Tag: cnv

FGFR inhibitors have been developed to inhibit FGFR activation and signal transduction; notwithstanding, currently the selection of intrahepatic cholangiocarcinoma (iCCA) patients for these drugs only relies on the detection of FGFR2 genetic alterations (GAs) in tumor tissues or circulating tumor DNAs, without concomitant assessment of FGFR2 signalling status. Accordingly, we…

Jan. 19, 2024 — Over 18 million people worldwide are annually diagnosed with cancer, with each case hiding many mutations in its genome. Understanding these mutations furthers cancer research, while also providing a deeper understanding to create possible cures, therapies and prevention strategies. The Triton Shared Computer Cluster at the…

Russell PSS, Nagaraj S, Vengadavaradan A, Russell S, Mammen PM, Shankar SR, et al. Prevalence of intellectual disability in India: a meta-analysis. World J Clin Pediatr. 2022;11:206–14. Article  PubMed  PubMed Central  Google Scholar  Winnepenninckx B, Rooms L, Kooy RF. Mental retardation: a review of the genetic causes. Br J Dev…

Gains and losses of genetic material can be almost any size: a single base pair or an entire chromosome spanning tens of millions. As genomic analysis technologies have evolved, researchers have separated these often medically relevant variants into bins based on their size and the methods used to detect them….

How to convert and annotate apt-probeset-genotype into PLINK format 2 Dear all, I called SNP genotypes of 100 Affy6 CEL files using apt-probeset-genotype from APT in order to perform a subsequent CNV analysis with PennCNV. As PennCNV doesn’t integrate SNP quality control procedure (move out SNP with genotype call <…

Fragment analysis separates and analyzes amplified PCR products according to fragments using a primer marked by a fluorescent label. ‍ Fragment Analysis can have many applications, such as: Linkage mapping Pathogen sub‐typing  Loss of Heterozygosity (LOH)  Animal breeding Genetic diversity Inter‐simple sequence repeat (ISSR)  Human, animal, and plant typing Microsatellite…

Whole-genome sequencing (WGS) analysis of early and advanced adenocarcinomas Whole-genome short read and long read sequencing datasets of 76 lung cancer specimens were analyzed. The datasets included newly generated data for 48 early small-sized lung adenocarcinoma cases (collectively called “Early-Ad” hereafter). These cases included 26 AIS (9 and 17 cases…

In a recent study published in the journal Nature, researchers investigated the previously underrepresented genomic diversity of four Aboriginal Australian communities. They used population-scale whole-genome (WGS) long-read sequencing. Study findings revealed unique alleles comprised of insertion-deletion variants, variable copy number regions, and structural variants, 62% of which are novel to…

Identification of DRGs in PCa Figure 1a showed the flow chart of this study. To explore the role of DRGs in PCa, we analyzed the gene expression profiles of these 15 DRGs in PCa patients. As shown in Fig. 1b, for ACTN4, TLN1, IQGAP1, CD2AP, FLNA, MYH9, MYL6, and ACTB genes, the…

Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…

Working with infercnv results for large datasets 0 I’m currently working with infercnv on a large dataset of 10x scRNA. I want to meaningfully visualise the results but with the resulting matrix of cnv results being so large it becomes prohibitive to visualise even with rasterisation. I was wondering if…

Lichtenstein P, Yip BH, Bjork C, Pawitan Y, Cannon TD, Sullivan PF, Hultman CM. Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study. Lancet. 2009;373(9659):234–9. Article  PubMed  Google Scholar  Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R,…

The affine gap design space for selecting variant representations As demonstrated in Fig. 1, the main issue with a difference-based format such as VCF is that often there are multiple reasonable sets of variant calls that can be used to represent the same final sequence relative to a reference FASTA. Since…

Introduction Respiratory tract infections are common and occur frequently. Rapid and accurate microbial detection is essential for timely and appropriate treatment. Traditional microbial detection methods have some limitations such as dependence on morphology, long duration, low sensitivity, and high variability.1,2 Metagenomic next-generation sequencing (mNGS) is a new detection technology characterized…

