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

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.


Other members

Selected Publications

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

Clinical, genomic, and epigenomic analyses of H3K27M-mutant diffuse midline glioma long-term survivors reveal a distinct group of tumors with MAPK pathway alterations.

Roberts HJ, Ji S, Picca A, (...), Pratt D, Waszak SM, Koschmann C

Acta neuropathologica – 2023 Oct 18

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