scholarly journals Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types

2020 ◽  
Vol 30 (3) ◽  
pp. 334-346 ◽  
Author(s):  
Akihiro Fujimoto ◽  
Masashi Fujita ◽  
Takanori Hasegawa ◽  
Jing Hao Wong ◽  
Kazuhiro Maejima ◽  
...  
Keyword(s):  
Microsatellite Instability ◽  
Comprehensive Analysis ◽  
Whole Genome ◽  
Cancer Types

scholarly journals Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Xiaoming Song ◽  
Qihang Yang ◽  
Yun Bai ◽  
Ke Gong ◽  
Tong Wu ◽  
...  
Keyword(s):  
Higher Plants ◽  
Extreme Environments ◽  
Gene Families ◽  
Comprehensive Analysis ◽  
Whole Genome ◽  
Flowering Genes ◽  
Database Construction ◽  
Myb Gene ◽  
Gene Coding ◽  
Lower Plants

AbstractSimple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher plants, showing that lower plants needed to adapt to early extreme environments. Four specific enriched functional terms in the lower plant Chlamydomonas reinhardtii were detected when it was compared with seven other higher plants. In addition, Guanylate_cyc existed in more genes of lower plants than of higher plants. In our PSSRD, we constructed an interactive plotting function in the chart interface, and users can easily view the detailed information of SSRs. All SSR information, including sequences, primers, and annotations, can be downloaded from our database. Moreover, we developed Web SSR Finder and Batch SSR Finder tools, which can be easily used for identifying SSRs. Our database was developed using PHP, HTML, JavaScript, and MySQL, which are freely available at http://www.pssrd.info/. We conducted an analysis of the Myb gene families and flowering genes as two applications of the PSSRD. Further analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene families. These SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future.

scholarly journals Comprehensive analysis of the transcriptional profile of the Mediator complex across human cancer types

Oncotarget ◽  
2016 ◽  
Vol 7 (17) ◽  
pp. 23043-23055 ◽  
Author(s):  
Isabella Syring ◽  
Niklas Klümper ◽  
Anne Offermann ◽  
Martin Braun ◽  
Mario Deng ◽  
...  
Keyword(s):  
Human Cancer ◽  
Comprehensive Analysis ◽  
Transcriptional Profile ◽  
Mediator Complex ◽  
Cancer Types

scholarly journals Comprehensive analysis of RNA-seq and whole genome sequencing data reveals no evidence for SARS-CoV-2 integrating into host genome

2021 ◽  
Author(s):  
Yu-Sheng Chen ◽  
Shuaiyao Lu ◽  
Bing Zhang ◽  
Tingfu Du ◽  
Wen-Jie Li ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rna Virus ◽  
Comprehensive Analysis ◽  
Host Genome ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Rna Seq ◽  
Sequencing Data ◽  
Infected Cells

SARS-CoV-2, as the causation of severe epidemic of COVID-19, is one kind of positive single-stranded RNA virus with high transmissibility. However, whether or not SARS-CoV-2 can integrate into host genome needs thorough investigation. Here, we performed both RNA sequencing (RNA-seq) and whole genome sequencing on SARS-CoV-2 infected human and monkey cells, and investigated the presence of host-virus chimeric events. Through RNA-seq, we did detect the chimeric host-virus reads in the infected cells. But further analysis using mixed libraries of infected cells and uninfected zebrafish embryos demonstrated that these reads are falsely generated during library construction. In support, whole genome sequencing also didn't identify the existence of chimeric reads in their corresponding regions. Therefore, the evidence for SARS-CoV-2's integration into host genome is lacking.

Comprehensive analysis of CTLA-4 in the tumor immune microenvironment of 33 cancer types

2020 ◽  
Vol 85 ◽  
pp. 106633
Author(s):  
Chufan Zhang ◽  
Jianing Chen ◽  
Qian Song ◽  
Xiaoyan Sun ◽  
Meijuan Xue ◽  
...  
Keyword(s):  
Comprehensive Analysis ◽  
Immune Microenvironment ◽  
Tumor Immune Microenvironment ◽  
Cancer Types

scholarly journals Landscape of Microsatellite Instability Across 39 Cancer Types

2017 ◽  
pp. 1-15 ◽  
Author(s):  
Russell Bonneville ◽  
Melanie A. Krook ◽  
Esko A. Kautto ◽  
Jharna Miya ◽  
Michele R. Wing ◽  
...  
Keyword(s):  
Microsatellite Instability ◽  
Mismatch Repair ◽  
Human Cancer ◽  
The Cancer Genome Atlas ◽  
Repair System ◽  
Multiple Cancer ◽  
External Data ◽  
Mismatch Repair System ◽  
Cancer Types ◽  
Genomic Microsatellites

