People_

Professor Vanessa Hayes

Petre Chair of Prostate Cancer Research
School of Medical Sciences

Details

Vanessa is the Petre Chair of Prostate Cancer Research in the School of Medical Sciences, heading the Ancestry & Health Genomics Laboratory located within the Charles Perkins Centre (CPC). The labs focus is on investigating the complexities of the human and cancer genome and how genomic variation has shaped human evolution and health. Our over-riding goal, to unlock the ancestral and mutagenic factors driving ethnic-geographic prostate cancer health disparity to deliver precision medicine to diagnose, treat and prevent specifically lethal disease. Our program of research is underpinned by expertise in genomic and data science, with a steadfast commitment to securing individualized cancer care options for patients worldwide. Our vision is to use patient-driven research that links genomic science with clinical science, specifically population science (or ancestry genomics). This multilayered approach is vital for investigating the entire spectrum of factors that can impact cancer progression and patient health outcomes.

Research interests

Human genomics, Human diversity, Genome Mapping, Prostate cancer, Cancer disparities, Cancer genomics, Complex Genomic Rearrangements, Bioinformatics, Biostatistics, Genetic epidemiology, Population genetics, Human evolution, Human migration, Human adaptation, Southern Africa, Indigenous genomics, Mitochondrial genomics, Genomic technology.

Current projects

Project 1: Mapping early human evolution through genomic diversity

No consensus exists on the origin and timeline of modern human evolution.The major reason is that inference methods used are highly dependent on available genetic data, both source and type.The literature is biased towards the study of recently diverged non-African populations and maternally-derived mitochondrial or partial genomic data. Modern humans have spent more time evolving inside Africa and as our team recently showed within southern Africa. The overall aim of this projectis to resolve modern human’s earliest evolution and associated survival (evolutionary fitness), by targeting the earliest diverged (oldest extant) and genetically diverse human populations, which are found in southern Africa. Merging southern African data with global population-wide resources, ancient human and archaic hominin fossils, and inferred ‘ghost’ populations, we will establish an evolutionary picture of global migrations, sub-population complexities and inter-species relatedness. Additionally, an aim of this project will be tocreate a human ancestral genomic frame of reference.

Project 2: Resolving the genomic basis for global/ethnic prostate cancer health disparities

Prostate cancer (PCa) burden is characterised by striking geographic and ethnic disparity.While incidence rates are highest in Australia, mortality rates are highest in Africa, specificallysouthern Africa where rates are 2.6-fold higher than Australia. This disparity is further alarming when considering the life expectancy of the average South African man is 20 years younger than his Australian brothers. Also, PCa is a genetic disease. While ones germline variation determines individual risk, acquired variants drive tumour evolution. Yet data has been lacking for Africa.In 2008, CIA-Hayes and colleagues initiated theSouthern African Prostate Cancer Study (SAPCS), withthe goal, toprovide evidence-based clinical, lifestyle and genomic data that underpins PCadisparities in African men. Recruiting over 2,500 men, the evidence is clear. PCa is asignificant health burden in southern Africa, with the risk of presenting with lethal disease 1.6-fold greater for men living in rural over urban communities. more recently the team has initiated the East African Prostate Cacner Study (EAPCS), which inpartnership with the SAPCS team have formed a network for African PCa genomic research efforts via the initiative of Dzomo. The SAPCS and EAPCS are committed to identifying the genetic basis for significant PCa health disparity.

Project 3: Resolving complex genomic rearrangements driving prostate cancer

Cancer is a genetic disease driven by the acquisition of oncogenic mutations. In prostate cancer these mutations may be complex resulting in extensive chromosomal rearrangements, including for example chromothripsis (chromosome shattering), chromoplexy (chains of balanced rearrangements), kataegis (clustered nucleotide substitutions), and telomere crisis, many which have only recently been reported. In this study we use cutting-edge genomic technologies and bioinformatic analytics to identify not only the extent of complex genome rearrangements acquired during prostate cancer progression, but determine how these phenomena interact to drive genomic instability and the relevance of this instability to disease progression and tumour evolution. The team is applying existing and developing new computational/mathematical methods to identify patterns (signature) in the occurrence of complex somatic genomic reconfigurations that might be uniquely ascribed to particular mutational process.

Associations

Affiliated positions: (i) Extraordinary Professor in the School of Health Systems & Public Health, University of Pretoria, South Africa, (ii) Honorary Professor in Health Sciences, University of Limpopo, in South Africa

Director: DoD-funded HEROIC Prostate Cacner Precision Health (PCaPH) Africa1K Consortium and TARGET Africa Project

Scientific Director: (i) Diversity inclusive Genome Study for Southern Africa (DiGS-SA), (ii)South African Prostate Cancer Study (SAPCS), (iii) East African Prostate Cancer Study (EAPCS)

