A Breast Cancer Polygenic Risk Score Validation in 15,490 Brazilians Using Exome Sequencing

Background/Objectives: Brazil has a highly admixed population. Polygenic risk scores (PRSs) have mostly been developed from European population studies, and their application to other populations is challenging. To assess the use of PRS for breast cancer (BC) risk in Brazil, we evaluated four PRSs i...

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Published in	Diagnostics (Basel) Vol. 15; no. 9; p. 1098
Main Authors	Eichemberger Rius, Flávia, Santa Cruz Guindalini, Rodrigo, Viana, Danilo, Salomão, Júlia, Gallo, Laila, Freitas, Renata, Bertolacini, Cláudia, Taniguti, Lucas, Imparato, Danilo, Antunes, Flávia, Sousa, Gabriel, Achjian, Renan, Fukuyama, Eric, Gregório, Cleandra, Ventura, Iuri, Gomes, Juliana, Taniguti, Nathália, Maistro, Simone, Krieger, José Eduardo, Zheng, Yonglan, Huo, Dezheng, Olopade, Olufunmilayo I., Azevedo Koike Folgueira, Maria Aparecida, Schlesinger, David
Format	Journal Article
Language	English
Published	Switzerland MDPI AG 25.04.2025 MDPI
Subjects	admixed population Breast cancer cancer genetics Cohort analysis Datasets Genetic aspects Genomes Health aspects Native North Americans next-generation sequencing (NGS) polygenic risk score (PRS) Precision medicine Regression analysis Risk factors Software Tumor proteins Womens health Brazil East Asia British Columbia Europe Africa breast cancer precision medicine cancer genetics admixed population next-generation sequencing (NGS) polygenic risk score (PRS)
Online Access	Get full text
ISSN	2075-4418 2075-4418
DOI	10.3390/diagnostics15091098

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Abstract	Background/Objectives: Brazil has a highly admixed population. Polygenic risk scores (PRSs) have mostly been developed from European population studies, and their application to other populations is challenging. To assess the use of PRS for breast cancer (BC) risk in Brazil, we evaluated four PRSs in the Brazilian population. Methods: We analyzed a Brazilian cohort composed of 6206 women with a history of breast cancer and 8878 unphenotyped adults as controls. Genomic variants were imputed from exomes, and scores were calculated for all samples. Results: After individuals with known pathogenic or likely pathogenic variants in BRCA1, BRCA2, PALB2, PTEN, or TP53 genes, and first-degree relatives of the probands were excluded, 5598 cases and 8767 controls remained. Four PRS models were compared, and PRS3820 achieved the best performance, with an odds ratio (OR) of 1.43 per standard deviation increase (p value < 0.001) and an OR of 1.88 (p value < 0.001) for the top decile. PRS3820 also performed well for different ancestry groups: East Asian majority (OR 1.59, p value 0.004), Non-European majority (OR 1.45, p value < 0.001), and European majority (OR 1.43, p value < 0.001). Conclusions: Among the different PRSs, PRS313 and PRS3820 could be validated in our Brazilian cohort, with the latter exhibiting the best performance. While further clinical studies are necessary to guide clinical practice, this work represents an important step toward improving BC precision medicine in Brazil.
AbstractList	Background/Objectives: Brazil has a highly admixed population. Polygenic risk scores (PRSs) have mostly been developed from European population studies, and their application to other populations is challenging. To assess the use of PRS for breast cancer (BC) risk in Brazil, we evaluated four PRSs in the Brazilian population. Methods: We analyzed a Brazilian cohort composed of 6206 women with a history of breast cancer and 8878 unphenotyped adults as controls. Genomic variants were imputed from exomes, and scores were calculated for all samples. Results: After individuals with known pathogenic or likely pathogenic variants in BRCA1, BRCA2, PALB2, PTEN, or TP53 genes, and first-degree relatives of the probands were excluded, 5598 cases and 8767 controls remained. Four PRS models were compared, and PRS3820 achieved the best performance, with an odds ratio (OR) of 1.43 per standard deviation increase (p value < 0.001) and an OR of 1.88 (p value < 0.001) for the top decile. PRS3820 also performed well for different ancestry groups: East Asian majority (OR 1.59, p value 0.004), Non-European majority (OR 1.45, p value < 0.001), and European majority (OR 1.43, p value < 0.001). Conclusions: Among the different PRSs, PRS313 and PRS3820 could be validated in our Brazilian cohort, with the latter exhibiting the best performance. While further clinical studies are necessary to guide clinical practice, this work represents an important step toward improving BC precision medicine in Brazil. Background/Objectives: Brazil has a highly admixed population. Polygenic risk scores (PRSs) have mostly been developed from European population studies, and their application to other populations is challenging. To assess the use of PRS for breast cancer (BC) risk in Brazil, we evaluated four PRSs in the Brazilian