Sebastian Martin Waszak

Biography

Sebastian M. Waszak is a Tenure-Track Assistant Professor of Life Sciences at the École Polytechnique Fédérale de Lausanne and an Associate Adjunct Professor of Neurology at the University of California, San Francisco. He is the Director of the Laboratory of Computational Neuro-Oncology at the Swiss Institute for Experimental Cancer Research. He obtained his PhD in Bioengineering and Biotechnology from the École Polytechnique Fédérale de Lausanne and specialized as a postdoctoral fellow in cancer genomics at the European Molecular Biology Laboratory. His research focuses on biomedical data science for children and young adults with brain tumours. He studies the genetic architecture and evolutionary history of brain tumours, develops novel technologies for minimally invasive and longitudinal molecular diagnostics in pediatric neuro-oncology, and studies cancer genomes in precision medicine clinical trials. He published 80 papers in basic science and medical journals (h-index 47; 17,000 citations), with first/senior author publications in Science (2013), Cell (2015), The Lancet Oncology (2018), Nature (2020a, 2020b), Clinical Cancer Research (2021),  and the Journal of Clinical Oncology (2020, 2023). He contributed and introduced novel entities to the 2021 WHO Classification of CNS Tumors and the 2023 WHO Classification of Genetic Tumor Syndromes. His research resulted in revised clinical practice guidelines and amendments to clinical trial protocols. He is a member of the Pacific Pediatric Neuro-Oncology Consortium (PNOC), the UCSF Pediatric DMG Tumor Board, and the DIPG/DMG National Brain Tumor Board.

Education

2014 Ph.D., Biotechnology/Bioengineering, École Polytechnique Fédérale de Lausanne, Switzerland
2010 Diplom-Ingenieur (FH), Bioinformatics, Hochschule Weihenstephan-Triesdorf, Germany
2009 Diplom Thesis, Population genomics, Weizmann Institute of Science, Israel

Professional Experience

2023 Tenure Track Assistant Professor, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
2021 Associate Adjunct Professor, Department of Neurology, University of California, San Francisco, United States
2021 Adjunct Researcher, Department of Pediatric Research, Rikshospitalet, Oslo University Hospital, Norway
2020 Group Leader, Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Norway
2014 Postdoctoral Fellow, Genome Biology Unit, European Molecular Biology Laboratory, Germany

Awards

2023 Poster Award, Annual Meeting of the Society for Neuro-Oncology, Canada
2022 Global Inclusion Award, Children's Brain Tumor Network, United States
2018 Postdoctoral Fellowship, European Molecular Biology Laboratory, Germany
2017 Early Career Award, Swiss Institute of Bioinformatics, Switzerland
2016 Postdoctoral Long-Term Fellowship, European Molecular Biology Organization, Germany
2015 Special Distinction for PhD Thesis, École Polytechnique Fédérale de Lausanne, Switzerland
2014 Early Postdoc.Mobility Fellowship, Swiss National Science Foundation, Switzerland
2013 Prime Spéciale du Doyen, École Polytechnique Fédérale de Lausanne, Switzerland
2009 Feinberg Graduate School Fellowship, Weizmann Institute of Science, Israel

