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El‐Wahsh S, Fellner A, Hobbs M, Copty J, Deveson I, Stevanovski I, Stoll M, Zhu D, Narayanan RK, Grosz B, Worgan L, Cheong PL, Yeow D, Rudaks L, Hasan MM, Hayes VM, Kennerson M, Kumar KR, Hayes M. An Inversion Affecting the GCH1 Gene as a Novel Finding in Dopa-Responsive Dystonia. Mov Disord Clin Pract 2024; 11:582-585. [PMID: 38497520 PMCID: PMC11078477 DOI: 10.1002/mdc3.14023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/23/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Affiliation(s)
- Shadi El‐Wahsh
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
| | - Avi Fellner
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
- The Neurogenetics Clinic, Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson HospitalPetah TikvaIsrael
| | - Matthew Hobbs
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Joe Copty
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Ira Deveson
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Igor Stevanovski
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Marion Stoll
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
| | - Danqing Zhu
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
| | - Ramesh K. Narayanan
- Northcott Neuroscience LaboratoryANZAC Research Institute—Sydney Local Health DistrictConcordNew South WalesAustralia
| | - Bianca Grosz
- Northcott Neuroscience LaboratoryANZAC Research Institute—Sydney Local Health DistrictConcordNew South WalesAustralia
| | - Lisa Worgan
- Clinical Genetics ServiceRoyal Prince Alfred HospitalSydneyNew South WalesAustralia
- Department of Medical GenomicsRoyal Prince Alfred HospitalSydneyNew South WalesAustralia
| | - Pak Leng Cheong
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Concord Clinical School, Sydney Medical School, Faculty of Health and MedicineUniversity of SydneySydneyNew South WalesAustralia
- Royal Prince Alfred Hospital, New South Wales Health PathologySydneyNew South WalesAustralia
- Institute of Precision Medicine and Bioinformatics, Sydney Local Health DistrictSydneyNew South WalesAustralia
| | - Dennis Yeow
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Concord Clinical School, Sydney Medical School, Faculty of Health and MedicineUniversity of SydneySydneyNew South WalesAustralia
- Neuroscience Research AustraliaSydneyNew South WalesAustralia
| | - Laura Rudaks
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Concord Clinical School, Sydney Medical School, Faculty of Health and MedicineUniversity of SydneySydneyNew South WalesAustralia
| | - Md Mehedi Hasan
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and HealthUniversity of SydneySydneyNew South WalesAustralia
| | - Vanessa M. Hayes
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and HealthUniversity of SydneySydneyNew South WalesAustralia
- School of Health Systems & Public HealthUniversity of PretoriaPretoriaSouth Africa
- Manchester Cancer Research CentreUniversity of ManchesterManchesterUK
| | - Marina Kennerson
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Northcott Neuroscience LaboratoryANZAC Research Institute—Sydney Local Health DistrictConcordNew South WalesAustralia
- Institute of Precision Medicine and Bioinformatics, Sydney Local Health DistrictSydneyNew South WalesAustralia
| | - Kishore R. Kumar
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Concord Clinical School, Sydney Medical School, Faculty of Health and MedicineUniversity of SydneySydneyNew South WalesAustralia
- Institute of Precision Medicine and Bioinformatics, Sydney Local Health DistrictSydneyNew South WalesAustralia
| | - Michael Hayes
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
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Huang R, Bornman MSR, Stricker PD, Simoni Brum I, Mutambirwa SBA, Jaratlerdsiri W, Hayes VM. The impact of telomere length on prostate cancer aggressiveness, genomic instability and health disparities. Sci Rep 2024; 14:7706. [PMID: 38565642 PMCID: PMC10987561 DOI: 10.1038/s41598-024-57566-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
The telomere repetitive TTAGGG motif at the ends of chromosomes, serves to preserve genomic integrity and chromosomal stability. In turn, genomic instability is a hallmark of cancer-implicating telomere disturbance. Prostate cancer (PCa) shows significant ancestral disparities, with men of African ancestry at the greatest risk for aggressive disease and associated genomic instability. Yet, no study has explored the role of telomere length (TL) with respect to ancestrally driven PCa health disparities. Patient- and technically-matched tumour-blood whole genome sequencing data for 179 ancestrally defined treatment naïve PCa patients (117 African, 62 European), we assessed for TL (blood and tumour) associations. We found shortened tumour TL to be associated with aggressive PCa presentation and elevated genomic instabilities, including percentage of genome alteration and copy number gains, in men of African ancestry. For European patients, tumour TL showed significant associations with PCa driver genes PTEN, TP53, MSH2, SETBP1 and DDX11L1, while shorter blood TL (< 3200 base pairs) and tumour TL (< 2861 base pairs) were correlated with higher risk for biochemical recurrence. Concurring with previous studies linking TL to PCa diagnosis and/or prognosis, for the first time we correlated TL differences with patient ancestry with important implications for future treatments targeting telomere dysfunction.
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Affiliation(s)
- Ruotian Huang
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - M S Riana Bornman
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, 0084, South Africa
| | - Phillip D Stricker
- Department of Urology, St Vincent's Hospital, Darlinghurst, NSW, 2010, Australia
| | - Ilma Simoni Brum
- Endocrine and Tumor Molecular Biology Laboratory, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa, 0208, South Africa
| | - Weerachai Jaratlerdsiri
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Vanessa M Hayes
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia.
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, 0084, South Africa.
- Manchester Cancer Research Centre, University of Manchester, Manchester, M20 4GJ, UK.
- Faculty of Health Sciences, University of Limpopo, Turfloop Campus, Sovenga, 0727, Limpopo, South Africa.
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3
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Soh PXY, Mmekwa N, Petersen DC, Gheybi K, van Zyl S, Jiang J, Patrick SM, Campbell R, Jaratlerdseri W, Mutambirwa SBA, Bornman MSR, Hayes VM. Prostate cancer genetic risk and associated aggressive disease in men of African ancestry. Nat Commun 2023; 14:8037. [PMID: 38052806 PMCID: PMC10697980 DOI: 10.1038/s41467-023-43726-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
African ancestry is a significant risk factor for prostate cancer and advanced disease. Yet, genetic studies have largely been conducted outside the context of Sub-Saharan Africa, identifying 278 common risk variants contributing to a multiethnic polygenic risk score, with rare variants focused on a panel of roughly 20 pathogenic genes. Based on this knowledge, we are unable to determine polygenic risk or differentiate prostate cancer status interrogating whole genome data for 113 Black South African men. To further assess for potentially functional common and rare variant associations, here we interrogate 247,780 exomic variants for 798 Black South African men using a case versus control or aggressive versus non-aggressive study design. Notable genes of interest include HCP5, RFX6 and H3C1 for risk, and MKI67 and KLF5 for aggressive disease. Our study highlights the need for further inclusion across the African diaspora to establish African-relevant risk models aimed at reducing prostate cancer health disparities.
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Affiliation(s)
- Pamela X Y Soh
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Naledi Mmekwa
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Desiree C Petersen
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kazzem Gheybi
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Smit van Zyl
- Faculty of Health Sciences, University of Limpopo, Turfloop Campus, South Africa
| | - Jue Jiang
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Sean M Patrick
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | | | - Weerachai Jaratlerdseri
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa, South Africa
| | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Vanessa M Hayes
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia.
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.
- Faculty of Health Sciences, University of Limpopo, Turfloop Campus, South Africa.
- Manchester Cancer Research Centre, University of Manchester, Manchester, M20 4GJ, UK.
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Gheybi K, Mmekwa N, Lebelo MT, Patrick SM, Campbell R, Nenzhelele M, Soh PXY, Obida M, Loda M, Shirindi J, Butler EN, Mutambirwa SBA, Bornman MSR, Hayes VM. Linking African ancestral substructure to prostate cancer health disparities. Sci Rep 2023; 13:20909. [PMID: 38017150 PMCID: PMC10684577 DOI: 10.1038/s41598-023-47993-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/21/2023] [Indexed: 11/30/2023] Open
Abstract
Prostate cancer (PCa) is a significant health burden in Sub-Saharan Africa, with mortality rates loosely linked to African ancestry. Yet studies aimed at identifying contributing risk factors are lacking within the continent and as such exclude for significant ancestral diversity. Here, we investigate a series of epidemiological demographic and lifestyle risk factors for 1387 men recruited as part of the multi-ethnic Southern African Prostate Cancer Study (SAPCS). We found poverty to be a decisive factor for disease grade and age at diagnosis, with other notably significant PCa associated risk factors including sexually transmitted diseases, erectile dysfunction, gynaecomastia, and vertex or complete pattern balding. Aligned with African American data, Black ethnicity showed significant risk for PCa diagnosis (OR = 1.44, 95% CI 1.05-2.00), and aggressive disease presentation (ISUP ≥ 4: OR = 2.25, 95% CI 1.49-3.40). New to this study, we demonstrate African ancestral population substructure associated PCa disparity, observing increased risk for advanced disease for the southern African Tsonga people (ISUP ≥ 4: OR = 3.43, 95% CI 1.62-7.27). Conversely, South African Coloured were less likely to be diagnosed with aggressive disease overall (ISUP ≥ 3: OR = 0.38, 95% 0.17-0.85). Understanding the basis for PCa health disparities calls for African inclusion, however, lack of available data has limited the power to begin discussions. Here, focusing on arguably the largest study of its kind for the African continent, we draw attention to the contribution of within African ancestral diversity as a contributing factor to PCa health disparities within the genetically diverse region of southern Africa.
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Affiliation(s)
- Kazzem Gheybi
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Naledi Mmekwa
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Maphuti Tebogo Lebelo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Sean M Patrick
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | | | | | - Pamela X Y Soh
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Muvhulawa Obida
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weil Cornell Medicine, New York Presbyterian-Weill Cornell Campus, New York, NY, USA
| | - Joyce Shirindi
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Eboneé N Butler
- Department of Epidemiology, University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa, South Africa
| | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Vanessa M Hayes
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia.
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.
- Manchester Cancer Research Centre, University of Manchester, Manchester, M20 4GJ, UK.
- Faculty of Health Sciences, University of Limpopo, Turfloop Campus, Sovenga, Limpopo, South Africa.
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Jiang J, Soh PXY, Mutambirwa SBA, Bornman MSR, Haiman CA, Hayes VM, Jaratlerdsiri W. ANO7 African-ancestral genomic diversity and advanced prostate cancer. Prostate Cancer Prostatic Dis 2023:10.1038/s41391-023-00722-x. [PMID: 37749167 DOI: 10.1038/s41391-023-00722-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/15/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023]
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 ANO7 in a study of 889 men from southern Africa, leveraging exomic genotyping array PCa case-control data (n = 780, 17 ANO7 alleles) and deep sequenced whole genome data for germline and tumour ANO7 interrogation (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 ANO7 as an inter-chromosomal PCa-related gene fusion partner in African derived tumours. CONCLUSIONS Here we provide not only validation for ANO7 as an African-relevant protein-altering PCa-risk locus, but additional evidence for a role of inherited and acquired ANO7 variance in the observed phenotypic heterogeneity and African-ancestral health disparity.
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Affiliation(s)
- Jue Jiang
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
| | - Pamela X Y Soh
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa, South Africa
| | - M S Riana Bornman
- School of Health Systems & Public Health, University of Pretoria, Pretoria, South Africa
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Vanessa M Hayes
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia.
- School of Health Systems & Public Health, University of Pretoria, Pretoria, South Africa.
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK.
| | - Weerachai Jaratlerdsiri
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia.
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Craddock J, Jiang J, Patrick SM, Mutambirwa SBA, Stricker PD, Bornman MSR, Jaratlerdsiri W, Hayes VM. Alterations in the Epigenetic Machinery Associated with Prostate Cancer Health Disparities. Cancers (Basel) 2023; 15:3462. [PMID: 37444571 DOI: 10.3390/cancers15133462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Prostate cancer is driven by acquired genetic alterations, including those impacting the epigenetic machinery. With African ancestry as a significant risk factor for aggressive disease, we hypothesize that dysregulation among the roughly 656 epigenetic genes may contribute to prostate cancer health disparities. Investigating prostate tumor genomic data from 109 men of southern African and 56 men of European Australian ancestry, we found that African-derived tumors present with a longer tail of epigenetic driver gene candidates (72 versus 10). Biased towards African-specific drivers (63 versus 9 shared), many are novel to prostate cancer (18/63), including several putative therapeutic targets (CHD7, DPF3, POLR1B, SETD1B, UBTF, and VPS72). Through clustering of all variant types and copy number alterations, we describe two epigenetic PCa taxonomies capable of differentiating patients by ancestry and predicted clinical outcomes. We identified the top genes in African- and European-derived tumors representing a multifunctional "generic machinery", the alteration of which may be instrumental in epigenetic dysregulation and prostate tumorigenesis. In conclusion, numerous somatic alterations in the epigenetic machinery drive prostate carcinogenesis, but African-derived tumors appear to achieve this state with greater diversity among such alterations. The greater novelty observed in African-derived tumors illustrates the significant clinical benefit to be derived from a much needed African-tailored approach to prostate cancer healthcare aimed at reducing prostate cancer health disparities.
