Hayes Lab Publications since 2010 (selected)

Soh PXY, Hayes VM. Common Genetic Variants Associated with Prostate Cancer Risk: The Need for African Inclusion. Eur Urol. 2023 Jul;84(1):22-24. doi: 10.1016/j.eururo.2023.04.006.

Mokoatle M, Marivate V, Mapiye D, Bornman R, Hayes VM. A review and comparative study of cancer detection using machine learning: SBERT and SimCSE application. BMC Bioinformatics. 2023 Mar 23;24(1):112. doi: 10.1186/s12859-023-05235-x.

Gheybi K, Jiang J, Mutambirwa SBA, Soh PXY, Kote-Jarai Z, Jaratlerdsiri W, Eeles RA, Bornman MSR, Hayes VM. Evaluating Germline Testing Panels in Southern African Males With Advanced Prostate Cancer. J Natl Compr Canc Netw. 2023 Mar;21(3):289-296.e3. doi: 10.6004/jnccn.2022.7097.

Hayes VM, Gong T, Mutambirwa SBA, Jaratlerdsiri W, Bornman MSR. African inclusion in prostate cancer genomic studies provides the first glimpses into addressing health disparities through tailored clinical care. Clin Transl Med. 2022;00:e1142.

Jaratlerdsiri W, Jiang J, Gong T, Patrick SM, Willet C, Chew T, Lyons RJ, Haynes AM, Pasqualim G, Louw M, Kench JG, Campbell R, Horvath LG, Chan EKF, Wedge DC, Sadsad R, Brum IS, Mutambirwa SBA, Stricker PD, Bornman MSR, Hayes VM. African-specific molecular taxonomy of prostate cancer. Nature. 2022 Sep;609(7927):552-559. doi: 10.1038/s41586-022-05154-6.

Gong T, Jaratlerdsiri W, Jiang J, Willet C, Chew T, Patrick SM, Lyons RJ, Haynes AM, Pasqualim G, Brum IS, Stricker PD, Mutambirwa SBA, Sadsad R, Papenfuss AT, Bornman RMS, Chan EKF, Hayes VM. Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers. Genome Med. 2022 Aug 31;14(1):100. doi: 10.1186/s13073-022-01096-w.

Burns D, Anokian E, Saunders EJ, Bristow RG, Fraser M, Reimand J, Schlomm T, Sauter G, Brors B, Korbel J, Weischenfeldt J, Waszak SM, Corcoran NM, Jung CH, Pope BJ, Hovens CM, Cancel-Tassin G, Cussenot O, Loda M, Sander C, Hayes VM, Dalsgaard Sorensen K, Lu YJ, Hamdy FC, Foster CS, Gnanapragasam V, Butler A, Lynch AG, Massie CE; CR-UK/Prostate Cancer UK, ICGC, The PPCG, Woodcock DJ, Cooper CS, Wedge DC, Brewer DS, Kote-Jarai Z, Eeles RA. Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study. Eur Urol. 2022 Aug;82(2):201-211. doi: 10.1016/j.eururo.2022.05.007.

Gong T, Hayes VM, Chan EKF. Detection of somatic structural variants from short-read next-generation sequencing data. Brief Bioinform. 2021 May 20;22(3):bbaa056. doi: 10.1093/bib/bbaa056.

Goncearenco A, LaBarre BA, Petrykowska HM, Jaratlerdsiri W, Bornman MSR, Turner SD, Hayes VM, Elnitski L. DNA methylation profiles unique to Kalahari KhoeSan individuals. Epigenetics. 2021 May;16(5):537-553. doi: 10.1080/15592294.2020.1809852.

Gong T, Hayes VM, Chan EKF. Shiny-SoSV: A web-based performance calculator for somatic structural variant detection. PLoS One. 2020 Aug 27;15(8):e0238108. doi: 10.1371/journal.pone.0238108.

Crumbaker M, Chan EKF, Gong T, Corcoran N, Jaratlerdsiri W, Lyons RJ, Haynes AM, Kulidjian AA, Kalsbeek AMF, Petersen DC, Stricker PD, Jamieson CAM, Croucher PI, Hovens CM, Joshua AM, Hayes VM. The Impact of Whole Genome Data on Therapeutic Decision-Making in Metastatic Prostate Cancer: A Retrospective Analysis. Cancers (Basel). 2020 May 7;12(5):1178. doi: 10.3390/cancers12051178.