population. Methods: We analyzed a Brazilian cohort composed of 6206 women with a history of breast cancer and 8878 unphenotyped adults as controls. Genomic variants were imputed from exomes, and scores were calculated for all samples. Results: After individuals with known pathogenic or likely pathogenic variants in BRCA1, BRCA2, PALB2, PTEN, or TP53 genes, and first-degree relatives of the probands were excluded, 5598 cases and 8767 controls remained. Four PRS models were compared, and PRS3820 achieved the best performance, with an odds ratio (OR) of 1.43 per standard deviation increase (p value < 0.001) and an OR of 1.88 (p value < 0.001) for the top decile. PRS3820 also performed well for different ancestry groups: East Asian majority (OR 1.59, p value 0.004), Non-European majority (OR 1.45, p value < 0.001), and European majority (OR 1.43, p value < 0.001). Conclusions: Among the different PRSs, PRS313 and PRS3820 could be validated in our Brazilian cohort, with the latter exhibiting the best performance. While further clinical studies are necessary to guide clinical practice, this work represents an important step toward improving BC precision medicine in Brazil.Background/Objectives: Brazil has a highly admixed population. Polygenic risk scores (PRSs) have mostly been developed from European population studies, and their application to other populations is challenging. To assess the use of PRS for breast cancer (BC) risk in Brazil, we evaluated four PRSs in the Brazilian population. Methods: We analyzed a Brazilian cohort composed of 6206 women with a history of breast cancer and 8878 unphenotyped adults as controls. Genomic variants were imputed from exomes, and scores were calculated for all samples. Results: After individuals with known pathogenic or likely pathogenic variants in BRCA1, BRCA2, PALB2, PTEN, or TP53 genes, and first-degree relatives of the probands were excluded, 5598 cases and 8767 controls remained. Four PRS models were compared, and PRS3820 achieved the best performance, with an odds ratio (OR) of 1.43 per standard deviation increase (p value < 0.001) and an OR of 1.88 (p value < 0.001) for the top decile. PRS3820 also performed well for different ancestry groups: East Asian majority (OR 1.59, p value 0.004), Non-European majority (OR 1.45, p value < 0.001), and European majority (OR 1.43, p value < 0.001). Conclusions: Among the different PRSs, PRS313 and PRS3820 could be validated in our Brazilian cohort, with the latter exhibiting the best performance. While further clinical studies are necessary to guide clinical practice, this work represents an important step toward improving BC precision medicine in Brazil. : Brazil has a highly admixed population. Polygenic risk scores (PRSs) have mostly been developed from European population studies, and their application to other populations is challenging. To assess the use of PRS for breast cancer (BC) risk in Brazil, we evaluated four PRSs in the Brazilian population. We analyzed a Brazilian cohort composed of 6206 women with a history of breast cancer and 8878 unphenotyped adults as controls. Genomic variants were imputed from exomes, and scores were calculated for all samples. After individuals with known pathogenic or likely pathogenic variants in , , , , or genes, and first-degree relatives of the probands were excluded, 5598 cases and 8767 controls remained. Four PRS models were compared, and PRS achieved the best performance, with an odds ratio (OR) of 1.43 per standard deviation increase ( value < 0.001) and an OR of 1.88 ( value < 0.001) for the top decile. PRS also performed well for different ancestry groups: East Asian majority (OR 1.59, value 0.004), Non-European majority (OR 1.45, value < 0.001), and European majority (OR 1.43, value < 0.001). Among the different PRSs, PRS and PRS could be validated in our Brazilian cohort, with the latter exhibiting the best performance. While further clinical studies are necessary to guide clinical practice, this work represents an important step toward improving BC precision medicine in Brazil. Background/Objectives : Brazil has a highly admixed population. Polygenic risk scores (PRSs) have mostly been developed from European population studies, and their application to other populations is challenging. To assess the use of PRS for breast cancer (BC) risk in Brazil, we evaluated four PRSs in the Brazilian population. Methods: We analyzed a Brazilian cohort composed of 6206 women with a history of breast cancer and 8878 unphenotyped adults as controls. Genomic variants were imputed from exomes, and scores were calculated for all samples. Results: After individuals with known pathogenic or likely pathogenic variants in BRCA1 , BRCA2 , PALB2 , PTEN , or TP53 genes, and first-degree relatives of the probands were excluded, 5598 cases and 8767 controls remained. Four PRS models were compared, and PRS 3820 achieved the best performance, with an odds ratio (OR) of 1.43 per standard deviation increase ( p value < 0.001) and