Abstract 2066: Visualization and analysis of cancer genomics data using UCSC Xena

UCSC Xena (http://xena.ucsc.edu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Researchers can easily view and explore public data, their own private data, or both using the Xena Browser. Private data are kept on the researcher's computer and are never uploaded to our public servers. We support Mac, Windows, and Linux.

Questions Xena can help you answer:

* Is overexpression of this gene associated with lower/higher survival?

* What genes are differentially expressed between these two groups of samples?

* What is the relationship between mutation, copy number, expression, etc for this gene?

Xena showcases seminal cancer genomics datasets from TCGA, the Pan-Cancer Atlas, GDC, PCAWG, ICGC, and more; a total of more than 1500 datasets across 50 cancer types. We support virtually any type of functional genomics data: SNPs, INDELs, copy number variation, gene expression, ATAC-seq, DNA methylation, exon-, transcript-, miRNA-, lncRNA-expression and structural variants. We also support clinical data such as phenotype information, subtype classifications and biomarkers. All of our data is available for download via python or R APIs, or using our URL links.

Our signature Visual Spreadsheet view shows multiple data types side-by-side enabling discovery of correlations across and within genes and genomic regions. We also have dynamic Kaplan-Meier survival analysis, powerful filtering and subgrouping, differential gene expression analysis, charts, statistical analyses, genomic signatures, and the ability to generate URLs to live views. We link out to the UCSC Genome Browser as well as MuPIT/CRAVAT and TumorMap.

New features include:

* Genome-wide differential gene expression analysis

* Select samples directly from the screen for filtering and creating subgroups

* Violin plots on any numerical data

* Loading of Microsoft Excel files

Our beta prototype site for visualizing single-cell data delivers million-cell-scale multi-omics data for interactive visualization in a web browser. Contact us for access to our beta prototype site.

If you use us please cite our publication in Nature Biotechnology: https://www.nature.com/articles/s41587-020-0546-8

Citation Format: Mary Goldman, Brian Craft, Jingchun Zhu, David Haussler. Visualization and analysis of cancer genomics data using UCSC Xena [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2066.

Removing the men who have sex with men blood donation deferral: Informing risk models using Canadian public health surveillance data

OBJECTIVE

Gay, bisexual and other men who have sex with men (gbMSM) were ineligible to donate blood in most countries since the 1980's. In Canada the deferral period has been incrementally decreased from lifetime to male-to-male sex in the last 3 months. Now a few countries have removed the deferral altogether. Risk models have been utilised to estimate the probability of an HIV positive donation being released into the blood supply and to inform incremental changes to the length of the deferral period. Here we use public health data to estimate the risk of HIV if the gbMSM deferral criteria were removed in Canada.

MATERIAL AND METHODS

We calculate the risk reduction among heterosexuals based on responses to standard risk questions routinely asked of donors. We assume gbMSM will donate at the same rate as heterosexual males. We apply the same risk reduction principle to HIV incidence and prevalence among gbMSM in the general population to evaluate the HIV risk without gbMSM time deferral. We model three scenarios where risk reduction is varied by assumptions about incidence and compliance with deferral criteria.

RESULTS

The estimates for all scenarios were not significantly different to the currently observed scenario which predicts a residual risk of 0.02 HIV positive per million donations (95% CI: 0.000006-0.09).

CONCLUSION

The models predict that removing the gbMSM deferral criteria would result in HIV residual risk similar to currently observed.

Abstract 5039: Visualization and analysis of cancer genomics data using UCSC Xena

UCSC Xena (http://xena.ucsc.edu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Researchers can easily view and explore public data, their own private data, or both using the Xena Browser. Private data are kept on the researcher's computer and are never uploaded to our public servers. The toll supports Mac, Windows, and Linux.

Questions Xena can help you answer:

1) Is overexpression of this gene associated with lower/higher survival?

2) What genes are differentially expressed between these two groups of samples?

3) What is the relationship between mutation, copy number, expression, etc for this gene?

Xena showcases seminal cancer genomics datasets from TCGA, the Pan-Cancer Atlas, GDC, PCAWG, ICGC, and more; a total of more than 1500 datasets across 50 cancer types. We support virtually any type of functional genomics data: SNPs, INDELs, copy number variation, gene expression, ATAC-seq, DNA methylation, exon-, transcript-, miRNA-, lncRNA-expression, and structural variants. We also support clinical data such as phenotype information, subtype classifications and biomarkers. All of our data is available for download via python or R APIs, or using our URL links.

