title: Evaluation of real-time quantitative PCR as a standard cytogenetic diagnostic tool for confirmation of microarray (aCGH) results and determination of inheritance.
abstract: OBJECTIVE
  To evaluate the use of real-time quantitative PCR (qPCR) as a diagnostic tool for follow up of abnormal microarray (aCGH) results.
  
  
  METHODS
  qPCR was performed on 207 samples with known aCGH results to detect chromosomal abnormality and determine the capability of qPCR. Eighty-four samples were processed and the results compared with the original aCGH result and with one or more of the alternative follow-up methods: aCGH, fluorescence in situ hybridization (FISH), or karyotyping. A separate cohort of 107 samples was used to determine critical threshold values for qPCR. A further 16 samples were assessed in reproducibility and sensitivity studies.
  
  
  RESULTS
  All qPCR findings were consistent with the original aCGH results, and qPCR was found to be a superior follow-up method compared to FISH and karyotyping. Critical threshold values were also determined from this study.
  
  
  CONCLUSIONS
  In this study, qPCR analysis identified all copy number changes. qPCR is an accurate, rapid, reliable, and inexpensive technique for confirming copy number changes, and for determining the inheritance of such abnormalities to aid interpretation of results. We also present the critical threshold values required for qPCR as a practical tool. This technique has now been successfully implemented as part of the clinical diagnostic service within our laboratory.
authors.affiliation: NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children , London, United Kingdom .
authors.forename: Rubin
authors.initials: R
authors.lastname: Wang
authors.forename: Jenny
authors.initials: J
authors.lastname: Carter
authors.forename: Nicholas
authors.initials: N
authors.lastname: Lench
mesh_terms: D016022:Case-Control Studies; D015331:Cohort Studies; D055028:Comparative Genomic Hybridization / Q000592:standards; D020732:Cytogenetic Analysis; D005260:Female; D006801:Humans; D040582:Inheritance Patterns / Q000235:genetics*; D008297:Male; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods* / Q000592:standards; D012680:Sensitivity and Specificity; D054928:Validation Studies as Topic
references.citation: Genome Res. 2004 Feb;14(2):287-95
references.pmid: 14762065
references.citation: Am J Med Genet A. 2008 Jan 1;146A(1):93-6
references.pmid: 18076123
references.citation: Alcohol Clin Exp Res. 2012 Sep;36(9):1512-8
references.pmid: 22702843
references.citation: Am J Hum Genet. 2010 May 14;86(5):749-64
references.pmid: 20466091
references.citation: Nat Genet. 2009 Aug;41(8):862-3
references.pmid: 19639023
references.citation: Pathol Biol (Paris). 2008 Sep;56(6):345-53
references.pmid: 18513889
references.citation: Am J Med Genet A. 2010 Jun;152A(6):1398-410
references.pmid: 20503314
references.citation: Science. 2007 Apr 20;316(5823):445-9
references.pmid: 17363630
references.citation: Hum Mutat. 2004 Apr;23(4):368-78
references.pmid: 15024731
references.citation: BMC Genomics. 2005 Dec 13;6:180
references.pmid: 16351727