Heyer EE, Deveson IW, Wooi D, Selinger CI, Lyons RJ, Hayes VM, O'Toole SA, Ballinger ML, Gill D, Thomas DM, Mercer TR, Blackburn J. Diagnosis of fusion genes using targeted RNA sequencing. Nat Commun. 2019 Mar 27;10(1):1388. doi: 10.1038/s41467-019-09374-9. Erratum in: Nat Commun. 2020 Apr 8;11(1):1810.

Petersen DC, Jaratlerdsiri W, van Wyk A, Chan EKF, Fernandez P, Lyons RJ, Mutambirw SBA, van der Merwe A, Venter PA, Bates W, Bornman MSR, Hayes VM. African KhoeSan ancestry linked to high-risk prostate cancer. BMC Med Genomics. 2019 Jun 4;12(1):82. doi: 10.1186/s12920-019-0537-0.

LaBarre BA, Goncearenco A, Petrykowska HM, Jaratlerdsiri W, Bornman MSR, Hayes VM, Elnitski L. MethylToSNP: identifying SNPs in Illumina DNA methylation array data. Epigenetics Chromatin. 2019 Dec 20;12(1):79. doi: 10.1186/s13072-019-0321-6.

Chan EKF, Timmermann A, Baldi BF, Moore AE, Lyons RJ, Lee SS, Kalsbeek AMF, Petersen DC, Rautenbach H, Förtsch HEA, Bornman MSR, Hayes VM. Human origins in a southern African palaeo-wetland and first migrations. Nature. 2019 Nov;575(7781):185-189. doi: 10.1038/s41586-019-1714-1. Erratum in: Nature. 2021 Apr;592(7852):E7.

Blackburn J, Vecchiarelli S, Heyer EE, Patrick SM, Lyons RJ, Jaratlerdsiri W, van Zyl S, Bornman MSR, Mercer TR, Hayes VM. TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: A focus on Africa. Prostate. 2019 Jul;79(10):1191-1196. doi: 10.1002/pros.23823.

Feng Y, Jaratlerdsiri W, Patrick SM, Lyons RJ, Haynes AM, Collins CC, Stricker PD, Bornman MSR, Hayes VM. Metagenomic analysis reveals a rich bacterial content in high-risk prostate tumors from African men. Prostate. 2019 Nov;79(15):1731-1738. doi: 10.1002/pros.23897.

Feng Y, Ramnarine VR, Bell R, Volik S, Davicioni E, Hayes VM, Ren S, Collins CC. Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer. BMC Genomics. 2019 Feb 18;20(1):146. doi: 10.1186/s12864-019-5457-z.

Hayes VM, Jaratlerdsiri W, Bornman MSR. Prostate cancer genomics and racial health disparity. Oncotarget. 2018 Nov 30;9(94):36650-36651. doi: 10.18632/oncotarget.26399.

Kalsbeek AMF, Chan EKF, Grogan J, Petersen DC, Jaratlerdsiri W, Gupta R, Lyons RJ, Haynes AM, Horvath LG, Kench JG, Stricker PD, Hayes VM. Altered mitochondrial genome content signals worse pathology and prognosis in prostate cancer. Prostate. 2018 Jan;78(1):25-31. doi: 10.1002/pros.23440.

Chan EKF, Cameron DL, Petersen DC, Lyons RJ, Baldi BF, Papenfuss AT, Thomas DM, Hayes VM. Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer. Genome Res. 2018 May;28(5):726-738. doi: 10.1101/gr.227975.117.

Hayes VM, Bornman MSR. Prostate Cancer in Southern Africa: Does Africa Hold Untapped Potential to Add Value to the Current Understanding of a Common Disease? J Glob Oncol. 2018 Sep;4:1-7. doi: 10.1200/JGO.2016.008862.

Jaratlerdsiri W, Chan EKF, Gong T, Petersen DC, Kalsbeek AMF, Venter PA, Stricker PD, Bornman MSR, Hayes VM. Whole-Genome Sequencing Reveals Elevated Tumor Mutational Burden and Initiating Driver Mutations in African Men with Treatment-Naïve, High-Risk Prostate Cancer. Cancer Res. 2018 Dec 15;78(24):6736-6746. doi: 10.1158/0008-5472.CAN-18-0254.

