Research Interests
My background in ecology and evolution has strongly influenced my research interests. The broad questions on processes and interactions within evolutionary systems are what interest me most. Modern high-throughput sequencing is an excellent tool to explore natural variation since it provides unparalleled resolution into the evolutionary process. While my undergraduate studies focused on organismal evolution and ecology, my postgraduate studies sparked my interest in investigating the evolutionary process on a microscopic scale. My postgraduate experience has provided me insight into evolution within an organism when looking at the genesis and evolution of cancer within a patient.
My research interests are now also underpinned by my enjoyment for writing software and creating tools for others to use. This has involved the sole development of, and contribution to, many internal and external pipelines, tools and platforms within the field of bioinformatics.
Patents
AU2016903841 & US20190267114A1. Gayevskiy, V. & Cowley, M.J (2017-ongoing). Device for presenting sequencing data. Google Patents: Link | PDF
Publications (* Indicates first authorship)
Weeden, C.E. & Gayevskiy, V. et al (2023) Early immune pressure initiated by tissue-resident memory T cells sculpts tumor evolution in non-small cell lung cancer. Cancer Cell, 41 (5), pp. 837-852. DOI: 10.1016/j.ccell.2023.03.019 | PDF
Sullivan, P.J. & Gayevskiy, V. et al (2023) Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications. Genome Biology, 24 (118), pp. 1-18. DOI: 10.1186/s13059-023-02936-7 | PDF
Leong, T.L. & … & Gayevskiy, V. et al (2023) Heterogeneity of tumour mutational burden in metastatic NSCLC demonstrated by endobronchial ultrasound sampling. Frontiers in Oncology, 13, pp. 1150349. DOI: 10.3389/fonc.2023.1150349 | PDF
Davis, R.L. & … & Gayevskiy, V. et al (2022) Use of Whole-Genome Sequencing for Mitochondrial Disease Diagnosis. Neurology, 99 (7), pp. e730-e742. DOI: 10.1212/WNL.0000000000200745 | PDF
Rius, R. & … & Gayevskiy, V. et al (2022) Biallelic pathogenic variants in COX11 are associated with an infantile-onset mitochondrial encephalopathy. Human Mutation. DOI: 10.1002/humu.24453 | PDF
Ewans, L.J. & … & Gayevskiy, V. et al (2022) Whole exome and genome sequencing in mendelian disorders: a diagnostic and health economic analysis. European Journal of Human Genetics. DOI: 10.1038/s41431-022-01162-2 | PDF
Palmer, E.E. & … & Gayevskiy, V. et al (2021) Diagnostic Yield of Whole Genome Sequencing After Nondiagnostic Exome Sequencing or Gene Panel in Developmental and Epileptic Encephalopathies. Neurology, 96 (13), pp. e1770-e1782. DOI: 10.1212/WNL.0000000000011655 | PDF
Mallawaarachchi, A.C. & … & Gayevskiy, V. et al (2021) Genomic diagnostics in polycystic kidney disease: an assessment of real-world use of whole-genome sequencing. European Journal of Human Genetics, 29, pp. 760-770. DOI: 10.1038/s41431-020-00796-4 | PDF
Wong, M. & … & Gayevskiy, V. et al (2020) Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer. Nature Medicine, 26, pp. 1742–1753. DOI: 10.1038/s41591-020-1072-4 | PDF
Sullivan, P. & … & Gayevskiy, V. et al (2020) Introme identifies non-canonical splice-altering variants in neuromuscular patients resulting in multiple new genetic diagnoses. Neuromuscular Disorders, 30, pp. S144. DOI: 10.1016/j.nmd.2020.08.330 | PDF
Riley, L.G. & … & Gayevskiy, V. et al (2020) The diagnostic utility of genome sequencing in a pediatric cohort with suspected mitochondrial disease. Genetics in Medicine, 22, pp. 1254–1261. DOI: 10.1038/s41436-020-0793-6 | PDF
* Leong, T.L. & Gayevskiy, V. et al (2019). Deep multi-region whole-genome sequencing reveals heterogeneity and gene-by-environment interactions in treatment-naive, metastatic lung cancer. Oncogene, 38, pp. 1661-1675. DOI: 10.1038/s41388-018-0536-1 | PDF
