Tag: CNA

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Conumee output as input for Gistic2.0 0 Hi Biostars! I am currently undertaking a CNA-analysis, in which i have access to methylation array data (Infinium EPIC). After generating CNV data through conumee, i would like to use this output for further processing using Gistic 2 to study CNAs at a…

NA values in conumee detail 0 Hi Biostars! I am currently performing a CNA-analysis on Illumina Infinium EPIC data. As i have genes of interest discovered through a separate RNA-seq analysis, i created g-ranges for these to study their CNA profile using conumee. However, after successfully running CNV.create_anno (i.e. creating…

Help locating TCGA data from cbioportal 0 Hi, I am a newbie, I want to locate the following files: data_RNA_Seq_v2_expression_median.txt data_linear_CNA.txt From what I read from other threads/google search, these data are supposed to come from cbioportal? But I can’t seem to locate these files in the cbioportal website! Any…

National Chung Hsing University researchers have created an artificial intelligence (AI)-powered irrigation calculator capable of reducing water use in rice farming by 20 percent. The calculator’s AI engine, which can identify the important physiological characteristics of a rice crop, provides detailed advice on irrigation within 10 to 15 seconds by…

LIFE-CHANGING: Certain people with B-cell acute lymphoblastic leukemia or relapsed or refractory diffuse large B-cell lymphoma are covered for about NT$8.19m People with two types of cancers who need treatment costing millions of New Taiwan dollars are now covered by the National Health Insurance (NHI) system. From Nov. 1, people…

Taipei, Nov. 3 (CNA) Patients with two types of cancers who get CAR T-cell treatment costing millions of Taiwan dollars will now be covered by Taiwan’s national health insurance (NHI) system, as the National Health Insurance Administration (NHIA) indicated in October. Starting Nov. 1, the treatment is covered under the…

Panel of tumors for CNV detection 1 Hi, I’m trying to detect somatic copy-number alterations in custom-targeted sequencing panel. Most of the tools and methods published for this sake requires matched normal sample or panel of normals. However, we have no normal samples. We do have dozens of tumor samples…

Paired tumor and normal DNA samples from 30 patients were subjected to WES at four ZPM laboratories with subsequent data analysis performed at five ZPM bioinformatic institutions (Fig. 1). DNA was originally derived from fresh-frozen samples that had been analyzed by WES within the multicenter MASTER (Molecularly Aided Stratification for…

Taipei, Oct. 16 (CNA) From November, patients with two types of cancers will be eligible to receive CAR T-cell treatment under Taiwan’s National Health Insurance (NHI) system, the National Health Insurance Administration (NHIA) said Sunday. The treatment, which takes immune T cells and modifies them with chimeric antigen receptors, or…

DOI: 10.18129/B9.bioc.TitanCNA     Subclonal copy number and LOH prediction from whole genome sequencing of tumours Bioconductor version: Release (3.13) Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome…

Hi, I am trying to run CONTROL-FREEC on diploid yeast samples to detect CNVs on a department cluster. The config file looks like this: [general] chrLenFile = yeast_chr.len ploidy = 2 window = 150000 #breakPointThreshold = -.002; #coefficientOfVariation = 0.062 chrFiles = /net/smith/vol1/home/student/FREEC-11.6b/data/test_sludge/yeast_files outputDir = /net/smith/vol1/home/student/FREEC-11.6b/data/test_sludge/output #degree=3 [sample] mateFile =…

How to distinguish between normal and malignant epithelial cells based on CNV? 1 One of the method that is used to find malignant cells in tumor scRNA-seq data is infercnv. This, this, and this papers used infercnv outputs to find cancer cells among other epithelial cells. They separate cancer and…

CNA score calculation per cell 0 Hello, I am analyzing single-cell RNA seq data, and I would like to get a CNA score per cell. I ran CNV estimation tools (like copykat and SCEVAN), and I get a CNA matrix output. I am interested in getting a CNA score per…

TAIPEI (Taiwan News) — An investigation found that the woman who visited a New Taipei indoor aquatic facility and subsequently died from a rare brain-eating amoeba infection had not visited other places for aquatic activities, according to health authorities. Marking the first such case in Taiwan in 12…

