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For determining copy number gains and losses, the R package CGH call was used [ 16].
In contrast, exome enrichment kits are generally not designed for the purpose of determining copy number states.
Primers, probes, and procedures for preparing RNA and determining copy numbers of RNA transcripts are in Supporting Information.
For determining copy numbers, we chose the 2-ΔΔCt method with a calibrator as described by [ 3].
The paralogue ratio test (PRT) is a simple, cost-effective method of accurately determining copy number by quantifying the amplification ratio between a target and reference amplicon.
We used an updated version of the previously described method to do CNV calling, ie., determining copy number gains and losses by changes in log2 signal intensity [ 31].
Similar(46)
PrimerBank primers could also be used for determining copy-number variation of a gene or splice isoform [ 53, 54].
HAPPY mapping can be extended to allow molecular copy-number counting (MCC), determining copy-numbers by counting the molecules present [ 21].
In particular, the substantial differential expression of TERT between genotypes in the two NSCLC subtypes suggests that genotype could play a role in determining copy-number amplification of TERT.
However, this single-pot strategy requires in silico masking of the coding sequences (exonic region) of the genome to determine copy number variation, which leads to incomplete transcripts from the cell.
In order to determine copy number changes, CGH-Explorer v. 3.1b was used [16].
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