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6. African-specific molecular taxonomy of prostate cancer

Author

Jaratlerdsiri, Weerachai, Jiang, Jue, Gong, Tingting, Patrick, Sean M., Willet, Cali, Chew, Tracy, Lyons, Ruth J., Haynes, Anne-Maree, Pasqualim, Gabriela, Louw, Melanie, Kench, James G., Campbell, Raymond, Horvath, Lisa G., Chan, Eva K. F., Wedge, David C., Sadsad, Rosemarie, Brum, Ilma Simoni, Mutambirwa, Shingai B. A., Stricker, Phillip D., Bornman, M. S. Riana, and Hayes, Vanessa M.

Published
2022
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8. Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study

Author

Burns, Daniel, Anokian, Ezequiel, Saunders, Edward J., Bristow, Robert G., Fraser, Michael, Reimand, Jüri, Schlomm, Thorsten, Sauter, Guido, Brors, Benedikt, Korbel, Jan, Weischenfeldt, Joachim, Waszak, Sebastian M., Corcoran, Niall M., Jung, Chol-Hee, Pope, Bernard J., Hovens, Chris M., Cancel-Tassin, Géraldine, Cussenot, Olivier, Loda, Massimo, Sander, Chris, Hayes, Vanessa M., Dalsgaard Sorensen, Karina, Lu, Yong-Jie, Hamdy, Freddie C., Foster, Christopher S., Gnanapragasam, Vincent, Butler, Adam, Lynch, Andy G., Massie, Charlie E., Woodcock, Dan J., Cooper, Colin S., Wedge, David C., Brewer, Daniel S., Kote-Jarai, Zsofia, and Eeles, Rosalind A.

Published
2022
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10. An Inversion Affecting the GCH1 Gene as a Novel Finding in Dopa‐Responsive Dystonia

Author

El‐Wahsh, Shadi, primary, Fellner, Avi, additional, Hobbs, Matthew, additional, Copty, Joe, additional, Deveson, Ira, additional, Stevanovski, Igor, additional, Stoll, Marion, additional, Zhu, Danqing, additional, Narayanan, Ramesh K., additional, Grosz, Bianca, additional, Worgan, Lisa, additional, Cheong, Pak Leng, additional, Yeow, Dennis, additional, Rudaks, Laura, additional, Hasan, Md Mehedi, additional, Hayes, Vanessa M., additional, Kennerson, Marina, additional, Kumar, Kishore R., additional, and Hayes, Michael, additional

Published
2024
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13. Linking African ancestral substructure to prostate cancer health disparities

Author

Gheybi, Kazzem, primary, Mmekwa, Naledi, additional, Lebelo, Maphuti Tebogo, additional, Patrick, Sean M., additional, Campbell, Raymond, additional, Nenzhelele, Mukudeni, additional, Soh, Pamela X. Y., additional, Obida, Muvhulawa, additional, Loda, Massimo, additional, Shirindi, Joyce, additional, Butler, Eboneé N., additional, Mutambirwa, Shingai B.A., additional, Bornman, M. S. Riana, additional, and Hayes, Vanessa M., additional

Published
2023
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18. Data from Cyclin D1 Splice Variants: Polymorphism, Risk, and Isoform-Specific Regulation in Prostate Cancer

Author

Comstock, Clay E.S., primary, Augello, Michael A., primary, Benito, Ruth Pe, primary, Karch, Jason, primary, Tran, Thai H., primary, Utama, Fransiscus E., primary, Tindall, Elizabeth A., primary, Wang, Ying, primary, Burd, Craig J., primary, Groh, Eric M., primary, Hoang, Hoa N., primary, Giles, Graham G., primary, Severi, Gianluca, primary, Hayes, Vanessa M., primary, Henderson, Brian E., primary, Le Marchand, Loic, primary, Kolonel, Laurence N., primary, Haiman, Christopher A., primary, Baffa, Raffaele, primary, Gomella, Leonard G., primary, Knudsen, Erik S., primary, Rui, Hallgeir, primary, Henshall, Susan M., primary, Sutherland, Robert L., primary, and Knudsen, Karen E., primary

Published
2023
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20. Supplementary Tables (Excel) from Whole-Genome Sequencing Reveals Elevated Tumor Mutational Burden and Initiating Driver Mutations in African Men with Treatment-Naïve, High-Risk Prostate Cancer

Author

Jaratlerdsiri, Weerachai, primary, Chan, Eva K.F., primary, Gong, Tingting, primary, Petersen, Desiree C., primary, Kalsbeek, Anton M.F., primary, Venter, Philip A., primary, Stricker, Phillip D., primary, Bornman, M.S. Riana, primary, and Hayes, Vanessa M., primary

