Abstract
Targeted sequencing, in which only a selected set of genomic loci are sequenced, enables a much higher coverage of each target than what is obtained using whole genome or exome sequencing. Multiplex PCR offers a simple and affordable technique for specific capture of target regions and can be easily adapted to generate next-generation sequencing (NGS)-ready amplicons. Here we describe a multiplex PCR (MxPCR) approach for capturing 13 leukemia-associated mutation hotspots followed by MiSeq sequencing that enables robust detection of mutations with a variant allele fraction (VAF) as low as 0.8% (0.008) in blood DNA.
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References
Kozarewa I et al (2015) Overview of target enrichment strategies. In: Current protocols in molecular biology. Wiley, Hoboken
Nguyen-Dumont T et al (2013) A high-plex PCR approach for massively parallel sequencing. Biotechniques 55(2):69–74
Quail MA et al (2011) Optimal enzymes for amplifying sequencing libraries. Nat Methods 9:10–11
Quail MA et al (2014) SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing. BMC Genomics 15(1):1–13
Shen Z et al (2010) MPprimer: a program for reliable multiplex PCR primer design. BMC Bioinformatics 11(1):1–7
Qu W, Zhang C (2015) Selecting specific PCR primers with MFEprimer. Methods Mol Biol 1275:201–213
McKerrell T et al (2015) Leukemia-associated somatic mutations drive distinct patterns of age-related clonal hemopoiesis. Cell Rep 10(8):1239–1245
Ford AM et al (1998) Fetal origins of the TEL-AML1 fusion gene in identical twins with leukemia. Proc Natl Acad Sci U S A 95(8):4584–4588
Kyle RA et al (2002) A long-term study of prognosis in monoclonal gammopathy of undetermined significance. N Engl J Med 346(8):564–569
Grove CS, Vassiliou GS (2014) Acute myeloid leukaemia: a paradigm for the clonal evolution of cancer? Dis Model Mech 7(8):941–951
Busque L et al (2012) Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis. Nat Genet 44(11):1179–1181
Genovese G et al (2014) Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence. N Engl J Med 371(26):2477–2487
Jacobs KB et al (2012) Detectable clonal mosaicism and its relationship to aging and cancer. Nat Genet 44(6):651–658
Jaiswal S et al (2014) Age-related clonal hematopoiesis associated with adverse outcomes. N Engl J Med 371(26):2488–2498
Laurie CC et al (2012) Detectable clonal mosaicism from birth to old age and its relationship to cancer. Nat Genet 44(6):642–650
Quail MA et al (2014) SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing. BMC Genomics 15:110
Li H et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079
Conte N et al (2013) Detailed molecular characterisation of acute myeloid leukaemia with a normal karyotype using targeted DNA capture. Leukemia 27(9):1820–1825
Nguyen-Dumont T et al (2013) Cross-platform compatibility of Hi-Plex, a streamlined approach for targeted massively parallel sequencing. Anal Biochem 442(2):127–129
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Park, N., Vassiliou, G. (2017). Design and Application of Multiplex PCR Seq for the Detection of Somatic Mutations Associated with Myeloid Malignancies. In: Fortina, P., Londin, E., Park, J., Kricka, L. (eds) Acute Myeloid Leukemia. Methods in Molecular Biology, vol 1633. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7142-8_6
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DOI: https://doi.org/10.1007/978-1-4939-7142-8_6
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Publisher Name: Humana Press, New York, NY
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Online ISBN: 978-1-4939-7142-8
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