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Affiliation(s)
- Jenna Craddock
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Jue Jiang
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
| | - Sean M Patrick
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa 0208, South Africa
| | - Phillip D Stricker
- Department of Urology, St Vincent's Hospital, Darlinghurst, NSW 2010, Australia
| | - M S Riana Bornman
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Weerachai Jaratlerdsiri
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
| | - Vanessa M Hayes
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
- Manchester Cancer Research Centre, University of Manchester, Manchester M20 4GJ, UK
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Soh PXY, Hayes VM. Common Genetic Variants Associated with Prostate Cancer Risk: The Need for African Inclusion. Eur Urol 2023:S0302-2838(23)02729-X. [PMID: 37100647 DOI: 10.1016/j.eururo.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/01/2023] [Indexed: 04/28/2023]
Affiliation(s)
- Pamela X Y Soh
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Health and Medicine, University of Sydney, Camperdown, Australia
| | - Vanessa M Hayes
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Health and Medicine, University of Sydney, Camperdown, Australia.
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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; 24:112. [PMID: 36959534 PMCID: PMC10037872 DOI: 10.1186/s12859-023-05235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/17/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Using visual, biological, and electronic health records data as the sole input source, pretrained convolutional neural networks and conventional machine learning methods have been heavily employed for the identification of various malignancies. Initially, a series of preprocessing steps and image segmentation steps are performed to extract region of interest features from noisy features. Then, the extracted features are applied to several machine learning and deep learning methods for the detection of cancer. METHODS In this work, a review of all the methods that have been applied to develop machine learning algorithms that detect cancer is provided. With more than 100 types of cancer, this study only examines research on the four most common and prevalent cancers worldwide: lung, breast, prostate, and colorectal cancer. Next, by using state-of-the-art sentence transformers namely: SBERT (2019) and the unsupervised SimCSE (2021), this study proposes a new methodology for detecting cancer. This method requires raw DNA sequences of matched tumor/normal pair as the only input. The learnt DNA representations retrieved from SBERT and SimCSE will then be sent to machine learning algorithms (XGBoost, Random Forest, LightGBM, and CNNs) for classification. As far as we are aware, SBERT and SimCSE transformers have not been applied to represent DNA sequences in cancer detection settings. RESULTS The XGBoost model, which had the highest overall accuracy of 73 ± 0.13 % using SBERT embeddings and 75 ± 0.12 % using SimCSE embeddings, was the best performing classifier. In light of these findings, it can be concluded that incorporating sentence representations from SimCSE's sentence transformer only marginally improved the performance of machine learning models.
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Affiliation(s)
- Mpho Mokoatle
- Department of Computer Science, University of Pretoria, Pretoria, South Africa.
| | - Vukosi Marivate
- Department of Computer Science, University of Pretoria, Pretoria, South Africa
| | | | - Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Vanessa M Hayes
- School of Medical Sciences, The University of Sydney, Sydney, Australia
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
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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; 21:289-296.e3. [PMID: 36898365 DOI: 10.6004/jnccn.2022.7097] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 11/07/2022] [Indexed: 03/12/2023]
Abstract
BACKGROUND Germline testing for prostate cancer is on the increase, with clinical implications for risk assessment, treatment, and management. Regardless of family history, NCCN recommends germline testing for patients with metastatic, regional, very-high-risk localized, and high-risk localized prostate cancer. Although African ancestry is a significant risk factor for aggressive prostate cancer, due to a lack of available data no testing criteria have been established for ethnic minorities. PATIENTS AND METHODS Through deep sequencing, we interrogated the 20 most common germline testing panel genes in 113 Black South African males presenting with largely advanced prostate cancer. Bioinformatic tools were then used to identify the pathogenicity of the variants. RESULTS After we identified 39 predicted deleterious variants (16 genes), further computational annotation classified 17 variants as potentially oncogenic (12 genes; 17.7% of patients). Rare pathogenic variants included CHEK2 Arg95Ter, BRCA2 Trp31Arg, ATM Arg3047Ter (2 patients), and TP53 Arg282Trp. Notable oncogenic variants of unknown pathogenicity included novel BRCA2 Leu3038Ile in a patient with early-onset disease, whereas patients with FANCA Arg504Cys and RAD51C Arg260Gln reported a family history of prostate cancer. Overall, rare pathogenic and early-onset or familial-associated oncogenic variants were identified in 6.9% (5/72) and 9.2% (8/87) of patients presenting with a Gleason score ≥8 or ≥4 + 3 prostate cancer, respectively. CONCLUSIONS In this first-of-its-kind study of southern African males, we provide support of African inclusion for advanced, early-onset, and familial prostate cancer genetic testing, indicating clinical value for 30% of current gene panels. Recognizing current panel limitations highlights an urgent need to establish testing guidelines for men of African ancestry. We provide a rationale for considering lowering the pathologic diagnostic inclusion criteria and call for further genome-wide interrogation to ensure the best possible African-relevant prostate cancer gene panel.
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Affiliation(s)
- Kazzem Gheybi
- Ancestry & Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Jue Jiang
- Ancestry & Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Mekgatho Health Sciences University, Dr. George Mukhari Academic Hospital, Medunsa, South Africa
| | - Pamela X Y Soh
- Ancestry & Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Zsofia Kote-Jarai
- Oncogenetics Team, The Institute of Cancer Research, Surrey, United Kingdom
| | - Weerachai Jaratlerdsiri
- Ancestry & Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Rosalind A Eeles
- Oncogenetics Team, The Institute of Cancer Research, Surrey, United Kingdom
| | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Vanessa M Hayes
- Ancestry & Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Camperdown, NSW, Australia.,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
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10
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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 2023; 13:e1142. [PMID: 36629046 PMCID: PMC9832422 DOI: 10.1002/ctm2.1142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 01/12/2023] Open
Affiliation(s)
- Vanessa M. Hayes
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and HealthUniversity of SydneyCamperdownAustralia
- Southern African Prostate Cancer Study, School of Health Systems and Public HealthUniversity of PretoriaPretoriaSouth Africa
| | - Tingting Gong
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and HealthUniversity of SydneyCamperdownAustralia
| | | | - Weerachai Jaratlerdsiri
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and HealthUniversity of SydneyCamperdownAustralia
| | - M. S. Riana Bornman
- Southern African Prostate Cancer Study, School of Health Systems and Public HealthUniversity of PretoriaPretoriaSouth Africa
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11
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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; 14:100. [PMID: 36045381 PMCID: PMC9434886 DOI: 10.1186/s13073-022-01096-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/28/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND African ancestry is a significant risk factor for advanced prostate cancer (PCa). Mortality rates in sub-Saharan Africa are 2.5-fold greater than global averages. However, the region has largely been excluded from the benefits of whole genome interrogation studies. Additionally, while structural variation (SV) is highly prevalent, PCa genomic studies are still biased towards small variant interrogation. METHODS Using whole genome sequencing and best practice workflows, we performed a comprehensive analysis of SVs for 180 (predominantly Gleason score ≥ 8) prostate tumours derived from 115 African, 61 European and four ancestrally admixed patients. We investigated the landscape and relationship of somatic SVs in driving ethnic disparity (African versus European), with a focus on African men from southern Africa. RESULTS Duplication events showed the greatest ethnic disparity, with a 1.6- (relative frequency) to 2.5-fold (count) increase in African-derived tumours. Furthermore, we found duplication events to be associated with CDK12 inactivation and MYC copy number gain, and deletion events associated with SPOP mutation. Overall, African-derived tumours were 2-fold more likely to present with a hyper-SV subtype. In addition to hyper-duplication and deletion subtypes, we describe a new hyper-translocation subtype. While we confirm a lower TMPRSS2-ERG fusion-positive rate in tumours from African cases (10% versus 33%), novel African-specific PCa ETS family member and TMPRSS2 fusion partners were identified, including LINC01525, FBXO7, GTF3C2, NTNG1 and YPEL5. Notably, we found 74 somatic SV hotspots impacting 18 new candidate driver genes, with CADM2, LSAMP, PTPRD, PDE4D and PACRG having therapeutic implications for African patients. CONCLUSIONS In this first African-inclusive SV study for high-risk PCa, we demonstrate the power of SV interrogation for the identification of novel subtypes, oncogenic drivers and therapeutic targets. Identifying a novel spectrum of SVs in tumours derived from African patients provides a mechanism that may contribute, at least in part, to the observed ethnic disparity in advanced PCa presentation in men of African ancestry.
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Affiliation(s)
- Tingting Gong
- grid.1013.30000 0004 1936 834XAncestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW Australia ,grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia ,grid.8547.e0000 0001 0125 2443Human Phenome Institute, Fudan University, Shanghai, China
| | - Weerachai Jaratlerdsiri
- grid.1013.30000 0004 1936 834XAncestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW Australia ,grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
| | - Jue Jiang
- grid.1013.30000 0004 1936 834XAncestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW Australia ,grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
| | - Cali Willet
- grid.1013.30000 0004 1936 834XSydney Informatics Hub, University of Sydney, Sydney, NSW Australia
| | - Tracy Chew
- grid.1013.30000 0004 1936 834XSydney Informatics Hub, University of Sydney, Sydney, NSW Australia
| | - Sean M. Patrick
- grid.49697.350000 0001 2107 2298School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Ruth J. Lyons
- grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
| | - Anne-Maree Haynes
- grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
| | - Gabriela Pasqualim
- grid.8532.c0000 0001 2200 7498Endocrine and Tumor Molecular Biology Laboratory, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil ,grid.411598.00000 0000 8540 6536Laboratory of Genetics, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Ilma Simoni Brum
- grid.8532.c0000 0001 2200 7498Endocrine and Tumor Molecular Biology Laboratory, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Phillip D. Stricker
- grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia ,grid.437825.f0000 0000 9119 2677Department of Urology, St. Vincent’s Hospital, Darlinghurst, NSW Australia
| | - Shingai B. A. Mutambirwa
- grid.461049.eDepartment of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa, Ga-Rankuwa, South Africa
| | - Rosemarie Sadsad
- grid.1013.30000 0004 1936 834XSydney Informatics Hub, University of Sydney, Sydney, NSW Australia
| | - Anthony T. Papenfuss
- grid.1042.70000 0004 0432 4889Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, Victoria Australia
| | - Riana M. S. Bornman
- grid.49697.350000 0001 2107 2298School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Eva K. F. Chan
- grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia ,grid.416088.30000 0001 0753 1056NSW Health Pathology, Sydney, Australia
| | - Vanessa M. Hayes
- grid.1013.30000 0004 1936 834XAncestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW Australia ,grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia ,grid.49697.350000 0001 2107 2298School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa ,grid.411732.20000 0001 2105 2799Faculty of Health Sciences, University of Limpopo, Turfloop Campus, Mankweng, South Africa
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12
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Mokoatle M, Mapiye D, Marivate V, Hayes VM, Bornman R. Discriminatory Gleason grade group signatures of prostate cancer: An application of machine learning methods. PLoS One 2022; 17:e0267714. [PMID: 35679280 PMCID: PMC9182297 DOI: 10.1371/journal.pone.0267714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/13/2022] [Indexed: 12/03/2022] Open
Abstract
One of the most precise methods to detect prostate cancer is by evaluation of a stained biopsy by a pathologist under a microscope. Regions of the tissue are assessed and graded according to the observed histological pattern. However, this is not only laborious, but also relies on the experience of the pathologist and tends to suffer from the lack of reproducibility of biopsy outcomes across pathologists. As a result, computational approaches are being sought and machine learning has been gaining momentum in the prediction of the Gleason grade group. To date, machine learning literature has addressed this problem by using features from magnetic resonance imaging images, whole slide images, tissue microarrays, gene expression data, and clinical features. However, there is a gap with regards to predicting the Gleason grade group using DNA sequences as the only input source to the machine learning models. In this work, using whole genome sequence data from South African prostate cancer patients, an application of machine learning and biological experiments were combined to understand the challenges that are associated with the prediction of the Gleason grade group. A series of machine learning binary classifiers (XGBoost, LSTM, GRU, LR, RF) were created only relying on DNA sequences input features. All the models were not able to adequately discriminate between the DNA sequences of the studied Gleason grade groups (Gleason grade group 1 and 5). However, the models were further evaluated in the prediction of tumor DNA sequences from matched-normal DNA sequences, given DNA sequences as the only input source. In this new problem, the models performed acceptably better than before with the XGBoost model achieving the highest accuracy of 74 ± 01, F1 score of 79 ± 01, recall of 99 ± 0.0, and precision of 66 ± 0.1.
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Affiliation(s)
- Mpho Mokoatle
- Department of Computer Science, University of Pretoria, Pretoria, South Africa
- * E-mail:
| | | | - Vukosi Marivate
- Department of Computer Science, University of Pretoria, Pretoria, South Africa
- School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Vanessa M. Hayes
- School of Medical Sciences, The University of Sydney, Sydney, Australia
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
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13
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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, 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; 82:201-211. [PMID: 35659150 DOI: 10.1016/j.eururo.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/06/2022] [Accepted: 05/10/2022] [Indexed: 11/15/2022]
Abstract
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 <1%) predicted-deleterious coding germline mutations were identified. Optimal multifactor and univariate Cox regression models were built to predict time to BCR after radical treatment, using germline variants grouped by functionally annotated gene sets. Models were tested for robustness using bootstrap resampling. RESULTS AND LIMITATIONS Optimal Cox regression multifactor models showed that rare predicted-deleterious germline variants in "Hallmark" gene sets were consistently associated with altered time to BCR. Three gene sets had a statistically significant association with risk-elevated outcome when modelling all samples: PI3K/AKT/mTOR, Inflammatory response, and KRAS signalling (up). PI3K/AKT/mTOR and KRAS signalling (up) were also associated among patients with higher-grade cancer, as were Pancreas-beta cells, TNFA signalling via NKFB, and Hypoxia, the latter of which was validated in the independent TCGA dataset. CONCLUSIONS We demonstrate for the first time that rare deleterious coding germline variants robustly associate with time to BCR after radical treatment, including cohort-independent validation. Our findings suggest that germline testing at diagnosis could aid clinical decisions by stratifying patients for differential clinical management. PATIENT SUMMARY Prostate cancer patients with particular genetic mutations have a higher chance of relapsing after initial radical treatment, potentially providing opportunities to identify patients who might need additional treatments earlier.
