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Background: Emergence of vaccine-escaping SARS-CoV-2 variants is a serious problem for global public health. The currently rampant Omicron has been shown to possess remarkable vaccine escape; however, the selection pressure exerted by vaccines might pave the way for other escape mutants in the near future. Materials & methods: For detection of neutralizing antibodies, the authors used the recently developed HiBiT-based virus-like particle neutralization test system. Sera after vaccination (two doses of Pfizer/BioNTech mRNA vaccine) were used to evaluate the neutralizing activity against various strains of SARS-CoV-2. Results: Beta+R346K, which was identified in the Philippines in August 2021, exhibited the highest vaccine resistance among the tested mutants. Surprisingly, Mu+K417N mutant exhibited almost no decrease in neutralization. Imdevimab retained efficacy against these strains. Conclusions: Mutations outside the receptor-binding domain contributed to vaccine escape. Both genomic surveillance and phenotypic analysis synergistically accelerate identifications of vaccine-escaping strains.

Tokyo Olympic and Paralympic Games, postponed for COVID-19 pandemic, were finally held in summer of 2021. Just before the games, alpha variant was being replaced with more contagious delta variant (B.1.617.2). AY.4 substrain AY.29, which harbors two additional characteristic mutations of 5239C>T (NSP3 Y840Y) and 5514T>C (NSP3 V932A), emerged in Japan and became the dominant strain in Tokyo by the time of the Olympic Games. As of October 18, 98 AY.29 samples are identified in 16 countries outside of Japan. Phylogenetic analysis and ancestral searches identified 46 distinct introductions of AY.29 strains into those 16 countries. United States has 44 samples with 10 distinct introductions, and United Kingdom has 13 distinct AY.29 strains introduced in 16 samples. Other countries or regions with multiple introductions of AY.29 are Canada, Germany, South Korea, and Hong Kong while Italy, France, Spain, Sweden, Belgium, Peru, Australia, New Zealand, and Indonesia have only one distinct strain introduced. There exists no unambiguous evidence that Olympic and Paralympic Games induced cross-border transmission of the delta substrain AY.29. Since most of unvaccinated countries are also under sampled for genome analysis with longer lead time for data sharing, it will take longer to capture the whole picture of cross-border transmissions of AY.29.

BACKGROUND: In metastatic breast cancer, Overall Response Rate (ORR) for checkpoint inhibitor monotherapy has been limited. Since Radiation Therapy (RT) stimulates anti-cancer immune responses, we evaluated safety and efficacy of a combinatorial therapy of RT with Nivolumab (a Programmed cell death protein 1 (PD-1) inhibitor) on HER2-negative metastatic breast cancer patients in a multicenter and non-randomized phase Ib/II study. PATIENTS AND METHODS: Patients with HER2-negative breast cancer, measurable metastasis (RECIST1.1) and at least one bone metastasis requiring radiation therapy were enrolled. The patients were divided into two cohorts, A and B. Cohort A constitutes estrogen and/or progesterone receptor-positive breast cancer patients that had 1 or 2 lines of endocrine therapy for the metastatic disease. Cohort B constitutes triple negative breast cancer patients that had two or more lines of chemotherapy for metastatic disease and anthracycline and taxane treatment for any disease setting. Single fraction RT of 8 Gy was delivered on day 0. Patients received 3 mg/kg Nivolumab intravenously every 2 weeks from day 1 until the disease progressed. Combined use of endocrine therapy of the physician’s choice was allowed in Cohort A. Primary endpoints were safety and ORR (RECIST1.1) in phase Ib and phase II, respectively. Secondary endpoints were Duration of Response (DOR), Disease Control Rate (DCR) and Progression-Free Survival (PFS). For translational research, we integrated time series multi-omics data that are correlated with Tumor Immune Microenvironment (TIME) to identify novel drug sensitivity-associated signatures using machine learning method. The multi-omics data included data from RNAseq, DNAseq, mass cytometry (CyTOF), multiple cytokines, human leukocyte antigen, radiomics, drug concentrations, tuberculin reaction using Peripheral Blood Mononuclear Cells (PBMCs), serum, plasma, imaging and Formalin-Fixed Paraffin-Embedded (FFPE) samples. RESULTS: 31 patients were enrolled from Jan 2017 to Nov 2018 and 29 patients (18 in Cohort A and 11 in Cohort B) were included in the full analysis set. While seven patients in Cohort A had received 1 or 2 lines of chemotherapy earlier for the metastatic disease, eight patients in Cohort B received three or more lines of chemotherapy. Dose limiting toxicities were not observed in phase Ib. In Cohort A, the ORR was 11.1% (90% with a Confidence Interval (CI) of 3.7-28.6). The best overall responses were: Partial Response (PR) in 2 patients (11.1%), Stable Disease (SD) in 11 patients (61.1%) and Progressive Disease (PD) in 5 patients (27.8%). In Cohort B, ORR was 0% as none of the patients responded to the treatment. The best overall responses were: SD in 4 patients (36.4%), PD in 6 patients (54.5%) and one patient (9.1%) was not evaluated (NE). While the DCR for Cohorts A and B were 72.2% (90% CI: 52.9-85.8) and 36.4% (90% CI: 17.5-60.6), respectively, the median PFS were 4 months (95% CI: 2.1-5.5 months) and 2 months (95% CI: 1.2-4.0 months), respectively. Common toxicities were mild; including 3 patients in Cohort A (16.7%) and 2 patients in Cohort B (18.2%) that experienced grade 3 or 4 toxicity. There were no deaths due to adverse effects. Furthermore, our integrated analysis identified novel candidates for drug sensitivity-associated signatures. CONCLUSIONS: The combination of RT and Nivolumab had a manageable safety profile and demonstrated clinically significant disease control outside the RT fields. Periodic abscopal response data and multi-omics data are also presented. (UMIN: UMIN000026046; ClinicalTrials.gov: NCT03430479). Citation Format: Masahiro Takada, Michio Yoshimura, Kosuke Kawaguchi, Takeshi Kotake, Ryuji Uozumi, Masako Kataoka, Takahiko Koyama, Hironori Kato, Hiroshi Yoshibayashi, Hirofumi Suwa, Wakako Tsuji, Hiroyasu Yamashiro, Tatsuki Kataoka, Hiroshi Ishiguro, Reitaro Tokumasu, Maya Honda, Rikiya Yamashita, Atsushi Yonezawa, Yuki Himoto, Natsuko Onishi, Laxmi Parida, Satoshi Morita, Masakazu Toi. A multicenter phase Ib/II study for evaluating safety and efficacy of Nivolumab in combination with radiation therapy in patients with HER2-negative metastatic breast cancer (KBCRN-B-002 trial) [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 P3-09-07.

