Molecular residual disease detection in resected, muscle-invasive urothelial cancer with a tissue-based comprehensive genomic profiling-informed personalized monitoring assay

Introduction

Circulating tumor DNA (ctDNA) detection postoperatively may identify patients with urothelial cancer at a high risk of relapse. Pragmatic tools building off clinical tumor next-generation sequencing (NGS) platforms could have the potential to increase assay accessibility.

Methods

We evaluated the widely available Foundation Medicine comprehensive genomic profiling (CGP) platform as a source of variants for tracking of ctDNA when analyzing residual samples from IMvigor010 (ClinicalTrials.gov identifier NCT02450331), a randomized adjuvant study comparing atezolizumab with observation after bladder cancer surgery. Current methods often involve germline sampling, which is not always feasible or practical. Rather than performing white blood cell sequencing to filter germline and clonal hematopoiesis (CH) variants, we applied a bioinformatic approach to select tumor (non-germline/CH) variants for molecular residual disease detection. Tissue-informed personalized multiplex polymerase chain reaction-NGS assay was used to detect ctDNA postsurgically (Natera).

Results

Across 396 analyzed patients, prevalence of potentially actionable alterations was comparable with the expected prevalence in advanced disease (13% FGFR2/3, 20% PIK3CA, 13% ERBB2, and 37% with elevated tumor mutational burden ≥10 mutations/megabase). In the observation arm, 66 of the 184 (36%) ctDNA-positive patients had shorter disease-free survival [DFS; hazard ratio (HR) = 5.77; 95% confidence interval (CI), 3.84-8.67; P < 0.0001] and overall survival (OS; HR = 5.81; 95% CI, 3.41-9.91; P < 0.0001) compared with ctDNA-negative patients. ctDNA-positive patients had improved DFS and OS with atezolizumab compared with those in observation (DFS HR = 0.56; 95% CI, 0.38-0.83; P = 0.003; OS HR = 0.66; 95% CI, 0.42-1.05). Clinical sensitivity and specificity for detection of postsurgical recurrence were 58% (60/103) and 93% (75/81), respectively.

Conclusion

We present a personalized ctDNA monitoring assay utilizing tissue-based FoundationOne® CDx CGP, which is a pragmatic and potentially clinically scalable method that can detect low levels of residual ctDNA in patients with resected, muscle-invasive bladder cancer without germline sampling.

[Effects and clinical significance of NLRP3 inflammasome activated by IL-17A in CRSwNP]

Objective: To investigate the effects and clinical significance of NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome activated by interleukin (IL)-17A in chronic rhinosinusitis with nasal polyps (CRSwNP). Methods: Patients underwent nasal endoscopic surgery in the Third Affiliated Hospital of Sun Yat-sen University from January 2020 to December 2021 were collected, including 28 CRSwNP (including 19 males and 9 females, aged 19 to 67 years), 22 chronic rhinosinusitis without nasal polyps (CRSsNP) and 22 controls. qRT-PCR was used to detect the expressions of IL-17A, NLRP3, IL-1β and IL-18 in the three groups, and their correlations were analyzed. The positions of IL-17A, NLRP3 and IL-18 in nasal polys were analyzed by immunofluorescence. Western Blotting and ELISA were employed to detect the expression of NLRP3, IL-1β and IL-18 in the human nasal epithelial cells after using IL-17A stimulation or IL-17A receptor inhibitor. Immunofluorescence was used to observe the NLRP3, IL-1β, and IL-18 protein expression after IL-17A stimulating human nasal epithelial cells, and after the use of IL-17A receptor inhibitor and NLRP3 inhibitor MCC950. The correlations between NLRP3, IL-1β, IL-18 and CT scores, nasal endoscopic scores, visual analogue scale (VAS) scores, and sino-nasal outcome test (SNOT) 22 scores of CRSwNP patients were analyzed. SPSS 20.0 software was used for statistical analysis. Results: The expressions of IL-17A, NLRP3, IL-1β and IL-18 in the tissues of CRSwNP patients were significantly higher than those in CRSsNP group(P=0.018,P<0.001,P=0.005, P=0.016) and the control group(all P<0.001). IL-17A was positively correlated with the expression of NLRP3, IL-1β, and IL-18(r ralue was 0.643,0.650,0.629,respectively, all P<0.05). IL-17A, NLRP3, and IL-18 were co-localized in the epithelial propria of polyp tissue. IL-17A stimulated the expressions of NLRP3, IL-1β, and IL-18 in human nasal epithelial cells. After the use of IL-17A receptor inhibitor, the expressions of NLRP3, IL-1β, and IL-18 were significantly down-regulated. After the use of NLRP3 inhibitor MCC950, IL-17A was significantly down-regulated to promote the expression of NLRP3, IL-1β, and IL-18. The expressions of NLRP3, IL-1β and IL-18 were positively correlated with CT, nasal endoscopy, VAS, and SNOT22 scores in patients with CRSwNP. Conclusions: IL-17A promotes the release of IL-1β and IL-18 by activating the NLRP3 inflammasome and aggravates the severity of the disease in CRSwNP.

[Establishment and behavioral evaluation of a mouse model of long-term free-choice alcohol drinking]

OBJECTIVE

To establish a model of long-term free drinking mouse by feeding mice with alcohol to simulate the state of human voluntary long-term drinking, and on this basis, to further discuss the evaluation criteria of long-term free drinking mice model in sports, anxiety and cognitive behavior.

METHODS

Forty six-week-old SPF C57BL/6 male mouse were randomly divided into two groups: Long-term free drinking group (n=20) and normal control group (n=20). The two groups were given solid feed normally. The long-term free drinking group was free to take 10% alcohol and water every day, while the normal drinking group only took water every day. The mice were fed for 7 months, and were evaluated by a series of behavioral methods, including Rota-rod test, balance beam test, open filed test, the elevated plus maze, two-box social behavior, new object recognition, Y maze and water maze.

RESULTS

With the increase of drinking days, the mice showed significant alcohol addiction in the alcohol preference test. With the increase of alcohol intake, the mice in the long-term free choice drinking group had slightly shiny fur and reduced diet. Compared with the control group, the weight gain began to slow down from the third month, and the weight decreased significantly by the sixth and seventh months (P=0.006, P < 0.001). The mice showed reduced balance locomotion ability (P=0.003, P=0.001) in the rotary bar and balance beam test. In the open field and elevated cross test, the mice had obvious anxiety-like behavior (P < 0.001). The mice showed decreased social ability in the two boxes of social behavior (P < 0.016). In the experiment of new object recognition and Y maze, the exploration of new object decreased (P=0.018, P=0.040). In the water maze, cognitive functions, such as learning and spatial memory were reduced (P < 0.001).

CONCLUSION

The successful establishment of the long-term free drinking mouse model is more convenient for us to carry out further research on the neural mechanism of alcohol addiction, and lays an experimental foundation for exploring the neural mechanism of alcohol addiction and related new targets.

Abstract P040: Mutational heterogeneity of colorectal cancers across ancestries and its implications for cancer early detection

Introduction: Early cancer detection with liquid biopsies has the potential to reduce mortality rates by improving screening strategies, adoption, and adherence. Towards this, a deeper understanding of the cancer genomic landscape among patients of different ethnicities is critical to ensure comparable performance across a broad population. In this study, we sought to understand how the mutational landscape of patients with colorectal cancer (CRC) varies across ethnicities. Methods: A total of 20,845 de-identified patients with stage I-IV CRC, who had undergone commercial personalized and tumor-informed ctDNA testing (SignateraTM) as of April 14, 2022, were eligible for inclusion in the study. We performed ancestry inference using Principal Component Analysis on single nucleotide polymorphisms (SNPs) and validated the predictions in a subset of 2,032 patients with whole exome sequencing data available along with self-reported ethnicity. Individuals were assigned to one of four major ethnic groups: African (AFR), European (EUR), East Asian (EAS) and South Asian (SAS). Results: Our cohort consisted of 69.1% EUR, 9.6% AFR, 20% EAS, and 1.3% SAS patients. On comparing the somatic driver mutations across ancestry groups, we observed APC mutations in 71% of EUR, 79% of AFR, 80% of EAS and 69% of SAS (p&lt;0.0001), KRAS mutations in 39% of EUR, 50% of AFR, 40% of EAS and 38% of SAS (p&lt;0.0001), and TP53 mutations in 64% in EUR, 64% in AFR, 74% in EAS and 69% in SAS (p&lt;0.0001) patients, respectively. The microsatellite instability (MSI) rates similarly varied across ancestral groups, with EUR ancestry (12.3%) having a significantly higher rate of MSI than AFR (8.9%) and EAS (7.5%) (p&lt;0.0001). Comparing the mutational patterns in left vs. right colon across 712 patients with available tumor location information, we found 64% of tumors in EAS to be left sided vs. 49% in EUR (p=0.0002). Left-sided tumors were enriched for MSI and RAS mutations and right-sided tumors were enriched for APC and TP53 mutations, confirming known differences in left- vs. right-sided colorectal tumors. Among left sided tumors, we also observed TP53 mutations in 79% of EAS as compared to 64% of EUR (p=0.001), APC mutations in 84% of EAS as compared to 70% of EUR (p=0.002) and RNF43 mutations in 1% of EAS as compared to 7% in EUR (p=0.002) suggesting differences in mechanisms of WNT pathway inactivation across ethnicities. Finally, we looked at the predicted performance of a cancer screening panel which is based on large and heterogeneous data and maximizes recurrent mutation coverage while minimizing panel size. Despite the differences in individual driver gene mutation frequency, we found that the mean number of mutations covered by the panel in AFR, EAS and SAS individuals relative to EUR was 1.07, 1.1 and 1.02, respectively. Conclusions: Our results demonstrate that the expected performance of a theoretical cancer screening panel was similar across the different ancestry groups despite differences in their somatic landscape.

Citation Format: Preethi Srinivasan, Boris Gutman, Vasily Aushev, Shruti Sharma, Taly Arbel, Hsin-Ta Wu, Meenakshi Malhotra, Raheleh Salari, Bernhard Zimmermann, Ryan Swenerton, Trupti Kawli, Breeana Mitchell, Matthew Rabinowitz, Alexey Aleshin, Johannes G. Reiter. Mutational heterogeneity of colorectal cancers across ancestries and its implications for cancer early detection. [abstract]. In: Proceedings of the AACR Special Conference: Precision Prevention, Early Detection, and Interception of Cancer; 2022 Nov 17-19; Austin, TX. Philadelphia (PA): AACR; Can Prev Res 2023;16(1 Suppl): Abstract nr P040.

Circulating tumor DNA monitoring for early recurrence detection in epithelial ovarian cancer

OBJECTIVE

Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy. We examined the utility of circulating tumor DNA (ctDNA) as a prognostic biomarker for EOC by assessing its relationship with patient outcome and CA-125, pre-surgically and during post-treatment surveillance.

METHODS

Plasma samples were collected from patients with stage I-IV EOC. Cohort A included patients with pre-surgical samples (N = 44, median follow-up: 2.7 years), cohort B and C included: patients with serially collected post-surgically (N = 12) and, during surveillance (N = 13), respectively (median follow-up: 2 years). Plasma samples were analyzed using a tumor-informed, personalized multiplex-PCR NGS assay; ctDNA status and CA-125 levels were correlated with clinical features and outcomes.

RESULTS

Genomic profiling was performed on the entire cohort and was consistent with that seen in TCGA. In cohort A, ctDNA-positivity was observed in 73% (32/44) of presurgical samples and was higher in high nuclear grade disease. In cohort B and C, ctDNA was only detected in patients who relapsed (100% sensitivity and specificity) and preceded radiological findings by an average of 10 months. The presence of ctDNA at a single timepoint after completion of surgery +/- adjuvant chemotherapy and serially during surveillance was a strong predictor of relapse (HR:17.6, p = 0.001 and p < 0.0001, respectively), while CA-125 positivity was not (p = 0.113 and p = 0.056).

CONCLUSIONS

The presence of ctDNA post-surgically is highly prognostic of reduced recurrence-free survival. CtDNA outperformed CA-125 in identifying patients at highest risk of recurrence. These results suggest that monitoring ctDNA could be beneficial in clinical decision-making for EOC patients.