Our signature Visual Spreadsheet view shows multiple data types side-by-side enabling discovery of correlations across and within genes and genomic regions. We also have dynamic Kaplan-Meier survival analysis, powerful filtering and subgrouping, differential gene expression analysis, charts, statistical analyses, genomic signatures, and the ability to generate URLs to live views. We link out to the UCSC Genome Browser as well as MuPIT/CRAVAT and TumorMap.

New features include:

- Genome-wide differential gene expression analysis

- New interface for filtering samples and creating subgroups

- New interface to create charts and graphs

- Violin plots on any numerical data

- Loading of Microsoft Excel files

- A new Publication Page showcasing publications and authors that use UCSC Xena

Our beta prototype for visualizing single-cell data delivers million-cell-scale multi-omics data for interactive visualization in a web browser.

Citation Format: Mary Goldman, Brian Craft, Jingchun Zhu, David Haussler. Visualization and analysis of cancer genomics data using UCSC Xena [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5039.

Making Tools that People Will Use: User-Centered Design in Computational Biology Research

User-Centered Design (UCD) focuses on deeply understanding the needs of users and ensuring these needs are met by tools and software. UCD methodology aims to make tools easier to use, reduce time spent in development and the need for user support, as well as make it easier to create and maintain documentation. The goal of UCD is to ultimately make a tool that meets user needs and is a pleasure to use. This workshop will give an overview of UCD and several examples of how UCD practices are already being used at several institutions. Attendees will leave with ideas of how to incorporate UCD into their tool development as well as general resources to get started.

Abstract 2466: Designing an intuitive visualization of BRCAness scores for clinicians

Objective: Genomic interrogation of tumors has changed the way we care for cancer patients. Monogenic, single mutation tests clearly and accurately define patient populations whose tumors will or will not likely respond to specific therapies. Next generation sequencing has enabled diagnostics derived from broader footprints, such as signatures of mutational processes. Currently, no universal guidelines exist on translating complex predictive signatures into the clinic, and their interpretability is a barrier to uptake by clinicians. Visually displaying genomic signatures may help clinicians interpret them. We designed a user-directed approach to developing understandable displays of an individual’s BRCAness signature through testing at clinical cancer conferences.

Materials and Methods: We adopted a two-stage approach to optimizing user-testing methods. First, 44 attendees at the 2018 Gastrointestinal Cancer Symposium participated in a tablet-based test of a visualization of a patient’s BRCAness signature. We refined our testing methods and continued tabled-based testing of 51 attendees at the 2018 American Society of Clinical Oncology. Participants viewed slides explaining the signature and visualization. They were asked to interpret a patient’s BRCAness signature when provided information both as text and as a visualization. Participants received one of three similar versions of the visualization.

Results: Participants interpreted patients’ BRCAness signatures faster when given a visual. When shown a visual indicating BRCAness scores of germline BRCA mutated tumors, participants interpreted the information fastest without sacrificing accuracy or confidence in their answer. Participants’ interpretation of an individual’s BRCAness signature was associated with their self-reported likelihood to recruit the individual to a clinical trial.

Conclusion: Visualizing distributions of BRCAness signatures with germline BRCA mutations displayed helped participants respond faster without sacrificing accuracy or confidence in their answer. Testing attendees at cancer conferences presents a potential platform to include clinicians and researchers in the development of genomics visualization tools.

Citation Format: Hannah R. Allegakoen, Mary Goldman, Bennett Caughey, Martin Consunji, Christopher C. Benz, David Haussler, Jingchun Zhu, Eric A. Collisson. Designing an intuitive visualization of BRCAness scores for clinicians [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 2466.

Abstract 911: UCSC Xena for cancer genomics visualization and interpretation

UCSC Xena (http://xena.ucsc.edu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Our unique Visual Spreadsheet shows multiple data types side-by-side enabling discovery of correlations across and within genes and genomic regions. We offer dynamic Kaplan-Meier survival analysis, powerful filtering and subgrouping, charts, statistical analyses, genomic signatures, comparative transcript views, and bookmarks. We link out to the UCSC Genome Browser, giving users additional genomic context for any gene or coordinate, as well as MuPIT/CRAVAT and TumorMap, to give users complementary views of the same data.