Selected Publications

• Flynn A, Waszak SM#, Weischenfeldt J#. Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer. Molecular Systems Biology (2024). doi:10.1038/s44320-024-00054-5. #corresponding authors
• Haas-Kogan DA, Aboian MS, Minturn JE, Leary SES, Abdelbaki MS, Goldman S, Elster JD, Kraya A, Lueder MR, Ramakrishnan D, von Reppert M, Liu KX, Rokita JL, Resnick AC, Solomon DA, Phillips JJ, Prados M, Molinaro AM, Waszak SM#, Mueller S#. Everolimus for Children With Recurrent or Progressive Low-Grade Glioma: Results From the Phase II PNOC001 Trial. Journal of Clinical Oncology. 2023 Nov 17; JCO2301838. #senior authors
• Roberts HJ*, Ji S*, Picca A, Sanson M, Garcia M, Snuderl M, Schüller U, Picart T, Ducray F, Green AL, Nakano Y, Sturm D, Abdullaev Z, Aldape K, Dang D, Kumar-Sinha C, Wu YM, Robinson D, Vo JN, Chinnaiyan AM, Cartaxo R, Upadhyaya SA, Mody R, Chiang J, Baker S, Solomon D, Venneti S, Pratt D, Waszak SM#, Koschmann C#. Clinical, genomic, and epigenomic analyses of H3K27M-mutant diffuse midline glioma long-term survivors reveal a distinct group of tumors with MAPK pathway alterations. Acta Neuropathologica. 2023 Oct 18; doi:10.1007/s00401-023-02640-7 #corresponding authors *first authors
• Venneti S*, Kawakibi AR*, Ji S*, Waszak SM*, Sweha SR*, Mota M*, Pun M*, Deogharkar A, Chung C, Tarapore RS, Ramage S, Chi A, Wen PY, Arrillaga-Romany I, Batchelor TT, Butowski NA, Sumrall A, Shonka N, Harrison RA, de Groot J, Mehta M, Hall MD, Daghistani D, Cloughesy TF, Ellingson BM, Beccaria K, Varlet P, Kim MM, Umemura Y, Garton H, Franson A, Schwartz J, Jain R, Kachman M, Baum H, Burant CF, Mottl SL, Cartaxo RT, John V, Messinger D, Qin T, Peterson E, Sajjakulnukit P, Ravi K, Waugh A, Walling D, Ding Y, Xia Z, Schwendeman A, Hawes D, Yang F, Judkins AR, Wahl D, Lyssiotis CA, de la Nava D, Alonso MM, Eze A, Spitzer J, Schmidt SV, Duchatel RJ, Dun MD, Cain JE, Jiang L, Stopka SA, Baquer G, Regan MS, Filbin MG, Agar NYR, Zhao L, Kumar-Sinha C, Mody R, Chinnaiyan A, Kurokawa R, Pratt D, Yadav VN, Grill J, Kline C, Mueller S, Resnick A, Nazarian J, Allen JE, Odia Y, Gardner SL, Koschmann C. Clinical efficacy of ONC201 in H3K27M-mutant diffuse midline gliomas is driven by disruption of integrated metabolic and epigenetic pathways. Cancer Discovery. 2023 Aug 16; http://dx.doi.org/10.1158/2159-8290.CD-23-0131; *equal contribution
• Waszak SM#, Bourdeaut F, Nichols KE, Walsh MF. ELP1-related medulloblastoma predisposition syndrome. WHO Classification of Tumours. Genetic Tumour Syndromes. 2023. #responsible author
• Kline C, Jain P, Kilburn L, Bonner ER, Gupta N, Crawford JR, Banerjee A, Packer RJ, Villanueva-Meyer J, Luks T, Zhang Y, Kambhampati M, Zhang J, Yadavilli S, Zhang B, Gaonkar KS, Rokita JL, Kraya A, Kuhn J, Liang W, Byron S, Berens M, Molinaro A, Prados M, Resnick A#, Waszak SM#, Nazarian J#, Mueller S#. Upfront Biology-Guided Therapy in Diffuse Intrinsic Pontine Glioma: Therapeutic, Molecular, and Biomarker Outcomes from PNOC003. Clinical Cancer Research. 2022 Sep 15;28(18):3965–78. #senior authors
• Pfister SM, Waszak SM. 14.0.0.20: ELP1-medulloblastoma syndrome. WHO Classification of Tumours. Central Nervous System Tumours. 2022
• Waszak SM*, Robinson GW*, Gudenas BL, Smith KS, Forget A, Kojic M, Garcia-Lopez J, Hadley J, Hamilton KV, Indersie E, Buchhalter I, Kerssemakers J, Jäger N, Sharma T, Rausch T, Kool M, Sturm D, Jones DTW, Vasilyeva A, Tatevossian RG, Neale G, Lombard B, Loew D, Nakitandwe J, Rusch M, Bowers DC, Bendel A, Partap S, Chintagumpala M, Crawford J, Gottardo NG, Smith A, Dufour C, Rutkowski S, Eggen T, Wesenberg F, Kjaerheim K, Feychting M, Lannering B, Schüz J, Johansen C, Andersen TV, Röösli M, Kuehni CE, Grotzer M, Remke M, Puget S, Pajtler KW, Milde T, Witt O, Ryzhova M, Korshunov A, Orr BA, Ellison DW, Brugieres L, Lichter P, Nichols KE, Gajjar A, Wainwright BJ, Ayrault O, Korbel JO, Northcott PA, Pfister SM. Germline Elongator mutations in Sonic Hedgehog medulloblastoma. Nature. 2020 Apr 1;580(7803):396–401. *first authors
• ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (Waszak SM*). Pan-cancer analysis of whole genomes. Nature. 2020 Feb 5;578(7793):82–93. *first author, germline working group
• Begemann M*, Waszak SM*, Robinson GW, Jäger N, Sharma T, Knopp C, Kraft F, Moser O, Mynarek M, Guerrini-Rousseau L, Brugieres L, Varlet P, Pietsch T, Bowers DC, Chintagumpala M, Sahm F, Korbel JO, Rutkowski S, Eggermann T, Gajjar A, Northcott P, Elbracht M, Pfister SM, Kontny U, Kurth I. Germline GPR161 Mutations Predispose to Pediatric Medulloblastoma. Journal of Clinical Oncology 2019 Oct 14;38(1):43–50. *first authors
• Waszak SM*, Northcott PA*, Buchhalter I, Robinson GW, Sutter C, Groebner S, Grund KB, Brugières L, Jones DTW, Pajtler KW, Morrissy AS, Kool M, Sturm D, Chavez L, Ernst A, Brabetz S, Hain M, Zichner T, Segura-Wang M, Weischenfeldt J, Rausch T, Mardin BR, Zhou X, Baciu C, Lawerenz C, Chan JA, Varlet P, Guerrini-Rousseau L, Fults DW, Grajkowska W, Hauser P, Jabado N, Ra YS, Zitterbart K, Shringarpure SS, De La Vega FM, Bustamante CD, Ng HK, Perry A, MacDonald TJ, Hernáiz Driever P, Bendel AE, Bowers DC, McCowage G, Chintagumpala MM, Cohn R, Hassall T, Fleischhack G, Eggen T, Wesenberg F, Feychting M, Lannering B, Schüz J, Johansen C, Andersen TV, Röösli M, Kuehni CE, Grotzer M, Kjaerheim K, Monoranu CM, Archer TC, Duke E, Pomeroy SL, Shelagh R, Frank S, Sumerauer D, Scheurlen W, Ryzhova MV, Milde T, Kratz CP, Samuel D, Zhang J, Solomon DA, Marra M, Eils R, Bartram CR, von Hoff K, Rutkowski S, Ramaswamy V, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Malkin D, Gajjar A, Korbel JO, Pfister SM. Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort. The Lancet Oncology. 2018 May 9;19(6):785–98. *first authors
• Waszak SM*, Delaneau O*, Gschwind AR, Kilpinen H, Raghav SK, Witwicki RM, Orioli A, Wiederkehr M, Panousis NI, Yurovsky A, Romano-Palumbo L, Planchon A, Bielser D, Padioleau I, Udin G, Thurnheer S, Hacker D, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Cell. 2015 Aug 20;162(5):1039–50. *first authors
• Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK, Witwicki RM, Migliavacca E, Yurovsky A, Lappalainen T, Hernandez N, Reymond A, Dermitzakis ET, Deplancke B. Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. Bioinformatics. 2013 Nov 18;30(2):165–71.
• Kilpinen H*, Waszak SM*, Gschwind AR*, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, Yurovsky A, Lappalainen T, Romano-Palumbo L, Planchon A, Bielser D, Bryois J, Padioleau I, Udin G, Thurnheer S, Hacker D, Core LJ, Lis JT, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science. 2013 Oct 17;342(6159):744–7. *first authors
• Massouras A*, Waszak SM*, Albarca-Aguilera M, Hens K, Holcombe W, Ayroles JF, Dermitzakis ET, Stone EA, Jensen JD, Mackay TFC, Deplancke B. Genomic variation and its impact on gene expression in Drosophila melanogaster. PLoS Genetics. 2012 Nov 15;8(11):e1003055.
• Raghav SK*, Waszak SM*, Krier I, Gubelmann C, Isakova A, Mikkelsen TS, Deplancke B. Integrative genomics identifies the corepressor SMRT as a gatekeeper of adipogenesis through the transcription factors C/EBPβ and KAISO. Molecular Cell. 2012 Apr 19;46(3):335–50.
• Waszak SM, Hasin Y, Zichner T, Olender T, Keydar I, Khen M, Stütz AM, Schlattl A, Lancet D, Korbel JO. Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity. PLoS Computational Biology. 2010 Nov 11;6(11):e1000988.