Published
2023
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21. Supplementary Data from Cyclin D1 Splice Variants: Polymorphism, Risk, and Isoform-Specific Regulation in Prostate Cancer

Author

Comstock, Clay E.S., primary, Augello, Michael A., primary, Benito, Ruth Pe, primary, Karch, Jason, primary, Tran, Thai H., primary, Utama, Fransiscus E., primary, Tindall, Elizabeth A., primary, Wang, Ying, primary, Burd, Craig J., primary, Groh, Eric M., primary, Hoang, Hoa N., primary, Giles, Graham G., primary, Severi, Gianluca, primary, Hayes, Vanessa M., primary, Henderson, Brian E., primary, Le Marchand, Loic, primary, Kolonel, Laurence N., primary, Haiman, Christopher A., primary, Baffa, Raffaele, primary, Gomella, Leonard G., primary, Knudsen, Erik S., primary, Rui, Hallgeir, primary, Henshall, Susan M., primary, Sutherland, Robert L., primary, and Knudsen, Karen E., primary

Published
2023
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22. Supplementary Tables (word) from Whole-Genome Sequencing Reveals Elevated Tumor Mutational Burden and Initiating Driver Mutations in African Men with Treatment-Naïve, High-Risk Prostate Cancer

Author

Jaratlerdsiri, Weerachai, primary, Chan, Eva K.F., primary, Gong, Tingting, primary, Petersen, Desiree C., primary, Kalsbeek, Anton M.F., primary, Venter, Philip A., primary, Stricker, Phillip D., primary, Bornman, M.S. Riana, primary, and Hayes, Vanessa M., primary

Published
2023
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23. Supplementary Figures from Whole-Genome Sequencing Reveals Elevated Tumor Mutational Burden and Initiating Driver Mutations in African Men with Treatment-Naïve, High-Risk Prostate Cancer

Author

Jaratlerdsiri, Weerachai, primary, Chan, Eva K.F., primary, Gong, Tingting, primary, Petersen, Desiree C., primary, Kalsbeek, Anton M.F., primary, Venter, Philip A., primary, Stricker, Phillip D., primary, Bornman, M.S. Riana, primary, and Hayes, Vanessa M., primary

Published
2023
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32. Germline determinants of the prostate tumor genome

Author

Houlahan, Kathleen E., primary, Yuan, Jiapei, additional, Schwarz, Tommer, additional, Livingstone, Julie, additional, Fox, Natalie S., additional, Jaratlerdsiri, Weerachai, additional, van Riet, Job, additional, Taraszka, Kodi, additional, Kurganovs, Natalie, additional, Zhu, Helen, additional, Sietsma Penington, Jocelyn, additional, Jung, Chol-Hee, additional, Yamaguchi, Takafumi N, additional, Jiang, Jue, additional, Heisler, Lawrence E, additional, Jovelin, Richard, additional, Ramanand, Susmita G, additional, Bell, Connor, additional, O’Connor, Edward, additional, Mutambirwa, Shingai B.A., additional, Seo, Ji-Heui, additional, Costello, Anthony J., additional, Pomerantz, Mark M., additional, Pope, Bernard J., additional, Zaitlen, Noah, additional, Kishan, Amar U., additional, Corcoran, Niall M., additional, Bristow, Robert G., additional, Waszak, Sebastian M., additional, Bornman, Riana M.S., additional, Gusev, Alexander, additional, Lolkema, Martijn P., additional, Weischenfeldt, Joachim, additional, Hung, Rayjean J., additional, He, Housheng H., additional, Hayes, Vanessa M., additional, Pasaniuc, Bogdan, additional, Freedman, Matthew L., additional, Hovens, Christopher M., additional, Mani, Ram S., additional, and Boutros, Paul C., additional

Published
2022
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33. Rare germline variants are associated with rapid biochemical recurrence after radical prostate cancer treatment : a PPCG study