Themes

Cancer, Healthy Ageing

Keywords

Ageing, Cancer, Genetics, Global health, Prostate

Approaches

Genetics, Risk Factors/Risk Assessment

Publications

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Journals

Mokoatle, M., Marivate, V., Mapiye, D., Bornman, M., Hayes, V. (2023). A review and comparative study of cancer detection using machine learning: SBERT and SimCSE application. BMC Bioinformatics, 24(1). [More Information]
Hayes, V., Gong, T., Mutambirwa, S., Jaratlerdsiri, W., Bornman, M. (2023). African inclusion in prostate cancer genomic studies provides the first glimpses into addressing health disparities through tailored clinical care. Clinical and Translational Medicine, 13(1), e1142. [More Information]
Craddock, J., Jiang, J., Patrick, S., Mutambirwa, S., Stricker, P., Bornman, M., Jaratlerdsiri, W., Hayes, V. (2023). Alterations in the Epigenetic Machinery Associated with Prostate Cancer Health Disparities. Cancers, 15(13). [More Information]
Jiang, J., Soh, P., Mutambirwa, S., Bornman, M., Haiman, C., Hayes, V., Jaratlerdsiri, W. (2023). ANO7 African-ancestral genomic diversity and advanced prostate cancer. Prostate Cancer and Prostatic Diseases. [More Information]
Gheybi, K., Jiang, J., Mutambirwa, S., Soh, P., Kote-Jarai, Z., Jaratlerdsiri, W., Eeles, R., Bornman, M., Hayes, V. (2023). Evaluating Germline Testing Panels in Southern African Males With Advanced Prostate Cancer. JNCCN Journal of the National Comprehensive Cancer Network, 21(3), 289-296. [More Information]
Soh, P., Mmekwa, N., Petersen, D., Gheybi, K., Van Zyl, S., Jiang, J., Patrick, S., Campbell, R., Jaratlerdsiri, W., Mutambirwa, S., Hayes, V., et al (2023). Prostate cancer genetic risk and associated aggressive disease in men of African ancestry. Nature Communications, 14(1), 8037. [More Information]
Ballard, J., Field, M., Edwards, R., Wilson, L., Koungoulos, L., Rosen, B., Chernoff, B., Dudchenko, O., Omer, A., Keilwagen, J., Hayes, V., et al (2023). The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology. GigaScience, 12. [More Information]
Jaratlerdsiri, W., Jiang, J., Gong, T., Patrick, S., Willet, C., Chew, T., Lyons, R., Haynes, A., Pasqualim, G., Louw, M., Sadsad, R., Hayes, V., et al (2022). African-specific molecular taxonomy of prostate cancer. Nature, 609(7927), 552-559. [More Information]
Mokoatle, M., Mapiye, D., Marivate, V., Hayes, V., Bornman, R. (2022). Discriminatory Gleason grade group signatures of prostate cancer: An application of machine learning methods. PloS One, 17(6-Jun). [More Information]
Gong, T., Jaratlerdsiri, W., Jiang, J., Willet, C., Chew, T., Patrick, S., Lyons, R., Haynes, A., Pasqualim, G., Brum, I., Sadsad, R., Hayes, V., et al (2022). Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers. Genome Medicine, 14(1). [More Information]
Burns, D., Anokian, E., Saunders, E., Bristow, R., Fraser, M., Reimand, J., Schlomm, T., Sauter, G., Brors, B., Korbel, J., Hayes, V., et al (2022). Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study. European Urology, 82(2), 201-211. [More Information]
Gong, T., Hayes, V., Chan, E. (2021). Detection of somatic structural variants from short-read next-generation sequencing data. Briefings in Bioinformatics, 22(3), bbaa056. [More Information]
Goncearenco, A., LaBarre, B., Petrykowska, H., Jaratlerdsiri, W., Bornman, M., Turner, S., Hayes, V., Elnitski, L. (2021). DNA methylation profiles unique to Kalahari KhoeSan individuals. Epigenetics, 16(5), 537-553. [More Information]
Field, M., Rosen, B., Dudchenko, O., Chan, E., Minoche, A., Edwards, R., Barton, K., Lyons, R., Tuipulotu, D., Hayes, V., et al (2020). Canfam-GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. GigaScience, 9(4), giaa027. [More Information]
Owen, K., Gearing, L., Zanker, D., Brockwell, N., Khoo, W., Roden, D., Cmero, M., Mangiola, S., Hong, M., Spurling, A., Hayes, V., et al (2020). Prostate cancer cell-intrinsic interferon signaling regulates dormancy and metastatic outgrowth in bone. EMBO Reports, 21(6), 1-24. [More Information]
Gong, T., Hayes, V., Chan, E. (2020). Shiny-SoSV: A web-based performance calculator for somatic structural variant detection. PloS One, 15(8), 1-20. [More Information]
Crumbaker, M., Chan, E., Gong, T., Corcoran, N., Jaratlerdsiri, W., Lyons, R., Haynes, A., Kulidjian, A., Kalsbeek, A., Petersen, D., Hayes, V., et al (2020). The impact of whole genome data on therapeutic decision-making in metastatic prostate cancer: A retrospective analysis. Cancers, 12(5), 1178. [More Information]
Petersen, D., Jaratlerdsiri, W., Van Wyk, A., Chan, E., Fernandez, P., Lyons, R., Mutambirw, S., Van Der Merwe, A., Venter, P., Bates, W., Hayes, V., et al (2019). African KhoeSan ancestry linked to high-risk prostate cancer. BMC Medical Genomics, 12(1), 1-7. [More Information]
Heyer, E., Deveson, I., Wooi, D., Selinger, C., Lyons, R., Hayes, V., O'Toole, S., Ballinger, M., Gill, D., Thomas, D., et al (2019). Diagnosis of fusion genes using targeted RNA sequencing. Nature Communications, 10(1), 1-12. [More Information]
