Tag: BRCA

mRNA vaccines against COVID-19 don’t modify humans, and don’t make them patentable or owned by any entities

CLAIM “if a human is injected with a GMO it becomes a patented piece of property from the government”, “they take away all your rights with mRNAs” DETAILS Factually inaccurate: U.S. law prohibits the patenting of human beings. Furthermore, mRNA vaccines don’t modify the human genome. Inadequate support: The 2013…

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Myriad Genetics to Submit Hereditary Cancer Risk Variants to ClinVar in 2023

NEW YORK – Myriad Genetics will begin submitting variants detected by its hereditary cancer risk test, including variants in BRCA1 and BRCA2 genes, to the public database ClinVar starting in the spring of 2023. The Salt Lake City-based company is infamous, derided, and even boycotted in certain circles in the…

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Figure 2 | Identification of Cytosolic DNA Sensor cGAS-STING as Immune-Related Risk Factor in Renal Carcinoma following Pan-Cancer Analysis

Expression landscape of the cGAS-STING sensor across human cancers. (a) The expression score of the cGAS-STING signal in paired tumor and nontumor tissues. (b) Significant difference of the cGAS-STING score between tumor and normal samples. BLCA: bladder urothelial carcinoma; BRCA: breast invasive carcinoma; CESC: cervical squamous cell carcinoma and endocervical…

Continue Reading Figure 2 | Identification of Cytosolic DNA Sensor cGAS-STING as Immune-Related Risk Factor in Renal Carcinoma following Pan-Cancer Analysis

Subtype and cell type specific expression of lncRNAs provide insight into breast cancer

lncRNA expression according to breast cancer clinicopathological subtypes To identify lncRNAs expressed by specific breast cancer subtypes or associated with clinicopathological features, we analyzed RNA-sequencing data from two large independent breast cancer cohorts: SCAN-B (n = 3455)17 and TCGA-BRCA (n = 1095). We focused on lncRNAs annotated in the Ensembl18 v93 non-coding reference transcriptome…

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Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer

Sampson, J. N. et al. Analysis of heritability and shared heritability based on genome-wide association studies for thirteen cancer types. J. Natl Cancer Inst. 107, djv279 (2015). PubMed  PubMed Central  Article  CAS  Google Scholar  Bosse, Y. & Amos, C. I. A decade of GWAS results in lung cancer. Cancer Epidemiol….

Continue Reading Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer

Alpelisib Plus Olaparib Phase 1b Clinical Trial for Patients With Advanced Triple-Negative Breast Cancer

For a study, researchers sought to present the breast cancer cohort. In a previous study, they reported on safety. They recommended a phase 2 dose (RP2D) of olaparib combined with the PI3Kα-specific inhibitor alpelisib in patients with high-grade serous ovarian cancer as studied in a phase 1b trial (NCT01623349). Investigators…

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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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Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant

Subjects Normal breast and tumor samples were obtained with the written informed consent from donors and appropriate approval from local ethical committees, with the detailed information described in the respective original publications: normal tissue9, METABRIC14, TCGA35. Differential allelic expression analysis DNA and total RNA from 64 samples of normal breast…

Continue Reading Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant

VCV000038126.28 Observations – ClinVar – NCBI

1 SCV000301220.2 Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Pathogenic reviewed by expert panel curation Breast-ovarian cancer, familial, susceptibility to, 2 (unknown ) germline Variant allele predicted to encode a truncated non-functional protein. 1 SCV000785901.2 Counsyl Pathogenic criteria provided,single submitter clinical testing Breast-ovarian cancer, familial, susceptibility to,…

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MND1 Expression as a Predictor of Breast Cancer Survival

Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…

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Role of CD68 in tumor immunity and prognosis prediction in pan-cancer

Expression of CD68 in pan-cancer First, to fully clarify the expression of CD68 in pan-cancer, we matched the GTEx normal samples with TCGA tumor samples (Fig. 1A). We found that the levels of CD68 were significantly elevated (P < 0.01) in colon adenocarcinoma (COAD), glioblastoma multiforme (GBM), kidney renal clear cell carcinoma (KIRC),…

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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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Molecular analysis of TCGA breast cancer histologic types

Breast cancer is classified into multiple distinct histologic types, and many of the rarer types have limited characterization. Here, we extend The Cancer Genome Atlas Breast Cancer (TCGA-BRCA) dataset with additional histologic type annotations, in a total of 1063 breast cancers. We analyze this extended dataset to define transcriptomic and…