Purpose Microsatellite instability (MSI) is a pattern of hypermutation that occurs at genomic microsatellites and is caused by defects in the mismatch repair system. Mismatch repair deficiency that leads to MSI has been well described in several types of human cancer, most frequently in colorectal, endometrial, and gastric adenocarcinomas. MSI is known to be both predictive and prognostic, especially in colorectal cancer; however, current clinical guidelines only recommend MSI testing for colorectal and endometrial cancers. Therefore, less is known about the prevalence and extent of MSI among other types of cancer. Methods Using our recently published MSI-calling software, MANTIS, we analyzed whole-exome data from 11,139 tumor-normal pairs from The Cancer Genome Atlas and Therapeutically Applicable Research to Generate Effective Treatments projects and external data sources across 39 cancer types. Within a subset of these cancer types, we assessed mutation burden, mutational signatures, and somatic variants associated with MSI. Results We identified MSI in 3.8% of all cancers assessed—present in 27 of tumor types—most notably adrenocortical carcinoma (ACC), cervical cancer (CESC), and mesothelioma, in which MSI has not yet been well described. In addition, MSI-high ACC and CESC tumors were observed to have a higher average mutational burden than microsatellite-stable ACC and CESC tumors. Conclusion We provide evidence of as-yet-unappreciated MSI in several types of cancer. These findings support an expanded role for clinical MSI testing across multiple cancer types as patients with MSI-positive tumors are predicted to benefit from novel immunotherapies in clinical trials.

Microsatellite instability status differentially associates with intratumoral immune microenvironment in human cancers

2020 ◽  
Author(s):  
Peng Zhang ◽  
Mingyue Liu ◽  
Ya Cui ◽  
Pan Zheng ◽  
Yang Liu
Keyword(s):  
Colorectal Cancer ◽  
Microsatellite Instability ◽  
Therapeutic Response ◽  
In Silico Analysis ◽  
Cancer Type ◽  
Clinical Responses ◽  
Stomach Adenocarcinoma ◽  
Immune Contexture ◽  
Cancer Types ◽  
The Impact

Abstract Based on clinical outcomes in colorectal cancer, high microsatellite instability (MSI-H) has recently been approved by the Food and Drug Administration (FDA) as a genetic test to select patients for immunotherapy targeting PD-1 and/or CTLA-4 without limitation to cancer type. However, it is unclear whether the MSI-H would broadly alter the tumor microenvironment to confer the therapeutic response of different cancer types to immunotherapy. To fill in this gap, we performed an in silico analysis of tumor immunity among different MSI statuses in five cancer types. We found that consistent with clinical responses to immunotherapy, MSI-H and non-MSI-H samples from colorectal cancer (COAD-READ) exhibited distinct infiltration levels and immune phenotypes. Surprisingly, the immunological difference between MSI-H and non-MSI-H samples was diminished in stomach adenocarcinoma and esophageal carcinoma (STAD-ESCA) and completely disappeared in uterine corpus endometrial carcinoma (UCEC). Regardless of cancer types, the abundance of tumor-infiltrating immune cells, rather than MSI status, strongly associated with the clinical outcome. Since preexisting antitumor immune response in the tumor (hot cancer) is accepted as a prerequisite to the therapeutic response to anti-PD-1/CTLA-4 immunotherapy, our data demonstrate that the impact of MSI varied on immune contexture will lead to the further evaluation of predictive immunotherapy responsiveness based on the universal biomarker of MSI status.

scholarly journals Ennet: construction of potential cancer-driving networks based on somatic enhancer mutations only

2017 ◽  
Author(s):  
Ya Cui ◽  
Yiwei Niu ◽  
Xueyi Teng ◽  
Dan Wang ◽  
Huaxia Luo ◽  
...  
Keyword(s):  
Neural Development ◽  
Somatic Mutations ◽  
Gene Interactions ◽  
Whole Genome ◽  
Sequencing Technology ◽  
Cancer Types ◽  
Cancer Drivers ◽  
New Perspective ◽  
Pan Cancer ◽  
Potential Cancer

AbstractWhole genome sequencing technology has facilitated the discovery of a large number of somatic mutations in enhancers (SMEs), whereas the utility of SMEs in tumorigenesis has not been fully explored. Here we present Ennet, a method to comprehensively investigate SMEs enriched networks (SME-networks) in cancer by integrating SMEs, enhancer-gene interactions and gene-gene interactions. Using Ennet, we performed a pan-cancer analysis in 2004 samples from 8 cancer types and found many well-known cancer drivers were involved in the SME-networks, includingESR1,SMAD3,MYC,EGFR,BCL2andPAX5. Meanwhile, Ennet also identified many new networks with less characterization but have potentially important roles in cancer, including a large SME-network in medulloblastoma (MB), which contains genes enriched in the glutamate receptor and neural development pathways. Interestingly, SME-networks are specific across cancer types, and the vast majority of the genes identified by Ennet have few mutations in gene bodies. Collectively, our work suggests that using enhancer-only somatic mutations can be an effective way to discover potential cancer-driving networks. Ennet provides a new perspective to explore new mechanisms for tumor progression from SMEs.

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