Dr Nic Waddell
Dr Nic Waddell obtained her PhD in molecular biology from the University of Leicester in the UK. She is head of the Medical Genomics Group and Coordinator of the Cancer Program at QIMR Berghofer Medical Research Institute. Prior to that she has been a post-doctoral researcher at the University of Queensland and QIMR Berghofer. She is a cancer researcher and collaborative bioinformatician who is an expert in the interpretation of next generation sequence data.
She played a key role in the Australian International Cancer Genome Consortia (ICGC) projects (PIs Grimmond, Biankin and Bowtell). She identified mutational signatures in pancreatic cancer that are linked to germline variants and treatment response, this work was published in Nature and has been cited over 1000 times. Dr Waddell is a member of the Queensland Genomics Health Alliance (QGHA) where she works with the community advisory group in ELSI areas such as community engagement and the development of guidelines to enable the clinical use of genomics. She is also a co-founder of a precision analytics company, genomiQa, who specialize in whole genome data analysis.
Her lab at QIMR Berghofer focuses on the genomics of several cancers including oesophageal, melanoma, mesothelioma and lung cancer. Her program of research also uses bioinformatic approaches to address clinical challenges in these diseases. Dr Waddell has >130 publications of which have been cited >21,000 times (Google Scholar) and her current H-index is 49. She has consistently published in high impact journals including articles in Nature, Nature Genetics and Nature Immunology. Dr Waddell is currently a CI on two Australian NHMRC project grants, an NHMRC Centre of Research Excellence grant, and holds an NHMRC Senior Research Fellowship.
Selected Publications
Newell F, Pires da Silva I, Johansson PA, Menzies AM, Wilmott JS, Addala V, Carlino MS, Rizos H, Nones K, Edwards JJ, Lakis V, Kazakoff SH, Mukhopadhyay P, Ferguson PM, Leonard C, Koufariotis LT, Wood S, Blank CU, Thompson JF, Spillane AJ, Saw RPM, Shannon KF, Pearson JV, Mann GJ, Hayward NK, Scolyer RA, Waddell N, Long GV. Multiomic profiling of checkpoint inhibitor-treated melanoma: Identifying predictors of response and resistance, and markers of biological discordance. Cancer Cell. 2022 Jan 10;40(1):88-102.e7. doi: 10.1016/j.ccell.2021.11.012. Epub 2021 Dec 23. PMID: 34951955.
Newell F, Wilmott JS, Johansson PA, Nones K, Addala V, Mukhopadhyay P, Broit N, Amato CM, Van Gulick R, Kazakoff SH, Patch AM, Koufariotis LT, Lakis V, Leonard C, Wood S, Holmes O, Xu Q, Lewis K, Medina T, Gonzalez R, Saw RPM, Spillane AJ, Stretch JR, Rawson RV, Ferguson PM, Dodds TJ, Thompson JF, Long GV, Levesque MP, Robinson WA, Pearson JV, Mann GJ, Scolyer RA, Waddell N, Hayward NK. Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity. Nat Commun. 2020 Oct 16;11(1):5259. doi: 10.1038/s41467-020-18988-3. PMID: 33067454; PMCID: PMC7567804.
Hayward NK, Wilmott JS, Waddell N, Johansson PA, Field MA, Nones K, Patch AM, Kakavand H, Alexandrov LB, Burke H, Jakrot V, Kazakoff S, Holmes O, Leonard C, Sabarinathan R, Mularoni L, Wood S, Xu Q, Waddell N, Tembe V, Pupo GM, De Paoli-Iseppi R, Vilain RE, Shang P, Lau LMS, Dagg RA, Schramm SJ, Pritchard A, Dutton-Regester K, Newell F, Fitzgerald A, Shang CA, Grimmond SM, Pickett HA, Yang JY, Stretch JR, Behren A, Kefford RF, Hersey P, Long GV, Cebon J, Shackleton M, Spillane AJ, Saw RPM, López-Bigas N, Pearson JV, Thompson JF, Scolyer RA, Mann GJ. Whole-genome landscapes of major melanoma subtypes. Nature. 2017 May 11;545(7653):175-180. doi: 10.1038/nature22071. Epub 2017 May 3. PMID: 28467829.