McCabe, M.J. & … & Gayevskiy, V. et al (2019) Development and validation of a targeted gene sequencing panel for application to disparate cancers. Scientific Reports, 9, 17052. DOI: 10.1038/s41598-019-52000-3 | PDF
Kumar, K.R. & … & Gayevskiy, V. et al (2019) Whole genome sequencing for the genetic diagnosis of heterogenous dystonia phenotypes. Parkinsonism and Related Disorders, 69, pp. 111-118. DOI: 10.1016/j.parkreldis.2019.11.004 | PDF
Cowley, M.J. & … & Gayevskiy, V. et al (2019) Reanalysis and optimisation of bioinformatic pipelines is critical for mutation detection. Human Mutation, 40 (4), pp. 374-379. DOI: 10.1002/humu.23699 | PDF
Palmer, E.E. & … & Gayevskiy, V. et al (2019) De Novo Variants Disrupting the HX Repeat Motif of ATN1 Cause a Recognizable Non-Progressive Neurocognitive Syndrome. The American Journal of Human Genetics, 104 (3), pp. 542-552. DOI: 10.1016/j.ajhg.2019.01.013 | PDF
McCabe, M.J. & … & Gayevskiy, V. et al (2019) Genomic stratification and liquid biopsy in a rare adrenocortical carcinoma (ACC) case, with dual lung metastases. Cold Spring Harbor Molecular Case Studies, 5: a003764. DOI: 10.1101/mcs.a003764 | PDF
Mueller, S.A. & … & Gayevskiy, V. et al (2019) Mutational Patterns in Metastatic Cutaneous Squamous Cell Carcinoma. Journal of Investigative Dermatology, 139 (7), pp. 1449-1458.e1. DOI: 10.1016/j.jid.2019.01.008 | PDF
Kim, A. & … & Gayevskiy, V. et al (2019) Increased Diagnostic Yield of Spastic Paraplegia with or Without Cerebellar Ataxia Through Whole-Genome Sequencing. The Cerebellum, 18 (4), pp. 781-790. DOI: 10.1007/s12311-019-01038-0 | PDF
Zammit, N.W. & … & Gayevskiy, V. et al (2019). Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity. Nature Immunology, 20, pp. 1299-1310. DOI: 10.1038/s41590-019-0492-0 | PDF
Rius, R. & … & Gayevskiy, V. et al (2019) Cryptic intronic NBAS variant reveals the genetic basis of recurrent liver failure in a child. Molecular Genetics and Metabolism, 136 (1), pp. 77-82. DOI: 10.1016/j.ymgme.2018.12.002 | PDF
Minoche, A.E. & … & Gayevskiy, V. et al (2019). Genome sequencing as a first-line genetic test in familial dilated cardiomyopathy. Genetics in Medicine, 21, pp. 650-662. DOI: 10.1038/s41436-018-0084-7 | PDF
Kirk, E.P. & … & Gayevskiy, V. et al (2019). Beyond the panel: preconception screening in consanguineous couples using the TruSight One "clinical exome". Genetics in Medicine, 21, pp. 608-612. DOI: 10.1038/s41436-018-0082-9 | PDF
* Gayevskiy, V. & Roscioli, T. & Dinger, M.E. & Cowley, M.J. (2019). Seave: a comprehensive web platform for storing and interrogating human genomic variation. Bioinformatics, 35 (1), pp. 122-125. DOI: 10.1093/bioinformatics/bty540 | PDF | GitHub
Tsoli M. & … & Gayevskiy V. et al (2018). Integration of genomics, high throughput drug screening, and personalized xenograft models as a novel precision medicine paradigm for high risk pediatric cancer. Cancer Biology & Therapy, 19 (12), pp. 1078-1087. DOI: 10.1080/15384047.2018.1491498 | PDF
Barnet M. & … & Gayevskiy V. et al (2018). Exploring the Germ-Line Contribution to Exceptional Response to PD-1/PD-L1 Inhibition in Patients with NSCLC by Whole Genome Sequencing. Journal of Thoracic Oncology, 13 (10), pp. S529. DOI: 10.1016/j.jtho.2018.08.726 | PDF
Ziegler, D.S. & … & Gayevskiy, V. et al (2018). Brief Report: Potent clinical and radiological response to larotrectinib in TRK fusion-driven high-grade glioma. British Journal of Cancer, 119, pp. 693-696. DOI: 10.1038/s41416-018-0251-2 | PDF
Kumar, K. & … & Gayevskiy, V. et al (2018). Expanding the spectrum of PEX16 mutations and novel insights into disease mechanisms. Molecular Genetics and Metabolism Reports, 16, pp. 46-51. DOI: 10.1016/j.ymgmr.2018.07.003 | PDF
Ewans, L.J. & … & Gayevskiy, V. et al (2018). Whole-exome sequencing reanalysis at 12 months boosts diagnosis and is cost-effective when applied early in Mendelian disorders. Genetics in Medicine, 20, pp. 1564–1574. DOI: 10.1038/gim.2018.39 | PDF
