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Intratumor heterogeneity is an important mediator of poor outcomes in many cancers, including breast cancer. Genetic subclones frequently contribute to this heterogeneity; however, their growth dynamics and interactions remain poorly understood. PIK3CA and HER2 alterations are known to coexist in breast and other cancers. Herein, we present data that describe the ability of oncogenic PIK3CA mutant cells to induce the proliferation of quiescent HER2 mutant cells through a cell contact–mediated mechanism. Interestingly, the HER2 cells proliferated to become the major subclone over PIK3CA counterparts both in vitro and in vivo. Furthermore, this phenotype was observed in both hormone receptor–positive and –negative cell lines, and was dependent on the expression of fibronectin from mutant PIK3CA cells. Analysis of human tumors demonstrated similar HER2:PIK3CA clonal dynamics and fibronectin expression. Our study provides insight into nonrandom subclonal architecture of heterogenous tumors, which may aid the understanding of tumor evolution and inform future strategies for personalized medicine.

Purpose:Existing cell-free DNA (cfDNA) methods lack the sensitivity needed for detecting minimal residual disease (MRD) following therapy. We developed a test for tracking hundreds of patient-specific mutations to detect MRD with a 1,000-fold lower error rate than conventional sequencing.Experimental Design:We compared the sensitivity of our approach to digital droplet PCR (ddPCR) in a dilution series, then retrospectively identified two cohorts of patients who had undergone prospective plasma sampling and clinical data collection: 16 patients with ER+/HER2− metastatic breast cancer (MBC) sampled within 6 months following metastatic diagnosis and 142 patients with stage 0 to III breast cancer who received curative-intent treatment with most sampled at surgery and 1 year postoperative. We performed whole-exome sequencing of tumors and designed individualized MRD tests, which we applied to serial cfDNA samples.Results:Our approach was 100-fold more sensitive than ddPCR when tracking 488 mutations, but most patients had fewer identifiable tumor mutations to track in cfDNA (median = 57; range = 2–346). Clinical sensitivity was 81% (n = 13/16) in newly diagnosed MBC, 23% (n = 7/30) at postoperative and 19% (n = 6/32) at 1 year in early-stage disease, and highest in patients with the most tumor mutations available to track. MRD detection at 1 year was strongly associated with distant recurrence [HR = 20.8; 95% confidence interval, 7.3–58.9]. Median lead time from first positive sample to recurrence was 18.9 months (range = 3.4–39.2 months).Conclusions:Tracking large numbers of individualized tumor mutations in cfDNA can improve MRD detection, but its sensitivity is driven by the number of tumor mutations available to track.

Liquid biopsies including circulating tumor cells (CTCs) and cell-free DNA (cfDNA) have enabled minimally invasive characterization of many cancers, but are rarely analyzed together. Understanding the detectability and genomic concordance of CTCs and cfDNA may inform their use in guiding cancer precision medicine. Here, we report the detectability of cfDNA and CTCs in blood samples from 107 and 56 patients with multiple myeloma (MM), respectively. Using ultra-low pass whole-genome sequencing, we find both tumor fractions correlate with disease progression. Applying whole-exome sequencing (WES) to cfDNA, CTCs, and matched tumor biopsies, we find concordance in clonal somatic mutations (~99%) and copy number alterations (~81%) between liquid and tumor biopsies. Importantly, analyzing CTCs and cfDNA together enables cross-validation of mutations, uncovers mutations exclusive to either CTCs or cfDNA, and allows blood-based tumor profiling in a greater fraction of patients. Our study demonstrates the utility of analyzing both CTCs and cfDNA in MM., Circulating tumor cells (CTCs) and cell-free DNA (cfDNA) enables characterization of a patient’s cancer. Here, the authors analyse CTCs, cfDNA, and tumor biopsies from multiple myeloma patients to show these approaches are complementary for mutation detection, together enabling a greater fraction of patient tumors to be profiled.

Purpose Cell-free DNA (cfDNA) offers the potential for minimally invasive genome-wide profiling of tumor alterations without tumor biopsy and may be associated with patient prognosis. Triple-negative breast cancer (TNBC) is characterized by few mutations but extensive somatic copy number alterations (SCNAs), yet little is known regarding SCNAs in metastatic TNBC. We sought to evaluate SCNAs in metastatic TNBC exclusively via cfDNA and determine if cfDNA tumor fraction is associated with overall survival in metastatic TNBC. Patients and Methods In this retrospective cohort study, we identified 164 patients with biopsy-proven metastatic TNBC at a single tertiary care institution who received prior chemotherapy in the (neo)adjuvant or metastatic setting. We performed low-coverage genome-wide sequencing of cfDNA from plasma. Results Without prior knowledge of tumor mutations, we determined tumor fraction of cfDNA for 96.3% of patients and SCNAs for 63.9% of patients. Copy number profiles and percent genome altered were remarkably similar between metastatic and primary TNBCs. Certain SCNAs were more frequent in metastatic TNBCs relative to paired primary tumors and primary TNBCs in publicly available data sets The Cancer Genome Atlas and METABRIC, including chromosomal gains in drivers NOTCH2, AKT2, and AKT3. Prespecified cfDNA tumor fraction threshold of ≥ 10% was associated with significantly worse metastatic survival (median, 6.4 v 15.9 months) and remained significant independent of clinicopathologic factors (hazard ratio, 2.14; 95% CI, 1.4 to 3.8; P < .001). Conclusion We present the largest genomic characterization of metastatic TNBC to our knowledge, exclusively from cfDNA. Evaluation of cfDNA tumor fraction was feasible for nearly all patients, and tumor fraction ≥ 10% is associated with significantly worse survival in this large metastatic TNBC cohort. Specific SCNAs are enriched and prognostic in metastatic TNBC, with implications for metastasis, resistance, and novel therapeutic approaches.

