Citations

Abstract CCGA [NCT02889978] is the largest study of cfDNA-based early cancer detection; the first CCGA learnings from multiple cfDNA assays are reported here. This prospective, multi-center, observational study has enrolled 10,012 of 15,000 demographically-balanced participants at 141 sites. Blood was collected from participants with newly diagnosed therapy-naive cancer (C, case) and participants without a diagnosis of cancer (noncancer [NC], control) as defined at enrollment. This preplanned substudy included 878 cases, 580 controls, and 169 assay controls (n=1627) across 20 tumor types and all clinical stages. All samples were analyzed by: 1) Paired cfDNA and white blood cell (WBC)-targeted sequencing (60,000X, 507 gene panel); a joint caller removed WBC-derived somatic variants and residual technical noise; 2) Paired cfDNA and WBC whole-genome sequencing (WGS; 35X); a novel machine learning algorithm generated cancer-related signal scores; joint analysis identified shared events; and 3) cfDNA whole-genome bisulfite sequencing (WGBS; 34X); normalized scores were generated using abnormally methylated fragments. In the targeted assay, non-tumor WBC-matched cfDNA somatic variants (SNVs/indels) accounted for 76% of all variants in NC and 65% in C. Consistent with somatic mosaicism (i.e., clonal hematopoiesis), WBC-matched variants increased with age; several were non-canonical loss-of-function mutations not previously reported. After WBC variant removal, canonical driver somatic variants were highly specific to C (e.g., in EGFR and PIK3CA, 0 NC had variants vs 11 and 30, respectively, of C). Similarly, of 8 NC with somatic copy number alterations (SCNAs) detected with WGS, 4 were derived from WBCs. WGBS data revealed informative hyper- and hypo-fragment level CpGs (1:2 ratio); a subset was used to calculate methylation scores. A consistent “cancer-like” signal was observed in <1% of NC participants across all assays (representing potential undiagnosed cancers). An increasing trend was observed in NC vs stages I-III vs stage IV (nonsyn. SNVs/indels per Mb [Mean±SD] NC: 1.01±0.86, stages I-III: 2.43±3.98; stage IV: 6.45±6.79; WGS score NC: 0.00±0.08, I-III: 0.27±0.98; IV: 1.95± 2.33; methylation score NC: 0±0.50; I-III: 1.02±1.77; IV: 3.94±1.70). These data demonstrate the feasibility of achieving >99% specificity for invasive cancer, and support the promise of cfDNA assay for early cancer detection. Additional data will be presented on detected plasma:tissue variant concordance and on multi-assay modeling. Citation Format: Alexander A. Aravanis, Geoffrey R. Oxnard, Tara Maddala, Earl Hubbell, Oliver Venn, Arash Jamshidi, Ling Shen, Hamed Amini, John A. Beausang, Craig Betts, Daniel Civello, Konstantin Davydov, Saniya Fazullina, Darya Filippova, Sante Gnerre, Samuel Gross, Chenlu Hou, Roger Jiang, Byoungsok Jung, Kathryn Kurtzman, Collin Melton, Shivani Nautiyal, Jonathan Newman, Joshua Newman, Cosmos Nicolaou, Richard Rava, Onur Sakarya, Ravi Vijaya Satya, Seyedmehdi Shojaee, Kristan Steffen, Anton Valouev, Hui Xu, Jeanne Yue, Nan Zhang, Jose Baselga, Rosanna Lapham, Daron G. Davis, David Smith, Donald Richards, Michael V. Seiden, Charles Swanton, Timothy J. Yeatman, Robert Tibshirani, Christina Curtis, Sylvia K. Plevritis, Richard Williams, Eric Klein, Anne-Renee Hartman, Minetta C. Liu. Development of plasma cell-free DNA (cfDNA) assays for early cancer detection: first insights from the Circulating Cell-Free Genome Atlas Study (CCGA) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-343.