Xena showcases seminal cancer genomics datasets from TCGA, the Pan-Cancer Atlas, PCAWG, GDC, GTEx, ICGC, and more; a total of more than 1500 datasets across 50 cancer types. We support virtually any type of functional genomics data. In addition to the commonly available SNPs, INDELs, copy number variation, and gene expression datasets, we support DNA methylation, exon-, transcript-, miRNA-, lncRNA-expression and structural variants. We also support clinical data such as phenotypes, subtype classifications and biomarkers. A recompute of TCGA, TARGET and GTEx datasets through the same bioinformatics pipeline allows users to compare expression between tumor and normal tissues. All of our data is available for download via our python API or through AWS S3 buckets.

A researcher can host their own data securely via private hubs running on a laptop or behind a firewall, with visual and analytical integration occurring only within the Xena Browser. The lightweight Xena Data Hubs are straightforward to install on Windows, Mac and Linux. Loading data is easy using either our application or command line interface.

Our newest features include:

* a new, more intuitive wizard to load your data into a local Hub

* URL bookmarks to save interactive views for yourself or to share with collaborators

* genomic signatures: dynamically build as a weighted sum over a set of genes

* hierarchically cluster a list of genes, regulons or probes

* upper vs lower quartile in a KM plot

Citation Format: Mary Goldman, Brian Craft, Jingchun Zhu, David Haussler. UCSC Xena for cancer genomics visualization and interpretation [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 911.

Platelet Inhibitory Drugs: An In Vivo Method of Evaluation in Patients

The measurement of platelet deposition in human thrombi is essential for the evaluation of platelet-inhibitory drugs and prosthetic materials for use in patients. The rate of 111Indiumlabelled platelet accumulation on Dacron arterial grafts was measured in 27 patients randomised to take either aspirin and dipyridamole (ASA + DPM) or placebo. Autologous platelets were labelled and re-injected seven days following surgery and the graft thrombogenidty index calculated as the daily rise in the ratio of emissions from the graft over a reference site.

The mean (± SD) thrombogenidty index in 12 patients undergoing femoro-popliteal bypass was 0.25 ± 0.09 on placebo and 0.16 ± 0.07 on ASA + DPM started pre-operatively (p Ã0.05). Post-operative ASA + DPM therapy started two days following platelet labelling in 15 patients with aorto-femoral grafts also significantly reduce thrombogenidty to 0.12 ± 0.05 compared with 0.25 ± 0.08 on placebo (p Ã0.01). In the latter patients the ratio of emissions from the graft over reference fell significantly on starting ASA + DPM, suggesting a net loss of platelets from the graft. These results indicate that the rate of in vivo platelet accumulation on Dacron grafts can be quantitated and that ASA + DPM reduced this rate in man.

Adsorption of ß2-Microglobulin on Dialysis Membranes: Comparison of Different Dialyzers and Effects of Reuse Procedures

In order to measure ß2-microglobulin adsorption on dialysis membranes, uremic plasma was passed through different dialyzers in a simulated hemodialysis circuit in which both plasma and dialysate compartments were organized as closed loops, the ultrafiltration pressure being adjusted to minimize water shifts. Under these conditions, comparison of the amounts of ß2-m in the plasma and dialysate compartments allowed us to calculate the binding of ß2-m to the membrane at different times of the procedure. Whereas cuprophane membrane (Gambro gf 180m, 1.8m2) did not bind ß2-m, AN69 (Filtral, 1.1 m2), high flux polysulfone (F60, 1.2m2) and modified polyamide (Polyflux 130, Gambro, 1.3m2) were found to adsorb 49 ± 8 mg (mean ± SEM), 17 ± 5 mg and 38 ± 4 mg of 82-m, respectively. These data were confirmed in trace labeling experiments with 125I-ß2-m. Adsorption was a saturable phenomenon occurring during the first 90 min of in vitro dialysis. After reuse with peracetic acid, the adsorption capacity of AN69 membrane was lowered to 20 ± 4 mg of ß2-m, contrasting with the unchanged adsorption after reuse with sodium hypochlorite. These data indicate that adsorption significantly contributes to ß2-m removal during hemodialysis with certain dialyzers and that reuse procedures may affect the propensity of dialysis membranes to bind 82-m.