Author

Burns, Daniel, Anokiana, Ezequiel, Saunders, Edward J, Bristow, Robert G, Fraser, Michael, Reimand, Jüri, Schlomm, Thorsten, Sauter, Guido, Brors, Benedikt, Korbeli, Jan, Weischenfeldt, Joachim, Waszak, Sebastian M, Corcoran, Niall M, Jung, Chol-Hee, Pope, Bernard J, Hovens, Chris M, Cancel-Tassin, Géraldine, Cussenot, Olivier, Loda, Massimo, Sander, Chris, Hayes, Vanessa M, Sorensen, Karina Dalsgaard, Lu, Yong-Jie, Hamdy, Freddie C, Foster, Christopher S, Gnanapragasam, Vincent, Butler, Adam, Lynch, Andy, Massie, Charlie E, CR-UK/Prostate Cancer UK, ICGC, The PPCG, Woodcock, Dan J, Cooper, Colin S, Wedge, David C, Brewer, Daniel S, Kote-Jarai, Zsofia, Eeles, Rosalind, University of St Andrews. School of Medicine, University of St Andrews. Statistics, University of St Andrews. Sir James Mackenzie Institute for Early Diagnosis, University of St Andrews. St Andrews Bioinformatics Unit, and University of St Andrews. Cellular Medicine Division

Subjects
MCC, RC0254, Prostate cancer, Pan Prostate Cancer Group, SDG 3 - Good Health and Well-being, RC0254 Neoplasms. Tumors. Oncology (including Cancer), Germline variants, QH426 Genetics, 3rd-DAS, QH426, Biochemical recurrence
Abstract

Funding: We acknowledge support from Cancer Research UK C5047/A14835/A22530/ A17528, C309/A11566, C368/A6743, A368/A7990, C14303/A17197 (Z.K.-J., S. Merson, N.C., S.E., D.L., T. Dadaev, M.A., E.B., J.B., G.A., P.W., B.A.-L., D.S.B., C.S.C., R.A.E.), the Dallaglio Foundation (CR-UK Prostate Cancer ICGC Project and Pan Prostate Cancer Group), PC-UK/Movember (Z.K.-J.), the NIHR support to The Biomedical Research Centre at The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust (Z.K.-J., N.D., S. Merson, N.C., S.E., D.L., T. Dadaev, S. Thomas, M.A., E.B., C.F., N.L., D.N., V.K., N.A., P.K., C.O., D.C., A.T., E.M., E.R., T. Dudderidge, S. Hazell, J.B., G.A., P.W., B.A.-L., D.S.B., C.S.C., R.A.E.), Cancer Research UK funding to The Institute of Cancer Research and the Royal Marsden NHS Foundation Trust CRUK Centre, the National Cancer Research Institute (National Institute of Health Research (NIHR) Collaborative Study: “Prostate Cancer: Mechanisms of Progression and Treatment (PROMPT)” (grant G0500966/75466) (D.E.N., V.G.), the Li Ka Shing Foundation (D.C.W., D.J.W.), Canadian Institutes of Health Research (CIHR) Project Grant (J.R.), and the Academy of Finland and Cancer Society of Finland (G.S.B.). D.M.B. is supported by Orchid. C.V.’s academic time was supported by the NIHR Oxford Biomedical Research Centre (Molecular Diagnostics Theme/Multimodal Pathology sub-theme). We also acknowledge support from the Bob Champion Cancer Trust, The Masonic Charitable Foundation successor to The Grand Charity, The King Family and the Stephen Hargrave Trust (C.S.C., D.S.B.). P.W. is a Cancer Research Life Fellow. We acknowledge core facilities provided by CRUK funding to the CRUK ICR Centre, the CRUK Cancer Therapeutics Unit and support for canSAR C35696/A23187 (P.W., G.A.). We would like to acknowledge The D. J Fielding Medical Research Trust for its support. Background: Germline variants explain more than a third of prostate cancer (PrCa) risk, but very few associations have been identified between heritable factors and clinical progression. Objective: To find rare germline variants that predict time to biochemical recurrence (BCR) after radical treatment in men with PrCa and understand the genetic factors associated with such progression. Design, setting, and participants: Whole-genome sequencing data from blood DNA were analysed for 850 PrCa patients with radical treatment from the Pan Prostate Cancer Group (PPCG) consortium from the UK, Canada, Germany, Australia, and France. Findings were validated using 383 patients from The Cancer Genome Atlas (TCGA) dataset. Outcome measurements and statistical analysis: A total of 15,822 rare (MAF

Published
2022

37. Additional file 1 of Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers

Author

Gong, Tingting, Jaratlerdsiri, Weerachai, Jiang, Jue, Willet, Cali, Chew, Tracy, Patrick, Sean M., Lyons, Ruth J., Haynes, Anne-Maree, Pasqualim, Gabriela, Brum, Ilma Simoni, Stricker, Phillip D., Mutambirwa, Shingai B. A., Sadsad, Rosemarie, Papenfuss, Anthony T., Bornman, Riana M. S., Chan, Eva K. F., and Hayes, Vanessa M.