Chan, E., Timmermann, A., Baldi, B., Moore, A., Lyons, R., Lee, S., Kalsbeek, A., Petersen, D., Rautenbach, H., Fortsch, H., Hayes, V., et al (2019). Human origins in a southern African palaeo-wetland and first migrations. Nature, 575(7781), 185-189. [More Information]
Feng, Y., Jaratlerdsiri, W., Patrick, S., Lyons, R., Haynes, A., Collins, C., Stricker, P., Bornman, M., Hayes, V. (2019). Metagenomic analysis reveals a rich bacterial content in high-risk prostate tumors from African men. The Prostate, 79(15), 1731-1738. [More Information]
Feng, Y., Ramnarine, V., Bell, R., Volik, S., Davicioni, E., Hayes, V., Ren, S., Collins, C. (2019). Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer. BMC Genomics, 20(1), 1-8. [More Information]
Labarre, B., Goncearenco, A., Petrykowska, H., Jaratlerdsiri, W., Bornman, M., Hayes, V., Elnitski, L. (2019). MethylToSNP: Identifying SNPs in Illumina DNA methylation array data. Epigenetics & Chromatin, 12(1), 1-14. [More Information]
Blackburn, J., Vecchiarelli, S., Heyer, E., Patrick, S., Lyons, R., Jaratlerdsiri, W., Van Zyl, S., Bornman, M., Mercer, T., Hayes, V. (2019). TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: A focus on Africa. The Prostate, 79(10), 1191-1196. [More Information]
Kalsbeek, A., Chan, E., Grogan, J., Petersen, D., Jaratlerdsiri, W., Gupta, R., Lyons, R., Haynes, A., Horvath, L., Kench, J., Hayes, V., et al (2018). Altered mitochondrial genome content signals worse pathology and prognosis in prostate cancer. The Prostate, 78(1), 25-31. [More Information]
Nair, S., Luu, P., Qu, W., Maddugoda, M., Huschtscha, L., Reddel, R., Chenevix-Trench, G., Toso, M., Kench, J., Horvath, L., Hayes, V., Rasko, J., Wong, J., et al (2018). Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten. Epigenetics & Chromatin, 11(1), 1-20. [More Information]
Chan, E., Cameron, D., Petersen, D., Lyons, R., Baldi, B., Papenfuss, A., Thomas, D., Hayes, V. (2018). Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer. Genome Research, 28(5), 726-738. [More Information]
Hayes, V., Jaratlerdsiri, W., Bornman, M. (2018). Prostate cancer genomics and racial health disparity. Oncotarget, 9(94), 36650-36651. [More Information]
Hayes, V., Bornman, M. (2018). Prostate Cancer in Southern Africa: Does Africa Hold Untapped Potential to Add Value to the Current Understanding of a Common Disease? Journal of Global Oncology, 4(4), 1-7. [More Information]
Jaratlerdsiri, W., Chan, E., Gong, T., Petersen, D., Kalsbeek, A., Venter, P., Stricker, P., Bornman, M., Hayes, V. (2018). Whole-Genome Sequencing Reveals Elevated Tumor Mutational Burden and Initiating Driver Mutations in African Men with Treatment-Naive, High-Risk Prostate Cancer. Cancer Research, 78(24), 6736-6746. [More Information]
Kalsbeek, A., Chan, E., Corcoran, N., Hovens, C., Hayes, V. (2017). Mitochondrial genome variation and prostate cancer: A review of the mutational landscape and application to clinical management. Oncotarget, 8(41), 71342-71357. [More Information]
Jaratlerdsiri, W., Chan, E., Petersen, D., Yang, C., Croucher, P., Bornman, M., Sheth, P., Hayes, V. (2017). Next generation mapping reveals novel large genomic rearrangements in prostate cancer. Oncotarget, 8(14), 23588-23602. [More Information]
Skoglund, P., Thompson, J., Prendergast, M., Mittnik, A., Sirak, K., Hajdinjak, M., Salie, T., Rohland, N., Mallick, S., Hayes, V., et al (2017). Reconstructing Prehistoric African Population Structure. Cell, 171(1), 59-71.e21. [More Information]
Kalsbeek, A., Chan, E., Grogan, J., Petersen, D., Jaratlerdsiri, W., Gupta, R., Lyons, R., Haynes, A., Horvath, L., Kench, J., Hayes, V., et al (2016). Mutational load of the mitochondrial genome predicts pathological features and biochemical recurrence in prostate cancer. Aging, 8(11), 2702-2712. [More Information]
McCrow, J., Petersen, D., Louw, M., Chan, E., Harmeyer, K., Vecchiarelli, S., Lyons, R., Bornman, M., Hayes, V. (2016). Spectrum of mitochondrial genomic variation and associated clinical presentation of prostate cancer in South African men. The Prostate, 76(4), 349-358. [More Information]
Chan, E., Hardie, R., Petersen, D., Beeson, K., Bornman, M., Smith, A., Hayes, V. (2015). Revised Timeline and Distribution of the Earliest Diverged Human Maternal Lineages in Southern Africa. PloS One, 10(3), 1-17. [More Information]
Stuchbery, R., Kurganovs, N., McCoy, P., Nelson, C., Hayes, V., Corcoran, N., Hovens, C. (2015). Target Acquired: Progress and Promise of Targeted Therapeutics in the Treatment of Prostate Cancer. Current Cancer Drug Targets, 15(5), 394-405. [More Information]
Tindall, E., Monare, R., Petersen, D., Van Zyl, S., Hardie, R., Segone, A., Venter, P., Rianna Bornman, M., Hayes, V. (2014). Clinical Presentation of Prostate Cancer in Black South Africans. The Prostate, 74(8), 880-891. [More Information]