BACKGROUND: Advances in imuuno-oncology (IO), i.e., a programmed cell death protein 1 (PD-1) inhibitors are revolutionizing cancer treatment by offering hope for a cure. However, the benefit of IO agents in metastatic breast cancer (MBC) is still limited. For immunotherapy to be successful, it is essential to understand the tumor immune contexture. Tumor immune microenvironment (TIME) alterations, such as increased effector-cell composition, inflamed immune cells, and the activated effector immune cells create conditions that enhance immunotherapy in MBC. The abscopal effect induced by Radiation therapy (RT) is known as a modulator of TIME. Then, abscopal effect is considered to be a systemic anti-tumor immune response. In this study, we integrated time series multi-omics data to identify alteration of the TIME signatures with RT combined with N\nivolumab, a PD-1 inhibitor, using a machine learning method. PATIENTS AND METHODS: This study was conducted as a translational research of the KBCRN-B-002 trial, which is a multicenter phase Ib/II study for evaluating the safety and efficacy of nivolumab in combination with RT in patients with HER2-negative MBC (Takada M et al. will make presentation the main results of the study. (UMIN: UMIN000026046; ClinicalTrials.gov: NCT03430479)). Twenty-nine patients were included in the translational analysis set. The multi-omics data included data from RNAseq, DNAseq, mass cytometry (CyTOF), multiple cytokines, human leukocyte antigen, radiomics, drug concentrations, tuberculin reaction using peripheral blood mononuclear cells (PBMCs), serum, plasma, imaging, and Formalin-Fixed Paraffin-Embedded (FFPE) samples. We collected time series data, which included data for the baseline, two weeks after starting therapy, four weeks after starting therapy, and the timing of progressive disease. For the integrated analysis, a unique machine learning method was developed. RESULTS: Our integrated analysis identified the alteration of the tumor immune microenvironment signatures using nivolumab combined with RT for MBC. These results included the signature of the immune cell composition, effector immune cells, and immune suppressor cells, via single-cell analysis using CyTOF. The types of analysis are given in the table. CONCLUSIONS: We identified candidates for TIME signatures for actionable hallmarks of RT combined with IO agent by our machine learning method. Type of AnalysisSampleTime PointBaseline2 Weeks4 WeeksProgressive DiseaseRNAseqFFPE✓RNAseqPBMCs✓✓✓✓DNAseqFFPE✓CyTOFPBMCs✓✓✓✓CytokinesSerum✓✓✓✓Nivolumab ConcentrationSerum✓✓✓✓TILsFFPE✓HLAPBMCs✓Tuberculin ReactionSkin✓ Citation Format: Kosuke Kawaguchi, Masahiro Takada, Takeshi Kotake, Michio Yoshimura, Ryuji Uozumi, Masako Kataoka, Takahiko Koyama, Reitaro Tokumasu, Maya Honda, Rikiya Yamashita, Atsushi Yonezawa, Yuki Himoto, Natsuko Onishi, Hironori Kato, Hiroshi Yoshibayashi, Hirofumi Suwa, Wakako Tsuji, Hiroyasu Yamashiro, Tatsuki Kataoka, Hiroshi Ishiguro, Laxmi Parida, Satoshi Morita, Masakazu Toi. Alteration of the tumor immune microenvironment signatures by nivolumab combined with radiation therapy for patients with metastatic breast cancer (Translational Research of the KBCRN-B-002 trial) [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 P4-10-33.

