bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analytical validation of digital cytometry (iSort) for leukocyte enumeration using stored blood.
Authors: Newman Aaron M. , Nakao Aki , Li Kathy , Liu Chih-Long , Mathi Kavita , Sigal Natalia , Maecker Holden , Diehn Maximilian , Alizadeh Ash A. 
Published: May 2020

3542 Background: Blood leukocyte enumeration is a cornerstone for clinical diagnosis and immune monitoring of diverse cancers and immunotherapies. Existing methods rely on intact/living cells and can thus be limiting due to handling time constraints and need for predefined antibody panels. While indirect cytometry methods including digital cytometry can overcome this limitation on archival specimens, their clinical performance has not been extensively characterized. We developed iSort, a novel transcriptome deconvolution method based on CIBERSORTx. Here, we comprehensively evaluated iSort and validated it against established diagnostic standards. Methods: We recruited 36 healthy adult blood donors and characterized their blood leukocyte profiles. We used several established clinical cytometry methods requiring intact cells in a CLIA laboratory including Complete Blood Count [CBC] and 6-color TBNK [TBNK]. We also immunophenotyped leukocytes by a research flow cytometry panel (FACS) and by mass cytometry (CyTOF). We then used these techniques as standards for validating leukocyte populations enumerated by iSort. iSort was performed on whole blood through deconvolution of 22 subsets from RNA-Seq. We assessed iSort’s analytical detection performance by spiking purified lymphocyte subsets into lymphodepleted human blood and by simulating blood mixtures using defined leukocyte mixtures within latin square designs. We assessed iSort concordance with an FDA approved IVD assay (TBNK) comparing distinct RNA-Seq library preparation chemistries. Results: iSort was highly correlated with TBNK/CBC across CD4 T, CD8 T, B cells, NK cells, monocytes, and neutrophils (r≥0.95). When comparing correlations to TBNK/CBC, we found no significant differences between iSort, CyTOF, and FACS, nor between RNA-Seq library chemistries. iSort demonstrated high linearity at low abundance levels (0.1 - 1%, r = 0.99, B-cells spiked into lymphodepleted blood samples after Rituximab) and at higher abundance levels (0.5 - 90%, r > 0.99) across lymphoid and myeloid subsets. iSort also showed high reproducibility among triplicate blood tubes for each population (median CV = 11%). Conclusions: iSort digital cytometry achieves highly accurate and robust leukocyte enumeration for diverse hematopoietic subsets. Given its favorable performance against existing clinical standards that require intact/living cells, iSort is a promising approach for the development of immunotherapy biomarkers.
Identification of FGFR2/3 fusions from clinical cfDNA NGS using a de novo fusion caller.
Authors: Yablonovitch Arielle , Gnerre Sante , Kiedrowski Lesli Ann , Yen Jennifer , Liu Leo , Helman Elena , Fairclough Stephen R , Nagy Rebecca , Chudova Darya , Talasaz AmirAli 
Published: May 2020

3545 Background: FGFR2/ 3 rearrangements are promising therapeutic targets, especially in advanced urothelial cancer (aUC) with FDA-approved erdafitinib. Liquid biopsy is an attractive non-invasive method to identify these fusions, but detection in cfDNA is technically challenging due to low tumor shedding levels, short molecules, and wide variation in gene partners. To address this, we developed an assembly-based fusion detection algorithm to call rearrangements in a de novo fashion without reliance on a fixed partner set and applied it to > 15,000 clinical samples. Methods: A cohort of 15,218 patients with mixed cancer types (including 698 aUC patients, as well as breast, cholangiocarcinoma, colorectal, and gastric), plus 276 healthy control samples were previously tested with Guardant360(R), a clinical 74-gene cfDNA NGS-based assay. The median unique molecule coverage was approximately 3,000 molecules sequenced to 15,000x read depth. Samples were reanalyzed in silico using the novel algorithm: in brief, reads aligned to candidate fusion breakpoints were assembled into de Bruijn graphs. Resulting contigs were aligned to the reference and filters were applied to remove technical artifacts. Results: The majority of FGFR2 (86%) and FGFR3 fusion partners (73%) in the mixed cancer cohort were observed only once, consistent with previous reports (Helsten 2016). FGFR3-TACC3 was the most common fusion, occurring in 72% of FGFR3 fusion-positive patients. In 37% of FGFR2 fusion positive patients, the de novo caller detected partners not previously described. In the aUC cohort, FGFR3 fusions were detected in 3.3% of patients, with 8/10 (80%) partner genes/intergenic regions occurring only once, which is in line with previous reports (Nassar 2018). No fusions were identified in 276 healthy control samples. In the mixed cancer cohort, common mutations co-occurring with FGFR2 fusions were FGFR2 N549K, PIK3CA H1047R, and TP53 R175H (5.6% each); KRAS Q61H was observed in 28% of patients with FGFR3 fusions. Conclusions: FGFR2/ 3 fusion partners detected by a highly specific assembly-based de novo fusion caller were heterogeneous and individually rare, highlighting the importance of a de novo approach. We observed an FGFR3 fusion prevalence in cfDNA from aUC patients that is comparable to previous reports for tissue testing, demonstrating an ability to capture targetable genomic rearrangements with plasma-based NGS in this patient population.
High intratumoral tryptophan metabolism is a poor predictor of response to pembrolizumab (pembro) in metastatic melanoma (MM): Results from a prospective trial using baseline C11-labeled alpha-methyl tryptophan (C11-AMT) PET imaging for response prediction.
Authors: Oldan Jorge D. , Ollila David W. , Giglio Ben C. , Smith Eric , Bouchard Deeanna M. , Ivanovic Marija , Lee Yueh Z. , Collichio Frances A. , Meyers Michael O. , Wallack Diana E. , Khandani Amir H. , Abernathy-Leinwand Amber , Long Patricia K. , Ezzell Jennifer Ashley , Trembath Dimitri G. , Li Zibo , Wong Terence Z. , Moschos Stergios J. 
Published: May 2020

3556 Background: Molecular imaging of metabolic pathways critical for effector T cell response other than glucose could predict response to PD1 inhibitors. We have previously shown that high expression of tryptophan metabolic pathway enzymes in stage III/IV melanoma correlates with reduced abundance of tumor-infiltrating lymphocytes (TILs, ASCO 2019, e21014). Here we investigated C11-AMT, a PET tracer that images tryptophan metabolism, as a predictor of response to pembro in patients (pts) with PD1 inhibitor-naïve MM. Methods: In this trial (NCT03089606) pts must have had measurable MM by RECIST, have undergone IV contrast CT, FDG-PET, and C11-AMT PET scan (30-40 min dynamic imaging), plus a mandatory tumor biopsy prior to pembro treatment. Results: 21 pts (16 males; 15 stage IV; median age 61) had all 3 baseline scans and evaluable research biopsies. 13 pts were non-progressors (CR = 4, PR = 6, and SD = 3). At a median f/u of 13.7 mons (2.8-25.1+), 6 pts are dead from MM, 11 are alive without MM and 4 are alive with MM. 46 tumor lesions were assessed by all 3 scans. Of the pts with tumor lesion, C11-AMT PET SUVmax < 7 and skewness < +0.3 of the tumor lesion with the highest C11-AMT SUVmax was associated with non-progression by RECIST (SUVmax < 7/skewness < +0.3 in progressors vs. non-progressors; Fisher’s 2-tail test p= 0.055). The corresponding association between baseline FDG-PET (SUVmax < 14 and skewness < +0.3) with treatment response was insignificant ( p= 0.08). There was a weak (Spearman ρ= 0.33) but significant correlation ( p= 0.001) in SUVmax between FDG-PET and C11-AMT among the 46 tumors analyzed. There was no significant correlation between melanoma-specific expression of the tryptophan- (TPH1, TPH2, IDO1, TDO2, LAT1) and glucose-metabolizing enzymes (GLUT1, HK1, HK3) by immunohistochemistry. Response to pembro trends to associate with present TILs (Fisher’s p= 0.087). Conclusions: Baseline C11-AMT PET imaging using simple radiomics measures (highest metabolic activity, SUVmax, and tumor heterogeneity, skewness) may better predict clinical benefit from pembro in MM than FDG PET. Variability in C11-AMT’s SUVmax cannot be solely explained by FDG-PET’s SUVmax, suggesting that these two imaging modalities may provide complementary information about intratumoral metabolic dysregulation that may relate with pembro response. Texture analysis using LifeX v4.0 will be presented at the meeting. Clinical trial information: NCT03089606 .
