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Gong J, Kim DM, Freeman MR, Kim H, Ellis L, Smith B, Theodorescu D, Posadas E, Figlin R, Bhowmick N, Freedland SJ. Genetic and biological drivers of prostate cancer disparities in Black men. Nat Rev Urol 2024; 21:274-289. [PMID: 37964070 DOI: 10.1038/s41585-023-00828-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2023] [Indexed: 11/16/2023]
Abstract
Black men with prostate cancer have historically had worse outcomes than white men with prostate cancer. The causes of this disparity in outcomes are multi-factorial, but a potential basis is that prostate cancers in Black men are biologically distinct from prostate cancers in white men. Evidence suggests that genetic and ancestral factors, molecular pathways involving androgen and non-androgen receptor signalling, inflammation, epigenetics, the tumour microenvironment and tumour metabolism are contributing factors to the racial disparities observed. Key genetic and molecular pathways linked to prostate cancer risk and aggressiveness have potential clinical relevance. Describing biological drivers of prostate cancer disparities could inform efforts to improve outcomes for Black men with prostate cancer.
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Affiliation(s)
- Jun Gong
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Daniel M Kim
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael R Freeman
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hyung Kim
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Leigh Ellis
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bethany Smith
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dan Theodorescu
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Edwin Posadas
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robert Figlin
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Neil Bhowmick
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stephen J Freedland
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Section of Urology, Durham VA Medical Center, Durham, NC, USA
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2
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Janivara R, Hazra U, Pfennig A, Harlemon M, Kim MS, Eaaswarkhanth M, Chen WC, Ogunbiyi A, Kachambwa P, Petersen LN, Jalloh M, Mensah JE, Adjei AA, Adusei B, Joffe M, Gueye SM, Aisuodionoe-Shadrach OI, Fernandez PW, Rohan TE, Andrews C, Rebbeck TR, Adebiyi AO, Agalliu I, Lachance J. Uncovering the genetic architecture and evolutionary roots of androgenetic alopecia in African men. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575396. [PMID: 38293167 PMCID: PMC10827056 DOI: 10.1101/2024.01.12.575396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Androgenetic alopecia is a highly heritable trait. However, much of our understanding about the genetics of male pattern baldness comes from individuals of European descent. Here, we examined a novel dataset comprising 2,136 men from Ghana, Nigeria, Senegal, and South Africa that were genotyped using a custom array. We first tested how genetic predictions of baldness generalize from Europe to Africa, finding that polygenic scores from European GWAS yielded AUC statistics that ranged from 0.513 to 0.546, indicating that genetic predictions of baldness in African populations performed notably worse than in European populations. Subsequently, we conducted the first African GWAS of androgenetic alopecia, focusing on self-reported baldness patterns at age 45. After correcting for present age, population structure, and study site, we identified 266 moderately significant associations, 51 of which were independent (p-value < 10-5, r2 < 0.2). Most baldness associations were autosomal, and the X chromosomes does not appear to have a large impact on baldness in African men. Finally, we examined the evolutionary causes of continental differences in genetic architecture. Although Neanderthal alleles have previously been associated with skin and hair phenotypes, we did not find evidence that European-ascertained baldness hits were enriched for signatures of ancient introgression. Most loci that are associated with androgenetic alopecia are evolving neutrally. However, multiple baldness-associated SNPs near the EDA2R and AR genes have large allele frequency differences between continents. Collectively, our findings illustrate how evolutionary history contributes to the limited portability of genetic predictions across ancestries.
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Affiliation(s)
- Rohini Janivara
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ujani Hazra
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Aaron Pfennig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Maxine Harlemon
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Department of Biology, Morgan State University, Baltimore, Maryland, USA
| | - Michelle S Kim
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Department of Human Genetics University of Michigan, Ann Arbor, Michigan, USA
| | | | - Wenlong C Chen
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Cancer Registry, National Institute for Communicable Diseases a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Paidamoyo Kachambwa
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
- Mediclinic Precise Southern Africa, Cape Town, South Africa
| | - Lindsay N Petersen
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
- Mediclinic Precise Southern Africa, Cape Town, South Africa
| | - Mohamed Jalloh
- Université Cheikh Anta Diop de Dakar, Dakar, Senegal
- Université Iba Der Thiam de Thiès, Thiès, Senegal
| | - James E Mensah
- Korle-Bu Teaching Hospital and University of Ghana Medical School, Accra, Ghana
| | - Andrew A Adjei
- Department of Pathology, University of Ghana Medical School, Accra, Ghana
| | | | - Maureen Joffe
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Oseremen I Aisuodionoe-Shadrach
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Centre, Abuja, Nigeria
| | - Pedro W Fernandez
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Thomas E Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Timothy R Rebbeck
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Ilir Agalliu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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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] [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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4
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Hoffmann TJ, Graff RE, Madduri RK, Rodriguez AA, Cario CL, Feng K, Jiang Y, Wang A, Klein RJ, Pierce BL, Eggener S, Tong L, Blot W, Long J, Rebbeck T, Lachance J, Andrews C, Adebiyi AO, Adusei B, Aisuodionoe-Shadrach OI, Fernandez PW, Jalloh M, Janivara R, Chen WC, Mensah JE, Agalliu I, Berndt SI, Shelley JP, Schaffer K, Machiela MJ, Freedman ND, Huang WY, Li SA, Goodman PJ, Till C, Thompson I, Lilja H, Van Den Eeden SK, Chanock SJ, Mosley JD, Conti DV, Haiman CA, Justice AC, Kachuri L, Witte JS. Genome-wide association study of prostate-specific antigen levels in 392,522 men identifies new loci and improves cross-ancestry prediction. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.27.23297676. [PMID: 37961155 PMCID: PMC10635224 DOI: 10.1101/2023.10.27.23297676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
We conducted a multi-ancestry genome-wide association study of prostate-specific antigen (PSA) levels in 296,754 men (211,342 European ancestry; 58,236 African ancestry; 23,546 Hispanic/Latino; 3,630 Asian ancestry; 96.5% of participants were from the Million Veteran Program). We identified 318 independent genome-wide significant (p≤5e-8) variants, 184 of which were novel. Most demonstrated evidence of replication in an independent cohort (n=95,768). Meta-analyzing discovery and replication (n=392,522) identified 447 variants, of which a further 111 were novel. Out-of-sample variance in PSA explained by our new polygenic risk score reached 16.9% (95% CI=16.1%-17.8%) in European ancestry, 9.5% (95% CI=7.0%-12.2%) in African ancestry, 18.6% (95% CI=15.8%-21.4%) in Hispanic/Latino, and 15.3% (95% CI=12.7%-18.1%) in Asian ancestry, and lower for higher age. Our study highlights how including proportionally more participants from underrepresented populations improves genetic prediction of PSA levels, with potential to personalize prostate cancer screening.