COVID-19 caused by SARS-CoV-2 was first identified in Japan on January 15th, 2020, soon after the pandemic originated in Wuhan, China. Subsequently, Japan experienced three distinct waves of the outbreak in the span of a year and has been attributed to new exogenous strains and evolving existing strains. Japan engaged very early on in tracking different COVID-19 strains and have sequenced approximately 5% of all confirmed cases. While Japan has enforced stringent airport surveillance on cross-border travelers and returnees, some carriers appear to have advanced through the quarantine stations undetected. In this study 30493 genomes sampled in Japan were analyzed to understand the strains, heterogeneity and temporal evolution of different SARS-CoV-2 strains. We identified 12 discrete strains with a substantial number of cases with most strains possessing the spike (S) D614G and nucleocapsid (N) 203_204delinsKR mutations. 155 distinct strains have been introduced into Japan and 39 of them were introduced after strict quarantine policy was implemented. In particular, the B.1.1.7 strain, that emerged in the United Kingdom (UK) in September 2020, has been circulating in Japan since late 2020 after eluding cross-border quarantine stations. Similarly, the B.1.351 strain dubbed the South African variant, P.1 Brazilian strain and R.1 strain with the spike E484K mutation have been detected in Japan. At least 14 exogenous B.1.1.7 sub-strains have been independently introduced in Japan as of late March 2021, and these strains carry mutations that give selective advantage including N501Y, H69_V70del, and E484K that confer increased transmissibility, reduced efficacy to vaccines and possible increased virulence. Furthermore, various strains, which harbor multiple variants in the PCR primers and the probe developed by National Institute of Infectious Disease (NIID), are emerging. It is imperative that the quarantine policy be revised, cross-border surveillance reinforced, and new public health measures implemented to mitigate further transmission of this deadly disease and to identify strains that may engender resistance to vaccines.

In personalized cancer genomic medicine, characterizing a patient’s molecular profile based on comprehensive information is important for maximizing treatment benefits. However, current cancer genome analysis is centered on single nucleotide variation (SNV), gene expression, and copy number variation (CNV) but places little emphasis on structural variations (SV) beside fusions. To date, investigation of SVs has been limited because SV analysis entails a cumbersome annotation process. This study describes the design, development, and implementation of an annotation tool for SV, termed SVAnnotator. Detailed annotation was performed on the results of SV detection of 2,781 whole genome samples from the ICGC/TCGA PanCancer Analysis of Whole Genomes (PCAWG) with identifications of fusion, exon skipping, gene disruption, and tandem duplication SVs. These annotations of SVs will facilitate understanding of molecular events and further enhance utilities of precision medicine in stratifications, pathogenicity assessments and drug responses. Frequent novel SV events in MACROD2, FHIT, WWOX and CCSER1 were observed across many cancers. Importantly, SV events were frequently identified in well-established tumor suppressor genes including RB1, NF1, PTEN and TP53. As such, it is plausible that potential therapeutic opportunities are overlooked when SV analysis is not appropriately performed. Given the frequency of SVs detected in our study, SVanalysis with detailed annotation should be a routine part of comprehensive precision medicine analysis, and further studies are warranted to enhance clinical benefits as well as our understanding of uncharacterized SV events.

Background The novel oral nucleoside antineoplastic agent trifluridine/tipiracil was approved for metastatic colorectal cancer in Japan in March 2014. In this post-marketing surveillance study, we investigated the safety and efficacy of trifluridine/tipiracil in a real-world setting, particularly haematological drug reactions classified according to the baseline renal and hepatic functions. Methods We investigated patients with metastatic colorectal cancer who received trifluridine/tipiracil during the first four treatment cycles prospectively. The patients typically received 35 mg/m2 trifluridine/tipiracil twice daily on days 1–5 and 8–12 every 28 days. The primary objective was to assess the safety of trifluridine/tipiracil, but its efficacy was also evaluated. Results Between July 2014 and June 2016, 860 patients were enrolled in the study, and the safety and efficacy of trifluridine/tipiracil were evaluated in 823 patients. Adverse drug reactions occurred in 89.7% of the patients. The most common adverse drug reactions were decreased white blood cell count (67.0%) and neutrophil count (63.9%). Haematological drug reactions of grade ≥3 were observed in 41.7% of the patients with normal renal function; 50.3, 65.6 and 78.9% of the patients had mild, moderate and severe renal impairments, respectively. Hepatic impairment was not associated with a higher incidence of haematological drug reactions. The median overall survival was 8.4 months, with a 1-year survival rate of 33.7%. Conclusion This post-marketing surveillance study further confirmed the safety and tolerability profile of trifluridine/tipiracil observed in a clinical study setting.

Number of confirmed cases of COVID-19 caused by SARS-CoV-2 exceeded 5 million as of May 21, 2020. Global average of the case fatality rate of COVID-19 is about 7% so far. There exist variations in case fatality rates among countries. Particularly, Singapore and Qatar have exceptionally low case fatality rates with 0.1% while France’s rate is almost 20%. Since no magic bullet treatment for COVID-19 exists, we investigated SARS-CoV-2 strains specific to Singapore in this study to identify a clade with low pathogenicity. Variant analysis revealed that a clade with variants ORF1ab L3606F, A4489V, S2015R, T2016K, and N P13L is common in Singapore. Based on our analysis of variants and historical case statistics, the clade is dominant in a recent surge. Therefore, we suggest that low case fatality rate of Singapore possibly is attributed to the clade. Although contribution of each variant to the low pathogenicity is not clear, L3606F alone does not accomplish such low pathogenicity from the comparison with case fatality data from Japan, where L3606F is dominant. Further investigation is necessary to conclude to validate this finding.

New coronavirus (SARS-CoV-2) treatments and vaccines are under development to combat COVID-19. Several approaches are being used by scientists for investigation, including (1) various small molecule approaches targeting RNA polymerase, 3C-like protease, and RNA endonuclease; and (2) exploration of antibodies obtained from convalescent plasma from patients who have recovered from COVID-19. The coronavirus genome is highly prone to mutations that lead to genetic drift and escape from immune recognition; thus, it is imperative that sub-strains with different mutations are also accounted for during vaccine development. As the disease has grown to become a pandemic, B-cell and T-cell epitopes predicted from SARS coronavirus have been reported. Using the epitope information along with variants of the virus, we have found several variants which might cause drifts. Among such variants, 23403A>G variant (p.D614G) in spike protein B-cell epitope is observed frequently in European countries, such as the Netherlands, Switzerland, and France, but seldom observed in China.

