Accurate detection of low-level mosaic mutations in pediatric acute lymphoblastic leukemia using single molecule tagging and deep-sequencing. Issue 7 (3rd July 2018)

• Record Type: Journal Article
• Authors: Yu, Jiangyan; Antić, Željko; van Reijmersdal, Simon V.; Hoischen, Alexander; Sonneveld, Edwin; Waanders, Esmé; Kuiper, Roland P.
• Is Part Of: Leukemia & lymphoma. Volume 59:Issue 7(2018)
• Page Start: 1690
• Page End: 1699
• Publication Date: 2018-07-03
• Subjects: Acute lymphoblastic leukemia -- low-level mosaic mutations -- deep sequencing -- molecular tagging -- single molecule Molecular Inversion Probes; Leukemia -- Periodicals; Lymphomas -- Periodicals; 616.99419
• DOI: 10.1080/10428194.2017.1390232
• Languages: English
• ISSNs: 1042-8194

Abstract

Abstract: 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.