an OR of 1.88 ( p value < 0.001) for the top decile. PRS 3820 also performed well for different ancestry groups: East Asian majority (OR 1.59, p value 0.004), Non-European majority (OR 1.45, p value < 0.001), and European majority (OR 1.43, p value < 0.001). Conclusions: Among the different PRSs, PRS 313 and PRS 3820 could be validated in our Brazilian cohort, with the latter exhibiting the best performance. While further clinical studies are necessary to guide clinical practice, this work represents an important step toward improving BC precision medicine in Brazil. Background/Objectives: Brazil has a highly admixed population. Polygenic risk scores (PRSs) have mostly been developed from European population studies, and their application to other populations is challenging. To assess the use of PRS for breast cancer (BC) risk in Brazil, we evaluated four PRSs in the Brazilian population. Methods: We analyzed a Brazilian cohort composed of 6206 women with a history of breast cancer and 8878 unphenotyped adults as controls. Genomic variants were imputed from exomes, and scores were calculated for all samples. Results: After individuals with known pathogenic or likely pathogenic variants in BRCA1, BRCA2, PALB2, PTEN, or TP53 genes, and first-degree relatives of the probands were excluded, 5598 cases and 8767 controls remained. Four PRS models were compared, and PRS[sub.3820] achieved the best performance, with an odds ratio (OR) of 1.43 per standard deviation increase (p value < 0.001) and an OR of 1.88 (p value < 0.001) for the top decile. PRS[sub.3820] also performed well for different ancestry groups: East Asian majority (OR 1.59, p value 0.004), Non-European majority (OR 1.45, p value < 0.001), and European majority (OR 1.43, p value < 0.001). Conclusions: Among the different PRSs, PRS[sub.313] and PRS[sub.3820] could be validated in our Brazilian cohort, with the latter exhibiting the best performance. While further clinical studies are necessary to guide clinical practice, this work represents an important step toward improving BC precision medicine in Brazil.
Audience	Academic
Author	Azevedo Koike Folgueira, Maria Aparecida Antunes, Flávia Taniguti, Nathália Viana, Danilo Gregório, Cleandra Salomão, Júlia Achjian, Renan Schlesinger, David Gomes, Juliana Ventura, Iuri Olopade, Olufunmilayo I. Eichemberger Rius, Flávia Zheng, Yonglan Freitas, Renata Santa Cruz Guindalini, Rodrigo Gallo, Laila Imparato, Danilo Sousa, Gabriel Fukuyama, Eric Taniguti, Lucas Maistro, Simone Bertolacini, Cláudia Krieger, José Eduardo Huo, Dezheng
AuthorAffiliation	6 Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA 3 Instituto D’Or de Pesquisa e Ensino (IDOR), Sao Paulo 01401-002, SP, Brazil 4 Instituto do Coração, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo (FMUSP), Sao Paulo 05403-900, SP, Brazil 5 Medicine and Human Genetics, Center for Clinical Cancer Genetics and Global Health, University of Chicago Medical Center, Chicago, IL 60637, USA 2 Comprehensive Center for Precision Oncology (C2PO), Centro de Investigação Translacional em Oncologia (CTO), Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo 01246-000, SP, Brazil 1 Mendelics, Sao Paulo 02511-000, SP, Brazil
AuthorAffiliation_xml	– name: 2 Comprehensive Center for Precision Oncology (C2PO), Centro de Investigação Translacional em Oncologia (CTO), Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo 01246-000, SP, Brazil – name: 5 Medicine and Human Genetics, Center for Clinical Cancer Genetics and Global Health, University of Chicago Medical Center, Chicago, IL 60637, USA – name: 6 Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA – name: 3 Instituto D’Or de Pesquisa e Ensino (IDOR), Sao Paulo 01401-002, SP, Brazil – name: 1 Mendelics, Sao Paulo 02511-000, SP, Brazil – name: 4 Instituto do Coração, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo (FMUSP), Sao Paulo 05403-900, SP, Brazil
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Snippet	Background/Objectives: Brazil has a highly admixed population. Polygenic risk scores (PRSs) have mostly been developed from European population studies, and... : Brazil has a highly admixed population. Polygenic risk scores (PRSs) have mostly been developed from European population studies, and their application to... Background/Objectives : Brazil has a highly admixed population. Polygenic risk scores (PRSs) have mostly been developed from European population studies, and...
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SubjectTerms	admixed population Breast cancer cancer genetics Cohort analysis Datasets Genetic aspects Genomes Health aspects Native North Americans next-generation sequencing (NGS) polygenic risk score (PRS) Precision medicine Regression analysis Risk factors Software Tumor proteins Womens health
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Title	A Breast Cancer Polygenic Risk Score Validation in 15,490 Brazilians Using Exome Sequencing
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