Next‐generation sequencing (NGS) has emerged as an affordable and reproducible means to query tumors for somatic genetic anomalies. To help interpret somatic NGS data, many institutions have created a molecular tumor board to analyze the results of NGS and make recommendations. This article evaluates the utility of cognitive computing systems to analyze data for clinical decision‐making., Background. Using next‐generation sequencing (NGS) to guide cancer therapy has created challenges in analyzing and reporting large volumes of genomic data to patients and caregivers. Specifically, providing current, accurate information on newly approved therapies and open clinical trials requires considerable manual curation performed mainly by human “molecular tumor boards” (MTBs). The purpose of this study was to determine the utility of cognitive computing as performed by Watson for Genomics (WfG) compared with a human MTB. Materials and Methods. One thousand eighteen patient cases that previously underwent targeted exon sequencing at the University of North Carolina (UNC) and subsequent analysis by the UNCseq informatics pipeline and the UNC MTB between November 7, 2011, and May 12, 2015, were analyzed with WfG, a cognitive computing technology for genomic analysis. Results. Using a WfG‐curated actionable gene list, we identified additional genomic events of potential significance (not discovered by traditional MTB curation) in 323 (32%) patients. The majority of these additional genomic events were considered actionable based upon their ability to qualify patients for biomarker‐selected clinical trials. Indeed, the opening of a relevant clinical trial within 1 month prior to WfG analysis provided the rationale for identification of a new actionable event in nearly a quarter of the 323 patients. This automated analysis took