Abstract Background Regular use of aspirin and other non-steroidal anti-inflammatory drugs (NSAIDs) is associated with lower risk of colorectal cancer (CRC). Genome-wide interaction analysis (GxE) has identified a few variants that may modify the effects of NSAIDs on CRC risk. However, limited statistical power remains a concern. Restricting analyses by using functional genomic information to aggregate variants into biologically relevant sets can reduce the number of tests, thereby increasing statistical power. We tested the interactions between variant models of gene expression and NSAIDs use on CRC risk. Methods Functional weights of each variant were estimated using PrediXcan based on jointly measured transcriptomes and genomes data of transverse colon tissues from the Genotype-Tissue Expression (GTEx) Project for all genes with sufficient heritability (≥1%). A mixed-effects model was used to assess the GxE effects in a gene among 9,917 incident CRC cases and 10,533 controls from 17 (nested) case-control studies from the Colon Cancer Family Registry (CCFR) and Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). GxE analysis was done by modeling the interaction between predicted gene expression and NSAID use (fixed effects), and residual variant-specific GxE effects that are not accounted for (random effects). Regular user of aspirin and/or non-aspirin NSAIDs was compared to non-regular users. False discovery rate (FDR) was used to account for multiple comparison and FDR≤0.2 was considered genome-wide significant. Secondary analysis was performed on significant genes and duration of use among users. Results Regular use of aspirin was higher among controls (30.3%) compared to cases (24.3%). Among the 4,842 genes tested, SORD significantly modified the effect of regular use of aspirin on CRC risk (p-interaction = 1.45×10-5; FDR=0.07). The SORD gene encodes sorbitol dehydrogenase (SORD), which oxidizes sorbitol to fructose in the polyol pathway. Decreased SORD concentrations were previously observed to dramatically increase in colorectal adenoma cells when compared to normal mucosa cells, suggesting the involvement of dysregulated polyol metabolisms in colorectal tumorigenesis. However, the duration of aspirin use was not statistically significantly associated with SORD gene expression on CRC risk (p=0.149) among 5,560 aspirin users. No significant interactions were observed between genetically determined colon gene expression levels and any NSAID use or non-aspirin NSAID use at FDR<0.2. Conclusions Incorporating functional information, we discovered a novel gene that may interact with aspirin use to confer CRC risk. These findings provide preliminary support for new biological insights that could help understand the chemopreventive mechanisms of aspirin on CRC. We aim to replicate these findings in additional studies. Citation Format: Xiaoliang Wang, Yu-Ru Su, Andrew T. Chan, Stephanie Bien, Sonja I. Bernt, Hermann Brenner, Graham Casey, Jenny Chang-Claude, Steven J. Gallinger, Robert W. Haile, Tabitha A. Harrison, Michael Hoffmeister, Mark A. Jenkins, Amit Joshi, Yi Lin, Noralane M. Lindor, Loic Le Marchand, Hongmei Nan, Polly A. Newcomb, John D. Potter, Martha L. Slattery, Steve N. Thibodeau, Emily White, Li Hsu, Ulrike Peters. Functionally informed genome-wide interaction analysis of nonsteroidal anti-inflammatory drugs on colorectal cancer risk [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 2965.

Purpose To determine the feasibility of shear wave elastography (SWE) with B‐mode ultrasound in predicting the stiffness of the rotator cuff muscle before arthroscopic rotator cuff repair to evaluate the difficulty of the surgical procedure, as well as to compare SWE with the Goutallier stage on magnetic resonance imaging (MRI). Methods Thirty‐eight patients with a full‐thickness supraspinatus tear requiring arthroscopic rotator cuff repair participated. The Goutallier stage of fatty infiltration on MRI was measured before surgery, as was the SWE modulus of the anterior superficial, anterior deep, posterior superficial, and posterior deep (PD) regions of the supraspinatus muscle. To measure the stiffness of the supraspinatus musculotendinous unit during surgery, the supraspinatus tendon was axially stretched until the anatomic insertion site was reached, and force per deformation was recorded. The correlation between stiffness of the supraspinatus and SWE value in each region of the supraspinatus muscle or Goutallier stage was determined. In addition, patients were divided into 2 groups: (1) In the complete footprint coverage group, greater than 50% of the footprint was covered during the stiffness measurement, and (2) in the incomplete footprint coverage group, less than 50% of the footprint was covered during the stiffness measurement. Differences in SWE value and Goutallier stage were measured between the 2 groups. Results The best correlation of stiffness with the SWE modulus of the PD muscle of the supraspinatus was R = 0.69, and the correlation of stiffness with the Goutallier stage on MRI was R = 0.48. The SWE value of the PD region was greater in the incomplete footprint coverage group than in the complete footprint coverage group, although the Goutallier stage was not significantly different. Conclusions The highest correlation with stiffness of the supraspinatus musculotendinous unit was with the SWE modulus of the PD muscle, as compared with SWE evaluation of the other regions or the Goutallier stage on MRI. Ultrasound SWE can predict the stiffness of the supraspinatus musculotendinous unit best. Clinical Relevance Rotator cuff retraction adds difficulty to arthroscopic rotator cuff repair. Ultrasound SWE may be used for presurgical planning.

LBA8501 Background: Plasma cfDNA genomic analysis is used widely for the care of advanced lung cancer, but its suitability for early stage lung cancer detection is not well established. CCGA (NCT02889978) is a prospective, multi-center, observational study launched for the development of a noninvasive assay for cancer detection. Methods: Blood was prospectively collected (N = 1627) from 749 controls (no cancer diagnosis) and 878 participants (pts) with newly-diagnosed untreated cancer in this preplanned substudy, including 127 pts with lung cancer. Three prototype sequencing assays were performed: paired cfDNA and white blood cell (WBC) targeted sequencing (507 genes, 60,000X) for single nucleotide variants/indels; paired cfDNA and WBC whole genome sequencing (WGS) for copy number variation (30X); and cfDNA whole genome bisulfite sequencing (WGBS) for methylation (30X). For each assay, a classification model using 10-fold cross-validation was developed for all pts with cancer, then evaluated in the pts with lung cancer; sensitivity was estimated at 95% specificity. Results: We evaluated pts with lung cancer (127) and a subset of controls (580) with similar ages (mean±SD yrs: 67±9, 60±13), 85% and 43% were ever-smokers, and 46% and 22% were men, respectively. Of 3055 nonsynonymous mutations detected across 122 evaluable pts with lung cancer, > 50% were detected in WBC consistent with clonal hematopoiesis (CH). Accounting for CH, sensitivity in 63 stage I-IIIA pts evaluable across all 3 assays was 48% (35-61, targeted), 54% (41-67, WGS), and 56% (43-68, WGBS); in 54 stage IIIB-IV pts it was 85% (73-93, targeted), 91% (80-97, WGS), and 93% (82-98, WGBS) . Similar sensitivities were observed across histological subtypes (adenocarcinoma, squamous cell, small cell). Comparison to tumor WGS and multi-assay classification will be reported. Conclusions: Early stage lung cancers are detectable in cfDNA using a genome-wide sequencing approach. For lung cancer detection using targeted assays, CH must be accounted for to minimize false positives. Assay optimization is ongoing to allow further clinical development in the intended use population. Clinical trial information: NCT02889978.

Background The purpose of this study is to assess the incidence of acromial stress fractures in a population of reverse shoulder arthroplasties (RSA) and determine potential risk factors for fracture. Patients and Methods Between August 2004 and December 2013, 1082 primary RSA were performed at a single institution. Twelve (1.11%) patients were diagnosed with a postoperative acromial stress fracture. This group was case-matched to a control group of 48 shoulders. Clinical and radiographic risk factors for fracture were assessed. Results Compared to controls, fractures were less satisfied with their outcome despite equivalent American Shoulder and Elbow Surgeons scores, pain scores, and range of motion. Osteoporosis was significantly associated with acromial fractures ( P = .027). A smaller lateral offset of the greater tuberosity, greater arm lengthening, and a thinner acromion were more common in the fracture group ( P = .026, P = .004, and P = .008, respectively). Conclusions In summary, postoperative acromial stress fractures appear to be incidental lesions with little influence on the outcome after RSA. The combination of a thin acromion and superior migration of the humeral head increase the risk of acromial fracture. Lateralized designs that do not excessively verticalize the deltoid line of pull on the acromion may decrease the risk of postoperative acromial fractures.

