Questions tagged [copy-number-variation]
Questions pertaining to variation in the number of copies of a chromosomal region.
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gene dosage vs copy number
In the online articles I'm reading, I see the authors mention gene dosage and copy number. My confusion is regarding if the two terms mean exactly the same thing - number of copies a gene occur in the ...
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Copy number deletion and high expression [duplicate]
I have a region that has significant CNV loss. But the expression for the genes in those regions is high compared to the expression found in the samples that don't have the regions lost. How can this ...
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Are there human genes that make a cell die when they undergo copy-number alterations?
I am trying to understand if there are known genes in the human genome where copy-number should be stable at a diploid level for the carrier cell to live.
I.e., are there lethal deletions or ...
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How do evolutionary forces influence the number of copies of the p53 gene?
p53 is an important tumor suppressor gene. Around 50% of cancers are associated with loss of function in p53.
Humans have only two copies of p53 in their genome (one on each homologous chromosome). ...
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Can CNVs have a phenotypic effect unrelated to the direct modification of transcriptional units?
I'd like to know how (or if) copy number variations can have a phenotypic effect unrelated to the direct disruption/movement/duplication of sequences for coding regions, promoters, enhancers etc.
I ...
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How to correlate CNV with transcriptomic data?
I have a list of differentially expressed genes. I want to correlate these genes with CNVs. I have downloaded the data from both TCGA and FireBrowse. But I am not able to understand how to do the ...
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What is the copy number of a given gene in GRCh37?
sorry for the naive question, but how do I determine what the copy number is in GRCh37 for a gene with multiple CNVs? (e.g. DRD4).
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Gene copies vs. gene paralogs - what's the difference?
I'm trying to get into the theory and practice of gene copy number variation (CNV) analysis, but there is something basic confusing me, which I couldn't yet figure out. Sorry if this is a dumb/trivial ...
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Breakpoint resolution for copy number variation analysis
I am reading [1].
One limitation of the Read Depth approach is that "the breakpoint resolution is often poor". Which is the meaning of low-resolution breakpoint in this case?
Breakpoint is ...
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Which matched normal(s) to use when computing CNAs from exome data with a Read-Depth approach
I want to use a Read-Depth algorithm to call copy number alterations (CNAs) from Whole Exome Sequencing data (WES) of a specific tumor.
I have a set of WES tumor samples, some of which also have the ...
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What does probe number and segmentation mean in copy number variation (CNV) data
In TCGA Copy number variation (CNV) data there is a column with title Num_Probes. What is the meaning of probe number with respect to the sample data below?
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Open databases for copy number variations similar to TCGA
The Cancer Genome Atlas(TCGA) has open data for copy number variation(CNV) from at least 10k different cancer patients. They offer two types of data, CNV data from tumor and CNV data from normal ...
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What's the difference between constitutional samples and tumor samples?
I think the tumor samples have two copies of the chromosomes. But for constitutional samples, do they only have one copy of the chromosomes?
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Copy number regulation & CNV
I have some genes which showed copy number loss between two groups. Now I want to see the copy number regulation of those genes. I really don't know about this concept. Can anyone please tell me ...
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How to compute CNV from TCGA data
TCGA provide CNV data for each cases like this.
I want to know, how can I calculate CNVs from this data? What are standard algorithms and methods used?
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What further research can the result of gene variation detection be used for [closed]
We do a research on a particular cancer (for e.g. breast cancer). Now, we have a result for the gene variation detection (VCF file). What next steps do we need to do? We don't have a clear picture ...
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Deciding a reasonable threshold for copy number variation in a CNV (SNP array) TCGA dataset
Is there a methodology to select a reasonable threshold for copy number variation in a CNV (SNP array) TCGA dataset, to define when there is a significative alteration?
Can I download CNV data for ...
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What's a segmented copy number profile
I am studying copy-number variation. I am reading
C. H. Mermel, S. E. Schumacher, B. Hill, M. L. Meyerson, R. Beroukhim, and G. Getz, “GISTIC2.0 facilitates sensitive and confident localization of ...
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How copy number variation thresholds are defined in GISTIC
I am having trouble trying to understand how GISTIC discretize copy number variation to values -2, -1, 0, 1, 2. I am using TCGA copy number variation for ColoRectal Adenocarcinoma.
In cBioPortal FAQ ...
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When do plasmids replicate relative to its host cell cycle?
For plasmids is so much shorter than their host cell's genome (about 1/1000 in my case), it will take only 1/1000 time for it to replicate.
With respect to cell cycle, when will that replication ...
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"Gold standard" for CNV detection methods?
Is there a generally accepted "gold standard" for testing the performance of CNV detection methods? I'm interested both in learning about existing datasets that may serve as gold standards for CNV ...
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How does the telomere repeat sequence vary in Eukaryotes?
Question:
How does the telomeric repeating sequence vary in non-vertebrate Eukaryotes? If you know the repeating sequence of a given species I would appreciate hearing it.
Background:
Telomerase is ...
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Is copy number variation dynamic?
Is there any evidence showing that copy number variation changes over time? I'm wanting to model interactions in expression level as a dynamic bayesian network, but an assumption my approach will need ...
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What is a focal copy number variation?
Often, genetics studies, especially genome wide ones, talk about "focal copy number variations" in genes or regions of the chromosome. I know what a copy number variation is. What does "focal" mean, ...
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What is the difference between copy number changes with and without allelic imbalance?
I require some clarification on copy number aberrations (structural gain and loss in chromosomes). From what I understand, gain/loss per se can be divided into two types.
Consider two alleles, A and ...
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What is the tRNA gene copy variation between different yeast strains?
I just started working on predicting steady-state protein levels from different codon usage bias measures. I have whole-genome sequences (it's NGS data) from different strains of S. cerevisiae and S. ...
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