tbuckley/cabot-search huggingface dataset:
Analytical validation of a 47-gene NGS panel for molecular profiling of myeloid neoplasms.
Authors: Sun Hee Rosenthal, Anna Gerasimova, Hai-Rong Li, Kevin Qu, Allan J Acab, Hansook K Chong, Xi Zhang, Quoclinh Nguyen, Alla Smolgovsky, David Wolfson, Andrew Grupe, Christopher Elzinga, Rebecca Chen, Renius Owen, Joseph J Catanese, Frederick KARL Racke, Felicitas L. Lacbawan
Journal: Journal of Clinical Oncology (2019)

e18526 Background: Molecular profiling can help diagnose, classify, and guide treatment of myeloid neoplasms. Next generation sequencing (NGS) is a powerful platform that can facilitate identification of actionable genetic alterations in multiple genes simultaneously. To serve clinical management needs, we developed and validated a NGS panel for 47 genes associated with diagnostic, prognostic, and/or therapeutic utilities for each of the subclasses of myeloid neoplasms: acute myeloid leukemia (AML, 42 genes), myelodysplastic syndrome (MDS, 36 genes), and myeloproliferative neoplasms (MPN, 26 genes). Methods: A total of 154 unique de-identified specimens were analyzed. Intra- and inter-assay precision studies were performed by standard laboratory practice. Single nucleotide variations (SNVs), insertions/deletions (indels), and FLT3 partial tandem duplications (PTD) were assessed for the entire coding regions of 23 genes and targeted exons of 24 genes. Target regions were captured by hybridization with complementary biotinylated DNA baits, and NGS was performed on an Illumina NextSeq500 instrument. Sequence reads obtained were analyzed using a bioinformatics pipeline that was developed in-house. At least 500 unique reads with base quality (Q) ≥20 (99% confidence) were required for coverage QC, except targets on X chromosome for male specimens, which required 250 unique reads. Results: On average, each sample generated 13.2 million reads, 100% (SD = 0.2%) mapped reads to the reference sequence, 61.7% (SD = 8.8%) on-target reads, and 1,952 (SD = 873) mean coverage. Data using ≥Q20 unique coverage of all target regions across all validation samples demonstrated that all target regions, even in the extreme end of GC spectrum (range: 12%-87%), met coverage requirements. Intra- and inter-assay precision studies, using 7 and 21 specimens, respectively, resulted in 100% concordance among replicates. An accuracy study of 131 unique specimens (a subset of the 154 specimens) yielded in 99.6% (755/758, 95% CI: 99.4%-100%) concordance for variants with allele frequencies ≥5% in comparison to other molecular methods including Sanger sequencing. No reportable variants were detected from any normal specimens (n = 17). Conclusions: We developed and validated a NGS panel for 47 genes with diagnostic, prognostic, and/or therapeutic utilities for each of the subclasses of myeloid neoplasms: AML (42 genes), MDS (36 genes), and MPN (26 genes). This panel will allow simultaneous analysis of the 47 genes with high sensitivity and specificity and may help manage clinical needs.
Right Atrial/Pulmonary Arterial Wedge Pressure Ratio in Primary and Mixed Constrictive Pericarditis
Authors: Jeong Hoon Yang, William R. Miranda, Barry A. Borlaug, Rick A. Nishimura, Hartzell V. Schaff, Kevin L. Greason, Joseph J. Maleszewski, Jae K. Oh
Journal: Journal of the American College of Cardiology (2019)
Life as a general practitioner
Authors: Jacqui Wise
Journal: BMJ (2019)

A GP is usually the first person a patient turns to for help and is a general expert in adult and paediatric medicine. One of the attractions of working as a GP is the variety—you never know who is going to walk through the door. Yes, there will undoubtedly be a lot of backaches and colds to deal with but a GP also needs to be able to spot red flag symptoms that might indicate a serious problem such as cancer.

A GP’s working week is divided up into sessions, each lasting half a day. A typical day will start at 8 am but could be earlier if the practice offers an early morning clinic. Appointments are usually 10 minutes long and the GP may see 18 to 20 patients during a morning surgery.

The time before and after the morning surgery may be spent dealing with paperwork such as going through correspondence, discharge summaries, out of hours reports, and test results. The GP may also need to make phone calls to patients or other healthcare professionals. After lunch the GP may need to visit patients at home or in care homes.