DMD is a degenerative, fatal, and incurable muscular dystrophy that is typically diagnosed between the ages of three and four. Affected boys have increasing muscle weakness and cardiorespiratory and orthopedic complications and are at risk of cognitive, behavioral, and language difficulties30. Suspected cases often undergo DMD gene mutation screening to…

Cell line and growth assays Cell lines were grown in Roswell Park Memorial Institute-1640 medium (RPMI-1640) with 1% penicillin–streptomycin (10,000 U ml−1) and 10% FBS or in Iscove’s modified Dulbecco’s medium (IMDM) with 1% penicillin–streptomycin (10,000 U ml−1), l-glutamine (200 mM) and 10% FBS in a humidified incubator with 5% CO2 maintained at 37 °C. Drugs…

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…

Introduction Patients with persistent, recurrent, or metastatic (P/R/M) cervical carcinoma respond poorly to treatment despite the best available therapeutic regimens, with a 5-year survival of 17%.1 Most of them are heavily pretreated with chemotherapy and/or radiotherapy, and many patients experience complications related to treatment or advanced disease, which exclude them…

TCGA/Broad Institute CNV Files Segment Mean 3 Hello everybody, I am trying to analyse CNV data from TCGA to get a measure of overall CNV per patient. When I download the Level 3 files taken from the SNP6 array, there is a column in the file called Segment_Mean. (Example at…

Introduction Lung cancer is one of the most common types of cancer worldwide and the leading cause of cancer death.1 The main category of lung cancer is non-small cell lung cancer, accounting for about 85%, and lung adenocarcinoma, as a kind of non-small cell lung cancer, is the most frequently…

Here, we report a proband with characteristic features of the clinical syndrome, including downward-slanting palpebral fissures; delayed development of bilateral optic nerve hypoplasia; facial deformity with a small mouth, thin lips, micrognathia, and blepharophimosis; short neck; abnormal deciduous teeth; and malformations of the thorax and short ribs. The proband showed…

Introduction: To investigate the molecular alterations of cuproptosis-related genes and to construct the cuproptosis-related circRNA-miRNA-mRNA networks in neovascular age-related macular degeneration (nAMD). Methods: The transcriptional profiles of laser-induced choroid neovascularization (CNV) mouse models and nAMD patient samples were obtained from sequencing and from the GEO database (GSE146887), respectively. The expression…

how to perform analysis with given copy number variation datasets between disease and control cohorts 0 Here I have two given copy number variation datasets of a disease cohort and a control cohort. I aimed to explore the possible association of copy number variation and disease phenotype. I wonder how…

how to get ER, PR and HER2 data from TCGA BRCA 2 Hi I have dowloaded the BRCA data from TCGA using TCGABiolinks I have done this: BRCARnaseqSE <- GDCprepare(query.a, directory = “BRCA_all”) sample.info <- SummarizedExperiment::colData(BRCARnaseqSE) Now I want to get data on ER, PR and HER2 – positive, negative…

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…

Introduction Ultrasound soft markers refer to small nonspecific variations in foetal structure found in prenatal ultrasound that are often associated with abnormal chromosome number or pathogenic copy number variations (CNVs).1,2 Common ultrasound soft markers include nuchal translucency (NT) thickness, nuchal fold (NF) thickness, nasal bone dysplasia, choroid plexus cyst, intracardiac…

Study design and sample collection To evaluate the accuracy and benchmark the optimal DP of LP GS in the detection of mosaicism, evaluation strategies were designed using simulated data and virtual samples, respectively (Fig. 1). The DNA of a total of 28 clinical samples (S1 ~ S28) (aborted fetal tissue, whole blood, chorionic…

GISTIC isn’t checking chromosome 23 / X 0 Hi, I have a problem with GISTIC apparently not checking for CNV on chromosome X. GISTIC2 runs without errors on my segmentation file with the supplied reference file refgenefile=refgenefiles/hg38.UCSC.add_miR.160920.refgene.mat My input file has CNV events in chromosome ’23’ but the GISTIC run…

Hello, I ran my analysis on GISTIC_2.0 version 6.15.30 on Gene Pattern. I have 58 samples of whole genome sequencing data with the seg copy number file. I prepared the input for gistic as stated in the literature and the forum: a txt file with 6 columns: sample, chromosome, start,…