A phase II study of talazoparib monotherapy in patients with wild-type BRCA1 and BRCA2 with a mutation in other homologous recombination genes

Talazoparib, a PARP inhibitor, is active in germline BRCA1 and BRCA2 (gBRCA1/2)-mutant advanced breast cancer, but its activity beyond gBRCA1/2 is poorly understood. We conducted Talazoparib Beyond BRCA ( NCT02401347 ), an open-label phase II trial, to evaluate talazoparib in patients with pretreated advanced HER2-negative breast cancer (n = 13) or other solid tumors (n = 7) with mutations in homologous recombination (HR) pathway genes other than BRCA1 and BRCA2. In patients with breast cancer, four patients had a Response Evaluation Criteria in Solid Tumors (RECIST) partial response (overall response rate, 31%), and three additional patients had stable disease of ≥6 months (clinical benefit rate, 54%). All patients with germline mutations in PALB2 (gPALB2; encoding partner and localizer of BRCA2) had treatment-associated tumor regression. Tumor or plasma circulating tumor DNA (ctDNA) HR deficiency (HRD) scores were correlated with treatment outcomes and were increased in all gPALB2 tumors. In addition, a gPALB2-associated mutational signature was associated with tumor response. Thus, talazoparib has been demonstrated to have efficacy in patients with advanced breast cancer who have gPALB2 mutations, showing activity in the context of HR pathway gene mutations beyond gBRCA1/2.

Circulating Tumor DNA After Neoadjuvant Chemotherapy in Breast Cancer Is Associated With Disease Relapse

PURPOSE

Detection of circulating tumor DNA (ctDNA) after neoadjuvant chemotherapy in patients with early-stage breast cancer may allow for early detection of relapse. In this study, we analyzed ctDNA using a personalized, tumor-informed multiplex polymerase chain reaction-based next-generation sequencing assay.

METHODS

Plasma samples (n = 157) from 44 patients were collected before neoadjuvant therapy (baseline), after neoadjuvant therapy and before surgery (presurgery), and serially postsurgery including a last follow-up sample. The primary end point was event-free survival (EFS) analyzed using Cox regression models.

RESULTS

Thirty-eight (86%), 41 (93%), and 38 (86%) patients had baseline, presurgical, and last follow-up samples, respectively. Twenty patients had hormone receptor-positive/human epidermal growth factor receptor 2-negative, 13 had triple-negative breast cancer, and 11 had human epidermal growth factor receptor 2-positive disease. Baseline ctDNA detection was observed in 22/38 (58%) patients and was significantly associated with Ki67 > 20% (P = .036) and MYC copy-number gain (P = .0025, false discovery rate = 0.036). ctDNA detection at presurgery and at last follow-up was observed in 2/41 (5%) and 2/38 (5%) patients, respectively. Eight relapses (seven distant and one local) were noted (median follow-up 3.03 years [range, 0.39-5.85 years]). After adjusting for pathologic complete response (pCR), ctDNA detection at presurgery and at last follow-up was associated with shorter EFS (hazard ratio [HR], 53; 95% CI, 4.5 to 624; P < .01, and HR, 31; 95% CI, 2.7 to 352; P < .01, respectively). Association between baseline detection and EFS was not observed (HR, 1.4; 95% CI, 0.3 to 5.9; P = .67).

CONCLUSION

The presence of ctDNA after neoadjuvant chemotherapy is associated with relapse in early-stage breast cancer, supporting interventional trials for testing the clinical utility of ctDNA monitoring in this setting.

Abstract 2796: ctDNA prognosis in adjuvant triple-negative breast cancer

Background: Triple negative breast cancer (TNBC) is the most aggressive breast cancer subtype, even in early stages. Evidence of molecular residual disease (MRD), after treatment with curative intent (surgery, chemotherapy), predating macroscopic recurrence can provide rationale for early therapeutic intervention, potentially improving patient outcomes. Longitudinal evaluation of circulating tumor DNA (ctDNA) is emerging as a promising early marker of treatment efficacy and recurrence, validated to pre-date recurrence by radiological imaging. However, data in early TNBC (eTNBC) are limited. Here we investigate the prognostic value of longitudinal ctDNA monitoring in eTNBC patients post-surgery and after adjuvant chemotherapy (ACT) using a custom bespoke ctDNA assay.

Methods: Tumor tissue and longitudinal post-surgical plasma samples were collected and analyzed from 186 patients enrolled in the phase 3 BEATRICE clinical study (NCT00528567). Samples from each patient were whole exome sequenced to identify up to 16 SNVs for ctDNA monitoring. ctDNA status was measured longitudinally and correlated with baseline prognostic factors as well as invasive disease free survival (iDFS) and overall survival (OS).

Results: Baseline ctDNA (b-ctDNA), evaluated post-surgery and prior to chemotherapy was detected in 19.9% (36/181) of patients. b-ctDNA was positively associated with large tumors and lymph node (LN) involvement, and negatively correlated with presence of stromal tumor infiltrating lymphocytes (TILs). b-ctDNA presence was a stronger predictor of shorter IDFS and OS compared to LN involvement (HR IDFS: 4.36 [2.47-7.7] vs 1.86 [1.08-3.19]; HR OS: 4.01 [1.6-10.07] vs 2.89 [1.39-6]]), respectively). Remarkably, b-ctDNA prognostic value was restricted to LN+ pts (HR IDFS: 10.94 [3.2-37.41]) vs LN- pts (HR IDFS 1.61 [0.49-5.36]). ctDNA positivity after ACT was observed in 21.5% (40/186) of patients and was associated with reduced IDFS and OS (HR: 8.36 [4.62-15.1] and 18.45 [6.79-50.17]), independent of LN involvement. Upon chemotherapy treatment, the median time to first ctDNA positivity occurrence was 13 months (range 3-42.3 mo) and the median lead time from ctDNA detection to radiographic recurrence was 6.1 months (range 0-30.5 mo). Akaike information criterion (AIC, p&lt;0.05) indicated that ctDNA detected post-surgery or post-chemotherapy identifies patients at the highest risk of disease progression even after adjustment for LN and TILs status as well as the tumor size.

Conclusions: ctDNA, both at post-surgery and post-ACT, provides additional prognostic value beyond the known risk factors of LN involvement, tumor size and TILs. Post-op ctDNA+ provides an independent and stronger indicator of poor prognosis than any other evaluated baseline covariates. Our data show that TNBC pts that are ctDNA+ post-surgery are at the highest risk of recurrence and death and are underserved by current SOC treatment.

Citation Format: Luciana Molinero, Derrick Renner, Hsin-Ta Wu, Nina Qi, Rajesh Patel, Ching-Wei Chang, Himanshu Sethi, Alexey Aleshin, Carlos Bais, David Cameron. ctDNA prognosis in adjuvant triple-negative breast cancer [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 2796.

Abstract LB111: Comparison of the predictive and prognostic significance of circulating tumor DNA in patients with high risk HER2-negative breast cancer receiving neoadjuvant chemotherapy

Background: We compared the predictive and prognostic value of ctDNA dynamics in high-risk hormone receptor-positive/HER2-negative (HR+/HER2-) and triple negative breast cancer (TNBC) receiving neoadjuvant chemotherapy (NAC) enrolled in the I-SPY 2 trial (NCT01042379). To our knowledge, this is the largest ctDNA study in breast cancer in the neoadjuvant setting.

Methods: Blood samples were collected at pre-treatment (T0), during treatment (T1 at 3 weeks, and T2 at 12 weeks) and after NAC (T3 at 24 weeks) from 106 HR+/HER2- and 97 TNBC patients. Plasma samples (n=734) were analyzed using a personalized and tumor-informed mPCR NGS-based ctDNA test (SignateraTM). Patients, all high risk for recurrence by MammaPrint, received paclitaxel-based treatment +/- experimental therapy followed by anthracycline. The median follow-up was 3.0 years (0.5 to 6.5). The predictive and prognostic value of ctDNA dynamics and status at different timepoints were examined. Our analysis is exploratory and does not adjust for other biomarkers.

Results: Pretreatment ctDNA positivity (Fisher p&lt;0.0001) and levels (mean tumor molecules/mL, MTM/mL, t test p=0.0062) were significantly higher in TNBC (90.7%, 14.7 MTM/mL) than in high risk HR+/HER2- (66.0%, 5.5 MTM/mL). Early and late ctDNA clearance during treatment (3 and 12 weeks of NAC) was predictive of pathologic complete response (pCR) and residual cancer burden (RCB), class 0-III, in TNBC but not HR+/HER2- (Table). In both subtypes: (1) ctDNA was a significant negative prognostic factor for distant recurrence-free survival (DRFS) at all timepoints (p&lt;0.05) except at pretreatment; (2) all patients who achieved pCR were ctDNA-negative after NAC; (3) among non-responding patients, ctDNA-negativity after NAC was associated with improved DRFS (Table).

Conclusions: The predictive value of ctDNA for prediction of pCR and RCB differed between subtypes (HR+/HER2- vs. TNBC), while similar prognostic value was observed. In TNBC, early clearance of ctDNA at 3 weeks was a significant predictor of favorable response to NAC. Compared to patients who were ctDNA-positive after NAC, ctDNA-negative status in both subtypes was associated with improved DRFS even in patients with residual cancer (no pCR or RCB-II/III). These findings could inform on the design of future studies that seek to demonstrate the utility of ctDNA in the curative setting.

Predictive and prognostic significance of ctDNA in early breast cancer in the neoadjuvant setting HR+HER2- (n=106) TNBC (n=97) Predictive value for prediction of pCR and RCB Fisher p-value Fisher p-value Early ctDNA clearance (between T0 and T1) and pCR 0.4521 &lt;0.0001 Late ctDNA clearance (between T0 and T2) and pCR 0.8071 0.0004 Early ctDNA clearance (between T0 and T1) and RCB (0-III) 0.1360 &lt;0.0001 Late ctDNA clearance (between T0 and T2) and RCB (0-III) 0.4869 0.0004 Early ctDNA clearance at T1 and pCR rates pCR rate pCR rate ctDNA clearance (ctDNA+ at T0/ctDNA- at T1) 21% 67% Late ctDNA clearance (betweeNo early clearance (ctDNA+ at T0/ctDNA+ at T1) 13% 14% Prognostic value for prediction of DRFS Log rank p-value Log rank p-value ctDNA at T3 and pCR vs no PCR 0.0002 &lt;0.0001 ctDNA at T3 and RCB (0-I vs II-III) 0.0110 &lt;0.0001 Timepoints: T0 - pretreatment; T1 - three weeks after treatment initiation; T2 - at 12 weeks, between paclitaxel-based and anthracycline regimens; T3- after neoadjuvant chemotherapy prior to surgery

Citation Format: Mark Jesus Mendoza Magbanua, Lamorna Brown Swigart, Derrick Renner, Svetlana Shchegrova, Gillian L. Hirst, Christina Yau, Denise M. Wolf, Hsin-Ta Wu, Ekaterina Kalashnikova, Amy L. Delson, A. Jo Chien, Debu Tripathy, Smita Asare, Raheleh Salari, Angel Rodriguez, Bernhard Zimmermann, Himanshu Sethi, Alexey Aleshin, Paul Billings, Rita Nanda, Hope S. Rugo, Laura J. Esserman, Minetta C. Liu, Angela DeMichele, Laura van 't Veer. Comparison of the predictive and prognostic significance of circulating tumor DNA in patients with high risk HER2-negative breast cancer receiving neoadjuvant chemotherapy [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 LB111.

[The expression profile and potential regulatory mechanism of ACE2 in chronic rhinosinusitis with nasal polyps]

Objective: To preliminarily analyze the expression of angiotensin-converting enzyme 2 (ACE2) and to investigate its potential regulatory mechanism in chronic rhinosinusitis with nasal polyps (CRSwNP). Methods: Patients underwent nasal endoscopic surgery in the Third Affiliated Hospital of Sun Yat-sen University from February 2020 to May 2021 were selected, including 17 males and 6 females, aging from 23 to 66 years old. Expression of ACE2 was evaluated via immunohistochemical staining in controls with non-chronic rhinosinusitis, non-eosinophilic CRSwNP (non-ECRSwNP), and eosinophilic CRSwNP (ECRSwNP) tissue, respectively. Correlations between ACE2 and the indicated Th1/Th2-related cytokines (IFN-γ, IL-4, IL-5, IL-13, IL-25, IL-33, TSLP and periostin) were analyzed based on GSE72713 dataset. Protein-protein interaction (PPI) network was constructed via string database, immune infiltration of GSE72713 dataset was evaluated using cibersort algorithm. ACE2 was comprehensively analyzed by microRNA regulatory network, gene set enrichment analysis (GSEA) and pharmacological analysis. Statistical analysis was performed using GraphPad 7.0 and SPSS 20.0 software. Results: ACE2 was up-regulated in non-ECRSwNP compared with ECRSwNP. Microarray analysis showed that ACE2 was positively correlated with IFN-γ while inversely correlated with IL-5, IL-13 and periostin significantly. Analysis of immune infiltration suggested that ACE2 expression correlated positively with the number of M1 macrophage while negatively with M2 macrophage. GSEA demonstrated that interferon-related signaling pathways were up-regulated in non-ECRSwNP, and miRNA-200B/miRNA-200C/miRNA-429 pathways targeting ACE2 were enriched in ECRSwNP. Results of pharmacological analysis indicated that ampicillin was able to promote the expression of ACE2 whereas acetaminophen could down regulated the expression of ACE2. Conclusion: Expression pattern of ACE2 is varied in non-ECRSwNP and ECRSwNP, which may be related to the different infiltration of indicated cytokines and different regulatory pathways of miRNA.