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Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma

Introduction Liver hepatocellular carcinoma (LIHC) is the most common type of primary cancer in the liver and third leading cause of cancer-related mortality worldwide (1). Although substantial improvements have been made in LIHC therapy, particularly in molecular targeted therapy and immunotherapy (2, 3), the 5-year survival rate of LIHC is…

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HTSeq Counts no longer available

HTSeq Counts no longer available 1 @vm-21340 Last seen 8 hours ago Brazil I’m working with breast cancer expression data from the TCGA-BRCA project. All my scripts were written to retrieve HTSeq counts from GDC, but they seem to have been removed from the GDC Data Portal. When using GDCquery,…

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Genomic and epigenomic alterations of the basal-like prognostic biomarkers.

a) Heatmap with dendrogram representing the unsupervised hierarchical clustering analysis based on CNVs data of TCGA-BRCA patients. The rows in the heatmap represent the 11 basal-like prognostic biomarkers. The columns correspond to basal-like and luminal A TCGA-BRCA patients: basal-like are indicated in dark blue and luminal A in green. The…

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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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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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The Evolving Treatment Landscape of Cholangiocarcinoma

Recent genomic profiling studies revealed that approximately 40% of patients with biliary tract cancers harbor actionable genomic mutations. The advances in the understanding and characterization of biliary tract cancers (BTCs), particularly intrahepatic cholangiocarcinoma (iCCA), and genomic profiling over the past decade have led to a rapid expansion of available treatment…

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Index of /runs/gdc/report_2018_02_16

Name Last modified Size Description Parent Directory   –   TCGA-ACC.2018_02_16.diced_metadata.tsv 2018-02-16 01:06 250K   TCGA-ACC.2018_02_16.high_res.heatmap.png 2018-02-16 01:08 73K   TCGA-ACC.2018_02_16.low_res.heatmap.png 2018-02-16 01:08 37K   TCGA-ACC.2018_02_16.sample_counts.tsv 2018-02-16 01:06 142   TCGA-BLCA.2018_02_16.diced_metadata.tsv 2018-02-16 01:06 1.2M   TCGA-BLCA.2018_02_16.high_res.heatmap.png 2018-02-16 01:08 90K   TCGA-BLCA.2018_02_16.low_res.heatmap.png 2018-02-16 01:08 53K   TCGA-BLCA.2018_02_16.sample_counts.tsv 2018-02-16 01:06 201  …

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r – ggplot: Try to plot boxplots with geom_rect on its background, but keep having error with object “variable” not found

I was almost desperate with this error after working on this for 4 hrs, googled and looked from past posts already. Here is my data structure: str(tcga_exp) ‘data.frame’: 11775 obs. of 5 variables: $ cohort: chr “BRCA-Basal.Tumor” “BRCA-LumA.Tumor” “BRCA-LumB.Tumor” “BRCA-LumA.Tumor” … $ exp : num 6.35 5.54 6.56 5.05 5.98…

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Identification of lipid metabolism-associated gene signature

Background Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer. Despite the dramatic improvement in breast cancer prognosis due to recent therapeutic advances, such as more effective adjuvant and neo-adjuvant chemotherapies, together with more radical and safer surgery, advances in early diagnosis and treatment over the…

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updated in-silico scoring system for missense variants

updated in-silico scoring system for missense variants 0 I have to compare and score the impact of missense mutations on PKD1/2 genes in human subjects. I found some literature on the subject, but the publication it’s 5 years old and they used a Grantham-based method from a 2006 publication on…

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BioChain announces expanded line of NGS characterized bio-samples for oncology researchers

NEWARK, Calif., Sept. 22, 2021 /PRNewswire/ — BioChain Institute, (“BioChain”), a leader in high quality processed bio-sample products, announced an expanded line of Next Generation Sequencing (NGS) characterized bio-samples encompassing a variety of cancer-related mutations available for preclinical drug development and as reference samples for CLIA labs.  “Scientists are looking for…

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Data Demonstrates Lucence Liquid Biopsy Test Can Track Treatment-Based ctDNA Changes

NEW YORK – At the European Society for Medical Oncology Congress this week, precision oncology assay developer Lucence presented data that demonstrated its amplicon-based LiquidHallmark assay could be used to personalize care for people with advanced urothelial carcinoma. LiquidHallmark is a laboratory-developed test based on the company’s AmpliMark next-generation sequencing platform…