147 Background: Fear of cancer recurrence (FCR) and related constructs are experienced by many cancer survivors and are consistently identified as important areas of need. This study adds to sparse literature on this topic by describing the prevalence of FCR and testing its associations with mental health status measures in a US sample of cancer survivors. Methods: Using the Medical Expenditure Panel Survey (MEPS) Experiences with Cancer Survivorship Supplement (n = 1,032), we examined socio-demographic, health and mental health characteristics of cancer survivors by their level of fear of cancer recurrence (none, low, high). Survey-weighted population-based estimates describe the prevalence of key variables. Multinomial logistic regression was used to test associations between validated measures of mental health status and individual characteristics, and levels of FCR in models unadjusted and controlling for socio-demographic and health characteristics. MEPS survey weights were applied in all analyses to account for the survey design. Results: Overall, 34% of cancer survivors reported no FCR, 54% reported low FCR, and 11% reported high FCR. Cancer survivors were at increased risk of reporting high FCR relative to no FCR if they had a low 12-item Short Form Health Survey (SF-12) Mental Component Summary (MCS) score (≤48) compared to high scores (odds ratio = 2.89; 95% confidence interval (CI) = 1.58, 5.32). Reporting depressive symptoms or psychological distress did not significantly increase the risk of reporting high or low FCR relative to no FCR. Conclusions: This study is the first to provide US population-based estimates of associations between FCR and individual, health and mental characteristics. Our results also provide valuable information on which survivors are most at-risk for FCR, and add to a new and growing literature supporting FCR as a multidimensional construct distinct from depression and distress. Future research is needed to more clearly differentiate FCR from other constructs, specifically anxiety disorders, and to identify clinically significant levels of FCR to better target survivors with the highest needs.

Background: Breast cancer (BC) may recur years to decades after initial treatment, leading to incurable, metastatic disease. Prior studies have shown blood biopsy can detect minimal residual disease (MRD), but not in all patients and often with very short lead time. Most efforts thus far have focused on tracking one or a few mutations via ctDNA, which may limit sensitivity. Here we sought to maximize the detection sensitivity of blood biopsies by tracking up to hundreds of individualized tumor mutations in cell-free DNA (cfDNA). Doing so enables us to break the detection ceiling imposed by the limited copies of each gene in the cell-free DNA in a blood draw. Methods: cfDNA was extracted from archival plasma samples (n=271) from 142 patients with stage 0-III BC enrolled prospectively onto two IRB-approved studies. We applied whole-exome sequencing (WES) to define up to several hundred mutations from each patient’s tumor. To limit potential errors, we employed strict criteria to select somatic SNVs to track using duplex sequencing in cfDNA. We required detection of ≥ 2 mutations for a cfDNA sample to be MRD+ and excluded any mutations also found in a patient’s own germline DNA. Results: We identified 142 patients treated for stage 0-III BC, who had postoperative blood and plasma samples available, and were monitored for distant recurrences for up to thirteen years. All patients had biopsy-proven BC, with 86 (61%) having HR+/HER2- BC, 31 (22%) having HR-/HER2-, or “triple negative” BC (TNBC), and 25 (18%) having HER2-positive disease. Three (2%) patients had stage 0 disease, 32 (23%) had stage I, 68 (42%) had stage II, and 39 (27%) had stage III BC at diagnosis. Archived plasma samples were collected post-operatively, at year 1, and at year 4. We created individualized assays targeting a median of 57 mutations (range 2 - 346) per patient. Reasoning that MRD status after completion of all local therapy and chemotherapy might best predict for distant recurrence, we conducted a landmark analysis at one year following surgery, and found all patients (n=6/6) with detectable MRD experienced recurrence (HR=21.2 (7.43-60.35)) in a median of 6.7 (range 3.4 - 15.8) months. Median lead time including all timepoints from first positive blood sample to recurrence was 18.9 (range: 3.4 - 39.2) months. Finally, in a multivariate model, MRD remained highly statistically significant independent of stage, subtype, and age at diagnosis. Conclusions: We present a novel approach to MRD tracking based on the premise that tracking many - rather than one or a handful of - mutations inherently increases sensitivity and that assay personalization maximizes sensitivity in a disease without multiple, recurrent mutations. To our knowledge, the lead time we show here is significantly longer than that seen in prior investigations, and if confirmed, could offer an opportunity to treat MRD long before the development of clinically apparent metastatic disease. Prospective studies are needed to determine whether earlier detection of MRD is clinically meaningful for patients. Citation Format: Heather A Parsons, Justin Rhoades, Sarah C. Reed, Greg Gydush, Priyanka Ram, Pedro Exman, Kan Xiong, Christopher Lo, Tianyu Li, Mark Fleharty, Greg Kirkner, Denisse Rotem, Ofir Cohen, Melissa Hughes, Shoshanna Rosenberg, Laura Collins, Kathy Miller, Brendan Blumenstiel, Carrie Cibulskis, Donna Neuberg, Samuel S. Freeman, Niall Lennon, Nikhil Wagle, Gavin Ha, Daniel G. Stover, Atish D. Choudhury, Gad Getz, Matthew Meyerson, Nancy U. Lin, Ian E. Krop, J. Christopher Love, G. Mike Makrigiorgos, Ann Partridge, Erika Mayer, Todd R. Golub, Viktor A. Adalsteinsson. Ultrasensitive detection of minimal residual disease in patients treated for breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-01-03.