Molecular residual disease (MRD) detection with a tissue comprehensive genomic profiling (CGP)-informed personalized monitoring assay: An exploratory analysis of the IMvigor-010 observation arm

448

Background: There is compelling rationale that detection of MRD following curative therapy may identify patients at high risk of relapse requiring intensified adjuvant therapy. Combining MRD detection with CGP creates an opportunity to offer MRD-guided treatment with precision cancer therapeutics. Here we analyze the observation arm of the IMvigor-010 study to understand the genomics of resected early stage bladder cancer and to validate CGP-informed personalized MRD detection in circulating tumor DNA (ctDNA). Methods: Using the resected tumor, tissue CGP was performed retrospectively with a 300+ gene assay, followed by MRD detection using FoundationOne Tracker (F1T). Briefly, coding, synonymous, and non-coding variants were selected from tumor tissue sequencing using an optimized algorithm that filters out non-tumor derived variants (germline, clonal hematopoiesis derived, sequencing artifacts). Tumor-informed personalized multiplex PCR-next generation sequencing (Natera) assay was designed and used to detect and quantify variant allelic frequency (VAF) in ctDNA from 182 patients. ctDNA levels were reported in mean tumor molecules per mL of plasma. F1T, a tissue-informed personalized monitoring assay, was performed on plasma samples collected at an MRD timepoint a median of 11 weeks post-surgery. Results: At the MRD timepoint, ctDNA was detected in 66/182 (36%). Focusing on the 66 ctDNA-positive patients, 58 had relapsed (88% PPV) at time of analysis. Median disease-free survival (DFS) from randomization was 3 months in ctDNA-positive vs not reached in ctDNA-negative population (HR = 5.7, 95% CI: 3.8-8.6, p <.0001). Median overall survival (OS) was 13 months in ctDNA-positive vs not reached in ctDNA-negative (HR = 5.7, 95% CI: 3.4-9.7, p <.0001). Potentially actionable CGP findings included FGFR2/3 short variants (SVs) and fusions (13%), ERBB2 SVs and amplifications (13%), PIK3CA SVs (20%), CDKN2A SVs and losses (41%) and tumor mutational burden (TMB) ≥10 mutations/Mb (35%). Conclusions: Tissue CGP-informed personalized MRD detection can detect low levels of residual ctDNA in patients with resected early stage bladder cancer, identifying a population with inferior DFS and OS. This technologic approach, synergizing regulatory-grade actionable CGP with ctDNA-based MRD detection, creates new opportunities for precision adjuvant therapy across a range of high-risk cancer types. Clinical trial information: NCT02450331.

Abstract P2-01-10: Detection of ctDNA following surgery predicts relapse in breast cancer patients receiving primary surgery

Introduction: Identification of Molecular Residual Disease (MRD) by circulating tumour DNA (ctDNA) analysis has the potential to transform the clinical management of patients with early breast cancer. We present results from a proof-of-principle study to assess ctDNA analysis following primary surgery to identify MRD and anticipate which patients are at risk of relapse. Methods: Early breast cancer patients receiving primary surgery for breast cancer (48 total), enrolled in the PlasmaDNA/ITH sample collection studies were included in the analysis. Tumour DNA from FFPE samples was whole exome sequenced to identify patient specific mutations and design personalized Signatera ctDNA assays. Plasma samples were collected pre-surgery (n=31), 1-14 weeks post-surgery and prior to adjuvant therapy (n=48), and following adjuvant chemotherapy (n=36). Cell free DNA was extracted from a total of 144 plasma samples (median volume 3.6ml, range 1.8-4.7ml) and sequenced with Signatera ctDNA assays. Primary objective was to assess whether relapse free survival (RFS) and distant metastasis free survival (DMFS) are worse in patients with ctDNA detected at the post-surgery timepoint compared to those without ctDNA detected. Results: Median age was 50.5 years, 34 had hormone receptor positive HER2 negative (HR+HER2-), 5 HER2 positive and 9 triple negative breast cancer (TNBC), 32 were stage 1-2 and 16 were stage 3-4. At a median follow-up of 60 months post-surgery, 8 patients had relapsed. ctDNA was detected in the single post-surgery timepoint in 29% (14/48) of patients, and detected in 62.5% (5/8) of patients who relapsed. RFS in patients with ctDNA detected at a single post-surgery timepoint was worse than those with no detected ctDNA although it was not statistically significant (Hazard Ratio (HR): 3.7; 95% CI, 0.9-15.6; P=0.07), while ctDNA detection associated with worse DMFS (HR: 5.6; 95% CI, 1.1-29-3; P=0.04). DMFS at 4 years follow-up in those with MRD ctDNA detection was 0.78 (95% CI 0.47-0.92) and those without MRD detection was 0.97 (95% CI 0.80-0.99). In patients with a pre-surgical timepoint (n=31), 64.5% (20/31) had ctDNA detected. Detection of ctDNA at either pre-surgery or post-surgery was associated with worse outcomes compared to no ctDNA detection at both RFS (HR: 7.9; 95% CI, 0.9-64.7; P=0.05) and DMFS (HR: 6.7; 95% CI, 0.8-55.8; P=0.07). Conclusions: In this proof-of-principle study of early-stage breast cancer patients, ctDNA-detected MRD at a single post-surgical timepoint was associated with distant metastasis free survival. The majority of patients with ctDNA detected MRD did not relapse, during the period of follow-up, possibly suggesting activity of adjuvant therapy in these patients. Further assessment is warranted on the prognostic impact of ctDNA MRD detection, and its possible role in adjuvant chemotherapy selection.

Citation Format: Isaac Garcia-Murillas, Rosalind J Cutts, Lara Ulrich, Matthew Beaney, Marie Robert, Maria Coakley, Catey Bunce, Giselle WalshCrestani, Sarah Hrebien, Ekaterina Kalashnikova, Hsin-Ta Wu, Scott Dashner, Himanshu Sethi, Alexey Aleshin, Alistair Ring, Alicia Okines, Ian E Smith, Mitch Dowsett, Peter Barry, Nicholas C Turner. Detection of ctDNA following surgery predicts relapse in breast cancer patients receiving primary surgery [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-01-10.

Abstract P2-01-06: Detection of circulating tumor DNA post neoadjuvant chemotherapy using a personalized assay is associated with disease relapse

Background: Approximately 30% of patients with early breast cancer present disease relapse after surgery, and technologies that enable the detection of circulating tumor DNA (ctDNA) were shown to identify them earlier than standard imaging. In the present study, we aimed to interrogate the value of the SignateraTM personalized ctDNA assay for early detection of disease relapse. Methods: The study included 52 early breast cancer patients undergoing neoadjuvant chemotherapy from an ongoing translational, single-center study at Jules Bordet Institute, Brussels, Belgium. From each patient, primary tumor tissue sections, blood sample for normal DNA, and serial plasma samples were sent to NATERA Inc for ctDNA detection using the SignateraTM assay. Plasma samples were collected before the initiation of neoadjuvant chemotherapy (baseline), after neoadjuvant chemotherapy, before surgery (pre-surgery), and at follow-up post-surgery. Whole exome sequencing (WES) was performed on the primary tumor tissue and matched normal DNA to design a patient-specific ctDNA assay. The unique set of SNV’s identified in WES were tracked in serial plasma samples. Associations between baseline ctDNA detection and standard clinicopathological characteristics and primary tumor point mutations or copy number aberrations were evaluated. Association between ctDNA detection, pathological complete response (pCR) and event-free survival (EFS) were explored. Fisher, Mann-Whitney and Kruskal-Wallis tests were used to compare variables. Log-rank tests and Cox regressions were used for survival analyses. Hazard ratios (HRs) and confidence intervals (CIs) were obtained from Cox regressions. For multivariable tests, logistic regressions were used for binary outcomes and Cox regressions for survival outcomes. P-values were obtained by comparing models with and without the variable of interest using Chi-square test in ANOVAs. Results: Forty-four out of 52 (85%) initially selected patients had the required tumor cellularity (≥ 20%) and adequate tumor DNA quantity and quality and had personalized ctDNA assays designed. In these 44 patients, 154 plasma samples were successfully processed including 38, 41, 75, 38 at baseline, pre-surgery, follow-up (any timepoint) and last follow-up timepoint, respectively. Twenty (45%) patients had hormone receptor positive/HER2-negative, 13 (30%) triple-negative and 11 (25%) HER2-positive breast cancers. Detection of ctDNA was observed in 22 of 38 (58%) patients at baseline and was significantly associated with Ki67&gt;20% and MYC copy number gain in the primary tumor. ctDNA detection at pre-surgery and at last follow-up was observed in 2 of 41 (5%) and 2 of 38 (5%) patients respectively. All patients who achieved pCR were ctDNA-negative at the pre-surgical time point. With a median follow-up of 3.03 years (range 0.39 - 5.85), we observed 8 relapses (7 distant and 1 local, respectively). After adjusting for pCR, ctDNA detection was associated with shorter EFS at pre-surgery and at last follow-up time points (HR: 53, 95% CI: 4.5-624, p&lt;0.01, and HR: 31, 95% CI: 2.7-352, p&lt;0.01, respectively), but not at baseline (HR: 1.4, 95% CI: 0.3-5.9, p=0.67). Conclusions: The detection of ctDNA post neoadjuvant chemotherapy is associated with disease relapse in early breast cancer supporting interventional trials in this setting.

Citation Format: Elisa Agostinetto, Frédéric Cailleux, Matteo Lambertini, Françoise Rothé, Hsin-Ta Wu, Mustafa Balcioglu, Himanshu Sethi, Delphine Vincent, Giulia Viglietti, Andrea Gombos, Andreas Papagiannis, Isabelle Veys, Ahmad Awada, Christos Sotiriou, Ekaterina Kalashnikova, Alexey Aleshin, Denis Larsimont, David Venet, Michail Ignatiadis. Detection of circulating tumor DNA post neoadjuvant chemotherapy using a personalized assay is associated with disease relapse [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-01-06.

Comprehensive genomic profiling (CGP)-informed personalized molecular residual disease (MRD) detection: An exploratory analysis from the PREDATOR study of metastatic colorectal cancer (mCRC) patients undergoing surgical resection

187

Background: Detection of MRD following metastatic liver resection in advanced CRC patients is associated with poor prognosis with high rate of relapse. Nevertheless, there is currently no standard of care to guide further therapy after curative intent surgery. MRD detection has the promise to be implemented into standard of care and guide treatment decision making. Here we establish feasibility of MRD detection using Foundation Medicine’s novel tissue-informed personalized monitoring assay, FoundationOne Tracker (F1T), in mCRC patients undergoing surgical resection with curative intent. Methods: Tissue-based CGP was performed retrospectively on a cohort of 72 patients from the PREDATOR trial. Trackable patient-specific single nucleotide variants were selected using a novel computational approach negating the need for buffy coat sequencing to filter germline variants. Personalized multiplex PCR was used to detect and evaluate prognostic value of ctDNA from plasma collected at MRD timepoint post-surgery (median 27 days, range 8-99.5). Median follow-up of patients in the overall population was 10.7 months (range: 0.9-53.8 months). Survival analyses were performed using the Kaplan-Meier Estimator and Cox regression. Results: Post-surgical F1T analysis was successful on 96% of cases (69/72). CGP analysis revealed at least one driver mutation in 57% of samples (41/72) including KRAS/NRAS (46%) and BRAF mutations (3%). MRD was detected in 45% (31/69) of patients, of which 94% (29/31) had progressed at the time of the data cut. Median progression -free survival (PFS) was 3.2 months (2.1-7.1) in ctDNA-positive vs 28 months (20.9-NA) in ctDNA-negative population (HR 5, CI 2.7-9.3, p<0.001). Median overall survival (OS) was 31.6 months in ctDNA-positive vs not reached in ctDNA-negative group (HR 27, CI 3.6-205, p<0.001). Conclusions: CGP-informed post-operative MRD detection is a strong prognostic biomarker and correlates with survival outcomes in patients with resected mCRC. F1T is a novel and convenient technological approach to MRD detection utilizing highly validated FMI testing to reveal potentially targetable mutations and inform personalized ctDNA monitoring. These results demonstrate the ability of F1T to accurately detect MRD in mCRC patients following surgical resection, without the need for germline sequencing.