The rise of machine learning and artificial intelligence has sparked a technological revolution, with industry giants utilizing these cutting-edge technologies to optimize processes, enhance the user experience, and uncover insightful data. In the bustling hub of AI and ML, two services – Vertex AI and Datadog – are transforming the…

Things are about to change. ML and AI applications are revolutionizing the way problems are solved in everything from complex medical and financial systems, to autonomous vehicles and personalized search algorithms. End-to-end machine learning platforms like Vertex AI provide critical guardrails for ML development and deployment — from feature engineering…

Forum:Superfreq result interpretation for amplification events from RNA-Seq 0 I have run superFreq on a couple of samples from gallbladder tissues along with OCUG and NOZ cell-line which have ERBB2 amplifications. The combined CNA heatmap that lists out the calls gene-wise can call the amplifications in these samples, but the…

YONGIN, South Korea, July 26, 2023 /PRNewswire/ — GC Genome Corporation, a leading genomic diagnostics company, announced the publication of a new study in Journal of the National Cancer Institute (JNCI), shedding light on the remarkable potential of utilizing circulating tumor DNA (ctDNA) copy number aberration (CNA) for prognosis prediction…

Data reporting No statistical methods were used to determine the sample size. The experiments were not randomized. Pathologists were blinded to the genetic alterations in each sample during histopathological evaluation. Participants and materials We enroled 207 female patients with breast cancer who underwent surgery at the Kyoto University Hospital and…

Liquid biopsy samples Patients with histological or cytological confirmation of chemotherapy-naive SCLC were recruited and consented at The Christie NHS Foundation Trust according to an ethically approved protocol (NHS Northwest 9 Research Ethical Committee). Informed written consent was obtained from all subjects. Experimental protocols were approved by the Institutional Review board of…

Clinical data The demographic data of the 254 HCC patients are presented in Table S1. We found that treatment received by HCC patients were associated with patient survival, as shown in Fig. S1. Somatic mutations The mutational landscape is shown in Fig. 1. The top 10 most common mutated genes were…

Characterization of genomic landscape We compared somatic variants, copy number alterations, and mutational burden between the primary and metastatic tumors of the ST and LT survival groups. Our cohort of patient tumors exhibited characteristics typical of those seen in previously sequenced HGSC tumors, such as nearly ubiquitous TP53 mutations, high…

Hi all, I attempted to download a list of multi assay experiments using cBioDataPack a moment ago. after cbio <- cBioPortal() studies <- getStudies(cbio, buildReport = TRUE) PedPanCanStudyIds<-studies[grepl(‘Ped’, studies$name, ignore.case=TRUE) & grepl(‘Pan’, studies$name, ignore.case=TRUE), ]$studyId I ran PedPanCanMaeList<-list(); setwd(oD) PedPanCanMaeList[[PedPanCanStudyIds[1]]]<-cBioDataPack(PedPanCanStudyIds[1]); saveRDS(PedPanCanMaeList[[ PedPanCanStudyIds[1] ]], file=paste0(‘./cBioPortal/’, PedPanCanStudyIds[1], ‘.Rds’) ) PedPanCanMaeList[[PedPanCanStudyIds[2]]]<-cBioDataPack(PedPanCanStudyIds[2]); saveRDS(PedPanCanMaeList[[ PedPanCanStudyIds[2]…

Do you want to contribute to top quality medical research? Do you want to work in the exciting field of single-cell cancer genomics and contribute to improve our understanding of how tumors evolve to treat them more effectively? A postdoc position in single-cell cancer omics bioinformatics is immediately available in…

Correct 18S data file ffor assing taxonomy 0 I wan to perform taxonomy identification using assign taxonomy and silva 18 S data set but i got this error message : Error in assignSpecies(seqs, refFasta = refFasta, allowMultiple = allowMultiple, : Incorrect reference file format for assignSpecies (this looks like a…

Copy Number Alteration and Loss or Heterozygosity 0 Dear all, I would appreciate having a piece of advice : Given the output from a copy number caller (FACETS, TitanCNA, Sequenza, Sclust) which criteria shall I apply on LogR and BAF (B allele frequency, minor allele frequency) in order to annotate…

Hi everyone, I want to perform a simulation with a piston on fused silica. I have tried read the fused silica file, extend the dimensions of the simulation box and create atoms of the piston in the upper part of the box (blank region) but it gave an error. So…

LEAKING TO CHINA: An academic said the source of genetic data leaks is the Chinese machines used for gene sequencing, raising national security concerns By Lee I-chia / Staff reporter Taiwan’s laws should be amended to help prevent genetic data from leaking to China and to establish a domestic genetic…

Generating variant read count matrix, total read count matrix and binary/ternary mutaion matrix for SNV from scDNAseq FASTQ files 0 Leung et al., 2017 paper mentioned in Fig 1 data processing for CRC patients was sequenced as single cell for both SNV (with MDA WGA) and CNA (with DOP-PCR) parallelly….