The Broad/IBM Cancer Resistance Project has partnered with Broad Genomics to pilot the use of cutting edge sequencing technology for the analysis of cell free DNA in blood biopsies. Working closely with the Broad's Cancer Program, Broad Genomics has developed a suite of liquid biopsy sequencing products designed to provide optimal flexibility in conducting research studies with a broad range of applications including; biomarker discovery, treatment resistance monitoring, and detection of minimal residual disease (MRD) post-surgery. Cell-free DNA is extracted from the blood, and a dual unique-molecular-indexed library is created. From this library, low coverage whole genome (ultra-low-pass 0.1x coverage) data is generated to survey sample quality and evaluate the tumor fraction in the liquid specimen. Utilizing the same library, additional assays can be selected for processing based on the research aim (Targeted Panel Assays, MRD Detection or Whole Exomes). Since our approach utilizes the same genomic material for whole genome and targeted sequencing assays, it is possible to maximize the information learned from each valuable and limited liquid biopsy specimen. Our study design takes advantage of the discovery potential of combined tissue-based sequencing and serial liquid biopsy analysis to elucidate mechanisms of cancer resistance by tracking the evolution of clonal and subclonal populations in patients samples over time. This collaboration will utilize the ultra-low-pass sequencing and whole exome sequencing together with custom analysis pipelines to correlate the genomic events with patient clinical data. We aim to process 3,000 samples from 1,000 patients over the next 3 years. To date we have processed close to 500 samples through the ultra-low-pass pipeline and 100 samples through the whole exome sequencing pipeline (results to be provided).The ability to successfully investigate treatment resistant cancers from non-invasive liquid biopsies presents new opportunities for identifying markers, understanding dynamics and monitoring tumor dissemination and clonal evolution. Citation Format: Gad Getz, Carrie Cibulskis, Ignaty Leshchiner, Megan Hanna, Dimitri Livitz, Kara Slowik, Chaya Levovitz, Filippo Utro, Kahn Rhrissorrakrai, Denisse Rotem, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Gavin Ha, Samuel S. Freeman, Christopher Lo, Mark Fleharty, Justin Abreu, Katie Larkin, Michelle Cipicchio, Brendan Blumenstiel, Matt DeFelice, Jonna Grimsby, Susanna Hamilton, Niall Lennon, Viktor A. Adalsteinsson, Laxmi Parida. Broad/IBM Project: Discovery of treatment resistance mechanisms through use of liquid biopsy genomics services [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3001.

Introduction: Precision medicine approaches to guide therapy selection require routine sampling of tumors. However, tumor biopsies are not always accessible and may be confounded by spatial heterogeneity. Liquid biopsies, including analysis of cell-free DNA (cfDNA), present a non-invasive alternative which may reflect multiple tumors in the body. Previous studies have demonstrated exome-wide concordance between single-site tumor biopsies and cfDNA, but little is known about how cfDNA reflects multiple lesions within a patient. Here we sought to determine how cfDNA reflects the body-wide tumor phylogeny, which will inform the use of cfDNA for cancer precision medicine. Methods: We identified 20 patients with pancreatic cancer who had undergone rapid autopsy. We then screened cfDNA tumor fraction and performed whole-exome sequencing of cfDNA and multiple tumor biopsies for 3 patients with cfDNA tumor fraction >10%. We inferred the tumor phylogeny and then developed a statistical approach to deconvolute the contributions to cfDNA from tumor phylogenetic nodes. Finally, we determined whether shared trunk mutations could be detected in cfDNA and tumor biopsies. Results: For each patient, we found mutations shared between all sites and cfDNA, including putative driver mutations. We found mutations which were clonal in multiple regions were detectable in cfDNA, whereas mutations private to individual sites were never clonal in cfDNA. Through our deconvolution analysis, we found that cfDNA could not be modeled as a simple linear combination of individual sites, but rather that cfDNA represented multiple nodes in the inferred phylogeny. For two pancreatic adenocarcinoma patients, the inferred ancestor of the metastases had high estimated contribution (>70%) to cfDNA, while the ancestors of the primaries had lower contributions ( Conclusions: Through analyzing cfDNA and synchronous tumor biopsies from the same patient, we find trunk mutations are enriched in cfDNA as compared to the average single-site biopsy. We also predict that cfDNA represents multiple nodes in the inferred phylogeny. In cases where tumor biopsies are inaccessible, we demonstrate that cfDNA might be a promising alternative to detect trunk SSNVs. These results suggest that cfDNA may be complementary to tumor biopsies for disease monitoring and treatment selection in personalized medicine. Citation Format: Samuel S. Freeman, Ziao Lin, Gavin Ha, Ignaty Leshchiner, Justin Rhoades, Dimitri Livitz, Daniel Rosebrock, Sarah C. Reed, Gregory Gydush, Christopher Lo, Denisse Rotem, Atish D. Choudhury, Daniel G. Stover, Heather A. Parsons, Jesse S. Boehm, J Christopher Love, Matthew Meyerson, Paul Grandgenett, Michael A. Hollingsworth, Viktor A. Adalsteinsson, Gad Getz. Liquid biopsies identify trunk mutations and reflect multiple tumors in a patient [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-225.