Molecular profiling of metastatic breast cancer (MBC) and target-based therapeutic matching in an Asian tertiary phase I oncology unit.
Authors: Walsh Robert John , Ngoi Natalie , Ong Rebecca Jia Min , Ow Samuel Guan Wei , Wong Andrea , Eng Lim Siew , Lim Yi Wan , Heong Valerie , Sundar Raghav , Soo Ross A. , Yong Wei-Peng , Chee Cheng Ean , Goh Boon Cher , Lee Soo-Chin , Tan David Shao Peng , Lim Joline Si Jing 
Published: May 2020

3561 Background: Somatic profiling of MBC has highlighted actionable mutations and driven trials of matched targeted therapy (tx). Previous phase I studies have reported improved outcomes following matched therapies with tumour molecular profiles. Here, we review next generation sequencing (NGS) and treatment outcomes of Asian MBC patients (pts) in the phase I unit of a tertiary centre. Methods: Pts with MBC referred to a phase I unit underwent NGS (n = 152). Tumour tissue was sequenced via the amplicon based Ion Ampliseq Cancer (IAC) v2 (50 genes) platform from 2014-2017 prior to institutional change to Foundation Medicine 1 (FM1) (324 genes) 2017-2019. Patients were counselled on findings and enrolled onto matched therapeutic trials where available. Results: NGS was successfully performed in 107 pts (IAC 46%, FM1 54%) of which tumour subtypes include hormone receptor positive 63%, triple negative breast cancer (TNBC) 28% and Her2 positive 19%. Median lines of prior tx for MBC was 4 (range 0-12). 89% had prior chemotherapy (CT), 57% prior endocrine therapy (ET). 72/107 (67%) sequenced patients had further treatment and 18 (25%) were matched to tx based on NGS findings (15 clinical trial, 3 off trial). Matching rates on both NGS platforms were similar (IAC 22% vs FM1 28%). Mutated pathways with potential matched tx included PIK3CA/AKT/PTEN (52%), DNA damage response (DRR) (15%), and FGFR (11%) pathways. PIK3 mutations were seen in 43% and associated with higher number of metastatic sites (p = 0.03); most prevalent aberrations were PIK3CA H1047R (41%) and PIK3CA E542K (13%). Matched cases were more heavily pretreated (mean lines of prior tx 5.3 matched vs 3.7, unmatched p = 0.05), and showed a median progression free survival (mPFS) of 24 weeks [w] and clinical benefit rate (complete/partial response or stable disease ≥ 12 weeks) of 53% on matched tx. Comparison by NGS platform showed improved mPFS for matched vs unmatched pts sequenced on FM1 vs IAC (FM1: 26 vs 19w, HR = 0.76 [95% CI: 0.3-1.9]; IAC: 8 vs 12w; HR = 1.21 [95% CI: 0.5-2.8]). Interestingly, 1 pt with SMARCB mutation, reportedly associated with the FGFR pathway, had a PFS of 70w on tx with a pan-FGFR inhibitor after progressing on 3 prior lines of tx (ET and CT). Conclusions: Molecular profiling of MBC in a phase I unit led to matched tx in 25% of cases. Matched pts showed encouraging mPFS with a suggestion of benefit in those matched after sequencing on a broader gene panel (FM1).
Machine learning radiomics signature on magnetic resonance imaging associated with phenotypes and disease-free survival in patients with breast cancer (RBC-01): A registry-based, multicenter cohort study.