What are the steps for Germline and Somatic CNV detection using CNVkit? 0 Hello, I have some basic questions regarding the CNV calling using CNVkit. I have tried to find the CNV caused between normal and tumor samples, but it was not clear which steps should be done respectively. For…

Job:Bioinformatics Research Associate, Genomics and Genetics 0 @jp-carter-15371 Last seen 7 hours ago Nashville, TN The Bioinformatics Research Associate is part of the Creative Data Solutions (CDS) Shared Resource at Vanderbilt University and is a key individual contributor responsible for performing bioinformatics analyses of genomic data sets, developing and implementing…

Understanding consensus CNV of PCAWG data 0 Hi everyone, I want to get the exact copy number of each gene for each sample in PCAWG I have located this PCAWG directory dcc.icgc.org/releases/PCAWG/consensus_cnv/gene_level_calls However, there are three files listed there: all_samples.consensus_CN.by_gene.170214.txt.gz all_samples.consensus_CN.minor_allele.by_gene.170313.txt.gz all_samples.consensus_level_calls.by_gene.170214.txt.gz I cannot find any description of these files…

What is the difference between CNV binning and aligning to gene? 0 Hi All, I have datasets of Whole Genome Seq of cancer and non-cancer cell. I would like to investigate the copy-number variation between the two conditions. After aligning read to reference genome, there would be two possible ways…

Introduction Since the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in 2019, this coronavirus has spread to more than 200 countries, cumulatively infecting 672 million people and causing 6.84 million deaths. Moreover, the emergence of numerous variant strains (α, β, γ, δ, and Omicron) presents a serious challenge for…

Oral and Poster Abstracts 652. Multiple Myeloma: Clinical and Epidemiological: Poster III Research, adult, Translational Research, assays, Plasma Cell Disorders, bioinformatics, Diseases, Lymphoid Malignancies, computational biology, Technology and Procedures, Study Population, Human, molecular testing, omics technologies Dor D. Abelman1,2, Jenna Eagles1*, Stephanie Pedersen1*,…

(Image Credit: AdobeStock) The topline results from the randomized, double-masked, sham-controlled, multicenter phase 3 GATHER2 24-month trial (NCT04435366) showed that avacincaptad pegol intravitreal solution (IZERVAY, Iveric Bio), a complement C5 inhibitor, met the primary objective of reducing the rate of geographic atrophy (GA) growth in patients treated monthly compared to…

Are XA: tagged reads == SA: tagged BWAMEM aligned reads? 1 I have a simple question. I am interested in reads with secondary alignments. I have a script that will parse out reads with secondary alignments for bwa-mem BAM files. These reads are tagged with SA: My problem is that…

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…

Specimen data All samples for MM, OV, BRCA, PDAC, UCEC, CRC, CESC/AD, SKCM and HNSCC, as well as 2 NATs for GBM and 1 NAT for ccRCC were collected with informed consent in concordance with Institutional Review Board (IRB) approval at the School of Medicine at Washington University in St…

Depth evaluation of LP GS. (A) Total detection sensitivity of LP GS for 155 CNVs. The dotted green line shows the optimal UAHRs (25 M). (B)Evaluation of the performance of LP GS using samples with 25 M UAHRs. For the 30 samples with positive CMA results, the left bar figure…

Total Sdic mRNA abundance positively correlates with Sdic copy number in testis Evidence for the presumed enhancing effect of gene duplication on the amount of gene product is mixed. Some studies indicated that no such, or a very limited, effect exists19,38,39,40,41, whereas others found a significant increase17,18,22,42,43. A possible explanation…

14 Oct 2023 Job Information Organisation/Company CNRS Department Institut de Recherche sur le Cancer et le Vieillissement, Nice Research Field Biological sciences » Biology Researcher Profile Recognised Researcher (R2) Country France Application Deadline 3 Nov 2023 – 23:59 (UTC) Type of Contract Temporary Job Status Full-time Hours Per Week 35…