To analyse genome variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2).Between 1 February and 1 May 2020, we downloaded 10 022 SARS CoV-2 genomes from four databases. The genomes were from infected patients in 68 countries. We identified variants by extracting pairwise alignment to the reference genome NC_045512, using the EMBOSS needle. Nucleotide variants in the coding regions were converted to corresponding encoded amino acid residues. For clade analysis, we used the open source software Bayesian evolutionary analysis by sampling trees, version 2.5.We identified 5775 distinct genome variants, including 2969 missense mutations, 1965 synonymous mutations, 484 mutations in the non-coding regions, 142 non-coding deletions, 100 in-frame deletions, 66 non-coding insertions, 36 stop-gained variants, 11 frameshift deletions and two in-frame insertions. The most common variants were the synonymous 3037C T (6334 samples), P4715L in the open reading frame 1ab (6319 samples) and D614G in the spike protein (6294 samples). We identified six major clades, (that is, basal, D614G, L84S, L3606F, D448del and G392D) and 14 subclades. Regarding the base changes, the C T mutation was the most common with 1670 distinct variants.We found that several variants of the SARS-CoV-2 genome exist and that the D614G clade has become the most common variant since December 2019. The evolutionary analysis indicated structured transmission, with the possibility of multiple introductions into the population.Analyser les variantes du génome de coronavirus 2 du syndrome respiratoire aigu sévère (SARS-CoV-2).Entre le 1Nous avons détecté 5775 variantes de génome distinctes, dont 2969 mutations faux-sens, 1965 mutations synonymes, 484 mutations dans les régions non codantes, 142 délétions non codantes, 100 délétions sans décalage du cadre de lecture, 66 insertions non codantes, 36 variantes de codon stop, 11 délétions entraînant un décalage du cadre de lecture, et 2 insertions sans décalage du cadre de lecture. Les variantes les plus fréquentes étaient les synonymes 3037C T (6334 échantillons), P4715L dans le cadre ouvert de lecture 1ab (6319 échantillons) et D614G dans la protéine de spicule (6294 échantillons). Nous avons identifié six clades majeurs (à savoir, de base, D614G, L84S, L3606F, D448del et G392D) et 14 sous-clades. Quant aux changements de base, la mutation C T était la plus répandue avec 1670 variantes distinctes.Nous avons constaté qu'il existait de nombreuses variantes du génome de SARS-CoV-2, et que le clade D614G était devenu la variante la plus commune depuis décembre 2019. L'analyse évolutive a indiqué une transmission structurée, avec une possibilité d'introductions multiples au sein de la population.Analizar las variantes del genoma del coronavirus tipo 2 del síndrome respiratorio agudo grave (SARS-CoV-2).Entre el 1 de febrero y el 1 de mayo de 2020, se registraron 10 022 genomas del CoV-2 del SARS en cuatro bases de datos. Los genomas eran de pacientes infectados ubicados en 68 países. Se identificaron variantes al extraer la alineación por pares del genoma de referencia NC_045512, por medio de EMBOSS Needle. Las variantes de los nucleótidos en las regiones codificantes se convirtieron en los correspondientes residuos de aminoácidos codificados. Para analizar los clados, se utilizó el programa informático de código abierto Bayesian evolutionary analysis by sampling trees, versión 2.5.Se identificaron 5775 variaciones diferentes del genoma, incluidas 2969 mutaciones con cambio de sentido, 1965 mutaciones sinónimas, 484 mutaciones en las regiones no codificantes, 142 supresiones no codificantes, 100 supresiones en la fase, 66 inserciones no codificantes, 36 variaciones de parada prematuras (Se determinó que existen diversas variaciones del genoma del SARS-CoV-2 y que el clado D614G es la variante más común desde diciembre de 2019. El análisis evolutivo indicó una transmisión estructurada, en la que existe la posibilidad de que se realicen múltiples inserciones en la población.الغرض تحليل الأشكال المختلفة لجينوم المتلازمة التنفسية الحادة الشديدة المعروفة باسم كورونا فيروس 2 (سارس كوف 2). الطريقة خلال الفترة ما بين 1 فبراير/شباط، و1 مايو/أيار 2020، قمنا بتنزيل 10022 من جينوم سارس كوف 2 من أربع قواعد بيانات. كانت الجينومات من المرضى حاملي العدوى في 68 دولة. قمنا بتحديد أشكال مختلفة عن طريق استخلاص تنسيق على شكل زوجي من الجينوم المرجعي NC_045512، باستخدام إبرة EMBOSS. تم تحويل الأشكال المختلفة من النيوكليتويد في مناطق الترميز إلى بقايا الحمض الأميني المشفر المقابل. وبالنسبة لتحليل كليد، فقد استخدمنا تحليل بايزان المتطور لبرنامج المصدر المفتوح، عن طريق تفرعات العينات، الإصدار 2.5. النتائج حددنا 5775 شكلاً مختلفاً ومتميزاً من الجينوم، بما في ذلك 2969 طفرة مُغلطة، و1965 طفرة متشابهة، و484 طفرة في المناطق غير المشفرة، و142 حالة حذف غير مشفرة، و100 حالة حذف في الإطار، و66 إدخال غير مشفر، و36 شكلاً مكتسبًا موقوفاً، و11 حالة حذف لإزاحة الإطار، وعمليتي إدراج داخل الإطار. كانت أكثر الأشكال المختلفة شيوعاً هي المشابه 3037CT (6334 عينة)، وP4715L في إطار القراءة المفتوحة 1ab (6319 عينة)، وD614G في بروتين الشوكي (6294 عينة). قمنا بتحديد ستة عوامل كليد أساسية (وهي القاعدي، وD614G، وL84S، وL3606FK، D448del، وG392D)، و14 عاملاً فرعياً من كليد. وبخصوص التغييرات القاعدية، فإن طفرة CT، كانت الأكثر شيوعاً في 1670 شكلاً مختلفاً ومتميزاً. الاستنتاج لقد اكتشفنا أن هناك العديد من الأشكال المختلفة من جينوم سارس كوف 2، وأن كليد D614G قد أصبح الشكل المختلف الأكثر شيوعاً منذ ديسمبر/كانون أول 2019. أشار التحليل المتطور إلى انتقال منظم، مع إمكانية الظهور المتعدد في السكان.旨在分析严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 的基因组变异体情况。.在 2020 年 2 月 1 日至 5 月 1 日期间，我们从四个数据库下载了 10,022 个严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 基因组。这些基因组来自 68 个国家的感染患者。我们通过使用凸出针提取参考基因组 NC_045512 的成对序列比对来确定变异体。编码区的核苷酸变体被转化为相应的编码氨基酸残基。我们使用基于抽样树的开源软件贝叶斯演化分析（2.5 版）进行支系分析。.我们确定了 5775 个不同的基因组变异体，包括 2969 个错义突变、1965 个同义突变、484 个非编码区突变、142 个非编码缺失、100 个框架内缺失、66 个非编码插入、36 个止损变异体、11 个移码缺失和 2 个框架内插入。最常见的变异是同义 3037C T（6334 个样本）、开放阅读框 1ab 中的 P4715L（6319 个样本）和纤突蛋白中的 D614G（6294 个样本）。我们确定了 6 大主要分支（即，基底、D614G、L84S、L3606F、D448del 和 G392D）和 14 个子分支。在基底变化方面，以 CT 突变最为常见，共有 1670 个不同的变异体。.我们发现严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 基因组存在多种变异体，其中 D614G 支系自 2019 年 12 月以来已成为最常见的变异体。演化分析表明，这是一种结构化传播，有可能多次传入人群中。.Проанализировать варианты геномов тяжелого острого респираторного синдрома, вызванного коронавирусом‑2 (SARS-CoV-2).В период между 1 февраля и 1 мая 2020 года авторы загрузили данные по 10 022 геномам вируса SARS CoV-2 из четырех баз данных. Геномы принадлежали инфицированным пациентам из 68 стран. Авторы идентифицировали варианты, извлекая и попарно сравнивая последовательности с эталонным геномом NC_045512, используя набор инструментов EMBOSS. Варианты нуклеотидной последовательности в кодирующих участках были преобразованы в соответствующие кодируемые аминокислотные остатки. Для анализа клад использовалось программное обеспечение с открытым кодом для байесовского эволюционного анализа деревьев выборки, версия 2.5.Было идентифицировано 5775 четких вариантов генома, в том числе 2969 миссенс-мутаций, 1965 синонимичных мутаций, 484 мутации в некодирующих участках, 142 некодирующие делеции, 100 делеций внутри рамки считывания, 66 некодирующих вставок, 36 вариантов изменения последовательности ДНК с новым стоп-кодоном, 11 делеций со сдвигом рамки и две вставки внутри рамки считывания. Чаще всего встречались синонимичная замена 3037C T (6334 образца), P4715L в открытой рамке считывания 1ab (6319 образцов) и D614G в белке «шипа» (6294 образца). Было выявлено шесть основных клад (базовая, D614G, L84S, L3606F, D448del и G392D) и 14 субклад. Что касается замены оснований, наиболее частой была мутация с заменой цитозина на тимин (CT), которая встречалась в 1670 вариантах.Авторы обнаружили существование нескольких вариантов генома SARS-CoV-2 и выяснили, что с декабря 2019 года наиболее распространенным вариантом является клада D614G. Эволюционный анализ продемонстрировал структурированную передачу генетических данных с возможностью многократной интродукции в популяцию.

