PMID- 32763409
OWN - NLM
STAT- MEDLINE
DCOM- 20211105
LR  - 20211105
IS  - 1943-7811 (Electronic)
IS  - 1525-1578 (Linking)
VI  - 22
IP  - 10
DP  - 2020 Oct
TI  - Design and Development of a Fully Synthetic Multiplex Ligation-Dependent Probe 
      Amplification-Based Probe Mix for Detection of Copy Number Alterations in 
      Prostate Cancer Formalin-Fixed, Paraffin-Embedded Tissue Samples.
PG  - 1246-1263
LID - S1525-1578(20)30426-8 [pii]
LID - 10.1016/j.jmoldx.2020.07.003 [doi]
AB  - DNA copy number alterations (CNAs) are promising biomarkers to predict prostate 
      cancer (PCa) outcome. However, fluorescence in situ hybridization (FISH) cannot 
      assess complex CNA signatures because of low multiplexing capabilities. Multiplex 
      ligation-dependent probe amplification (MLPA) can detect multiple CNAs in a 
      single PCR assay, but PCa-specific probe mixes available commercially are 
      lacking. Synthetic MLPA probes were designed to target 10 CNAs relevant to PCa: 
      5q15-21.1 (CHD1), 6q15 (MAP3K7), 8p21.2 (NKX3-1), 8q24.21 (MYC), 10q23.31 (PTEN), 
      12p13.1 (CDKN1B), 13q14.2 (RB1), 16p13.3 (PDPK1), 16q23.1 (GABARAPL2), and 
      17p13.1 (TP53), with 9 control probes. In cell lines, CNAs were detected when the 
      cancer genome was as low as 30%. Compared with FISH in radical prostatectomy 
      formalin-fixed, paraffin-embedded samples (n = 18: 15 cancers and 3 matched 
      benign), the MLPA assay showed median sensitivity and specificity of 80% and 93%, 
      respectively, across all CNAs assessed. In the validation set (n = 40: 20 tumors 
      sampled in two areas), the respective sensitivity and specificity of MLPA 
      compared advantageously with FISH and TaqMan droplet digital PCR (ddPCR) when 
      assessing PTEN deletion (FISH: 85% and 100%; ddPCR: 100% and 83%) and PDPK1 gain 
      (FISH: 100% and 92%; ddPCR: 93% and 100%). This new PCa probe mix accurately 
      identifies CNAs by MLPA across multiple genes using low quality and quantities 
      (50 ng) of DNA extracted from clinical formalin-fixed, paraffin-embedded samples.
CI  - Copyright (c) 2020 Association for Molecular Pathology and American Society for 
      Investigative Pathology. Published by Elsevier Inc. All rights reserved.
FAU - Ebrahimizadeh, Walead
AU  - Ebrahimizadeh W
AD  - Division of Urology, Department of Surgery, McGill University and the Research 
      Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
FAU - Guerard, Karl-Philippe
AU  - Guerard KP
AD  - Division of Urology, Department of Surgery, McGill University and the Research 
      Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
FAU - Rouzbeh, Shaghayegh
AU  - Rouzbeh S
AD  - Division of Urology, Department of Surgery, McGill University and the Research 
      Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
FAU - Bramhecha, Yogesh M
AU  - Bramhecha YM
AD  - Division of Urology, Department of Surgery, McGill University and the Research 
      Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
FAU - Scarlata, Eleonora
AU  - Scarlata E
AD  - Division of Urology, Department of Surgery, McGill University and the Research 
      Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
FAU - Brimo, Fadi
AU  - Brimo F
AD  - Department of Pathology, McGill University and the Research Institute of the 
      McGill University Health Centre, Montreal, Quebec, Canada.
FAU - Patel, Palak G
AU  - Patel PG
AD  - Department of Pathology, Queen's University, Kingston, Ontario, Canada.
FAU - Jamaspishvili, Tamara
AU  - Jamaspishvili T
AD  - Department of Pathology, Queen's University, Kingston, Ontario, Canada.
FAU - Aprikian, Armen G
AU  - Aprikian AG
AD  - Division of Urology, Department of Surgery, McGill University and the Research 
      Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
FAU - Berman, David
AU  - Berman D
AD  - Department of Pathology, Queen's University, Kingston, Ontario, Canada.
FAU - Bartlett, John M S
AU  - Bartlett JMS
AD  - Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, 
      Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, 
      Ontario, Canada; Edinburgh Cancer Research Centre, University of Edinburgh, 
      Edinburgh, United Kingdom.
FAU - Chevalier, Simone
AU  - Chevalier S
AD  - Division of Urology, Department of Surgery, McGill University and the Research 
      Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
FAU - Lapointe, Jacques
AU  - Lapointe J
AD  - Division of Urology, Department of Surgery, McGill University and the Research 
      Institute of the McGill University Health Centre, Montreal, Quebec, Canada. 
      Electronic address: jacques.lapointe@mcgill.ca.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20200804
PL  - United States
TA  - J Mol Diagn
JT  - The Journal of molecular diagnostics : JMD
JID - 100893612
RN  - 0 (DNA Probes)
RN  - 0 (DNA, Neoplasm)
RN  - 1HG84L3525 (Formaldehyde)
SB  - IM
MH  - Cell Line, Tumor
MH  - DNA Copy Number Variations/*genetics
MH  - DNA Probes/*metabolism
MH  - DNA, Neoplasm/genetics
MH  - Formaldehyde/*chemistry
MH  - Genome, Human
MH  - Humans
MH  - Limit of Detection
MH  - Male
MH  - *Nucleic Acid Amplification Techniques
MH  - *Paraffin Embedding
MH  - Prostatic Neoplasms/*genetics
MH  - Reproducibility of Results
MH  - *Tissue Fixation
EDAT- 2020/08/09 06:00
MHDA- 2021/11/06 06:00
CRDT- 2020/08/09 06:00
PHST- 2020/02/14 00:00 [received]
PHST- 2020/06/24 00:00 [revised]
PHST- 2020/07/15 00:00 [accepted]
PHST- 2020/08/09 06:00 [pubmed]
PHST- 2021/11/06 06:00 [medline]
PHST- 2020/08/09 06:00 [entrez]
AID - S1525-1578(20)30426-8 [pii]
AID - 10.1016/j.jmoldx.2020.07.003 [doi]
PST - ppublish
SO  - J Mol Diagn. 2020 Oct;22(10):1246-1263. doi: 10.1016/j.jmoldx.2020.07.003. Epub 
      2020 Aug 4.