Authors: Yao Herui , Yu Yunfang , Tan Yujie , Hu Qiugen , Ouyang Jie , Chen Yongjian , Gu Yang , Li Anlin , He Zifan , Yang Yaping , Chen Kai , Ma Jiafan , Li Chenchen , Ma Mudi , Li Xiaohong , Zhong Haitao , Ou Qiyun , Wu Zhuo , Su Fengxi , Song Erwei 
Published: May 2020

3563 Background: The early stage breast cancer patients can vary in disease-free survival (DFS), innovative predictors evaluate the prognostic capacity are urgently needed. We aimed to develop and independently validate a radiomics signature based on MRI associated with phenotypes and DFS in patients with breast cancer and to establish a radiomics nomogram that incorporates the radiomics signature and clinicopathological findings using computational algorithms. Methods: In this multicenter, retrospective, cohort study, we analyzed preoperative contrast–enhanced MRI data from the prospective cohort study (n = 123) of patients who had been treated with neoadjuvant chemotherapy in phase 3 trials and independent cohort (n = 438) at the Sun Yat-sen Memorial Hospital as training cohort to develop the radiomic signature, and validated it in validation cohort (Foshan cohort, n = 121; Dongguan cohort, n = 89) between November 17, 2011, and September 21, 2019, and validated in TGCA cohort (n = 84). Machine-learning algorithm to identify robust imaging subtypes and evaluated their clinical and biologic relevance. A nomogram combining the radiomic signature and clinicopathological findings to predict individual survival based on Cox regression model. The primary endpoint was disease-free survival (DFS). This study is registered with ClinicalTrials.gov, number NCT04003558, and Chinese Clinical Trail Registry, number ChiCTR1900024020. Results: A total of 855 breast cancer patients were included. Radiomics signature was generated to classify patients into high-risk and low-risk groups in the Guangzhou training cohort. Patients with low-risk scores in the training cohort had higher DFS (hazard ratio [HR] 0.55, 95% CI 0.31 to 0.99; P= 0.045) than patients with high-risk scores, and validated in in validation cohort (HR 0.14, 95% CI 0.03 to 0.62; P= 0.003). The nomogram combined radiomics score with clinicopathological factors could accurately predict DFS benefits in training cohort (C-index = 0.83; AUC, 1, 2, 3-year were 0.80, 0.85, 0.82, respectively) and validated in validation cohorts. Conclusions: The radiomics signature are significantly associated with the DFS in patients with breast cancer. Combining the radiomics nomogram improved individualized DFS pretiction. Clinical trial information: NCT04003558 .
High-risk breast cancer genes at 8q22-24 and their role in over 5,000 patients evaluated with the 70-gene risk of recurrence assay.
Authors: Diab Sami , Socoteanu Matei P. , Encarnacion Carlos A. , Osborne Cynthia R. C. , Hendricks Carolyn B. , McIntyre Kristi , Thomas Vibha Taneja , Bhaskaran Rajith , Mittempergher Lorenza , Menicucci Andrea , Audeh William , O'Shaughnessy Joyce ,   FLEX Investigators' Group
Published: May 2020

3569 Background: Previous studies have shown that CCNE2 expression is higher in patients’ cancers resistant to CDK4/6 inhibitors. Increased expression of CCNE2, MTDH, or TSPYL5, genes contained within the 70-gene risk of distant recurrence signature (70GS), has also been implicated in breast oncogenesis, poor prognosis, and chemoresistance. These genes are located on chromosome region 8q22.1, one of the most recurrently amplified regions out of all 70GS genes in breast tumors (Fatima et al. 2017). MYC, located on 8q24, is overexpressed in 40% of all breast cancers (BC). Here we examined the expression of CCNE2, MTDH, and TSPYL5 in relation to 70GS risk and the 80-gene molecular subtype signature (80GS), and their correlation with MYC expression in early stage BC patients. Methods: CCNE2, MTDH, TSPYL5, and MYC mRNA expression was measured in 5022 BC samples sent to Agendia (Irvine, CA) for 70GS and 80GS testing, which included FFPE microarray full-transcriptome data. 70GS was used to stratify patients into Ultra Low Risk (UL), Low Risk (LR), High Risk (HR), and Ultra High Risk (UH). Both 70GS and 80GS were used to classify patient samples into Luminal A, Luminal B, HER2, or Basal type. Wilcoxon rank sum test was used to assess