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Getting exon sequences for all human genes

Getting exon sequences for all human genes 2 Hi everyone, I would be very grateful if you could help me. I want to download the sequences of all the exons for each human gene. I went to ensembl biomart and tried to do it for BRCA2 first (this was a…

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The Current Molecular Treatment Landscape of Advanced Colorectal Cancer and Need for the COLOMATE Platform

Next-Generation Sequencing Utilizing Tumor Tissue and/or Blood The identification of actionable genomic alterations in tumors such as mCRC was once performed by Sanger DNA sequencing of tumor DNA that was extracted from fixed paraffin-embedded tumor tissue, but this has now been replaced by next-generation sequencing (NGS), which allows for larger-scale…

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High tumor mutation burden and DNA repair gene mutations

Introduction Anaplastic lymphoma kinase (ALK)‑fusion genes represent a small but important part of oncogenic driver mutations in NSCLC, accounting for approximately 3%‑7% of all cases worldwide.1,2 Small molecule tyrosine kinase inhibitors (TKIs) are the standard therapy for ALK-rearranged NSCLC. Crizotinib, a first-generation TKI, is the most widely used targeted drug…

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Personalized profiles for disease risk must capture all facets of health

Providing the best possible care for an individual means having a better understanding of their risks of developing disease. The goal is to have personalized answers when people need to know whether, for instance, preventive surgery makes sense, a given medicine is likely to be risky or a certain diet…

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Revealing biomarkers associated with PARP inhibitors based on genetic interactions in cancer genome

This article was originally published here Comput Struct Biotechnol J. 2021 Aug 10;19:4435-4446. doi: 10.1016/j.csbj.2021.08.007. eCollection 2021. ABSTRACT Poly (ADPribose) polymerase inhibitors (PARPis) are clinically approved drugs designed according to the concept of synthetic lethality (SL) interaction. It is crucial to expand the scale of patients who can benefit from…

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Genome-wide synthetic lethal screen unveils novel CAIX-NFS1/xCT axis as a targetable vulnerability in hypoxic solid tumors

Abstract The metabolic mechanisms involved in the survival of tumor cells within the hypoxic niche remain unclear. We carried out a synthetic lethal CRISPR screen to identify survival mechanisms governed by the tumor hypoxia–induced pH regulator carbonic anhydrase IX (CAIX). We identified a redox homeostasis network containing the iron-sulfur cluster…

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pughlab/inspire-genomics: Pan-cancer analysis of genomic and immune landscape profiles of metastatic solid tumors treated with pembrolizumab

Contents Serial circulating tumor DNA (ctDNA) monitoring is emerging as a non-invasive strategy to predict and monitor immune checkpoint blockade (ICB) therapeutic efficacy across cancer types. Yet, limited data exist to show the relationship between ctDNA dynamics and tumor genome and immune microenvironment in patients receiving ICB. Here, we present…

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Predicting and characterizing a cancer dependency map of tumors with deep learning

INTRODUCTION The development of novel cancer therapies requires knowledge of specific biological pathways to target individual tumors and eradicate cancer cells. Toward this goal, the landscape of genetic vulnerabilities of cancer, or the cancer dependency map, is being systematically profiled. Using RNA interference (RNAi) loss-of-function screens, Marcotte et al. (1),…

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Overall survival and Event free survival

Overall survival and Event free survival 0 Hello everyone. I have a simple question. How do I calculate the overall survival (OS) rate and Event-free survival (EFS) using TCGA-BRCA clinical data? which column must be used for each one? Also, can I use the first quartile as my risk score…

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Differential expression analysis of TCGA data based on tumor staging

Hi everyone I wanted to analyze TCGA-BRCA data for identifying DEGs in different TNM stages (I to IV) between Normal and Tumor. How to change the following code to get the DEGs based on the staging? CancerProject <- “TCGA-BRCA” DataDirectory <- paste0(“../GDC/”,gsub(“-“,”_”,CancerProject)) FileNameData <- paste0(DataDirectory, “_”,”HTSeq_Counts”,”.rda”) query <- GDCquery(project =…

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Survival Analysis Cut-off

Survival Analysis Cut-off 0 Hello guys, I am doing a survival analysis using TCGA-BRCA project data. I am trying different cut-offs to separate my samples into high and low risk groups, but since it is my first time I would like to ask a question just to be fully sure…

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