Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA

• Verfasst von: Jann, Johann-Christoph [VerfasserIn]
• Verfasst von: Nowak, Daniel [VerfasserIn]
• Verfasst von: Nolte, Florian [VerfasserIn]
• Verfasst von: Fey, Stephanie [VerfasserIn]
• Verfasst von: Nowak, Verena [VerfasserIn]
• Verfasst von: Obländer, Julia [VerfasserIn]
• Verfasst von: Pressler, Jovita [VerfasserIn]
• Verfasst von: Palme, Iris [VerfasserIn]
• Verfasst von: Xanthopoulos, Christina [VerfasserIn]
• Verfasst von: Fabarius, Alice [VerfasserIn]
• Verfasst von: Schlenk, Richard Friedrich [VerfasserIn]
• Verfasst von: Hofmann, Wolf-Karsten [VerfasserIn]
• Verfasst von: Mossner, Maximilian [VerfasserIn]
• Titel: Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA
• Verf.angabe: Johann-Christoph Jann, Daniel Nowak, Florian Nolte, Stephanie Fey, Verena Nowak, Julia Obländer, Jovita Pressler, Iris Palme, Christina Xanthopoulos, Alice Fabarius, Uwe Platzbecker, Aristoteles Giagounidis, Katharina Götze, Anne Letsch, Detlef Haase, Richard Schlenk, Gesine Bug, Michael Lübbert, Arnold Ganser, Ulrich Germing, Claudia Haferlach, Wolf-Karsten Hofmann, Maximilian Mossner
• E-Jahr: 2017
• Jahr: 9 June 2017
• Umfang: 11 S.
• Fussnoten: Published online first 9 June 2017 ; Gesehen am 30.07.2018
• Titel Quelle: Enthalten in: Journal of medical genetics
• Ort Quelle: London : BMJ Publishing Group, 1964
• Jahr Quelle: 2017
• Band/Heft Quelle: 54(2017), 9, Seite 640-650
• ISSN Quelle: 1468-6244
• DOI: doi:10.1136/jmedgenet-2017-104528
• Datenträger: Online-Ressource
• Sprache: eng
• Sach-SW: Chromosomal deletion
• Sach-SW: deletion 5q
• Sach-SW: myelodysplastic syndrome
• Sach-SW: PCR
• Sach-SW: short tandem repeats
• K10plus-PPN: 1578052874

Abstract

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.