Tag: TP53

Dog lymphoma, new genetic mutations discovered. Hopes for man too

TURIN – Large B cell lymphoma is one of the most frequent cancers in dogs and is considered a good model for the study of the same pathology in humans. The study was published in the prestigious Nature journal, Lab Animal. Researchers of a European team coordinated by the professor…

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Differences in Germline Variant Spectrum Between Black and White Men With Prostate Cancer

By Matthew StengerPosted: 6/13/2022 10:50:00 AM Last Updated: 6/13/2022 10:00:21 AM In a study presented at the 2022 ASCO Annual Meeting (Abstract 10502) and simultaneously published in JCO Precision Oncology, Veda N. Giri, MD, and colleagues found that Black men with prostate cancer exhibited a lower frequency and narrower spectrum…

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Our genetic strength in numbers

Although it’s 20 years since the first human genome was sequenced – that is, the entire collection of our DNA – our ability to ‘read’ our own instruction manual is no less astounding. We now know we have around three billion chemical base pairs that provide the code for approximately…

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Integrative analysis of eQTL and GWAS summary statistics reveals transcriptomic alteration in Alzheimer brains | BMC Medical Genomics

Significant gene-AD associations With the GWAS summary data from the IGAP and eQTL summary data from BRAINEAC, we performed both SMR and HEIDI tests to estimate the gene-AD associations in three human brain regions: frontal cortex, temporal cortex, and hippocampal regions. For the frontal cortex and hippocampal regions, we obtained…

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Interphase Fluorescence in situ Hybridization of Bone Marrow Smears of Multiple Myeloma

Here, we present a protocol for improving the success of interphase fluorescence in situ hybridization detection on bone marrow smears from multiple myeloma patients. The application of Fluorescence In Situ Hybridization called FISH to genetic risk stratification in multiple myeloma is essential. The critical part of FISH reports is not…

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Biomea Fusion Reports Preclinical Data on BMF-219 and Trial

Covalent menin inhibitor BMF-219 showed strong cytotoxic activity as a single agent at similar concentrations across multiple preclinical patient derived (PDX) models ex vivo, including diffuse large B-cell lymphoma (DLBCL), multiple myeloma (MM), colorectal cancer (CRC), non-small cell lung cancer (NSCLC), and pancreatic cancer Single agent BMF-219 demonstrated pronounced anti-cancer activity…

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Pandas merge rows with different operations for each column

import pandas as pd df = pd.DataFrame({‘case_id’:[‘1’, ‘1’, ‘1’,’2′,’2′,’2′], ‘Gene’:[‘KRAS’,’SMAD4′,’TP53′,’TP000′,’SMAD000′,’TP000′], ‘ch_a’:[0,1,0,0,0,0], ‘ch_b’:[0,0,0,1,1,0], ‘ch_c’:[0,0,0,1,1,0]}) case_id Gene ch_a ch_b ch_c 0 1 KRAS 0 0 0 1 1 SMAD4 1 0 0 2 1 TP53 0 0 0 3 2 TP000 0 1 1 4 2 SMAD000 0 1 1 5 2…

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Characterization of Blood- Based Molecular Profiling in Pancreatic Adenocarcinoma

Introduction Most cases of pancreatic adenocarcinoma (PDAC) are diagnosed in the metastatic or locally advanced stage. It is the fourth leading cause of cancer death in the United States,1,2 with a 5-year overall survival (OS) around 10% in this country2 despite years of research and therapeutic development. For those patients…

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Hypoxic Characteristic Genes Predict Response to Immunotherapy for Urothelial Carcinoma

This article was originally published here Front Cell Dev Biol. 2021 Nov 25;9:762478. doi: 10.3389/fcell.2021.762478. eCollection 2021. ABSTRACT Objective: Resistance to immune checkpoint inhibitors (ICIs) has been a massive obstacle to ICI treatment in metastatic urothelial carcinoma (MUC). Recently, increasing evidence indicates the clinical importance of the association between hypoxia…

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BRCA2 Linked to Inferior Outcomes of Treatment With CDK4/6 Inhibitors Plus Endocrine Therapy

An analysis of germline-somatic interactions in breast cancer tumors revealed novel associations relevant to the disease’s progression and treatment resistance. For example, the study presented at the 2021 San Antonio Breast Cancer Symposium (SABCS) showed that carriers of the BRCA2 mutation had inferior outcomes to treatment with first-line CDK4/6 inhibitors…