Data collection for HRD prediction model training and validation For the development of the HRD prediction model, 1854 samples (WGS data) from the pan-cancer analysis of whole genomes9 (PCAWG) and 560 breast cancer samples (SNP array data)16 are collected. To obtain a high-confidence training dataset of HRD, samples with BRCA1/2…

NEW YORK — Researchers have uncovered genetic and gene expression changes in the organs of patients who died of precision treatment-resistant metastatic cutaneous melanoma. The patients had initially benefited from treatments such as MAPK inhibitors (MAPKi) and immune checkpoint blockade (ICB) but later acquired resistance and succumbed to the disease….

Hey there, I just started to work with WisecondorX for NIPT analysis. Everything went smooth until I get to the prediction step. When I use this command I get the error below; code; WisecondorX predict V350129651_L04_79.npz /data/storeData/project/1_Projects/NIPT/NIPT-REF/NIPT_REF_npz/niptref_mg.100kb.npz /data/storeData/project/1_Projects/NIPT/nipt_1/V350129651_L04_79 –plot –bed “[INFO – 2023-04-27 13:46:42]: Starting CNA prediction [INFO – 2023-04-27…

Activation of the polyamine-hypusine circuit is a hallmark of human cancer and of MYC-driven lymphoma. A, Copy number alterations (CNA) of EIF5A and EIFA2 (left), and of DHPS and DOHH (right) across different cancer types. Abbreviations for the indicated TCGA datasets are: prostate = PRAD; Liver Hepatocellular = LIHC; Diffuse…

Multi-omics analyses of the ICC samples Following multiregional sampling of primary ICC cases, we performed multi-omics analyses, including genome, transcriptome, proteome, and metabolome analysis. We used 10 (67 samples), 11 (88 samples), 10 (49 samples) and 10 (49 samples) ICC cases for WES, whole-transcriptome sequencing, proteomic analysis, and metabolomic analysis,…

fitting a copy number profile to know CNV signatures 0 Dear all, I would like to ask for a suggestion on whether I could fit a CNA profile of a sample that I do have to known CNV signatures. I have used the package sigminer, that seems to focus entirely…

The Google Data Cloud & AI Summit is an annual event and a part of Google’s digital cloud summit series. It focuses on revealing insights, solutions, business transformation opportunities, and the latest innovations in Google Data Cloud for AI, databases, data analytics, and business intelligence to enthusiasts, developers, business users,…

Taipei, April 11 (CNA) Taiwanese researchers have discovered a distinct new species of clam native to the Tamsui River that was previously thought to have originated in Japan. According to the Council of Agriculture, researchers stumble across the new species while working alongside the Tamsui Fisherman’s Association to restore clam…

allelic copy number variation 0 Dear all, I am working with sequenza output that has the following format – 1st line (www.ncbi.nlm.nih.gov/pmc/articles/PMC4269342/ ; Sequenza estimates the allelic specific copy numbers). How can I transform this output into numerical allele specific copy-numbers shown on the 2nd line ? chromosome position base.ref…

CNA plots with gene names using GISTIC 0 I have the GISTIC plots with amplification and deletion for my data but the plots show chromosome region where as I want to have gene names on the peak positions. I have attach a demo diagram below. visualization CNA GISTIC • 72…

Okay, so I initially suggested that I deliver the content of this blog as an interpretive dance video. My suggestion was turned down, and I’m sure you’re as disappointed as I am. But dancing or not, I’m really excited about Generative AI support in Vertex AI.  Vertex AI was launched…

alelle – specific CNA/LOH 0 Dear all, I would appreciate having your help on the following : I would like to use a software that is called scarHRD to measure the degree of homologous recombination deficiency (HRD) in cancer cells. The link to the scarHRD package is : github.com/sztup/scarHRD ScarHRD…