Abstract 552: Circulating tumor DNA predicts disease recurrence in ovarian cancer patients

Introduction: Epithelial ovarian, fallopian tube, and peritoneal cancer (EOC) is the most lethal gynecologic malignancy with a 5-year survival rate of 47%. While primary treatment generally results in remission, most patients relapse within 3 years. CA-125 is a commonly used biomarker for recurrence detection, however, it lacks specificity and is not associated with improved survival. Here we examine the utility of circulating tumor DNA (ctDNA) as a biomarker for EOC by assessing its relationship to patient outcome and CA-125 when measured pre-surgically and during patient monitoring.

Methods: This study included patients diagnosed with stage I-IV EOC with plasma samples collected pre-surgically (n=44) and a group of patients (n=22) with serially collected samples after surgery. Median follow-up for patients with pre-surgical samples and with prospectively collected samples was 29 months (range: 6-150) and 15 months (range: 0.6-26), respectively. Whole exome sequencing was performed on patient tumors and matched normal tissue to design patient-specific ctDNA assays (bespoke mPCR NGS assay) for variant detection in plasma samples. The relationship between ctDNA status, CA-125 levels, and recurrence-free survival (RFS) were evaluated (Fisher's exact, log-rank test).

Results: Among patients with presurgical plasma samples high-grade serous was the most common histological subtype 66% (29/44). Endometrioid represented 11% (5/44) of tumors and 23% (10/44) were tumors of other epithelial subtypes. In this cohort 75% (33/44) had early-stage disease, 7% (3/44) were metastatic and 18% (8/44) had the unstaged disease. The presence of ctDNA was observed in 73% of samples at baseline with detection rates of 69% (20/29) for serous and 80% (4/5) for endometrioid histologies. Pre-surgical ctDNA detection was significantly associated with a higher grade (p=0.003). All patients with ctDNA negative status at baseline (n=12) survived until the end of follow-up (median: 25 months), while 3 deaths were observed among ctDNA positive patients (n=32; p=0.003).

In the sub-cohort of patients with prospective post-surgical plasma collection, ctDNA was observed in samples of all patients who relapsed (7/7; 100% sensitivity). ctDNA detection preceded radiological findings by a median of 9 months (range: 2-36). None of the patients with ctDNA negative status within 6 months after enrollment experienced disease progression (13/13; 100% specificity). The presence of ctDNA was observed to be a strong predictor of relapse (HR: 12.75, 95%CI: 1.7-94 p&lt;0.0001), while CA-125 was not significantly associated with RFS (HR: 1.3, 95%CI: 0.3-6.3; p=0.09).

Conclusions: The presence of ctDNA post-surgically is highly prognostic of decreased RFS and was found to be a stronger predictor of disease progression than CA-125 monitoring. These results suggest that monitoring ctDNA could be a useful tool in clinical decision making for patients with EOC.

Citation Format: Jocelyn S. Chapman, William E. Pierson, Karen Smith-McCune, Geovanni Pineda, Reena M. Vattakalam, Alexandra Ross, Meredith A. Mills, Carlos J. Suarez, Tracy Davis, Robert P. Edwards, Michelle Boisen, James M. Ford, June Y. Hou, Hsin-Ta Wu, Scott Dashner, Ekaterina Kalashnikova, Angel Rodriguez, Bernhard Zimmermann, Sarah Sawyer, Himanshu Sethi, Alexey Aleshin. Circulating tumor DNA predicts disease recurrence in ovarian cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 552.

Abstract PD9-02: Personalized ctDNA as a predictive biomarker in high-risk early stage breast cancer (EBC) treated with neoadjuvant chemotherapy (NAC) with or without pembrolizumab (P)

Background: In the I-SPY 2 TRIAL, the addition of P to standard NAC resulted in more than doubling of the pathologic complete response (pCR) rates for both hormone receptor-positive (HR+)/HER2- and triple-negative (TN) early breast cancer (EBC) patients (pts) compared to NAC only (Nanda et al, JAMA Oncol, 2020). At 3 years, distant recurrence-free survival (DRFS) rates in pts with pCR following NAC+P was &gt;95%. We hypothesized that ctDNA can serve as a predictive biomarker of response and survival in pts treated with NAC.

Methods: A personalized ctDNA test (Signatera) was performed on 511 serial plasma samples from 138 pts with high-risk HR+/HER2- (n=77) or TN (n=61) stage II/III EBC. Pts received P with paclitaxel (Tx) followed by AC (P arm, n=42) or standard NAC only (n=96), an exploratory subset of pts evaluated for P efficacy. Plasma was collected; pretreatment (T0), 3 weeks after treatment initiation (T1), between Tx+/-P and AC regimens (T2), and prior to surgery (T3). ctDNA was deemed positive with a minimum of 2 of the pt specific tumor mutation fragments detected in cfDNA. Association of ctDNA with response and survival was analyzed using logistic and Cox regressions with pCR and DRFS as endpoints. Median follow-up was 2.8 years.

Results: Detection of ctDNA decreased over time (P arm: T0-81%, T1-50%, T2-19%, T3-3%) and NAC only: T0-82%, T1-65%, T2-26%, T3-10%).

ctDNA data at T0 and T1 was available for 96% (132/138) of pts in P arm or NAC only (Table). Among ctDNA+ patients at baseline, clearance at T1 was significantly associated with pCR (OR=1.92, ctDNA+/-; OR=0.27, ctDNA+/+; LR p&lt;0.001). This association remained significant after adjustment for HR status and treatment (LR p&lt;0.001) and P arm or NAC only (P: LR p=0.03; NAC: LR p=0.01).

ctDNA data at T0, T1, and T2 was available for 86% (118/138) pts. (Table). Among all ctDNA+ pts at baseline, dynamics through T2 was associated with pCR (OR=1.44, ctDNA+/-/-; OR=0.33, ctDNA+/+/-, OR=0.12, ctDNA+/+/+; LR p=0.0011). This association remained significant when adjusted for HR status and treatment (LR p&lt;0.001). Analysis within individual treatments showed significant association for NAC (LR p=0.040) and a non-significant trend in NAC+P (LR p=0.063), likely due to smaller sample size.

All pts who achieved pCR were ctDNA- at T3 (n=34). Among those who failed to achieve pCR (n=81), DRFS was significantly better in ctDNA- (n=72/81; 20 in P and 52 in NAC) versus ctDNA+ pts (n=9/81; 1 in P and 8 in NAC) (adjusted HR 0.13; 95% CI 0.05-0.37).

Conclusions: These exploratory results align with our previous findings that early clearance of ctDNA during NAC treatment was significantly associated with increased likelihood of achieving pCR. Additionally, we show that ctDNA clearance can be an early surrogate marker for therapy response assessment. Residual ctDNA after neoadjuvant treatment was a significant predictor of metastatic recurrence and death. Personalized monitoring of ctDNA during the course of NAC is feasible and provides information that can be combined with imaging and pathology, and may help to optimize decision making for de-escalation or escalation of therapy. Larger studies are ongoing.

ctDNA dynamics and pCRctDNA status at T0 and T1 (n=132)ctDNA status at T0, T1, and T2 (n=118)ctDNA-/-ctDNA+/-ctDNA+/+ctDNA-/-/-ctDNA+/-/-ctDNA+/+/-ctDNA+/+/+Total, n (%)24 (18)28 (21)80 (61)22 (19)24 (20)43 (36)27 (23)pCR, n (%)9 (38)15 (54)11 (14)9 (41)12 (50)8 (19)2 (7)No pCR, n (%)15 (63)13 (46)69 (86)13 (59)12 (50)35 (81)25 (93)

Citation Format: Mark Jesus M Magbanua, Denise Wolf, Derrick Renner, Svetlana Shchegrova, Lamorna Brown Swigart, Christina Yau, Gillian Hirst, Hsin-Ta Wu, Ekaterina Kalashnikova, Antony Tin, Amy Delson, Douglas Yee, Angela DeMichele, Raheleh Salari, Angel Rodriguez, Bernhard Zimmermann, Himanshu Sethi, Alexey Aleshin, Paul Billings, Laura Esserman, Minetta Liu, Rita Nanda, Laura van ‘t Veer, I-SPY 2 Investigators. Personalized ctDNA as a predictive biomarker in high-risk early stage breast cancer (EBC) treated with neoadjuvant chemotherapy (NAC) with or without pembrolizumab (P) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD9-02.

Characterization of clonal hematopoiesis of indeterminate potential mutations from germline whole exome sequencing data

1525

Background: Clonal hematopoiesis of Indeterminate Potential (CHIP) is an age-related phenomenon where somatic mutations accumulate in cells of the blood or bone marrow. It is a source of biological noise that causes false-positives in ctDNA analysis and is present in up to 20% of individuals over the age of 70. The presence of CHIP has been linked to an increased risk of hematologic cancers and cardiovascular disease. The Signatera assay filters CHIP mutations through tumor tissue and germline sequencing thereby reducing false-positive results and focuses on tumor-specific mutations for each patient. Methods: Whole exome sequencing data (average depth ~250x) analyzed from patients’ buffy coat (n = 159) was used to characterize CHIP mutations. Variant calling was performed using Freebayes variant caller with allele frequency threshold between 1% and 10%. Following which variant annotation and selection was performed based on the top 54 genes that are most implicated in myeloid disorders. The selected variants were further screened based on the reported variants in the literature and/or the Catalog of Somatic Mutations in Cancer (COSMIC). Results: The analysis revealed an average of 0.14 (0-2) CHIP mutations per patient with an average variant allele frequency of 3.49% (1%-8.5%). The most common CHIP mutations were observed in DNMT3A, (n = 17), TET2 (n = 7) and TP53 (n = 7) genes. The percentage of patients with at least 1 mutation found in DNMT3A, TET2, and TP53 were 4.2%, 1.94%, and 1.38%, respectively. Other genes containing CHIP mutation included CEBPA, ETV6, HRAS, PDGFRA, NRAS, KMT2A, EZH2, GATA2, GNAS at a frequency below 1%. CHIP mutations were not observed in patients younger than 40 years, but they increased in frequency with every decade of life thereafter. The incidence of CHIP increased from 0.04 for the 40-50 yrs age group to 0.18 for individuals older than 60. Further analysis of associations between incidence of CHIP and cancer type, prior exposure to chemotherapy as well as longitudinal evolution of CHIP mutations during cytotoxic treatment are underway and will be presented. Conclusions: CHIP, a common finding in the elderly population is an important factor to consider in ctDNA analysis and most frequently involves DNMT3A, TET2, and TP53 genes. The frequency of CHIP can be impacted by a number of other factors such as cytotoxic chemo- or radiotherapy.

[Scenario-based study of medical resource requirement rapid assessment under the COVID-19 pandemic]

Objective: COVID-19 outbreak is still under global pandemic. China is facing the risks of importation and local rebound of COVID-19. Under the circumstances, preparations for medical resources are in urgently needed. Methods: Based on current understanding of the disease, we set up five scenarios and use the infectious disease transmission dynamic and pandemic theoretical static models to evaluate the demand for medical resources. Results: Different epidemic strength and strategies of disease control and prevention resulted in different levels of medical resource request, and active control strategy and effective measures could significantly decrease the requirement. During the epidemic rising phase, the cost of prevention and control measures and the requirement of professional response capacities would increase with potential high risk of medical resource demand sharply increasing. Conclusion: Regions with different economic level, population scale, and different prevention and control capabilities should all initiate scientific assessment of medical resource requirement under emergency response and prepare for possible future rebound and epidemic.