Skoglund P, Thompson JC, Prendergast ME, Mittnik A, Sirak K, Hajdinjak M, Salie T, Rohland N, Mallick S, Peltzer A, Heinze A, Olalde I, Ferry M, Harney E, Michel M, Stewardson K, Cerezo-Román JI, Chiumia C, Crowther A, Gomani-Chindebvu E, Gidna AO, Grillo KM, Helenius IT, Hellenthal G, Helm R, Horton M, López S, Mabulla AZP, Parkington J, Shipton C, Thomas MG, Tibesasa R, Welling M, Hayes VM, Kennett DJ, Ramesar R, Meyer M, Pääbo S, Patterson N, Morris AG, Boivin N, Pinhasi R, Krause J, Reich D. Reconstructing Prehistoric African Population Structure. Cell. 2017 Sep 21;171(1):59-71.e21. doi: 10.1016/j.cell.2017.08.049.

Kalsbeek AMF, Chan EKF, Corcoran NM, Hovens CM, Hayes VM. Mitochondrial genome variation and prostate cancer: a review of the mutational landscape and application to clinical management. Oncotarget. 2017 Aug 4;8(41):71342-71357. doi: 10.18632/oncotarget.19926.

Kalsbeek AMF, Chan EKF, Grogan J, Petersen DC, Jaratlerdsiri W, Gupta R, Lyons RJ, Haynes AM, Horvath LG, Kench JG, Stricker PD, Hayes VM. Altered mitochondrial genome content signals worse pathology and prognosis in prostate cancer. Prostate. 2018 Jan;78(1):25-31. doi: 10.1002/pros.23440.

Jaratlerdsiri W, Chan EKF, Petersen DC, Yang C, Croucher PI, Bornman MSR, Sheth P, Hayes VM. Next generation mapping reveals novel large genomic rearrangements in prostate cancer. Oncotarget. 2017 Apr 4;8(14):23588-23602. doi: 10.18632/oncotarget.15802.

McCrow JP, Petersen DC, Louw M, Chan EK, Harmeyer K, Vecchiarelli S, Lyons RJ, Bornman MS, Hayes VM. Spectrum of mitochondrial genomic variation and associated clinical presentation of prostate cancer in South African men. Prostate. 2016 Mar;76(4):349-58. doi: 10.1002/pros.23126.

Kalsbeek AM, Chan EF, Grogan J, Petersen DC, Jaratlerdsiri W, Gupta R, Lyons RJ, Haynes AM, Horvath LG, Kench JG, Stricker PD, Hayes VM. Mutational load of the mitochondrial genome predicts pathological features and biochemical recurrence in prostate cancer. Aging (Albany NY). 2016 Oct 5;8(11):2702-2712. doi: 10.18632/aging.101044.

Stuchbery R, Kurganovs NJ, McCoy PJ, Nelson CC, Hayes VM, Corcoran NM, Hovens CM. Target Acquired: Progress and Promise of Targeted Therapeutics in the Treatment of Prostate Cancer. Curr Cancer Drug Targets. 2015;15(5):394-405. doi: 10.2174/1568009615666150416113453.

Chan EK, Hardie RA, Petersen DC, Beeson K, Bornman RM, Smith AB, Hayes VM. Revised timeline and distribution of the earliest diverged human maternal lineages in southern Africa. PLoS One. 2015 Mar 25;10(3):e0121223. doi: 10.1371/journal.pone.0121223.

Pang AW, Macdonald JR, Yuen RK, Hayes VM, Scherer SW. Performance of high-throughput sequencing for the discovery of genetic variation across the complete size spectrum. G3 (Bethesda). 2014 Jan 10;4(1):63-5. doi: 10.1534/g3.113.008797.

Tindall EA, Monare LR, Petersen DC, van Zyl S, Hardie RA, Segone AM, Venter PA, Bornman MS, Hayes VM. Clinical presentation of prostate cancer in black South Africans. Prostate. 2014 Jun;74(8):880-91. doi: 10.1002/pros.22806.

