Human TaqMan™ Copy Number Reference Assays are run with human TaqMan™ Copy Number Assays in a duplex real-time PCR reaction to detect and measure copy number variations (CNVs) and smaller regions in the human genome. Two options for genes that can be used as endogenous reference genes in humans are offered: RNase P and TERT. TaqMan™ Copy Number Reference Assays are designed to unique genomic sequences in the reference genome assembly (build GRCh38) and are required for relative quantitation of copy number targets.

TaqMan™ Copy Number Assays quantitate the gene of interest and normalize to an endogenous reference gene known to be present in two copies in a diploid genome. Please note that TaqMan™ Copy Number Reference Assays are species specific.

RNase P: The Standard Reference Gene Option
TaqMan™ Copy Number Reference Assays have a VIC™ dye–labeled TAMRA™ probe and reference sequence–specific forward and reverse primers. The assays are not primer-limited.

TaqMan™ Copy Number Reference Assay RNase P is recommended as the standard reference assay for copy number analysis. This assay detects the Ribonuclease P RNA component H1 (H1RNA) gene (RPPH1) on chromosome 14, cytoband 14q11.2. The assay location is chr.14:20343370 on build GRCh38. It has an 87 bp amplicon that maps within the single exon RPPH1 gene.

TaqMan™ Copy Number Reference Assay TERT is an alternative reference assay; it is recommended in the event that the RNase P assay functions poorly with a sample because of chromosomal aberrations or other issues. This assay targets the telomerase reverse transcriptase (TERT) gene located on chromosome 5, cytoband 5p15.33. The assay location is chr5:1253257 on build GRCh38. It has an 88 bp amplicon that maps within exon 16 of the TERT gene.

Simplest Copy Number Analysis Workflow
TaqMan™ Copy Number Assays have the simplest workflow of all currently available copy number analysis methods. The test assay (FAM™ dye–labeled), the reference assay (VIC™ dye–labeled), your sample DNA, and TaqMan™ Master Mix are combined and then run on an Applied Biosystems™ real-time PCR system using the standard TaqMan™ Copy Number Assay protocol. On average, setup to primary analysis takes only 3–4 hr (including an approximately 2 hour PCR run).

Powerful Data analysis Software
CopyCaller™ Software was developed specifically for TaqMan™ Copy Number Assay data analysis. This free, easy-to-use software utilizes a graphical interface that quickly calculates the possible copy numbers for a set of samples in a run. It also gives a confidence value for each copy number call, and has outlier functionality.