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5
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Rebbeck T, Janivara R, Chen W, Hazra U, Baichoo S, Agalliu I, Kachambwa P, Simonti C, Brown L, Tambe S, Kim M, Harlemon M, Jalloh M, Muzondiwa D, Naidoo D, Ajayi O, Snyper N, Niang L, Diop H, Ndoye M, Mensah J, Darkwa-Abrahams A, Biritwum R, Adjei A, Adebiyi A, Shittu O, Ogunbiyi O, Adebayo S, Nwegbu M, Ajibola H, Oluwole O, Jamda M, Pentz A, Haiman C, Spies P, Van der Merwe A, Cook M, Chanock SJ, Berndt SI, Watya S, Lubwama A, Muchengeti M, Doherty S, Smyth N, Lounsbury D, Fortier B, Rohan T, Jacobson J, Neugut A, Hsing A, Gusev A, Aisuodionoe-Shadrach O, Joffe M, Adusei B, Gueye S, Fernandez P, McBride J, Andrews C, Petersen L, Lachance J. Heterogeneous genetic architectures and evolutionary genomics of prostate cancer in Sub-Saharan Africa. RESEARCH SQUARE 2023:rs.3.rs-3378303. [PMID: 37886553 PMCID: PMC10602179 DOI: 10.21203/rs.3.rs-3378303/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Men of African descent have the highest prostate cancer (CaP) incidence and mortality rates, yet the genetic basis of CaP in African men has been understudied. We used genomic data from 3,963 CaP cases and 3,509 controls recruited in Ghana, Nigeria, Senegal, South Africa, and Uganda, to infer ancestry-specific genetic architectures and fine-mapped disease associations. Fifteen independent associations at 8q24.21, 6q22.1, and 11q13.3 reached genome-wide significance, including four novel associations. Intriguingly, multiple lead SNPs are private alleles, a pattern arising from recent mutations and the out-of-Africa bottleneck. These African-specific alleles contribute to haplotypes with odds ratios above 2.4. We found that the genetic architecture of CaP differs across Africa, with effect size differences contributing more to this heterogeneity than allele frequency differences. Population genetic analyses reveal that African CaP associations are largely governed by neutral evolution. Collectively, our findings emphasize the utility of conducting genetic studies that use diverse populations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Maxwell Nwegbu
- University of Abuja Teaching Hospital and Cancer Science Center
| | - Hafees Ajibola
- University of Abuja Teaching Hospital and Cancer Science Center
| | - Olabode Oluwole
- University of Abuja and University of Abuja Teaching Hospital
| | - Mustapha Jamda
- University of Abuja Teaching Hospital and Cancer Science Center
| | | | | | | | | | | | | | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda
| | | | | | - Mazvita Muchengeti
- National Institute for Communicable Diseases a Division of the National Health Laboratory Service
| | | | | | | | | | | | | | | | - Ann Hsing
- Stanford University School of Medicine
| | | | | | | | | | | | | | - Jo McBride
- Centre for Proteomic and Genomic Research
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6
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Chen F, Madduri RK, Rodriguez AA, Darst BF, Chou A, Sheng X, Wang A, Shen J, Saunders EJ, Rhie SK, Bensen JT, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Stanford JL, Zheng W, Sanderson M, John EM, Park JY, Xu J, Wang Y, Berndt SI, Huff CD, Yeboah ED, Tettey Y, Lachance J, Tang W, Rentsch CT, Cho K, Mcmahon BH, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Sellers TA, Yamoah K, Murphy AB, Crawford DC, Patel AV, Bush WS, Aldrich MC, Cussenot O, Petrovics G, Cullen J, Neslund-Dudas CM, Stern MC, Kote-Jarai Z, Govindasami K, Cook MB, Chokkalingam AP, Hsing AW, Goodman PJ, Hoffmann TJ, Drake BF, Hu JJ, Keaton JM, Hellwege JN, Clark PE, Jalloh M, Gueye SM, Niang L, Ogunbiyi O, Idowu MO, Popoola O, Adebiyi AO, Aisuodionoe-Shadrach OI, Ajibola HO, Jamda MA, Oluwole OP, Nwegbu M, Adusei B, Mante S, Darkwa-Abrahams A, Mensah JE, Diop H, Van Den Eeden SK, Blanchet P, Fowke JH, Casey G, Hennis AJ, Lubwama A, Thompson IM, Leach R, Easton DF, Preuss MH, Loos RJ, Gundell SM, Wan P, Mohler JL, Fontham ET, Smith GJ, Taylor JA, Srivastava S, Eeles RA, Carpten JD, Kibel AS, Multigner L, Parent MÉ, Menegaux F, Cancel-Tassin G, Klein EA, Andrews C, Rebbeck TR, Brureau L, Ambs S, Edwards TL, Watya S, Chanock SJ, Witte JS, Blot WJ, Michael Gaziano J, Justice AC, Conti DV, Haiman CA. Evidence of Novel Susceptibility Variants for Prostate Cancer and a Multiancestry Polygenic Risk Score Associated with Aggressive Disease in Men of African Ancestry. Eur Urol 2023; 84:13-21. [PMID: 36872133 PMCID: PMC10424812 DOI: 10.1016/j.eururo.2023.01.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/14/2022] [Accepted: 01/24/2023] [Indexed: 03/06/2023]
Abstract
BACKGROUND Genetic factors play an important role in prostate cancer (PCa) susceptibility. OBJECTIVE To discover common genetic variants contributing to the risk of PCa in men of African ancestry. DESIGN, SETTING, AND PARTICIPANTS We conducted a meta-analysis of ten genome-wide association studies consisting of 19378 cases and 61620 controls of African ancestry. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Common genotyped and imputed variants were tested for their association with PCa risk. Novel susceptibility loci were identified and incorporated into a multiancestry polygenic risk score (PRS). The PRS was evaluated for associations with PCa risk and disease aggressiveness. RESULTS AND LIMITATIONS Nine novel susceptibility loci for PCa were identified, of which seven were only found or substantially more common in men of African ancestry, including an African-specific stop-gain variant in the prostate-specific gene anoctamin 7 (ANO7). A multiancestry PRS of 278 risk variants conferred strong associations with PCa risk in African ancestry studies (odds ratios [ORs] >3 and >5 for men in the top PRS decile and percentile, respectively). More importantly, compared with men in the 40-60% PRS category, men in the top PRS decile had a significantly higher risk of aggressive PCa (OR = 1.23, 95% confidence interval = 1.10-1.38, p = 4.4 × 10-4). CONCLUSIONS This study demonstrates the importance of large-scale genetic studies in men of African ancestry for a better understanding of PCa susceptibility in this high-risk population and suggests a potential clinical utility of PRS in differentiating between the risks of developing aggressive and nonaggressive disease in men of African ancestry. PATIENT SUMMARY In this large genetic study in men of African ancestry, we discovered nine novel prostate cancer (PCa) risk variants. We also showed that a multiancestry polygenic risk score was effective in stratifying PCa risk, and was able to differentiate risk of aggressive and nonaggressive disease.