Why 99% coverage at 20X depth for sequencing? 0 Hi, I’m new to sequencing. I don’t understand why most labs set this metric and how they derive these specific values, rather than 95%, or 30X for example. How do they tie in with statistics as well? Does it have to…

Hi, I’m new to sequencing. I don’t understand why most labs set this metric and how they derive these specific values, rather than 95%, or 30X for example. How do they tie in with statistics as well? Does it have to do with an error rate of 1%? Or does…

The Center of Excellence (CoE) in Data Science and Bioinformatics at LabCorp Information Technology department applies various data science disciplines (including artificial intelligence, machine learning, graph databases, statistics, bioinformatics, and natural language processing) to our clinical, operational and financial challenges, and creates opportunities to enhance the value of our offerings…

Data simulation Short nanopore sequencing runs yield sparse and random coverage of the genome. To enable model training, we generate simulated sparse nanopore runs based on microarray data. To this end, N simulated reads are randomly sampled from the read length distribution (D) and assigned a start mapping position in…

Introduction Hypertrophic cardiomyopathy (HCM), characterized by asymmetric hypertrophy of the ventricular wall, is a condition where the heart becomes thickened without a distinct inducement.1,2 Epidemiological investigation shows that the estimated prevalence rate of HCM in the general population is 1:500.3,4 The clinical manifestations vary greatly, with no symptoms and mild…

Received: 28 August 2023 / Revised: 3 October 2023 / Accepted: 6 October 2023 / Published: 9 October 2023 Round 1 Reviewer 1 Report Dear authors, After consideration, I have some recommendations and concerns that I believe will improve the quality and impact of your manuscript. While the manuscript provides…

. 2023 Oct 5;21(10):e3002313. doi: 10.1371/journal.pbio.3002313. eCollection 2023 Oct. Xiaoyu Liao  1 , Wenzhi Li  1 , Kaibo Lin  1 , Wei Jin  1 , Shaozhen Zhang  1 , Yao Wang  1 , Meng Ma  1 , Yating Xie  1 , Weina Yu  1 , Zhiguang Yan  1 , Hongyuan Gao  1 , Leiwen Zhao  1 , Jiqiang Si  1 , Yun Wang …

Several human diseases arise due to defects in mitochondrial DNA (mtDNA), which is distinct from nuclear DNA and is inherited only from maternal ancestors. The prevention of these diseases by mitochondrial replacement (MR) therapy involves the risk of increasing mtDNA mutations, which can subsequently lead to mitochondrial genetic drift. A…

The Position The Discovery team and Data Analysis Team (DAT) at Veracyte are seeking an experienced bioinformatics scientist to drive next-generation sequencing (NGS) assay development and biomarker discovery in a vibrant group eager to explore and innovate where few have gone before.You will work at the intersection of the established…

(MENAFN– GlobeNewsWire – Nasdaq) Akari’s priority pipeline programs remain on track to begin enrollment in the registrational nomacopan Phase 3 clinical trials in pediatric and adult HSCT-TMA and start PAS-nomacopan clinical trials in geographic atrophy (GA) Granted orphan drug designation from the European Commission for treatment in hematopoietic stem cell…

Approval of Fresenius Kabi’s Tocilizumab Biosimilar in the EU:  On September 19, 2023, Fresenius Kabi announced that the European Commission (EC) granted marketing authorization for TYENNE (tocilizumab), a biosimilar referencing Roche’s ROACTEMRA.  TYENNE is the first tocilizumab biosimilar approved in the EU.  TYENNE received approval for both subcutaneous (prefilled syringe…

IZERVAY achieved a significant reduction in geographic atrophy growth compared to placebo at 24 months. Astellas Pharma has announced positive 24-month topline results from the GATHER2 Phase 3 clinical study of IZERVAY, developed by its subsidiary Iveric Bio who recently secured regulatory approval in the US for the therapy. IZERVAY,…

1. Introduction Newborn screening (NBS) plays a vital role in healthcare systems for the prompt identification of individuals who may develop one of a set of rare, but severe health conditions [1]. In the UK, for example, dried blood spot (DBS) specimens are routinely collected at 4–5 days of age…

