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. 2019 Jan;102(1):87-96.
doi: 10.1111/ejh.13179. Epub 2018 Nov 22.

Mate pair sequencing improves detection of genomic abnormalities in acute myeloid leukemia

Umut Aypar  1 , Stephanie A Smoley  1 , Beth A Pitel  1 , Kathryn E Pearce  1 , Roman M Zenka  2 , George Vasmatzis  3 , Sarah H Johnson  3 , James B Smadbeck  3 , Jess F Peterson  1 , Katherine B Geiersbach  1 , Daniel L Van Dyke  1 , Erik C Thorland  1 , Robert B Jenkins  1 , Rhett P Ketterling  1 , Patricia T Greipp  1 , Hutton M Kearney  1 , Nicole L Hoppman  1 , Linda B Baughn  1
Affiliations

Mate pair sequencing improves detection of genomic abnormalities in acute myeloid leukemia

Umut Aypar et al. Eur J Haematol. 2019 Jan.

Abstract

Objective: Acute myeloid leukemia (AML) can be subtyped based on recurrent cytogenetic and molecular genetic abnormalities with diagnostic and prognostic significance. Although cytogenetic characterization classically involves conventional chromosome and/or fluorescence in situ hybridization (FISH) assays, limitations of these techniques include poor resolution and the inability to precisely identify breakpoints.

Method: We evaluated whether an NGS-based methodology that detects structural abnormalities and copy number changes using mate pair sequencing (MPseq) can enhance the diagnostic yield for patients with AML.

Results: Using 68 known abnormal and 20 karyotypically normal AML samples, each recurrent primary AML-specific abnormality previously identified in the abnormal samples was confirmed using MPseq. Importantly, in eight cases with abnormalities that could not be resolved by conventional cytogenetic studies, MPseq was utilized to molecularly define eight recurrent AML-fusion events. In addition, MPseq uncovered two cryptic abnormalities that were missed by conventional cytogenetic studies. Thus, MPseq improved the diagnostic yield in the detection of AML-specific structural rearrangements in 10/88 (11%) of cases analyzed.

Conclusion: Utilization of MPseq represents a precise, molecular-based technique that can be used as an alternative to conventional cytogenetic studies for newly diagnosed AML patients with the potential to revolutionize the diagnosis of hematologic malignancies.

Keywords: MPseq; acute myeloid leukemia; molecular cytogenetics.

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Conflict of interest statement

Algorithms described in this manuscript are licensed to WholeGenome LLC owned by George Vasmatzis.

Figures

Figure 1
Figure 1
Schematic of MPseq AML workflow. Blood or bone marrow samples are processed into fixed cells or extracted for genomic DNA. Fixed cell pellets are processed for karyotype and/or FISH analysis. Genomic DNA is extracted, prepared using the Illumina Nextera Mate Pair library preparation kit and sequenced on a HiSeq 2500. Reads are aligned to the reference genome with BIMA and variants are detected using SVAtools. Two algorithms are utilized for variant detection; junction detection and CNVDetect which also incorporates aneuploidy detection and resulting data are visualized
Figure 2
Figure 2
(panel A and B) Representative junction plots of the classic‐AML rearrangements to be detected by this assay. Each junction plot shows the lowest number chromosome on the top and the higher number on the bottom. Each black line represents a junction between two rearranged fragments with blue in the forward orientation and red in the reverse. Copy state is shown by the gray shaded area on the far top and bottom of the plot. All this data taken together allows for reconstruction of the abnormal region
Figure 3
Figure 3
Sample 78‐BM classified as a normal sample for this verification because we reported a normal karyotype shown in A and normal KMT2A break‐apart FISH B, top figure. MPseq junction plot confirming an insertion of exons 9‐24 of MLLT10 (NM_004641) into intron 9 of KMT2A (NM_005933) in C and confirmed using an MLLT10/KMT2A D‐FISH probe B, bottom figure
See this image and copyright information in PMC

References

    1. Grimwade D, Ivey A, Huntly BJ. Molecular landscape of acute myeloid leukemia in younger adults and its clinical relevance. Blood. 2016;127(1):29‐41. - PMC - PubMed
    1. De Kouchkovsky I, Abdul‐Hay M. Acute myeloid leukemia: a comprehensive review and 2016 update. Blood Cancer J. 2016;6(7):e441. - PMC - PubMed
    1. Arber DA, Orazi A, Hasserjian R, et al. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016;127(20):2391‐2405. - PubMed
    1. Leonard JP, Martin P, Roboz GJ. Practical implications of the 2016 revision of the World Health Organization classification of lymphoid and myeloid neoplasms and acute leukemia. J Clin Oncol. 2017;35(23):2708‐2715. - PubMed
    1. Aypar U, Knudson RA, Pearce KE, Wiktor AE, Ketterling RP. Development of an NPM1/MLF1 D‐FISH probe set for the detection of t(3;5)(q25;q35) identified in patients with acute myeloid leukemia. J Mol Diagn. 2014;16(5):527‐532. - PubMed

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