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Questions tagged [copy-number-variation]

Questions pertaining to variation in the number of copies of a chromosomal region.

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1answer
67 views

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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1answer
189 views

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 defined ...
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1answer
22 views

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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1answer
653 views

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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1answer
93 views

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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1answer
50 views

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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1answer
99 views

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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3answers
1k views

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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0answers
46 views

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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2answers
354 views

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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2answers
529 views

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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1answer
2k views

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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1answer
721 views

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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0answers
164 views

“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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2answers
664 views

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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1answer
89 views

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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1answer
8k views

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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1answer
881 views

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 ...
14
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2answers
362 views

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. ...