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Affiliation(s)
| | | | | | - Robert G Bristow
- Manchester Cancer Research Centre and CRUK Manchester Institute, The University of Manchester, Manchester, UK
| | - Michael Fraser
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada; Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Medical Biophysics & Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Guido Sauter
- University Medical Centre Hamburg - Eppendorf, Hamburg, Germany
| | - Benedikt Brors
- German Cancer Research Center (DKFZ), Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Jan Korbel
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Joachim Weischenfeldt
- Charité - Universitätsmedizin Berlin, Berlin, Germany; Biotech Research & Innovation Centre (BRIC) & Finsen Laboratory, University of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - Niall M Corcoran
- Department of Surgery, The University of Melbourne, Grattan Street, Parkville, Victoria, Australia; Department of Urology, Royal Melbourne Hospital, Parkville, Victoria, Australia; Melbourne Bioinformatics, The University of Melbourne, Grattan Street, Victoria, Australia
| | - Chol-Hee Jung
- The University of Melbourne, Grattan Street, Parkville, Victoria, Australia
| | - Bernard J Pope
- Department of Surgery, The University of Melbourne, Grattan Street, Parkville, Victoria, Australia; Royal Melbourne Hospital, Melbourne, Parwille, Victoria, Australia
| | - Chris M Hovens
- Melbourne Bioinformatics, The University of Melbourne, Grattan Street, Victoria, Australia; The University of Melbourne, Grattan Street, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, The Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Géraldine Cancel-Tassin
- CeRePP, Hopital Tenon, Paris, France; Sorbonne Universite, GRC n°5 Predictive Onco-Urology, APHP, Tenon Hospital, Paris, France
| | - Olivier Cussenot
- CeRePP, Hopital Tenon, Paris, France; Sorbonne Universite, GRC n°5 Predictive Onco-Urology, APHP, Tenon Hospital, Paris, France
| | - Massimo Loda
- Department of Pathology & Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vanessa M Hayes
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia; School of Medical Sciences, University of Sydney, Charles Perkins Centre, Camperdown, NSW, Australia
| | - Karina Dalsgaard Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark; Department of Clinical Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Yong-Jie Lu
- Centre for Biomarker and Therapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
| | | | | | - Adam Butler
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Andy G Lynch
- School of Medicine, University of St Andrews, St Andrews, Fife, UK; School of Mathematics & Statistics, St Andrews, Fife, UK
| | - Charlie E Massie
- CRUK Cambridge Institute, Hutchison MRC Research Centre, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
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- CR-UK/Prostate Cancer UK, ICGC, The Pan Prostate Cancer Group, UK
| | - Dan J Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
| | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - David C Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, UK; The Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK
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14
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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 2020; 16:537-553. [PMID: 32892676 PMCID: PMC8078743 DOI: 10.1080/15592294.2020.1809852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Genomes of KhoeSan individuals of the Kalahari Desert provide the greatest understanding of single nucleotide diversity in the human genome. Compared with individuals in industrialized environments, the KhoeSan have a unique foraging and hunting lifestyle. Given these dramatic environmental differences, and the responsiveness of the methylome to environmental exposures of many types, we hypothesized that DNA methylation patterns would differ between KhoeSan and neighbouring agropastoral and/or industrial Bantu. We analysed Illumina HumanMethylation 450 k array data generated from blood samples from 38 KhoeSan and 42 Bantu, and 6 Europeans. After removing CpG positions associated with annotated and novel polymorphisms and controlling for white blood cell composition, sex, age and technical variation we identified 816 differentially methylated CpG loci, out of which 133 had an absolute beta-value difference of at least 0.05. Notably SLC39A4/ZIP4, which plays a role in zinc transport, was one of the most differentially methylated loci. Although the chronological ages of the KhoeSan are not formally recorded, we compared historically estimated ages to methylation-based calculations. This study demonstrates that the epigenetic profile of KhoeSan individuals reveals differences from other populations, and along with extensive genetic diversity, this community brings increased accessibility and understanding to the diversity of the human genome.
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Affiliation(s)
- Alexander Goncearenco
- Genomic Functional Analysis Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brenna A LaBarre
- Genomic Functional Analysis Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.,Graduate Program in Bioinformatics, Boston University, Boston, MA, USA
| | | | - Weerachai Jaratlerdsiri
- Laboratory for Human Comparative & Prostate Cancer Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Stephen D Turner
- Division of Biomedical Informatics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Vanessa M Hayes
- Laboratory for Human Comparative & Prostate Cancer Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia.,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.,Faculty of Health Sciences, University of Limpopo, Sovenga, South Africa.,Sydney Medical School, University of Sydney, Camperdown, Australia
| | - Laura Elnitski
- Genomic Functional Analysis Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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15
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Owen KL, Gearing LJ, Zanker DJ, Brockwell NK, Khoo WH, Roden DL, Cmero M, Mangiola S, Hong MK, Spurling AJ, McDonald M, Chan C, Pasam A, Lyons RJ, Duivenvoorden HM, Ryan A, Butler LM, Mariadason JM, Giang Phan T, Hayes VM, Sandhu S, Swarbrick A, Corcoran NM, Hertzog PJ, Croucher PI, Hovens C, Parker BS. Prostate cancer cell-intrinsic interferon signaling regulates dormancy and metastatic outgrowth in bone. EMBO Rep 2020; 21:e50162. [PMID: 32314873 PMCID: PMC7271653 DOI: 10.15252/embr.202050162] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/15/2020] [Accepted: 03/20/2020] [Indexed: 12/11/2022] Open
Abstract
The latency associated with bone metastasis emergence in castrate-resistant prostate cancer is attributed to dormancy, a state in which cancer cells persist prior to overt lesion formation. Using single-cell transcriptomics and ex vivo profiling, we have uncovered the critical role of tumor-intrinsic immune signaling in the retention of cancer cell dormancy. We demonstrate that loss of tumor-intrinsic type I IFN occurs in proliferating prostate cancer cells in bone. This loss suppresses tumor immunogenicity and therapeutic response and promotes bone cell activation to drive cancer progression. Restoration of tumor-intrinsic IFN signaling by HDAC inhibition increased tumor cell visibility, promoted long-term antitumor immunity, and blocked cancer growth in bone. Key findings were validated in patients, including loss of tumor-intrinsic IFN signaling and immunogenicity in bone metastases compared to primary tumors. Data herein provide a rationale as to why current immunotherapeutics fail in bone-metastatic prostate cancer, and provide a new therapeutic strategy to overcome the inefficacy of immune-based therapies in solid cancers.
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16
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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; 12:E1178. [PMID: 32392735 PMCID: PMC7280976 DOI: 10.3390/cancers12051178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/21/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND While critical insights have been gained from evaluating the genomic landscape of metastatic prostate cancer, utilizing this information to inform personalized treatment is in its infancy. We performed a retrospective pilot study to assess the current impact of precision medicine for locally advanced and metastatic prostate adenocarcinoma and evaluate how genomic data could be harnessed to individualize treatment. METHODS Deep whole genome-sequencing was performed on 16 tumour-blood pairs from 13 prostate cancer patients; whole genome optical mapping was performed in a subset of 9 patients to further identify large structural variants. Tumour samples were derived from prostate, lymph nodes, bone and brain. RESULTS Most samples had acquired genomic alterations in multiple therapeutically relevant pathways, including DNA damage response (11/13 cases), PI3K (7/13), MAPK (10/13) and Wnt (9/13). Five patients had somatic copy number losses in genes that may indicate sensitivity to immunotherapy (LRP1B, CDK12, MLH1) and one patient had germline and somatic BRCA2 alterations. CONCLUSIONS Most cases, whether primary or metastatic, harboured therapeutically relevant alterations, including those associated with PARP inhibitor sensitivity, immunotherapy sensitivity and resistance to androgen pathway targeting agents. The observed intra-patient heterogeneity and presence of genomic alterations in multiple growth pathways in individual cases suggests that a precision medicine model in prostate cancer needs to simultaneously incorporate multiple pathway-targeting agents. Our whole genome approach allowed for structural variant assessment in addition to the ability to rapidly reassess an individual's molecular landscape as knowledge of relevant biomarkers evolve. This retrospective oncological assessment highlights the genomic complexity of prostate cancer and the potential impact of assessing genomic data for an individual at any stage of the disease.
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Affiliation(s)
- Megan Crumbaker
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, Randwick, NSW 2031, Australia
- Kinghorn Cancer Centre, Department of Medical Oncology, St. Vincent’s Hospital, Darlinghurst, NSW 2010, Australia
| | - Eva K. F. Chan
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, Randwick, NSW 2031, Australia
| | - Tingting Gong
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
- Central Clinical School, University of Sydney, Sydney, Camperdown, NSW 2050, Australia
| | - Niall Corcoran
- Australian Prostate Cancer Research Centre Epworth, Richmond, VIC 3121, Australia;
- Department of Surgery, University of Melbourne, Melbourne, VIC 3010, Australia
- Division of Urology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Weerachai Jaratlerdsiri
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
| | - Ruth J. Lyons
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
| | - Anne-Maree Haynes
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
| | - Anna A. Kulidjian
- Department of Orthopedic Surgery, Scripps Clinic, La Jolla, CA 92037, USA.;
- Orthopedic Oncology Program, Scripps MD Anderson Cancer Center, La Jolla, CA 92037, USA
| | - Anton M. F. Kalsbeek
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
| | - Desiree C. Petersen
- The Centre for Proteomic and Genomic Research, Cape Town 7925, South Africa;
| | - Phillip D. Stricker
- Department of Urology, St. Vincent’s Hospital, Darlinghurst, NSW 2010, Australia;
| | - Christina A. M. Jamieson
- Department of Urology, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA;
| | - Peter I. Croucher
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Randwick, NSW 2031, Australia
| | - Christopher M. Hovens
- Australian Prostate Cancer Research Centre Epworth, Richmond, VIC 3121, Australia;
- Department of Surgery, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Anthony M. Joshua
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, Randwick, NSW 2031, Australia
- Kinghorn Cancer Centre, Department of Medical Oncology, St. Vincent’s Hospital, Darlinghurst, NSW 2010, Australia
| | - Vanessa M. Hayes
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, Randwick, NSW 2031, Australia
- Central Clinical School, University of Sydney, Sydney, Camperdown, NSW 2050, Australia
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17
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Gong T, Hayes VM, Chan EKF. Detection of somatic structural variants from short-read next-generation sequencing data. Brief Bioinform 2020; 22:5831479. [PMID: 32379294 PMCID: PMC8138798 DOI: 10.1093/bib/bbaa056] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 03/05/2020] [Accepted: 03/29/2020] [Indexed: 01/09/2023] Open
Abstract
Somatic structural variants (SVs), which are variants that typically impact >50 nucleotides, play a significant role in cancer development and evolution but are notoriously more difficult to detect than small variants from short-read next-generation sequencing (NGS) data. This is due to a combination of challenges attributed to the purity of tumour samples, tumour heterogeneity, limitations of short-read information from NGS and sequence alignment ambiguities. In spite of active development of SV detection tools (callers) over the past few years, each method has inherent advantages and limitations. In this review, we highlight some of the important factors affecting somatic SV detection and compared the performance of seven commonly used SV callers. In particular, we focus on the extent of change in sensitivity and precision for detecting different SV types and size ranges from samples with differing variant allele frequencies and sequencing depths of coverage. We highlight the reasons for why some SV callers perform well in some settings but not others, allowing our evaluation findings to be extended beyond the seven SV callers examined in this paper. As the importance of large SVs become increasingly recognized in cancer genomics, this paper provides a timely review on some of the most impactful factors influencing somatic SV detection that should be considered when choosing SV callers.
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Affiliation(s)
| | - Vanessa M Hayes
- Corresponding authors: Eva K.F. Chan, New South Wales Health Pathology, Newcastle, NSW 2300, Australia. E-mail: ; Vanessa M. Hayes, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia. Tel.: +61-2-9355-5841; Fax: +61 2-2-9295-8151; E-mail:
| | - Eva K F Chan
- Corresponding authors: Eva K.F. Chan, New South Wales Health Pathology, Newcastle, NSW 2300, Australia. E-mail: ; Vanessa M. Hayes, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia. Tel.: +61-2-9355-5841; Fax: +61 2-2-9295-8151; E-mail:
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18
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Field MA, Rosen BD, Dudchenko O, Chan EKF, Minoche AE, Edwards RJ, Barton K, Lyons RJ, Tuipulotu DE, Hayes VM, D. Omer A, Colaric Z, Keilwagen J, Skvortsova K, Bogdanovic O, Smith MA, Aiden EL, Smith TPL, Zammit RA, Ballard JWO. 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 2020; 9:giaa027. [PMID: 32236524 PMCID: PMC7111595 DOI: 10.1093/gigascience/giaa027] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/29/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The German Shepherd Dog (GSD) is one of the most common breeds on earth and has been bred for its utility and intelligence. It is often first choice for police and military work, as well as protection, disability assistance, and search-and-rescue. Yet, GSDs are well known to be susceptible to a range of genetic diseases that can interfere with their training. Such diseases are of particular concern when they occur later in life, and fully trained animals are not able to continue their duties. FINDINGS Here, we provide the draft genome sequence of a healthy German Shepherd female as a reference for future disease and evolutionary studies. We generated this improved canid reference genome (CanFam_GSD) utilizing a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. The GSD assembly is ∼80 times as contiguous as the current canid reference genome (20.9 vs 0.267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer scaffolds (429 vs 3,310) than the current canid reference genome CanFamv3.1. Two chromosomes (4 and 35) are assembled into single scaffolds with no gaps. BUSCO analyses of the genome assembly results show that 93.0% of the conserved single-copy genes are complete in the GSD assembly compared with 92.2% for CanFam v3.1. Homology-based gene annotation increases this value to ∼99%. Detailed examination of the evolutionarily important pancreatic amylase region reveals that there are most likely 7 copies of the gene, indicative of a duplication of 4 ancestral copies and the disruption of 1 copy. CONCLUSIONS GSD genome assembly and annotation were produced with major improvement in completeness, continuity, and quality over the existing canid reference. This resource will enable further research related to canine diseases, the evolutionary relationships of canids, and other aspects of canid biology.
