Peifer, Martin - assoc. RG 16

Computational cancer genomics

Prof. Dr. Martin Peifer
Prof. Dr. Martin Peifer

Department for Translational Genomics | CMMC Research Center

CMMC - PI - assoc. RG 16

mpeifer@uni-koeln.de

+49 221 478 96863

Lab Website

CMMC Profile Page

Curriculum Vitae (CV)

Publications on PubMed

Department for Translational Genomics | CMMC Research Center

Robert-Koch-Str. 21

50931 Cologne

About

The development of massively parallel sequencing has fueled genome-centric cancer research. This technology has enabled us to sequence entire cancer genomes and transcriptomes in a relatively short period of time. However, the data produced by this approach is highly complex and difficult to analyze in order to extract the biologically relevant information. Within our group we are developing new computational methods and analyze sequencing data from tumor specimens.

Research Focus

We develop and apply computational methods to cancer genome sequencing data. This includes methods call somatic genome alterations such as point mutations, copy number changes, and rearrangements. Furthermore, we develop computational tools for integrative genome analyses, to reconstruct tumor evolution, and recently to analyze single cell sequencing data (both on RNA and DNA). We mostly work on tumor types such as lung cancer, neuroblastoma, and B-cell lymphoma.

Goals and Approach

With the help of these methods, we aim to better understand tumorigenesis, clonal evolution of cancer cells, and therapy resistance. We are an interdisciplinary team and provide new computational approaches to analyze and interpret high-throughput cancer sequencing data. 

Figure

Fig.: Tumor phylogenies and clonal dynamics in 65 patients with small cell lung cancer (adapted from George et al. Nature 2024).

Lab Website

For more information, please check Peifer Lab. 

  1. George J*, Maas L, Abedpour N, Cartolano M, Kaiser L, Fischer RN, Scheel AH, Weber JP, Hellmich M, Bosco G, Volz C, Mueller C, Dahmen I, John F, Alves CP, Werr L, Panse JP, Kirschner M, Engel-Riedel W, Jürgens J, Stoelben E, Brockmann M, Grau S, Sebastian M, Stratmann JA, Kern J, Hummel HD, Hegedüs B, Schuler M, Plönes T, Aigner C, Elter T, Toepelt K, Ko YD, Kurz S, Grohé C, Serke M, Höpker K, Hagmeyer L, Doerr F, Hekmath K, Strapatsas J, Kambartel KO, Chakupurakal G, Busch A, Bauernfeind FG, Griesinger F, Luers A, Dirks W, Wiewrodt R, Luecke A, Rodermann E, Diel A, Hagen V, Severin K, Ullrich RT, Reinhardt HC, Quaas A, Bogus M, Courts C, Nürnberg P, Becker K, Achter V, Büttner R, Wolf J, Peifer M*, Thomas RK*. Evolutionary trajectories of small cell lung cancer under therapy. Nature, 2024; 627(8005): 880-889. * co-last authors
     
  2. Rosswog C, Bartenhagen C, Welte A, Kahlert Y, Hemstedt N, Lorenz W, Cartolano M, Ackermann S, Perner S, Vogel W, Altmüller J, Nürnberg P, Hertwig F, Göhring G, Lilienweiss E, Stütz AM, Korbel JO, Thomas RK, Peifer M*, and Fischer M*. Chromothripsis followed by circular recombination drives oncogene amplification in human cancer. Nature Genetics, 2021; 53(12):1673-1685.* co-last authors
     
  3. Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vzquez-Garca I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher SE, Fan Y, Fittall M, Drews RM, Yao X, Watkins TBK, Lee J, Schlesner M, Zhu H, Adams DJ, McGranahan N, Swanton C, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan Ke, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, and Van Loo P, PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell, 2021; 184:2239-2254.e39.
     
  4. Cartolano M, Abedpour N, Achter V, Yang TP, Ackermann S, Fischer M and Peifer M. CaMuS: simultaneous fitting and de novo imputation of cancer mutational signature. Scientific Reports, 2020; 10:19316.
     