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Affiliation(s)
- Fei Chen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Burcu F Darst
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alisha Chou
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xin Sheng
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anqi Wang
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jiayi Shen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeannette T Bensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sue A Ingles
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rick A Kittles
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Sara S Strom
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - William B Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Esther M John
- Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Ying Wang
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Yao Tettey
- Department of Pathology, University of Ghana, Accra, Ghana; Korle Bu Teaching Hospital, Accra, Ghana
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Christopher T Rentsch
- Yale School of Medicine, New Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Kelly Cho
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Jamaica Plain, MA, USA
| | - Benjamin H Mcmahon
- Theoretical Biology Division, Los Alamos National Lab, Los Alamos, NM, USA
| | | | - Andrew A Adjei
- Department of Pathology, University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana
| | | | | | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Kosj Yamoah
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA; Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Melinda C Aldrich
- Division of Epidemiology, Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Olivier Cussenot
- Department of Urology and Predictive Onco-Urology Group, Sorbonne Université, GRC 5 Predictive Onco-Urology, APHP-Sorbonne Université, Paris, France; CeRePP, Tenon Hospital, Paris, France
| | - Gyorgy Petrovics
- Department of Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jennifer Cullen
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA; Department of Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | - Mariana C Stern
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Ann W Hsing
- Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Bettina F Drake
- Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer J Hu
- The University of Miami School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Jacob M Keaton
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jacklyn N Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Nashville, TN, USA
| | - Peter E Clark
- Atrium Health/Levine Cancer Institute, Charlotte, NC, USA
| | | | | | | | - Olufemi Ogunbiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Michael O Idowu
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Olufemi Popoola
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Akindele O Adebiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Oseremen I Aisuodionoe-Shadrach
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Hafees O Ajibola
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Mustapha A Jamda
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Olabode P Oluwole
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Maxwell Nwegbu
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | | | | | | | | | - Halimatou Diop
- Laboratoires Bacteriologie et Virologie, Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente, Northern California, Oakland, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Pascal Blanchet
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, Guadeloupe, France
| | - Jay H Fowke
- Department of Preventive Medicine, Division of Epidemiology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Graham Casey
- Department of Public Health Science, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Anselm J Hennis
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | | | - Ian M Thompson
- CHRISTUS Santa Rosa Medical Center Hospital, San Antonio, TX, USA
| | - Robin Leach
- Department of Urology, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susan M Gundell
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peggy Wan
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - James L Mohler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Elizabeth T Fontham
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Gary J Smith
- Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA; Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Shiv Srivastava
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Rosaline A Eeles
- The Institute of Cancer Research, London, UK; Royal Marsden NHS Foundation Trust, London, UK
| | - John D Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adam S Kibel
- Department of Urology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Luc Multigner
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Rennes, France
| | - Marie-Élise Parent
- Epidemiology and Biostatistics Unit, Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, Canada
| | - Florence Menegaux
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif Cédex, France; Paris-Sud University, Villejuif Cédex, France
| | - Geraldine Cancel-Tassin
- Department of Urology and Predictive Onco-Urology Group, Sorbonne Université, GRC 5 Predictive Onco-Urology, APHP-Sorbonne Université, Paris, France; CeRePP, Tenon Hospital, Paris, France
| | - Eric A Klein
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Caroline Andrews
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA; Glickman Urological & Kidney Institute, Cleveland, OH, USA
| | - Timothy R Rebbeck
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - Laurent Brureau
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, Guadeloupe, France
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; International Epidemiology Institute, Rockville, MD, USA
| | - J Michael Gaziano
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA
| | - Amy C Justice
- Yale School of Medicine, New Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA
| | - David V Conti
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher A Haiman
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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7
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Dauda B, Molina SJ, Allen DS, Fuentes A, Ghosh N, Mauro M, Neale BM, Panofsky A, Sohail M, Zhang SR, Lewis ACF. Ancestry: How researchers use it and what they mean by it. Front Genet 2023; 14:1044555. [PMID: 36755575 PMCID: PMC9900027 DOI: 10.3389/fgene.2023.1044555] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Background: Ancestry is often viewed as a more objective and less objectionable population descriptor than race or ethnicity. Perhaps reflecting this, usage of the term "ancestry" is rapidly growing in genetics research, with ancestry groups referenced in many situations. The appropriate usage of population descriptors in genetics research is an ongoing source of debate. Sound normative guidance should rest on an empirical understanding of current usage; in the case of ancestry, questions about how researchers use the concept, and what they mean by it, remain unanswered. Methods: Systematic literature analysis of 205 articles at least tangentially related to human health from diverse disciplines that use the concept of ancestry, and semi-structured interviews with 44 lead authors of some of those articles. Results: Ancestry is relied on to structure research questions and key methodological approaches. Yet researchers struggle to define it, and/or offer diverse definitions. For some ancestry is a genetic concept, but for many-including geneticists-ancestry is only tangentially related to genetics. For some interviewees, ancestry is explicitly equated to ethnicity; for others it is explicitly distanced from it. Ancestry is operationalized using multiple data types (including genetic variation and self-reported identities), though for a large fraction of articles (26%) it is impossible to tell which data types were used. Across the literature and interviews there is no consistent understanding of how ancestry relates to genetic concepts (including genetic ancestry and population structure), nor how these genetic concepts relate to each other. Beyond this conceptual confusion, practices related to summarizing patterns of genetic variation often rest on uninterrogated conventions. Continental labels are by far the most common type of label applied to ancestry groups. We observed many instances of slippage between reference to ancestry groups and racial groups. Conclusion: Ancestry is in practice a highly ambiguous concept, and far from an objective counterpart to race or ethnicity. It is not uniquely a "biological" construct, and it does not represent a "safe haven" for researchers seeking to avoid evoking race or ethnicity in their work. Distinguishing genetic ancestry from ancestry more broadly will be a necessary part of providing conceptual clarity.
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Affiliation(s)
- Bege Dauda
- Center for Global Genomics and Health Equity, University of Pennsylvania, Philadelphia, PA, United States
| | - Santiago J. Molina
- Department of Sociology, Northwestern University, Evanston, IL, United States
| | - Danielle S. Allen
- Edmond & Lily Safra Center for Ethics, Harvard University, Cambridge, MA, United States
| | - Agustin Fuentes
- Department of Anthropology, Princeton University, Princeton, NJ, United States
| | - Nayanika Ghosh
- Department of the History of Science, Harvard University, Cambridge, MA, United States
| | - Madelyn Mauro
- Edmond & Lily Safra Center for Ethics, Harvard University, Cambridge, MA, United States
| | - Benjamin M. Neale
- Broad Institute of Harvard and MIT, Cambridge, MA, United States
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Aaron Panofsky
- Institute for Society & Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Public Policy, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Sociology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Mashaal Sohail
- Centro de Ciencias Genomicas (CCG), Universidad Nacional Autonoma de Mexico (UNAM), Cuernavaca, Morelos, Mexico
| | - Sarah R. Zhang
- University of California, Berkeley, Berkeley, CA, United States
| | - Anna C. F. Lewis
- Edmond & Lily Safra Center for Ethics, Harvard University, Cambridge, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
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8
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Translational Bioinformatics for Human Reproductive Biology Research: Examples, Opportunities and Challenges for a Future Reproductive Medicine. Int J Mol Sci 2022; 24:ijms24010004. [PMID: 36613446 PMCID: PMC9819745 DOI: 10.3390/ijms24010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Since 1978, with the first IVF (in vitro fertilization) baby birth in Manchester (England), more than eight million IVF babies have been born throughout the world, and many new techniques and discoveries have emerged in reproductive medicine. To summarize the modern technology and progress in reproductive medicine, all scientific papers related to reproductive medicine, especially papers related to reproductive translational medicine, were fully searched, manually curated and reviewed. Results indicated whether male reproductive medicine or female reproductive medicine all have made significant progress, and their markers have experienced the progress from karyotype analysis to single-cell omics. However, due to the lack of comprehensive databases, especially databases collecting risk exposures, disease markers and models, prevention drugs and effective treatment methods, the application of the latest precision medicine technologies and methods in reproductive medicine is limited.