© 2018 Elsevier Inc. Nearly all prostate cancer deaths are from metastatic castration-resistant prostate cancer (mCRPC), but there have been few whole-genome sequencing (WGS) studies of this disease state. We performed linked-read WGS on 23 mCRPC biopsy specimens and analyzed cell-free DNA sequencing data from 86 patients with mCRPC. In addition to frequent rearrangements affecting known prostate cancer genes, we observed complex rearrangements of the AR locus in most cases. Unexpectedly, these rearrangements include highly recurrent tandem duplications involving an upstream enhancer of AR in 70%–87% of cases compared with

Brain tumors often require invasive neurosurgical procedures for diagnosis and tissue acquisition to guide precision medicine. Detection of tumor-derived cell-free DNA (cfDNA) would facilitate tumor profiling without risk of surgery-related morbidity and provide a means of tumor surveillance. Our aim is to validate a sample collection procedure and develop highly sensitive and specific methodologies to detect tumor-derived cfDNA in CSF, plasma and urine from pediatric patients with brain tumors to identify clinically relevant genomic alterations. Since July 2016, we have collected blood, urine and CSF samples from 192 patients across all histological subtypes at Dana-Farber Cancer Institute/Boston Children’s Hospital. In parallel, we sequenced the tumors to identify tumor-specific genomic alterations. We optimized a method to process cfDNA and perform ultra-low pass whole genome sequencing (ULP-WGS) using unique molecular identifiers, confirming we can reliably construct sequencing libraries from CSF-, plasma- and urine-derived cfDNA. ULP-WGS has also been used to assess sequencing library quality, copy number variations (CNVs) and tumor fraction. The vast majority of samples undergoing ULP-WGS exhibited no CNVs, consistent with either absence in the tumor or low levels of tumor-derived cfDNA. To distinguish between these, we developed a hybrid capture sequencing panel covering 46 genes, allowing identification of specific mutations and fusions more common in pediatric brain tumors. We are currently assessing the specificity and sensitivity of our assays for detection of tumor-derived cfDNA. Our results will provide insights regarding the feasibility of cfDNA assays to guide clinical care in children with brain tumors.

195 Background: Quantification of circulating free DNA (cfDNA) has been proposed both as a prognostic biomarker and as a biomarker of response and resistance to therapy. However, dynamics of cfDNA derived from both tumor and non-cancerous tissues through dense longitudinal monitoring over the course of treatment with multiple therapeutic modalities have not been well described. Methods: CfDNA isolated from banked and prospectively collected plasma samples from pts with metastatic castration-resistant prostate cancer (mCRPC) was subject to ultra-low pass (~0.1x coverage) whole genome sequencing (ULP-WGS). The fraction of cfDNA derived from tumor rather than non-cancerous tissues (i.e. the tumor fraction, or TFx) in each sample was estimated using a novel computational tool called ichorCNA, and was correlated with clinical features and response to therapy. Results: 663 plasma samples from 140 pts were included (median 3 samples/pt; range 1-20). TFx was correlated with the number of bone metastases (median TFx = 0.014 with no bone mets, 0.047 with 1-3, 0.190 for 4+), and with the presence of distant visceral mets (p < 0.0001). In multi-variate analysis, TFx was positively correlated with Alk Phos (p = 0.0227) and negatively correlated with Hgb (p < 0.001), but was not correlated with PSA (p = 0.75). All new treatment starts leading to > = 30% PSA decline at > = 6 weeks were associated with a decline in TFx from baseline when baseline TFx was > 7% (median TFx change -92.2%, range -70.3% to -100%); however, TFx in patients being subsequently maintained on secondary hormonal therapy without radiographic progression was quite dynamic. The total yield of cfDNA derived from both tumor and non-cancerous tissues tracked closely with TFx, and did not markedly change with initiation of therapies expected to lead to generalized tissue damage, such as chemotherapy and radiation, over the time scales examined. Conclusions: Decline in TFx is a promising biomarker for initial response to therapy, but subsequent temporary rises in TFx do not necessarily indicate the cessation of clinical benefit from secondary hormonal therapies. Analysis of cfDNA may allow a window into short-term tumor dynamics not easily assayed through other methods.

