PT  - JOURNAL ARTICLE
AU  - Johann-Christoph Jann
AU  - Daniel Nowak
AU  - Florian Nolte
AU  - Stephanie Fey
AU  - Verena Nowak
AU  - Julia Obländer
AU  - Jovita Pressler
AU  - Iris Palme
AU  - Christina Xanthopoulos
AU  - Alice Fabarius
AU  - Uwe Platzbecker
AU  - Aristoteles Giagounidis
AU  - Katharina Götze
AU  - Anne Letsch
AU  - Detlef Haase
AU  - Richard Schlenk
AU  - Gesine Bug
AU  - Michael Lübbert
AU  - Arnold Ganser
AU  - Ulrich Germing
AU  - Claudia Haferlach
AU  - Wolf-Karsten Hofmann
AU  - Maximilian Mossner
TI  - Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA
AID  - 10.1136/jmedgenet-2017-104528
DP  - 2017 Jun 09
TA  - Journal of Medical Genetics
PG  - jmedgenet-2017-104528
4099  - http://jmg.bmj.com/content/early/2017/06/09/jmedgenet-2017-104528.short
4100  - http://jmg.bmj.com/content/early/2017/06/09/jmedgenet-2017-104528.full
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.