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9
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Kim MS, Naidoo D, Hazra U, Quiver MH, Chen WC, Simonti CN, Kachambwa P, Harlemon M, Agalliu I, Baichoo S, Fernandez P, Hsing AW, Jalloh M, Gueye SM, Niang L, Diop H, Ndoye M, Snyper NY, Adusei B, Mensah JE, Abrahams AOD, Biritwum R, Adjei AA, Adebiyi AO, Shittu O, Ogunbiyi O, Adebayo S, Aisuodionoe-Shadrach OI, Nwegbu MM, Ajibola HO, Oluwole OP, Jamda MA, Singh E, Pentz A, Joffe M, Darst BF, Conti DV, Haiman CA, Spies PV, van der Merwe A, Rohan TE, Jacobson J, Neugut AI, McBride J, Andrews C, Petersen LN, Rebbeck TR, Lachance J. Testing the generalizability of ancestry-specific polygenic risk scores to predict prostate cancer in sub-Saharan Africa. Genome Biol 2022; 23:194. [PMID: 36100952 PMCID: PMC9472407 DOI: 10.1186/s13059-022-02766-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 09/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genome-wide association studies do not always replicate well across populations, limiting the generalizability of polygenic risk scores (PRS). Despite higher incidence and mortality rates of prostate cancer in men of African descent, much of what is known about cancer genetics comes from populations of European descent. To understand how well genetic predictions perform in different populations, we evaluated test characteristics of PRS from three previous studies using data from the UK Biobank and a novel dataset of 1298 prostate cancer cases and 1333 controls from Ghana, Nigeria, Senegal, and South Africa. RESULTS Allele frequency differences cause predicted risks of prostate cancer to vary across populations. However, natural selection is not the primary driver of these differences. Comparing continental datasets, we find that polygenic predictions of case vs. control status are more effective for European individuals (AUC 0.608-0.707, OR 2.37-5.71) than for African individuals (AUC 0.502-0.585, OR 0.95-2.01). Furthermore, PRS that leverage information from African Americans yield modest AUC and odds ratio improvements for sub-Saharan African individuals. These improvements were larger for West Africans than for South Africans. Finally, we find that existing PRS are largely unable to predict whether African individuals develop aggressive forms of prostate cancer, as specified by higher tumor stages or Gleason scores. CONCLUSIONS Genetic predictions of prostate cancer perform poorly if the study sample does not match the ancestry of the original GWAS. PRS built from European GWAS may be inadequate for application in non-European populations and perpetuate existing health disparities.
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Affiliation(s)
- Michelle S Kim
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr, Atlanta, GA, 30332, USA
| | - Daphne Naidoo
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | - Ujani Hazra
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr, Atlanta, GA, 30332, USA
| | - Melanie H Quiver
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr, Atlanta, GA, 30332, USA
| | - Wenlong C Chen
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
| | - Corinne N Simonti
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr, Atlanta, GA, 30332, USA
| | | | - Maxine Harlemon
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr, Atlanta, GA, 30332, USA
| | - Ilir Agalliu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Pedro Fernandez
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Ann W Hsing
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | | | | | - Lamine Niang
- Universite Cheikh Anta Diop de Dakar, Dakar, Senegal
| | | | - Medina Ndoye
- Universite Cheikh Anta Diop de Dakar, Dakar, Senegal
| | | | | | - James E Mensah
- Korle-Bu Teaching Hospital and University of Ghana Medical School, Accra, Ghana
| | - Afua O D Abrahams
- Korle-Bu Teaching Hospital and University of Ghana Medical School, Accra, Ghana
| | - Richard Biritwum
- Korle-Bu Teaching Hospital and University of Ghana Medical School, Accra, Ghana
| | - Andrew A Adjei
- Department of Pathology, University of Ghana Medical School, Accra, Ghana
| | | | | | | | - Sikiru Adebayo
- College of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - Maxwell M Nwegbu
- College of Health Sciences, University of Abuja and University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Hafees O Ajibola
- College of Health Sciences, University of Abuja and University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Olabode P Oluwole
- College of Health Sciences, University of Abuja and University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Mustapha A Jamda
- College of Health Sciences, University of Abuja and University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Elvira Singh
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
| | - Audrey Pentz
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd, Johannesburg, South Africa
| | - Maureen Joffe
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd, Johannesburg, South Africa.,MRC Developmental Pathways to Health Research Unit, Department of Pediatrics, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Burcu F Darst
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David V Conti
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher A Haiman
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Petrus V Spies
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - André van der Merwe
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Thomas E Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Judith Jacobson
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Alfred I Neugut
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Jo McBride
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | | | | | - Timothy R Rebbeck
- Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr, Atlanta, GA, 30332, USA.
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10
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Role of Polygenic Risk Score in Cancer Precision Medicine of Non-European Populations: A Systematic Review. Curr Oncol 2022; 29:5517-5530. [PMID: 36005174 PMCID: PMC9406904 DOI: 10.3390/curroncol29080436] [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: 06/06/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022] Open
Abstract
The development of new screening methods and diagnostic tests for traits, common diseases, and cancer is linked to the advent of precision genomic medicine, in which health care is individually adjusted based on a person’s lifestyle, environmental influences, and genetic variants. Based on genome-wide association study (GWAS) analysis, rapid and continuing progress in the discovery of relevant single nucleotide polymorphisms (SNPs) for traits or complex diseases has increased interest in the potential application of genetic risk models for routine health practice. The polygenic risk score (PRS) estimates an individual’s genetic risk of a trait or disease, calculated by employing a weighted sum of allele counts combined with non-genetic variables. However, 98.38% of PRS records held in public databases relate to the European population. Therefore, PRSs for multiethnic populations are urgently needed. We performed a systematic review to discuss the role of polygenic risk scores in advancing precision medicine for different cancer types in multiethnic non-European populations.