Afternoon surgery usually runs from 3 pm until 5.30 pm with another 15 to 20 patients seen. Some practices may also take last minute urgent cases after …
Abstract 5116: Benchmarking the HLA typing performance of three HLA assay and two software
Authors: Rui Meng, Tao Zhu, Yu Gong, Yanan Chen, Hua Dong, Ye Yizhou, Fugen Li, Ping Liu, Minya Yao
Journal: Cancer Research (2019)

Abstract Background:The adaptive immune response intrinsically depends on hyper variable human leukocyte antigen (HLA) genes. Correct HLA typing is crucial for successful donor-patient matching in organ transplantation and recently is also an emerging biomarker for immune checkpoint inhibitor. With the great progress on next generation sequencing (NGS) technology, sequencing accuracy and throughput have increased while the cost for data have decreased faster than Moore's Law, thus HLA tying by NGS has been widely used from laboratory to clinic. Method:We tested three NGS assay for HLA typing and two recently published HLA typing software from 24 samples. Three assays involve two target capture methods (WES and HLA target sequencing) and one amplification sequencing method. Two software involve Xhla and HLAHD, respectively. First, we compared 3 assay performance based on PE150 read length and xHLA software by both 4 alleles and 8 alleles. Second, we compared the performance of two widespread HLA typing software xHLA and HLA-HD according to different assay type, read depth, read length and speed. Results:First of all, for PE150 datasets on three assay, the accuracy rate of HLAHD is all 100%, while xhla in WES is 99%, amplicom 98.6%, target HLA sequencing 100%. On reads length evaluation, the accuracy of HLAHD decreases gradually from PE150 to PE100 and PE75, and the capture method is more sensitive to reads length than the amplification assay, while Xhla is very robust on read length. On coverage evaluation, when the amplicom sequencing data was down-sampled 500X to 10X, the accuracy of HLAHHD and XHLA is both 100% in 50X and above and decrease gradually when less than 50X. In terms of time, with the increase in sequencing depth, running time for both software increase. HLAHD prediction from fastq file is longer than that from bam file, especially when the panel data is relatively large, the time will increase exponentially. Conclusions:Our benchmarking dataset show that current HLA assay and computational methods for HLA typing generally provide satisfactory results, while different assay type matched with different software, read depth and read length do affect the performance. Citation Format: Rui Meng, Tao Zhu, Yu Gong, Yanan Chen, Hua Dong, Ye Yizhou, Fugen Li, Ping Liu, Minya Yao. Benchmarking the HLA typing performance of three HLA assay and two software [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5116.
Role of ethnicity in thrombotic and hemorrhagic complications of myeloproliferative neoplasms.
Authors: Andrew Peseski, Antoine Saliba, Hamid Sayar
Journal: Journal of Clinical Oncology (2019)

e18555 Background: Philadelphia-chromosome negative myeloproliferative neoplasms (MPN) are a group of hematologic malignancies with known complications of hemorrhage and thrombosis. Age and a previous history of thrombosis are well-documented risk factors for future vascular events. Variations in the rates of these complications among ethnicities and sexes have not been extensively explored. Methods: Our retrospective analysis included 301 adult patients with a diagnosis of MPN without a history of thrombosis or hemorrhagic event seen at the Indiana University Simon Cancer Center between 1992 and 2019. Relationships between ethno-racial backgrounds and vascular complications and disease outcomes were evaluated using multivariate logistic regression analysis and Cox regression models. Results: Two hundred seventy-one patients (90.0%) were Caucasian and 30 patients (10.0%) were non-Caucasian. Non-Caucasian patients were comprised of African America, Asian, and Middle Eastern ethnicities. Median age at diagnosis was 56 years, and 43.9% were male. No association was found between the incidence of thrombotic complications and ethnicity using the log-rank test ( p 0.68). The incidence of hemorrhagic events was significantly increased in non-Caucasian patients (OR = 4.33; 95% CI [1.15 – 16.36], p 0.03). Patients with higher hemoglobin concentration at diagnosis were at a significantly lower risk of bleeding complications (OR = 0.79; 95% CI [0.65 – 0.95], p 0.01). Non-Caucasian patients were at 2.98 times (95% CI [1.19 – 7.44], p 0.02) higher risk when vascular complications were pooled together. Our models also showed that male sex (OR = 0.14; 95% CI [.02 – .98], p 0.048) and a higher platelet count at the time of diagnosis (OR = 0.99; 95% CI [.993 –.999], p 0.03) had a marginally significant association with decreased rate of progression to acute myeloid leukemia. Conclusions: This study suggests that in patients without a history of thrombosis or bleeding, non-Caucasian ethnicity was associated with an increased adjusted risk of hemorrhagic complications in patients with MPN. This observation may inform future studies to further characterize those disparities in outcomes at the genetic or socioeconomic level.
Research of miR-30b in Cisplatin Resistance of Human NK/T Cell Lymphoma Lines SNK-6 and YTS Cells By Targeting CCL22
Authors: Rong Liang, Jian hong Wang, Fang Liu, Xiao hui Duan, Xia Cai Hao, Liang Zhang, Michael Wang, Xiang -xiang Liu, Yan Hua Guo, Zhe Wang, Hailong Tang, Ljie Yang
Journal: Blood (2018)
Abstract 399: ctDNA a promising predictive marker for treatment with PD-1 inhibitors in KRAS mutated NSCLC after platinum based chemotherapy
Authors: T.Jeroen.N. Hiltermann, Lucie B.M. Hijmering-Kappelle, Maria L. Aguirre Azpurua, Anthonie.J. vd Wekken, Birgitta.I. Hiddinga, Wim Timens, Harry.J.M. Groen, Ed Schuuring
Journal: Cancer Research (2019)