Morris, A., Heinze, A., Chan, E., Smith, A., Hayes, V. (2014). First Ancient Mitochondrial Human Genome from a Pre-Pastoralist Southern African. Genome Biology and Evolution, 6(10), 2647-2453. [More Information]
Pang, A., MacDonald, J., Yuen, R., Hayes, V., Scherer, S. (2014). Performance of high-throughput sequencing for the discovery of genetic variation across the complete size spectrum. G3: Genes, Genomes, Genetics, 4(1), 63-65. [More Information]
Tindall, E., Bornman, M., Van Zyl, S., Segone, A., Monare, L., Venter, P., Hayes, V. (2013). Addressing the contribution of previously described genetic and epidemiological risk factors associated with increased prostate cancer risk and aggressive disease within men from South Africa. BMC Urology, 13, 1-12. [More Information]
Petersen, D., Libiger, O., Tindall, E., Hardie, R., Hannick, L., Glashoff, R., Mukerji, M., Fernandez, P., Haacke, W., Schork, N., et al (2013). Complex patterns of genomic admixture within southern Africa. PLoS Genetics, 9(3), 1-17. [More Information]
Muhlbradt, E., Ma, J., Severi, G., Ortner, E., Hayes, V., Hoang, H., Stampfer, M., Giles, G., Pollak, M., Gelmann, E. (2013). Variant NKX3.1 and Serum IGF-1: Investigation of Interaction in Prostate Cancer. Genes and Cancer, 4(11-12), 535-545. [More Information]
Saunders, D., Tindall, E., Shearer, R., Roberson, J., Decker, A., Wilson, J., Hayes, V. (2012). A novel SERPINA1 mutation causing serum Alpha1-Antitrypsin Deficiency. PloS One, 7(12), 1-5. [More Information]
Tindall, E., Severi, G., Hoang, H., Southey, M., English, D., Hopper, J., Giles, G., Hayes, V. (2012). Interleukin-6 promoter variants, prostate cancer risk, and survival. The Prostate, 72(16), 1701-1707. [More Information]
Miller, W., Hayes, V., Ratan, A., Petersen, D., Wittekindt, N., Miller, J., Walenz, B., Knight, J., Qi, J., Zhao, F., et al (2011). Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proceedings of the National Academy of Sciences of the United States of America, 108(30), 12348-12353. [More Information]
Hayes, V., Venter, P., Mphahlele, M. (2011). Helping hand for genomics in Africa. Nature, 476(7359), 152-152.
Hayes, V. (2011). Indigenous Genomics. Science, 332, 639-639.
Ratan, A., Zhang, Y., Hayes, V., Schuster, S., Miller, W. (2010). Calling SNPs without a reference sequence. BMC Bioinformatics, 11, 130. [More Information]
Schuster, S., Miller, W., Ratan, A., Tomsho, L., Giardine, B., Kasson, L., Harris, R., Petersen, D., Zhao, F., Hayes, V., et al (2010). Complete Khoisan and Bantu genomes from southern Africa. Nature, 463(7283), 943-947. [More Information]
Tindall, E., Severi, G., Hoang, H., Ma, C., Fernandez, P., Southey, M., English, D., Hopper, J., Heynes, C., Tangye, S., et al (2010). Comprehensive analysis of the cytokine rich chromosome 5q31.1 region suggests a role for IL-4 gene variants in prostate cancer risk. Carcinogenesis, 31(10), 1748-1754. [More Information]
Tindall, E., Hayes, V. (2010). Comprehensive sequence analysis of the human IL23A gene defines new variation content and high rate of evolutionary conservation. DNA Research, 172(2), 117-122. [More Information]
Patterson, N., Petersen, D., van der Ross, R., Sudoyo, H., Glashoff, R., Marzuki, S., Reich, D., Hayes, V. (2010). Genetic structure of a unique admixed population: implications for medical research. Human Molecular Genetics, 19(3), 411-419. [More Information]
Tindall, E., Hayes, V., Petersen, D. (2010). Inflammatory genetic markers of prostate cancer risk. Cancers, 2(2), 1198-1220. [More Information]
Tindall, E., Petersen, D., Nikolaysen, S., Miller, W., Schuster, S., Hayes, V. (2010). Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation. BMC Research Notes, 3, 1-6. [More Information]
Miller, W., Wright, S., Zhang, Y., Schuster, S., Hayes, V. (2010). Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species. Biocomputing (Year), 2010, 43-53.
Stone, J., Gurrin, L., Hayes, V., Southey, M., Hopper, J., Byrnes, G. (2010). Sibship analysis of associations between SNP haplotypes and a continuous trait with application to mammographic density. Genetic epidemiology, 34(4), 309-318. [More Information]
Tindall, E., Hoang, H., Southey, M., English, D., Hopper, J., Giles, G., Severi, G., Hayes, V. (2010). The 4q27 locus and prostate cancer risk. BMC Cancer, 10, 1-6. [More Information]
van Loo, K., van Schijndel, J., van Zweeden, M., van Manen, D., Trip, M., Petersen, D., Schuitemaker, H., Hayes, V., Martens, G. (2009). Correlation between HIV-1 seropositivity and prevalence of a gamma-secretase polymorphism in two distinct ethnic populations. Journal of Medical Virology, 81(11), 1847-1851. [More Information]
Comstock, C., Augello, M., Pe Benito, R., karch, J., Tran, T., Utama, F., Tindall, E., Wang, Y., Burd, C., Hayes, V., et al (2009). Cyclin D1 splice variants: polymorphism, risk, and isoform-specific regulation in prostate cancer. Clinical Cancer Research, 15(17), 5338-5349. [More Information]