Cell free DNA (cfDNA) has been shown to be an emerging non-invasive biomarker to monitor tumor progression in cancer patients. Elevated cfDNA has been found not only from tumors, but also from normal tissues. Thus, the identification of cfDNA’s tissue-of-origin is critical to understand the mechanism of cfDNA release and tumor progression. Recent efforts to identify cfDNA’s tissue-of-origin begin to utilize cfDNA’s epigenomic status, such as DNA methylation and nucleosome spacing. However, both of these methods have limitations: (1) For nucleosome positioning, lack of reference nucleosome maps in different tumor and normal tissues has limited its application to tissue-of-origin deconvolution; (2) For DNA methylation, large DNA degradation during whole genome bisulfite sequencing (WGBS) library preparation, even with current low-input DNA technology, is still the major hurdle for its clinical application, although extensive DNA methylation studies by WGBS in tumor and normal tissues during the last decade have provided many reference maps. Very recently, a pioneer study showed significant differences between DNA fragment lengths of methylated and unmethylated cfDNA. Taking advantage of this experimental observation, we developed a machine learning approach to infer the base pair resolution DNA methylation level from fragment size information in whole genome sequencing (WGS). The predicted DNA methylation, from not only high coverage but also dozens of ultra-low-pass WGS (ULP-WGS), showed high concordance with the ground truth DNA methylation level from WGBS in the same cancer patients. Furthermore, by using hundreds of WGBS datasets from different tumor and normal tissues/cells as the reference map, we deconvoluted cfDNA’s tissue-of-origin status by inferred DNA methylation level at ULP-WGS from thousands of breast/prostate cancer samples and healthy individuals. The cfDNA’s tissue-of-origin status in cancer patients showed high concordance with confirmed metastasis tissues from physicians. Interestingly, some clinical information, such as cancer grades/stages, seemed to be correlated with cfDNA’s tissue-of-origin status. Overall, our methods here pave the road for cfDNA’s application in clinical diagnosis and monitoring. Citation Format: Yaping Liu, Sarah Reed, Atish D. Choudhury, Heather A. Parsons, Daniel G. Stover, Gavin Ha, Gregory Gydush, Justin Rhoades, Denisse Rotem, Samuel Freeman, Viktor Adalsteinsson, Manolis Kellis. Identify tissue-of-origin in cancer cfDNA by whole genome sequencing [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 5689. doi:10.1158/1538-7445.AM2017-5689

1092 Background: Triple-negative breast cancer (TNBC) is a poor prognosis breast cancer subset characterized by relatively few mutations but extensive copy number alterations (CNAs). Cell-free DNA (cfDNA) offers the potential to overcome infrequent tumor biopsies in metastatic TNBC (mTNBC) and interrogate the genomics of chemotherapy resistance. Methods: 506 archival or fresh plasma samples were identified from 164 patients with mTNBC who had previously received chemotherapy. We performed low coverage sequencing to determine genome-wide copy number and estimate ‘tumor fraction’ of cfDNA (TFx). In patient samples with TFx >10%, we identified regions that were significantly gained or lost using GISTIC2.0. We compared CNAs of mTNBCs with primary TNBCs from a publicly-available dataset, METABRIC (TNBC n=277). Results: We successfully obtained high quality, low coverage whole genome sequencing data for 478 (94.5%) plasma samples from 158 patients, with 1 to 14 samples per patient. Archival samples had significantly higher average cfDNA per mL plasma and TFx than fresh samples, potentially due to later average line of therapy. Average TFx of first blood draw was significantly higher in patients with liver metastases (TFx 28.3% vs. 14.4%, p=1.1e-7). 101/158 patients (63.9%) had at least one sample with TFx >10%, our threshold for high confidence CNA calls. Most alterations significantly enriched in chemotherapy-resistant mTNBCs were chromosomal gains, including NOTCH2 and ERCC1. Median overall survival from time of first blood draw was 9 months, and TFx was highly correlated independent of metastatic line of therapy, age at metastatic diagnosis, BRCA status, and primary stage: adjusted hazard ratio between 4th and 1stquartiles = 4.29 (95% CI 1.66-11.1; p=0.0008). Conclusions: It is feasible to perform genome-level copy number analysis from cfDNA in both archival and fresh samples from patients with mTNBC. Copy number alterations enriched in mTNBC may have implications in the understanding of metastasis, therapeutic resistance, and novel therapeutic targets. ‘Tumor fraction’ of cfDNA is correlated with overall survival and may be an independent prognostic marker in mTNBC.

1076 Background: The Metastatic Breast Cancer Project is a nationwide research study, launched in Oct 2015 in collaboration with patients (pts) and advocacy groups, that directly engages pts through social media and seeks to empower them to share their experiences, clinical information, and samples to accelerate research. Methods: MBC pts enroll by providing their information at mbcproject.org. Pts are sent a saliva kit and asked to mail back a sample which is used to extract germline DNA. We contact pts medical providers and obtain medical records (MRs) and stored tumor samples. Pts may also submit a blood sample, used to extract cell free DNA (cfDNA). Whole exome sequencing (WES) is performed on tumor, germline, and cfDNA; transcriptome sequencing is performed on tumor. Clinical and genomic data are used to generate genomic landscapes in pt subgroups and to identify mechanisms of response and resistance to therapies. Data are shared widely through public databases. Pts receive regular study updates. Results: In 12 months, 2908 MBC pts from 50 states enrolled. 95% completed the 16-question survey about their cancer, treatments, and demographics. 1730 (60%) completed the online consent form. 100-200 pts continue to enroll monthly. To date, 1539 saliva kits were mailed and 1120 samples were received (73%). 992 unique treating institutions were reported by pts, including 733 institutions reported by only 1 pt each and 5 institutions reported by more than 40 pts each. We have obtained MRs from 253 patients (67% yield) and tumor samples from 85 pts (67% yield). WES was successfully completed for 79 tumors of 88 attempted (90%). WES has been performed on initial cfDNA samples. Conclusions: A direct-to-patient approach enabled rapid identification of thousands of MBC pts willing to share MRs, saliva, and tumor samples, including many with rare phenotypes. Remote acquisition of MRs, saliva, tumor, and blood for pts located throughout the US is feasible. We estimate that for ~33% of consenting patients, we can obtain medical records, saliva, and tumor tissue. Genomic analysis of tumor and cfDNA from subgroups including young pts, pts with extraordinary responses, and pts with de novo MBC will be presented.