[Clinical factors of pathological complete response after neoadjuvant chemoradiotherapy in rectal cancer]

Objective: To explore the feasibility of clinical factors to predict the pathological complete response after neoadjuvant chemoradiotherapy in rectal cancer. Methods: A retrospective analysis was performed on clinical factors of 162 patients with rectal cancer, who underwent neoadjuvant chemoradiotherapy in the General Hospital of People's Liberation Army from January 2011 to December 2018.According to the postoperative pathological results, the patients were divided into pathological complete response (pCR) group and non-pathological complete response group (non-pCR group) to check the predictive clinical factors for pCR. Results: Twenty-eight cases achieved pCR after neoadjuvant chemoradiation (17.3%, 28/162). Univariate analysis showed that patients with higher differentiation (P=0.024), tumor occupation of the bowel lumen≤1/2 (P=0.006), earlier clinical T stage (P=0.013), earlier clinical N stage (P=0.009), the time interval between neoadjuvant chemoradiotherapy and surgery>49 days (P=0.006), and maximum tumor diameter≤5 cm (P=0.019) were more likely to obtain pCR, and the differences werestatistically significant. Multivariate analysis showed that tumor occupation of the bowel lumen≤1/2 (P=0.01), maximum tumor diameter≤5 cm (P=0.035), and the interval>49 days (P=0.009) were independent factors in predicting pCR after neoadjuvant therapy. Conclusion: Tumor occupation of the bowel lumen, maximum tumor diameter, and the time interval between neoadjuvant chemoradiotherapy and surgery can predict the pCR in rectal cancer.

[Changing trend in prognosis of primary hypopharyngeal carcinoma and reason analysis: date comparison of 2003-2007 and 2010-2014 in a single centre]

Objective: To explore changing trend in prognosis of primary hypopharyngeal carcinoma and to analyze the reasons at the Eye, Ear, Nose and Throat Hospital of Fudan University. Methods: We retrospectively analyzed the clinical data of 461 patients with primary hypopharyngeal carcinoma treated at the Eye, Ear, Nose and Throat Hospital of Fudan University from 2003 to 2007 (Group 1) and 2010 to 2014 (Group 2) according to the inclusion criteria. 142 from Group 1, including 133 males and 9 females, rangedfrom 38 to 82 years old and 319 from Group 2, including 313 males and 6 females, ranged from 39 to 81 years old, were included in this work. The laryngeal function preservation rate, survival outcome, application and effect of pre-and post-operative adjuvant therapy were compared. SPSS 24.0 was used for statistical analyses. Results: There were 62 patients with early disease (T1-2N0) including 18 in Group 1 and 44 in Group 2, in whom 3 (16.7%) underwent surgical procedures with laryngeal function preservation in Group 1, while, 30 (68.2%) underwent laryngeal function preservation surgery in Group 2. The laryngeal function preservation rate showed an obviously upward trend in recent years (χ(2)=13.617, P<0.001), whereas, the recurrence-free survival rate (RFS) and overall survival rate (OS) showed no significant differences between two groups (P=0.469 and 0.808, respectively). Among the 399 patients with advanced disease, 124 were in Group 1 and 275 in Group 2. After propensity score matching (PSM) was used, the OS rate was significantly higher for Group 2 than Group 1 (P=0.017), while the application of laryngeal function preservation surgery was significantly higher in Group 2 (χ(2)=4.686, P=0.030). The application rates of preoperative adjuvant therapy and postoperative adjuvant chemotherapy were significantly higher in group 2 than in group 1 (χ(2)=5.687, P=0.017; χ(2)=19.407, P<0.001). Conclusion: The application of laryngeal function preserving surgery significantly increases the retention rate of laryngeal functions in patients with early-stage hypopharyngeal carcinoma, with similar long-term survival outcomes. The application of comprehensive treatment including preoperative adjuvant therapy and postoperative adjuvant treatments, especially postoperative chemoradiotherapy, shows an obvious increase in the function preservation rate and long-term survival in patients with advanced hypopharyngeal carcinoma.

Abstract P5-01-04: Personalized monitoring of circulating tumor DNA during neoadjuvant therapy in high-risk early stage breast cancer reflects response and risk of metastatic recurrence

Background: The detection of circulating tumor DNA (ctDNA) during neoadjuvant therapy (NAT) may serve as an early indicator of emerging resistance and disease progression. In this study, we analyzed ctDNA from high-risk early breast cancer patients who received NAT and definitive surgery in the I-SPY 2 TRIAL (NCT01042379). We hypothesized that ctDNA can serve as a biomarker of response and survival in this setting.

Methods: ctDNA analysis was performed on 291 plasma samples from 84 high-risk stage II and III breast cancer patients randomized either to an investigational agent MK-2206, an AKT inhibitor, in combination with paclitaxel followed by doxorubicin and cyclophosphamide (AC) (n=52)—or standard-of-care (paclitaxel followed by AC) (n=32). HER2+ patients also received trastuzumab. Serial plasma was collected at pretreatment (T0), at 3 weeks after initiation of paclitaxel treatment (T1), between paclitaxel and AC regimens (T2), and after NAT prior to surgery (T3).

A personalized ctDNA test was designed to detect a set of 16 patient-specific somatic variants, initially identified from whole exome sequencing of pretreatment tumor, then tested in plasma samples. Regions containing the somatic variants were amplified from cell-free DNA using specific polymerase chain reaction primers. Amplified products were subjected to ultra-deep sequencing (mean: 94,000x) to detect somatic variants. Association between ctDNA and clinicopathologic variables was assessed using Fisher’s exact test. Association of ctDNA with response and survival was analyzed using logistic and Cox regressions, respectively. The survival endpoint of the study was distant disease-free survival. The median follow-up was 4.8 years.

Results: At pretreatment (T0), 61 of the 84 (73%) patients had detectable ctDNA. Pretreatment (T0) ctDNA positivity and levels (mean mutant molecules per mL of plasma) were significantly associated with increased tumor burden (clinical T stage T3/T4), more aggressive tumor biology (higher Mammaprint scores) and subtype (HER2+ and Triple negative). CtDNA detection during NAT decreased over time (T0- 73%; T1- 35%; T2- 14%; T3- 9%).

Of the 84 patients, 23 (27%) achieved pCR and all were ctDNA-negative after NAT (T3), while all 6 patients who had detectable ctDNA at T3 did not achieve pCR. Patients who cleared ctDNA early at T1 (n=27, 48% pCR rate) had significantly increased probability of achieving a pathologic complete response (pCR) compared to those who remained ctDNA-positive (n=29, 17% pCR rate; Odds ratio=4.33, Likelihood ratio p=0.012).

Patients who were ctDNA-positive at T3 (n=6) had significantly increased risk of metastatic recurrence (HR 14.7; 95% CI 1.6-131.5) compared to those who achieved pCR and were ctDNA-negative (n=17). The risk of metastatic recurrence in patients who cleared ctDNA during NAT was not significantly different from those who were negative at T0 and remained negative by T3 (hazard ratio, HR: 2.1, 95% CI: 0.22-20.2). Interestingly, patients who were ctDNA-negative (n=37) but failed to achieve pCR had similar risk of metastatic recurrence with those who achieved pCR (HR 1.4; 95% CI 0.15-13.5).

Conclusions: Early clearance of ctDNA during NAT was significantly associated with increased likelihood of achieving pCR. Residual ctDNA after NAT was a significant predictor of metastatic recurrence, while clearance of ctDNA at any point during NAT was associated with improved outcomes. Taken together, personalized monitoring of ctDNA during NAT may aid in real-time assessment of treatment response and help fine-tune pCR as a surrogate endpoint of survival. Validation studies in a larger cohort are warranted.

Citation Format: Mark Jesus M Magbanua, Lamorna Brown-Swigart, Gillian Hirst, Christina Yau, Denise Wolf, Hsin-Ta Wu, Antony Tin, Svetlana Shchegrova, Himanshu Sethi, Raheleh Salari, Alexey Aleshin, Maggie Louie, Bernhard Zimmermann, Angela DeMichele, Minetta Liu, Amy Delson, Amy Jo Chien, Smita Asare, Laura Esserman, I-SPY 2 TRIAL Consortium, Laura van't Veer. Personalized monitoring of circulating tumor DNA during neoadjuvant therapy in high-risk early stage breast cancer reflects response and risk of metastatic recurrence [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 P5-01-04.

Fetal heart rate variability responsiveness to maternal stress, non-invasively detected from maternal transabdominal ECG

PURPOSE

Prenatal stress (PS) during pregnancy affects in utero- and postnatal child brain-development. Key systems affected are the hypothalamic-pituitary-adrenal axis and the autonomic nervous system (ANS). Maternal- and fetal ANS activity can be gauged non-invasively from transabdominal electrocardiogram (taECG). We propose a novel approach to assess couplings between maternal (mHR) and fetal heart rate (fHR) as a new biomarker for PS based on bivariate phase-rectified signal averaging (BPRSA). We hypothesized that PS exerts lasting impact on fHR.

METHODS

Prospective case-control study matched for maternal age, parity, and gestational age during the third trimester using the Cohen Perceived Stress Scale (PSS-10) questionnaire with PSS-10 over or equal 19 classified as stress group (SG). Women with PSS-10 < 19 served as control group (CG). Fetal electrocardiograms were recorded by a taECG. Coupling between mHR and fHR was analyzed by BPRSA resulting in fetal stress index (FSI). Maternal hair cortisol, a memory of chronic stress exposure for 2-3 months, was measured at birth.

RESULTS

538/1500 pregnant women returned the questionnaire, 55/538 (10.2%) mother-child pairs formed SG and were matched with 55/449 (12.2%) consecutive patients as CG. Maternal hair cortisol was 86.6 (48.0-169.2) versus 53.0 (34.4-105.9) pg/mg (p = 0.029). At 36 + 5 weeks, FSI was significantly higher in fetuses of stressed mothers when compared to controls [0.43 (0.18-0.85) versus 0.00 (- 0.49-0.18), p < 0.001].

CONCLUSION

Prenatal maternal stress affects the coupling between maternal and fetal heart rate detectable non-invasively a month prior to birth. Lasting effects on neurodevelopment of affected offspring should be studied.

TRIAL REGISTRATION

Clinical trial registration: NCT03389178.

Analysis of Plasma Cell-Free DNA by Ultradeep Sequencing in Patients With Stages I to III Colorectal Cancer

Importance

Novel sensitive methods for detection and monitoring of residual disease can improve postoperative risk stratification with implications for patient selection for adjuvant chemotherapy (ACT), ACT duration, intensity of radiologic surveillance, and, ultimately, outcome for patients with colorectal cancer (CRC).

Objective

To investigate the association of circulating tumor DNA (ctDNA) with recurrence using longitudinal data from ultradeep sequencing of plasma cell-free DNA in patients with CRC before and after surgery, during and after ACT, and during surveillance.

Design, Setting, and Participants

In this prospective, multicenter cohort study, ctDNA was quantified in the preoperative and postoperative settings of stages I to III CRC by personalized multiplex, polymerase chain reaction-based, next-generation sequencing. The study enrolled 130 patients at the surgical departments of Aarhus University Hospital, Randers Hospital, and Herning Hospital in Denmark from May 1, 2014, to January 31, 2017. Plasma samples (n = 829) were collected before surgery, postoperatively at day 30, and every third month for up to 3 years.

Main Outcomes and Measures

Outcomes were ctDNA measurement, clinical recurrence, and recurrence-free survival.

Results

A total of 130 patients with stages I to III CRC (mean [SD] age, 67.9 [10.1] years; 74 [56.9%] male) were enrolled in the study; 5 patients discontinued participation, leaving 125 patients for analysis. Preoperatively, ctDNA was detectable in 108 of 122 patients (88.5%). After definitive treatment, longitudinal ctDNA analysis identified 14 of 16 relapses (87.5%). At postoperative day 30, ctDNA-positive patients were 7 times more likely to relapse than ctDNA-negative patients (hazard ratio [HR], 7.2; 95% CI, 2.7-19.0; P < .001). Similarly, shortly after ACT ctDNA-positive patients were 17 times (HR, 17.5; 95% CI, 5.4-56.5; P < .001) more likely to relapse. All 7 patients who were ctDNA positive after ACT experienced relapse. Monitoring during and after ACT indicated that 3 of the 10 ctDNA-positive patients (30.0%) were cleared by ACT. During surveillance after definitive therapy, ctDNA-positive patients were more than 40 times more likely to experience disease recurrence than ctDNA-negative patients (HR, 43.5; 95% CI, 9.8-193.5 P < .001). In all multivariate analyses, ctDNA status was independently associated with relapse after adjusting for known clinicopathologic risk factors. Serial ctDNA analyses revealed disease recurrence up to 16.5 months ahead of standard-of-care radiologic imaging (mean, 8.7 months; range, 0.8-16.5 months). Actionable mutations were identified in 81.8% of the ctDNA-positive relapse samples.