Morris AG, Heinze A, Chan EK, Smith AB, Hayes VM. First ancient mitochondrial human genome from a prepastoralist southern African. Genome Biol Evol. 2014 Sep 10;6(10):2647-53. doi: 10.1093/gbe/evu202.

Petersen DC, Libiger O, Tindall EA, Hardie RA, Hannick LI, Glashoff RH, Mukerji M; Indian Genome Variation Consortium, Fernandez P, Haacke W, Schork NJ, Hayes VM. Complex patterns of genomic admixture within southern Africa. PLoS Genet. 2013;9(3):e1003309. doi: 10.1371/journal.pgen.1003309.

Tindall EA, Bornman MS, van Zyl S, Segone AM, Monare LR, Venter PA, Hayes VM. 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 Urol. 2013 Dec 29;13:74. doi: 10.1186/1471-2490-13-74.

Saunders DN, Tindall EA, Shearer RF, Roberson J, Decker A, Wilson JA, Hayes VM. A novel SERPINA1 mutation causing serum alpha(1)-antitrypsin deficiency. PLoS One. 2012;7(12):e51762. doi: 10.1371/journal.pone.0051762.

Tindall EA, Severi G, Hoang HN, Southey MC, English DR, Hopper JL, Giles GG, Hayes VM; Australian Prostate Cancer BioResource. Interleukin-6 promoter variants, prostate cancer risk, and survival. Prostate. 2012 Dec 1;72(16):1701-7. doi: 10.1002/pros.22557.

Hayes VM, Venter PA, Mphahlele MJ. Helping hand for genomics in Africa. Nature. 2011 Aug 10;476(7359):152. doi: 10.1038/476152c.

Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J, Walenz B, Knight J, Qi J, Zhao F, Wang Q, Bedoya-Reina OC, Katiyar N, Tomsho LP, Kasson LM, Hardie RA, Woodbridge P, Tindall EA, Bertelsen MF, Dixon D, Pyecroft S, Helgen KM, Lesk AM, Pringle TH, Patterson N, Zhang Y, Kreiss A, Woods GM, Jones ME, Schuster SC. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12348-53. doi: 10.1073/pnas.1102838108.

Hayes V. Indigenous genomics. Science. 2011 May 6;332(6030):639. doi: 10.1126/science.1205999.

Tindall EA, Hayes VM, Petersen DC. Inflammatory genetic markers of prostate cancer risk. Cancers (Basel). 2010 Jun 8;2(2):1198-220. doi: 10.3390/cancers2021198.

Tindall EA, Hoang HN, Southey MC, English DR, Hopper JL, Giles GG, Severi G, Hayes VM. The 4q27 locus and prostate cancer risk. BMC Cancer. 2010 Feb 25;10:69. doi: 10.1186/1471-2407-10-69.

Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM. Complete Khoisan and Bantu genomes from southern Africa. Nature. 2010 Feb 18;463(7283):943-7. doi: 10.1038/nature08795.

Miller W, Wright SJ, Zhang Y, Schuster SC, Hayes VM. Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species. Pac Symp Biocomput. 2010:43-53. doi: 10.1142/9789814295291_0006.

Patterson N, Petersen DC, van der Ross RE, Sudoyo H, Glashoff RH, Marzuki S, Reich D, Hayes VM. Genetic structure of a unique admixed population: implications for medical research. Hum Mol Genet. 2010 Feb 1;19(3):411-9. doi: 10.1093/hmg/ddp505.

Tindall EA, Hayes VM. Comprehensive sequence analysis of the human IL23A gene defines new variation content and high rate of evolutionary conservation. DNA Res. 2010 Apr;17(2):117-22. doi: 10.1093/dnares/dsq003.

Tindall EA, Severi G, Hoang HN, Ma CS, Fernandez P, Southey MC, English DR, Hopper JL, Heyns CF, Tangye SG, Giles GG, Hayes VM; Australian Prostate Cancer BioResource. Comprehensive analysis of the cytokine-rich chromosome 5q31.1 region suggests a role for IL-4 gene variants in prostate cancer risk. Carcinogenesis. 2010 Oct;31(10):1748-54. doi: 10.1093/carcin/bgq081.