Abstract

Additional file 1: Figure S1. Concordant SV call generation from Manta and GRIDSS. Figure S2. Summary of SVs in each type, compared to other studies. Figure S3. CIRCOS plot of hyper-SV mutated tumours. Figure S4. The spread of SV breakpoints and samples in each 1 Mbp genomic bin. Figure S5. TMPRSS2-ERG fusion with interstitial region retention. Table S1. Clinical and pathological characteristics of 180 prostate cancer patients included in this study. Table S2. Biallelic assessment of CDK12 in hyper-duplicated samples. Table S3. Biallelic assessment of BRCA2 in hyper-deleted samples.

Published
2022
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38. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

Author

Miller, Webb, Hayes, Vanessa M., Ratan, Aakrosh, Petersen, Desiree C., Wittekindt, Nicola E., Miller, Jason, Walenz, Brian, Knight, James, Qi, Ji, Zhao, Fangqing, Wang, Qingyu, Bedoya-Reina, Oscar C., Katiyar, Neerja, Tomsho, Lynn P., Kasson, Lindsay McClellan, Hardie, Rae-Anne, Woodbridge, Paula, Tindall, Elizabeth A., Bertelsen, Mads Frost, Dixon, Dale, Pyecroft, Stephen, Helgen, Kristofer M., Lesk, Arthur M., Pringle, Thomas H., Patterson, Nick, Zhang, Yu, Kreiss, Alexandre, Woods, Gregory M., Jones, Menna E., and Schuster, Stephan C.

Published
2011

41. ANO7African-ancestral genomic diversity and advanced prostate cancer

Author

Jiang, Jue, Soh, Pamela X. Y., Mutambirwa, Shingai B. A., Bornman, M. S. Riana, Haiman, Christopher A., Hayes, Vanessa M., and Jaratlerdsiri, Weerachai

Abstract

Background: Prostate cancer (PCa) is a significant health burden for African men, with mortality rates more than double global averages. The prostate specific Anoctamin 7 (ANO7) gene linked with poor patient outcomes has recently been identified as the target for an African-specific protein-truncating PCa-risk allele. Methods: Here we determined the role of ANO7in a study of 889 men from southern Africa, leveraging exomic genotyping array PCa case-control data (n= 780, 17 ANO7alleles) and deep sequenced whole genome data for germline and tumour ANO7interrogation (n= 109), while providing clinicopathologically matched European-derived sequence data comparative analyses (n= 57). Associated predicted deleterious variants (PDVs) were further assessed for impact using computational protein structure analysis. Results: Notably rare in European patients, we found the common African PDV p.Ile740Leu (rs74804606) to be associated with PCa risk in our case-control analysis (Wilcoxon rank-sum test, false discovery rate/FDR = 0.03), while sequencing revealed co-occurrence with the recently reported African-specific deleterious risk variant p.Ser914* (rs60985508). Additional findings included a novel protein-truncating African-specific frameshift variant p.Asp789Leu, African-relevant PDVs associated with altered protein structure at Ca2+binding sites, early-onset PCa associated with PDVs and germline structural variants in Africans (Linear regression models, −6.42 years, 95% CI = −10.68 to −2.16, P-value = 0.003) and ANO7as an inter-chromosomal PCa-related gene fusion partner in African derived tumours. Conclusions: Here we provide not only validation for ANO7as an African-relevant protein-altering PCa-risk locus, but additional evidence for a role of inherited and acquired ANO7variance in the observed phenotypic heterogeneity and African-ancestral health disparity.

Published
2023
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45. Risk for HIV-1 infection associated with a common CXCL 12 (SDF1) polymorphism and CXCR4 variation in an African population

Author

Petersen, Desiree C., Glashoff, Richard H., Shrestha, Sadeep, Bergeron, Julie, Laten, Annette, Gold, Bert, van Rensburg, Estrelita Janse, Dean, Michael, and Hayes, Vanessa M.

Subjects
Genetic polymorphisms -- Research, Gene mutations -- Research, Africans -- Genetic aspects, Genetic research, Health
Abstract

A study was conducted on African people to analyze the stromal cell derived factor 1 (SDF1)-3'A single nucleotide polymorphism (SNP) and performed mutation screening for polymorphic markers in the chemokine receptor 4 (CXCR4) gene to determine existence of significant associations with susceptibility to HIV-1 infection. Comprehensive mutation analysis of the CXCR4 gene confirmed a high degree of genetic conservation within the coding region of African ancient populations.

Published
2005

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