Publications

84. Flynn A, Waszak SM#, Weischenfeldt J#. Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer. Mol Syst Biol (2024). doi:10.1038/s44320-024-00054-5. #corresponding authors

83. Mueller S, Kline C, Franson A, van der Lugt J, Prados M, Waszak SM, Plasschaert S, Molinaro AM, Koschmann C, Nazarian J. Rational combination platform trial design for children and young adults with Diffuse Midline Glioma: a report from PNOC. Neuro Oncol. 2023. doi:10.1093/neuonc/noad181.

82. Haas-Kogan DA, Aboian MS, Minturn JE, Leary SES, Abdelbaki MS, Goldman S, Elster JD, Kraya A, Lueder MR, Ramakrishnan D, von Reppert M, Liu KX, Rokita JL, Resnick AC, Solomon DA, Phillips JJ, Prados M, Molinaro AM, Waszak SM#, Mueller S#. Everolimus for Children With Recurrent or Progressive Low-Grade Glioma: Results From the Phase II PNOC001 Trial. Journal of Clinical Oncology. 2023 Nov 17; JCO2301838. #senior authors

81. Roberts HJ, Ji S, Picca A, Sanson M, Garcia M, Snuderl M, Schüller U, Picart T, Ducray F, Green AL, Nakano Y, Sturm D, Abdullaev Z, Aldape K, Dang D, Kumar-Sinha C, Wu YM, Robinson D, Vo JN, Chinnaiyan AM, Cartaxo R, Upadhyaya SA, Mody R, Chiang J, Baker S, Solomon D, Venneti S, Pratt D, Waszak SM#, Koschmann C#. Clinical, genomic, and epigenomic analyses of H3K27M-mutant diffuse midline glioma long-term survivors reveal a distinct group of tumors with MAPK pathway alterations. Acta Neuropathologica. 2023 Oct 18; doi:10.1007/s00401-023-02640-7. #corresponding authors

80. Bonner ER, Dawood A, Gordish-Dressman H, Eze A, Bhattacharya S, Yadavilli S, Mueller S, Waszak SM#, Nazarian J#. Pan-cancer atlas of somatic core and linker histone mutations. npj Genomic Medicine. 2023 Aug 28;8(1):1–14. #corresponding authors

79. Venneti S*, Kawakibi AR*, Ji S*, Waszak SM*, Sweha SR*, Mota M*, Pun M*, Deogharkar A, Chung C, Tarapore RS, Ramage S, Chi A, Wen PY, Arrillaga-Romany I, Batchelor TT, Butowski NA, Sumrall A, Shonka N, Harrison RA, de Groot J, Mehta M, Hall MD, Daghistani D, Cloughesy TF, Ellingson BM, Beccaria K, Varlet P, Kim MM, Umemura Y, Garton H, Franson A, Schwartz J, Jain R, Kachman M, Baum H, Burant CF, Mottl SL, Cartaxo RT, John V, Messinger D, Qin T, Peterson E, Sajjakulnukit P, Ravi K, Waugh A, Walling D, Ding Y, Xia Z, Schwendeman A, Hawes D, Yang F, Judkins AR, Wahl D, Lyssiotis CA, de la Nava D, Alonso MM, Eze A, Spitzer J, Schmidt SV, Duchatel RJ, Dun MD, Cain JE, Jiang L, Stopka SA, Baquer G, Regan MS, Filbin MG, Agar NYR, Zhao L, Kumar-Sinha C, Mody R, Chinnaiyan A, Kurokawa R, Pratt D, Yadav VN, Grill J, Kline C, Mueller S, Resnick A, Nazarian J, Allen JE, Odia Y, Gardner SL, Koschmann C. Clinical efficacy of ONC201 in H3K27M-mutant diffuse midline gliomas is driven by disruption of integrated metabolic and epigenetic pathways. Cancer Discovery. 2023 Aug 16; http://dx.doi.org/10.1158/2159-8290.CD-23-0131; *equal contribution

78. Sanjaya P, Maljanen K, Katainen R, Waszak SM; Genomics England Research Consortium; Aaltonen LA, Stegle O, Korbel JO, Pitkänen E. Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping. Genome Med. 2023 Jul 7;15(1):47.
 