Using Copy Number Alterations detected in other studies for the same tumor cell line 0 Hello everybody, It is my first time working with cancer genomes and I have some doubts. I found this study in which they provide a lot of different sequencing data for the cell line HCC1395,…

DOI: 10.18129/B9.bioc.ChAMPdata   Data Packages for ChAMP package Bioconductor version: Release (3.16) Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis. Author: Yuan Tian [ctb,aut], Tiffany Morris [cre,aut], Lee Stirling [ctb] and Andrew Teschendorff [ctb] Maintainer: Yuan Tian <champ450k at gmail.com> Citation (from within…

I want to plot the EnrichedHeatmap using the GenomicRanges of my CNA data. The normalizeToMatrix function returned mat1, which is filled with 0, resulting in Error: You should have at least two distinct break values. when I try to plot it. library(EnrichedHeatmap) library(GenomicRanges) library(data.table) library(ChIPseeker) library(tibble) library(AnnotationHub) library(IlluminaHumanMethylation450kanno.ilmn12.hg19) library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb…

Generative AI, that is, the ability to create text, images, code, videos, audio and more from simple natural language prompts is poised to welcome a new way of transforming user experience and how people interact with information. Google Cloud has announced that its new generative AI capabilities are now available…

Generative AI is poised to usher in a new wave of interactive, multimodal experiences that transform how we interact with information, brands, and one another. Harnessing the power of decades of Google’s research, innovation, and investment in AI, Google Cloud is bringing businesses and governments the ability to generate text,…

Google on Tuesday unveiled a ‘magic wand’ that creates marketing blogs, training plans and other text documents for users. The announcement is the tech giant’s new generative AI system rolling out to Google Workspace, adding new capabilities to Docs, Sheets, Slides and Gmail. The system will be able to summarize message threads…

Interpreting ASCAT CNV output 1 Hello, I have two queries w.r.t ASCAT CNV data: How does one go about getting the total copy number for a given locus or chromosome from the ASCAT CNV.output results. What is the optimal way to filter the dataset to reduce the noise? I would…

Ka/Ks and dn/ds are usually considered to be the same thing (also named ω). However, estimation of KaKs using seqinr and dnds using ape give different results. The two estimators refer to the same paper for details, although seqinr also refer to other papers. Calling dnds function, we cna understand…

Entry EC 1.7.1.4                  Enzyme                                  Name nitrite reductase [NAD(P)H];nitrite reductase (reduced nicotinamide adenine dinucleotide (phosphate));assimilatory nitrite reductase (ambiguous);nitrite reductase [NAD(P)H2];NAD(P)H2:nitrite oxidoreductase;nit-6 (gene name) Class Oxidoreductases;Acting on other nitrogenous compounds as donors;With NAD+ or NADP+ as acceptorBRITE hierarchy Sysname ammonia:NAD(P)+ oxidoreductase Reaction(IUBMB) NH3 + 3 NAD(P)+ + 2 H2O = nitrite + 3 NAD(P)H…

In general, more than half of MDS patients are diagnosed at age 75 years or older, and the incidence rate of MDS in patients under 50 years of age is as low as less than 1 per 100,000)3. The median number of gene mutations in patients with MDS has been found to…

Early detection (pancreatic cancer) cfMeDIP-seq, 5hmC sequencing LR elastic-net Hierarchical clustering, t-SNE, LR with elastic-net penalization Methylation (5mC-5hmC) 208 (72/136) 24-feature 5mC, 27-features 5hmC, 51-features combined model SML, UML Combined 5mC and 5hmC AUC of 0.997 (sensitivity 0.938, specificity 0.955) Median total reads: 17.4 M, 0.8 nonduplicate mapping rate pms.cd120.com/PDAC/index.html…

Introduction Cancer is a large group of diseases that have the same basic properties that are caused by cell division or uncontrolled cell proliferation. This irregular process of division produces a mass of cells in an organ or tissue, which leads to the formation of tumours.1,2 Cancer became one of…

Job Posting for Scientist II, Bioinformatics at PTC Therapeutics, Inc. Job Description Summary: The Scientist II, Bioinformatics is responsible for planning and performing scientific experiments that contribute to PTC’s research and drug discovery activities. The Scientist II is also responsible for communicating experimental results to his/her supervisor and…