353 Background: Currently, there are no FDA-approved blood biomarkers for the prognosis or prediction of outcomes in urothelial carcinoma (UC). The telomerase reverse transcriptase ( TERT) promoter is recurrently mutated at high frequency in UC (50%). These mutations have been correlated with tumor recurrence and survival. Tumor cell-free DNA (cfDNA) with somatic genomic alterations can be found in the plasma of cancer patients and has the potential for use as a non-invasive cancer biomarker. Detection of TERT promoter mutations in cfDNA might be used as a prognostic tool to monitor disease outcome in UC patients. We set out to detect tumor cfDNA and TERT promoter mutations in cfDNA from patients with UC at different stages. Methods: UC patients receiving chemotherapy in the neoadjuvant, first or second-line metastatic setting had blood collected either before or during therapy. cfDNA was isolated from ~1ml plasma samples using the QIAmp (Qiagen) kit. Samples underwent ultra-low pass whole genome sequencing (ULP-WGS) to determine whether tumor cfDNA could be detected in these samples. TERT promoter mutations were detected using a sensitive qPCR assay. Results: 40 plasma samples from a total of 32 patients with urothelial carcinoma were analyzed. Sufficient amounts of plasma cfDNA were obtained for library construction and ULP-WGS in 11 patients. 6 of these 11 patients were determined to be positive for detectable tumor cfDNA and of these, all were metastatic and 50% (3/6) were positive for a TERT promoter mutation. In total, 8 out of 40 samples (20%) were positive for a TERT promoter mutation, including samples from two patients where total cfDNA yield was insufficient for library construction. A total of ~20% of patients with metastatic disease were positive for TERT promoter mutations in cfDNA. The low percentage of samples having sufficient cfDNA most likely reflects the low volume of plasma used. Conclusions: TERT promoter mutations were identified in cfDNA of UC patients. ULP-WGS showed tumor cfDNA in patients with a high tumor burden and metastatic disease. TERTpromoter mutations in cfDNA could potentially be used as a non-invasive method for detection of disease. These results have implications for the use of cfDNA in the evaluation of advanced UC.

73 Background: Little research has assessed whether and how technology can support early palliative care. Our team developed a HIPAA-compliant, cloud-based Personal Health Network (PHN) with a secure, online network of family, caregivers, clinicians and service providers designated by the patient; symptom reporting/management resources; and support for communication among network members via audio/video conferencing, messaging, and document sharing. This study examines PHN usability and acceptance, and identifies additional functions for early palliative care. Methods: Patients undergoing chemotherapy in a Comprehensive Cancer Center (n = 19) and their caregivers (n = 17) watched video demonstrations of the technology, participated in semi-structured interviews, and completed surveys measuring computer self-efficacy, PHN usability and acceptance. Results: Most participants were male with college education; mean age was 58 years. Most had a tablet or desktop computer (75%), a mobile phone (94%) and believed that technology improves the security of medication information (66%). At the same time, only 44% used email to contact healthcare providers and 30% used the internet to connect with others for support and information. Most reported the PHN was easy to learn and use and was an efficient and useful tool for patient-driven social networking, team communication, care coordination and symptom management. Participants suggested adapting the PHN to support spiritual and emotional needs and advance care planning. Common concerns included skepticism about receipt of timely responses from providers to symptom reports and the need for ongoing support for older adults with limited technology experience. Conclusions: These preliminary findings support adaption of the PHN to support palliative care components identified as important to patients and caregivers and further PHN usability and acceptance testing in larger, more diverse samples. The results also underscore the need for systems to support technology users, to clarify expectations of response time with patients and caregivers, and to assure these expectations can be met by healthcare providers.

