A Simple Variable Number of Tandem Repeat-Based Genotyping Strategy for the Detection of Handling Errors and Validation of Sample Identity in Biobanks.
Biobanking biological samples involve multiple handling, processing, and labeling steps. Each step may be a source of error, which if unnoticed or uncorrected may have consequences for research. We aimed to develop a simple and inexpensive genotyping method that would be valuable to detect such errors and confirm sample identity. For this purpose, seven variable number of tandem repeat (VNTR) loci were selected, analyzed by polymerase chain reaction (PCR) amplification, and organized in a PCR-based DNA profiling algorithm that proved useful to minimize the number of steps required for the procedure. Match probability calculations suggest that this method/algorithm has the potential to discriminate every participant of a biobank. As a proof of concept, the algorithm was applied on samples taken from the PROCURE Prostate Cancer Biobank. It was applied on 403 DNA samples from 101 randomly chosen patients who provided prostate tissues at surgery and blood at two to three different time points over a period of up to 7 years. A unique DNA profile requiring the analysis of no more than four VNTR loci (D16S83, D17S5, D1S80, D19S20) was successfully obtained for each of the 101 cases studied and led to the identification of two mismatches among the 403 samples evaluated (0.5% error rate). Further investigations using the same genotyping method revealed that one of the errors was due to tissue mishandling and that the other was due to tissue mislabeling. These errors, typical to the complex biobanking process, highlight the importance to implement a routine genotyping method as part of quality assurance in biobanking.
1 McGill University Health Centre and Research Institute , Montréal, Canada .|2 PROCURE Alliance , Montréal, Canada .
Charles
C
Pellerin
1 McGill University Health Centre and Research Institute , Montréal, Canada .|2 PROCURE Alliance , Montréal, Canada .
Ginette
G
McKercher
1 McGill University Health Centre and Research Institute , Montréal, Canada .|2 PROCURE Alliance , Montréal, Canada .
Armen G
AG
Aprikian
3 Montréal University Health Centre , Montréal, Canada .
Fred
F
Saad
4 Québec University Health Centre , Québec, Canada .
Louis
L
Lacombe
5 Sherbrooke University Health Centre , Sherbrooke, Canada .
Michel
M
Carmel
1 McGill University Health Centre and Research Institute , Montréal, Canada .|2 PROCURE Alliance , Montréal, Canada .
Simone
S
Chevalier
D000465:Algorithms; D018070:Biological Specimen Banks / Q000592:standards; D016172:DNA Fingerprinting / Q000379:methods*; D006801:Humans; D008297:Male; D018598:Minisatellite Repeats; D016133:Polymerase Chain Reaction; D011471:Prostatic Neoplasms / Q000235:genetics / Q000473:pathology; D013048:Specimen Handling / Q000592:standards*
VNTR; biobanking; prostate cancer; quality assurance