Abstract Introduction: Immunotherapy is a breakthrough in non-small cell lung cancer (NSCLC), showing long lasting responses in metastasized disease. However, only a limited number of patients responds to treatment. Selection of patients by known biomarkers (eg PD-L1, TMB) and combining PD-(L)1 inhibitors with other treatments (eg. chemotherapy or CTLA4 inhibitors) enriches the population for responders, however still around 60% do not respond with a durable response. We hypothesized that in KRAS mutant positive advanced NSCLC the detection of changes of ctDNA levels will be a relevant predictive marker in immunotherapy ( and stronger than eg PD-L1 expression in tumor tissue).. Purpose: To test ctDNA as an early predictive marker for durable response in KRAS mutated lung cancer, in patients treated with PD-1 inhibitors after progression on platinum containing chemotherapy. Methods: Patients with advanced NSCLC treated with nivolumab with a known KRAS or BRAF mutation from primary biopsy, with disease progression after platinum based chemotherapy are eligible. ctDNA obtained from EDTA plasma at baseline, 1, 2, 4, 6 weeks and thereafter every 12 weeks compared to durable response as primary outcome (ie. benefit from treatment&amp;gt; 6month). Secondary outcomes were tumor response according to RECISTv1.1, progression-free and overall survival. ctDNA was determined and analyzed using a digital droplet PCR assay (Biorad) that was confirmed by a second technique (Idylla). ctDNA was categorized according to its response pattern in time: increasing, decreasing and undetectable KRAS mutant allele frequencies over time. Results: In this ongoing study 31 patients with a known KRAS and 2 patients with a BRAF mutation participated. 24 (72%) had detectable levels of KRAS (n=22) or BRAF (n=2) in plasma. Concordance between Idylla and ddPCR was good and correlation was high (R2 =0,52). Of first 27 patients ctDNA increasing n=11, decreasing n=10, no change n=6. Data on all included patients will be presented. Conclusion: Early detection of decreasing KRAS/BRAF mutant alleles in ctDNA predicted durable tumor responses, and increasing levels were associated with early disease progression. Citation Format: T.Jeroen.N. Hiltermann, Lucie B.M. Hijmering-Kappelle, Maria L. Aguirre Azpurua, Anthonie.J. vd Wekken, Birgitta.I. Hiddinga, Wim Timens, Harry.J.M. Groen, Ed Schuuring. ctDNA a promising predictive marker for treatment with PD-1 inhibitors in KRAS mutated NSCLC after platinum based chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 399.
Abstract 17131: No Harmful Effects of a Selective SGLT2-Inhibitor in Contrast to Impairment of Cardiac Energy Metabolism by Phlorizin During Ischemia-Reperfusion Injury in Mice
Authors: Akira Yoshii, Tomohisa Nagoshi, Yusuke Kashiwagi, Haruka Kimura, Yoshiro Tanaka, Keiichi Ito, Takuya Yoshino, Toshikazu D Tanaka, Michihiro Yoshimura
Journal: Circulation (2017)