Conclusions and Relevance

Circulating tumor DNA analysis can potentially change the postoperative management of CRC by enabling risk stratification, ACT monitoring, and early relapse detection.

Personalized Detection of Circulating Tumor DNA Antedates Breast Cancer Metastatic Recurrence

PURPOSE

Up to 30% of patients with breast cancer relapse after primary treatment. There are no sensitive and reliable tests to monitor these patients and detect distant metastases before overt recurrence. Here, we demonstrate the use of personalized circulating tumor DNA (ctDNA) profiling for detection of recurrence in breast cancer.

EXPERIMENTAL DESIGN

Forty-nine primary patients with breast cancer were recruited following surgery and adjuvant therapy. Plasma samples (n = 208) were collected every 6 months for up to 4 years. Personalized assays targeting 16 variants selected from primary tumor whole-exome data were tested in serial plasma for the presence of ctDNA by ultradeep sequencing (average >100,000X).

RESULTS

Plasma ctDNA was detected ahead of clinical or radiologic relapse in 16 of the 18 relapsed patients (sensitivity of 89%); metastatic relapse was predicted with a lead time of up to 2 years (median, 8.9 months; range, 0.5-24.0 months). None of the 31 nonrelapsing patients were ctDNA-positive at any time point across 156 plasma samples (specificity of 100%). Of the two relapsed patients who were not detected in the study, the first had only a local recurrence, whereas the second patient had bone recurrence and had completed chemotherapy just 13 days prior to blood sampling.

CONCLUSIONS

This study demonstrates that patient-specific ctDNA analysis can be a sensitive and specific approach for disease surveillance for patients with breast cancer. More importantly, earlier detection of up to 2 years provides a possible window for therapeutic intervention.

Bespoke circulating tumor DNA (ctDNA) analysis as a predictive biomarker in solid tumor patients (pts) treated with single-agent pembrolizumab (P)

2542

Background: Limited data exist in the clonal dynamics of serial ctDNA as a predictive biomarker in advanced solid tumor pts receiving immune checkpoint blockade. Methods: Pts with mixed solid tumors received single agent P (anti-PD-1) 200 mg IV Q3wks in the investigator-initiated phase II INSPIRE trial (NCT02644369). ctDNA was assayed at baseline (B) and start of cycle 3 (C3) using a pt-specific amplicon-based NGS assay (Signatera™). Samples were considered ctDNA positive if ≥2 of 16 pt-specific targets met the qualifying confidence score threshold. Results: Results of 70 pts are presented. Demographics: male 46%; median age=60 yrs (range 21–82); head and neck (20%), triple negative breast (14%) and ovarian (14%) cancers comprised the major malignancies. Median no. of P cycles=4 (range 2–35); follow up was 14m (range 2–29); RECIST responses: CR 2.9% (n=2), PR 17% (n=12), CBR (CR+PR+SD≥6 cycles) 31% (n=22), RECIST/clinical PD (n=43/10; 65%/15%). Median PFS=3.3m and median OS=17.8m. 68/70 pts had ctDNA detected at baseline (median=16/16 variants) demonstrating 97% sensitivity. Table shows correlation of ΔctDNA (ctDNAB compared to ctDNAC3) with clinical efficacy parameters, whereas ctDNAB values did not reach statistical significance. Conclusions: A strong correlation exists between ΔctDNA with OS, PFS, CBR and ORR with P, suggesting it is a potential predictive biomarker in pts with mixed solid tumors. Clinical trial information: NCT02644369. [Table: see text]

Early Detection of Metastatic Relapse and Monitoring of Therapeutic Efficacy by Ultra-Deep Sequencing of Plasma Cell-Free DNA in Patients With Urothelial Bladder Carcinoma

PURPOSE

Novel sensitive methods for early detection of relapse and for monitoring therapeutic efficacy may have a huge impact on risk stratification, treatment, and ultimately outcome for patients with bladder cancer. We addressed the prognostic and predictive impact of ultra-deep sequencing of cell-free DNA in patients before and after cystectomy and during chemotherapy.

PATIENTS AND METHODS

We included 68 patients with localized advanced bladder cancer. Patient-specific somatic mutations, identified by whole-exome sequencing, were used to assess circulating tumor DNA (ctDNA) by ultra-deep sequencing (median, 105,000×) of plasma DNA. Plasma samples (n = 656) were procured at diagnosis, during chemotherapy, before cystectomy, and during surveillance. Expression profiling was performed for tumor subtype and immune signature analyses.

RESULTS

Presence of ctDNA was highly prognostic at diagnosis before chemotherapy (hazard ratio, 29.1; P = .001). After cystectomy, ctDNA analysis correctly identified all patients with metastatic relapse during disease monitoring (100% sensitivity, 98% specificity). A median lead time over radiographic imaging of 96 days was observed. In addition, for high-risk patients (ctDNA positive before or during treatment), the dynamics of ctDNA during chemotherapy was associated with disease recurrence (P = .023), whereas pathologic downstaging was not. Analysis of tumor-centric biomarkers showed that mutational processes (signature 5) were associated with pathologic downstaging (P = .024); however, no significant correlation for tumor subtypes, DNA damage response mutations, and other biomarkers was observed. Our results suggest that ctDNA analysis is better associated with treatment efficacy compared with other available methods.

CONCLUSION

ctDNA assessment for early risk stratification, therapy monitoring, and early relapse detection in bladder cancer is feasible and provides a basis for clinical studies that evaluate early therapeutic interventions.

[Outcome of neck dissection for 154 cN0/cN1 patients with squamous cell carcinoma of hypopharynx and prognostic analysis]

Objective: To determine the relationship between nodal disease distribution patterns and oncological outcome and optimum management of cN0/cN1 patients with hypopharyngeal squamous cell carcinoma (HPSCC). Methods: The collected clinical data and the follow-up disease-free survival (DFS) information from 154 patients with HPSCC treated between 2001 and 2014 in Eye Ear Nose and Throat Hospital of Fudan University were retrospectively analyzed. Kaplan-Meier method was used to calculate DFS rate. Log-rank test and Cox regression model were performed to evaluate the survival prognostic factors for univariate and multivariate analyses. Results: Among 154 patients (63 cN0 patients, 91 cN1 patients) with HPSCC,in whom 148 were male, 6 were female, with an arerage age of (58.6±9.9), 63 cN0 patients received lateral neck dissection, of whom 9 were histologically positive nodes. Particularly, occult metastasis rate was 15.6%(7/45) for HPSCC in pyriform sinus and 18.2%(2/11) for HPSCC in posterior pharyngeal wall. Among 91 cN1 HPSCC, 34 underwent radical neck dissection and 54 underwent selective neck dissection. DFS for patients(T3-4N1) with radical neck dissection was lower than that for patient with selective neck dissection(15.2% vs.39.5%, χ(2)=5.153, P<0.05). The DFS of cN0 HPSCC was overestimated by the false-negative patients (cN0→pN+) for cN0 HPSCC and the DFS of cN1 HPSCC was underestimated by the false-positive(cN1→pN0) for cN1 HPSCC. Conclusions: For cN1 HPSCC, compared with radical neck dissection, selective neck dissection may be considered as a more adequate method for removal of metastatic lymph nodes. Postoperative combined therapy and follow-up strategy should be established according to pathological N staging.

[Prospective cohort study on the risks of pre-pregnancy overweight, excessive gestational weight gain on macrosomia]

Objective: To investigate the risks of pre-pregnancy overweight, excessive gestational weight gain on macrosomia. Methods: We conducted one hospital-based cohort study, focusing on pregnant women from January 2015. All pregnant women attending to this hospital for maternal check-ups, were included in our cohort and followed to the time of delivery. Data related to general demographic characteristics, pregnancy and health status of those pregnant women, was collected and maternal pre-pregnant BMI and maternal weight gain were calculated. Logistic regression was used to explore the risk difference of pre-pregnancy BMI, excessive gestational weight gain on macrosomia. Results: The overall incidence of macrosomia in our cohort appeared as 6.6% (149/2 243). After adjusting the confounding factors including age and histories on pregnancy, pre-pregnancy overweight/obesity was associated with higher risks of macrosomia (OR=3.12, 95%CI: 1.35-7.22, P=0.008; OR=2.99, 95%CI: 1.17-7.63, P=0.022) when comparing to those with normal pre-pregnancy weight. Cesarean delivery and sex of the offspring were associated with higher risk of macrosomia, while excessive gestational weight gain showed no significant difference (OR=1.41, 95%CI: 0.96-2.09, P=0.084). Our data showed that Macrosomia was statistically associated with gestational weight gain (P=0.002). After controlling parameters as age, history of pregnancy and related complications of the pregnant women, results from the logistic regression showed that women with gestational inadequate weight gain having reduced risks to deliver macrosomia, when compared to those pregnant women with adequate weight gain (OR=0.52, 95%CI: 0.30-0.90, P=0.019). Conclusion: Pre-pregnancy overweight and obesity were on higher risks to macrosomia.

[Efficacy and economic evaluation of sublingual immunotherapy with Dermatophagoides farinae drops in patients with allergic rhinitis and allergic asthma]

Objective:To evaluate the efficacy and economics of sublingual immunotherapy (SLIT) with Dermatophagoides farinae drops in patients with allergic rhinitis and allergic asthma. Method:Two hundred and three patients (aged 4-60 yr) with allergic rhinitis and allergic asthma induced by house dust mites were retrospectively analyzed. Eighty-six patients were treated by SLIT with standardized Dermatophagoides farina drops and pharmacotherapy (SLIT group), while 117 patients were treated by standardized pharmacotherapy (drug group). Patients were followed up for 2 years with one visit in every 3 months. Total nasal syptom score (TNSS), total rhinitis medicine score (TRMS), daytime asthma syptom score (DASS), nighttime asthma syptom score (NASS), total asthma medicine score (TAMS) and treatment charge were recorded at each visit. Result:There was no significant difference between two groups in TNSS, TRMS, DASS, NASS, TAMS before treatment (all P>0.05). After 1-year or 2-year duration, there were significant differences between the SLIT group and drug group in TNSS, TMSS, DASS, NASS, TAMS (all P<0.01). After 1-year or 2-year duration, the symptom scores and medication scores of SLIT group significantly decreased compared with those before treatment (all P<0.01). In terms of treatment charge, although direct cost of SLIT group was a little higher than that of drug group, the indirect cost of SLIT group was remarkably lower than that of drug group, showing significant difference (P<0.01). Conclusion:SLIT with Dermatophagoides farinae drops is effective in patients with allergic rhinitis and allergic asthma, which may also reduce indirect cost.

[Retrospective analysis of 760 laryngeal squamous cell carcinoma patients treated with open laryngeal function-preserving operations]

Objective:To explore the fundamental clinical characteristics and survival prognostic factors of laryngeal squamous cell carcinoma (LSCC) patients treated with open laryngeal function-preserving operations. Method: The collected clinical data and the follow-up survival information from 760 patients with LSCC undergoing open laryngeal function-preserving operations between January 2005 and December 2010 in Eye & ENT Hospital of Fudan University were retrospectively analyzed. Kaplan-Meier was applied to calculate survival rates. Log-rank test and Cox regression model were performed to evaluate the survival prognostic factors for univariate and multivariate analysis. Result: Among the enrolled 760 cases, 697 patients were glottic cancer, followed by 59 cases in supraglottis and 4 cases in subglottis. The number of laryngeal cancer patients staged in T1 to T4 was 222, 420, 112 and 6, respectively. 27 patients had positive cervical lymph nodes. There were 220, 408, 111 and 21 patients with clinical stage Ⅰ to Ⅳ, respectively. The 5-year overall survival (OS), disease free survival (DFS) and disease specific survival (DSS) rates were 89.3%, 83.9% and 89.8%, respectively. Multivariate Cox analysis indicated that clinical stage and second primary tumor were independent influencing factors for the OS rate, while, age, primary site, pathological differentiation, T stage, clinical stage and surgical margin were independent risk factors for tumor recurrence and progression (P<0.05). Conclusion: Open laryngeal function-preserving operation is a crucial therapeutic strategy applicable to LSCC patients in early and selected advanced stage in China. Early diagnosis and therapy, and sufficient safety surgical margin are keys for improving the survival rate and reducing the risk of relapse for laryngeal cancer patients.