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Affiliation(s)
- Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield Road, Cairns, QLD 4878, Australia
- John Curtin School of Medical Research, Australian National University, Garran Rd, Canberra, ACT 2600, Australia
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Baltimore Ave, Beltsville, MD 20705, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
- Center for Theoretical and Biological Physics, Rice University, Main St, Houston, TX 77005, USA
| | - Eva K F Chan
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Andre E Minoche
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical School, University of New South Wales Sydney, Victoria Street, Darlinghurst NSW 2010, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Kirston Barton
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Ruth J Lyons
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Vanessa M Hayes
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
- Central Clinical School, University of Sydney, Parramatta Road, Camperdown, NSW 2050, Australia
| | - Arina D. Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Ksenia Skvortsova
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Martin A Smith
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
- Center for Theoretical and Biological Physics, Rice University, Main St, Houston, TX 77005, USA
- Broad Institute of MIT and Harvard, Main St, Cambridge, MA 02142, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, ShanghaiTech University, Huaxia Middle Rd, Pudong 201210, China
| | - Timothy P L Smith
- US Meat Animal Research Center, Agricultural Research Service USDA, Rd 313, Clay Center, NE 68933, USA
| | - Robert A Zammit
- Vineyard Veterinary Hospital, Windsor Rd, Vineyard, NSW 2765, Australia
| | - J William O Ballard
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
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19
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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; 12:79. [PMID: 31861999 PMCID: PMC6923858 DOI: 10.1186/s13072-019-0321-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/09/2019] [Indexed: 12/16/2022] Open
Abstract
Background Current array-based methods for the measurement of DNA methylation rely on the process of sodium bisulfite conversion to differentiate between methylated and unmethylated cytosine bases in DNA. In the absence of genotype data this process can lead to ambiguity in data interpretation when a sample has polymorphisms at a methylation probe site. A common way to minimize this problem is to exclude such potentially problematic sites, with some methods removing as much as 60% of array probes from consideration before data analysis. Results Here, we present an algorithm implemented in an R Bioconductor package, MethylToSNP, which detects a characteristic data pattern to infer sites likely to be confounded by polymorphisms. Additionally, the tool provides a stringent reliability score to allow thresholding on SNP predictions. We calibrated parameters and thresholds used by the algorithm on simulated and real methylation data sets. We illustrate findings using methylation data from YRI (Yoruba in Ibadan, Nigeria), CEPH (European descent) and KhoeSan (southern African) populations. Our polymorphism predictions made using MethylToSNP have been validated through SNP databases and bisulfite and genomic sequencing. Conclusions The benefits of this method are threefold. First, it prevents extensive data loss by considering only SNPs specific to the individuals in the study. Second, it offers the possibility to identify new polymorphisms in samples for which there is little known about the genetic landscape. Third, it identifies variants as they exist in functional regions of a genome, such as in CTCF (transcriptional repressor) sites and enhancers, that may be common alleles or personal mutations with potential to deleteriously affect genomic regulatory activities. We demonstrate that MethylToSNP is applicable to the Illumina 450K and Illumina 850K EPIC array data and is also backwards compatible to the 27K methylation arrays. Going forward, this kind of nuanced approach can increase the amount of information derived from precious data sets by considering samples of the project individually to enable more informed decisions about data cleaning.
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Affiliation(s)
- Brenna A LaBarre
- Graduate Program in Bioinformatics, Boston University, Boston, MA, USA.,Genomic Functional Analysis Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 49 Convent Dr., Bethesda, MD, 20892, USA
| | - Alexander Goncearenco
- Genomic Functional Analysis Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 49 Convent Dr., Bethesda, MD, 20892, USA
| | - Hanna M Petrykowska
- Genomic Functional Analysis Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 49 Convent Dr., Bethesda, MD, 20892, USA
| | - Weerachai Jaratlerdsiri
- Laboratory for Human Comparative & Prostate Cancer Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Hatfield, Pretoria, South Africa
| | - Vanessa M Hayes
- Laboratory for Human Comparative & Prostate Cancer Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Health Systems and Public Health, University of Pretoria, Hatfield, Pretoria, South Africa.,Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Laura Elnitski
- Genomic Functional Analysis Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 49 Convent Dr., Bethesda, MD, 20892, USA.
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20
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Feng Y, Jaratlerdsiri W, Patrick SM, Lyons RJ, Haynes A, Collins CC, Stricker PD, Bornman MR, Hayes VM. Metagenomic analysis reveals a rich bacterial content in high-risk prostate tumors from African men. Prostate 2019; 79:1731-1738. [PMID: 31454437 PMCID: PMC6790596 DOI: 10.1002/pros.23897] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 08/06/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Inflammation is a hallmark of prostate cancer (PCa), yet no pathogenic agent has been identified. Men from Africa are at increased risk for both aggressive prostate disease and infection. We hypothesize that pathogenic microbes may be contributing, at least in part, to high-risk PCa presentation within Africa and in turn the observed ethnic disparity. METHODS Here we reveal through metagenomic analysis of host-derived whole-genome sequencing data, the microbial content within prostate tumor tissue from 22 men. What is unique about this study is that patients were separated by ethnicity, African vs European, and environments, Africa vs Australia. RESULTS We identified 23 common bacterial genera between the African, Australian, and Chinese prostate tumor samples, while nonbacterial microbes were notably absent. While the most abundant genera across all samples included: Escherichia, Propionibacterium, and Pseudomonas, the core prostate tumor microbiota was enriched for Proteobacteria. We observed a significant increase in the richness of the bacterial communities within the African vs Australian samples (t = 4.6-5.5; P = .0004-.001), largely driven by eight predominant genera. Considering core human gut microbiota, African prostate tissue samples appear enriched for Escherichia and Acidovorax, with an abundance of Eubacterium associated with host tumor hypermutation. CONCLUSIONS Our study provides suggestive evidence for the presence of a core, bacteria-rich, prostate microbiome. While unable to exclude for fecal contamination, the observed increased bacterial content and richness within the African vs non-African samples, together with elevated tumor mutational burden, suggests the possibility that bacterially-driven oncogenic transformation within the prostate microenvironment may be contributing to aggressive disease presentation in Africa.
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Affiliation(s)
- Ye Feng
- Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
- Institute of Translational MedicineZhejiang University School of MedicineHangzhouChina
| | - Weerachai Jaratlerdsiri
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstNew South WalesAustralia
| | - Sean M. Patrick
- School of Health Systems and Public HealthUniversity of PretoriaPretoriaSouth Africa
| | - Ruth J. Lyons
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstNew South WalesAustralia
| | - Anne‐Maree Haynes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstNew South WalesAustralia
| | - Colin C. Collins
- Vancouver Prostate CentreVancouverCanada
- Department of UrologyUniversity of British ColumbiaVancouverCanada
| | - Phillip D. Stricker
- Department of UrologySt Vincent's Hospital SydneyDarlinghurstNew South WalesAustralia
| | - M.S. Riana Bornman
- School of Health Systems and Public HealthUniversity of PretoriaPretoriaSouth Africa
| | - Vanessa M. Hayes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstNew South WalesAustralia
- School of Health Systems and Public HealthUniversity of PretoriaPretoriaSouth Africa
- St Vincent's Clinical SchoolUniversity of New South Wales SydneySydneyNew South WalesAustralia
- Central Clinical School, Faculty of Medicine and HealthUniversity of SydneyCamperdownNew South WalesAustralia
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21
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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; 575:185-189. [PMID: 31659339 DOI: 10.1038/s41586-019-1714-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 09/24/2019] [Indexed: 01/17/2023]
Abstract
Anatomically modern humans originated in Africa around 200 thousand years ago (ka)1-4. Although some of the oldest skeletal remains suggest an eastern African origin2, southern Africa is home to contemporary populations that represent the earliest branch of human genetic phylogeny5,6. Here we generate, to our knowledge, the largest resource for the poorly represented and deepest-rooting maternal L0 mitochondrial DNA branch (198 new mitogenomes for a total of 1,217 mitogenomes) from contemporary southern Africans and show the geographical isolation of L0d1'2, L0k and L0g KhoeSan descendants south of the Zambezi river in Africa. By establishing mitogenomic timelines, frequencies and dispersals, we show that the L0 lineage emerged within the residual Makgadikgadi-Okavango palaeo-wetland of southern Africa7, approximately 200 ka (95% confidence interval, 240-165 ka). Genetic divergence points to a sustained 70,000-year-long existence of the L0 lineage before an out-of-homeland northeast-southwest dispersal between 130 and 110 ka. Palaeo-climate proxy and model data suggest that increased humidity opened green corridors, first to the northeast then to the southwest. Subsequent drying of the homeland corresponds to a sustained effective population size (L0k), whereas wet-dry cycles and probable adaptation to marine foraging allowed the southwestern migrants to achieve population growth (L0d1'2), as supported by extensive south-coastal archaeological evidence8-10. Taken together, we propose a southern African origin of anatomically modern humans with sustained homeland occupation before the first migrations of people that appear to have been driven by regional climate changes.
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Affiliation(s)
- Eva K F Chan
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Axel Timmermann
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea. .,Pusan National University, Busan, South Korea.
| | - Benedetta F Baldi
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Andy E Moore
- Department of Geology, Rhodes University, Grahamstown, South Africa
| | - Ruth J Lyons
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Sun-Seon Lee
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea.,Pusan National University, Busan, South Korea
| | - Anton M F Kalsbeek
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Desiree C Petersen
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,The Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | - Hannes Rautenbach
- Climate Change and Variability, South African Weather Service, Pretoria, South Africa.,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.,Akademia, Johannesburg, South Africa
| | | | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia. .,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia. .,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa. .,Faculty of Health Sciences, University of Limpopo, Sovenga, South Africa. .,Central Clinical School, University of Sydney, Sydney, New South Wales, Australia.
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22
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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; 79:1191-1196. [PMID: 31090091 PMCID: PMC6617820 DOI: 10.1002/pros.23823] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/11/2019] [Accepted: 04/17/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND The androgen-regulated gene TMPRSS2 to the ETS transcription factor gene ERG fusion is the most common genomic alteration acquired during prostate tumorigenesis and biased toward men of European ancestry. In contrast, African American men present with more advanced disease, yet their tumors are less likely to acquire TMPRSS2-ERG. Data for Africa is scarce. METHODS RNA was made available for genomic analyses from 181 prostate tissue biopsy cores from Black South African men, 94 with and 87 without pathological evidence for prostate cancer. Reverse transcription polymerase chain reaction was used to screen for the TMPRSS2-ERG fusion, while transcript junction coordinates and isoform frequencies, including novel gene fusions, were determined using targeted RNA sequencing. RESULTS Here we report a frequency of 13% for TMPRSS2-ERG in tumors from Black South Africans. Present in 12/94 positive versus 1/87 cancer negative prostate tissue cores, this suggests a 92.62% predictivity for a positive cancer diagnosis (P = 0.0031). At a frequency of almost half that reported for African Americans and roughly a quarter of that reported for men of European ancestry, acquisition of TMPRSS2-ERG appears to be inversely associated with aggressive prostate cancer. Further support was provided by linking the presence of TMPRSS2-ERG to low-grade disease in younger patients (P = 0.0466), with higher expressing distal ERG fusion junction coordinates. CONCLUSIONS Only the second study of its kind for the African continent, we support a link between TMPRSS2-ERG status and prostate cancer racial health disparity beyond the borders of the United States. We call for urgent evaluation of androgen deprivation therapy within Africa.