expression differences. Results: The expression of CCNE2, MTDH, and TSPYL5 significantly correlated with each other and was higher in HR patients compared to LR patients (p < 0.001) and higher in UH patients compared to HR patients (p < 0.001). Expression of these genes was highest in Basal type tumors, 83% of which were UH, followed by Luminal B type tumors, and lowest in Luminal A type tumors. CCNE2 and MYC expression was elevated in LR compared to UL patients (p < 0.001 and p = 0.0043). There was no difference in MYC expression between HR vs. LR or UH vs. HR. Lastly, there was no association between the expression of 8q22.1 genes and MYC in any 70GS subgroup. Conclusions: Within the 70GS, CCNE2, MTDH, and TSPYL5 have similar expression patterns and when overexpressed may identify an UH cohort of BC. This observation, in addition to their physical proximity at 8q22.1 suggests a possible amplicon in this region. The highest expression of CCNE2, MTDH, and TSPYL5 associated with UH patients and is concordant with previous studies that support the role of these genes in BC metastasis. Furthermore, this analysis suggests MYC may not stratify patients based on metastatic potential. These data may be clinically relevant for stratifying patients in ongoing clinical trials evaluating response and resistance to targeted therapies in early stage BC.
Comparison of recurrence patterns after surgery and radiation therapy with 68Ga-PSMA-11 PET/CT in nonmetastatic castrate-sensitive prostate cancer patients: A single-center post-hoc retrospective analysis in 787 patients.
Authors: Armstrong Wesley R , Thin Pan , Nguyen Kathleen , Alano Rejah M. , Booker Kiara M , Gartmann Jeannine , Lok Vincent , Lira Stephanie , Czernin Johannes , Kishan Amar Upadhyaya , Nickols Nicholas George , Calais Jeremie 
Published: May 2020

3577 Background: 20 to 50% of prostate cancer (PCa) patients undergoing radical prostatectomy (RP) or definitive radiation therapy (dRT) will experience disease recurrence. However, anatomical recurrence patterns may differ depending on the therapeutic approaches. The aim of this post-hoc retrospective analysis was to investigate if the relapse pattern as assessed by 68Ga-PSMA-11 PET/CT was different depending on the type of local pelvic therapy (RP, dRT, salvage RT (SRT), pelvic lymph node dissection (PLND), pelvic lymph node RT (PLNRT)) in patients with non-metastatic castrate sensitive (nmCS) recurrent disease after primary definitive therapy. Methods: Patients who underwent a 68Ga-PSMA-11 PET/CT for nmCS PCa recurrent disease after primary definitive therapy were screened from a database of 4 prospective studies (NCT02940262, NCT03515577, NCT04050215, NCT03582774). Patients who underwent primary staging (n = 95), without definitive therapy (n = 68), with known metastatic disease (M1) (n = 68) or with castrate resistant (CR) disease (n = 291) were excluded. We examined the relationship between recurrence patterns as assessed by 68Ga-PSMA-11 PET/CT (PROMISE criteria) and prior local treatments: i) RP, ii) dRT, iii) RP + SRT. Results: 787 patients were included in the analysis. Positive scan rates were 60%, 94% and 75% in RP, dRT and RP + SRT populations, respectively. Median pre-scan PSA levels were 0.50 (0.02-72.5) ng/ml, 4.4 (0.1-202) ng/ml, and 1.07 (0.04-33) ng/ml for patients who underwent RP (n = 464), dRT (n = 109) and post-RP SRT (n = 214). Median time to first recurrence was 27.7 after RP and 54.6 months after dRT (p = < 0.0001). Patients who underwent RP had lower local recurrence (LR) pattern (T+) rates by PSMA PET than those with dRT (99/464; 21% vs 69/109; 63%; p = < 0.0001). Nodal metastasis (N1) positivity rate was similar between RP and dRT (179/464; 39% vs 43/109; 39%; p = 0.87). Extrapelvic metastasis (M1) positivity rate was lower for RP than dRT (93/464; 20% vs 51/109; 47%; p = < 0.0001). Median time from post-RP SRT to second recurrence was 22.3 months. In patients who had a second recurrence after RP and SRT the positivity rate of LR (T+), N1 disease and M1 disease by PSMA PET/CT was 12% (24/214), 46% (99/214) and 44% (95/214). Conclusions: In this cohort of patients with nmCS PCa recurrent disease after primary definitive therapy, the patterns of failure differ based on prior local treatments.