  5. Klein S*, Quaas A, Noh KW, Cartolano M, Abedpour N, Mauch C, Quantius J, Reinhardt HC, Büttner R, Martin M* and Doris Helbig*. Integrative Analysis of Pleomorphic Dermal Sarcomas Reveals Fibroblastic Differentiation and Susceptibility to Immunotherapy. Clinical Cancer Research, 2020; 26:5638-5645. *co-last authors
     
  6. Ackermann S †, Cartolano M †, Hero B, Welte A, Kahlert Y, Roderwieser A, Bartenhagen C, Walter E, Gecht J, Kerschke L, Volland R, Menon R, Heuckmann JM, Gartlgruber M, Hartlieb S, Henrich KO, Okonechnikov K, Altmüller J, Nürnberg P, Lefever S, de Wilde B, Sand F, Ikram F, Rosswog C, Fischer J, Theissen J, Hertwig F, Singhi AD, Simon T, Vogel W, Perner S, Krug B, Schmidt M, Rahmann S, Achter V, Lang U, Vokuhl C, Ortmann M, Büttner R, Eggert A, Speleman F, O’Sullivan RJ, Thomas RK, Berthold F†, Vandesompele J†, Schramm A†, Westermann F †, Schulte JH †, Peifer M †, Fischer M †. A mechanistic classification of clinical phenotypes in neuroblastoma. Science, 2018; 7;362(6419):1165-1170. †equal contribution
     
  7. Cun Y, Yang TP, Achter V, Lang U, Peifer M. Copy-number analysis and inference of subclonal populations in cancer genomes using Sclust. Nature Protocols, 2018; 13(6):1488-1501.
     
  8. Peifer M, Hertwig F, Roels F, Dreidax D, Gartlgruber M, Menon R, Krämer A, Roncaioli JL, Sand F, Heuckmann JM, Ikram F, Schmidt R, Ackermann S, Engesser A, Kahlert Y, Vogel W, Altmüller J, Nürnberg P, Thierry-Mieg J, Thierry-Mieg D, Mariappan A, Heynck S, Mariotti E, Henrich KO, Gloeckner C, Bosco G, Leuschner I, Schweiger MR, Savelyeva L, Watkins SC, Shao C, Bell E, Höfer T, Achter V, Lang U, Theissen J, Volland R, Saadati M, Eggert A, de Wilde B, Berthold F, Peng Z, Zhao C, Shi L, Ortmann M, Büttner R, Perner S, Hero B, Schramm A, Schulte JH, Herrmann C, O'Sullivan RJ, Westermann F, Thomas RK, Fischer M. Telomerase activation by genomic rearrangements in high-risk neuroblastoma. Nature, 2015; 29;526(7575):700-4.
     
  9. George J, Lim JS, Jang SJ, Cun Y, Ozretic L, Leenders F, Lu X, Fernandez-Cuesta L, Bosco G, Nguyen C, Berg J, Müller C, Dahmen I, Jahchan N, Yang D, Karnezis AN, Vaka D, Torres A, Menon R, Wang MS, Stuetz A, Korbel J, Wilkerson M, Hayes N, Engelmann D, Pützer B, Vlasic I, Seidel D, Pinther B, Schaub B, Becker C, Altmüller J, Yokota J, Khono T, Iwakawa R, Muley T, Peterson I, … Nürnberg P, Reinhardt HC, Perner S, Heukamp LC, Büttner R, Haas SA, Brambilla E, Peifer M*, Sage J*, Thomas RK*. Comprehensive genomic profiling of small cell lung cancer. Nature, 2015; 6; 524(7563):47-53. doi: 10.1038/nature14664. *co-last authors
     