77. Kolodziejczak AS, Guerrini-Rousseau L, Planchon JM, Ecker J, Selt F, Mynarek M, Obrecht D, Sill M, Autry RJ, Zhao E, Hirsch S, Amouyal E, Dufour C, Ayrault O, Torrejon J, Waszak SM, Ramaswamy V, Pentikainen V, Demir HA, Clifford SC, Schwalbe EC, Massimi L, Snuderl M, Galbraith K, Karajannis MA, Hill K, Li BK, Walsh M, White CL, Redmond S, Loizos L, Jakob M, Kordes UR, Schmid I, Hauer J, Blattmann C, Filippidou M, Piccolo G, Scheurlen W, Farrag A, Grund K, Sutter C, Pietsch T, Frank S, Schewe DM, Malkin D, Ben-Arush M, Sehested A, Wong TT, Wu KS, Liu YL, Carceller F, Mueller S, Stoller S, Taylor MD, Tabori U, Bouffet E, Kool M, Sahm F, von Deimling A, Korshunov A, von Hoff K, Kratz CP, Sturm D, Jones DTW, Rutkowski S, van Tilburg CM, Witt O, Bougeard G, Pajtler KW, Pfister SM, Bourdeaut F, Milde T. Clinical outcome of pediatric medulloblastoma patients with Li-Fraumeni syndrome. Neuro Oncol. 2023 Jun 28:noad114.

76. Waszak SM#, Bourdeaut F, Nichols KE, Walsh MF. ELP1-related medulloblastoma predisposition syndrome. WHO Classification of Tumours. Genetic Tumour Syndromes. 2023. #responsible author

75. Frioux C, Ansorge R, Özkurt E, Ghassemi Nedjad C, Fritscher J, Quince C, Waszak SM, Hildebrand F. Enterosignatures define common bacterial guilds in the human gut microbiome. Cell Host Microbe. 2023 Jun 13:S1931-3128(23)00217-2.

74. Jackson ER, Duchatel RJ, Staudt DE, Persson ML, Mannan A, Yadavilli S, Parackal S, Game S, Chong WC, Jayasekara WSN, Grand ML, Kearney PS, Douglas AM, Findlay IJ, Germon ZP, McEwen HP, Beitaki TS, Patabendige A, Skerrett-Byrne DA, Nixon B, Smith ND, Day B, Manoharan N, Nagabushan S, Hansford JR, Govender D, McCowage GB, Firestein R, Howlett M, Endersby R, Gottardo NG, Alvaro F, Waszak SM, Larsen MR, Colino-Sanguino Y, Valdes-Mora F, Rakotomalala A, Meignan S, Pasquier E, André N, Hulleman E, Eisenstat DD, Vitanza NA, Nazarian J, Koschmann C, Mueller S, Cain JE, Dun MD. ONC201 in Combination with Paxalisib for the Treatment of H3K27-Altered Diffuse Midline Glioma. Cancer Res. 2023 May 17;OF1–17.

73. Houlahan KE, Livingstone J, Fox NS, Kurganovs N, Zhu H, Sietsma Penington J, Jung CH, Yamaguchi TN, Heisler LE, Jovelin R, Costello AJ, Pope BJ, Kishan AU, Corcoran NM, Bristow RG, Waszak SM, Weischenfeldt J, He HH, Hung RJ, Hovens CM, Boutros PC. A polygenic two-hit hypothesis for prostate cancer. J Natl Cancer Inst. 2023 Apr 11;115(4):468–72.

72. Kratz CP, Smirnov D, Autry R, Jäger N, Waszak SM, Großhennig A, Berutti R, Wendorff M, Hainaut P, Pfister SM, Prokisch H, Ripperger T, Malkin D. Reply to Li and colleagues. J Natl Cancer Inst [Internet]. 2023 Apr 2; Available from: http://dx.doi.org/10.1093/jnci/djad057

71. Kratz CP, Smirnov D, Autry R, Jäger N, Waszak SM, Großhennig A, Berutti R, Wendorff M, Hainaut P, Pfister SM, Prokisch H, Ripperger T, Malkin D. Reply to Evans and Woodward. J Natl Cancer Inst. 2023 Feb 8;115(2):231–2.

70. Messinger D, Harris MK, Cummings JR, Thomas C, Yang T, Sweha SR, Woo R, Siddaway R, Burkert M, Stallard S, Qin T, Mullan B, Siada R, Ravindran R, Niculcea M, Dowling AR, Bradin J, Ginn KF, Gener MAH, Dorris K, Vitanza NA, Schmidt SV, Spitzer J, Li J, Filbin MG, Cao X, Castro MG, Lowenstein PR, Mody R, Chinnaiyan A, Desprez PY, McAllister S, Dun MD, Hawkins C, Waszak SM, Venneti S, Koschmann C, Yadav VN. Therapeutic targeting of prenatal pontine ID1 signaling in diffuse midline glioma. Neuro Oncol. 2023 Jan 5;25(1):54–67.