The confluence of genomic technologies and cognitive computing has brought us to the doorstep of widespread usage of personalized medicine. Cognitive systems, such as Watson for Genomics (WG), integrate massive amounts of new omic data with the current body of knowledge to assist physicians in analyzing and acting on patient's genomic profiles.

Introduction: Breast cancer subtyping is still not fully agreed among oncologists. Today, many guidelines separate patients into four subtypes, luminal A, luminal B, Her2 positive, and triple negative breast cancers. However, distinction between luminal A and luminal B cases is not clear cut although many use Ki67 index. As more treatment options including immune checkpoint blockade are available, it is imperative to define strata and to find optimum treatments for each stratum. Method: TCGA BRCA transcriptome data (BRCA-UQ) is used, which has a sample size of 1089. We employed topological data analysis (TDA) which can handle high dimensional nature of transcriptome data in elegant manner. For characterization of the clusters, we used clinical data such as metastasis status, tumor sizes, age of diagnosis, survival, and pathological data and molecular data including PIK3CA, TP53, GATA3 mutations, MYC amplification, 8p23.2 deletion, 16q24.3 deletion, and tumor mutation burden (TMB). In addition, state of tumor microenvironment is assessed using CD45 expression for tumor infiltrating leukocytes (TIL) and HOXD12 expression for cancer associated fibroblast (CAF). Results: TDA cleanly clustered breast cancer transcriptome data separating ER+, Her2+ and triple negative cases. However, among ER+ cases, boundary between Luminal A and Luminal B is vague except for ER+/Her2+ cases. In ER+ cases, there are four clusters with poor prognosis. One has PIK3CA mutation, high MYC, and low TIL. Another cluster is characterized by GATA3 mutations. The other has low TIL and PIK3CA mutations. Also, high CAF cluster coincides with poor prognosis ones. Conclusions: The study revealed complexity behind ER+ breast cancer stratification from molecular and clinical perspectives. A TDA based method will likely to classify a patient into a right stratum better than conventional methods. Identified clusters with high TIL and high TMB which are good candidates for immune checkpoint blockade. Further study on identification of optimal treatments for each stratum will be warranted. Citation Format: Takahiko Koyama, Aldo G. Saenz, Laxmi Parida. Topological data analysis revealed complexity behind ER positive breast cancer subtypes in TCGA transcriptome data [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2497.

e15046 Background: Advances in immuno-oncology (IO), i.e., programmed cell-death protein 1 (PD-1) inhibitors, are revolutionizing cancer treatment by offering hope for a cure. However, the benefit of IO agents in metastatic breast cancer (MBC) remains limited. For immunotherapy to be successful, it is essential to understand the tumor immune contexture. Systemic immune alterations, such as the signature of peripheral blood mononuclear cells (PBMC) and cytokine expression, are one of the hallmarks of successful immunotherapy in MBC. The abscopal effect induced by radiation therapy (RT) is known to be a modulator of systemic immune alterations, and the abscopal effect is considered as a systemic anti-tumor immune response. In this study, we integrated time series multi-omics data in order to identify alteration of the immune signatures after RT combined with nivolumab, a PD-1 inhibitor, using a longitudinal liquid biopsy with artificial intelligence. Methods: This study was conducted as translational research, part of the KBCRN-B-002 trial, which is a multicenter phase Ib/II study evaluating the safety and efficacy of nivolumab in combination with RT in patients with HER2-negative MBC (UMIN: UMIN000026046). Twenty-nine patients were included in the translational analysis set. The multi-omics data included data from RNAseq, mass cytometry (CyTOF) and multiple cytokines, using PBMC, serum and plasma. We collected time series data, which covered the baseline, two weeks after starting therapy, four weeks after starting therapy and the timing of progressive disease. For integrated analysis of the multi-omics data, a machine-learning method was developed. Results: Our integrated analysis (involving a longitudinal liquid biopsy and machine-learning method) identified an apparent cluster of responder groups and alteration of the systemic immune signatures. Single-cell analysis using CyTOF results including the signature of the immune cell composition, effector immune cells and immune suppressor cells. Conclusions: Our method clustered responders well and identified candidates of the systemic immune signatures for actionable hallmarks of RT combined with IO agent by a longitudinal liquid biopsy. Clinical trial information: NCT03430479 .

Background Prompted by the revolution in high-throughput sequencing and its potential impact for treating cancer patients, we initiated a clinical research study to compare the ability of different sequencing assays and analysis methods to analyze glioblastoma tumors and generate real-time potential treatment options for physicians. Methods A consortium of seven institutions in New York City enrolled 30 patients with glioblastoma and performed tumor whole genome sequencing (WGS) and RNA sequencing (RNA-seq; collectively WGS/RNA-seq); 20 of these patients were also analyzed with independent targeted panel sequencing. We also compared results of expert manual annotations with those from an automated annotation system, Watson Genomic Analysis (WGA), to assess the reliability and time required to identify potentially relevant pharmacologic interventions. Results WGS/RNAseq identified more potentially actionable clinical results than targeted panels in 90% of cases, with an average of 16-fold more unique potentially actionable variants identified per individual; 84 clinically actionable calls were made using WGS/RNA-seq that were not identified by panels. Expert annotation and WGA had good agreement on identifying variants [mean sensitivity = 0.71, SD = 0.18 and positive predictive value (PPV) = 0.80, SD = 0.20] and drug targets when the same variants were called (mean sensitivity = 0.74, SD = 0.34 and PPV = 0.79, SD = 0.23) across patients. Clinicians used the information to modify their treatment plan 10% of the time. Conclusion These results present the first comprehensive comparison of technical and machine augmented analysis of targeted panel and WGS/RNA-seq to identify potential cancer treatments.