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11
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Chen F, Darst BF, Madduri RK, Rodriguez AA, Sheng X, Rentsch CT, Andrews C, Tang W, Kibel AS, Plym A, Cho K, Jalloh M, Gueye SM, Niang L, Ogunbiyi OJ, Popoola O, Adebiyi AO, Aisuodionoe-Shadrach OI, Ajibola HO, Jamda MA, Oluwole OP, Nwegbu M, Adusei B, Mante S, Darkwa-Abrahams A, Mensah JE, Adjei AA, Diop H, Lachance J, Rebbeck TR, Ambs S, Gaziano JM, Justice AC, Conti DV, Haiman CA. Validation of a multi-ancestry polygenic risk score and age-specific risks of prostate cancer: A meta-analysis within diverse populations. eLife 2022; 11:78304. [PMID: 35801699 PMCID: PMC9322982 DOI: 10.7554/elife.78304] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background We recently developed a multi-ancestry polygenic risk score (PRS) that effectively stratifies prostate cancer risk across populations. In this study, we validated the performance of the PRS in the multi-ancestry Million Veteran Program and additional independent studies. Methods Within each ancestry population, the association of PRS with prostate cancer risk was evaluated separately in each case-control study and then combined in a fixed-effects inverse-variance-weighted meta-analysis. We further assessed the effect modification by age and estimated the age-specific absolute risk of prostate cancer for each ancestry population. Results The PRS was evaluated in 31,925 cases and 490,507 controls, including men from European (22,049 cases, 414,249 controls), African (8794 cases, 55,657 controls), and Hispanic (1082 cases, 20,601 controls) populations. Comparing men in the top decile (90-100% of the PRS) to the average 40-60% PRS category, the prostate cancer odds ratio (OR) was 3.8-fold in European ancestry men (95% CI = 3.62-3.96), 2.8-fold in African ancestry men (95% CI = 2.59-3.03), and 3.2-fold in Hispanic men (95% CI = 2.64-3.92). The PRS did not discriminate risk of aggressive versus nonaggressive prostate cancer. However, the OR diminished with advancing age (European ancestry men in the top decile: ≤55 years, OR = 7.11; 55-60 years, OR = 4.26; >70 years, OR = 2.79). Men in the top PRS decile reached 5% absolute prostate cancer risk ~10 years younger than men in the 40-60% PRS category. Conclusions Our findings validate the multi-ancestry PRS as an effective prostate cancer risk stratification tool across populations. A clinical study of PRS is warranted to determine whether the PRS could be used for risk-stratified screening and early detection. Funding This work was supported by the National Cancer Institute at the National Institutes of Health (grant numbers U19 CA214253 to C.A.H., U01 CA257328 to C.A.H., U19 CA148537 to C.A.H., R01 CA165862 to C.A.H., K99 CA246063 to B.F.D, and T32CA229110 to F.C), the Prostate Cancer Foundation (grants 21YOUN11 to B.F.D. and 20CHAS03 to C.A.H.), the Achievement Rewards for College Scientists Foundation Los Angeles Founder Chapter to B.F.D, and the Million Veteran Program-MVP017. This research has been conducted using the UK Biobank Resource under application number 42195. This research is based on data from the Million Veteran Program, Office of Research and Development, and the Veterans Health Administration. This publication does not represent the views of the Department of Veteran Affairs or the United States Government.
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Affiliation(s)
- Fei Chen
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, United States
| | - Burcu F Darst
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, United States.,Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | | | | | - Xin Sheng
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, United States
| | - Christopher T Rentsch
- Yale School of Medicine, New Haven, United States.,VA Connecticut Healthcare System, West Haven, United States.,London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Caroline Andrews
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, United States
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Adam S Kibel
- Department of Surgery, Urology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Anna Plym
- Department of Surgery, Urology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Kelly Cho
- VA Boston Healthcare System, Boston, United States.,Division of Aging, Brigham and Women's Hospital, Boston, United States
| | | | | | | | - Olufemi J Ogunbiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Olufemi Popoola
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Akindele O Adebiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Oseremen I Aisuodionoe-Shadrach
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Hafees O Ajibola
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Mustapha A Jamda
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Olabode P Oluwole
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Maxwell Nwegbu
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | | | | | | | | | | | - Halimatou Diop
- Laboratoires Bacteriologie et Virologie, Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States
| | - Timothy R Rebbeck
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, United States
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - J Michael Gaziano
- VA Boston Healthcare System, Boston, United States.,Division of Aging, Brigham and Women's Hospital, Boston, United States.,Department of Medicine, Harvard Medical School, Boston, United States
| | - Amy C Justice
- Yale School of Medicine, New Haven, United States.,VA Connecticut Healthcare System, West Haven, United States
| | - David V Conti
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, United States
| | - Christopher A Haiman
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, United States
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12
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Ndlovu S, Hlongwa M, Ginindza T. Mapping evidence on the risk factors associated with pediatric cancers in sub-Saharan Africa: a scoping review. Syst Rev 2022; 11:58. [PMID: 35379332 PMCID: PMC8978411 DOI: 10.1186/s13643-022-01931-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The rarity and heterogeneity of pediatric cancers make it difficult to assess risk factors associated with the development of cancer in this group. This also determines the quantity and quality of evidence for etiological factors linked to pediatric cancers. Evidence on the risk factors associated with pediatric cancers is scarce; however, it has been accumulating slowly over the years. As the disease burden shifts from communicable to non-communicable diseases, most of these low- to middle-income countries (LMICs) find themselves overburdened with changing health care priorities and needs. In sub-Saharan Africa, it is of major importance to pay particular attention to risk factors associated with pediatric cancer. OBJECTIVE To map evidence on risk factors associated with pediatric cancers in sub-Saharan Africa (SSA). METHODS This review was guided by Arksey and O'Malley's framework for conducting scoping reviews. Four electronic databases were searched in December 2018, and another manual search was conducted in February 2022 to include newly published eligible articles. The databases searched included PubMed and Health Source: Nursing/Academic Edition. We also searched articles from an academic search engine, Google scholar. This review included articles reporting the relevant outcomes of this study and articles reporting cancers in children in the 0-15 years age range. This review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) extension for scoping reviews (PRISMA-ScR): checklist and explanation. RESULTS We retrieved 7391 articles from the initial database. The final number of studies that were included for data extraction was 15. Evidence from the retrieved studies suggests that most childhood cancers in the SSA region are infection-induced. The type of cancer mostly reported is Burkitt Lymphoma and is diagnosed mostly in the tropical region of SSA. The type of risk factors was divided into three types: infection-induced, genetic, and demographic risk factors. Overall, based on the articles retrieved, there was limited evidence on the risk factors associated with pediatric cancers in SSA. CONCLUSION The limited evidence on the risk factors coupled with the lack of evidence on the true burden of these malignancies in the SSA hampers efforts to set priorities for childhood cancer control. Formulation of effective preventative (where possible) measures and treatment regimens will need proper assessment of risk factors.
