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01-09-2019 | Lymphoma | Original Article

Comprehensive detection of chromosomal translocations in lymphoproliferative disorders by massively parallel sequencing

Authors: Philippe Szankasi, Ashini Bolia, Michael Liew, Jonathan A. Schumacher, Elaine P. S. Gee, Anna P. Matynia, K. David Li, Jay L. Patel, Xinjie Xu, Mohamed E. Salama, Todd W. Kelley

Published in: Journal of Hematopathology | Issue 3/2019

Abstract

Balanced translocations have diagnostic and prognostic value in B-cell lymphoproliferative disorders (LPDs). Most of these translocations involve the juxtaposition of a strong immunoglobulin (Ig) enhancer to proto-oncogenes, such as BCL2, BCL6, and MYC, leading to their overexpression. These rearrangements generally do not result in mRNA fusions, and fluorescent in situ hybridization (FISH) remains the gold standard for assessing of recurrent translocations in LPDs. With the growing use of massively parallel sequencing for the detection of both point mutations and large structural rearrangements, we aimed at evaluating the utility of this method for the molecular work-up of B-cell LPDs side by side with FISH. We describe a method using solution capture for enrichment of known translocation breakpoints and massively parallel sequencing for the detection of balanced translocation in formalin-fixed tissues with a B-cell LPD. We detected a total of 57 rearrangements with a high concordance of 94.2% when compared to FISH. We detected translocations between BCL2, BCL6, and MYC and the three Ig loci and non-Ig loci, including novel partners for MYC and BCL6. In addition, massively parallel sequencing allowed a detailed analysis of the structure of the resulting chromosomal fusions. Our comparison shows the feasibility of using massively parallel sequencing for detecting balanced translocations in B-cell LPDs and advantages and disadvantages to both methods, and how they can complement each other.

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Kuppers R, Dalla-Favera R (2001) Mechanisms of chromosomal translocations in B cell lymphomas. Oncogene 20(40):5580–5594. https://doi.org/10.1038/sj.onc.1204640 CrossRefPubMed

Goossens T, Klein U, Kuppers R (1998) Frequent occurrence of deletions and duplications during somatic hypermutation: implications for oncogene translocations and heavy chain disease. Proc Natl Acad Sci U S A 95(5):2463–2468CrossRefPubMedPubMedCentral

Espinet B, Bellosillo B, Melero C, Vela MC, Pedro C, Salido M, Pijuan L, Florensa L, Besses C, Serrano S, Sole F (2008) FISH is better than BIOMED-2 PCR to detect IgH/BCL2 translocation in follicular lymphoma at diagnosis using paraffin-embedded tissue sections. Leuk Res 32(5):737–742. https://doi.org/10.1016/j.leukres.2007.09.010 CrossRefPubMed

Shen W, Szankasi P, Sederberg M, Schumacher J, Frizzell KA, Gee EP, Patel JL, South ST, Xu X, Kelley TW (2016) Concurrent detection of targeted copy number variants and mutations using a myeloid malignancy next generation sequencing panel allows comprehensive genetic analysis using a single testing strategy. Br J Haematol 173(1):49–58. https://doi.org/10.1111/bjh.13921 CrossRefPubMed

Akasaka H, Akasaka T, Kurata M, Ueda C, Shimizu A, Uchiyama T, Ohno H (2000) Molecular anatomy of BCL6 translocations revealed by long-distance polymerase chain reaction-based assays. Cancer Res 60(9):2335–2341PubMed

Ohno H (2006) Pathogenetic and clinical implications of non-immunoglobulin: BCL6 translocations in B-cell non-Hodgkin’s lymphoma. J Clin Exp Hematopathol : JCEH 46(2):43–53CrossRef

Bouamar H, Abbas S, Lin AP, Wang L, Jiang D, Holder KN, Kinney MC, Hunicke-Smith S, Aguiar RC (2013) A capture-sequencing strategy identifies IRF8, EBF1, and APRIL as novel IGH fusion partners in B-cell lymphoma. Blood 122(5):726–733. https://doi.org/10.1182/blood-2013-04-495804 CrossRefPubMedPubMedCentral

Akasaka T, Akasaka H, Yonetani N, Ohno H, Yamabe H, Fukuhara S, Okuma M (1998) Refinement of the BCL2/immunoglobulin heavy chain fusion gene in t(14;18)(q32;q21) by polymerase chain reaction amplification for long targets. Genes Chromosom Cancer 21(1):17–29CrossRefPubMed

Burmeister T, Molkentin M, Schwartz S, Gokbuget N, Hoelzer D, Thiel E, Reinhardt R (2013) Erroneous class switching and false VDJ recombination: molecular dissection of t(8;14)/MYC-IGH translocations in Burkitt-type lymphoblastic leukemia/B-cell lymphoma. Mol Oncol 7(4):850–858. https://doi.org/10.1016/j.molonc.2013.04.006 CrossRefPubMedPubMedCentral

10.