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Affiliation(s)
- James Blackburn
- Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstAustralia
- St. Vincent's Clinical SchoolFaculty of Medicine, UNSWSydneyAustralia
| | - Stefano Vecchiarelli
- Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstAustralia
| | - Erin E. Heyer
- Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstAustralia
| | - Sean M. Patrick
- School of Health Systems and Public HealthUniversity of PretoriaGezinaSouth Africa
| | - Ruth J. Lyons
- Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstAustralia
| | | | - Smit van Zyl
- University of Limpopo, Turfloop CampusSovengaSouth Africa
| | - M. S. Riana Bornman
- School of Health Systems and Public HealthUniversity of PretoriaGezinaSouth Africa
| | - Tim R. Mercer
- Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstAustralia
- St. Vincent's Clinical SchoolFaculty of Medicine, UNSWSydneyAustralia
- Altius Institute for Biomedical SciencesSeattleWashington
| | - Vanessa M. Hayes
- Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstAustralia
- St. Vincent's Clinical SchoolFaculty of Medicine, UNSWSydneyAustralia
- School of Health Systems and Public HealthUniversity of PretoriaGezinaSouth Africa
- University of Limpopo, Turfloop CampusSovengaSouth Africa
- Sydney Medical SchoolUniversity of SydneyCamperdownAustralia
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23
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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; 12:82. [PMID: 31164124 PMCID: PMC6549381 DOI: 10.1186/s12920-019-0537-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 05/21/2019] [Indexed: 02/08/2023] Open
Abstract
Backgrounds Genetic diversity is greatest within Africa, in particular the KhoeSan click-speaking peoples of southern Africa. South African populations represent admixture fractions including differing degrees of African, African-KhoeSan and non-African genetic ancestries. Within the United States, African ancestry has been linked to prostate cancer presentation and mortality. Together with environmental contributions, genetics is a significant risk factor for high-risk prostate cancer, defined by a pathological Gleason score ≥ 8. Methods Using genotype array data merged with ancestry informative reference data, we investigate the contribution of African ancestral fractions to high-risk prostate cancer. Our study includes 152 South African men of African (Black) or African-admixed (Coloured) ancestries, in which 40% showed high-risk prostate cancer. Results Genetic fractions were determined for averaging an equal African to non-African genetic ancestral contribution in the Coloured; we found African ancestry to be linked to high-risk prostate cancer (P-value = 0.0477). Adjusting for age, the associated African ancestral fraction was driven by a significant KhoeSan over Bantu contribution, defined by Gleason score ≥ 8 (P-value = 0.02329) or prostate specific antigen levels ≥20 ng/ml (P-value = 0.03713). Additionally, we observed the mean overall KhoeSan contribution to be increased in Black patients with high-risk (11.8%) over low-risk (10.9%) disease. Linking for the first time KhoeSan ancestry to a common modern disease, namely high-risk prostate cancer, we tested in this small study the validity of using KhoeSan ancestry as a surrogate for identifying potential high-risk prostate cancer risk loci. As such, we identified four loci within chromosomal regions 2p11.2, 3p14, 8q23 and 22q13.2 (P-value = all age-adjusted < 0.01), two of which have previously been associated with high-risk prostate cancer. Conclusions Our study suggests that ancient KhoeSan ancestry may be linked to common modern diseases, specifically those of late onset and therefore unlikely to have undergone exclusive selective pressure. As such we show within a uniquely admixed South African population a link between KhoeSan ancestry and high-risk prostate cancer, which may explain the 2-fold increase in presentation in Black South Africans compared with African Americans. Electronic supplementary material The online version of this article (10.1186/s12920-019-0537-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Desiree C Petersen
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, NSW, 2010, Australia.,Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia.,Centre for Proteomic and Genomic Research (CPGR), 1st Floor, St. Peters Mall, Cnr. Anzio and Main Road, Observatory, Cape Town, 7925, South Africa
| | - Weerachai Jaratlerdsiri
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, NSW, 2010, Australia
| | - Abraham van Wyk
- Division of Anatomical Pathology, NHLS Tygerberg and Stellenbosch University, Tygerberg, South Africa
| | - Eva K F Chan
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, NSW, 2010, Australia.,Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia
| | - Pedro Fernandez
- Division of Urology, Department of Surgical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ruth J Lyons
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, NSW, 2010, Australia
| | - Shingai B A Mutambirw
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa, South Africa
| | - Andre van der Merwe
- Division of Urology, Department of Surgical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Philip A Venter
- Faculty of Health Sciences, University of Limpopo, Mankweng, South Africa
| | - William Bates
- Division of Anatomical Pathology, NHLS Tygerberg and Stellenbosch University, Tygerberg, South Africa
| | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Vanessa M Hayes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, NSW, 2010, Australia. .,Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia. .,Faculty of Health Sciences, University of Limpopo, Mankweng, South Africa. .,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa. .,Central Clinical School, University of Sydney, Camperdown, NSW, Australia.
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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; 10:1388. [PMID: 30918253 PMCID: PMC6437215 DOI: 10.1038/s41467-019-09374-9] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 02/22/2019] [Indexed: 01/05/2023] Open
Abstract
Fusion genes are a major cause of cancer. Their rapid and accurate diagnosis can inform clinical action, but current molecular diagnostic assays are restricted in resolution and throughput. Here, we show that targeted RNA sequencing (RNAseq) can overcome these limitations. First, we establish that fusion gene detection with targeted RNAseq is both sensitive and quantitative by optimising laboratory and bioinformatic variables using spike-in standards and cell lines. Next, we analyse a clinical patient cohort and improve the overall fusion gene diagnostic rate from 63% with conventional approaches to 76% with targeted RNAseq while demonstrating high concordance for patient samples with previous diagnoses. Finally, we show that targeted RNAseq offers additional advantages by simultaneously measuring gene expression levels and profiling the immune-receptor repertoire. We anticipate that targeted RNAseq will improve clinical fusion gene detection, and its increasing use will provide a deeper understanding of fusion gene biology. Rapid and accurate detection of fusion genes is important in cancer diagnostics. Here, the authors demonstrate that targeted RNA sequencing provides fast, sensitive and quantitative gene fusion detection and overcomes the limitations of approaches currently in clinical use.
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Affiliation(s)
- Erin E Heyer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Ira W Deveson
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia
| | - Danson Wooi
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia
| | - Christina I Selinger
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, 2050, NSW, Australia
| | - Ruth J Lyons
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia.,Faculty of Health Sciences, University of Limpopo, Turfloop Campus, Mankweng, 0727, South Africa.,School of Health Systems and Public Health, University of Pretoria, Pretoria, 0002, South Africa.,Central Clinical School, University of Sydney, Sydney, 2006, NSW, Australia
| | - Sandra A O'Toole
- St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, 2050, NSW, Australia.,Central Clinical School, University of Sydney, Sydney, 2006, NSW, Australia.,The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,Australian Clinical Labs, Sydney, 2010, NSW, Australia
| | - Mandy L Ballinger
- The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Devinder Gill
- Department of Haematology, Princess Alexandra Hospital, Brisbane, 4102, QLD, Australia
| | - David M Thomas
- The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Tim R Mercer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia. .,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia. .,Altius Institute for Biomedical Sciences, Seattle, 98121, WA, USA.
| | - James Blackburn
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia. .,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia.
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25
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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; 20:146. [PMID: 30777011 PMCID: PMC6379980 DOI: 10.1186/s12864-019-5457-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/16/2019] [Indexed: 12/29/2022] Open
Abstract
Background Prostate cancer (PCa) is the most common malignant neoplasm among men in many countries. Since most precancerous and cancerous tissues show signs of inflammation, chronic bacterial prostatitis has been hypothesized to be a possible etiology. However, establishing a causal relationship between microbial inflammation and PCa requires a comprehensive analysis of the prostate microbiome. The aim of this study was to characterize the microbiome in prostate tissue of PCa patients and investigate its association with tumour clinical characteristics as well as host expression profiles. Results The metagenome and metatranscriptome of tumour and the adjacent benign tissues were assessed in 65 Chinese radical prostatectomy specimens. Escherichia, Propionibacterium, Acinetobacter and Pseudomonas were abundant in both metagenome and metatranscriptome, thus constituting the core of the prostate microbiome. The biodiversity of the microbiomes could not be differentiated between the matched tumour/benign specimens or between the tumour specimens of low and high Gleason Scores. The expression profile of ten Pseudomonas genes was strongly correlated with that of eight host small RNA genes; three of the RNA genes may negatively associate with metastasis. Few viruses could be identified from the prostate microbiomes. Conclusions This is the first study of the human prostate microbiome employing an integrated metagenomics and metatranscriptomics approach. In this Chinese cohort, both metagenome and metatranscriptome analyses showed a non-sterile microenvironment in the prostate of PCa patients, but we did not find links between the microbiome and local progression of PCa. However, the correlated expression of Pseudomonas genes and human small RNA genes may provide tantalizing preliminary evidence that Pseudomonas infection may impede metastasis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5457-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | | | - Robert Bell
- Vancouver Prostate Centre, Vancouver, Canada
| | | | | | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.,St Vincent's Clinical School, University of New South Wales, Randwick, NSW, Australia
| | - Shancheng Ren
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China.
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26
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Affiliation(s)
- Vanessa M Hayes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Randwick, NSW, Australia; Central Clinical School, University of Sydney, Camperdown, NSW, Australia; School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Weerachai Jaratlerdsiri
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Randwick, NSW, Australia; Central Clinical School, University of Sydney, Camperdown, NSW, Australia; School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - M S Riana Bornman
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Randwick, NSW, Australia; Central Clinical School, University of Sydney, Camperdown, NSW, Australia; School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
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27
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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; 4:1-7. [PMID: 30241160 PMCID: PMC6223485 DOI: 10.1200/jgo.2016.008862] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Vanessa M Hayes
- Vanessa M. Hayes, University of Sydney, University of New South Wales, and Garvan Institute of Medical Research, Sydney, Australia; and University of Limpopo, Limpopo, South Africa and; Vanessa M. Hayes and M.S. Riana Bornman, University of Pretoria, Pretoria South Africa
| | - M S Riana Bornman
- Vanessa M. Hayes, University of Sydney, University of New South Wales, and Garvan Institute of Medical Research, Sydney, Australia; and University of Limpopo, Limpopo, South Africa and; Vanessa M. Hayes and M.S. Riana Bornman, University of Pretoria, Pretoria South Africa
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28
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Jaratlerdsiri W, Chan EK, Gong T, Petersen DC, Kalsbeek AM, Venter PA, Stricker PD, Bornman MR, 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; 78:6736-6746. [DOI: 10.1158/0008-5472.can-18-0254] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/05/2018] [Accepted: 09/04/2018] [Indexed: 11/16/2022]
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29
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Nair SS, Luu PL, Qu W, Maddugoda M, Huschtscha L, Reddel R, Chenevix-Trench G, Toso M, Kench JG, Horvath LG, Hayes VM, Stricker PD, Hughes TP, White DL, Rasko JEJ, Wong JJL, Clark SJ. Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten. Epigenetics Chromatin 2018; 11:24. [PMID: 29807544 PMCID: PMC5971424 DOI: 10.1186/s13072-018-0194-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/21/2018] [Indexed: 12/24/2022] Open
Abstract
Background Comprehensive genome-wide DNA methylation profiling is critical to gain insights into epigenetic reprogramming during development and disease processes. Among the different genome-wide DNA methylation technologies, whole genome bisulphite sequencing (WGBS) is considered the gold standard for assaying genome-wide DNA methylation at single base resolution. However, the high sequencing cost to achieve the optimal depth of coverage limits its application in both basic and clinical research. To achieve 15× coverage of the human methylome, using WGBS, requires approximately three lanes of 100-bp-paired-end Illumina HiSeq 2500 sequencing. It is important, therefore, for advances in sequencing technologies to be developed to enable cost-effective high-coverage sequencing. Results In this study, we provide an optimised WGBS methodology, from library preparation to sequencing and data processing, to enable 16–20× genome-wide coverage per single lane of HiSeq X Ten, HCS 3.3.76. To process and analyse the data, we developed a WGBS pipeline (METH10X) that is fast and can call SNPs. We performed WGBS on both high-quality intact DNA and degraded DNA from formalin-fixed paraffin-embedded tissue. First, we compared different library preparation methods on the HiSeq 2500 platform to identify the best method for sequencing on the HiSeq X Ten. Second, we optimised the PhiX and genome spike-ins to achieve higher quality and coverage of WGBS data on the HiSeq X Ten. Third, we performed integrated whole genome sequencing (WGS) and WGBS of the same DNA sample in a single lane of HiSeq X Ten to improve data output. Finally, we compared methylation data from the HiSeq 2500 and HiSeq X Ten and found high concordance (Pearson r > 0.9×). Conclusions Together we provide a systematic, efficient and complete approach to perform and analyse WGBS on the HiSeq X Ten. Our protocol allows for large-scale WGBS studies at reasonable processing time and cost on the HiSeq X Ten platform. Electronic supplementary material The online version of this article (10.1186/s13072-018-0194-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shalima S Nair
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Phuc-Loi Luu
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Wenjia Qu
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Madhavi Maddugoda
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Lily Huschtscha
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Roger Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | | | | | - James G Kench
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Lisa G Horvath
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia.,Clinical Prostate Cancer Research, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Chris O'Brien Lifehouse, Camperdown, NSW, Australia
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Phillip D Stricker
- Department of Urology, St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Timothy P Hughes
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Australian Leukaemia and Lymphoma Group, Melbourne, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia.,Department of Haematology, SA Pathology, Adelaide, SA, Australia
| | - Deborah L White
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Australian Leukaemia and Lymphoma Group, Melbourne, Australia.,Faculty of Health Science and Faculty of Science, University of Adelaide, Adelaide, SA, Australia.,Australian Genomic Health Alliance, Melbourne, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, Australia
| | - Justin J-L Wong
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Susan J Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia. .,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia. .,Epigenetics Research Program, The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW, 2010, Australia.