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2023

Mokoatle, M., Marivate, V., Mapiye, D., Bornman, M., Hayes, V. (2023). A review and comparative study of cancer detection using machine learning: SBERT and SimCSE application. BMC Bioinformatics, 24(1). [More Information]
Hayes, V., Gong, T., Mutambirwa, S., Jaratlerdsiri, W., Bornman, M. (2023). African inclusion in prostate cancer genomic studies provides the first glimpses into addressing health disparities through tailored clinical care. Clinical and Translational Medicine, 13(1), e1142. [More Information]
Craddock, J., Jiang, J., Patrick, S., Mutambirwa, S., Stricker, P., Bornman, M., Jaratlerdsiri, W., Hayes, V. (2023). Alterations in the Epigenetic Machinery Associated with Prostate Cancer Health Disparities. Cancers, 15(13). [More Information]
Jiang, J., Soh, P., Mutambirwa, S., Bornman, M., Haiman, C., Hayes, V., Jaratlerdsiri, W. (2023). ANO7 African-ancestral genomic diversity and advanced prostate cancer. Prostate Cancer and Prostatic Diseases. [More Information]
Gheybi, K., Jiang, J., Mutambirwa, S., Soh, P., Kote-Jarai, Z., Jaratlerdsiri, W., Eeles, R., Bornman, M., Hayes, V. (2023). Evaluating Germline Testing Panels in Southern African Males With Advanced Prostate Cancer. JNCCN Journal of the National Comprehensive Cancer Network, 21(3), 289-296. [More Information]
Soh, P., Mmekwa, N., Petersen, D., Gheybi, K., Van Zyl, S., Jiang, J., Patrick, S., Campbell, R., Jaratlerdsiri, W., Mutambirwa, S., Hayes, V., et al (2023). Prostate cancer genetic risk and associated aggressive disease in men of African ancestry. Nature Communications, 14(1), 8037. [More Information]
Ballard, J., Field, M., Edwards, R., Wilson, L., Koungoulos, L., Rosen, B., Chernoff, B., Dudchenko, O., Omer, A., Keilwagen, J., Hayes, V., et al (2023). The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology. GigaScience, 12. [More Information]

show 4 more

2022

Jaratlerdsiri, W., Jiang, J., Gong, T., Patrick, S., Willet, C., Chew, T., Lyons, R., Haynes, A., Pasqualim, G., Louw, M., Sadsad, R., Hayes, V., et al (2022). African-specific molecular taxonomy of prostate cancer. Nature, 609(7927), 552-559. [More Information]
Mokoatle, M., Mapiye, D., Marivate, V., Hayes, V., Bornman, R. (2022). Discriminatory Gleason grade group signatures of prostate cancer: An application of machine learning methods. PloS One, 17(6-Jun). [More Information]
Gong, T., Jaratlerdsiri, W., Jiang, J., Willet, C., Chew, T., Patrick, S., Lyons, R., Haynes, A., Pasqualim, G., Brum, I., Sadsad, R., Hayes, V., et al (2022). Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers. Genome Medicine, 14(1). [More Information]
Burns, D., Anokian, E., Saunders, E., Bristow, R., Fraser, M., Reimand, J., Schlomm, T., Sauter, G., Brors, B., Korbel, J., Hayes, V., et al (2022). Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study. European Urology, 82(2), 201-211. [More Information]