Albinger-Hegyi A, Hochreutener B, Abdou MT, Hegyi I, Dours-Zimmermann MT, Kurrer MO, Heitz PU, Zimmermann DR (2002) High frequency of t(14;18)-translocation breakpoints outside of major breakpoint and minor cluster regions in follicular lymphomas: improved polymerase chain reaction protocols for their detection. Am J Pathol 160(3):823–832. https://doi.org/10.1016/S0002-9440(10)64905-X CrossRefPubMedPubMedCentral

11.

Murga Penas EM, Callet-Bauchu E, Ye H, Gazzo S, Berger F, Schilling G, Albert-Konetzny N, Vettorazzi E, Salles G, Wlodarska I, Du MQ, Bokemeyer C, Dierlamm J (2010) The t(14;18)(q32;q21)/IGH-MALT1 translocation in MALT lymphomas contains templated nucleotide insertions and a major breakpoint region similar to follicular and mantle cell lymphoma. Blood 115(11):2214–2219. https://doi.org/10.1182/blood-2009-08-236265 CrossRefPubMed

12.

Fan H, Gulley ML, Gascoyne RD, Horsman DE, Adomat SA, Cho CG (1998) Molecular methods for detecting t(11;14) translocations in mantle-cell lymphomas. Diagn Mol Pathol 7(4):209–214CrossRefPubMed

13.

Baens M, Steyls A, Dierlamm J, De Wolf-Peeters C, Marynen P (2000) Structure of the MLT gene and molecular characterization of the genomic breakpoint junctions in the t(11;18)(q21;q21) of marginal zone B-cell lymphomas of MALT type. Genes Chromosom Cancer 29(4):281–291CrossRefPubMed

14.

Yonetani N, Ueda C, Akasaka T, Nishikori M, Uchiyama T, Ohno H (2001) Heterogeneous breakpoints on the immunoglobulin genes are involved in fusion with the 5′ region of BCL2 in B-cell tumors. Japn J Cancer Res : Gann 92(9):933–940CrossRef

15.

Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv

16.

Rausch T, Zichner T, Schlattl A, Stutz AM, Benes V, Korbel JO (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28(18):i333–i339. https://doi.org/10.1093/bioinformatics/bts378 CrossRefPubMedPubMedCentral

17.

Liew M, Rowe L, Clement PW, Miles RR, Salama ME (2016) Validation of break-apart and fusion MYC probes using a digital fluorescence in situ hybridization capture and imaging system. J Pathol Inform 7:20. https://doi.org/10.4103/2153-3539.181764 CrossRefPubMedPubMedCentral

18.

Ueda C, Akasaka T, Kurata M, Maesako Y, Nishikori M, Ichinohasama R, Imada K, Uchiyama T, Ohno H (2002) The gene for interleukin-21 receptor is the partner of BCL6 in t(3;16)(q27;p11), which is recurrently observed in diffuse large B-cell lymphoma. Oncogene 21(3):368–376. https://doi.org/10.1038/sj.onc.1205099 CrossRefPubMed

19.

Yoshida S, Kaneita Y, Aoki Y, Seto M, Mori S, Moriyama M (1999) Identification of heterologous translocation partner genes fused to the BCL6 gene in diffuse large B-cell lymphomas: 5’-RACE and LA - PCR analyses of biopsy samples. Oncogene 18(56):7994–7999. https://doi.org/10.1038/sj.onc.1203293 CrossRefPubMed

20.

Bakhshi A, Wright JJ, Graninger W, Seto M, Owens J, Cossman J, Jensen JP, Goldman P, Korsmeyer SJ (1987) Mechanism of the t(14;18) chromosomal translocation: structural analysis of both derivative 14 and 18 reciprocal partners. Proc Natl Acad Sci U S A 84(8):2396–2400CrossRefPubMedPubMedCentral

21.

Halper-Stromberg E, Steranka J, Giraldo-Castillo N, Fuller T, Desiderio S, Burns KH (2013) Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies. BMC Genomics 14:565. https://doi.org/10.1186/1471-2164-14-565 CrossRefPubMedPubMedCentral

22.

Cotter F, Price C, Zucca E, Young BD (1990) Direct sequence analysis of the 14q+ and 18q- chromosome junctions in follicular lymphoma. Blood 76(1):131–135PubMedCrossRef

23.