How to find positions with higher depth relative to their surroundings 2 Hello. I try to find positions that have higher depth significantly than their surroundings. Is there a good way to do this? Currently I have depth per position data from samtools depth. depth python samtools • 73 views…

(Image Credit: AdobeStock/MIND AND I) Astellas Pharma Inc. announced positive 24-month topline results from the Phase 3 GATHER2 (NCT04435366) clinical trial evaluating the efficacy and safety of avacincaptad pegol (ACP) intravitreal solution (Izervay, Iveric Bio), a complement C5 inhibitor for the treatment of geographic atrophy (GA) secondary to age-related macular…

CNV calling 1 Hello all, Can anyone please suggest the best open source CNV calling tool that is available, having a decent specificty and sensitivity. I am using cn.MOPS and ExomeDepth, currently. But I want to improve the pipeline to get more accurate results. Please suggest. Thanks NGS Variant CNV…

Stoneking, M. An Introduction to Molecular Anthropology (Wiley, 2017). Fuhlrott, J. C. & Schaaffhausen, H. Über die Knochenfunde aus dem Neandertal bei Mettmann. Verhandlungen naturwissenschaftlicher-historischer Ver. preussisch Rheinl. Westfal. Correspondenz-Bl. 14, 50–52 (1857). Google Scholar  Meyer, M. et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos…

Best Tools and Practices for CNV Variant Calling in WES Data 0 Hi Everyone, What are the best tools for CNV variant calling in the context of whole exome sequencing (WES) analysis? I’m currently working on a project focused on CNV detection in autistic subjects, where we aim to strike…

Mice All animal use was approved by the Department of Comparative Medicine at the Massachusetts Institute of Technology (MIT) and the Institutional Animal Care and Use Committee under protocol no. 0714-076-17. Mice were housed with a 12-h light/12-h dark cycle with temperatures in the range 20–22 °C and 30–70% humidity. KrasLSL-G12D…

The median age of the patients was 55 years (range 13–74). Median time between SOT and PTLD was 95 months (range 2–338). Most patients had stage IV disease (n = 13, 76%) with a median metabolic tumor volume (MTV) of 302 mL (range 5–2070 mL). Lactate dehydrogenase (LDH) levels ranged from 210 to 5068 (Additional file…

The PositionRoche Sequencing Solutions (RSS), a business within Roche Diagnostics, focused on developing a disruptive Next-Generation Sequencing (NGS) platform along with a portfolio of reagents, assays and informatics solutions for multiple disease areas. We are looking for a Principal Bioinformatics Scientist in the NGS Algorithms and Applications team to support…

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 =…

Genetic Cancers: Welcome back to “The Science Of Health”, ABP Live’s health column. Last time, in the health column, we discussed the difference between small cell lung cancers and non-small cell lung cancers, and explained why small cell lung cancers are less common than non-small cell lung cancers, despite the…

Sentrix Array Genotyping 0 Hi all, I am currently trying to figure out how to work with genotyping data generated by a Sentrix array. The data I have is an output file from the Illumina GenomeStudio Software, namely a SampleName_FinalReport.txt file which contains the columns Sample ID , Sample Name,…

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…

Testing for measurable residual disease (MRD) in persons with plasma cell myeloma (PCM) after therapy correlates with therapy outcomes including progression-free survival (PFS) and survival (reviewed in refs. [1, 2]). Most MRD-testing in this setting uses multi-parameter flow cytometry (MPFC) but prediction accuracy is imperfect with C-statistics of only about…

PRESS RELEASE Published September 5, 2023 DNA plays a crucial role in human growth and development. Irreparable DNA damage caused by external environmental factors leads to disease, which may be transmitted to future generations through genetic material. Common genetic disorders in humans can be divided into four broad categories: chromosomal,…

Forum:ISCN annotation for SV/CN VCF files 0 Hi I’m trying to annotate the output of a VCF file that contains SV and CNV calls from long read sequencing. The conventional tools work well enough, but I can find anything that will annotate with the ISCN annotation for the whole VCF…