Scarpa A…Waddell N, Biankin AV, Grimmond SM, et al. Whole-genome landscape of pancreatic neuroendocrine tumours. Nature. 2017 Mar 2;543(7643):65-71. doi: 10.1038/nature21063. Epub 2017 Feb 15. Erratum in: Nature. 2017 Sep 27;: PMID: 28199314.
Waddell N, Pajic M, Patch AM, et al. Whole genomes redefine the mutational landscape of pancreatic cancer. Nature 518, 495–501 (2015). https://doi.org/10.1038/nature14169
Biankin AV, Waddell N, Kassahn KS, Gingras MC, et al. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature. 2012 Nov 15;491(7424):399-405. doi: 10.1038/nature11547. Epub 2012 Oct 24. PMID: 23103869; PMCID: PMC3530898.
Nones K, Waddell N, Wayte N, Patch AM, Bailey P, Newell F, Holmes O, Fink JL, Quinn MCJ, Tang YH, Lampe G, Quek K, Loffler KA, Manning S, Idrisoglu S, Miller D, Xu Q, Waddell N, Wilson PJ, Bruxner TJC, Christ AN, Harliwong I, Nourse C, Nourbakhsh E, Anderson M, Kazakoff S, Leonard C, Wood S, Simpson PT, Reid LE, Krause L, Hussey DJ, Watson DI, Lord RV, Nancarrow D, Phillips WA, Gotley D, Smithers BM, Whiteman DC, Hayward NK, Campbell PJ, Pearson JV, Grimmond SM, Barbour AP. Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis. Nat Commun. 2014 Oct 29;5:5224. doi: 10.1038/ncomms6224. PMID: 25351503; PMCID: PMC4596003.
Yap M, Johnston RL, Foley H, MacDonald S, Kondrashova O, Tran KA, Nones K, Koufariotis LT, Bean C, Pearson JV, Trzaskowski M, Waddell N. Verifying explainability of a deep learning tissue classifier trained on RNA-seq data. Sci Rep. 2021 Jan 29;11(1):2641. doi: 10.1038/s41598-021-81773-9. PMID: 33514769; PMCID: PMC7846764.
Shamsani J, Kazakoff SH, Armean IM, McLaren W, Parsons MT, Thompson BA, O'Mara TA, Hunt SE, Waddell N, Spurdle AB. A plugin for the Ensembl Variant Effect Predictor that uses MaxEntScan to predict variant spliceogenicity. Bioinformatics. 2019 Jul 1;35(13):2315-2317. doi: 10.1093/bioinformatics/bty960. PMID: 30475984; PMCID: PMC6596880.
Cowley MJ, Pinese M, Kassahn KS, Waddell N, Pearson JV, Grimmond SM, Biankin AV, Hautaniemi S, Wu J. PINA v2.0: mining interactome modules. Nucleic Acids Res. 2012 Jan;40(Database issue):D862-5. doi: 10.1093/nar/gkr967. Epub 2011 Nov 8. PMID: 22067443; PMCID: PMC3244997.
Kassahn KS, Holmes O, Nones K, Patch AM, Miller DK, Christ AN, Harliwong I, Bruxner TJ, Xu Q, Anderson M, Wood S, Leonard C, Taylor D, Newell F, Song S, Idrisoglu S, Nourse C, Nourbakhsh E, Manning S, Wani S, Steptoe A, Pajic M, Cowley MJ, Pinese M, Chang DK, Gill AJ, Johns AL, Wu J, Wilson PJ, Fink L, Biankin AV, Waddell N, Grimmond SM, Pearson JV. Somatic point mutation calling in low cellularity tumors. PLoS One. 2013 Nov 8;8(11):e74380. doi: 10.1371/journal.pone.0074380. PMID: 24250782; PMCID: PMC3826759.
Song S, Nones K, Miller D, Harliwong I, Kassahn KS, Pinese M, Pajic M, Gill AJ, Johns AL, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu Q, Newell F, Cowley MJ, Wu J, Wilson P, Fink L, Biankin AV, Waddell N, Grimmond SM, Pearson JV. qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles. PLoS One. 2012;7(9):e45835. doi: 10.1371/journal.pone.0045835. Epub 2012 Sep 25. PMID: 23049875; PMCID: PMC3457972.