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Affiliation(s)
- Sehlisiwe Ndlovu
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa.
| | - Mbuzeleni Hlongwa
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa.,Burden of Disease Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Themba Ginindza
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
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Benafif S, Ni Raghallaigh H, McGrowder E, Saunders EJ, Brook MN, Saya S, Rageevakumar R, Wakerell S, James D, Chamberlain A, Taylor N, Hogben M, Benton B, D’Mello L, Myhill K, Mikropoulos C, Bowen‐Perkins H, Rafi I, Ferris M, Beattie A, Kuganolipava S, Sevenoaks T, Bower J, Kumar P, Hazell S, deSouza NM, Antoniou A, Bancroft E, Kote‐Jarai Z, Eeles R. The BARCODE1 Pilot: a feasibility study of using germline single nucleotide polymorphisms to target prostate cancer screening. BJU Int 2022; 129:325-336. [PMID: 34214236 PMCID: PMC9292247 DOI: 10.1111/bju.15535] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/09/2021] [Accepted: 06/23/2021] [Indexed: 12/22/2022]
Abstract
OBJECTIVES To assess the feasibility and uptake of a community-based prostate cancer (PCa) screening programme selecting men according to their genetic risk of PCa. To assess the uptake of PCa screening investigations by men invited for screening. The uptake of the pilot study would guide the opening of the larger BARCODE1 study recruiting 5000 men. SUBJECTS AND METHODS Healthy males aged 55-69 years were invited to participate via their general practitioners (GPs). Saliva samples were collected via mailed collection kits. After DNA extraction, genotyping was conducted using a study specific assay. Genetic risk was based on genotyping 130 germline PCa risk single nucleotide polymorphisms (SNPs). A polygenic risk score (PRS) was calculated for each participant using the sum of weighted alleles for 130 SNPs. Study participants with a PRS lying above the 90th centile value were invited for PCa screening by prostate magnetic resonance imaging (MRI) and biopsy. RESULTS Invitation letters were sent to 1434 men. The overall study uptake was 26% (375/1436) and 87% of responders were eligible for study entry. DNA genotyping data were available for 297 men and 25 were invited for screening. After exclusions due to medical comorbidity/invitations declined, 18 of 25 men (72%) underwent MRI and biopsy of the prostate. There were seven diagnoses of PCa (38.9%). All cancers were low-risk and were managed with active surveillance. CONCLUSION The BARCODE1 Pilot has shown this community study in the UK to be feasible, with an overall uptake of 26%. The main BARCODE1 study is now open and will recruit 5000 men. The results of BARCODE1 will be important in defining the role of genetic profiling in targeted PCa population screening. Patient Summary What is the paper about? Very few prostate cancer screening programmes currently exist anywhere in the world. Our pilot study investigated if men in the UK would find it acceptable to have a genetic test based on a saliva sample to examine their risk of prostate cancer development. This test would guide whether men are offered prostate cancer screening tests. What does it mean for patients? We found that the study design was acceptable: 26% of men invited to take part agreed to have the test. The majority of men who were found to have an increased genetic risk of prostate cancer underwent further tests offered (prostate MRI scan and biopsy). We have now expanded the study to enrol 5000 men. The BARCODE1 study will be important in examining whether this approach could be used for large-scale population prostate cancer screening.
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Affiliation(s)
- Sarah Benafif
- Oncogenetics TeamInstitute of Cancer ResearchLondonUK
| | | | - Eva McGrowder
- Oncogenetics TeamInstitute of Cancer ResearchLondonUK
| | | | - Mark N. Brook
- Oncogenetics TeamInstitute of Cancer ResearchLondonUK
| | - Sibel Saya
- Oncogenetics TeamInstitute of Cancer ResearchLondonUK
- The University of MelbourneMelbourneVictoriaAustralia
| | | | | | - Denzil James
- Oncogenetics TeamInstitute of Cancer ResearchLondonUK
| | | | - Natalie Taylor
- Cancer Genetics Unit and Academic Urology UnitRoyal Marsden NHS Foundation TrustLondonUK
| | - Matthew Hogben
- Cancer Genetics Unit and Academic Urology UnitRoyal Marsden NHS Foundation TrustLondonUK
| | - Barbara Benton
- Cancer Genetics Unit and Academic Urology UnitRoyal Marsden NHS Foundation TrustLondonUK
| | - Lucia D’Mello
- Cancer Genetics Unit and Academic Urology UnitRoyal Marsden NHS Foundation TrustLondonUK
| | - Kathryn Myhill
- Cancer Genetics Unit and Academic Urology UnitRoyal Marsden NHS Foundation TrustLondonUK
| | | | | | | | | | | | | | | | | | - Pardeep Kumar
- Cancer Genetics Unit and Academic Urology UnitRoyal Marsden NHS Foundation TrustLondonUK
| | - Steven Hazell
- Cancer Genetics Unit and Academic Urology UnitRoyal Marsden NHS Foundation TrustLondonUK
| | | | - Antonis Antoniou
- Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Elizabeth Bancroft
- Oncogenetics TeamInstitute of Cancer ResearchLondonUK
- Cancer Genetics Unit and Academic Urology UnitRoyal Marsden NHS Foundation TrustLondonUK
| | | | - Rosalind Eeles
- Oncogenetics TeamInstitute of Cancer ResearchLondonUK
- Cancer Genetics Unit and Academic Urology UnitRoyal Marsden NHS Foundation TrustLondonUK
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Quiver MH, Lachance J. Adaptive eQTLs reveal the evolutionary impacts of pleiotropy and tissue-specificity while contributing to health and disease. HGG ADVANCES 2022; 3:100083. [PMID: 35047867 PMCID: PMC8756519 DOI: 10.1016/j.xhgg.2021.100083] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/21/2021] [Indexed: 11/24/2022] Open
Abstract
Large numbers of expression quantitative trait loci (eQTLs) have recently been identified in humans, and many of these regulatory variants have large allele frequency differences between populations. Here, we conducted genome-wide scans of selection to identify adaptive eQTLs (i.e., eQTLs with large population branch statistics). We then tested if tissue pleiotropy affects whether eQTLs are more or less likely to be adaptive and identified tissues that have been key targets of positive selection during the last 100,000 years. Top adaptive eQTL outliers include rs1043809, rs66899053, and rs2814778 (a SNP that is associated with malaria resistance). We found that effect sizes of eQTLs were negatively correlated with population branch statistics and that adaptive eQTLs affect two-thirds as many tissues as do non-adaptive eQTLs. Because the tissue breadth of an eQTL can be viewed as a measure of pleiotropy, these results imply that pleiotropy inhibits adaptation. The proportion of eQTLs that are adaptive varies by tissue, and we found that eQTLs that regulate expression in testis, thyroid, blood, or sun-exposed skin are enriched for signatures of positive selection. By contrast, eQTLs that regulate expression in the cerebrum or female-specific tissues have a relative lack of adaptive outliers. Scans of selections also reveal that many adaptive eQTLs are closely linked to disease-associated loci. Taken together, our results indicate that eQTLs have played an important role in recent human evolution.
