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Protocol for M3P: A Comprehensive and Clinical Oriented Targeted Sequencing Panel for Routine Molecular Analysis in Multiple Myeloma

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Multiple Myeloma

Abstract

Over the past 10 years next generation sequencing (NGS) approaches deciphered a large number of genomes from a wide variety of tumor types. However, despite most relevant findings, this technology has not yet been implemented into standard diagnostic workflows. Broad access to NGS technology is still limited, sequencing/analysis times exceed clinically relevant timeframes and despite huge cuts, costs remain significant. We proposed a custom-tailored gene panel, which focuses on a selected number of relevant genes and developed a clinically oriented NGS targeted sequencing approach for the molecular characterization of Multiple Myeloma (MM) tumors, allowing the description of the tumor genetic heterogeneity and its changes under selective pressure of antitumor therapy, in a more cost effective and faster turnaround timeframe.

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References

  1. Bolli N, Avet-Loiseau H, Wedge DC, Van Loo P, Alexandrov LB, Martincorena I, Dawson KJ, Iorio F, Nik-Zainal S, Bignell GR, Hinton JW, Li Y, Tubio JM, McLaren S, OM S, Butler AP, Teague JW, Mudie L, Anderson E, Rashid N, Tai YT, Shammas MA, Sperling AS, Fulciniti M, Richardson PG, Parmigiani G, Magrangeas F, Minvielle S, Moreau P, Attal M, Facon T, Futreal PA, Anderson KC, Campbell PJ, Munshi NC (2014) Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nat Commun 5:2997. https://doi.org/10.1038/ncomms3997

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Cancer Genome Atlas Research N (2013) Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med 368(22):2059–2074. https://doi.org/10.1056/NEJMoa1301689

    Article  CAS  Google Scholar 

  3. Lohr JG, Stojanov P, Carter SL, Cruz-Gordillo P, Lawrence MS, Auclair D, Sougnez C, Knoechel B, Gould J, Saksena G, Cibulskis K, McKenna A, Chapman MA, Straussman R, Levy J, Perkins LM, Keats JJ, Schumacher SE, Rosenberg M, Multiple Myeloma Research C, Getz G, Golub TR (2014) Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy. Cancer Cell 25(1):91–101. https://doi.org/10.1016/j.ccr.2013.12.015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Walker BA, Boyle EM, Wardell CP, Murison A, Begum DB, Dahir NM, Proszek PZ, Johnson DC, Kaiser MF, Melchor L, Aronson LI, Scales M, Pawlyn C, Mirabella F, Jones JR, Brioli A, Mikulasova A, Cairns DA, Gregory WM, Quartilho A, Drayson MT, Russell N, Cook G, Jackson GH, Leleu X, Davies FE, Morgan GJ (2015) Mutational spectrum, copy number changes, and outcome: results of a sequencing study of patients with newly diagnosed myeloma. J Clin Oncol 33(33):3911–3920. https://doi.org/10.1200/JCO.2014.59.1503

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Kortuem KM, Braggio E, Bruins L, Barrio S, Shi CS, Zhu YX, Tibes R, Viswanatha D, Votruba P, Ahmann G, Fonseca R, Jedlowski P, Schlam I, Kumar S, Bergsagel PL, Stewart AK (2016) Panel sequencing for clinically oriented variant screening and copy number detection in 142 untreated multiple myeloma patients. Blood Cancer J 6:e397. https://doi.org/10.1038/bcj.2016.1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Kortum KM, Mai EK, Hanafiah NH, Shi CX, Zhu YX, Bruins L, Barrio S, Jedlowski P, Merz M, Xu J, Stewart RA, Andrulis M, Jauch A, Hillengass J, Goldschmidt H, Bergsagel PL, Braggio E, Stewart AK, Raab MS (2016) Targeted sequencing of refractory myeloma reveals a high incidence of mutations in CRBN and Ras pathway genes. Blood 128(9):1226–1233. https://doi.org/10.1182/blood-2016-02-698092

