Questions tagged [cancer]

An abnormal growth of cells that can threaten an individual's life. Cancerous cells are very proliferative and can spread to other parts of the body, creating metastases.

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How to interpret the Copy Number from pseudocount depmap portal file?

Do you know how to interpret the Copy Number (CN) file from the depmap portal: CCLE_gene_cn.csv. This is an already normalized file with pseudo count + 1. In this ...
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36 views

What are Dummy fastqs?

I had to do a file transfer for in our system to run from fastqs and I came across the term "dummy fastq", not sure what exactly it means and what is the purpose of it in the workflow. Can ...
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building complex drug-dna for AMBER software

I will appreciate if you can please clarify some of my doubts about drug-DNA complex. I want to study the drug-DNA simulation using AMBER. I did go through all the tutorials video on youtube but ...
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367 views

How can I calculate loss of heterozygosity (LOH) in NGS sequencing data?

I'm analyzing a tumor sample and a healthy sample from the same patient. I want to use sciClone to look at tumor clonality. One input is the genomic regions that need to be excluded due to LOH. I have ...
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Is there any database about the abundance of proteins in urine of healthy patients?

I have a dataset about adundance of urine proteins from cancer patients. I would like to compare these abundance levels to healthy patients' urine proteins. However I don't have any data with healthy ...
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Using grep to get lines from a file (.tsv) that contain specific samples listed in a sample file (.tsv)

So I have a file, let's call it pcawg.tsv. It's formatted like the one down below. ...
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1answer
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Important genes beyond PAM50 for breast cancer classification

Note: this question has also been asked on Biostars I am currently trying to complete a Breast Cancer Classification task using Neural Networks. I have experimented with using my full dataset of gene ...
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Ccle miRna data units

Does anybody know what units the mirna expression data on ccle is in? I saw the pipeline in the original paper but it doesn't mention units. Original paper: https://www.nature.com/articles/s41586-019-...
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Clusters in scRNA of Glioblastoma

There is a scRNA dataset on Glioblastoma from 10xgenomics. Unfortunately, there seems to be no research paper related to that data. Question 0 : May be there is paper ? How to find it ? I am not ...
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Bacterial DNA at the tail of transcriptome reads. What does that mean?

I am assembling a transcriptome obtained from the Internet. The transcriptome was extracted from a human cancer tissue that had been previously grafted into a mouse. I have detected that many ...
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114 views

Survival analysis using CoxPH - Effect of covariates

Hi and sorry for the long post in advance, I'm doing a survival analysis of lung cancer patients using Python's lifelines package. According to the documentation, the function ...
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Portals besides the National Cancer Institute GDC Data Portal for downloading histology slides

I am downloading sample slides (in svs format) from the GDC Portal for a convolutional neural network model, but I also need normal tissue slides to perform classification. There are some normal ...
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389 views

What would be a reasonable healthy data set/control group to compare with a cell line from TCGA?

Assume I want to run a simple machine learning of healthy/non healthy classification, how can I use TCGA where it has only data of people with cancer. What do usually people do for example for study ...
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66 views

Comparing AUCs: Discrimination of same Control from different Test Group - paired or unpaired? miRNA

I want to compare two AUCs using a bootstraping method from pROC package (roc.test). I have done a classification using Logistic Regression and Serum miRNAs as prediction factors. The Controls are in ...
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How to aggregate multiple MAF files together?

I have cancer genomic data (tumor/normal whole exome sequencing) from 50 patients that received the same type of treatment, half of whom responded. These come in the form of 50 .maf files, along with ...
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228 views

How are PDO and PDX used in computational and predicative models for tumour biology?

There are wet methods: Patient-derived models: Patient Derived Xenograft (PDX) and Patient Derived Organoids (PDO) to reflect tumor biology. Are there any databases or computational tools that use ...
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1answer
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Are there databases or resources that contain expression of proteins or genes before and after cancer treatment?

Are there databases that contain information about gene or protein expression before and after targeted therapy or chemotherapy? I am curious about different cancer cell lines or cancer types. Any ...
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Can we use GTEx data as control data for TCGA data?

I am using Recount2 TCGA data and was wondering is it right to use GTEx data as control data for this. I would really appreciate your views on this?
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Database for germline copy number variations in cancer

I am interested in looking at germline copy number variations in individuals that are at high risk of developing cancer. Are there any databases where I can look, if a CNV seen in our test case has ...
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Building cancer gene database

I am trying to build a database of different cancer genes i.e lung cancer, throat cancer etc. Searched through NCBI website by searching for nucleotide sequences, but I am unable to find appropriate ...
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Finding genes especific to microenvironment

I have RNA-seq .bam files for 3 patients, tumour and its matched derived model, namely organoid, but I don't have any matched normal sample. Differentially expressed genes between a tumour and its ...
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992 views

How to interpret fish plot in R

I am working on subclonal evolution of multiple myeloma. After literature survey, I found people use Fish plot to represent tumor evolution. The example of fish plot can be found here. But I am not ...
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197 views

GDC data portal cancer subtype

I need to use Gene Expression quantification data (using HTSeq-FPKM-UQ) for breast cancer data on the gdc portal (https://portal.gdc.cancer.gov/repository) to classify breast cancer subtypes (luminal ...
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104 views

Information about control data

I am putting this question because I did not find any useful information from internet because of limited access. My question is related to control (or normal) data that we use for somatic mutation ...
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389 views

Why the t-test for a specific gene shows different value compared to differential analysis?

