RT Journal Article
SR Electronic
T1 Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA
JF Journal of Medical Genetics
JO J Med Genet
FD BMJ Publishing Group Ltd
SP jmedgenet-2017-104528
DO 10.1136/jmedgenet-2017-104528
A1 Johann-Christoph Jann
A1 Daniel Nowak
A1 Florian Nolte
A1 Stephanie Fey
A1 Verena Nowak
A1 Julia Obländer
A1 Jovita Pressler
A1 Iris Palme
A1 Christina Xanthopoulos
A1 Alice Fabarius
A1 Uwe Platzbecker
A1 Aristoteles Giagounidis
A1 Katharina Götze
A1 Anne Letsch
A1 Detlef Haase
A1 Richard Schlenk
A1 Gesine Bug
A1 Michael Lübbert
A1 Arnold Ganser
A1 Ulrich Germing
A1 Claudia Haferlach
A1 Wolf-Karsten Hofmann
A1 Maximilian Mossner
YR 2017
UL http://jmg.bmj.com/content/early/2017/06/09/jmedgenet-2017-104528.abstract
AB Background Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings.Methods For precise determination of del(5q) cell fractions, we developed an inexpensive multiplex-PCR assay requiring only nanograms of DNA that simultaneously measures allelic imbalances of 12 independent short tandem repeat markers.Results Application of this method to n=1142 samples from n=260 individuals revealed strong intermarker concordance (R²=0.77–0.97) and reproducibility (mean SD: 1.7%). Notably, the assay showed accurate quantification via standard curve assessment (R²>0.99) and high concordance with paired FISH measurements (R²=0.92) even with subnanogram amounts of DNA. Moreover, cytogenetic response was reliably confirmed in del(5q) patients with myelodysplastic syndromes treated with lenalidomide. While the assay demonstrated good diagnostic accuracy in receiver operating characteristic analysis (area under the curve: 0.97), we further observed robust correlation between bone marrow and peripheral blood samples (R²=0.79), suggesting its potential suitability for less-invasive clonal monitoring.Conclusions In conclusion, we present an adaptable tool for quantification of chromosomal aberrations, particularly in problematic samples, which should be easily applicable to further tumour entities.