Accurate detection of low-level mosaic mutations in pediatric acute lymphoblastic leukemia using single molecule tagging and deep-sequencing

Jiangyan Yu, Željko Antić, Simon V van Reijmersdal, Alexander Hoischen, Edwin Sonneveld, Esmé Waanders, Roland P Kuiper

Onderzoeksoutput: Bijdrage aan tijdschriftArtikelpeer review

Samenvatting

Pathogenic mutations in relapse-associated genes in pediatric acute lymphoblastic leukemia may improve risk stratification when detected at subclonal levels at primary diagnosis. However, to detect subclonal mutations upfront, a deep-sequencing approach with high specificity and sensitivity is required. Here, we performed a proof-of-principle study to detect low-level mosaic RAS pathway mutations by deep sequencing using random tagging-based single molecule Molecular Inversion Probes (smMIPs). The smMIP-based approach could sensitively detect variants with allele frequency as low as 0.4%, which could all be confirmed by other techniques. In comparison, with standard deep-sequencing techniques we reached a detection threshold of only 2.5%, which hampered detection of seven low-level mosaic mutations representing 24% of all detected mutations. We conclude that smMIP-based deep-sequencing outperforms standard deep-sequencing techniques by showing lower background noise and high specificity, and is the preferred technology for detecting mutations upfront, particularly in genes in which mutations show limited clustering in hotspots.

Originele taal-2Engels
Pagina's (van-tot)1690-1699
Aantal pagina's10
TijdschriftLeukemia & lymphoma
Volume59
Nummer van het tijdschrift7
DOI's
StatusGepubliceerd - jul. 2018

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