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How to copy number in the SPA Evaluation

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just hello my name is Daniel Harrigan and today Ill be talking about how to run copy number variation analysis todays talk Ill address a couple of questions namely what is a copy number variant and how do we detect it with genotype data what does the CNB file format look like and what is CNB analysis output look like finally how do I use this to run CNB burden and Association tests so what is a copy number variant well I Define it here as a subset of structural variation involving a gain or duplication or a loss slash deletion of genomic sequence now I call it a subset of structural variation because structural variation can Encompass basically any change in the length of a genomic sequence that can be as small as a single base pair insertion or deletion now most Snips that we we think of are just substitutions so the actual size of the genome isnt changed with a single nucleotide polymorphism foreign but a structural variant can Encompass anything from very small all the way to en

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How do you find the copy number of a gene?

Firstly, you can use PCR or qPCR to determine the exact number of mRNA or DNA copies, which is rather a very simple method where you generate a standard curve with a known quantity of your gene of interest and determine the copies of the target in an unknown sample. After real time PCR you will have the CT.

How is CNV calculated?

The CNV is simply given by the ratio of the estimated concentration of the target gene to the estimated concentration of the reference gene.

What is copy number and how it is measured?

The copy number of the region present in the sample of genomic DNA then is obtained by dividing the number of target regions present on the coverslip by the number of genomes scanned.

How do you find the copy number of a plasmid?

This can easily be achieved with a copy number calculator, all you need to know is the concentration of DNA in your sample in ng/l and the length of your template in base pairs. The concentration of DNA in the sample is normally determined using a quantification tool based on fluorometry or spectrophotometry.

How do you assess copy number?

Copy number variation can be detected with various types of tests such as fluorescent in situ hybridization, comparative genomic hybridization and with high-resolution array-based tests based on array comparative genomic hybridization (or aCGH), SNP array technologies and high resolution microarrays that include copy

How do you measure copy number?

This is done by measuring the lengths of individual hybridization signals from sequence-specific probes. Therefore, the effective copy number of each region is the sum of the lengths of the measured hybridization signals divided by the known length of the respective regions (Eq.

How do you detect CNV?

There are four main methods of detecting CNVs with NGS data: Read-Pair (RP) Split-Read (SR) Read-Depth (RD) Assembly (AS)

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