Overhauser effects in non-conducting solids at 1.2 K

Recently, it was observed that protons in non-conducting solids doped with 1,3-bisdiphenylene-2-phenylallyl (BDPA) or its sulfonated derivative (SA-BDPA) can be polarized through Overhauser effects via resonant microwave irradiation. These effects were present under magic angle spinning conditions in magnetic fields between 5 and 18.8 T and at temperatures near 100 K. This communication reports similar effects in static samples at 6.7 T and, more importantly, at temperatures as low as 1.2 K, in a different dynamic regime than in the previous study. Our results provide new information towards understanding the mechanism of the Overhauser effect in non-conducting solids. We discuss possible origins of the fluctuations that can give rise to an Overhauser effect at such low temperatures.

Abstract SY10-02: Pan-cancer study of recurrent and heterogeneous RNA aberrations and association with whole-genome variants

Whole-exome sequencing studies have transformed our understanding of recurrent somatic mutations that contribute to cancer pathogenesis; however, these studies limit our ability to identify cancer-associated mutations to those that cause protein-coding changes. To more comprehensively catalogue cancer-associated gene alterations, we have extensively characterized tumor transcriptomes from 1,220 donors with matched whole-genome sequence data to identify recurrent RNA-level aberrations. Specifically, we created a unified RNA-Seq analysis pipeline including sequence alignment and quality control and subsequently identified gene alterations through outlier detection from estimated gene expression levels, alternative splicing, alternative transcription starts, and allele-specific expression and through identified RNA-edited sites and gene fusions. Our data represent an extensive catalog of RNA aberrations for each gene across 27 cancer types. We have also tested for genetic associations with these RNA phenotypes. Using an integrative analysis approach, we have mapped genome-wide cis and trans effects on individual RNA phenotypes, considering both common germline variants as well as somatic SNVs in gene promoters, enhancers, and intronic and other regions. Many of the regulatory associations we identify are not accessible by exome sequencing, underlining the importance of whole-genome sequence data. Utilizing this RNA-centric view, we have identified genes that are recurrently altered, yet have not been previously characterized as cancer genes or identified through DNA-level driver gene analysis. To identify further supporting evidence that these recurrent alterations are potential drivers, we identified genes with mutually exclusive RNA-level alterations. Our findings reveal new insights into selective advantages of somatic changes and molecular mechanisms of cancer. This work is by the Transcriptome Working Group of the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium and authors are listed in alphabetical order.

Citation Format: Samirkumar Amin, Philip Awadalla, Andrew Biankin, Paul Boutros, Alvis Brazma, Angela Norie Brooks, Claudia Calabrese, David Chang, Aurélien Chateigner, Ken Chen, Zechen Chong, Brian Craft, Chad Creighton, Deniz Demircioğlu, Nuno Fonseca, Milana Frenkel-Morgenstern, Gad Getz, Jonathan Göke, Mary Goldman, Liliana Greger, Syed Haider, Yao He, Katherine Hoadley, Yuan Ji, Andre Kahles, Ekta Khurana, Jan Korbel, Kjong Lehmann, Han Liang, Fenglin Liu, Maximillian Marin, Matthew Meyerson, Akinyemi Ojesina, Francis Ouellette, Chandra Pedamallu, Marc Perry, Gunnar Rätsch, Roland Schwarz, Yuichi Shiraishi, Cameron Soulette, Oliver Stegle, Patrick Tan, Alfonso Valencia, Linda Xiang, Christina Yung, Junjun Zhang, Fan Zhang, Zemin Zhang, Jingchun Zhu. Pan-cancer study of recurrent and heterogeneous RNA aberrations and association with whole-genome variants [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 SY10-02. doi:10.1158/1538-7445.AM2017-SY10-02

Abstract 5270: The UCSC Xena system for integrating and visualizing functional genomics

UCSC Xena (http://xena.ucsc.edu/) is a bioinformatics tool to visualize functional genomics data from multiple sources simultaneously, including both public and private data. The Xena system consists of a set of federated data hubs and the Xena browser, which integrates across hubs, providing one location to analyze and visualize all data. The lightweight Xena data hubs are straightforward to install on Windows, Mac and Linux operating systems and easily allow hub administrators to authenticate users, ensuring that only authorized users have access to secure data. Loading data into a Xena hub is easy using either our application or command line interface. Hosting public data from major projects, such as TCGA, on public Xena hubs gives users access without having to download these large datasets. The Xena system makes it easy to aggregate across many hubs, allowing users to integrate public datasets and private secure data together or view them separately. This system of the browser and hubs helps researchers combine new or preliminary results from their laptops or internal servers, or even data from a new paper, securely with vetted data from the public sphere.