show 1 more

2021

Gong, T., Hayes, V., Chan, E. (2021). Detection of somatic structural variants from short-read next-generation sequencing data. Briefings in Bioinformatics, 22(3), bbaa056. [More Information]
Goncearenco, A., LaBarre, B., Petrykowska, H., Jaratlerdsiri, W., Bornman, M., Turner, S., Hayes, V., Elnitski, L. (2021). DNA methylation profiles unique to Kalahari KhoeSan individuals. Epigenetics, 16(5), 537-553. [More Information]

2020

Field, M., Rosen, B., Dudchenko, O., Chan, E., Minoche, A., Edwards, R., Barton, K., Lyons, R., Tuipulotu, D., Hayes, V., et al (2020). Canfam-GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. GigaScience, 9(4), giaa027. [More Information]
Owen, K., Gearing, L., Zanker, D., Brockwell, N., Khoo, W., Roden, D., Cmero, M., Mangiola, S., Hong, M., Spurling, A., Hayes, V., et al (2020). Prostate cancer cell-intrinsic interferon signaling regulates dormancy and metastatic outgrowth in bone. EMBO Reports, 21(6), 1-24. [More Information]
Gong, T., Hayes, V., Chan, E. (2020). Shiny-SoSV: A web-based performance calculator for somatic structural variant detection. PloS One, 15(8), 1-20. [More Information]
Crumbaker, M., Chan, E., Gong, T., Corcoran, N., Jaratlerdsiri, W., Lyons, R., Haynes, A., Kulidjian, A., Kalsbeek, A., Petersen, D., Hayes, V., et al (2020). The impact of whole genome data on therapeutic decision-making in metastatic prostate cancer: A retrospective analysis. Cancers, 12(5), 1178. [More Information]

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2019

Petersen, D., Jaratlerdsiri, W., Van Wyk, A., Chan, E., Fernandez, P., Lyons, R., Mutambirw, S., Van Der Merwe, A., Venter, P., Bates, W., Hayes, V., et al (2019). African KhoeSan ancestry linked to high-risk prostate cancer. BMC Medical Genomics, 12(1), 1-7. [More Information]
Heyer, E., Deveson, I., Wooi, D., Selinger, C., Lyons, R., Hayes, V., O'Toole, S., Ballinger, M., Gill, D., Thomas, D., et al (2019). Diagnosis of fusion genes using targeted RNA sequencing. Nature Communications, 10(1), 1-12. [More Information]
Chan, E., Timmermann, A., Baldi, B., Moore, A., Lyons, R., Lee, S., Kalsbeek, A., Petersen, D., Rautenbach, H., Fortsch, H., Hayes, V., et al (2019). Human origins in a southern African palaeo-wetland and first migrations. Nature, 575(7781), 185-189. [More Information]
Feng, Y., Jaratlerdsiri, W., Patrick, S., Lyons, R., Haynes, A., Collins, C., Stricker, P., Bornman, M., Hayes, V. (2019). Metagenomic analysis reveals a rich bacterial content in high-risk prostate tumors from African men. The Prostate, 79(15), 1731-1738. [More Information]
Feng, Y., Ramnarine, V., Bell, R., Volik, S., Davicioni, E., Hayes, V., Ren, S., Collins, C. (2019). Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer. BMC Genomics, 20(1), 1-8. [More Information]
Labarre, B., Goncearenco, A., Petrykowska, H., Jaratlerdsiri, W., Bornman, M., Hayes, V., Elnitski, L. (2019). MethylToSNP: Identifying SNPs in Illumina DNA methylation array data. Epigenetics & Chromatin, 12(1), 1-14. [More Information]
Blackburn, J., Vecchiarelli, S., Heyer, E., Patrick, S., Lyons, R., Jaratlerdsiri, W., Van Zyl, S., Bornman, M., Mercer, T., Hayes, V. (2019). TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: A focus on Africa. The Prostate, 79(10), 1191-1196. [More Information]