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Kortum KM, Zhu YX, Shi CX, Jedlowski P, Stewart AK (2015) Cereblon binding molecules in multiple myeloma. Blood Rev 29(5):329–334. https://doi.org/10.1016/j.blre.2015.03.003

    Article  CAS  PubMed  Google Scholar 

  8. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29(1):24–26. https://doi.org/10.1038/nbt.1754

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME (2007) Microarray-based genomic selection for high-throughput resequencing. Nat Methods 4(11):907–909. https://doi.org/10.1038/nmeth1109

    Article  CAS  PubMed  Google Scholar 

  10. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26(10):1135–1145. https://doi.org/10.1038/nbt1486

    Article  CAS  PubMed  Google Scholar 

  11. Barrio S, Shanafelt TD, Ojha J, Chaffee KG, Secreto C, Kortum KM, Pathangey S, Van-Dyke DL, Slager SL, Fonseca R, Kay NE, Braggio E (2017) Genomic characterization of high-count MBL cases indicates that early detection of driver mutations and subclonal expansion are predictors of adverse clinical outcome. Leukemia 31(1):170–176. https://doi.org/10.1038/leu.2016.172

    Article  CAS  PubMed  Google Scholar 

  12. Kortum KM, Langer C, Monge J, Bruins L, Zhu YX, Shi CX, Jedlowski P, Egan JB, Ojha J, Bullinger L, Kull M, Ahmann G, Rasche L, Knop S, Fonseca R, Einsele H, Stewart AK, Braggio E (2015) Longitudinal analysis of 25 sequential sample-pairs using a custom multiple myeloma mutation sequencing panel (MP). Ann Hematol 94(7):1205–1211. https://doi.org/10.1007/s00277-015-2344-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Kortum KM, Langer C, Monge J, Bruins L, Egan JB, Zhu YX, Shi CX, Jedlowski P, Schmidt J, Ojha J, Bullinger L, Liebisch P, Kull M, Champion MD, Van Wier S, Ahmann G, Rasche L, Knop S, Fonseca R, Einsele H, Stewart AK, Braggio E (2015) Targeted sequencing using a 47 gene multiple myeloma mutation panel (M(3) P) in -17p high risk disease. Br J Haematol 168(4):507–510. https://doi.org/10.1111/bjh.13171

    Article  CAS  PubMed  Google Scholar 

  14. Kortuem KM, Stewart AK, Bruins LA, Ahmann G, Vasmatzis G, Rajkumar SV, Kumar S, Dispenzieri A, Lacy MQ, Gertz MA, Fonseca R, Champion M, Bergsagel PL, Braggio E (2014) Development and results of a multiple myeloma specific custom 77-gene mutation panel for clinical targeted sequencing. Blood 124:169

    Article  Google Scholar 

  15. Kortüm KM, Braggio E, Sonneveld P, Bruins L, Barrio S, Hofste BD, van Duin M, Mai EK, Hanafiah N, Goldschmidt H, Knop S, Rasche L, Langer C, Kull M, LB, Engelhardt M, Martinez-Lopez J, Einsele H, Raab MS, Stewart AK (2015) Overview of 500 Multiple Myeloma (MM) patients analyzed by targeted sequencing at Mayo Clinic. Meeting abstract: individualizing Medicine Meeting 2015, Mayo Clinic

    Google Scholar 

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Correspondence to Klaus Martin Kortüm .

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Barrio, S. et al. (2018). Protocol for M3P: A Comprehensive and Clinical Oriented Targeted Sequencing Panel for Routine Molecular Analysis in Multiple Myeloma. In: Heuck, C., Weinhold, N. (eds) Multiple Myeloma. Methods in Molecular Biology, vol 1792. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-7865-6_8

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  • DOI: https://doi.org/10.1007/978-1-4939-7865-6_8

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-7864-9

  • Online ISBN: 978-1-4939-7865-6

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