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Jaratlerdsiri W, Jiang J, Gong T, Patrick SM, Willet C, Chew T, Lyons RJ, Haynes AM, Pasqualim G, Louw M, Kench JG, Campbell R, Horvath LG, Chan EKF, Wedge DC, Sadsad R, Brum IS, Mutambirwa SBA, Stricker PD, Bornman MSR, Hayes VM. African-specific molecular taxonomy of prostate cancer. Nature 2022; 609:552-559. [PMID: 36045292 PMCID: PMC9477733 DOI: 10.1038/s41586-022-05154-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/27/2022] [Indexed: 12/24/2022]
Abstract
Prostate cancer is characterized by considerable geo-ethnic disparity. African ancestry is a significant risk factor, with mortality rates across sub-Saharan Africa of 2.7-fold higher than global averages1. The contributing genetic and non-genetic factors, and associated mutational processes, are unknown2,3. Here, through whole-genome sequencing of treatment-naive prostate cancer samples from 183 ancestrally (African versus European) and globally distinct patients, we generate a large cancer genomics resource for sub-Saharan Africa, identifying around 2 million somatic variants. Significant African-ancestry-specific findings include an elevated tumour mutational burden, increased percentage of genome alteration, a greater number of predicted damaging mutations and a higher total of mutational signatures, and the driver genes NCOA2, STK19, DDX11L1, PCAT1 and SETBP1. Examining all somatic mutational types, we describe a molecular taxonomy for prostate cancer differentiated by ancestry and defined as global mutational subtypes (GMS). By further including Chinese Asian data, we confirm that GMS-B (copy-number gain) and GMS-D (mutationally noisy) are specific to African populations, GMS-A (mutationally quiet) is universal (all ethnicities) and the African-European-restricted subtype GMS-C (copy-number losses) predicts poor clinical outcomes. In addition to the clinical benefit of including individuals of African ancestry, our GMS subtypes reveal different evolutionary trajectories and mutational processes suggesting that both common genetic and environmental factors contribute to the disparity between ethnicities. Analogous to gene-environment interaction-defined here as a different effect of an environmental surrounding in people with different ancestries or vice versa-we anticipate that GMS subtypes act as a proxy for intrinsic and extrinsic mutational processes in cancers, promoting global inclusion in landmark studies.
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Affiliation(s)
- Weerachai Jaratlerdsiri
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
- Genomics and Epigenetic Theme, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Jue Jiang
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
- Genomics and Epigenetic Theme, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Tingting Gong
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
- Genomics and Epigenetic Theme, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Sean M Patrick
- School of Health Systems & Public Health, University of Pretoria, Pretoria, South Africa
| | - Cali Willet
- Sydney Informatics Hub, University of Sydney, Darlington, New South Wales, Australia
| | - Tracy Chew
- Sydney Informatics Hub, University of Sydney, Darlington, New South Wales, Australia
| | - Ruth J Lyons
- Genomics and Epigenetic Theme, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Anne-Maree Haynes
- Genomics and Epigenetic Theme, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Gabriela Pasqualim
- Endocrine and Tumor Molecular Biology Laboratory (LABIMET), Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratory of Genetics, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Melanie Louw
- National Health Laboratory Services, Johannesburg, South Africa
| | - James G Kench
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and Central Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | | | - Lisa G Horvath
- Genomics and Epigenetic Theme, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Medical Oncology, Chris O'Brien Lifehouse, Royal Prince Alfred Hospital and Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Eva K F Chan
- Genomics and Epigenetic Theme, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- NSW Health Pathology, Sydney, New South Wales, Australia
| | - David C Wedge
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Rosemarie Sadsad
- Sydney Informatics Hub, University of Sydney, Darlington, New South Wales, Australia
| | - Ilma Simoni Brum
- Endocrine and Tumor Molecular Biology Laboratory (LABIMET), 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, South Africa
| | - Phillip D Stricker
- Genomics and Epigenetic Theme, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Urology, St Vincent's Hospital, Darlinghurst, New South Wales, Australia
| | - M S Riana Bornman
- School of Health Systems & 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, New South Wales, Australia.
- Genomics and Epigenetic Theme, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.
- School of Health Systems & Public Health, University of Pretoria, Pretoria, South Africa.
- Faculty of Health Sciences, University of Limpopo, Mankweng, South Africa.
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Jeffet J, Margalit S, Michaeli Y, Ebenstein Y. Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale. Essays Biochem 2021; 65:51-66. [PMID: 33739394 PMCID: PMC8056043 DOI: 10.1042/ebc20200021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method's basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method's resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.