The largest public Xena hub, based at UCSC, currently hosts an expanding set of searchable data, including 806 public datasets from several large consortiums including TCGA (The Cancer Genome Atlas), ICGC (International Cancer Genome Consortium), Treehouse Childhood Cancer Project, CCLE (Cancer Cell Line Encyclopedia), and more. Xena hubs are flexible enough to handle most data types, including gene, exon, miRNA and protein expression, copy number, DNA methylation and somatic mutation data along with phenotypes, subtype classifications and genomic biomarkers. Dynamic Kaplan-Meier survival analysis helps investigators to assess survival stratification by any information while scatter plots and bar graphs offer new insights into the data. Integration with Galaxy gives users access to a myriad of bioinformatics tools for further analysis and hypothesis testing.

Citation Format: Mary Goldman, Brian Craft, Jingchun Zhu, Teresa Swatloski, Melissa Cline, David Haussler. The UCSC Xena system for integrating and visualizing functional genomics. [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 5270.

The Effect of Compression on Venous Haemodynamics Assessed by Quantitative Photoplethysmography

Background:

The purpose of this study was to examine quantitatively the effect of compression stockings on venous haemodynamics at the level of the ankle.

Methods:

To obtain quantifiable results, a computer-controlled photoplethysmographic system was used to measure the displacement of local blood volume induced by exercise (exercise displacement volume, EDV) and by tilting the subject (tilt displacement volume, TDV). The test was repeated after application of class I compression stockings 20–30 mmHg). The ratio EDV/TDV is considered to represent the efficiency of the veno-muscular pump. Three groups of subjects were studied: a control group ( n = 8), patients with telangiectases ( n = 10) and a group with large varices ( n = 11).

Results:

The application of external compression had a quantifiable and beneficial effect on venous haemodynamics and was most significantly documented by an increase in veno-muscular efficiency (EDV/TDV) from 28% to 44% in the varicose vein patients. Statistically significant increases of EDV/TDV could also be identified in the telangiectatic patients and normal subjects. EDV also showed an increase with compression stockings; however, statistical significance was only reached in the varicose vein group.

Conclusion:

External compression (class 1 compression stockings) significantly improved venous haemodynamic indices, especially in patients with varicose veins. Quantitative photoplethysmography used in this study permits a fast, non-invasive and quantifiable evaluation of venous haemodynamics of the lower extremities.

Electron-scale measurements of magnetic reconnection in space

Magnetic reconnection is a fundamental physical process in plasmas whereby stored magnetic energy is converted into heat and kinetic energy of charged particles. Reconnection occurs in many astrophysical plasma environments and in laboratory plasmas. Using measurements with very high time resolution, NASA's Magnetospheric Multiscale (MMS) mission has found direct evidence for electron demagnetization and acceleration at sites along the sunward boundary of Earth's magnetosphere where the interplanetary magnetic field reconnects with the terrestrial magnetic field. We have (i) observed the conversion of magnetic energy to particle energy; (ii) measured the electric field and current, which together cause the dissipation of magnetic energy; and (iii) identified the electron population that carries the current as a result of demagnetization and acceleration within the reconnection diffusion/dissipation region.

Development of standard definitions for surveillance of complications related to blood donation

Standard definitions of donor reactions allow each blood establishment to monitor donor adverse events and compare with other organizations to develop best practices. The ISBT Haemovigilance Working Party leads a multi-organizational effort to update the 2008 ISBT standard for surveillance of complications related to blood donation. Revised definitions have been developed and endorsed by the ISBT, AABB, International Haemovigilance Network (IHN) and other international organizations.

Effect of hyperbaric oxygen therapy on amphotericin-B induced acute renal failure in rats

AIM

Acute renal injury may occur after amphotericin B (AmB) administration. The hypothesized injury mechanism is renal vasoconstriction and direct toxic damage. Hyperbaric oxygen therapy (HBO) is indicated for treatment of many ischemic events but not for acute renal failure (ARF). The aim of this study was to investigate the role of HBO therapy in AmB induced ARF.

METHODS

ARF was induced in 41 Sprague-Dawley rats by a single dose of 75 mg/kg AmB. The rats were randomly divided into two groups; one group was treated with daily HBO for 3 consecutive days. The control group received no HBO treatment. Parameters of renal function were taken on the 5th day after AmB administration.