CONTRA for CNV detection. troubleshooting 4 Hi Biostars Users, I would like to know if you have encountered this issue while working with CONTRA tool for detecting CNVs in targeted NGS. In fact, my analysis is “stopping” at the binning process with no error message, I have checked all the…

WES CNV analysis 0 Hi, I am new to CNV analysis and beginner in R language. I am trying to call germline CNVs using exome data using ExomeDepth. I only have the raw data with hg38 reference. If you have the ExomeDepth scripts to run on hg38 reference. Kindly share…

InferCNV results interpretation 0 I’d been looking for a way to distinguish cancer cells from other epithelial cells in tumor scRNA-seq data and found inferCNV method. It finds cells with large-scale chromosomal deletions or insertions from scRNA-seq data based on “normal” cell references. I followed their test running on pediatric…

In a recent study published in Stem Cell Reports, researchers evaluated the use of a dual clustered regularly interspaced short palindromic repeats (CRISPR)-Cas3 system for inducing multi-exon skipping (MES) among Duchenne muscular dystrophy (DMD)-patient-derived induced pluripotent stem cells (iPSCs). Study: Dual CRISPR-Cas3 system for inducing multi-exon skipping in DMD patient-derived iPSCs. Image…

how to filter a multi-sample VCF file based on 0/0 genotype numbers 1 I created one multi-sample VCF file using CNVcaller program. When I checked VCF file, realized that some variants only have one 0/1 or 1/1 genotype and rest of genotypes for other samples are as 0/0. Based on…

Cell culture IMR90, 4T1, CT26, RAW264.7 and B16F10 cell lines were purchased from the American Type Culture Collection and cultured in MEM (IMR90), DMEM (B16F10, RAW264.7) or RPMI (4T1, IMR90, CT26) supplemented with 10% FBS in the presence of penicillin (50 U ml−1) and streptomycin (50 μg ml−1). All cells were found to be…

Marshall, C. R. et al. Structural variation of chromosomes in autism spectrum disorder. Am. J. Hum. Genet. 82, 477–488 (2008). Article  CAS  PubMed  PubMed Central  Google Scholar  Egolf, L. E. et al. Germline 16p11.2 microdeletion predisposes to neuroblastoma. Am. J. Hum. Genet. 105, 658–668 (2019). Article  CAS  PubMed  PubMed Central …

Short-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), and exome sequencing (ES). To assess the…

Coverage plot of a complete genome 2 In a paper I was reading i have found the attached image. It shows the duplication of specific chromosomes in different yeast strains after treatment with antibiotics. I was wondering how can one plot the whole genome in such a way? Are there…

CNV benchmarking 0 Hi, I know how to do small germline variants benchmarking and now I want to do the same for germline CNV, to calculate sensitivity and specificity/precision. Can you suggest me what standard sample to run on the sequencer, where to find it’s true CNV set and any…

We are searching for a persistent Principal Scientist II Bioinformatics to join our energetic team at F. Hoffmann-La Roche Ltd in Mississauga, ON.Growing your career as a Full Time Principal Scientist II Bioinformatics is an incredible opportunity to develop key skills.If you are strong in leadership, critical thinking and have…

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…

Detecting CNV’s (copy number variation) in haploid yeast cells 0 Hey all, I have whole-genome-sequencing data from 22 yeast strains grown in lab evolution experiments. I want to compute copy number variation to see whether a specific gene/chromosome was duplicated throughout the experiment. I am struggling to find a good,…

Genome assembly, annotation, and overview We assembled a chromosome-scale genome of a GS E. indica plant using PacBio Sequel II and long-range interaction (Hi-C) datasets. The assembly consists of nine chromosomes spanning 509,878,742 base pairs estimated to be ~97.8% complete by Benchmarking Universal Single-Copy Orthologs (BUSCO)28 analysis with an LTR…

NEW YORK – With a combination of multiomic analyses and machine learning, an international team has tracked down endometrial carcinoma (EC) subtypes, along with potential predictive models, treatment targets, and markers for treatment response. “Analysis of this independent cohort, incorporating pre-existing EC tumor and cell line cohorts, has not only…