Background: Flexor tendon injury is common, and tendon reconstruction is indicated clinically if the primary repair fails or cannot be performed immediately after tendon injury. The purpose of the current study was to compare clinically standard extrasynovial autologous graft (EAG) tendon and intrasynovial allogeneic graft (IAG) that had both undergone biolubricant surface modification in a canine in vivo model. Methods: Twenty-four flexor digitorum profundus (FDP) tendons from the second and fifth digits of 12 dogs were used for this study. In the first phase, a model of failed FDP tendon repair was created. After 6 weeks, the ruptured FDP tendons with a scarred digit were reconstructed with the use of either EAG or IAG tendons treated with carbodiimide-derivatized hyaluronic acid and lubricin. At 12 weeks after tendon reconstruction, the digits were harvested for functional, biomechanical, and histologic evaluations. Results: The tendon failure model was a clinically relevant and reproducible model for tendon reconstruction. The IAG group demonstrated improved digit function with decreased adhesion formation, lower digit work of flexion, and improved graft gliding ability compared with the EAG group. However, the IAG group had decreased healing at the distal tendon-bone junction. Our histologic findings verified the biomechanical evaluations and, further, showed that cellular repopulation of allograft at 12 weeks after reconstruction is still challenging. Conclusions: FDP tendon reconstruction using IAG with surface modification has some beneficial effects for reducing adhesions but demonstrated inferior healing at the distal tendon-bone junction compared with EAG. These mixed results indicate that vitalization and turnover acceleration are crucial to reducing failure of reconstruction with allograft. Clinical Relevance: Flexor tendon reconstruction is a common surgical procedure. However, postoperative adhesion formation may lead to unsatisfactory clinical outcomes. In this study, we developed a potential flexor tendon allograft using chemical and tissue-engineering approaches. This technology could improve function following tendon reconstruction.

Abstract BACKGROUND Clinical trials NRG/NSABP B-31 and Alliance/NCCTG N9831 demonstrated that trastuzumab added to chemotherapy extended disease-free survival (DFS) in breast cancer patients (pts) in the adjuvant setting (Romond et al). However, the degree of trastuzumab benefit varies among pts. We previously described an 8-gene model that was predictive for trastuzumab benefit, which was validated in an independent cohort of B-31 patients (Pogue-Geile 2013). The 8-gene signature subtyped B-31 pts in an independent validation cohort into three trastuzumab benefit groups: one with large benefit HR=0.27, one with medium benefit HR=0.56, and one with little to no benefit HR=1.56. The purpose of this study was to validate the 8-gene model in pts enrolled into N9831, which tested the efficacy of adding trastuzumab to doxorubicin plus cyclophosphamide → paclitaxel by randomizing pts into one of three arms: chemotherapy only (Arm A), trastuzumab given after chemotherapy (Arm B), or trastuzumab given concurrently with chemotherapy (Arm C). METHODS NCounter data, consisting of 8 predictive genes and 4 house-keeping genes, for 1,379 patients enrolled into N9831 were used to assign each patient to one of the three benefit groups. Assignments to one of the three trastuzumab benefit groups based on the 8-gene model were made by the NSABP/NRG Pathology Laboratory Biostatistician, who was blinded to outcome data. Predictions were sent to N9831 investigators and accuracy of predictions were tested in pts enrolled into arms A and C (N=892) using Cox models adjusted for age, nodes, ER/PR status, tumor size, and grade. Recurrence-free survival (RFS) and DFS were used as endpoints. RESULTS Tumors from N9831were placed into one of the three trastuzumab benefit groups based on the 8-gene signature. The N9831 pts in the predicted-large benefit group had a hazard ratio (HR) of 0.47, P=0.0006, pts in the predicted-medium benefit group had an HR of 0.6, P=0.02, and the predicted-low benefit group had an HR of 1.54, P=0.375. The interaction P value was significant at 0.019 in adjusted Cox models. The RFS at 10 years for trastuzumab-treated pts was 72%, 83%, and 83% in the low, medium, and large benefit groups, respectively. CONCLUSIONS The 8-gene signature developed in a discovery cohort and validated in an independent cohort of B-31 pts has now been validated in N9831. Many anti-HER2 therapies such as lapatinib, afatinib, neratinib, pertuzumab, and TDM-1 have been approved for treatment in metastatic breast cancer pts and although these agents have shown responses, the actual improvements in outcomes in pts is variable and it is not known which pts actually receive benefit. Thus this signature may be clinically useful in identifying pts who may benefit from additional treatment beyond trastuzumab or for stratification of pts enrolled into clinical trials testing new anti-HER2 therapies. SUPPORT U10CA180868, -180822, UG1CA189867, U24CA196067, the PA DOH, which disclaims certain responsibilities, Genentech, Inc., and the Breast Cancer Research Foundation. Citation Format: Pogue-Geile KL, Song N, Serie DJ, Thompson EA. The NSABP/NRG 8-gene signature accurately predicts degree of benefit from trastuzumab in Alliance/NCCTG N9831: Validation of the 8-gene signature in an independent clinical trial [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD3-18.