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30
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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; 28:726-738. [PMID: 29618486 PMCID: PMC5932612 DOI: 10.1101/gr.227975.117] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 03/21/2018] [Indexed: 01/21/2023]
Abstract
Genomic rearrangements are common in cancer, with demonstrated links to disease progression and treatment response. These rearrangements can be complex, resulting in fusions of multiple chromosomal fragments and generation of derivative chromosomes. Although methods exist for detecting individual fusions, they are generally unable to reconstruct complex chained events. To overcome these limitations, we adopted a new optical mapping approach, allowing megabase-length genome maps to be reconstructed and rearranged genomes to be visualized without loss of integrity. Whole-genome mapping (Bionano Genomics) of a well-studied highly rearranged liposarcoma cell line resulted in 3338 assembled consensus genome maps, including 72 fusion maps. These fusion maps represent 112.3 Mb of highly rearranged genomic regions, illuminating the complex architecture of chained fusions, including content, order, orientation, and size. Spanning the junction of 147 chromosomal translocations, we found a total of 28 Mb of interspersed sequences that could not be aligned to the reference genome. Traversing these interspersed sequences using short-read sequencing breakpoint calls, we were able to identify and place 399 sequencing fragments within the optical mapping gaps, thus illustrating the complementary nature of optical mapping and short-read sequencing. We demonstrate that optical mapping provides a powerful new approach for capturing a higher level of complex genomic architecture, creating a scaffold for renewed interpretation of sequencing data of particular relevance to human cancer.
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Affiliation(s)
- Eva K F Chan
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, New South Wales 2010, Australia.,St Vincent's Clinical School, University of New South Wales, New South Wales 2052, Australia
| | - Daniel L Cameron
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - Desiree C Petersen
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, New South Wales 2010, Australia.,St Vincent's Clinical School, University of New South Wales, New South Wales 2052, Australia
| | - Ruth J Lyons
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, New South Wales 2010, Australia
| | - Benedetta F Baldi
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, New South Wales 2010, Australia
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Victoria 3010, Australia.,Department of Mathematics and Statistics, University of Melbourne, Victoria 3010, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia.,Bioinformatics and Cancer Genomics, Peter MacCallum Cancer Centre, Victoria 3002, Australia
| | - David M Thomas
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, New South Wales 2010, Australia.,Cancer Division, Garvan Institute of Medical Research, New South Wales 2010, Australia
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, New South Wales 2010, Australia.,St Vincent's Clinical School, University of New South Wales, New South Wales 2052, Australia.,School of Health Systems and Public Health, University of Pretoria, Hatfield 0002, South Africa.,Central Clinical School, University of Sydney, New South Wales 2006, Australia
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31
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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; 78:25-31. [PMID: 29134670 DOI: 10.1002/pros.23440] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/29/2017] [Indexed: 01/24/2023]
Abstract
BACKGROUND Mitochondrial genome (mtDNA) content is depleted in many cancers. In prostate cancer, there is intra-glandular as well as inter-patient mtDNA copy number variation. In this study, we determine if mtDNA content can be used as a predictor for prostate cancer staging and outcomes. METHODS Fresh prostate cancer biopsies from 115 patients were obtained at time of surgery. All cores underwent pathological review, followed by isolation of cancer and normal tissue. DNA was extracted and qPCR performed to quantify the total amount of mtDNA as a ratio to genomic DNA. Differences in mtDNA content were compared for prostate cancer pathology features and disease outcomes. RESULTS We showed a significantly reduced mtDNA content in prostate cancer compared with normal adjacent prostate tissue (mean difference 1.73-fold, P-value <0.001). Prostate cancer with increased mtDNA content showed unfavorable pathologic characteristics including, higher disease stage (PT2 vs PT3 P-value = 0.018), extracapsular extension (P-value = 0.02) and a trend toward an increased Gleason score (P-value = 0.064). No significant association was observed between changes in mtDNA content and biochemical recurrence (median follow up of 107 months). CONCLUSIONS Contrary to other cancer types, prostate cancer tissue shows no universally depleted mtDNA content. Rather, the change in mtDNA content is highly variable, mirroring known prostate cancer genome heterogeneity. Patients with high mtDNA content have an unfavorable pathology, while a high mtDNA content in normal adjacent prostate tissue is associated with worse prognosis.
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Affiliation(s)
- Anton M F Kalsbeek
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Medical Sciences, University of New South Wales Sydney, Randwick, New South Wales, Australia
| | - Eva K F Chan
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Medical Sciences, University of New South Wales Sydney, Randwick, New South Wales, Australia
| | - Judith Grogan
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Cancer Research Division, The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Desiree C Petersen
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Medical Sciences, University of New South Wales Sydney, Randwick, New South Wales, Australia
| | - Weerachai Jaratlerdsiri
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Ruta Gupta
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Cancer Research Division, The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Ruth J Lyons
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Anne-Maree Haynes
- Cancer Research Division, The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Lisa G Horvath
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Cancer Research Division, The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia
| | - James G Kench
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Cancer Research Division, The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Phillip D Stricker
- Department of Urology, St. Vincent's Hospital, Darlinghurst, New South Wales, Australia
| | - Vanessa M Hayes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Medical Sciences, University of New South Wales Sydney, Randwick, New South Wales, Australia
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Cancer Research Division, The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
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32
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Kalsbeek AMF, Chan EFK, 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) 2017; 8:2702-2712. [PMID: 27705925 PMCID: PMC5191864 DOI: 10.18632/aging.101044] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/20/2016] [Indexed: 12/31/2022]
Abstract
Prostate cancer management is complicated by extreme disease heterogeneity, which is further limited by availability of prognostic biomarkers. Recognition of prostate cancer as a genetic disease has prompted a focus on the nuclear genome for biomarker discovery, with little attention given to the mitochondrial genome. While it is evident that mitochondrial DNA (mtDNA) mutations are acquired during prostate tumorigenesis, no study has evaluated the prognostic value of mtDNA variation. Here we used next-generation sequencing to interrogate the mitochondrial genomes from prostate tissue biopsies and matched blood of 115 men having undergone a radical prostatectomy for which there was a mean of 107 months clinical follow-up. We identified 74 unique prostate cancer specific somatic mtDNA variants in 50 patients, providing significant expansion to the growing catalog of prostate cancer mtDNA mutations. While no single variant or variant cluster showed recurrence across multiple patients, we observe a significant positive correlation between the total burden of acquired mtDNA variation and elevated Gleason Score at diagnosis and biochemical relapse. We add to accumulating evidence that total acquired genomic burden, rather than specific mtDNA mutations, has diagnostic value. This is the first study to demonstrate the prognostic potential of mtDNA mutational burden in prostate cancer.
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Affiliation(s)
- Anton M F Kalsbeek
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,School of Medical Sciences, University of New South Wales, Randwick, NSW 2031, Australia
| | - Eva F K Chan
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,School of Medical Sciences, University of New South Wales, Randwick, NSW 2031, Australia
| | - Judith Grogan
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW 2050, Australia.,Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Desiree C Petersen
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,School of Medical Sciences, University of New South Wales, Randwick, NSW 2031, Australia
| | - Weerachai Jaratlerdsiri
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Ruta Gupta
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW 2050, Australia.,Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Ruth J Lyons
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Anne-Maree Haynes
- Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Lisa G Horvath
- Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,Chris O'Brien Lifehouse, Missenden Road, Camperdown, NSW 2050, Australia
| | - James G Kench
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW 2050, Australia.,Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Phillip D Stricker
- Department of Urology, St. Vincent's Hospital, Darlinghurst, NSW 2010, Australia
| | - Vanessa M Hayes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,School of Medical Sciences, University of New South Wales, Randwick, NSW 2031, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW 2050, Australia
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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; 171:59-71.e21. [PMID: 28938123 PMCID: PMC5679310 DOI: 10.1016/j.cell.2017.08.049] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 07/01/2017] [Accepted: 08/29/2017] [Indexed: 02/06/2023]
Abstract
We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations. PAPERCLIP.
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Affiliation(s)
- Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | | | - Mary E Prendergast
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA
| | - Alissa Mittnik
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archeological Sciences, Eberhard-Karls-University, Tuebingen 72070, Germany
| | - Kendra Sirak
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA; School of Archaeology and Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Tasneem Salie
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alexander Peltzer
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; Integrative Transcriptomics, Centre for Bioinformatics, University of Tuebingen, Tuebingen 72076, Germany
| | - Anja Heinze
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica I Cerezo-Román
- Department of Geography and Anthropology, California State Polytechnic University, Pomona, Pomona, CA 91768, USA
| | - Chrissy Chiumia
- Malawi Department of Museums and Monuments, Lilongwe 3, Malawi
| | - Alison Crowther
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; School of Social Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | | | - Katherine M Grillo
- Department of Archaeology and Anthropology, University of Wisconsin - La Crosse, La Crosse, WI 54601, USA
| | - I Taneli Helenius
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Richard Helm
- Canterbury Archaeological Trust, Canterbury CT1 2LU, UK
| | - Mark Horton
- Department Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK
| | - Saioa López
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - John Parkington
- Department of Archaeology, University of Cape Town, Cape Town 7700, South Africa
| | - Ceri Shipton
- McDonald Institute for Archaeological Research, Cambridge CB2 3ER, UK; British Institute in Eastern Africa, Nairobi 30710, Kenya
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Ruth Tibesasa
- Department of Anthropology and Archaeology, University of Pretoria, Pretoria 0083, South Africa
| | - Menno Welling
- African Studies Centre Leiden, Leiden University, Leiden 2300 RB, Netherlands; African Heritage Ltd, Zomba, Malawi
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia; School of Health Systems and Public Health, University of Pretoria, Gezina 0031, South Africa
| | - Douglas J Kennett
- Department of Anthropology and Institutes for Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA
| | - Raj Ramesar
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Nick Patterson
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alan G Morris
- Department of Archaeology, University of Cape Town, Cape Town 7700, South Africa
| | - Nicole Boivin
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, University College Dublin, Dublin 4, Ireland; Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archeological Sciences, Eberhard-Karls-University, Tuebingen 72070, Germany
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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Kalsbeek AM, Chan EK, 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; 8:71342-71357. [PMID: 29050365 PMCID: PMC5642640 DOI: 10.18632/oncotarget.19926] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/26/2017] [Indexed: 12/17/2022] Open
Abstract
Prostate cancer is a genetic disease. While next generation sequencing has allowed for the emergence of molecular taxonomy, classification is restricted to the nuclear genome. Mutations within the maternally inherited mitochondrial genome are known to impact cancer pathogenesis, as a result of disturbances in energy metabolism and apoptosis. With a higher mutation rate, limited repair and increased copy number compared to the nuclear genome, the clinical relevance of mitochondrial DNA (mtDNA) variation requires deeper exploration. Here we provide a systematic review of the landscape of prostate cancer associated mtDNA variation. While the jury is still out on the association between inherited mtDNA variation and prostate cancer risk, we collate a total of 749 uniquely reported prostate cancer associated somatic mutations. Support exists for number of somatic events, extent of heteroplasmy, and rate of recurrence of mtDNA mutations, increasing with disease aggression. While, the predicted pathogenic impact for recurrent prostate cancer associated mutations appears negligible, evidence exists for carcinogenic mutations impacting the cytochrome c oxidase complex and regulating metastasis through elevated reactive oxygen species production. Due to a lack of lethal cohort analyses, we provide additional unpublished data for metastatic disease. Discussing the advantages of mtDNA as a prostate cancer biomarker, we provide a review of current progress of including elevated mtDNA levels, of a large somatic deletion, acquired tRNAs mutations, heteroplasmy and total number of somatic events (mutational load). We confirm via meta-analysis a significant association between mtDNA mutational load and pathological staging at diagnosis or surgery (p < 0.0001).
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Affiliation(s)
- Anton M.F. Kalsbeek
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Medical Faculty, University of New South Wales, Randwick, New South Wales, Australia
| | - Eva K.F. Chan
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Medical Faculty, University of New South Wales, Randwick, New South Wales, Australia
| | - Niall M. Corcoran
- Australian Prostate Cancer Research Centre Epworth, Richmond, Victoria, Australia
- Departments of Urology and Surgery, Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher M. Hovens
- Australian Prostate Cancer Research Centre Epworth, Richmond, Victoria, Australia
- Departments of Urology and Surgery, Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Vanessa M. Hayes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Medical Faculty, University of New South Wales, Randwick, New South Wales, Australia
- Central Clinical School, University of Sydney, Camperdown, New South Wales, Australia
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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; 8:23588-23602. [PMID: 28423598 PMCID: PMC5410329 DOI: 10.18632/oncotarget.15802] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 02/15/2017] [Indexed: 12/27/2022] Open
Abstract
Complex genomic rearrangements are common molecular events driving prostate carcinogenesis. Clinical significance, however, has yet to be fully elucidated. Detecting the full range and subtypes of large structural variants (SVs), greater than one kilobase in length, is challenging using clinically feasible next generation sequencing (NGS) technologies. Next generation mapping (NGM) is a new technology that allows for the interrogation of megabase length DNA molecules outside the detection range of single-base resolution NGS. In this study, we sought to determine the feasibility of using the Irys (Bionano Genomics Inc.) nanochannel NGM technology to generate whole genome maps of a primary prostate tumor and matched blood from a Gleason score 7 (4 + 3), ETS-fusion negative prostate cancer patient. With an effective mapped coverage of 35X and sequence coverage of 60X, and an estimated 43% tumor purity, we identified 85 large somatic structural rearrangements and 6,172 smaller somatic variants, respectively. The vast majority of the large SVs (89%), of which 73% are insertions, were not detectable ab initio using high-coverage short-read NGS. However, guided manual inspection of single NGS reads and de novo assembled scaffolds of NGM-derived candidate regions allowed for confirmation of 94% of these large SVs, with over a third impacting genes with oncogenic potential. From this single-patient study, the first cancer study to integrate NGS and NGM data, we hypothesise that there exists a novel spectrum of large genomic rearrangements in prostate cancer, that these large genomic rearrangements are likely early events in tumorigenesis, and they have potential to enhance taxonomy.