69. Pfister SM, Waszak SM. 14.0.0.20: ELP1-medulloblastoma syndrome. WHO Classification of Tumours. Central Nervous System Tumours. 2022.

68. Kratz CP, Smirnov D, Autry R, Jäger N, Waszak SM, Großhennig A, Berutti R, Wendorff M, Hainaut P, Pfister SM, Prokisch H, Ripperger T, Malkin D. Heterozygous BRCA1 and BRCA2 and Mismatch Repair Gene Pathogenic Variants in Children and Adolescents With Cancer. J Natl Cancer Inst. 2022 Nov 14;114(11):1523–32.

67. Kline C, Jain P, Kilburn L, Bonner ER, Gupta N, Crawford JR, Banerjee A, Packer RJ, Villanueva-Meyer J, Luks T, Zhang Y, Kambhampati M, Zhang J, Yadavilli S, Zhang B, Gaonkar KS, Rokita JL, Kraya A, Kuhn J, Liang W, Byron S, Berens M, Molinaro A, Prados M, Resnick A#, Waszak SM#, Nazarian J#, Mueller S#. Upfront Biology-Guided Therapy in Diffuse Intrinsic Pontine Glioma: Therapeutic, Molecular, and Biomarker Outcomes from PNOC003. Clin Cancer Res. 2022 Sep 15;28(18):3965–78. #senior authors

66. Przystal JM, Cianciolo Cosentino C, Yadavilli S, Zhang J, Laternser S, Bonner ER, Prasad R, Dawood AA, Lobeto N, Chin Chong W, Biery MC, Myers C, Olson JM, Panditharatna E, Kritzer B, Mourabit S, Vitanza NA, Filbin MG, de Iuliis GN, Dun MD, Koschmann C, Cain JE, Grotzer MA, Waszak SM, Mueller S, Nazarian J. Imipridones affect tumor bioenergetics and promote cell lineage differentiation in diffuse midline gliomas. Neuro Oncol. 2022 Sep 1;24(9):1438–51.

65. Guerrini-Rousseau L, Masliah-Planchon J, Waszak SM, Alhopuro P, Benusiglio PR, Bourdeaut F, Brecht IB, Del Baldo G, Dhanda SK, Garrè ML, Gidding CEM, Hirsch S, Hoarau P, Jorgensen M, Kratz C, Lafay-Cousin L, Mastronuzzi A, Pastorino L, Pfister SM, Schroeder C, Smith MJ, Vahteristo P, Vibert R, Vilain C, Waespe N, Winship IM, Evans DG, Brugieres L. Cancer risk and tumour spectrum in 172 patients with a germline SUFU pathogenic variation: a collaborative study of the SIOPE Host Genome Working Group. J Med Genet. 2022 Jun 29;59(11):1123–32.

64. Burns D, Anokian E, Saunders EJ, Bristow RG, Fraser M, Reimand J, Schlomm T, Sauter G, Brors B, Korbel J, Weischenfeldt J, Waszak SM, Corcoran NM, Jung CH, Pope BJ, Hovens CM, Cancel-Tassin G, Cussenot O, Loda M, Sander C, Hayes VM, Dalsgaard Sorensen K, Lu YJ, Hamdy FC, Foster CS, Gnanapragasam V, Butler A, Lynch AG, Massie CE, CR-UK/Prostate Cancer UK, ICGC, The PPCG, Woodcock DJ, Cooper CS, Wedge DC, Brewer DS, Kote-Jarai Z, Eeles RA. Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study. Eur Urol. 2022 May 31;82(2):201–11.

63. Llimos G, Gardeux V, Koch U, Kribelbauer JF, Hafner A, Alpern D, Pezoldt J, Litovchenko M, Russeil J, Dainese R, Moia R, Mahmoud AM, Rossi D, Gaidano G, Plass C, Lutsik P, Gerhauser C, Waszak SM, Boettiger A, Radtke F, Deplancke B. A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation. Nat Commun. 2022 Apr 19;13(1):2042.

62. Findlay IJ, De Iuliis GN, Duchatel RJ, Jackson ER, Vitanza NA, Cain JE, Waszak SM, Dun MD. Pharmaco-proteogenomic profiling of pediatric diffuse midline glioma to inform future treatment strategies. Oncogene. 2021 Nov 10;41(4):461–75.

61. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 May 5;35(7):2002–16.

60. Bonner ER, Waszak SM, Grotzer MA, Mueller S, Nazarian J. Mechanisms of imipridones in targeting mitochondrial metabolism in cancer cells. Neuro Oncol. 2021 Apr 12;23(4):542–56.

59. Llamazares-Prada M, Espinet E, Mijošek V, Schwartz U, Lutsik P, Tamas R, Richter M, Behrendt A, Pohl ST, Benz NP, Muley T, Warth A, Heußel CP, Winter H, Landry JJM, Herth FJ, Mertens TC, Karmouty-Quintana H, Koch I, Benes V, Korbel JO, Waszak SM, Trumpp A, Wyatt DM, Stahl HF, Plass C, Jurkowska RZ. Versatile workflow for cell type-resolved transcriptional and epigenetic profiles from cryopreserved human lung. JCI Insight [Internet]. 2021 Mar 22;6(6). Available from: http://dx.doi.org/10.1172/jci.insight.140443

58. Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L, PCAWG Consortium. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020 Sep 21;11(1):4748.

57. Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, PCAWG Tumour Subtypes and Clinical Translation, Boutros PC, PCAWG Consortium. Sex differences in oncogenic mutational processes. Nat Commun. 2020 Aug 28;11(1):4330.

56. Erarslan-Uysal B, Kunz JB, Rausch T, Richter-Pechańska P, van Belzen IA, Frismantas V, Bornhauser B, Ordoñez-Rueada D, Paulsen M, Benes V, Stanulla M, Schrappe M, Cario G, Escherich G, Bakharevich K, Kirschner-Schwabe R, Eckert C, Loukanov T, Gorenflo M, Waszak SM, Bourquin JP, Muckenthaler MU, Korbel JO, Kulozik AE. Chromatin accessibility landscape of pediatric T-lymphoblastic leukemia and human T-cell precursors. EMBO Mol Med. 2020 Aug 5;12(9):e12104.

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49. Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Campbell PJ, PCAWG Consortium. Patterns of somatic structural variation in human cancer genomes. Nature. 2020 Feb 5;578(7793):112–21.

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46. Zapatka M, Borozan I, Brewer DS, Iskar M, Grundhoff A, Alawi M, Desai N, Sültmann H, Moch H, Pathogens P, Cooper CS, Eils R, Ferretti V, Lichter P, PCAWG Consortium. The landscape of viral associations in human cancers. Nat Genet. 2020 Feb 5;52(3):320–30.

45. Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA, PCAWG Structural Variation Working Group, PCAWG Consortium. Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nat Genet. 2020 Feb 5;52(3):294–305.

44. Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PA, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine KM, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH, PCAWG Structural Variation Working Group, Campbell PJ, Tubio JMC, PCAWG Consortium. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2020 Feb 5;52(3):306–19.

43. Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y, Han L, Kim HL, Nakagawa H, Park K, Campbell PJ, Liang H, PCAWG Consortium. Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet. 2020 Feb 5;52(3):342–52.

42. Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS, PCAWG Drivers and Functional Interpretation Group, Johnson R, PCAWG Consortium. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Commun Biol. 2020 Feb 5;3(1):56.

41. Yakneen S, Waszak SM, PCAWG Technical Working Group, Gertz M, Korbel JO, PCAWG Consortium. Butler enables rapid cloud-based analysis of thousands of human genomes. Nat Biotechnol. 2020 Feb 5;38(3):288–92.

40. Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A, PCAWG Drivers and Functional Interpretation Working Group, Reimand J, Stuart JM, Raphael BJ, PCAWG Consortium. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun. 2020 Feb 5;11(1):729.

39. Jiao W, Atwal G, Polak P, Karlic R, Cuppen E, PCAWG Tumor Subtypes and Clinical Translation Working Group, Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris QD, Stein LD, PCAWG Consortium. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nat Commun. 2020 Feb 5;11(1):728.

38. Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group, Reimand J, PCAWG Consortium. Integrative pathway enrichment analysis of multivariate omics data. Nat Commun. 2020 Feb 5;11(1):735.