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Disease Causing Mutations Databases or database for predicting the functional consiquence of the mutation

Disease Causing Mutations Databases or database for predicting the functional consiquence of the mutation 1 I would like to analyze the functional consequence of the mutation in the protein-coding region of the human genome like in TP53 or EGFR etc. I tried Annovar, VEP, SIFT, polyphen, etc but as far…

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PLOS Papers on Y-Chromosome Sequencing, Blood Methylation Markers, CLL Mutations

In PLOS Genetics, a Belgian team led by investigators at KU Leuven presents a Y-chromosome-specific sequencing strategy for targeting informative Y-chromosome SNPs (Y-SNPs) and short tandem repeats (Y-STRs). The investigators’ CSYseq method “simultaneously identifies slow mutating Y-SNPs as evolution markers and rapidly mutating Y-STRs as patrilineage markers,” they say, noting…

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ZhaozzReal/SNV_IPA: Detect SNV-associated intronic polyadenylation events from standard RNAseq data

Description Somatic single nucleotide variants (SNVs) in cancer genome affect gene expression through various mechanisms depending on their genomic location. In this study, we found that somatic SNVs near splice site are associated with abnormal intronic polyadenylation (IPA) . Here we give examples to show how to detect SNV-associated IPA…

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Prognostic Biomarkers Identified for Pancreatic Ductal Adenocarcinoma Using Whole Genome Sequencing

Possible biomarkers for prognosis and clinical outcomes were identified, through the use whole exome sequencing and RNA sequencing, as therapeutic targets for patients with pancreatic ductal adenocarcinoma (PDAC), according to a recent study. The study, published in Therapeutic Advances in Medical Oncology, also reconfirmed genomic landscapes, major driver mutations, and…

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Genomic Analysis of Lung Cancer in Never Smokers Identifies Three Molecular Subtypes

A genomic analysis of lung cancer in people with no history of smoking has found that a majority of these tumors arise from the accumulation of mutations caused by natural processes in the body. The international team of scientists, led by researchers at the National Cancer Institute (NCI), carried out…

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Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection | Genome Biology

Stochastic Amplicon Ligation. DNA samples for oncology sequencing are typically extracted from FFPE tissues and can have average lengths of less than 500 nt due to accumulated chemical damage [18]. We developed the Stochastic Amplicon Ligation (SAL) method to enzymatically concatenate many short DNA molecules together to utilize the long-read…

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Gene mutation analysis in papillary thyroid carcinoma

Introduction Thyroid tumors are the most common malignant tumors of the endocrine system, and their incidence has been increasing in the recent decades. Currently, there are some target drugs that can effectively treat PTC, and next-generation sequencing (NGS) can be used for targeted therapy. In order to make better informed…

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Doubts with Stacked barplot using R ggplot2

Doubts with Stacked barplot using R ggplot2 0 Hello! I am trying to plot some data using R but I am having some problems doing it. I have a data frame with two columns (genes and and type of mutation) and looks like: genes variant MLH1 Intronic ATR 5′ UTR…

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Analysis of the Prognostic Significance of Circulating Tumor DNA in Metastatic Castrate Resistant Prostate Cancer

This article was originally published here Clin Genitourin Cancer. 2021 Jul 31:S1558-7673(21)00151-8. doi: 10.1016/j.clgc.2021.07.012. Online ahead of print. ABSTRACT BACKGROUND: There has been considerable interest in ctDNA next generation sequencing platforms to assess genomic alterations in mCRPC given its accessibility and identification of temporal genomic data. PATIENTSAND METHODS: In this…

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looking for interaction tools

looking for interaction tools 0 Hello, I am searching for a tool which can identify list of human genes directly regulated by a specific gene (for example : TP53). I have explored GeneMANIA and some other tools (STRING and inBio Discover) but I am not sure about the interactions which…

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Integrated bioinformatics analysis to identify abnormal CC

Introduction In recent years, the morbidity and mortality of colon cancer have increased rapidly, both being ranked fourth worldwide. Although surgery-based comprehensive treatments improve the prognosis of colon cancer, because of the lack of available means for early diagnosis, the mortality level remains high for patients with advanced-stage cancer. The…

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Using joiningdata/lollipops to make lollipop chart

Using joiningdata/lollipops to make lollipop chart 0 I’m having trouble downloading and using pbnjay’s lollipop I went and downloaded the mac version and opened up “lollipops” in the command line. I closed the terminal and then opened it again, and tried: lollipops TP53 R273C R175H T125 R248Q but go the…

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