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Affiliation(s)
- Melanie H Quiver
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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15
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Darst BF, Hughley R, Pfennig A, Hazra U, Fan C, Wan P, Sheng X, Xia L, Andrews C, Chen F, Berndt SI, Kote-Jarai Z, Govindasami K, Bensen JT, Ingles SA, Rybicki BA, Nemesure B, John EM, Fowke JH, Huff CD, Strom SS, Isaacs WB, Park JY, Zheng W, Ostrander EA, Walsh PC, Carpten J, Sellers TA, Yamoah K, Murphy AB, Sanderson M, Crawford DC, Gapstur SM, Bush WS, Aldrich MC, Cussenot O, Petrovics G, Cullen J, Neslund-Dudas C, Kittles RA, Xu J, Stern MC, Chokkalingam AP, Multigner L, Parent ME, Menegaux F, Cancel-Tassin G, Kibel AS, Klein EA, Goodman PJ, Stanford JL, Drake BF, Hu JJ, Clark PE, Blanchet P, Casey G, Hennis AJM, Lubwama A, Thompson IM, Leach RJ, Gundell SM, Pooler L, Mohler JL, Fontham ETH, Smith GJ, Taylor JA, Brureau L, Blot WJ, Biritwum R, Tay E, Truelove A, Niwa S, Tettey Y, Varma R, McKean-Cowdin R, Torres M, Jalloh M, Magueye Gueye S, Niang L, Ogunbiyi O, Oladimeji Idowu M, Popoola O, Adebiyi AO, Aisuodionoe-Shadrach OI, Nwegbu M, Adusei B, Mante S, Darkwa-Abrahams A, Yeboah ED, Mensah JE, Anthony Adjei A, Diop H, Cook MB, Chanock SJ, Watya S, Eeles RA, Chiang CWK, Lachance J, Rebbeck TR, Conti DV, Haiman CA. A Rare Germline HOXB13 Variant Contributes to Risk of Prostate Cancer in Men of African Ancestry. Eur Urol 2022; 81:458-462. [PMID: 35031163 PMCID: PMC9018520 DOI: 10.1016/j.eururo.2021.12.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/06/2021] [Accepted: 12/22/2021] [Indexed: 11/17/2022]
Abstract
A rare African ancestry-specific germline deletion variant in HOXB13 (X285K, rs77179853) was recently reported in Martinican men with early-onset prostate cancer. Given the role of HOXB13 germline variation in prostate cancer, we investigated the association between HOXB13 X285K and prostate cancer risk in a large sample of 22 361 African ancestry men, including 11 688 prostate cancer cases. The risk allele was present only in men of West African ancestry, with an allele frequency in men that ranged from 0.40% in Ghana and 0.31% in Nigeria to 0% in Uganda and South Africa, with a range of frequencies in men with admixed African ancestry from North America and Europe (0-0.26%). HOXB13 X285K was associated with 2.4-fold increased odds of prostate cancer (95% confidence interval [CI] = 1.5-3.9, p = 2 × 10-4), with greater risk observed for more aggressive and advanced disease (Gleason ≥8: odds ratio [OR] = 4.7, 95% CI = 2.3-9.5, p = 2 × 10-5; stage T3/T4: OR = 4.5, 95% CI = 2.0-10.0, p = 2 × 10-4; metastatic disease: OR = 5.1, 95% CI = 1.9-13.7, p = 0.001). We estimated that the allele arose in West Africa 1500-4600 yr ago. Further analysis is needed to understand how the HOXB13 X285K variant impacts the HOXB13 protein and function in the prostate. Understanding who carries this mutation may inform prostate cancer screening in men of West African ancestry. PATIENT SUMMARY: A rare African ancestry-specific germline deletion in HOXB13, found only in men of West African ancestry, was reported to be associated with an increased risk of overall and advanced prostate cancer. Understanding who carries this mutation may help inform screening for prostate cancer in men of West African ancestry.
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Affiliation(s)
- Burcu F Darst
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
| | - Raymond Hughley
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Aaron Pfennig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ujani Hazra
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Caoqi Fan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Peggy Wan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xin Sheng
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lucy Xia
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Caroline Andrews
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - Fei Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | | | - Koveela Govindasami
- The Institute of Cancer Research, Sutton, London, UK; Royal Marsden NHS Foundation Trust, London, UK
| | - Jeannette T Bensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sue A Ingles
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Esther M John
- Department of Epidemiology & Population Health and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jay H Fowke
- Division of Epidemiology, Department of Preventive Medicine, The University of Tennessee Health Science Center, TN, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Sara S Strom
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - William B Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Patrick C Walsh
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - John Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Kosj Yamoah
- Department of Radiation Oncology and Cancer Epidemiology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Dana C Crawford
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - William S Bush
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Olivier Cussenot
- CeRePP & Sorbonne Universite, GRC n° 5, AP-HP, Tenon Hospital, Paris, France
| | - Gyorgy Petrovics
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jennifer Cullen
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Rick A Kittles
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Mariana C Stern
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | | | - Luc Multigner
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) -UMR_S 1085, Rennes, France
| | - Marie-Elise Parent
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, University of Quebec, Laval, Quebec, Canada
| | - Florence Menegaux
- Université Paris-Saclay, Université Paris-Sud, CESP (Center for Research in Epidemiology and Population Health), Inserm, Team Cancer-Environment, Villejuif, France
| | | | - Adam S Kibel
- Division of Urology, Brigham and Women's Hospital/Dana-Farber Cancer Institute, Boston, MA, USA; Washington University, St. Louis, MO, USA
| | - Eric A Klein
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Bettina F Drake
- Department of Surgery, Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Peter E Clark
- Atrium Health/Levine Cancer Institute, Charlotte, NC, USA
| | - Pascal Blanchet
- CHU de Guadeloupe, Univ Antilles, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) -UMR_S 1085, Rennes, France
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Anselm J M Hennis
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA; George Alleyne Chronic Disease Research Centre and Faculty of Medical Sciences, The University of the West Indies, Bridgetown, Barbados
| | - Alexander Lubwama
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Ian M Thompson
- CHRISTUS Santa Rosa Health System and The University of Texas Health Science Center, San Antonio, TX, USA
| | - Robin J Leach
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Susan M Gundell
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Loreall Pooler
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - James L Mohler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Elizabeth T H Fontham
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Gary J Smith
- Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jack A Taylor
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA; Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Laurent Brureau
- CHU de Guadeloupe, Univ Antilles, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) -UMR_S 1085, Rennes, France
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana
| | | | | | - Yao Tettey
- Korle Bu Teaching Hospital, Accra, Ghana; University of Ghana Medical School, Accra, Ghana
| | - Rohit Varma
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | - Roberta McKean-Cowdin
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Mina Torres
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | | | | | | | - Olufemi Ogunbiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | | | - Olufemi Popoola
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Akindele O Adebiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Oseremen I Aisuodionoe-Shadrach
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Maxwell Nwegbu
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | | | | | | | - Edward D Yeboah
- Korle Bu Teaching Hospital, Accra, Ghana; University of Ghana Medical School, Accra, Ghana
| | | | | | - Halimatou Diop
- Laboratoires Bacteriologie et Virologie, Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Stephen Watya
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda; Uro Care, Kampala, Uganda
| | - Rosalind A Eeles
- The Institute of Cancer Research, Sutton, London, UK; Royal Marsden NHS Foundation Trust, London, UK
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Timothy R Rebbeck
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - David V Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - 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; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
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Fernandez PW. Prostate Cancer Genomics Research Disparities in Africa: Advancing Knowledge in Resource Constrained Settings. Cancer Control 2022; 29:10732748221095952. [PMID: 35475404 PMCID: PMC9087236 DOI: 10.1177/10732748221095952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Prostate cancer disproportionately affects men of African descent and it is
estimated that Africa will bear the highest disease burden in the next decade.