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Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sapir Margalit
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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Goldrich DY, LaBarge B, Chartrand S, Zhang L, Sadowski HB, Zhang Y, Pham K, Way H, Lai CYJ, Pang AWC, Clifford B, Hastie AR, Oldakowski M, Goldenberg D, Broach JR. Identification of Somatic Structural Variants in Solid Tumors by Optical Genome Mapping. J Pers Med 2021; 11:142. [PMID: 33670576 PMCID: PMC7921992 DOI: 10.3390/jpm11020142] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
Genomic structural variants comprise a significant fraction of somatic mutations driving cancer onset and progression. However, such variants are not readily revealed by standard next-generation sequencing. Optical genome mapping (OGM) surpasses short-read sequencing in detecting large (>500 bp) and complex structural variants (SVs) but requires isolation of ultra-high-molecular-weight DNA from the tissue of interest. We have successfully applied a protocol involving a paramagnetic nanobind disc to a wide range of solid tumors. Using as little as 6.5 mg of input tumor tissue, we show successful extraction of high-molecular-weight genomic DNA that provides a high genomic map rate and effective coverage by optical mapping. We demonstrate the system's utility in identifying somatic SVs affecting functional and cancer-related genes for each sample. Duplicate/triplicate analysis of select samples shows intra-sample reliability but also intra-sample heterogeneity. We also demonstrate that simply filtering SVs based on a GRCh38 human control database provides high positive and negative predictive values for true somatic variants. Our results indicate that the solid tissue DNA extraction protocol, OGM and SV analysis can be applied to a wide variety of solid tumors to capture SVs across the entire genome with functional importance in cancer prognosis and treatment.
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Affiliation(s)
- David Y. Goldrich
- Department of Otolaryngology—Head and Neck Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (D.Y.G.); (B.L.); (D.G.)
| | - Brandon LaBarge
- Department of Otolaryngology—Head and Neck Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (D.Y.G.); (B.L.); (D.G.)
| | - Scott Chartrand
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.C.); (L.Z.)
| | - Lijun Zhang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.C.); (L.Z.)
| | - Henry B. Sadowski
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Yang Zhang
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Khoa Pham
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Hannah Way
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Chi-Yu Jill Lai
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Andy Wing Chun Pang
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Benjamin Clifford
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Alex R. Hastie
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - Mark Oldakowski
- Bionano Genomics, San Diego, CA 92121, USA; (H.B.S.); (Y.Z.); (K.P.); (H.W.); (C.-Y.J.L.); (A.W.C.P.); (B.C.); (A.R.H.); (M.O.)
| | - David Goldenberg
- Department of Otolaryngology—Head and Neck Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (D.Y.G.); (B.L.); (D.G.)
| | - James R. Broach
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.C.); (L.Z.)
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Bahcivan A, Gamsizkan M, Kantarcioglu Coskun S, Cangur S, Yuksel A, Ceyhan A, Onal B. KRAS, BRAF, PIK3CA mutation frequency of radical prostatectomy samples and review of the literature. Aging Male 2020; 23:1627-1641. [PMID: 33878842 DOI: 10.1080/13685538.2021.1901274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE The molecular basis of prostate cancer is highly heterogeneous. Our study aimed to perform the mutation analysis of KRAS, BRAF, PIK3CA, and immunohistochemical (IHC) evaluation of EGFR, HER2, p16, and PTEN to demonstrate new areas for targeted therapies. METHODS A total of 24 prostatectomy samples diagnosed with adenocarcinoma were analyzed by microarray hybridization. Also, these samples were IHC stained for EGFR, HER2, P16, and PTEN. The cases were divided into two groups based on low and high Gleason scores. All findings were compared with the clinicopathological parameters of the patients. RESULTS While KRAS mutation was in 3/24 (12.5%) of our cases, BRAF and PIK3CA mutations were not detected. There was no significant difference between the groups in terms of KRAS mutation frequency. HER2 was immunohistochemically negative in all samples. There was no correlation between EGFR, P16 immunopositivity, and clinicopathological features. CONCLUSION KRAS mutation frequency is similar to those in Asian populations. BRAF and PIK3CA mutation frequencies have been reported in the literature in the range of 0-15% and 0-10.4%, respectively, consistent with our study findings. HER2 immunoexpression is a controversial issue in the literature. EGFR and p16 expressions may not correlate with the stage.
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Affiliation(s)
- Atike Bahcivan
- Department of Pathology, Duzce University, Duzce, Turkey
| | | | | | - Sengul Cangur
- Department of Biostatistics and Medical Informatics, Duzce University, Duzce, Turkey
| | | | - Aysegul Ceyhan
- Department of Pathology, Duzce University, Duzce, Turkey
| | - Binnur Onal
- Department of Pathology, Duzce University, Duzce, Turkey
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Shiny-SoSV: A web-based performance calculator for somatic structural variant detection. PLoS One 2020; 15:e0238108. [PMID: 32853264 PMCID: PMC7451576 DOI: 10.1371/journal.pone.0238108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/10/2020] [Indexed: 11/19/2022] Open
Abstract
Somatic structural variants are an important contributor to cancer development and evolution. Accurate detection of these complex variants from whole genome sequencing data is influenced by a multitude of parameters. However, there are currently no tools for guiding study design nor are there applications that could predict the performance of somatic structural variant detection. To address this gap, we developed Shiny-SoSV, a user-friendly web-based calculator for determining the impact of common variables on the sensitivity, precision and F1 score of somatic structural variant detection, including choice of variant detection tool, sequencing depth of coverage, variant allele fraction, and variant breakpoint resolution. Using simulation studies, we determined singular and combinatoric effects of these variables, modelled the results using a generalised additive model, allowing structural variant detection performance to be predicted for any combination of predictors. Shiny-SoSV provides an interactive and visual platform for users to easily compare individual and combined impact of different parameters. It predicts the performance of a proposed study design, on somatic structural variant detection, prior to the commencement of benchwork. Shiny-SoSV is freely available at https://hcpcg.shinyapps.io/Shiny-SoSV with accompanying user’s guide and example use-cases.
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