Vaandrager JW, Schuuring E, Philippo K, Kluin PM (2000) V(D)J recombinase-mediated transposition of the BCL2 gene to the IGH locus in follicular lymphoma. Blood 96(5):1947–1952PubMedCrossRef

24.

Joos S, Falk MH, Lichter P, Haluska FG, Henglein B, Lenoir GM, Bornkamm GW (1992) Variable breakpoints in Burkitt lymphoma cells with chromosomal t(8;14) translocation separate c-myc and the IgH locus up to several hundred kb. Hum Mol Genet 1(8):625–632CrossRefPubMed

25.

Joos S, Haluska FG, Falk MH, Henglein B, Hameister H, Croce CM, Bornkamm GW (1992) Mapping chromosomal breakpoints of Burkitt’s t(8;14) translocations far upstream of c-myc. Cancer Res 52(23):6547–6552PubMed

26.

Einerson RR, Law ME, Blair HE, Kurtin PJ, McClure RF, Ketterling RP, Flynn HC, Dogan A, Remstein ED (2006) Novel FISH probes designed to detect IGK-MYC and IGL-MYC rearrangements in B-cell lineage malignancy identify a new breakpoint cluster region designated BVR2. Leukemia 20(10):1790–1799. https://doi.org/10.1038/sj.leu.2404340 CrossRefPubMed

27.

Henglein B, Synovzik H, Groitl P, Bornkamm GW, Hartl P, Lipp M (1989) Three breakpoints of variant t(2;8) translocations in Burkitt’s lymphoma cells fall within a region 140 kilobases distal from c-myc. Mol Cell Biol 9(5):2105–2113CrossRefPubMedPubMedCentral

28.

Copie-Bergman C, Cuilliere-Dartigues P, Baia M, Briere J, Delarue R, Canioni D, Salles G, Parrens M, Belhadj K, Fabiani B, Recher C, Petrella T, Ketterer N, Peyrade F, Haioun C, Nagel I, Siebert R, Jardin F, Leroy K, Jais JP, Tilly H, Molina TJ, Gaulard P (2015) MYC-IG rearrangements are negative predictors of survival in DLBCL patients treated with immunochemotherapy: a GELA/LYSA study. Blood 126(22):2466–2474. https://doi.org/10.1182/blood-2015-05-647602 CrossRefPubMed

29.

Chong LC, Ben-Neriah S, Slack GW, Freeman C, Ennishi D, Mottok A, Collinge B, Abrisqueta P, Farinha P, Boyle M, Meissner B, Kridel R, Gerrie AS, Villa D, Savage KJ, Sehn LH, Siebert R, Morin RD, Gascoyne RD, Marra MA, Connors JM, Mungall AJ, Steidl C, Scott DW (2018) High-resolution architecture and partner genes of MYC rearrangements in lymphoma with DLBCL morphology. Blood Adv 2(20):2755–2765. https://doi.org/10.1182/bloodadvances.2018023572 CrossRefPubMedPubMedCentral

30.

Zhu G, Benayed R, Ho C, Mullaney K, Sukhadia P, Rios K, Berry R, Rubin BP, Nafa K, Wang L, Klimstra DS, Ladanyi M, Hameed MR (2019) Diagnosis of known sarcoma fusions and novel fusion partners by targeted RNA sequencing with identification of a recurrent ACTB-FOSB fusion in pseudomyogenic hemangioendothelioma. Mod Pathol 32(5):609–620. https://doi.org/10.1038/s41379-018-0175-7 CrossRefPubMed

31.

Kim B, Lee H, Shin S, Lee ST, Choi JR (2019) Clinical evaluation of massively parallel RNA sequencing for detecting recurrent gene fusions in hematologic malignancies. J Mol Diagn 21(1):163–170. https://doi.org/10.1016/j.jmoldx.2018.09.002 CrossRefPubMed

Title: Comprehensive detection of chromosomal translocations in lymphoproliferative disorders by massively parallel sequencing
Authors: Philippe Szankasi
Ashini Bolia
Michael Liew
Jonathan A. Schumacher
Elaine P. S. Gee
Anna P. Matynia
K. David Li
Jay L. Patel
Xinjie Xu
Mohamed E. Salama
Todd W. Kelley
Publication date: 01-09-2019
Publisher: Springer Berlin Heidelberg
Keywords: Lymphoma
Mucosa Associated Lymphoid Tissue
Published in: Journal of Hematopathology / Issue 3/2019
Print ISSN: 1868-9256
Electronic ISSN: 1865-5785
DOI: https://doi.org/10.1007/s12308-019-00360-0

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Comprehensive detection of chromosomal translocations in lymphoproliferative disorders by massively parallel sequencing

Abstract

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