Tag: CNA

Group comparison of CNA between primary and metastatic samples

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…

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Analytics Insight Announces ‘Top 10 Data Science Leaders of 2021’

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…

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Genome-Wide cfDNA Analysis Detects Therapy Response in B-Cell Lymphoma – Hematology

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…

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Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data

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…

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Copy Number to Log2_ratio for autosomal

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…

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Get Allele specific copy number regions from WGS data using ASCAT?

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…

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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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KEGG ENZYME: 1.14.12.17

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 =…

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Single cell DNA sequencing reveals punctuated and gradual clonal evolution in hepatocellular carcinoma

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…

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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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Difference between linear and log2 CNA values

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!…

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Copy number differences between groups

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…

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