To date, there have been reports of three balanced translocations and one microdeletion involving 12q24 associated with hypogonadism or KS1,2,3,4. In a case reported in 1983, all three brothers of Vietnamese Chinese origin were found to have severe primary hypogonadism with a karyotype of 46,XY,t(1;12)(p32;q24)3. Another case, published in 1990,…

SUMMARY: Bioinformatics scientist responsible for designing, developing, evaluating, maintaining, and optimizing genomic/genetic data, workflows, and tools, as well as visualizing and communicating key results to stakeholders. QUALIFICATIONS: Education: Master’s or higher degree in Bioinformatics, Computer Science or genetic/genomic relate biological Science and/with two (2) years of experience on genomic data…

In a recent study published in JAMA Network Open, a group of researchers compared the efficacy of proactive genome sequencing and a medically actionable gene panel in identifying potential risk for pediatric-onset disorders in healthy newborns and children. Study: At-Risk Genomic Findings for Pediatric-Onset Disorders From Genome Sequencing vs Medically…

Job overview In this position, you will contribute to the development of new algorithms for DNA, RNA, and Methylation analysis for cancer diagnosis. Your contributions will be used at leading top-tier academic institutions, cancer centers, and biopharmaceutical companies who are in pursuit of better diagnosis and treatments. You will be…

Dear Biostars, I am trying to prepare some published data to test a CNV filtration method I am working on. I would really like to use data from Conrad et al (2007), mostly because it is highly cited – and easy to access. Link here www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-142?query=E-MTAB-142. Unfortunately, Aglient tech is…

Integrate transcriptomics and CNV 1 Dear Community, I have two omics datasets (WGS and transcriptomics) on tumor/normal cells. I have performed CNV calling on genomics data and DEG on transcriptomics data. Is there any methods/ approach to compare among these two dataset? Best, CNV omics • 181 views • link…

M6A regulators are likely to have a significant effect on HBV-related HCC Twenty m6A regulators, including 12 readers, 7 writers, and 1 eraser, were identified in the TCGA and GEO cohorts. The correlation network provided interactive information among the m6A regulators. The ratio of somatic mutations and CNV for the…

Genomics Revolutionizing Hospital Systems Bleeding edge Industrialization of Genomics: A Novel Business Opportunity to a Hospital System – to Calibrate by Whole Genome DNA Analytics, the Efficacy of Chemotherapy Drugs: Wider Global implications. Guest Article – By Ram Ramanujam, Founder-President &CEO, Propinquity Therapeutics, A RNA CGT Company, Bangalore, India. The…

CNV Annotation of Segmentation Files For Canine 0 Hi all, I have several copy number segmentation files that have been aligned to CanFam4 (canine). I just need to match the chromosomal coordinates on the segmentation files with the corresponding gene annotations. I know there is software for humans that is…

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…

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…

Hello all, I have plotted an oncoprint following this link but i am facing trouble in arranging the labels and modifying annotations, here is the code i have used. Input: Sample1 Sample2 Sample3 Sample4 Sample5 Gene1 “” “Nonsense” “” “” “Nonsense” “Nonsense” Gene2 “” “” “” “” “” “” Gene3…

Boger B, Fachi MM, Vilhena RO, Cobre AF, Tonin FS, Pontarolo R. Systematic review with meta-analysis of the accuracy of diagnostic tests for COVID-19. Am J Infect Control. 2021;49(1):21–9. doi.org/10.1016/j.ajic.2020.07.011. Article  CAS  PubMed  Google Scholar  Sule WF, Oluwayelu DO. Real-time RT-PCR for COVID-19 diagnosis: challenges and prospects. Pan Afr Med…

Unlocking the Potential of CRAM Files: The New VarSeq 2.3.0 Release for Enhanced Plotting, Coverage Analysis, and CNV Detection The CRAM (Compressed Reference-oriented Alignment Map) file format was conceived in 2011 as a more space-efficient way to store alignment…

I tried to upload vcf of SV from HiFi CNV and pbsv into Franklin (by genoox) 0 Hi I tried to upload vcf of SV from HiFi CNV and pbsv into Franklin (by genoox). For inherited disease family case, I used 1 file of merged vcf for SNV from Deeptrio,…