Underlying genomic factors may contribute to prostate cancer disparities;
however, it is unclear whether Africa has prioritised genomics research toward
addressing these disparities. A Pubmed review was performed of publications
spanning a 15-year period, with specific focus on prostate cancer genomics
research that included samples from Africa and investigators in Africa. Data are
presented on research publications from Africa relative to similar publications
from different geographical regions, and more specifically, the extent of
disparities and the contributions to prostate cancer knowledge as a result of
genomics research that included African samples and African institutions.
Limited publication output may reflect the infrastructure and funding challenges
in Africa. Widespread cooperation should be fostered by sharing capacity and
leveraging existing expertise to address the growing cancer burden facing the
continent.
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Affiliation(s)
- Pedro W Fernandez
- Division of Urology, 26697Stellenbosch University, Cape Town, South Africa
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17
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Diversity in cancer genomics research is a matter of equity and scientific discovery. Genet Med 2021; 24:549-551. [PMID: 34906472 DOI: 10.1016/j.gim.2021.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/24/2022] Open
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18
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Medulloblastoma recurrence and metastatic spread are independent of colony-stimulating factor 1 receptor signaling and macrophage survival. J Neurooncol 2021; 153:225-237. [PMID: 33963961 DOI: 10.1007/s11060-021-03767-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 04/26/2021] [Indexed: 01/01/2023]
Abstract
PURPOSE Tumor infiltration by immunosuppressive myeloid cells or tumor-associated macrophages (TAMs) contributes to tumor progression and metastasis. In contrast to their adult counterparts, higher TAM signatures do not correlate with aggressive tumor behavior in pediatric brain tumors. While prominent TAM infiltrates exist before and after radiation, the degree to which irradiated macrophages and microglia support progression or leptomeningeal metastasis remains unclear. Patients with medulloblastoma often present with distant metastases and tumor recurrence is largely incurable, making them prime candidates for the study of novel approaches to prevent neuroaxis dissemination and recurrence. METHODS Macrophage depletion was achieved using CSF-1 receptor inhibitors (CSF-1Ri), BLZ945 and AFS98, with or without whole brain radiation in a variety of medulloblastoma models, including patient-derived xenografts bearing Group 3 medulloblastoma and a transgenic Sonic Hedgehog (Ptch1+/-, Trp53-/-) medulloblastoma model. RESULTS Effective reduction of microglia, TAM, and spinal cord macrophage with CSF-1Ri resulted in negligible effects on the rate of local and spinal recurrences or survival following radiation. Results were comparable between medulloblastoma subgroups. While notably few tumor-infiltrating lymphocytes (TILs) were detected, average numbers of CD3+ TILs and FoxP3+ Tregs did not differ between groups following treatment and tumor aggressiveness by Ki67 proliferation index was unaltered. CONCLUSION In the absence of other microenvironmental influences, medulloblastoma-educated macrophages do not operate as tumor-supportive cells or promote leptomeningeal recurrence in these models. Our data add to a growing body of literature describing a distinct immunophenotype amid the medulloblastoma microenvironment and highlight the importance of appropriate pediatric modeling prior to clinical translation.
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Zaaijer S, Capes-Davis A. Ancestry matters: Building inclusivity into preclinical study design. Cell 2021; 184:2525-2531. [PMID: 33989545 DOI: 10.1016/j.cell.2021.03.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Human cell lines (CLs) are key assets for biomedicine but lack ancestral diversity. Here, we explore why genetic diversity among cell-based models is essential for making preclinical research more equitable and widely translatable. We lay out practical actions that can be taken to improve inclusivity in study design.
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Affiliation(s)
- Sophie Zaaijer
- Cornell Tech, New York, NY, USA; FIND Genomics, New York, NY, USA.
| | - Amanda Capes-Davis
- CellBank Australia, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
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20
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Acheampong E, Adu EA, Obirikorang C, Amoah G, Afriyie OO, Yorke J, Anto EO, Gyamfi MA, Acheampong EN, Gyasi-Sarpong CK, Yeboah FA. Association of genetic variants with prostate cancer in Africa: a concise review. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00157-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Abstract
Background
Prostate cancer (PCa) has one of the highest heritability of all major cancers, where the genetic contribution has been documented, and knowledge about the molecular genetics of the disease is increasing. However, the extent and aspects to which genetic variants explain PCa heritability in Africa are limited.
Main body
In this review, we summarize studies that highlight how identified genetic variants explain differences in PCa incidence and presentation across ethnic groups. We also present the knowledge gaps in PCa genetics in Africa and why Africa represents an untapped potential ground for genetic studies on PCa. A significant number of genome-wide association studies, linkage, and fine-mapping analyses have been conducted globally, and that explains 30–33% of PCa heritability. The African ancestry has a significant mention in PCa incidence and presentation. To date, the candidate gene approach has replicated 23 polymorphisms including dinucleotide and trinucleotide repeats in 16 genes. CYP17-rs743572, CYP3A4-rs2740574, CYP3A5-rs776746, CYP3A43-rs501275, and haplotype blocks, containing these variants, are significantly associated with PCa among some population groups but not others. With the few existing studies, the extent of genetic diversity in Africa suggests that genetic associations of PCa to African ancestry go beyond nucleotide sequence polymorphisms, to a level of environmental adaptation, which may interpret genetic risk profiles. Also, the shreds of evidence suggest that evolutionary history contributes to the high rates of PCa relative to African ancestry, and genetic associations do not always replicate across populations.
Conclusion
The genetic architecture of PCa in Africa provides important contributions to the global understanding of PCa specifically the African-ancestry hypothesis. There is a need for more prostate cancer consortiums to justify the heritable certainties of PCa among Africans, and emphasis should be placed on the genetic epidemiological model of PCa in Africa.
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Chikowore T, Kamiza AB, Oduaran OH, Machipisa T, Fatumo S. Non-communicable diseases pandemic and precision medicine: Is Africa ready? EBioMedicine 2021; 65:103260. [PMID: 33639396 PMCID: PMC7921515 DOI: 10.1016/j.ebiom.2021.103260] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 01/12/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022] Open
Abstract
Non-communicable diseases (NCDs) kill more than 41 million people every year, accounting for 71% of all deaths globally. The prevalence of NCDs is estimated to be higher than that of infectious diseases in Africa by 2030. Precision medicine may help with early identification of cases, resulting in timely prevention and improvement in the efficacy of treatments. However, Africa has been lagging behind in genetic research, a key component of the precision medicine initiative. A number of genomic research initiatives which could lead to translational genomics are emerging on the African continent which includes the Non-communicable Diseases Genetic Heritage Study (NCDGHS) and the Men of African Descent and Carcinoma of the Prostate (MADCaP) Network. These offer a promise that precision medicine can be applied in African countries. This review evaluates the advances of genetic studies for cancer, hypertension, type 2 diabetes and body mass index (BMI) in Africa.
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Affiliation(s)
- Tinashe Chikowore
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Abram Bunya Kamiza
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tafadzwa Machipisa
- Hatter Institute for Cardiovascular Diseases Research in Africa (HICRA), Department of Medicine, University of Cape Town, Cape Town, South Africa; Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, 237 Barton Street East, Hamilton, ON L8L 2 × 2, Canada
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research group, MRC/UVRI and LSHTM, Uganda; London School of Hygiene and Tropical Medicine London UK; H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria.
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