Waszak lab
The Laboratory of Computational Neuro-Oncology studies the genetic and molecular architecture of pediatric brain tumours, develops novel technologies for rapid and longitudinal diagnostics in pediatric neuro-oncology, and studies the evolution of pediatric gliomas in response to targeted therapies. Our research aims to advance diagnostics in pediatric neuro-oncology and to optimize therapeutic decision-making with real-time data about cancer cell states. Our group is affiliated with the Swiss Institute for Experimental Cancer Research at the École Polytechnique Fédérale de Lausanne and the Department of Neurology at the University of California, San Francisco. ...
Research projects
✓ Digital neuro-pathology. To perform intra- and interoperative diagnostics for patients with pediatric brain tumours based on artificial intelligence and digital tissue slides.
✓ Liquid biopsy in neuro-oncology. To develop methods for multi-modal and longitudinal monitoring of pediatric brain tumours based on cell-free DNA whole genome sequencing.
✓ Clinical cancer genomics. To study the evolution of pediatric gliomas in response to targeted therapies.
Latest publications
Germline analysis of an international cohort of pediatric diffuse midline glioma patients.
Mateos MK, Ajuyah P, Fuentes-Bolanos N, (...), Wong-Erasmus M, Cowley MJ, Ziegler DS
Neuro-oncology – 2025 Mar 12
The Germline and Somatic Origins of Prostate Cancer Heterogeneity.
Yamaguchi TN, Houlahan KE, Zhu H, (...), Reimand J, Hovens CM, Boutros PC
Cancer discovery – 2025 Feb 13
Germline pathogenic variation impacts somatic alterations and patient outcomes in pediatric CNS tumors.
Corbett RJ, Kaufman RS, McQuaid SW, (...), MacFarland SP, Rokita JL, Diskin SJ
medRxiv : the preprint server for health sciences – 2025 Feb 6
Genetic ancestry superpopulations show distinct prevalence and outcomes across pediatric central nervous system tumors from the PBTA and PNOC.
Corbett RJ, Gullickson CC, Geng Z, (...), Mueller S, Rokita JL, Kline C
Neuro-oncology – 2025 Jan 23
Germline loss-of-function variant in the E3 ubiquitin ligase TRAF2 in a young adult patient with medulloblastoma: a case report.
Vo JN, Franson A, Waszak SM, (...), Becker N, Chinnaiyan AM, Robinson DR
Acta neuropathologica communications – 2024 Dec 20
Copy-number dosage regulates telomere maintenance and disease-associated pathways in neuroblastoma.
Burkert M, Blanc E, Thiessen N, (...), Schulte JH, Ohler U, Schwarz RF
iScience – 2024 Sep 10
Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer.
Flynn A, Waszak SM, Weischenfeldt J
Molecular systems biology – 2024 Jul 18
Rational combination platform trial design for children and young adults with diffuse midline glioma: A report from PNOC.
Mueller S, Kline C, Franson A, (...), Molinaro AM, Koschmann C, Nazarian J
Neuro-oncology – 2024 May 3
Team
Other members
Selected Publications
Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer.
Flynn A, Waszak SM, Weischenfeldt J
Molecular systems biology – 2024 Jul 18
Everolimus for Children With Recurrent or Progressive Low-Grade Glioma: Results From the Phase II PNOC001 Trial.
Haas-Kogan DA, Aboian MS, Minturn JE, (...), Molinaro AM, Waszak SM, Mueller S
Journal of clinical oncology : official journal of the American Society of Clinical Oncology – 2023 Nov 17
Clinical Efficacy of ONC201 in H3K27M-Mutant Diffuse Midline Gliomas Is Driven by Disruption of Integrated Metabolic and Epigenetic Pathways.
Venneti S, Kawakibi AR, Ji S, (...), Odia Y, Gardner SL, Koschmann C
Cancer discovery – 2023 Nov 1
Upfront Biology-Guided Therapy in Diffuse Intrinsic Pontine Glioma: Therapeutic, Molecular, and Biomarker Outcomes from PNOC003.
Kline C, Jain P, Kilburn L, (...), Waszak SM, Nazarian J, Mueller S
Clinical cancer research : an official journal of the American Association for Cancer Research – 2022 Sep 15
Germline Elongator mutations in Sonic Hedgehog medulloblastoma.
Waszak SM, Robinson GW, Gudenas BL, (...), Korbel JO, Northcott PA, Pfister SM
Nature – 2020 Apr 1
Pan-cancer analysis of whole genomes.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
Nature – 2020 Feb 5
Germline GPR161 Mutations Predispose to Pediatric Medulloblastoma.
Begemann M, Waszak SM, Robinson GW, (...), Pfister SM, Kontny U, Kurth I
Journal of clinical oncology : official journal of the American Society of Clinical Oncology – 2019 Oct 14
Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort.
Waszak SM, Northcott PA, Buchhalter I, (...), Gajjar A, Korbel JO, Pfister SM
The Lancet. Oncology – 2018 May 9
Population Variation and Genetic Control of Modular Chromatin Architecture in Humans.
Waszak SM, Delaneau O, Gschwind AR, (...), Reymond A, Deplancke B, Dermitzakis ET
Cell – 2015 Aug 20
Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.
Waszak SM, Kilpinen H, Gschwind AR, (...), Reymond A, Dermitzakis ET, Deplancke B
Bioinformatics (Oxford, England) – 2013 Nov 18
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription.
Kilpinen H, Waszak SM, Gschwind AR, (...), Reymond A, Deplancke B, Dermitzakis ET
Science (New York, N.Y.) – 2013 Oct 17
Genomic variation and its impact on gene expression in Drosophila melanogaster.
Massouras A, Waszak SM, Albarca-Aguilera M, (...), Jensen JD, Mackay TF, Deplancke B
PLoS genetics – 2012 Nov 15
Integrative genomics identifies the corepressor SMRT as a gatekeeper of adipogenesis through the transcription factors C/EBPβ and KAISO.
Raghav SK, Waszak SM, Krier I, (...), Isakova A, Mikkelsen TS, Deplancke B
Molecular cell – 2012 Apr 19
Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity.
Waszak SM, Hasin Y, Zichner T, (...), Schlattl A, Lancet D, Korbel JO
PLoS computational biology – 2010 Nov 11
WHO Classification of Tumours. Genetic Tumour Syndromes. ELP1-related medulloblastoma predisposition syndrome.
Waszak SM, Bourdeaut F, Nichols KE, Walsh MF
WHO Classification of Tumours. 2023; 5th ed. Vol. 6. – 2023
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