I have RNA-Seq data for LUNG cancer. 370 tumor and 50 Normal. For differential analysis initially I did some filtering and kept approx. 19k genes for further analysis. I used edgeR. With a FC > or &...
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How transcription factor influence gene expression?

I am studying about gene regularity network(GRN). I'm interested to work on cancer detection to find start reasons of this particular illness. I'm trying to find out how the transcription factor(TF) ...
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EMT/EMT-like processes in bioinformatics to study cancer progression

First I am not sure why, but it seems EMT can be used to infer the status of cancer progression. What kind of databases are there for the EMT process in the context of cancer? I saw this book which ...
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Meaning of category in MutSigCV

I am trying to understand the working of MutSigCV. But I am not sure about some terms used in MAF file format which is category. According to MutSigCV, every mutation can be divided into the following ...
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Tumor sample and heterozygous SNVs: what is the genotype of the normal cells?

In the following picture, you can see that in normal cells (yellow) we have two copies of each gene, while in tumor cells (violet), we just have one copy due to a clonal mono-allelic deletion. I do ...
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Use of heterozygous SNPs in cancer research: why?

When reading about allelic fraction (AF) and SNPs in cancer research, they always mention the fact that they're using heterozygous SNPs (informative SNPs). Why is this? Why can't we use homozygous ...
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3answers
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Somatic tumor only variant calling?

I'm evaluating possibilites for somatic tumor variant calling without paired-normal samples. I'm aware of the consequences without a normal sample. All the popular variant calling tools such as ...
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1answer
93 views

Difference between copy number neutral reads and active reads

In this paper, the authors talk about copy number neutral reads (as reads that equally represent parental chromosomes) and active reads (as reads from only one parent chromosome): We reasoned that ...
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1answer
464 views

Is there a publicly available tumor-normal sample?

I am looking for a publicly available matched tumor-normal sample. I need Illumina fastq reads (or an aligned bam file, since I could extract the reads from it) from a tumor and a matching, non-tumor ...
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108 views

How can I use annotations to remove variants not relevant to cancer risk?

I currently have ~180 whole germlines and around 10M SNPs/indels. I would like to build a predictive model using Machine Learning (ML) techniques to predict cancer risk according to these germline ...
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297 views

Database of copy number alterations in different cancer types

Is there a database of somatic copy number alterations (CNAs) in different cancer types? That is, annotations of which CNAs are more commonly seen in different cancer types.
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COSMIC Genotypes and Phenotypes

I'm trying to find files containing genotypes and phenotypes for cell lines in COSMIC. On their downloads page I found links for mutation data, which I guess could be converted to genotypes, but I ...
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Working with the additional cell lines in NCI-60

NCI-60 has additional cell lines, but when I get results from CellMiner they are not included in there. Namely, the genes such as: DLD-1(Colon), ...
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Using data mining of papers in order to derive genomic connections [closed]

Are there any examples of researchers data mining articles and papers (e.g., from pubmed or google scholar) in order to derive relations between genes and diseases?
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How to access the patient-derived xenografts (PDXs) repository?

I saw this nature news item, it sounds that Cellminer is obsolete, is it right? What are the new tools to analyze the "new cell lines"? Where's the PDX repository? What about the European initiative ...
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GRCh38 vcf file with common cancer mutations

Is there a vcf file on the GRCh38 assembly with common cancer mutations I can download somewhere? Maybe from one of the big international cancer genomics consortia? By common, I mean whichever ...
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436 views

Searching for gene expression data by cell line

I have two cancer cell lines (OCI-Ly18 & riva) that I want to find gene expression data for, but I'm not aware of many gene expression databases that allow searching by cell-line without searching ...
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203 views

Detecting structural variants with MinION data

Working on various cancers I have an interest in detecting structural variation (SV) in human, we've successfully used various tools like Pindel, SVDetect, Manta, and LUMPY, to name a few for ...
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Tumor purity/contamination/admixture estimation

Can anyone recommend a good tool for estimating the tumor content given a matched tumor and normal file for DNA NGS whole genome sequencing data or whole exome data? Is it possible to estimate this ...