RESULTS

Forty-one rats were treated with AmB, 21 received HBO and 20 served as controls. Body weight loss following the administration of AmB was 13.5+14.7% in the HBO treated rats, as opposed to 24.6+5% in the control group (P=0.004). Serum creatinine and urea were 0.49+0.13 mg/dL and 200.63+87.82 mg/dL in the treatment group and 0.70+0.22 mg/dL and 368.01+169.35 mg/dL, respectively in the control (P=0.001).

CONCLUSION

In this model of AmB-induced ARF, HBO treatment alleviated renal injury as reflected by changes in serum creatinine and urea levels.

Abstract P4-08-01: Assessing the safety and feasibility of efficient hypothesis testing in patients with metastatic triple negative breast cancer

We hypothesize that new insights into how cancers progress and respond to treatment will come from clinical trials that i) extensively characterize the molecular features of a patient’s cancer; ii) use results to predict drug susceptibilities; iii) treat in accordance with these predictions; and iv) learn from individual patient outcomes to iterate and improve over time. To investigate the feasibility of this type of clinical study, we launched the "Intensive Trial of OMics in Cancer" (ITOMIC) for patients with metastatic triple negative breast cancer (TNBC) (Clinicaltrials.gov ID: NCT01957514). Eligible patients have metastatic TNBC, are platinum-naive, and are scheduled to receive Cisplatin. Biopsies are performed under carefully controlled conditions prior to Cisplatin – starting all subjects on a common treatment path, and uncoupling the time needed for specimen analysis from immediate therapy. Biopsies are repeated upon completion of Cisplatin and following subsequent therapies. A subset of specimens is chosen for whole Exome Sequencing, deep sequencing of a panel of cancer associated genes, and RNA-sequencing. De-identified results are placed on a web-based server for analysis and discussed at a meeting of the ITOMIC tumor board. A report describing results and potential therapies is provided to the subject’s oncologist. Treatment decisions are left to the discretion of the oncologist. If a decision is taken to pursue treatments identified in our report we offer assistance in accessing those treatments.

Ten patients have been screened and seven have enrolled. Subjects range in age from 40 to 77 years and all but one has received extensive prior treatment for metastatic TNBC. All seven underwent an initial set of biopsies, targeting between two and five metastatic sites. For most metastatic sites, multiple core needle passes are performed. All subjects tolerated the biopsies well without significant adverse events, and all started treatment with Cisplatin. Three subjects completed Cisplatin and underwent a second round of biopsies.

Potential targets for therapy were identified in 5 of the first 6 subjects, and three subjects have received four predicted therapies: 1) a patient with somatic loss of BRCA1 and two linked FGFR2 activating mutations, who was treated first with Veliparib through a single-patient IND and then switched to Ponatinib which produced a partial response; 2) a patient with a novel missense ROS1 mutation treated with crizotinib; and 3) a patient with CYP3A4 copy gain treated with cyclophosphamide.

Conclusion: Our early experience indicates that this approach is feasible and may increase the efficiency of learning from patients with advanced cancer.

Citation Format: C Anthony Blau, Colin Pritchard, Michael O Dorschner, Sibel Blau, Brigham Mecham, Elisabeth Mahen, VK Gadi, Wayne Monsky, Kimberly Burton, Arturo Ramirez, Jackie Stilwell, Eric Kladjian, Carol Collins, Jeannine S McCune, William S Noble, Julie Gralow, Frank Senecal, Linda Dhaene, Nicole Kuderer, Jennifer Specht, Chaozhong Song, Carla Grandori, Nathan Price, Mary Goldman, Aime Radenbaugh, David Haussler, Jingchun Zhu. Assessing the safety and feasibility of efficient hypothesis testing in patients with metastatic triple negative breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-08-01.

The UCSC Cancer Genomics Browser: update 2015

The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a web-based application that integrates relevant data, analysis and visualization, allowing users to easily discover and share their research observations. Users can explore the relationship between genomic alterations and phenotypes by visualizing various -omic data alongside clinical and phenotypic features, such as age, subtype classifications and genomic biomarkers. The Cancer Genomics Browser currently hosts 575 public datasets from genome-wide analyses of over 227 000 samples, including datasets from TCGA, CCLE, Connectivity Map and TARGET. Users can download and upload clinical data, generate Kaplan–Meier plots dynamically, export data directly to Galaxy for analysis, plus generate URL bookmarks of specific views of the data to share with others.