217 Background: Treatment summaries (TSs) and survivorship care plans (SCPs) were expected to bridge patient-provider communication challenges and better address the unique needs of cancer survivors. While interest in TSs and SCPs has been growing, acceptance and implementation has been slow and findings from studies of their effectiveness have been mixed, overall. Our study examines independent associations of receipt of TSs and SCPs with psychosocial outcomes of cancer survivors. Methods: The study sample included survivors completing the 2012 LIVESTRONG Survey for People Affected by Cancer (n = 5,156). Logistic regression was used to model three distinct psychosocial outcomes: having relationship concerns (yes/no), distress (defined as a rating of 6 or higher on the NCCN Distress Thermometer), and moderate or severe cancer-specific worry (yes/no) as functions of TS receipt, SCP receipt and important confounding variables (age, sex, race/ethnicity, marital status, employment, income, education and health insurance). Results: Among cancer survivors, only 51% received a TS and only 16% received a SCP. Survivors who received a TS or SCP had significantly lower odds of relationship concerns (TS: OR = 0.62; 95% CI 0.52, 0.75; SCP: OR = 0.73; 95% CI 0.57, 0.94); distress (TS: OR = 0.74; 95% CI 0.65, 0.85; SCP: OR = 0.81; 95% CI 0.68, 0.97); and moderate or severe cancer-specific worry (TS: OR = 0.76; 95% CI: 0.67-0.85; SCP: OR = 0.78; 95% CI: 0.67-0.92). Other covariates consistently associated with psychosocial concerns included younger age, being unemployed and income ≤ $60,000. Conclusions: Many cancer survivors do not receive a TS or SCP. Receipt of either document was associated with reporting better psychosocial outcomes, suggesting that TSs and SCPs may not be reaching cancer survivors with psychosocial health problems. Survivors with psychosocial concerns may benefit from targeted survivorship care.

189 Background: When a parent is diagnosed with cancer, family functioning may be disrupted, placing children at risk. Little is known, however, about the parenting experiences of cancer survivors. Methods: Among cancer survivors with children age ≤ 20 years at diagnosis (n = 2,375) in the 2012 LIVESTRONG Survey for People Affected by Cancer, we used logistic regression to model the odds that 1) children were not fully emotionally supported or that 2) cancer affected survivors’ ability to provide care for their children. Odds ratios (OR) and 95% confidence intervals (CI) were calculated. Predictors included age of youngest child at diagnosis ( ≤ 10 years versus 11-20 years), survivor report of high distress, and confidence obtaining emotional support. Models also controlled for important sociodemographic covariates. Results: Among survivors, 50% reported that their children were not fully emotionally supported, and 58% reported that cancer affected their ability to provide care for their children. Significant predictors of children not being fully emotionally supported included: government insurance (OR 1.5; 95% CI 1.0-2.1); annual income ≤ $60,000 (OR 1.6; 95% CI 1.3-2.1); being retired (OR 1.7; 95% CI 1.2-2.4); or female (OR 1.4; 95% CI 1.1-1.7). Significant predictors of cancer interfering with the ability to provide care for children included: female sex (OR 2.2; 95% CI 1.8-2.7), survivor report of high distress (OR 1.6, 95% CI 1.4-2.0), having a child ≤ 10 years (OR 2.5; 95% CI 2.0-3.2), or a child who was not fully emotionally supported (OR 1.5; 95% CI 1.3-1.9). Survivors with confidence in their ability to obtain emotional support were less likely to report that cancer interfered with their ability to provide care (OR 0.8; 95% CI 0.6-0.9). Conclusions: Many cancer survivors with young children at diagnosis report that cancer or its treatment affects their ability to provide care, or that their children are not fully emotionally supported. Increased attention to the psychosocial needs of parenting cancer survivors is warranted, particularly among women, those with public insurance, lower incomes, children ≤ 10 years and survivors who report high distress levels or inadequate emotional support.

190 Background: Recent national reports highlight the dramatically rising costs of cancer care and its impact on financial hardship among survivors. Comparatively little attention, however, has been paid to the contributions of family and friends in unpaid caregiving roles—specifically, the impact of caregiving on caregivers jobs and work life. Methods: Using data collected in the 2012 LIVESTRONG Survey of People Affected by Cancer, we examined the prevalence of cancer survivors reporting that they had a friend or family member providing care to them during or after cancer treatment. Then, among those reporting they had a caregiver employed at that time, we used logistic regression to examine caregiver work modifications (i.e., paid time, unpaid time off, changing hours or duties, or making a change in employment status. All models controlled for survivor age at diagnosis, sex, race/ethnicity, income, education and employment status as potential predictors. Results: Of the respondents (n = 6310), 88% reported a family member or friend provided care as follows (in non-mutually exclusive categories): spouses (64%), friends (47%), parents (40%), siblings (31%), children (28%) or other family member (14%). Among survivors with employed caregivers (n = 4,984), 41% reported that their caregiver made a work modification; of these 57% took paid time off, 41% took unpaid time off, 4% switched from full time to part time and 3% took early retirement. Caregivers were more likely to make work modifications for survivors with low (versus high) income or education and for unemployed (versus employed) survivors. The age of the survivor was also a significant factor, with caregivers making more work modifications for younger survivors (ages 18-64) compared to older survivors (age > 65)—with ORs of caregiver work modfications increasing from 1.70 to 6.92 in a dose response by survivor age. Conclusions: Family and friends provide care to a majority of individuals with cancer and many make substantial modifications to their work—contributions which are not routinely counted in estimates of the cost of cancer care. Interventions may be warranted to support caregivers, particular those of survivors with lower income, less education and those of younger age.