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Affiliation(s)
- Weerachai Jaratlerdsiri
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Eva K F Chan
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Australia.,St Vincent's Clinical School, University of New South Wales, Randwick, Australia
| | - Desiree C Petersen
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Australia.,St Vincent's Clinical School, University of New South Wales, Randwick, Australia
| | - Claire Yang
- Bionano Genomics Inc., San Diego, California, USA
| | - Peter I Croucher
- St Vincent's Clinical School, University of New South Wales, Randwick, Australia.,Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Randwick, Australia
| | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Palak Sheth
- Bionano Genomics Inc., San Diego, California, USA
| | - Vanessa M Hayes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Australia.,St Vincent's Clinical School, University of New South Wales, Randwick, Australia.,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.,Central Clinical School, University of Sydney, Camperdown, Australia
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36
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Kalsbeek AM, Chan EF, Grogan J, Petersen DC, Jaratlerdsiri W, Gupta R, Lyons RJ, Haynes AM, Horvath LG, Kench JG, Stricker PD, Hayes VM. Mitochondrial genome content is decreased in prostate cancer overall, but increased in high grade cancer. Pathology 2017. [DOI: 10.1016/j.pathol.2016.12.300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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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 2016; 15:394-405. [PMID: 25882061 DOI: 10.2174/1568009615666150416113453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 11/30/2014] [Accepted: 11/30/2014] [Indexed: 11/22/2022]
Abstract
Cancer is fundamentally a genomic disease caused by mutations or rearrangements in the DNA or epigenetic machinery of a patient. An emerging field in cancer treatment targets key aberrations arising from the mutational landscape of an individual patient's disease rather than employing a cancer-wide cytotoxic therapy approach. In prostate cancer in particular, where there is an observed variation in response to standard treatments between patients with disease of a similar pathological stage and grade, mutationdirected treatment may grow to be a viable tool for clinicians to tailor more effective treatments. This review will describe a number of mutations across multiple forms of cancer that have been successfully antagonised by targeted therapeutics including their identification, the development of targeted compounds to combat them and the development of resistance to these therapies. This review will continue to examine these same mutations in the treatment and management of prostate cancer; the prevalence of targetable mutations in prostate cancer, recent clinical trials of targeted-agents and the potential or limitations for their use.
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Affiliation(s)
| | | | | | | | | | | | - Christopher M Hovens
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, Victoria, Australia.
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38
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McCrow JP, Petersen DC, Louw M, Chan EKF, Harmeyer K, Vecchiarelli S, Lyons RJ, Bornman MSR, Hayes VM. Spectrum of mitochondrial genomic variation and associated clinical presentation of prostate cancer in South African men. Prostate 2016; 76:349-58. [PMID: 26660354 PMCID: PMC4832339 DOI: 10.1002/pros.23126] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/05/2015] [Indexed: 01/09/2023]
Abstract
BACKGROUND Prostate cancer incidence and mortality rates are significantly increased in African-American men, but limited studies have been performed within Sub-Saharan African populations. As mitochondria control energy metabolism and apoptosis we speculate that somatic mutations within mitochondrial genomes are candidate drivers of aggressive prostate carcinogenesis. METHODS We used matched blood and prostate tissue samples from 87 South African men (77 with African ancestry) to perform deep sequencing of complete mitochondrial genomes. Clinical presentation was biased toward aggressive disease (Gleason score >7, 64%), and compared with men without prostate cancer either with or without benign prostatic hyperplasia. RESULTS We identified 144 somatic mtDNA single nucleotide variants (SNVs), of which 80 were observed in 39 men presenting with aggressive disease. Both the number and frequency of somatic mtDNA SNVs were associated with higher pathological stage. CONCLUSIONS Besides doubling the total number of somatic PCa-associated mitochondrial genome mutations identified to date, we associate mutational load with aggressive prostate cancer status in men of African ancestry.
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Affiliation(s)
| | - Desiree C. Petersen
- J. Craig Venter InstituteLa JollaCalifornia
- Laboratory for Human Comparative and Prostate Cancer GenomicsGarvan Institute of Medical ResearchDarlinghurst, SydneyNSWAustralia
- Faculty of MedicineUniversity of New SouthWales Australia, RandwickNSWAustralia
| | - Melanie Louw
- Department of PathologyUniversity of PretoriaSouth Africa
| | - Eva K. F. Chan
- Laboratory for Human Comparative and Prostate Cancer GenomicsGarvan Institute of Medical ResearchDarlinghurst, SydneyNSWAustralia
- Faculty of MedicineUniversity of New SouthWales Australia, RandwickNSWAustralia
| | - Katherine Harmeyer
- J. Craig Venter InstituteLa JollaCalifornia
- Laboratory for Human Comparative and Prostate Cancer GenomicsGarvan Institute of Medical ResearchDarlinghurst, SydneyNSWAustralia
| | - Stefano Vecchiarelli
- Laboratory for Human Comparative and Prostate Cancer GenomicsGarvan Institute of Medical ResearchDarlinghurst, SydneyNSWAustralia
| | - Ruth J. Lyons
- Laboratory for Human Comparative and Prostate Cancer GenomicsGarvan Institute of Medical ResearchDarlinghurst, SydneyNSWAustralia
| | - M. S. Riana Bornman
- School of Health Systems and Public HealthUniversity of PretoriaSouth Africa
| | - Vanessa M. Hayes
- J. Craig Venter InstituteLa JollaCalifornia
- Laboratory for Human Comparative and Prostate Cancer GenomicsGarvan Institute of Medical ResearchDarlinghurst, SydneyNSWAustralia
- Faculty of MedicineUniversity of New SouthWales Australia, RandwickNSWAustralia
- School of Health Systems and Public HealthUniversity of PretoriaSouth Africa
- Central Clinical SchoolUniversity of SydneyCamperdown, SydneyNSWAustralia
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Hayes VM, Tindall EA, Bornman R. Abstract B22: Significance of ethnic-based disparities in prostate cancer risk and outcomes. Cancer Epidemiol Biomarkers Prev 2015. [DOI: 10.1158/1538-7755.disp14-b22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Ethnic-based disparities have been significantly associated with prostate cancer incidence, age and pathological/biochemical presentation, and mortality. Risk for these parameters are lowest in Asian men relative to men of European ancestry, while the highest in men of African ancestry, in particular African-Americans. Limited studies have, however, addressed clinical presentation and contributing factors within the context of Africa. We established the Southern African Prostate Cancer Study (SAPCS), a unique resource to investigate clinical presentation and risk factors within non-migrant Africans. Enrolling over 1000 men to date we report skewing towards significantly higher prostate specific antigen (PSA) levels in cases (83.0% present with a PSA≥20mg/L; median PSA=98.8mg/L) relative to men with no detectable PCa (18.5% present with a PSA≥20mg/L; median PSA=9.1mg/L). Compared with African-Americans, non-migrant Africans presented with significantly more aggressive disease defined by Gleason score >7 (17% and 36%, respectively) and PSA≥20mg/L (17.2% and 83.2%, respectively), which is further exasperated in men from rural versus urban localities. To determine if the observed clinical presentation is driven by genetics and/or environmental factors, we investigated the power for the most significant genome-wide association study (GWAS) identified PCa risk alleles (n=46) as well as epidemiological measures to predict PCa status and/or disease outcomes within the SAPCS. While we show no evidence that previously defined PCa risk alleles predict disease status within Africa, we show associations with family history of cancer, diabetes, current sexual activity and erectile dysfunction, balding pattern, frequent aspirin usage and high PSA levels. We propose that the SAPCS provides a unique non-PSA tested resource to enhance our understanding that drives significant disparities in PCa associated with ethnic background.
Citation Format: Vanessa M. Hayes, Elizabeth A. Tindall, Riana Bornman. Significance of ethnic-based disparities in prostate cancer risk and outcomes. [abstract]. In: Proceedings of the Seventh AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 9-12, 2014; San Antonio, TX. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2015;24(10 Suppl):Abstract nr B22.
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Chan EKF, Hardie RA, Petersen DC, Beeson K, Bornman RMS, Smith AB, Hayes VM. Revised timeline and distribution of the earliest diverged human maternal lineages in southern Africa. PLoS One 2015; 10:e0121223. [PMID: 25807545 PMCID: PMC4373779 DOI: 10.1371/journal.pone.0121223] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/29/2015] [Indexed: 02/05/2023] Open
Abstract
The oldest extant human maternal lineages include mitochondrial haplogroups L0d and L0k found in the southern African click-speaking forager peoples broadly classified as Khoesan. Profiling these early mitochondrial lineages allows for better understanding of modern human evolution. In this study, we profile 77 new early-diverged complete mitochondrial genomes and sub-classify another 105 L0d/L0k individuals from southern Africa. We use this data to refine basal phylogenetic divergence, coalescence times and Khoesan prehistory. Our results confirm L0d as the earliest diverged lineage (∼172 kya, 95%CI: 149–199 kya), followed by L0k (∼159 kya, 95%CI: 136–183 kya) and a new lineage we name L0g (∼94 kya, 95%CI: 72–116 kya). We identify two new L0d1 subclades we name L0d1d and L0d1c4/L0d1e, and estimate L0d2 and L0d1 divergence at ∼93 kya (95%CI:76–112 kya). We concur the earliest emerging L0d1’2 sublineage L0d1b (∼49 kya, 95%CI:37–58 kya) is widely distributed across southern Africa. Concomitantly, we find the most recent sublineage L0d2a (∼17 kya, 95%CI:10–27 kya) to be equally common. While we agree that lineages L0d1c and L0k1a are restricted to contemporary inland Khoesan populations, our observed predominance of L0d2a and L0d1a in non-Khoesan populations suggests a once independent coastal Khoesan prehistory. The distribution of early-diverged human maternal lineages within contemporary southern Africans suggests a rich history of human existence prior to any archaeological evidence of migration into the region. For the first time, we provide a genetic-based evidence for significant modern human evolution in southern Africa at the time of the Last Glacial Maximum at between ∼21–17 kya, coinciding with the emergence of major lineages L0d1a, L0d2b, L0d2d and L0d2a.
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Affiliation(s)
- Eva K. F. Chan
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia
- Faculty of Medicine, University of New South Wales Australia, Randwick, NSW, Australia
| | - Rae-Anne Hardie
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia
- Faculty of Medicine, University of New South Wales Australia, Randwick, NSW, Australia
| | - Desiree C. Petersen
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia
- Faculty of Medicine, University of New South Wales Australia, Randwick, NSW, Australia
- J. Craig Venter Institute, 4120 Torrey Pines Road, La Jolla, California, 92037, United States of America
| | - Karen Beeson
- J. Craig Venter Institute, 4120 Torrey Pines Road, La Jolla, California, 92037, United States of America
| | - Riana M. S. Bornman
- School of Health Systems and Public Health, University of Pretoria, Hatfield, South Africa
| | - Andrew B. Smith
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
| | - Vanessa M. Hayes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia
- Faculty of Medicine, University of New South Wales Australia, Randwick, NSW, Australia
- J. Craig Venter Institute, 4120 Torrey Pines Road, La Jolla, California, 92037, United States of America
- School of Health Systems and Public Health, University of Pretoria, Hatfield, South Africa
- Central Clinical School, The University of Sydney, Camperdown, NSW, Australia
- * E-mail:
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Abstract
The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-speaking forager peoples of southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semidesert regions of Namibia and Botswana, whereas archeological, historical, and genetic evidence promotes a once broader southerly dispersal of click-speaking peoples including southward migrating pastoralists and indigenous marine-foragers. No genetic data have been recovered from the indigenous peoples that once sustained life along the southern coastal waters of Africa prepastoral arrival. In this study we generate a complete mitochondrial genome from a 2,330-year-old male skeleton, confirmed through osteological and archeological analysis as practicing a marine-based forager existence. The ancient mtDNA represents a new L0d2c lineage (L0d2c1c) that is today, unlike its Khoe-language based sister-clades (L0d2c1a and L0d2c1b) most closely related to contemporary indigenous San-speakers (specifically Ju). Providing the first genomic evidence that prepastoral Southern African marine foragers carried the earliest diverged maternal modern human lineages, this study emphasizes the significance of Southern African archeological remains in defining early modern human origins.
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Affiliation(s)
- Alan G Morris
- Department of Human Biology, University of Cape Town, South Africa
| | - Anja Heinze
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Eva K F Chan
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Andrew B Smith
- Department of Archeology, University of Cape Town, South Africa
| | - Vanessa M Hayes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia Genomeic Medicine Group, J. Craig Venter Institute, La Jolla, California Central Clinical School, The University of Sydney, Camperdown, New South Wales, Australia Department of Urology, University of Pretoria, South Africa Medical Faculty, University of New South Wales, Randwick, New South Wales, Australia
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Tindall EA, Monare LR, Petersen DC, van Zyl S, Hardie RA, Segone AM, Venter PA, Bornman MSR, Hayes VM. Clinical presentation of prostate cancer in black South Africans. Prostate 2014; 74:880-91. [PMID: 24723425 PMCID: PMC4135056 DOI: 10.1002/pros.22806] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/12/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND Compared with White Americans, Black American men are at a significant increased risk of presenting with prostate cancer (PCa) and associated mortality, suggesting a link to African-ancestry. However, PCa status within Africa is largely unknown. We address the clinical presentation of PCa within Black South African men. METHODS Over 1,000 participants with or without PCa have enrolled in the Southern African Prostate Cancer Study (SAPCS). Using genome-wide profiling we establish a unique within Africa population substructure. Adjusting for age, clinical variables were assessed, compared against Black Americans and between rural and urban localities while addressing potential socio-demographic confounders. RESULTS We report a significant difference in the distribution of prostate specific antigen (PSA) levels skewed towards higher PSA levels in the PCa cases (83.0% present with a PSA ≥ 20 µg/L; median PSA = 98.8 µg/L) relative to men with no detectable PCa (18.5% present with a PSA ≥ 20 µg/L; median PSA = 9.1 µg/L). Compared with Black Americans, Black South Africans presented with significantly more aggressive disease defined by Gleason score >7 (17% and 36%, respectively) and PSA ≥ 20 µg/L (17.2% and 83.2%, respectively). We report exasperated disease aggression defined by Gleason score >7 (P = 0.0042) and poorly differentiated tumor grade (P < 0.0001) within rural versus urban localities. CONCLUSION Black South African men present with higher PSA levels and histopathological tumor grade compared with Black Americans, which is further escalated in men from rural localities. Our data suggests that lack of PSA testing may be contributing to an aggressive PCa disease phenotype within South African men.