Abstract A33: Exploring pediatric cancer genomics with the UCSC Cancer Genomics Browser

The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) is a set of web-based tools to display, investigate and analyze cancer genomics data and associated clinical data. Experimental quantities such as gene expression levels, copy number variation and somatic mutations are displayed next to clinical features such as age of onset and cancer subtype. Users can interactively group or sort data by clinical features to dynamically explore how genomic aberrations relate to clinical outcomes. Integrated Kaplan–Meier plots help investigators assess how clinical or genomic values impact long-term survival. The browser currently hosts data from 144 cancer studies including TCGA, CCLE and LINCS. It can display data from multiple studies at once, facilitating cross-cancer comparisons.

We are currently interested in hosting new pediatric cancer datasets, and can offer either public or protected access as appropriate.

Figure 1 illustrates the power of this approach. It compares patterns of somatic mutations in pediatric high-risk neuroblastoma, a cancer of the peripheral nervous system (Pugh, Morozova et al, Nature Genetics 2013) to those in two adult cancers of the central nervous system: lower grade glioma (LGG, TCGA) and glioblastoma multiforme (GBM, TCGA), and contrasts the age of the patient with frequency of mutations in the Alpha Thalassemia/Mental Retardation Syndrome X-linked (ATRX) gene. The data for all three cancers is sorted by the age of the patient, with yellow being the oldest. The age ranges overlap: the oldest neuroblastoma patients are 16, while the youngest LGG and GBM patients are 14 and 21 respectively. While the three cancers show distinct patterns of somatic mutations, all three show frequent mutations in the ATRX gene in older teens or young adults.

This suggests that these cancers may share age-related subtypes with similar genomic signatures. These subtypes may indicate the age-dependent importance of ATRX in the development of both central and peripheral nervous systems, and may ultimately highlight common therapeutic avenues for the two groups of diseases.

This data set can be explored at the UCSC Cancer Genomics Browser at https://genome-cancer.ucsc.edu/proj/site/hgHeatmap/#?bookmark=pc

Citation Format: Melissa Cline, Olena Morozova, Teresa Swatloski, Brian Craft, Mary Goldman, David Haussler, Jingchun Zhu. Exploring pediatric cancer genomics with the UCSC Cancer Genomics Browser. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A33.

Measuring respiratory symptoms in clinical trials of COPD: reliability and validity of a daily diary

BACKGROUND

Although respiratory symptoms are characteristic features of COPD, there is no standardised method for quantifying their severity in stable disease.

OBJECTIVE

To evaluate the EXACT-Respiratory Symptom (E-RS) measure, a daily diary comprising 11 of the 14 items in the Exacerbations of Chronic Pulmonary Disease Tool (EXACT).

METHODS

Qualitative: patient focus group and interviews to address content validity. Quantitative: secondary data analyses to test reliability and validity.

RESULTS

Qualitative: n=84; mean (SD) age 65 (10) years, FEV1 1.2(0.4) L; 44% male. Subject descriptions of their respiratory symptoms were consistent with E-RS content and structure. Quantitative: n=188; mean (SD) age 66 (10) years, FEV1 1.2(0.5) L; 50% male. Factor analysis (FA) showed 3 subscales: RS-Breathlessness, RS-Cough & Sputum, and RS-Chest Symptoms; second-order FA supported a general factor and total score. Reliability (total and subscales): 0.88, 0.86, 0.73, 0.81; 2-day test-retest ICC: 0.90, 0.86, 0.87, 0.82, respectively.

VALIDITY

Total scores correlated significantly (p < 0.0001) with SGRQ Total (r=0.75), Symptoms (r=0.66), Activity (r=0.57), Impact (r=0.70) scores; subscale correlations were also significant (r=0.26, p < 0.05 (RS-Chest Symptoms with Activity) to r=0.69, p < 0.0001 (RS-Cough & Sputum with Symptoms). RS-Breathlessness correlated with rescue medication use (r=0.32, p < 0.0001), clinician-reported mMRC (r=0.33, p < 0.0001), and FEV1% predicted (r=-0.17, p < 0.05). E-RS scores differentiated groups based on chronic bronchitis diagnosis (p < 0.01-0.001), smoking status (p < 0.05-0.001), and rescue medication use (p < 0.05-0.0001).

CONCLUSIONS

Results suggest the RS-Total is a reliable and valid instrument for evaluating respiratory symptom severity in stable COPD. Further study of sensitivity to change is warranted.