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2018

Kalsbeek, A., Chan, E., Grogan, J., Petersen, D., Jaratlerdsiri, W., Gupta, R., Lyons, R., Haynes, A., Horvath, L., Kench, J., Hayes, V., et al (2018). Altered mitochondrial genome content signals worse pathology and prognosis in prostate cancer. The Prostate, 78(1), 25-31. [More Information]
Nair, S., Luu, P., Qu, W., Maddugoda, M., Huschtscha, L., Reddel, R., Chenevix-Trench, G., Toso, M., Kench, J., Horvath, L., Hayes, V., Rasko, J., Wong, J., et al (2018). Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten. Epigenetics & Chromatin, 11(1), 1-20. [More Information]
Chan, E., Cameron, D., Petersen, D., Lyons, R., Baldi, B., Papenfuss, A., Thomas, D., Hayes, V. (2018). Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer. Genome Research, 28(5), 726-738. [More Information]
Hayes, V., Jaratlerdsiri, W., Bornman, M. (2018). Prostate cancer genomics and racial health disparity. Oncotarget, 9(94), 36650-36651. [More Information]
Hayes, V., Bornman, M. (2018). Prostate Cancer in Southern Africa: Does Africa Hold Untapped Potential to Add Value to the Current Understanding of a Common Disease? Journal of Global Oncology, 4(4), 1-7. [More Information]
Jaratlerdsiri, W., Chan, E., Gong, T., Petersen, D., Kalsbeek, A., Venter, P., Stricker, P., Bornman, M., Hayes, V. (2018). Whole-Genome Sequencing Reveals Elevated Tumor Mutational Burden and Initiating Driver Mutations in African Men with Treatment-Naive, High-Risk Prostate Cancer. Cancer Research, 78(24), 6736-6746. [More Information]

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2017

Kalsbeek, A., Chan, E., Corcoran, N., Hovens, C., Hayes, V. (2017). Mitochondrial genome variation and prostate cancer: A review of the mutational landscape and application to clinical management. Oncotarget, 8(41), 71342-71357. [More Information]
Jaratlerdsiri, W., Chan, E., Petersen, D., Yang, C., Croucher, P., Bornman, M., Sheth, P., Hayes, V. (2017). Next generation mapping reveals novel large genomic rearrangements in prostate cancer. Oncotarget, 8(14), 23588-23602. [More Information]
Skoglund, P., Thompson, J., Prendergast, M., Mittnik, A., Sirak, K., Hajdinjak, M., Salie, T., Rohland, N., Mallick, S., Hayes, V., et al (2017). Reconstructing Prehistoric African Population Structure. Cell, 171(1), 59-71.e21. [More Information]

2016

Kalsbeek, A., Chan, E., Grogan, J., Petersen, D., Jaratlerdsiri, W., Gupta, R., Lyons, R., Haynes, A., Horvath, L., Kench, J., Hayes, V., et al (2016). Mutational load of the mitochondrial genome predicts pathological features and biochemical recurrence in prostate cancer. Aging, 8(11), 2702-2712. [More Information]
McCrow, J., Petersen, D., Louw, M., Chan, E., Harmeyer, K., Vecchiarelli, S., Lyons, R., Bornman, M., Hayes, V. (2016). Spectrum of mitochondrial genomic variation and associated clinical presentation of prostate cancer in South African men. The Prostate, 76(4), 349-358. [More Information]

2015

Chan, E., Hardie, R., Petersen, D., Beeson, K., Bornman, M., Smith, A., Hayes, V. (2015). Revised Timeline and Distribution of the Earliest Diverged Human Maternal Lineages in Southern Africa. PloS One, 10(3), 1-17. [More Information]
Stuchbery, R., Kurganovs, N., McCoy, P., Nelson, C., Hayes, V., Corcoran, N., Hovens, C. (2015). Target Acquired: Progress and Promise of Targeted Therapeutics in the Treatment of Prostate Cancer. Current Cancer Drug Targets, 15(5), 394-405. [More Information]

2014

Tindall, E., Monare, R., Petersen, D., Van Zyl, S., Hardie, R., Segone, A., Venter, P., Rianna Bornman, M., Hayes, V. (2014). Clinical Presentation of Prostate Cancer in Black South Africans. The Prostate, 74(8), 880-891. [More Information]
Morris, A., Heinze, A., Chan, E., Smith, A., Hayes, V. (2014). First Ancient Mitochondrial Human Genome from a Pre-Pastoralist Southern African. Genome Biology and Evolution, 6(10), 2647-2453. [More Information]
Pang, A., MacDonald, J., Yuen, R., Hayes, V., Scherer, S. (2014). Performance of high-throughput sequencing for the discovery of genetic variation across the complete size spectrum. G3: Genes, Genomes, Genetics, 4(1), 63-65. [More Information]

2013

Tindall, E., Bornman, M., Van Zyl, S., Segone, A., Monare, L., Venter, P., Hayes, V. (2013). Addressing the contribution of previously described genetic and epidemiological risk factors associated with increased prostate cancer risk and aggressive disease within men from South Africa. BMC Urology, 13, 1-12. [More Information]
Petersen, D., Libiger, O., Tindall, E., Hardie, R., Hannick, L., Glashoff, R., Mukerji, M., Fernandez, P., Haacke, W., Schork, N., et al (2013). Complex patterns of genomic admixture within southern Africa. PLoS Genetics, 9(3), 1-17. [More Information]
Muhlbradt, E., Ma, J., Severi, G., Ortner, E., Hayes, V., Hoang, H., Stampfer, M., Giles, G., Pollak, M., Gelmann, E. (2013). Variant NKX3.1 and Serum IGF-1: Investigation of Interaction in Prostate Cancer. Genes and Cancer, 4(11-12), 535-545. [More Information]

