A Simple, Universal, and Cost-Efficient Digital PCR Method for the Targeted Analysis of Copy Number Variations.
Clin Chem
; 65(9): 1153-1160, 2019 09.
Article
in En
| MEDLINE
| ID: mdl-31292136
ABSTRACT
BACKGROUND:
Rare copy number variations (CNVs) are a major cause of genetic diseases. Simple targeted methods are required for their confirmation and segregation analysis. We developed a simple and universal CNV assay based on digital PCR (dPCR) and universal locked nucleic acid (LNA) hydrolysis probes.METHODS:
We analyzed the mapping of the 90 LNA hydrolysis probes from the Roche Universal ProbeLibrary (UPL). For each CNV, selection of the optimal primers and LNA probe was almost automated; probes were reused across assays and each dPCR assay included the CNV amplicon and a reference amplicon. We assessed the assay performance on 93 small and large CNVs and performed a comparative cost-efficiency analysis.RESULTS:
UPL-LNA probes presented nearly 20000000 occurrences on the human genome and were homogeneously distributed with a mean interval of 156 bp. The assay accurately detected all the 93 CNVs, except one (<200 bp), with coefficient of variation <10%. The assay was more cost-efficient than all the other methods.CONCLUSIONS:
The universal dPCR CNV assay is simple, robust, and cost-efficient because it combines a straightforward design allowed by universal probes and end point PCR, the advantages of a relative quantification of the target to the reference within the same reaction, and the high flexibility of the LNA hydrolysis probes. This method should be a useful tool for genomic medicine, which requires simple methods for the interpretation and segregation analysis of genomic variations.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
DNA
/
Polymerase Chain Reaction
/
DNA Copy Number Variations
Type of study:
Health_economic_evaluation
Limits:
Humans
/
Male
Language:
En
Journal:
Clin Chem
Journal subject:
QUIMICA CLINICA
Year:
2019
Document type:
Article
Affiliation country: