Tag: cnv

Control-FREEC output

Control-FREEC output 0 Hello everybody, I’m using the tool Control-FREEC to evaluate the CNVs in my data, but I have some doubts about the _ratio.txt file in output. As far as I understood by both the paper and the documentation, this file should report the ratio (that, if I’m correct,…

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Who are the leading innovators in DNA polymorphism detection for the pharmaceutical industry?

The pharmaceutical industry continues to be a hotbed of innovation, with activity driven by the evolution of new treatment paradigms, the gravity of unmet need, as well as the growing importance of technologies such as pharmacogenomics, digital therapeutics, and artificial intelligence (AI). In the last three years alone, there have…

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Genome-wide identification of disease-causing copy number variations in 450 individuals with anorectal malformations

CNV analysis After the application of quality filter step I (gender mismatch), two patients were excluded. Through step II (call rate <98%), 40 patients were discarded and after step III (exceeded double of standard deviation), 12 more patients were excluded. In the remaining 396 individuals with ARM, a total of…

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ParseCNV2: efficient sequencing tool for copy number variation genome-wide association studies

Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007;17:1665–74. Article  CAS  PubMed  PubMed Central  Google Scholar  Chang CC, Chow CC, Tellier LC, Vattikuti S,…

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UCSC Genome Browser | Encyclopedia MDPI

1. History Initially built and still managed by Jim Kent, then a graduate student, and David Haussler, professor of Computer Science (now Biomolecular Engineering) at the University of California, Santa Cruz in 2000, the UCSC Genome Browser began as a resource for the distribution of the initial fruits of the…

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CNV Pipeline Options

The following are the top-level options that are shared with the DRAGEN Host Software to control the CNV pipeline. You can input a BAM or CRAM file into the CNV pipeline. If you are using the DRAGEN mapper and aligner, you can use FASTQ files. …

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UK Biobank Copy Number-Based GWAS Discovers New Associations With Human Traits

NEW YORK – A new set of analytical tools is making it possible to systematically search for links between copy number variants and complex human traits or conditions, according to a study by a pair of investigators at the European Molecular Biology Laboratory’s European Bioinformatics Institute. “[W]e present a robust…

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How to get the total number of unique genes affected by Pathogenic SNPs in dbSNP?

How to get the total number of unique genes affected by Pathogenic SNPs in dbSNP? 0 In dbVar I have been able to get the total number of unique genes affected by deletions, insertions and duplication which report classified this CNV as pathogenic. Now, I would like to do the…

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Senior Scientist Applied Bioinformatics Job In San Francisco, CA 94103| TechCareers

At Bristol Myers Squibb, we are inspired by a single vision – transforming patients’ lives through science. In oncology, hematology, immunology and cardiovascular disease – and one of the most diverse and promising pipelines in the industry – each of our passionate colleagues contribute to innovations that drive meaningful change….

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Within analysis, low-coverage whole-genome sequencing out of cfDNA was held to examine blood plasma away from patients with spine metastasis

Within analysis, low-coverage whole-genome sequencing out of cfDNA was held to examine blood plasma away from patients with spine metastasis An analysis pipe is made and you will verified to evaluate the brand new CNV condition within the cfDNA, in order to determine whether brand new CIN score, that has…

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Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

Cell-type annotation scRNA-seq data were filtered to discard low-quality cells and doublets (Supplementary Fig. 1, Extended Data Fig. 1 and Methods). Supervised clustering (Reference Component Analysis v2 (RCA2)) at low resolution grouped cells into 11 major cell types (Extended Data Fig. 1). To identify epithelial cell subtypes, we initially analyzed…

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AndyMSSMLab/PHEWAS_in_CNV: Scripts used for performing PheWAS analysis in CNVs

GitHub – AndyMSSMLab/PHEWAS_in_CNV: Scripts used for performing PheWAS analysis in CNVs This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to…

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Genetic and chemotherapeutic influences on germline hypermutation

DNM filtering in 100,000 Genomes Project We analysed DNMs called in 13,949 parent–offspring trios from 12,609 families from the rare disease programme of the 100,000 Genomes Project. The rare disease cohort includes individuals with a wide array of diseases, including neurodevelopmental disorders, cardiovascular disorders, renal and urinary tract disorders, ophthalmological…

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Genomic Study Reveals Recurrent Inversion Variants, Instability Effects