2012

Saunders, D., Tindall, E., Shearer, R., Roberson, J., Decker, A., Wilson, J., Hayes, V. (2012). A novel SERPINA1 mutation causing serum Alpha1-Antitrypsin Deficiency. PloS One, 7(12), 1-5. [More Information]
Tindall, E., Severi, G., Hoang, H., Southey, M., English, D., Hopper, J., Giles, G., Hayes, V. (2012). Interleukin-6 promoter variants, prostate cancer risk, and survival. The Prostate, 72(16), 1701-1707. [More Information]

2011

Miller, W., Hayes, V., Ratan, A., Petersen, D., Wittekindt, N., Miller, J., Walenz, B., Knight, J., Qi, J., Zhao, F., et al (2011). Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proceedings of the National Academy of Sciences of the United States of America, 108(30), 12348-12353. [More Information]
Hayes, V., Venter, P., Mphahlele, M. (2011). Helping hand for genomics in Africa. Nature, 476(7359), 152-152.
Hayes, V. (2011). Indigenous Genomics. Science, 332, 639-639.

2010

Ratan, A., Zhang, Y., Hayes, V., Schuster, S., Miller, W. (2010). Calling SNPs without a reference sequence. BMC Bioinformatics, 11, 130. [More Information]
Schuster, S., Miller, W., Ratan, A., Tomsho, L., Giardine, B., Kasson, L., Harris, R., Petersen, D., Zhao, F., Hayes, V., et al (2010). Complete Khoisan and Bantu genomes from southern Africa. Nature, 463(7283), 943-947. [More Information]
Tindall, E., Severi, G., Hoang, H., Ma, C., Fernandez, P., Southey, M., English, D., Hopper, J., Heynes, C., Tangye, S., et al (2010). Comprehensive analysis of the cytokine rich chromosome 5q31.1 region suggests a role for IL-4 gene variants in prostate cancer risk. Carcinogenesis, 31(10), 1748-1754. [More Information]
Tindall, E., Hayes, V. (2010). Comprehensive sequence analysis of the human IL23A gene defines new variation content and high rate of evolutionary conservation. DNA Research, 172(2), 117-122. [More Information]
Patterson, N., Petersen, D., van der Ross, R., Sudoyo, H., Glashoff, R., Marzuki, S., Reich, D., Hayes, V. (2010). Genetic structure of a unique admixed population: implications for medical research. Human Molecular Genetics, 19(3), 411-419. [More Information]
Tindall, E., Hayes, V., Petersen, D. (2010). Inflammatory genetic markers of prostate cancer risk. Cancers, 2(2), 1198-1220. [More Information]
Tindall, E., Petersen, D., Nikolaysen, S., Miller, W., Schuster, S., Hayes, V. (2010). Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation. BMC Research Notes, 3, 1-6. [More Information]
Miller, W., Wright, S., Zhang, Y., Schuster, S., Hayes, V. (2010). Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species. Biocomputing (Year), 2010, 43-53.
Stone, J., Gurrin, L., Hayes, V., Southey, M., Hopper, J., Byrnes, G. (2010). Sibship analysis of associations between SNP haplotypes and a continuous trait with application to mammographic density. Genetic epidemiology, 34(4), 309-318. [More Information]
Tindall, E., Hoang, H., Southey, M., English, D., Hopper, J., Giles, G., Severi, G., Hayes, V. (2010). The 4q27 locus and prostate cancer risk. BMC Cancer, 10, 1-6. [More Information]

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2009

van Loo, K., van Schijndel, J., van Zweeden, M., van Manen, D., Trip, M., Petersen, D., Schuitemaker, H., Hayes, V., Martens, G. (2009). Correlation between HIV-1 seropositivity and prevalence of a gamma-secretase polymorphism in two distinct ethnic populations. Journal of Medical Virology, 81(11), 1847-1851. [More Information]
Comstock, C., Augello, M., Pe Benito, R., karch, J., Tran, T., Utama, F., Tindall, E., Wang, Y., Burd, C., Hayes, V., et al (2009). Cyclin D1 splice variants: polymorphism, risk, and isoform-specific regulation in prostate cancer. Clinical Cancer Research, 15(17), 5338-5349. [More Information]

Selected Grants

2023

Genomic bases for African geo-ethnic prostate cancer health disparity, Hayes V, Jaratlerdsiri W, National Institutes of Health (USA)/Research Grant

2022

TRANSFER IN: HEROIC Prostate Cancer Precision Health (PCaPH) Africa1K - Powering precision health to improve prostate cancer outcomes in Africa. V. Hayes, Hayes V, US Department of Defence (USA)/Prostate Cancer Research Program
High-risk prostate cancer in southern Africa: Unravelling the genome and exposome (TARGET Africa), Hayes V, US Department of Defence (USA)/Prostate Cancer Research Program

2020

Mutational signatures of DDT: the role of a controversial persistent endocrine disrupting pollutant on prostate cancer aetiology, Hayes V, Bornman M, National Health and Medical Research Council (NHMRC)/Ideas Grant