miniaturized HH and compare its concordances with the standard high definition echocardiography study(STD).

Methods

Between April and May of 2016 adult patients who were scheduled to regular STD, were also submitted to a HH exam. Experienced sonographers performed and an experienced echocardiographer reviewed the STD exam, and an experienced echocardiographer performed and reviewed the HH study - reviewers were blinded to the other study results. STD exams included 2-dimensional images, Color Doppler and hemodynamics analysis. With the HH hemodynamic assessment was not performed as the machine does not include such technology. Agreement between the reports was analyzed.

Results

110 patients were included. Mean age was 62.4 ± 16.7 years. The κ values(Table) show good correlation between HH and STD on the analysis of left ventricular global and segment functions, right ventricle size and function, mitral and aortic stenosis. On the evaluation of left ventricle hypertrophy, mitral and aortic regurgitations the correlation was modest, while poor correlation was found for pulmonary and tricuspid regurgitations.

Conclusion

In a daily practice scenario with experienced hands, HH demonstrates good results for the assessment of ventricles size and function, while the evaluation of right heart valves was the least reliable performance. Dissemination of HH should occur with considerations and caution.

K Values for Echocardiography Analysis Echocardiography analysis K value Global estimated LV dysfunction 0.85 Wall motion abnormalities 0.78 LV hypertrophy 0.6 RV size 0.83 RV function 0.82 Mitral regurgitation 0.42 Aortic regurgitation 0.56 Mitral stenosis 0.96 Aortic stenosis 0.82 Tricuspid regurgitation 0.26 Pulmonary regurgitation 0.25 LV: left ventricle; RV: right ventricle.