Background Significant numbers of variants detected in cancer patients are often left labeled only as variants of unknown significance (VUS). In order to expand precision medicine to a wider population, we need to extend our knowledge of pathogenicity and drug response in the context of VUS’s. Methods In this study, we analyzed variants from AACR Project GENIE Consortium APG (Cancer Discov 7:818-831, 2017) and compared them to the COSMIC database Forbes et al. (Nucleic Acids Res 43:D805-811, 2015) to identify recurrent variants that would merit further study. We filtered out known hotspot variants, inactivating variants in tumor suppressors, and likely benign variants by comparing with COSMIC and ExAC Lee et al. (Science 337:967-971, 2012). Results We have identified 45,933 novel variants with unknown significance unique to GENIE. In our analysis, we found on average six variants per patient where two could be considered as pathogenic or likely pathogenic and the majority are VUS’s. More importantly, we have discovered 730 recurrent variants that appear more than 3 times in GENIE but less than 3 in COSMIC. If we combine the recurrences of GENIE and COSMIC for all variants, 2586 are newly identified as occurring more than 3 times than when using COSMIC alone. Conclusions Although it would be inappropriate to blindly accept these recurrent variants as pathogenic, they may warrant higher priority than other observed VUS’s. These newly identified recurrent variants might affect the molecular profiles of approximately 1 in 6 patients. Further analysis and characterization of these variants in both research and clinical contexts will improve patient treatments and the development of new therapeutics. Electronic supplementary material The online version of this article (10.1186/s12885-019-5313-1) contains supplementary material, which is available to authorized users.

The instability of the cylindrical D 6 h structure in [6]cycloparaphenylene, the non-zero dihedral angles between adjacent paraphenylene units, is investigated from the viewpoint of the pseudo Jahn–Teller effect, wherein the driving forces are orbital vibronic couplings of the deformation modes between occupied and unoccupied orbitals. We show that the overlap densities between the frontier orbitals including the highest occupied molecular orbital (HOMO) and a certain unoccupied/occupied molecular orbital mainly contribute to the instability. The results of vibronic coupling density analysis justify the strong coupling of the unoccupied orbital with the HOMO.

Introduction: Many cancer patients suffer from metastasis in bone, brain, liver and lung. However, understanding of metastasis in molecular level is quite limited. To improve survival rate and quality of life, preventing metastasis is crucial. In this study, we analyzed transcriptomic data with tumor node metastasis (TNM) classification from The Cancer Genome Atlas (TCGA) to identify genes associated with metastasis. Method: TCGA samples in 20 solid tumor types with both transcriptome and TNM annotation data are used. To obtain the best cut point separating cohorts of high and low gene expression, Hothorn and Lausen’s method is used. A contingency table is created with expression separated by the the cut point and presence of staging T, N, M for each gene. Association between the staging category and the gene was calculated with Fisher’s exact test. Results: In total, 13,220 distinct genes including miRNAs are associated with either lymph node or distant metastasis for some cancer types with a loose criteria of p-value < 1.0e-3. Among them, we identified 1,357 genes with p-value < 1.0e-8. ADAMTS12, AURKB, BUB1, C17orf53, CCNA2, CEP55, EPR1, KIF4A, KIF11, KRT80, MELK, MKI67, NCAPG, NEIL3, PBK, PLK1, RRM2, TPX2, miR139, miR30a, miR375, and miR379 appear most commonly in lymph node metastasis for many cancer types. Likewise, NOP56, PKD1L2, miR150, miR365, miR9, miR149, miR210, miR425, miR675, and miR937 are most commonly associated genes in distant metastasis. Many of these genes have been already reported in association with metastasis. Conclusions: This study created comprehensive list of metastasis associated genes for the 20 solid tumors in TCGA. They would be useful as diagnostic and prognostic biomarkers; however, we found therapeutically relevant genes such as PLK1, AURKB, MET, MELK, CDK1, BUB1, and PBK. Some adhesion molecules associated with a particular cancer type might explain its organ destination preference. Among distant metastatic miRNAs discovered, metastasis promoting miRNAs in high abundance might be engaged in homing as exosomal miRNAs by reprogramming destination niche in favor of migrating tumor cells. Further work to reveal metastasis mechanism and to discover some pharmaceutical agents to prevent metastasis will be conducted. Citation Format: Takahiko Koyama, Laxmi Parida. Identification of novel genes associated with metastasis from TCGA transcriptomic data [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 2771.