Phase I study of the combination of alisertib (MLN8237) and gemcitabine in advanced solid tumors.
Authors: Huynh Jasmine , Chen Justin , Kim Edward Jae-Hoon , Gandara David R. , Semrad Thomas John , Riess Jonathan W. , Li Tianhong , Wu Chun-Yi , Zhang Chao , Yu Aiming , Matsukuma Karen , Kelly Karen 
Published: May 2020

3589 Background: Aurora Kinase A (AKA) is a key mitotic regulator overexpressed in multiple solid tumors. This open-label dose escalation and expansion phase I study evaluated the safety and tolerability of alisertib (MLN8237), an oral AKA inhibitor, in combination with gemcitabine. Methods: In dose escalation, patients (pts) > 18y with refractory solid tumors received 28-day cycles of gemcitabine on days 1, 8, 15 and alisertib twice daily on days 1-3, 8-10, and 15-17. Gemcitabine was given at 1000mg/m2. Four dose levels (DL) of alisertib (20-50mg) were given per 3+3 design to investigate dose limiting toxicities (DLT) in cycle 1, to determine maximum tolerated dose (MTD) and recommended phase II dose (RP2D). In dose expansion, advanced pancreatic adenocarcinoma pts received the MTD dose twice daily on a modified dosing schedule to allow for pharmacokinetic (PK) evaluation. Anti-tumor activity was assessed by response rate (RECIST 1.1) and progression-free survival (PFS). PK evaluation of plasma gemcitabine and alisertib was performed on all pts enrolled in the dose expansion. PK sampling was performed before treatment, immediately after gemcitabine infusion, and at other pre-specified post-infusion timepoints. Results: Twenty-six pts were treated in total: 21 pts in dose escalation and 5 pts in dose expansion. Overall, median age was 57y [42-82]; 50% male; 62% PS 1 (16 pts); 2 [0-7] median prior therapies. In the dose escalation phase, 9 tumor types were included and NSCLC was most common (7 pts). Maximum administered dose (DL4) achieved 900 mg alisertib per cycle and was tolerated (1 DLT in 6 pts). The dose expansion phase enrolled 5 pts with advanced pancreatic adenocarcinoma; median age 63y [48-82]; 60% male; 60% PS 1 (3 pts); 2 [1-2] median prior therapies. Grade ≥3 TRAEs were observed in 73% of all pts and were predominantly hematologic, including neutropenia (54%), leukopenia (50%), and lymphopenia (31%). Similar TRAEs were seen at DL4; all 14 pts experienced neutropenia with 64% experiencing grade ≥3 neutropenia. Fourteen of 23 evaluable pts (61%) had stable disease and 2 pts (9%) had partial response (PR) as best overall response. Median PFS was 2.9 months (95% CI 2.0-4.2). Analysis of PK data is ongoing and will be reported. Conclusions: Alisertib can be safely administered with gemcitabine. RP2D for alisertib is 50 mg PO BID in combination with full dose gemcitabine. Best response was at least stable disease in a majority of pts with PR observed in 9% of this heavily pretreated group of patients. Most grade ≥3 TRAEs were hematologic. Results of PK studies will also be reported. Clinical trial information: NCT01924260 .