Hemodialysis clearance of glyphosate following a life-threatening ingestion of glyphosate-surfactant herbicide

CONTEXT

Ingestion of glyphosate-surfactant herbicides (GlySH) can result in acute kidney injury, electrolyte abnormalities, acidosis, cardiovascular collapse, and death. In severe toxicity, the use of hemodialysis is reported, but largely unsupported by kinetic analysis. We report the dialysis clearance of glyphosate following a suicidal ingestion of a glyphosate-containing herbicide.

CASE DETAILS

A 62-year-old man was brought to the emergency department (ED) 8.5 h after drinking a bottle of commercial herbicide containing a 41% solution of glyphosate isopropylamine, in polyoxyethyleneamine (POEA) surfactant and water. He was bradycardic and obtunded with respiratory depression necessitating intubation and mechanical ventilation. Initial laboratory results were significant for the following: pH, 7.11; PCO2, 64 mmHg; PO2, 48 mmHg; potassium, 7.8 mEq/L; Cr 3.3, mg/dL; bicarbonate, 22 mEq/L; anion gap, 18 mEq/L; and lactate, 7.5 mmol/L. Acidosis and hyperkalemia persisted despite ventilation and fluid resuscitation. The patient underwent hemodialysis 16 h post ingestion, after which he demonstrated resolution of acidosis and hyperkalemia, and improvement in clinical status. Serum glyphosate concentrations were drawn prior to, during, and after hemodialysis. The extraction ratio and hemodialysis clearance were calculated to be 91.8% and 97.5 mL/min, respectively.

DISCUSSION

We demonstrate the successful clearance of glyphosate using hemodialysis, with corresponding clinical improvement in a patient with several poor prognostic factors (advanced age, large volume ingested, and impaired consciousness). The effects of hemodialysis on the surfactant compound are unknown. Hemodialysis can be considered when severe acidosis and acute kidney injury complicate ingestion of glyphosate-containing products.

Abstract P3-08-18: Association of tamoxifen use and ovarian aging in patients with invasive or pre-invasive breast cancer

Background: The use of tamoxifen has been shown to delay the recovery of chemotherapy-induced amenorrhea, however the independent impact of long-term endocrine therapy on ovarian aging is not known, and to our knowledge, has never been directly investigated. Understanding the effect of endocrine therapy on ovarian aging will help breast cancer patients of reproductive age make more informed and empowered decisions regarding their treatment. The aim of this study is to explore the relationship between tamoxifen therapy and age onset of menopause.

Methods: We conducted a retrospective cohort study using patients identified through the UCSF Cancer Registry and UCSF SPORE database. Women who were diagnosed with Stage 1-3 invasive or in situ breast cancer between 1985 and 2011, who were premenopausal at the time of diagnosis and who did not receive systemic chemotherapy were included. Patients with recurrent disease and prior ovarian surgery were excluded. Eligibility was confirmed by telephone, and online or paper surveys were distributed to eligible subjects only. Age onset of menopause was the primary endpoint of the study and was defined as the age at which a woman had her last period and no menses for 12 months. Age onset of menopause was assessed through surveys. The primary analysis compared age onset of menopause between subjects who received tamoxifen for any duration and control subjects who never received tamoxifen. Secondary analyses were performed using a Cox proportional hazards model to determine whether duration of tamoxifen exposure and age of tamoxifen initiation impacted age onset of menopause in subjects treated with tamoxifen.

Results: A total of 1137 potential subjects believed to meet eligibility criteria were identified and called, and 649 subjects were reached. Eligibility was confirmed by phone in 340 subjects. A total of 336 subjects consented to participate in the study, and 262 (78%) completed and returned the survey. 227 subjects were included in the primary analysis of which 110 subjects received prior tamoxifen, and 117 subjects received no prior tamoxifen. At the time of the survey, 16.3% vs. 20.2% of patients under age 50 that were exposed and not exposed to tamoxifen entered menopause, respectively. The median age onset of menopause was 50.94 and 51.34 for the tamoxifen and no tamoxifen groups, respectively. The hazard ratio between these groups was 1.077 which was not statistically significant (p = 0.6917). No association (p = 0.55) was found between the duration of tamoxifen use and the age onset of menopause. When controlling for tamoxifen duration, there was no significant difference (p = 0.93) in age onset of menopause between subjects who initiated tamoxifen prior to age 45 and those who initiated at age 45 or older.

Conclusion: These data suggest that tamoxifen alone is not associated with an earlier age onset of menopause, and that tamoxifen use, in the absence of systemic chemotherapy, is unlikely to significantly accelerate ovarian aging.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-08-18.