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Affiliation(s)
| | - L Richard Monare
- Department of Urology, University of LimpopoMedunsa, South Africa
| | - Desiree C Petersen
- J. Craig Venter InstituteLa Jolla, California
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research and The Kinghorn Cancer CentreDarlinghurst, New South Wales, Australia
| | - Smit van Zyl
- Department of Urology, University of LimpopoMedunsa, South Africa
| | - Rae-Anne Hardie
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research and The Kinghorn Cancer CentreDarlinghurst, New South Wales, Australia
| | - Alpheus M Segone
- Department of Urology, University of LimpopoMedunsa, South Africa
| | - Philip A Venter
- Department of Medical Sciences, University of LimpopoTurfloop, South Africa
| | - MS Riana Bornman
- Department of Urology, University of PretoriaPretoria, South Africa
| | - Vanessa M Hayes
- J. Craig Venter InstituteLa Jolla, California
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research and The Kinghorn Cancer CentreDarlinghurst, New South Wales, Australia
- Department of Medical Sciences, University of LimpopoTurfloop, South Africa
- Sydney Medical School, University of SydneyCamperdown, New South Wales, Australia
- *Correspondence to: Professor Vanessa M. Hayes, Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, Australia. E-mail:
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Tindall EA, Bornman MSR, 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; 13:74. [PMID: 24373635 PMCID: PMC3882498 DOI: 10.1186/1471-2490-13-74] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 12/24/2013] [Indexed: 11/30/2022] Open
Abstract
Background Although African ancestry represents a significant risk factor for prostate cancer, few studies have investigated the significance of prostate cancer and relevance of previously defined genetic and epidemiological prostate cancer risk factors within Africa. We recently established the Southern African Prostate Cancer Study (SAPCS), a resource for epidemiological and genetic analysis of prostate cancer risk and outcomes in Black men from South Africa. Biased towards highly aggressive prostate cancer disease, this is the first reported data analysis. Methods The SAPCS is an ongoing population-based study of Black men with or without prostate cancer. Pilot analysis was performed for the first 837 participants, 522 cases and 315 controls. We investigate 46 pre-defined prostate cancer risk alleles and up to 24 epidemiological measures including demographic, lifestyle and environmental factors, for power to predict disease status and to drive on-going SAPCS recruitment, sampling procedures and research direction. Results Preliminary results suggest that no previously defined risk alleles significantly predict prostate cancer occurrence within the SAPCS. Furthermore, genetic risk profiles did not enhance the predictive power of prostate specific antigen (PSA) testing. Our study supports several lifestyle/environmental factors contributing to prostate cancer risk including a family history of cancer, diabetes, current sexual activity and erectile dysfunction, balding pattern, frequent aspirin usage and high PSA levels. Conclusions Despite a clear increased prostate cancer risk associated with an African ancestry, experimental data is lacking within Africa. This pilot study is therefore a significant contribution to the field. While genetic risk factors (largely European-defined) show no evidence for disease prediction in the SAPCS, several epidemiological factors were associated with prostate cancer status. We call for improved study power by building on the SAPCS resource, further validation of associated factors in independent African-based resources, and genome-wide approaches to define African-specific risk alleles.
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Affiliation(s)
| | | | | | | | | | | | - Vanessa M Hayes
- J, Craig Venter Institute, Genomic Medicine Group, San Diego, CA, USA.
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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:e51762. [PMID: 23251618 PMCID: PMC3520848 DOI: 10.1371/journal.pone.0051762] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 11/06/2012] [Indexed: 12/02/2022] Open
Abstract
Mutations in the SERPINA1 gene can cause deficiency in the circulating serine protease inhibitor α1-Antitrypsin (α1AT). α1AT deficiency is the major contributor to pulmonary emphysema and liver disease in persons of European ancestry, with a prevalence of 1 in 2500 in the USA. We present the discovery and characterization of a novel SERPINA1 mutant from an asymptomatic Middle Eastern male with circulating α1AT deficiency. This 49 base pair deletion mutation (T379Δ), originally mistyped by IEF, causes a frame-shift replacement of the last sixteen α1AT residues and adds an extra twenty-four residues. Functional analysis showed that the mutant protein is not secreted and prone to intracellular aggregation.
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Affiliation(s)
- Darren N Saunders
- Cancer Research Program, Garvan Institute of Medical Research, Sydney, Australia.
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Tindall EA, Severi G, Hoang HN, Southey MC, English DR, Hopper JL, Giles GG, Hayes VM. Interleukin-6 promoter variants, prostate cancer risk, and survival. Prostate 2012; 72:1701-7. [PMID: 22782910 DOI: 10.1002/pros.22557] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 06/12/2012] [Indexed: 12/20/2022]
Abstract
BACKGROUND Inflammation has been implicated in prostate cancer (PCa) pathogenesis. Promoter DNA variants responsible for differential expression of key cytokines may therefore influence susceptibility to PCa. METHODS Two interleukin-6 (IL-6) promoter variants, -174G>C and -6331T>C, were genotyped for association with PCa risk and survival using the Risk Factors for Prostate Cancer Study (RFPCS, 825 cases and 732 controls) and the Melbourne Collaborative Cohort Study (MCCS, 818 cases and 1,745 controls). Impact of genotypes on IL-6 transcriptional activity was measured using Low Density Arrays. RESULTS A significant increase in IL-6 transcriptional activity in malignant compared to benign prostate tissue supports a role for IL-6 in PCa. The -174G>C variant showed no association with PCa risk, overall survival, or IL-6 transcriptional activity. The -6331 C-allele was significantly associated with an increased risk in the RFPCS (OR = 1.29, 95% CI = 1.08-1.54), but not in the MCCS. In the MCCS however, cases presenting with a CC genotype conferred a higher risk of mortality (HR = 2.27, 95% CI = 1.34-3.85), which was maintained although reduced overall in the pooled analysis with RFPCS (HR = 1.68, 95% CI = 1.10-2.54). Furthermore, we associate the minor C-allele with a significant decrease in IL-6 transcriptional activity. CONCLUSIONS While our study refutes a role for IL-6 -174G>C, it is the first to implicate -6331T>C with PCa risk and poor survival. Our observation that -6331T>C has a significant impact on IL-6 transcriptional activity, calls for further investigations into the role of this variant as a novel PCa biomarker.
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Affiliation(s)
- Elizabeth A Tindall
- Cancer Genetics Group, Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Randwick, New South Wales, Australia
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Hayes VM. Treasure Caves
Cradle of Humankind
World Heritage Site Sterkfontein 1911, South Africa www.cradleofhumankind.co.za. Science 2012. [DOI: 10.1126/science.1211058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Our reviewer visits a World Heritage Site in South Africa that preserves the source of several important hominin fossils.
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Affiliation(s)
- Vanessa M. Hayes
- The reviewer is at the J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA 92121, USA
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Abstract
Background The most common application for the next-generation sequencing technologies is resequencing, where short reads from the genome of an individual are aligned to a reference genome sequence for the same species. These mappings can then be used to identify genetic differences among individuals in a population, and perhaps ultimately to explain phenotypic variation. Many algorithms capable of aligning short reads to the reference, and determining differences between them have been reported. Much less has been reported on how to use these technologies to determine genetic differences among individuals of a species for which a reference sequence is not available, which drastically limits the number of species that can easily benefit from these new technologies. Results We describe a computational pipeline, called DIAL (De novo Identification of Alleles), for identifying single-base substitutions between two closely related genomes without the help of a reference genome. The method works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to determine small insertions/deletions. We evaluate the software's effectiveness using published Roche/454 sequence data from the genome of Dr. James Watson (to detect heterozygous positions) and recent Illumina data from orangutan, in each case comparing our results to those from computational analysis that uses a reference genome assembly. We also illustrate the use of DIAL to identify nucleotide differences among transcriptome sequences. Conclusions DIAL can be used for identification of nucleotide differences in species for which no reference sequence is available. Our main motivation is to use this tool to survey the genetic diversity of endangered species as the identified sequence differences can be used to design genotyping arrays to assist in the species' management. The DIAL source code is freely available at http://www.bx.psu.edu/miller_lab/.
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Affiliation(s)
- Aakrosh Ratan
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, USA.
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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; 10:69. [PMID: 20184734 PMCID: PMC2841665 DOI: 10.1186/1471-2407-10-69] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 02/25/2010] [Indexed: 12/13/2022] Open
Abstract
Background Chronic inflammation is considered to be implicated in the development of prostate cancer. In this study we are the first to investigate a potential association between variants in an autoimmune related region on chromosome 4q27 and prostate cancer risk. This region harbors two cytokine genes IL-2 and the recently described IL-21. Methods We genotyped six variants previously associated with autoimmune disease (namely rs13151961, rs13119723, rs17388568, rs3136534, rs6822844 and rs6840978) and one functional IL-2 promoter variant (rs2069762) for possible association with prostate cancer risk using the Australian Risk Factors for Prostate Cancer case-control Study. Results Overall, our results do not support an association between the seven variants at position 4q27 and prostate cancer risk. Per allele odds ratios (ORs) were not significantly different from 1 (all P-values = 0.06). However, we found suggestive evidence for a significant association between the presence of the rs13119723 variant (located in a protein of unknown function) and men with a family history of prostate cancer in first-degree relatives (P-value for interaction 0.02). The per allele OR associated with this variant was significantly higher than 1 (2.37; 95% C.I. = 1.01-5.57). Conclusions We suggest that genetic variation within the chromosome 4q27 locus might be associated with prostate cancer susceptibility in men with a family history of the disease. Furthermore, our study alludes to a potential role of unknown protein KIAA1109 in conferring this risk.
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Affiliation(s)
- Elizabeth A Tindall
- Cancer Genetics Group, Children's Cancer Institute Australia for Medical Research, Sydney Children's Hospital, High St, Randwick, NSW, Australia
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Tindall EA, Petersen DC, Nikolaysen S, Miller W, Schuster SC, Hayes VM. Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation. BMC Res Notes 2010; 3:39. [PMID: 20175893 PMCID: PMC2848685 DOI: 10.1186/1756-0500-3-39] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2010] [Accepted: 02/22/2010] [Indexed: 11/29/2022] Open
Abstract
Background High-throughput custom designed genotyping arrays are a valuable resource for biologically focused research studies and increasingly for validation of variation predicted by next-generation sequencing (NGS) technologies. We investigate the Illumina GoldenGate chemistry using custom designed VeraCode and sentrix array matrix (SAM) assays for each of these applications, respectively. We highlight applications for interpretation of Illumina generated genotype cluster plots to maximise data inclusion and reduce genotyping errors. Findings We illustrate the dramatic effect of outliers in genotype calling and data interpretation, as well as suggest simple means to avoid genotyping errors. Furthermore we present this platform as a successful method for two-cluster rare or non-autosomal variant calling. The success of high-throughput technologies to accurately call rare variants will become an essential feature for future association studies. Finally, we highlight additional advantages of the Illumina GoldenGate chemistry in generating unusually segregated cluster plots that identify potential NGS generated sequencing error resulting from minimal coverage. Conclusions We demonstrate the importance of visually inspecting genotype cluster plots generated by the Illumina software and issue warnings regarding commonly accepted quality control parameters. In addition to suggesting applications to minimise data exclusion, we propose that the Illumina cluster plots may be helpful in identifying potential in-put sequence errors, particularly important for studies to validate NGS generated variation.
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Affiliation(s)
- Elizabeth A Tindall
- Cancer Genetics Group, Children's Cancer Institute Australia for Medical Research, Sydney Children's Hospital, High Street, Randwick, NSW 2031, Australia.
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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; 17:117-22. [PMID: 20154336 PMCID: PMC2853383 DOI: 10.1093/dnares/dsq003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A newly described heterodimeric cytokine, interleukin-23 (IL-23) is emerging as a key player in both the innate and the adaptive T helper (Th)17 driven immune response as well as an initiator of several autoimmune diseases. The rate-limiting element of IL-23 production is believed to be driven by expression of the unique p19 subunit encoded by IL23A. We set out to perform comprehensive DNA sequencing of this previously under-studied gene in 96 individuals from two evolutionary distinct human population groups, Southern African Bantu and European. We observed a total of 33 different DNA variants within these two groups, 22 (67%) of which are currently not reported in any available database. We further demonstrate both inter-population and intra-species sequence conservation within the coding and known regulatory regions of IL23A, supporting a critical physiological role for IL-23. We conclude that IL23A may have undergone positive selection pressure directed towards conservation, suggesting that functional genetic variants within IL23A will have a significant impact on the host immune response.
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Affiliation(s)
- Elizabeth A Tindall
- Cancer Genetics Group, Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
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