Although recent large clinical trials showed that selective SGLT2 inhibitors (SGLT2i) reduced cardiovascular events in diabetic patients, the direct effects of cardiac SGLT inhibition and its funct...
First-line therapy of T-cell lymphoma: Allogeneic or autologous transplantation for consolidation—Final results of the AATT study.
Authors: Norbert Shmitz, Lorenz Truemper, Marita Ziepert, Kamal Bouabdallah, Guillaume Cartron, Maike Nickelsen, Noel Jean Milpied, Christian Gisselbrecht, Gerald Wulf, Sébastien Maury, Emmanuel Gyan, Arnaud Jaccard, Laurence De Leval, Philippe Gaulard, Andreas Rosenwald, Birte Friedrichs, Peter Reimer, Martin Wilhelm, Bettina Altmann, Olivier Tournilhac
Journal: Journal of Clinical Oncology (2019)

7503 Background: In patients (pts) with peripheral T-cell lymphoma (PTCL) results of first-line therapy remain poor; guidelines recommend consolidation with autologous transplantation (autoSCT) in transplant-eligible pts. AATT (Autologous or Allogeneic Transplantation in T-cell lymphoma) sought to improve first-line therapy and compared alloSCT with autoSCT. Methods: This was a prospective randomized trial comparing autoSCT with alloSCT in younger pts (18-60 yrs) with newly diagnosed PTCL who had achieved CR, PR, or SD after 4 courses of CHOEP and 1 course of DHAP. Pts were to receive BEAM followed by autoSCT or myeloablative conditioning (fludarabine, busulfan, cyclophosphamide) followed by alloSCT from a matched related or unrelated donor. Primary endpoint was 3-year event-free survival (EFS). The study was stopped prematurely after a pre-planned interim analysis (JCO 33, 2015, suppl 8507a). Results: 103 pts randomized upfront to autoSCT (n=54) or alloSCT (n=49) formed the full analysis set. Median age was 50 years, 63% were male. 36 pts (35%) could not proceed to transplantation mostly due to early progression. Median observation time for EFS was 42 months. 3-year EFS and overall survival (OS) did not significantly differ between alloSCT and autoSCT (EFS: 43% (95% CI29-57%) vs. 38% (25-52%), p=0.58, OS: 57% (43-71%) vs. 70% (57-82%) (p=0.41). Comparing pts who actually received autoSCT (n=41) or alloSCT (n=26) EFS, PFS, and OS also showed no significant difference. No patient relapsed but eight pts (31%) died of treatment-related mortality (TRM) after alloSCT compared to 13 relapses (36%) but no TRM observed after autoSCT. Comparison of pts with aaIPI 2/3 vs. 0/1 showed significant differences for all endpoints. Conclusions: AlloSCT or autoSCT given to consolidate response in pts with PTCL showed no significant survival differences. While exerting a strong GvL-effect alloSCT resulted in substantial TRM. For younger pts with PTCL autoSCT remains the preferred consolidation, in particular, because pts. relapsing after autoSCT can be successfully salvaged with alloSCT. Clinical trial information: 2007-001052-39.
Abstract 15952: Mortality Reduction with Administration of Abciximab During Primary Percutaneous Coronary Intervention is Confined to ST-Segment Elevation Myocardial Infarction Patients with Complex Lesions
Authors: Allan Z Iversen, Soren Galatius, Sune Pedersen, Ulrik Abildgaard, Jan S Jensen
Journal: Circulation (2012)

Background: The optimal timing of administration of the glycoprotein IIb/IIIa inhibitor abciximab (up-stream or in-cath-lab) in patients with ST-segment elevation myocardial infarction (STEMI) unde...
K-Ras mutation in liquid biopsy and tumor tissue correlation in patients with pancreatic cancer
Authors: E. Perdomo Zaldivar, E. Inga, T. Cano, M. Gómez, M. Toledano Fonseca, G. Saavedra Garcia, B. Rodriguez Alonso, R. Rodriguez Alonso, A. Rodriguez Ariza, E. Aranda
Journal: Annals of Oncology (2019)
Abstract LB-076: Personal neoantigen immunotherapy in hepatocellular carcinoma
Authors: Sui Peng, Zhenwei Peng, Lixia Xu, Jie Mei, Longqing Tang, Yanyan Han, Ming Kuang
Journal: Cancer Research (2019)