[The prevalence and influencing factors of work-related musculoskeletal disorders of oilfield workover workers]

Objective: To investigate work-related musculoskeletal disorders (WMSDs) of workover workers in an oilfield and explore the influencing factors. Methods: In June 2016, 685 workover workers were selected as working group, and 191 other workers exposed to toxic and harmful operations were selected as control group. Cross sectional investigation was conducted by self-made questionnaire, and the influencing factors of musculoskeletal disorders were analyzed by unconditional multivariate Logistic regression. Results: The total annual prevalence of WMSDs for workover workers was 90.5%, with the highest prevalence of low back pain of 71.5%. The prevalence of WMSDs increased with the increase of service age, and the difference between the drinkers was higher than that of the non drinkers (P<0.05) . Multivariate Logistic regression analysis showed that working age, drinking and the posture of lifting heavy objects were risk factors for WMSDs in workover workers. Conclusion: The WMSDs appears to be a serious problem in oilfield workover workers. Corresponding measures should be taken to prevent the risk factors and control the occurrence of diseases effectively.

Abstract 3653: Sequencing of plasma cfDNA from patients with locally advanced bladder cancer for surveillance and therapeutic efficacy monitoring

Minimally invasive methods for assessment of tumor burden, early detection of disease relapse and for monitoring therapeutic efficacy are needed to improve individualized follow-up and treatment for patients diagnosed with bladder cancer. The ability to predict pathologic complete response after neoadjuvant chemotherapy (NAC) through detection of ctDNA in plasma may enable strategies for bladder preservation. The aim of the study was to use patient-specific mutations to identify residual disease, metastatic relapse and to monitor treatment response in longitudinally collected plasma samples. For this, 50 patients diagnosed with locally advanced muscle-invasive bladder cancer (MIBC) and scheduled for chemotherapy were prospectively recruited between 2013 and 2017. In total, 42 patients received four cycles of cisplatin-based NAC prior to cystectomy and 82% showed response (pathologic downstaging). Eight patients received 2-6 cycles of cisplatin-based first-line chemotherapy due to diagnosis of T4b or lymph node metastasis prior to cystectomy (3CR, 2PR, 2PD, 1 ongoing). So far, 8/50 patients (16%) experienced disease relapse and three patients had metastatic progression. The mean follow-up time after radical cystectomy (RC) was 320 days (65-973); the mean follow-up time for disease-free patients was 397 days (119-778). Whole-exome sequencing (106x mean target coverage) of tumor and germline DNA was performed from a time point before systemic treatment. MUTECT2 identified a mean of 33 high (6-121), 340 (67-2838) moderate and 223 (29-2955) low-impact SNVs or insertion-deletions (InDels) per tumor. High-impact mutations in known cancer genes such as TP53 (60%), KDM6A (34%), ARID1A (32%), RB1 (28%), BRCA2 (26%), FGFR3 (22%) and ERCC2 (20%) were identified with no significant difference between responders vs nonresponders. Signatures 2, 13 (APOBEC), and 3 (BRCA) were frequently identified, with signature 13 being more prevalent in nonresponders (p=0.05). Personalized, multiplex-PCR assay-panels were individually designed, targeting each patient's tumor-specific mutations in plasma. Targeted sequencing was performed using cfDNA from 4-16 longitudinally collected plasma from each patient taken pre- and post-systemic therapy and at scheduled control visits after RC. In a blinded fashion, ctDNA was analyzed and results were compared to pathologic response and radiographic imaging data for each patient. Conclusion: Preliminary results indicated that analysis of plasma cfDNA is an appropriate method to detect metastatic relapse after RC and to monitor treatment efficacy. Here we perform a larger ctDNA study, applying direct sequencing of plasma cfDNA using highly sensitive NGS methods to determine clinical applicability of the method. Data collection is ongoing and all details will be presented at the AACR 2018 meeting.

Citation Format: Karin Birkenkamp-Demtröder, Emil Christensen, Shruti Sharma, Ann Taber, Mads Agerbæk, Himanshu Sethi, Hsin-Ta Wu, Svetlana Shchegrova, Philippe Lamy, Iver Nordentoft, Ryan Swenerton, Samantha Navarro, Tony Tin, Ramya Srinivasan, John So, Spenser Alexander, Solomon Moshkevich, Bernhard Zimmermann, Cheng-Ho Jimmy Lin, Jørgen Bjerggaard Jensen, Lars Dyrskjøt. Sequencing of plasma cfDNA from patients with locally advanced bladder cancer for surveillance and therapeutic efficacy monitoring [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 3653.

Abstract 1590: Personalized circulating tumor DNA analysis to monitor colorectal cancer

Early detection of disease recurrence has shown to improve survival in patients with early-stage colorectal cancer (CRC) (Pita-Fernandez et al., 2015). Detection of circulating tumor DNA (ctDNA) postoperatively in patients with stage II colon cancer provides direct evidence of residual disease and identifies patients at high risk of recurrence (Tie et al., 2016). Previous studies have performed ctDNA analysis to monitor tumor burden in early-stage CRC using small gene panel sequencing or digital droplet PCR (ddPCR) assays to detect specific variants (Tie et al., 2016, Reinert et al., 2016). Building upon these previous studies, here we use a personalized multiplex ctDNA technology measuring 16 mutations specific to each patient's tumor respectively to assess minimal residual disease postoperatively and to monitor treatment response in CRC. Our study includes 130 patients diagnosed with stage I-III CRC treated with intended curative surgery. Of the 130 patients, 80 received adjuvant chemotherapy for a duration of six months. For 119 patients, one pre-operative and one post-operative plasma sample were available. In addition, longitudinally-collected plasma samples were available from 78 of 130 patients for early detection of disease recurrence and to determine their relationship with imaging and carcinoembryonic antigen (CEA) during a 3-year post-operative surveillance period.

To identify patient-specific tumor mutation signatures, whole-exome sequencing of CRC tissue and germline DNA is used. Patient specific multiplex-PCR assay panels are designed to target 16 tumor-specific single-nucleotide variants (SNVs) in plasma. Targeted sequencing is then performed on plasma samples collected pre- and post-operative and during adjuvant therapy. We then correlate ctDNA status to the clinical outcome, including CEA and radiographic imaging, for each patient. Data collection is ongoing and results will be presented at the AACR 2018 meeting.

Conclusion. This study provides a novel methodology to detect minimal residual disease postoperatively and to monitor treatment efficacy in CRC using a personalized multiplex-PCR approach. The performance of this patient-specific ctDNA technology will be compared to the current standard of care for monitoring disease burden.

References:

S. Pita-Fernàndez, et al. Ann. Oncol. 26, 644–656 (2015).

Tie J, et al. Sci Transl Med. 2016 Jul 6;8(346):346ra92.

Reinert T. Gut. 2016 Apr;65(4):625-34.

Citation Format: Thomas Reinert, Tenna V. Henriksen, Mads H. Rasmussen, Himanshu Sethi, Shruti Sharma, Hsin-Ta Wu, Dina Hafez, Prashanthi Natarajan, Scott Dashner, Mustafa Balcioglu, Ann Nguyen, Derrick Renner, Bernhard Zimmermann, Lene H- Iversen, Mogens R. Madsen, Cheng-Ho Jimmy Lin, Claus L. Andersen. Personalized circulating tumor DNA analysis to monitor colorectal cancer [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 1590.

[Clinical value of acoustic radiation force impulse technique to predict esophageal and gastric varices in patients with biliary atresia]

Objective: To investigate the clinical value of acoustic radiation force impulse (ARFI)technique in predicting esophageal and gastric varices in patients with biliary atresia after Kasai portoenterostomy. Methods: A total of 42 patients with biliary atresia after Kasai portoenterostomy were collected from September 2015 to May 2016 in Tianjin First Central Hospital.ARFI technique was used to measure the stiffness of liver and spleen, and 28 healthy children as control.According to the result of CT examination , patients with biliary atresia were divided into two groups , twenty-three patients with esophageal and gastric varices(A group) and nineteen patients without esophageal and gastric varices (B group), Comparing the difference of liver and spleen stiffness between the two groups.The ROC curve analysis was carried out to test the diagnostic power of effective parameter. Results: The ARFI value of liver (2.98±0.80) m/s and spleen (3.00±0.33) m/s of patients with biliary atresia was significantly higher than that of control group((1.10±0.16) m/s, (2.12±0.32) m/s), the differences had statistical significance (both P<0.01). Between group A and group B, the spleen ARFI value of group A(3.16±0.26) m/s was higher than group B(2.83±0.32) m/s, the difference had statistical significance (P<0.01), whereas there was no statistical difference of liver ARFI value between two group((2.93±0.65), (3.02±0.96) m/s)(P>0.05). The cut-off ARFI value of spleen to diagnose esophageal and gastric varices in biliary atresia was 3.02 m/s, and the biggest area under the ROC curve, sensitivity, and specificity were 0.81, 78.6% and 84.5%, respectively. Conclusion: ARFI can be used as a noninvasive method to predict the presence of esophageal and gastric varices in patients with biliary atresia after Kasai portoenterostomy.

Non-invasive acquisition of fetal ECG from the maternal xyphoid process: a feasibility study in pregnant sheep and a call for open data sets

OBJECTIVE

The utility of fetal heart rate (FHR) monitoring can only be achieved with an acquisition sampling rate that preserves the underlying physiological information on the millisecond time scale (1000 Hz rather than 4 Hz). For such acquisition, fetal ECG (fECG) is required, rather than the ultrasound to derive FHR. We tested one recently developed algorithm, SAVER, and two widely applied algorithms to extract fECG from a single-channel maternal ECG signal recorded over the xyphoid process rather than the routine abdominal signal.

APPROACH

At 126dG, ECG was attached to near-term ewe and fetal shoulders, manubrium and xyphoid processes (n  =  12). fECG served as the ground-truth to which the fetal ECG signal extracted from the simultaneously-acquired maternal ECG was compared. All fetuses were in good health during surgery (pH 7.29  ±  0.03, pO₂ 33.2  ±  8.4, pCO₂ 56.0  ±  7.8, O₂Sat 78.3  ±  7.6, lactate 2.8  ±  0.6, BE  -0.3  ±  2.4).

MAIN RESULT

In all animals, single lead fECG extraction algorithm could not extract fECG from the maternal ECG signal over the xyphoid process with the F1 less than 50%.

SIGNIFICANCE

The applied fECG extraction algorithms might be unsuitable for the maternal ECG signal over the xyphoid process, or the latter does not contain strong enough fECG signal, although the lead is near the mother's abdomen. Fetal sheep model is widely used to mimic various fetal conditions, yet ECG recordings in a public data set form are not available to test the predictive ability of fECG and FHR. We are making this data set openly available to other researchers to foster non-invasive fECG acquisition in this animal model.

[Long-term efficacy of supracricoid partial laryngectomy for 298 patients with laryngeal carcinoma]

Objective: To evaluate the oncologic and functional outcomes of supracricoid partial laryngectomy (SCPL) in the treatment of laryngeal carcinoma. Methods: A total of 298 laryngeal carcinoma patients who underwent SCPL treatment from January 2005 to December 2013 were reviewed retrospectively. Clinical data of demographic and clinical characteristics, postoperative complications, rehabilitation information, recurrence and metastasis were analysed. Survival and local control were used to evaluate the clinical outcome.Data were analyzed by SPSS 23.0 software. Results: Thirty-one patients with supraglottic carcinoma underwent cricohyoidoepiglottopexy (CHEP)and 267 with glottic carcinoma underwent cricohyoidopexy (CHP) were enrolled in this study. The mean duration of followed up was 74 months, ranging from 12 to 146 months. Fifty-four cases died at last follow-up. With respect to 31 patients with supraglottic carcinoma, 5- and 10-year overall survival rates and disease specific survival rates all were 78.1%; 5- and 10-year disease free survival rates were 72.1% and 63.7% respectively; and 5- and 10-year local control rates were both 84.2%. In 267 patients with glottic carcinoma, 5- and 10-year overall survival rates were 85.8% and 77.1% respectively; 5- and 10-year disease specific survival rates were 86.6% and 78.4% respectively; 5- and 10-year disease free survival rates were 80.6% and 74.2% respectively; and 5- and 10-year local control rates were 90.0% and 89.4% respectively. The survival rate of patients with glottic carcinoma at stage T1 was higher than that at stage T2 or T3, and the disease free survival rate of patients with early stage was superior than that of patients with advance stage. Cox regression analysis showed that tumor stage T2, and T3, tumor recurrence, and tumor metastasis were independent risk factors for survival. Furthermore, nasogastric feeding tube removal rate was 100% and the decannulation rates of SCPL were 96% in the patients with SCPL. Conclusions: SCPL is a safe procedure with tumor resection for laryngeal carcinoma, with preserving of swallowing, respiration, and phonation functions, and has excellent survival and local control rates. This procedure could be considered as a standard function-sparing treatment for selected patients with laryngeal carcinoma of stages T1b-T3.

