Comparison qPCR study for selecting a valid single copy gene for measuring absolute telomere length.

ABSTRACT

Telomere shortening is a well-known biomarker for biological aging. A previous review of the methods used to measure telomere length (TL) noted how challenging it is to compare results from different studies using diverse methodological techniques. The most commonly used high throughput method for measuring average TL is the quantitative PCR (qPCR) method, where there are two protocols available; the relative TL and the absolute TL (aTL) method. All qPCR methods have similarities in that they use two different primer sets to measure the telomere repeat sequence (TTAGGG)n and a single copy gene region to calculate the average TL, (T/S) ratio. The difference between the relative TL and the aTL assay lies with the introduction of duplex oligomer standards to identify TL in kilobase pairs rather than using the traditional relative TL, T/S ratio method. Problems were noted using 36B4 (RPLP0), which was originally used as a suitable single copy gene qPCR assay. A previous aTL publication attempted to replace the 36B4 (RPLP0) single copy gene using the Interferon beta 1 gene (IFNB1) but results showed a lack of agreement with the TL results when compared to the DNAmTL assay. Here, we compare the two single copy gene assays previously used for the aTL assay and offer an alternative IFNB1 single copy gene assay without non-specific priming amplification to provide more consistent diploid copy number determination and a more robust and reproducible assay for measuring absolute TL.