Abstract Hepatocellular carcinoma (HCC) is one of the most common cancers and the leading causes of mortality in China with limited therapeutic options. To investigate whether neoantigens could induce tumor specific immune responses in patients with HCC, neoantigen stimulating cellular therapy (neo-MASCT) was applied after radical resection. Neo-MASCT was a cell-based immunotherapy with injections of mature dendritic cells (DCs) loaded with a peptide pool of multiple shared tumor associated antigens (TAAs) and several personalized neoantigens followed by autologous T cells stimulated by these DCs. To obtain neoantigens, fresh tumor samples were acquired immediately after biopsy or surgery for subsequently WES and RNAseq. All mutations including SNV, non-frame shift insert/deletion (Indel), and neoORF were detected by comparing NGS data from tumors to normal tissues. All neo-epitope candidates were predicted by our own proprietary algorithm MASNEO according to the patient’s HLA class I genotypes. Long neoantigen peptides containing 25-31 amino acids with higher affinities were selected for further synthesis and treatment. Peptides containing multiple neo-epitopes were preferred. Until now, eight patients had received neo-MASCT, and seven of them were tested for specific immune responses against both TAAs and neoantigens using IFNγ Elispot assay. The results showed that Neo-MASCT induced TAA-specific immune responses in five patients (5/7, 71%), and induced neoantigen-specific immune responses in six patients (6/7, 86%), respectively. One patient demonstrated specific T cell responses against all the five neoantigen peptides (5/5, 100%) after neo-MASCT treatment. The average responsive rate of neoantigens was 65% (22/34 peptides) in the six responding patients. In conclusion, our results demonstrate that neo-MASCT is well-tolerated in HCC patients and elicits immune responses against multiple tumor antigens, especially personalized neoantigens. We will continuously monitor the immune responses against neoantigens, and use the results to train and optimize our predicting algorithm. We will also evaluate the clinical benefit of neo-MASCT in further clinical trials with more patients. Citation Format: Sui Peng, Zhenwei Peng, Lixia Xu, Jie Mei, Longqing Tang, Yanyan Han, Ming Kuang. Personal neoantigen immunotherapy in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-076.
Abstract 1740: Characterization of CDK9 role in the DNA damage response
Authors: Thales C. Nepomuceno, Guilherme Suarez-Kurtz, Alvaro N. Monteiro, Marcelo A. Carvalho
Journal: Cancer Research (2019)

Abstract Introduction: The DNA damage response (DDR) is a well-coordinated pathway capable of sensing and repairing different types of DNA damage. Double-strand break (DSB) lesions activate the ATM-CHK2 axis, which is responsible for the cell cycle arrest, prompting cells for DNA repair. DSBs are primarily repaired through two distinct pathways: homology-directed recombination (HR) and non-homologous end-joining (NHEJ). BRCA1 and 53BP1 play an important role in DDR by orchestrating the decision between HR and NHEJ, but the precise mechanisms regarding both pathways are not entirely understood. Previously, our group identified the putative interaction of the cyclin-dependent kinase 9 (CDK9) with BRCA1 and BARD1 (BRCA1-associated RING domain 1). CDK9 is a component of the positive transcription elongation complex and has been implicated in genome integrity maintenance associated with the replication stress response. More recently, we characterized CDK9 as a DDR player by modulating BRCA1 recruitment to DNA damaged sites and consequently the HR pathway. We also showed that cells lacking CDK9 failure to form RAD51, but not 53BP1, ionizing radiation-induced foci (IRIF) and are characterized by an increased sensitivity to DSBs Methods and Results: Here we show that the CDK9-BRCA1 interaction occurs through BRCA1 N-terminal region in a BRCA1-BARD1 heterodimer formation-dependent manner. We also identified a CDK9 mutant (E369A) that abrogates the CDK9-BRCA1 interaction (through BRCA1 C-terminal region). Moreover, we characterized CHK2 as a novel CDK9-interaction partner, through ectopic GST-pulldown and constitutive co-immunoprecipitation assays. Further, cells lacking CDK9 are deficient in promoting G2/M arrest after IR-induced DNA damage. We also identified new CDK9 interactions in a DDR-related context using a TAP-MS approach. Conclusion: Collectively, our data suggest a role for CDK9 in the DDR through DNA damage repair and cell cycle checkpoint regulation Citation Format: Thales C. Nepomuceno, Guilherme Suarez-Kurtz, Alvaro N. Monteiro, Marcelo A. Carvalho. Characterization of CDK9 role in the DNA damage response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1740.
Studies Evaluating Statin Adherence and Outcome Should Adjust for Smoking Persistence and Antiplatelet Treatment Discontinuation—Reply
Authors: Fatima Rodriguez, David J. Maron, Paul A. Heidenreich
Journal: JAMA Cardiology (2019)

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