MACHETE is a new CRISPR-based technique developed by researchers at the Sloan Kettering Institute (SKI) to study large-scale genetic deletions efficiently in laboratory models. People are already calling it the Machete Paper. Still, lead authors Francisco “Pancho” Barriga and Kaloyan Tsanov of the Sloan Kettering Institute don’t want the name…

Sample preparation and sequencing The method of sample collection and processing is described in a companion article (ref. 23). Sequencing and basic bioinformatic processing of DNA-, RNA- and ATAC-seq data are included there as well. Gene expression normalization and filtering The number of non-ribosomal protein-coding genes on the 23 canonical chromosome pairs…

How can you score CNV for each sample (with TCGA data)? 0 Hi, I’m looking at TCGA CNV data, and trying to get a sense of how copy number altered each sample is. TCGA gives “Segment_Mean” values for varying sized regions of the genome for each sample, which to my…

Group comparison of CNA between primary and metastatic samples 1 Dear all, I am trying to find significantly different CNA between human cancer primary samples and their metastatic samples. My data is from WGS and I have already segmentaiton file. GISTIC2.0 provides significant CNA evet in a cohort, but does…

SAN JOSE, Calif. & HYDERABAD, India, November 24, 2021–(BUSINESS WIRE)–Analytics Insight has named ‘Top 10 Data Science Leaders of 2021’ in its November magazine issue. The issue focuses on trailblazing leaders who are changing the industry dynamics with top-notch data science skills. The magazine issue recognizes ten leaders who are…

Image: The Bio-Rad QX200 Droplet Digital PCR (ddPCR) reader (Photo courtesy of University of California Santa Barbara) Diffuse large B-cell lymphoma (DLBCL) is the most common, aggressive type of non-Hodgkin lymphoma. Although 50% to 60% of individuals achieve cure with chemoimmunotherapy, outcomes are poor for relapsed/refractory disease. Chimeric antigen receptor…

Somatic point mutation calling suggests Mutect2 is best for subclonal variants We applied four somatic variant callers (Mutect211, Strelka212, VarScan213 and Lancet14) to a highly mutated tumour dataset (S3R3) at 100% tumour purity across all sequencing depths. Runtimes differed substantially between methods, with Strelka2 being fastest and Mutect2 taking longest…

Copy Number to Log2_ratio for autosomal 0 Hi, I want to transform some ASCAT data into log2_r values. The file contains at total copy number column. I would then take fold ratio of the total copy number versus the natural ploidy, correct? Can I assume the natural ploidy for all…

Get Allele specific copy number regions from WGS data using ASCAT? 0 Hi, I have some paired samples(normal vs. tumour) and want to do allele specific CNA analysis. can you help me to check if I use the right pipeline? I use bcftools mpileup and call to call snp from…

Organoid culture of small intestinal cells and lentiviral transduction C57BL/6J mice and BALB/cAnu/nu immune-deficient nude mice were purchased from CLEA Japan (Tokyo, Japan). The small intestine was harvested from wild-type male C57BL/6J mice at 3–5 weeks of age (Additional file 1: Figure S9A). Crypts were purified and dissociated into single cells,…

Entry EC 1.14.12.17               Enzyme                                  Name nitric oxide dioxygenase Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donorBRITE hierarchy Sysname nitric oxide,NAD(P)H:oxygen oxidoreductase Reaction(IUBMB) 2 nitric oxide + 2 O2 + NAD(P)H =…

Footnotes Grant support This work is jointly supported by National Natural Science Foundation of China (82173035, 81802813,82030079, 81972656, 81988101, and 81902401), the National Science and Technology Major Project of China (2018ZX10723204), the Michigan Medicine and Peking University Health Science Center Joint Institute for Translational and Clinical Research (BMU2020JI005), Natural Science…

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),…

Difference between linear and log2 CNA values 0 Hi, Simply what the title is asking. Cbioportal allows for either Log2 cna values or linear cna values. Is this simply how the values were normalized? Is there a way to differentiate between the two value types by seeing the numbers? Thanks!…

Copy number differences between groups 0 Analogous to differential expression with RNA data, is there a statistic or tool to analyze the frequency of copy number alterations between two groups? I had imagined this to be a Chi-square performed like 20,000 times (each gene) to see if that particular gene…