NEW YORK – A team from Germany, the US, and Italy has tallied recurrent inversions across dozens of human genomes, providing a look at haplotypes containing these polymorphisms, mechanisms that lead to new inversions, and inversion ties to genetic instability and related microdeletion or duplication conditions. The findings appeared in…

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N6-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance | Military Medical Research

Bioinformatics analyses revealed the involvement of m6A modification in cervical cancer progression To better understand whether and how m6A regulators contribute to cervical cancer progression, we first identified 9 m6A writers (WTAP, ZC3H13, METTL3, METTL14, METTL16, VIRMA, RBM15B, RBM15, and CBLL1), 15 m6A readers (FMR1, hnRNPA2B1, hnRNPC, YTHDF1/2/3, YTHDC1/2, LRPPRC,…

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aCGH – Allie: Result by abbreviation

1  array comparative genomic hybridization(1473 times) Neoplasms(306 times) FISH (238 times)CNVs (135 times)MLPA (72 times) 2003 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. 2  array CGH(43 times) Neoplasms(12 times) CNVs (7 times)FISH (3 times)ID (3 times) 2003 Combined array comparative genomic hybridization and…

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Color hiring Software Engineer, Bioinformatics in Remote

About Color Color’s mission is to help people lead the healthiest lives that science and medicine can offer. We launched in April 2015 with a simple, affordable genetic test to help people understand their risk for hereditary cancer. In 2017, we added coverage for hereditary heart conditions. Between them, cancer…

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BTG2 gene predicts poor outcome in PT-DLBCL

Introduction Primary testicular diffuse large B-cell lymphoma (PT-DLBCL) is a rare and aggressive form of mature B-cell lymphoma.1–3 PT-DLBCL was the most common type of testicular tumor in men aged over 60 and characterized by painless uni- or bilateral testicular masses with infrequent constitutional symptoms.4–6 PT-DLBCL shows significant extranodal tropism,…

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R: PC gamma

PCgamma {GSAgm} R Documentation PC gamma Description For GSA of SNP data, the following two-step procedure is implemented (see Biernacka et al[1] for more details on the method). Step 1: Principal components analysis for SNPs within a gene is completed with the components needed to explain 80 percent of the…

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CD Genomics: Bioinformatics-Analysis Division Provides Genotyping Analysis Service for Studying Genetic Variations

New York, USA – February 23, 2022 – The Bioinformatics-analysis division is a new division of CD Genomics that provides reliable next-generation and third-generation high-throughput sequencing data analysis, comprehensive technology services, database construction, and other related data analysis services. CD Genomics recently launched various types of genotyping analysis services, including…

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Copy number variants calling from WES data through eXome hidden Markov model (XHMM) identifies additional 2.5% pathogenic genomic imbalances smaller than 30 kb undetected by array-CGH

It has been estimated that Copy Number Variants (CNVs) account for 10%-20% of patients affected by Developmental Disorder (DD)/Intellectual Disability (ID). Although array comparative genomic hybridization (array-CGH) represents the gold-standard for the detection of genomic imbalances, common Agilent array-CGH 4 × 180 kb arrays fail to detect CNVs smaller than…

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How can you score CNV for each sample (with TCGA data)?

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…

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CNV calling for wgs of S. pombe

CNV calling for wgs of S. pombe 0 Hi, Can anyone help to do CNV calling of WGS data of S.Pombe? I have 1 normal sample and 3 samples treated with a suppressor. I used Control-FREEC but did not get the right result. Can anyone help, how to do germline…

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Comparison of CNV analysis methods: Array CGH vs NGS

Rare genetic disorders are caused by variants in major functional genes. Most are SNV or INDEL variants, but SVs, such as CNVs or chromosomal variants, can also be the cause. Recently, a large-scale study has also been published showing that CNVs were identified in 11-12% more infants and children with…

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A genomic mutation spectrum of collecting duct carcinoma in the Chinese population

This article was originally published here BMC Med Genomics. 2022 Jan 3;15(1):1. doi: 10.1186/s12920-021-01143-2. ABSTRACT BACKGROUND: Renal collecting duct carcinoma (CDC) is a rare and lethal subtype of renal cell carcinoma (RCC). The genomic profile of the Chinese population with CDC remains unclear. In addition, clinical treatments are contradictory. In…

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Reliability of Cell-Free DNA (cfDNA) Next Generation Sequencing in Predicting Chromosomal Structural Abnormalities and Cytogenetic-Risk Stratification of Patients with Myeloid Neoplasms