Objective:To analyze a glioblastoma tumor specimen with 3 different platforms and compare potentially actionable calls from each.Methods:Tumor DNA was analyzed by a commercial targeted panel. In addition, tumor-normal DNA was analyzed by whole-genome sequencing (WGS) and tumor RNA was analyzed by RNA sequencing (RNA-seq). The WGS and RNA-seq data were analyzed by a team of bioinformaticians and cancer oncologists, and separately by IBM Watson Genomic Analytics (WGA), an automated system for prioritizing somatic variants and identifying drugs.Results:More variants were identified by WGS/RNA analysis than by targeted panels. WGA completed a comparable analysis in a fraction of the time required by the human analysts.Conclusions:The development of an effective human-machine interface in the analysis of deep cancer genomic datasets may provide potentially clinically actionable calls for individual patients in a more timely and efficient manner than currently possible.ClinicalTrials.gov identifier:NCT02725684.

Introduction: 98% of mutations are non-coding mutations. Thus far, most non-coding mutations are ignored or merely classified as variant of unknown significance with a few exceptions, despite the fact that non-coding region plays significant role in regulations and other important biological processes. Although they would not be directly druggable, these non-coding mutations might be important for cancer etiology, response to treatments and prognosis assessments. Method: Mutations in non-coding genes, intron, upstream and downstream, and intergenic regions are collected from COSMIC and TCGA as defined in Ensemble GRCh37.75 gene definition and hg19 RefSeq. Over 15 million non-coding mutations are analyzed for recurrence over 10 samples. Mutations in neighborhood of IG genes and dbSNP150 polymorphisms are removed from further investigation. We analyzed remaining mutations for possible super enhancer and transcription factor binding. Result: 911 distinct recurrent mutations are identified. Promoter mutations in protein coding genes like MPRS31, NUDFB9, SZT2, WASF3 in addition to TERT are discovered. Intronic mutations of well-known cancer genes such as HIF1A, NF1, KMT2C, and ATR are discovered with their associated cancer type specificity. As for non-coding RNA's, lincRNA CROCCP2, LINC00969 and miRNA MIR4477 appear frequently. Only 182 mutations are reluctantly classified as intergenic; intergenic loci RP11-96F8.1-KSR1P1, MLLT10P1-DEFB115, and bP-21201H5.1-IGHV1OR21-1 contain unusually high recurrent mutations. Conclusion: Many non-coding mutations worth further investigation are found. Still, it is quite possible that many of these mutations might be artifacts resulting from paralogous alignments, gene definition compatibility and other technical issues. Importantly, we discovered novel intronic mutations in genes already associated with treatments. Mutations in intergenic regions might be involved in regulatory mechanisms and chromosomal structures. Understanding these non-coding mutations will further refine our understanding of biology as well as cancer. Citation Format: Takahiko Koyama, Laxmi Parida. Analysis of noncoding mutations in cancer revealed novel potentially pathogenic recurrent mutations [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 2353.

We report the results of a special drug use-results survey that used medication diaries about compliance to tegafur/uracil (UFT) adjuvant chemotherapy in patients who had undergone complete resection for non-small cell lung cancer. Between April1 , 2008, and March 31, 2010, 2,527 patients were enrolled. Of these patients, 2,411 and 1,811 were evaluated for treatment and compliance, respectively. The 2-year treatment completion rate was 59.1% in 2,093 of the 2,411 patients, excluding 318 patients with treatment failure owing to recurrence. The results were comparable with those from The Japan Lung Cancer Research Group on PostsurgicalAdjuvant Chemotherapy (JLCRG). The main reasons of the treatment failure were gastrointestinaland hepatic disorders. The proportion of patients with @75% compliance was 95.3% (1,726/1,811), and most of the patients who kept their medication diaries exhibited good compliance.

We have reported that two endoperoxides, N-89 and N-251, synthesized in 2001, possess potent antimalarial activities. Aiming at their eventual use for curing malaria in humans, we have been investigating various aspects of their antimalarial actions. Here we show that N-89 and N-251 inhibit the growth of Plasmodium falciparum within human erythrocytes in vitro at its lifecycle stage 'trophozoite' specifically. It is known that artemisinin compounds, which are currently used for curing malaria, have other stage-specificities. Therefore, it is likely that the antimalarial mechanism of N-89 and N-251 differs from those of artemisinin compounds. As malaria parasites resistant to artemisinin-based combination therapy are currently emerging in some tropical regions, N-89 and N-251 are candidates for overcoming these new problems.

Next-generation sequencing (NGS) is an attractive tool for prospective use in the field of clinical oncology. However, for this purpose, further innovations are necessary including medical informatics which links somatic mutations to clinical intervention. This process is currently labor-intensive, involving experienced curators who pick up the relevant evidence among a growing body of knowledge and translate it into medical practice. We organized a clinical sequencing team, called as IMSUT Tumor Board, and have been integrating clinical and genomic information in hematological malignancies with the aid of a cognitive computing (CC) system. Genomic DNA was prepared from malignant cell fractions and normal tissues in each patient, and subjected to comparative NGS, mainly targeted deep sequencing with ready-made panels and, on demand, whole exome sequencing. Sequence data was analyzed using a pipeline of in-house semi-automated medical informatics, namely YOKOMON-GO. CC was used to identify candidate driver mutations and pathways in each patient, from which pathogenic information as well as applicable drug information was deduced. A summary of NGS data was reported and discussed in IMSUT Tumor Board to deliberate upon potentially actionable findings. Up to date, we have performed NGS analysis on 90 patients with AML, MDS, MPN, et al., among which informative and actionable findings could be obtained in 50 and 18 patients, respectively. Six patients actually received treatments motivated in IMSUT Tumor Board. Our preliminary results indicate that CC can be well suited to clinical sequencing. Disclosures Koyama: IBM: Employment.