  10. Peifer M, Fernández-Cuesta L, Sos ML, George J, Seidel D, Kasper LH, Plenker D, Leenders F, Sun R, Zander T, Menon R, Koker M, Dahmen I, Müller C, Di Cerbo V, Schildhaus HU, Altmüller J, Baessmann I, Becker C, de Wilde B, Vandesompele J, Böhm D, Ansén S, Gabler F, Wilkening I, Heynck S, Heuckmann JM, Lu X, Carter SL, Cibulskis K, Banerji S, Getz G, Park KS, Rauh D, Grütter C, Fischer M, Pasqualucci L, Wright G, Wainer Z, Russell P, Petersen I, Chen Y, Stoelben E, Ludwig C, Schnabel P, Hoffmann H, Muley T, Brockmann M, Engel-Riedel W, Muscarella LA, Fazio VM, Groen H, Timens W, Sietsma H, Thunnissen E, Smit E, Heideman DA, Snijders PJ, Cappuzzo F, Ligorio C, Damiani S, Field J, Solberg S, Brustugun OT, Lund-Iversen M, Sänger J, Clement JH, Soltermann A, Moch H, Weder W, Solomon B, Soria JC, Validire P, Besse B, Brambilla E, Brambilla C, Lantuejoul S, Lorimier P, Schneider PM, Hallek M, Pao W, Meyerson M, Sage J, Shendure J, Schneider R, Büttner R, Wolf J, Nürnberg P, Perner S, Heukamp LC, Brindle PK, Haas S, Thomas RK. Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nature Genetics, 2012; 44(10):1104-10. 

Publication Record on PubMed - Martin Peifer

2024 (up to June)
  • Garcia-Marquez MA, Thelen M, Bauer E, Maas L, Wennhold K, Lehmann J, Keller D, Nikolic M, George J, Zander T, Schroder W, Muller P, Yazbeck AM, Bruns C, Thomas R, Gathof B, Quaas A, Peifer M, Hillmer AM, von Bergwelt-Baildon M, and Schlosser HA (2024). Germline homozygosity and allelic imbalance of HLA-I are common in esophagogastric adenocarcinoma and impair the repertoire of immunogenic peptides. J Immunother Cancer12. doi:10.1136/jitc-2023-007268.
2023
  • Flumann R, Hansen J, Pelzer BW, Nieper P, Lohmann T, Kisis I, Riet T, Kohlhas V, Nguyen PH, Peifer M, Abedpour N, Bosco G, Thomas RK, Kochanek M, Knufer J, Jonigkeit L, Beleggia F, Holzem A, Buttner R, Lohneis P, Meinel J, Ortmann M, Persigehl T, Hallek M, Calado DP, Chmielewski M, Klein S, Gothert JR, Chapuy B, Zevnik B, Wunderlich FT, von Tresckow B, Jachimowicz RD, Melnick AM, Reinhardt HC, and Knittel G (2023). Distinct Genetically Determined Origins of Myd88/BCL2-Driven Aggressive Lymphoma Rationalize Targeted Therapeutic Intervention Strategies. Blood Cancer Discov 4, 78-97. doi:10.1158/2643-3230.BCD-22-0007.
     
  • Koerner L, Schmiel M, Yang TP, Peifer M, Buettner R, and Pasparakis M (2023). NEMO- and RelA-dependent NF-kappaB signaling promotes small cell lung cancer. Cell Death Differ 30, 938-951. doi:10.1038/s41418-023-01112-5.
     
  • Rosswog C, Fassunke J, Ernst A, Schomig-Markiefka B, Merkelbach-Bruse S, Bartenhagen C, Cartolano M, Ackermann S, Theissen J, Blattner-Johnson M, Jones B, Schramm K, Altmuller J, Nurnberg P, Ortmann M, Berthold F, Peifer M, Buttner R, Westermann F, Schulte JH, Simon T, Hero B, and Fischer M (2023). Genomic ALK alterations in primary and relapsed neuroblastoma. Br J Cancer 128, 1559-1571. doi:10.1038/s41416-023-02208-y.

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