37. Cmero M, Yuan K, Ong CS, Schröder J, PCAWG Evolution and Heterogeneity Working Group, Corcoran NM, Papenfuss T, Hovens CM, Markowetz F, Macintyre G, PCAWG Consortium. Inferring structural variant cancer cell fraction. Nat Commun. 2020 Feb 5;11(1):730.

36. Rubanova Y, Shi R, Harrigan CF, Li R, Wintersinger J, Sahin N, Deshwar AG, PCAWG Evolution and Heterogeneity Working Group, Morris QD, PCAWG Consortium. Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nat Commun. 2020 Feb 5;11(1):731.

35. Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, Creighton CJ, PCAWG Consortium. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun. 2020 Feb 5;11(1):736.

34. Bhandari V, Li CH, Bristow RG, Boutros PC, PCAWG Consortium. Divergent mutational processes distinguish hypoxic and normoxic tumours. Nat Commun. 2020 Feb 5;11(1):737.

33. Shuai S, PCAWG Drivers and Functional Interpretation Working Group, Gallinger S, Stein LD, PCAWG Consortium. Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nat Commun. 2020 Feb 5;11(1):734.

32. Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M, PCAWG-Structural Variation Working Group, Brors B, Rippe K, Jones DTW, Feuerbach L, PCAWG Consortium. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun. 2020 Feb 5;11(1):733.

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12. Gubelmann C, Schwalie PC, Raghav SK, Röder E, Delessa T, Kiehlmann E, Waszak SM, Corsinotti A, Udin G, Holcombe W, Rudofsky G, Trono D, Wolfrum C, Deplancke B. Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network. Elife. 2014 Aug 27;3:e03346.

11. Hammer C, Degenhardt F, Priebe L, Stütz AM, Heilmann S, Waszak SM, Schlattl A, Mangold E, Hoffmann P, Nöthen MM, Rietschel M, Rappold G, Korbel J, Cichon S, Niesler B, MooDS Consortium. A common microdeletion affecting a hippocampus- and amygdala-specific isoform of tryptophan hydroxylase 2 is not associated with affective disorders. Bipolar Disord. 2014 Apr 23;16(7):764–8.

10. Waszak SM, Deplancke B. Rounding up natural gene expression variation during development. Dev Cell. 2013 Dec 23;27(6):601–3.

9. Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK, Witwicki RM, Migliavacca E, Yurovsky A, Lappalainen T, Hernandez N, Reymond A, Dermitzakis ET, Deplancke B. Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. Bioinformatics. 2013 Nov 18;30(2):165–71.

8. Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, Yurovsky A, Lappalainen T, Romano-Palumbo L, Planchon A, Bielser D, Bryois J, Padioleau I, Udin G, Thurnheer S, Hacker D, Core LJ, Lis JT, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science. 2013 Oct 17;342(6159):744–7.

7. Gubelmann C, Waszak SM, Isakova A, Holcombe W, Hens K, Iagovitina A, Feuz JD, Raghav SK, Simicevic J, Deplancke B. A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks. Mol Syst Biol. 2013 Aug 6;9:682.

6. Massouras A*, Waszak SM*, Albarca-Aguilera M, Hens K, Holcombe W, Ayroles JF, Dermitzakis ET, Stone EA, Jensen JD, Mackay TFC, Deplancke B. Genomic variation and its impact on gene expression in Drosophila melanogaster. PLoS Genet. 2012 Nov 15;8(11):e1003055.

5. Olender T, Waszak SM, Viavant M, Khen M, Ben-Asher E, Reyes A, Nativ N, Wysocki CJ, Ge D, Lancet D. Personal receptor repertoires: olfaction as a model. BMC Genomics. 2012 Aug 21;13:414.

4. Raghav SK*, Waszak SM*, Krier I, Gubelmann C, Isakova A, Mikkelsen TS, Deplancke B. Integrative genomics identifies the corepressor SMRT as a gatekeeper of adipogenesis through the transcription factors C/EBPβ and KAISO. Mol Cell. 2012 Apr 19;46(3):335–50.

3. Schlattl A, Anders S, Waszak SM, Huber W, Korbel JO. Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions. Genome Res. 2011 Aug 23;21(12):2004–13.

2. Waszak SM, Hasin Y, Zichner T, Olender T, Keydar I, Khen M, Stütz AM, Schlattl A, Lancet D, Korbel JO. Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity. PLoS Comput Biol. 2010 Nov 11;6(11):e1000988.

1. Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO, Snyder M. Variation in transcription factor binding among humans. Science. 2010 Mar 18;328(5975):232–5.