Oral and Poster Abstracts 617. Acute Myeloid Leukemias: Biomarkers, Molecular Markers and Minimal Residual Disease in Diagnosis and Prognosis: Poster III Translational Research Maher Albitar, MD1*, Andrew Ip, MD, MSc2, Andre H. Goy, MD3*, Jeffrey Justin Estella, BS, MS1*, Ivan De Dios, BS1*,…

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Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model | BMC Biology

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,…

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which tool can I use to detect CNVs?

which tool can I use to detect CNVs? 0 Hi everyone, I have performed target sequencing on tumour samples (with MiSeq, Illumina). I must perform CNV detection, which tool do you suggest me to use ? (I do not have the normal samples, only tumour samples). Thanks, Elisa calling CNV…

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ABOUT affymetrix genotyping console (GTC) software and TCGA CNV workflow

ABOUT affymetrix genotyping console (GTC) software and TCGA CNV workflow 0 The TCGA CNV workflow uses Birdsuite to estimate raw copy number (CN). The affymetrix genotyping console (GTC) use similar algorithm developed by broad. Is GTC used to estimate raw CN, too? Otherwise, could GTC output files that could be…

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Is it possible to report the allele frequency of integer copy numbers >= 3?

Is it possible to report the allele frequency of integer copy numbers >= 3? 0 I am using cn.mops which reports integer CNV for samples (eg CN1, CN3, CN4, CN5, etc.) I hope to report haplotype frequency of detected CNVs, but I am struggling to understand if this is possible….

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getting different value list from GATK gc content and CANOES

getting different value list from GATK gc content and CANOES 0 I was trying to run codes from this paper “A machine-learning approach for accurate detection of copy-number variants from exome sequencing” I need to get data from GATK GC content and CANOES and combined them, but I got a…

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HRD score LST?

HRD score LST? 1 I am confused about the calculation of LST score for the HRD score. Looking at the description of such a package that does this calculation (scarHRD): In the LST figure B, I don’t understand why the 2nd “X” in chromosome 1 is marked as an “X”….

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Principal Software Engineer 1 – Bioinformatics Job in California

Summary: Our engineering team specializes in developing a fast and accurate FPGA-accelerated platform called DRAGEN, for the secondary analysis of NGS data. Team activities are two-fold: 1) algorithm design of analysis methods to discover variants, and, 2) highly-efficient HW/SW implementation for fast run time. The platform covers a wide…

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InferCNV how to choose the right reference?

InferCNV how to choose the right reference? 1 Hello everyone! Could you help me to choose the correct reference for scRNA data if I need to identify CNVs among the malignant clusters that are represented as immune cells with an epithelial phenotype (CTC). What is more correct to take healthy…

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Your reference doesn’t appear to be indexed. Please run the mkref tool.

cellranger-dna: Your reference doesn’t appear to be indexed. Please run the mkref tool. 1 I received the following error when running cellranger-dna: “Your reference doesn’t appear to be indexed. Please run the mkref tool”. The reference that I used was downloaded from 10X database. I thought the reference was already…

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From idat Illumina Infinium MethylationEPIC to CNV analysis for homo/hetero-zigous deletion

From idat Illumina Infinium MethylationEPIC to CNV analysis for homo/hetero-zigous deletion 0 Hi, My group works on cancer and we have difficulty on a little part of our last project about malignant pleuric mesothelioma. I’m looking for help in the analysis of .idat from genome-wide DNA methylation profiles obtained via…

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Dissecting Cancer with Single-cell DNA Sequencing & Multi-omics | Learning Center

CANCER & SINGLE-CELL ANALYSIS The heterogeneity and dynamism of cancer present formidable challenges to understanding and treating the disease. As discussed in the last section, tumor evolution often leads to considerable genetic variation across clones. But the complexity of tumors does not stop at the level of DNA. Intratumoral phenotypic…

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gender determination and chrX CN calls

gender determination and chrX CN calls 1 I’m running CNVKit in amplicon mode on a set of tumor bam files generated with a small amplicon panel of 45 genes. The panel includes just one gene on chrX, and none on chrY. My reference is generated by 10 normal male samples…

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Default CNV call thresholds for haplotype chromosome s

Default CNV call thresholds for haplotype chromosome s 0 Hi, I confuse a topic that about the CNV call. The default thresholds are -1.1 => 0, -0.25 => 1, 0.2 => 2, 0.7 => 3 for discrete copy number. But these thresholds doesn’t work for chrY and chrX. What is…

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