Identifying structural variants using linked-read sequencing data

MOTIVATION

Structural variation, including large deletions, duplications, inversions, translocations and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing. This technology labels all reads that originate from a small number (∼5 to 10) DNA molecules ∼50 Kbp in length with the same molecular barcode. These barcoded reads contain long-range sequence information that is advantageous for identification of structural variants.

RESULTS

We present Novel Adjacency Identification with Barcoded Reads (NAIBR), an algorithm to identify structural variants in linked-read sequencing data. NAIBR predicts novel adjacencies in an individual genome resulting from structural variants using a probabilistic model that combines multiple signals in barcoded reads. We show that NAIBR outperforms several existing methods for structural variant identification-including two recent methods that also analyze linked-reads-on simulated sequencing data and 10X whole-genome sequencing data from the NA12878 human genome and the HCC1954 breast cancer cell line. Several of the novel somatic structural variants identified in HCC1954 overlap known cancer genes.

AVAILABILITY AND IMPLEMENTATION

Software is available at compbio.cs.brown.edu/software.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

[Ovarian tumor associated with anti-N-methyl-D-aspartate receptor encephalitis: a report of 15 cases]

Objective: To summarize the clinical features of patients with ovarian tumor and anti-N-methyl-D-aspartate receptor(NMDAR) encephalitis, and to explore the influence of operation patterns on the prognosis. Methods: The clinical information of patients with ovarian tumor and anti-NMDAR encephalitis in The 3rd Affiliated Hospital of Sun Yat-Sen University and The Zhujiang Hospital of Southern Medical University were collected and analyzed. Results: There were 15 patients were enrolled in this study, with the average age of 24.5±5.0 years old. The most frequent first symptom was psychosis. The main clinical features were psychosis, seizures, conscious disturbance, autonomic dysfunction, dyskinesia, central hypoventilation and impaired memory. Most patients' symptoms were relieved after immunotherapy and surgery. The number of favorable prognosis of patients (mRS score 0-2) with ovariectomy was higher than that of the patients with ovarian cystectomy (5 vs 3). But the difference had no statistical significance (P=0.529). Conclusions: For young female patients with psychosis, we should be alert to the possibility of anti-NMDAR encephalitis and screen for tumor. Treated with immunotherapy and operation, most patients can get a favorable prognosis.

[Immunotherapy for head and neck squamous cell carcinoma]

Head and neck squamous cell carcinoma(HNSCC) is the sixth most common malignancies of human beings. The prognosis of advanced HNSCC is poor despite improvements in traditional treatment strategies including surgery, chemotherapy, and radiotherapy. Cancer immunotherapy is the use of the immune system to treat cancer, which provides a sustained antitumor reaction but an absense of chemoresistance. Cancer immunotherapy is becoming the forth treatment strategy towards cancer. Therefore, we reviewed the current state of immunotherapy for HNSCC.

[The clinical characteristics and treatment outcomes of 386 patients with hypopharyngeal cancer]

OBJECTIVE

To investigate the clinical characteristics, surgical treatment outcomes and prognostic factors of hypopharyngeal carcinoma.

METHODS

A retrospective review of the Eye & ENT Hospital of Fudan University patients' database between January 2003 and June 2013 was conducted and a total of 386 patients were enrolled in the study. Patients' clinical and oncological information was collected and survival rates were analyzed using Kaplan-Meier curves. Prognostic factors were evaluated with multivariate Cox model survival analysis.

RESULTS

Among the 386 patients 95.9% were males and 4.1% were females, with an average age of (58.4±9.4) years. The primary tumor sites were pyriform sinus (76.7%), posterior hypopharyngeal wall (17.3%) and postcricoid region (6.0%). There were 31(8.0%), 83(21.5%), 175(45.3%) and 97(25.1%) patients with stage T1 to T4, respectively, 99(25.6%), 74(19.2%), 181(46.9%) and 32(8.3%) patients with stage N0 to N3, respectively , and 3 patients with distant metastasis to lung on initial diagnosis. Second primary cancers were found in 28 cases (7.3%). The 5-year overall survival (OS), disease specific survival (DSS) and disease free survival (DFS) were 45.8%, 48.1% and 46.0% respectively according to Kaplan-Meier survival curves. Multivariate Cox regression model showed significant association between 5-year overall survival rate and T stage (P<0.001), N stage (P=0.003) and second primary tumors (P=0.017). Advanced T stage and lymphovascular invasion were associated with a higher rate of recurrence (P<0.001).

CONCLUSIONS

Hypopharyngeal squamous cell carcinoma has a dismal prognosis, with high rates of submucosal infiltration, cervical lymph node metastasis and distant metastasis. Treatment choices should be made according to TNM stage and overall health conditions in order to achieve ideal oncologic and functional results. Surgery with postoperative chemoradiation therapy is the main treatment for advanced-stage hypopharyngeal cancer.

[Reconstruction of tissue defects after resection of tonsillar cancer by mandibular swing approach]

Objective:To explore the reconstruction methods of oropharyngeal defects after resection of tonsillar cancer by mandibular swing approach.Method:Twenty four cases of patients with tonsillar carcinoma hospitalized in our institution from January, 2010 to December, 2015 were analyzed. Based on the degree and extent of tissue defects, they were divided into three categories.①Small defects, including loss of tonsillar fossa and pharyngeal arches; ②Moderate defects, including small defects of soft palate or tongue root besides lateropharyngeal defects; ③Large defects, including large defects of soft palate and tongue root besides lateropharyngeal defects. The tissue defects of 8 patients belonged to small defects, of whom 4 cases were repaired with mid-thick skin and the others were restored by radial forearm flaps. There were 5 cases of patients with moderate oropharyngeal defects after surgery of tonsillar carcinoma. These defects were reconstructed by radial forearm flaps(2 cases) and anterolateral femoral skin flaps (3 cases) respectively, while the remaining large defects of 11 patients were renovated using pectoralis major myocutaneous flaps(9 cases) and anterolateral femoral skin flaps(2 cases). Result:All the patients healed by first intention after surgery.Four transplanted skin grafts on the regions of small defects survived completely.5 cases of radial forearm flaps and anterolateral femoral skin flaps also survived well, whereas only one radial forearm flap suffered from vascular crisis leading to failure at 5 days postoperatively. The necrotic flaps were then removed by submaxillary space and oral cavity and the wounds were self-healed. The tissue defects were successfully repaired by pectoralis major myocutaneous flaps. Although the surgical wounds swelled, they were obviously relieved half a year later. In the tonsillar cancer patients encroached on soft palates, one occurred nasopharyngeal reflux and 3 spoke vaguely but understandably. The other patients' function of chewing, deglutition, respiration and speech were restored well. Conclusion:Small defects after resection by mandibular swing approach could be repaired by mid-thick skin or radial forearm flaps. Moderate defects of T3 tonsillar cancer could be restored using radial forearm flaps or anterolateral femoral skin flaps, while anterolateral femoral skin flaps or pectoralis major myocutaneous flaps could reconstructed the large defects of T3 or T4 tonsillar cancer.

Optimization of PAM-4 transmitters based on lumped silicon photonic MZMs for high-speed short-reach optical links

We demonstrate how to optimize the performance of PAM-4 transmitters based on lumped Silicon Photonic Mach-Zehnder Modulators (MZMs) for short-reach optical links. Firstly, we analyze the trade-off that occurs between extinction ratio and modulation loss when driving an MZM with a voltage swing less than the MZM's V_π. This is important when driver circuits are realized in deep submicron CMOS process nodes. Next, a driving scheme based upon a switched capacitor approach is proposed to maximize the achievable bandwidth of the combined lumped MZM and CMOS driver chip. This scheme allows the use of lumped MZM for high speed optical links with reduced RF driver power consumption compared to the conventional approach of driving MZMs (with transmission line based electrodes) with a power amplifier. This is critical for upcoming short-reach link standards such as 400Gb/s 802.3 Ethernet. The driver chip was fabricated using a 65nm CMOS technology and flip-chipped on top of the Silicon Photonic chip (fabricated using IMEC's ISIPP25G technology) that contains the MZM. Open eyes with 4dB extinction ratio for a 36Gb/s (18Gbaud) PAM-4 signal are experimentally demonstrated. The electronic driver chip has a core area of only 0.11mm2 and consumes 236mW from 1.2V and 2.4V supply voltages. This corresponds to an energy efficiency of 6.55pJ/bit including Gray encoder and retiming, or 5.37pJ/bit for the driver circuit only.

[Clinical and pathological analysis of 1116 cases of vocal cord polyp]

Objective:The aim of this study is to investigate the clinical and pathological features of vocal cord polyp. Method:Retrospective analyzed the clinical and pathological data of 1116 cases in vocal cord polyp patients treated with suspension microlaryngoscopic surgery. Result:The bradycardia was observed in 170 cases(15.2%) during the suspension of laryngoscope under general anesthesia. In this case，the suspension was stopped or the laryngoscope was taken out of mouth and atropine was administrated by intravenous injection. After that, heartbeat gradually accelerated and approached to normal,then the suspension was begun again to complete microlaryngoscopic surgery. Among the 1116 cases,1094(98%) were cured,22(2%) were improved，and no case was invalid. No pharyngeal injury was in 865 cases(77.5%). Mild,moderate and severe palatoglossal arch injury was observed in 139 (12.5%)cases，86(7.7%)cases,and 26 (2.3%) cases，respectively. The incidences of epithelial hyperplasia and dysplasia in vocal cord polyp were 35.3% and 5.0%, respectively. The prevalence rates of epithelial hyperplasia and dysplasia in male and female patients of vocal cord polyp were 76.2%,23.8% (P <0.01) and 78.6%,21.4% (P <0.01),respectively. And the prevalence rates of keratinization and parakeratosis in male and female patients were 93.1%,6.9% (P <0.01) and 93.1%,6.9% (P <0.01),respectively.The incidence of keratinization in patients of no epithelial hyperplasia, epithelial hyperplasia and epithelial dysplasia were 2.1%,18.2% and 30.3%,respectively，with significant difference in pairwise comparison.Conclusion:High incidence of vocal cord polyp is at the age from 31 to 60 years old.Although laryngomicrosurgery is an effective treatment for vocal cord polyp, pharyngeal injury and laryngopharyngeal vagal reflex should be noticed during the operation.In addition,vocal cord polyps in male patients are susceptible to epithelial dysplasia and keratinization.

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

We describe a comprehensive genomic characterization of adrenocortical carcinoma (ACC). Using this dataset, we expand the catalogue of known ACC driver genes to include PRKAR1A, RPL22, TERF2, CCNE1, and NF1. Genome wide DNA copy-number analysis revealed frequent occurrence of massive DNA loss followed by whole-genome doubling (WGD), which was associated with aggressive clinical course, suggesting WGD is a hallmark of disease progression. Corroborating this hypothesis were increased TERT expression, decreased telomere length, and activation of cell-cycle programs. Integrated subtype analysis identified three ACC subtypes with distinct clinical outcome and molecular alterations which could be captured by a 68-CpG probe DNA-methylation signature, proposing a strategy for clinical stratification of patients based on molecular markers.

CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer

Cancer is a heterogeneous disease with different combinations of genetic alterations driving its development in different individuals. We introduce CoMEt, an algorithm to identify combinations of alterations that exhibit a pattern of mutual exclusivity across individuals, often observed for alterations in the same pathway. CoMEt includes an exact statistical test for mutual exclusivity and techniques to perform simultaneous analysis of multiple sets of mutually exclusive and subtype-specific alterations. We demonstrate that CoMEt outperforms existing approaches on simulated and real data. We apply CoMEt to five different cancer types, identifying both known cancer genes and pathways, and novel putative cancer genes.