241 Background: An estimated 13.7 million cancer survivors live in the United States, a population projected to reach 18 million in 2022. Late- and long-term psychological and emotional effects of cancer can be severe and unfortunately, often go unrecognized and untreated. Few population based data exist that capture psychosocial outcomes across the cancer continuum, from active treatment through survivorship. Methods: We analyzed the Medical Expenditure Panel Survey (MEPS) Experiences with Cancer Survivorship Supplement (n=1,592) to examine psychosocial outcomes among active treatment and survivorship patients across the post-treatment trajectory. Survey-weighted regression models were used to determine the risk of depression (PHQ-2), psychological distress (K-6) and cancer-specific worry related to recurrence. The primary independent variable was post-treatment survivorship status, categorized in years (1-2; 3-4; 5-9; 10-20; >21years) compared to active treatment as the reference group. All models were adjusted for plausible confounding variables (age, sex, race/ethnicity, marital status, employment, income, education, health insurance and health status). Estimates are generalizable to US non-institutionalized populations. Results: No significant difference in the risk of depression (PHQ-2) or psychological distress (K-6) was evident between those in active treatment and cancer survivors at any time post-treatment and those in active treatment. In contrast, cancer-specific worry was significantly higher among those respondents in active treatment (OR 4.3; 95% CI: 2.8, 6.6) compared to those post-treatment. Within the post-treatment survivorship categories, cancer-specific worry generally declined with time post-treatment; however these associations were only significant among those whose treatment was more than 20 years ago (OR= 0.12; 95% CI: 0.04, 0.36) relative to those in active treatment. Conclusions: Psychosocial concerns are pervasive among cancer survivors and are similar to concerns among individuals undergoing active treatment. These findings highlight unmet psychosocial needs among cancer survivors and demonstrate the importance of targeted interventions across the survivorship continuum.

246 Background: Recent national reports highlight gaps in the quality of health care received by the growing population of cancer survivors in the United States. A deeper understanding of the health care experiences of cancer survivors and related disparities could inform interventions designed to address these gaps. Methods: Data from the 2011 Medical Expenditures Panel Survey Household Component and Experiences with Cancer Survivorship Supplement (n=1,592) were used to compare health care experiences of survivors those those of individuals in active treatment. Logistic regression models of three outcomes (receipt of necessary care; detailed discussions with providers about late or long-term side effects of cancer treatment; and detailed discussions with providers about lifestyle or health recommendations e.g., diet, exercise, quitting smoking) were controlled for potential confounding variables including age, sex, health insurance status, education, race/ethnicity, and marital status. Survey weights were applied to account for the complex sampling design and estimates are generalizable to the US civilian, non-institutionalized population. Results: Most respondents (96%), whether or not they were in active treatment, reported they had received all medical care, tests, or treatments that they or their providers believed were necessary. Fewer survivors, compared to respondents in active treatment, reported their providers had discussed late or long-term side effects (37% versus 61%; p

238 Background: The prevalence of cancer in the US continues to increase, with 18.1 million projected survivors by 2020. Few recent population-based studies have examined cancer-related work and financial disparities in this growing population. Methods: Cancer-related work modifications (e.g., changing to a flexible schedule or less demanding job, early or delayed retirement, extended or unpaid time off) and financial difficulties (e.g., debt, worry about medical bills, bankruptcy) were examined in the 2011 Medical Expenditures Panel Survey Experiences with Cancer Survivorship Supplement (n=1,592). Survey-weighted logistic regression was used to model the odds of having any work modification or financial difficulty and negative binomial regression to model counts of these outcomes as functions of survivorship status (i.e., active treatment

3 Background: The number of cancer survivors in the US surpassed 13 million in 2012. In response to rising costs or care and greater demand for services, recent national reports and policies promote cancer care coordination to reduce costly and potentially avoidable services such as Emergency Department (ED) visits. Such efforts must be informed by reliable estimates and improved understanding of ED use and costs among oncology patients. This study quantifies the extent to which cancer survivors use the ED compared to individuals with other chronic conditions and estimates related annual expenses. Methods: Data from the 2008-2011 Medical Expenditure Panel Survey (MEPS) and survey-weighted regression models were used to determine the odds of any ED use (logistic), counts of ED visits (negative binomial) and mean annual medical expenditures attributed to ED use (generalized linear models) in three groups of respondents: cancer survivors, those with chronic conditions other than cancer, and those with neither (reference group). All models were adjusted for important confounding variables (age, sex, race/ethnicity, education, health insurance and health status). Estimates are generalizable to US non-institutionalized populations. Results: Among individuals with cancer, other chronic conditions, and neither condition, 17%, 15% and 9% visited the ED, respectively. Mean annual expenditures attributed to ED use among those with visits were $1471 (95% CI: $1262-$1678), $1517 (95% CI:$1395-$1640) and $1106 (95% CI: $984-$1228). Cancer survivors and individuals with other chronic conditions consistently had significantly higher ED use and costs than did the reference group. The likelihood of having any ED visit was similar between cancer survivors and those with other conditions, however cancer survivors incurred more visits (IRR: 1.17; 95% CI: 1.01, 1.36). Conclusions: ED use and expenditures are substantial among cancer survivors and equal or exceed the same outcomes in individuals with other chronic conditions. Future research is recommended to explore specific areas of unmet health need that may be driving increased frequency of ED visits in the growing population of cancer survivors.