De Sousa, S.M. & … & Gayevskiy, V. et al (2017). Germline variants in familial pituitary tumour syndrome genes are common in young patients and families with additional endocrine tumours. European Journal of Endocrinology, 176 (5), pp. 635-644. DOI: 10.1530/EJE-16-0944 | PDF
Balasubramaniam, S. & … & Gayevskiy, V. et al (2017). EPG5-Related Vici Syndrome: A Primary Defect of Autophagic Regulation with an Emerging Phenotype Overlapping with Mitochondrial Disorders. JIMD Reports. DOI: 10.1007/8904_2017_71 | PDF
Balasubramaniam, S. & … & Gayevskiy, V. et al (2017). Unique presentation of cutis laxa with Leigh-like syndrome due to ECHS1 deficiency. Journal of Inherited Metabolic Disease, 40 (5), pp. 745-747. DOI: 10.1007/s10545-017-0036-4 | PDF
Riley, L.R. & … & Gayevskiy, V. et al (2017). A SLC39A8 variant causes manganese deficiency, and glycosylation and mitochondrial disorders. Journal of Inherited Metabolic Disease, 40 (2), pp. 261-269. DOI: 10.1007/s10545-016-0010-6 | PDF
Heimer, G. & … & Gayevskiy, V. et al (2016). MECR Mutations Cause Childhood-Onset Dystonia and Optic Atrophy, a Mitochondrial Fatty Acid Synthesis Disorder. The American Journal for Human Genetics, 99 (6), pp. 1229-1244. DOI: 10.1016/j.ajhg.2016.09.021 | PDF
* Gayevskiy, V. & Lee, S. & Goddard, M.R. (2016). European derived Saccharomyces cerevisiae colonisation of New Zealand vineyards aided by humans. FEMS Yeast Research, 16 (7), fow091. DOI: 10.1093/femsyr/fow091 | PDF
Kumar, K.R. & … & Gayevskiy, V. et al (2016). Defining the genetic basis of early onset hereditary spastic paraplegia using whole genome sequencing. Neurogenetics, 17, pp. 265-270. DOI: 10.1007/s10048-016-0495-z | PDF
Merlevede, J. & … & Gayevskiy, V. et al (2016) Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents. Nature Communications, 7:10767 DOI: 10.1038/ncomms10767 | PDF
* Gayevskiy, V. & Goddard, M.R. (2016) Saccharomyces eubayanus and Saccharomyces arboricola reside in North Island native New Zealand forests. Environmental Microbiology, 18 (4), pp. 1137-1147. DOI: 10.1111/1462-2920.13107 | PDF
Rogers, S. & … & Gayevskiy, V. et al (2015). Dataset from the global phosphoproteomic mapping of early mitotic exit in human cells. Data in Brief, 5, pp. 45-52. DOI: 10.1016/j.dib.2015.08.010 | PDF
McCloy, R. & … & Gayevskiy, V. et al (2015). Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs. Molecular and Cellular Proteomics, 14 (8), pp. 2194-2212. DOI: 10.1074/mcp.M114.046938 | PDF
* Gayevskiy V. & Klaere S. & Knight S. & Goddard M.R. (2014) ObStruct: A Method to Objectively Analyse Factors Driving Population Structure Using Bayesian Ancestry Profiles. PLoS ONE, 9 (1): e85196. DOI: 10.1371/journal.pone.0085196 | PDF
* Gayevskiy, V. & Goddard, M.R. (2012). Geographic delineations of yeast communities and populations associated with vines and wines in New Zealand. The ISME Journal, 6 (7), pp. 1281-1290. DOI: 10.1038/ismej.2011.195 | PDF
Conferences
2016 - AGTA Conference Poster
2015 - AGTA Conference Poster
2014 - NZMEC Symposium Talk
2014 - NZ Phylogenomics Meeting Talk
2011 - Romeo Bragato Conference Talk
2010 - New Zealand Microbiological Society (NZMS) Conference Talk
Teaching
2017 - Taught the sections on cancer genomics, bioinformatics for clinicians, introduction to Seave and copy number/structural variants at the Clinical Genomics Workshop hosted by the Kinghorn Centre for Clinical Genomics in Hong Kong. Ran two practical workshop sessions on using Seave to diagnose patients with rare disease and validate variants using IGV.
2016 - Taught the copy number variation and variant filtration sections of the Cancer Genomics Workshop hosted by BioPlatforms Australia in Melbourne.
2015 - Taught the copy number variation and variant filtration sections of the Cancer Genomics Workshop hosted by BioPlatforms Australia in Canberra.
2015 - Short talk on Seave at the Clinical Genomics workshop hosted at the Kinghorn Centre for Clinical Genomics.