Dataset Information

The Brazilian Initiative on Precision Medicine (BIPMed): fostering genomic data-sharing of underrepresented populations.

ABSTRACT: The development of precision medicine strategies requires prior knowledge of the genetic background of the target population. However, despite the availability of data from admixed Americans within large reference population databases, we cannot use these data as a surrogate for that of the Brazilian population. This lack of transferability is mainly due to differences between ancestry proportions of Brazilian and other admixed American populations. To address the issue, a coalition of research centres created the Brazilian Initiative on Precision Medicine (BIPMed). In this study, we aim to characterise two datasets obtained from 358 individuals from the BIPMed using two different platforms: whole-exome sequencing (WES) and a single nucleotide polymorphism (SNP) array. We estimated allele frequencies and variant pathogenicity values from the two datasets and compared our results using the BIPMed dataset with other public databases. Here, we show that the BIPMed WES dataset contains variants not included in dbSNP, including 6480 variants that have alternative allele frequencies (AAFs) >1%. Furthermore, after merging BIPMed WES and SNP array data, we identified 809,589 variants (47.5%) not present within the 1000 Genomes dataset. Our results demonstrate that, through the incorporation of Brazilian individuals into public genomic databases, BIPMed not only was able to provide valuable knowledge needed for the implementation of precision medicine but may also enhance our understanding of human genome variability and the relationship between genetic variation and disease predisposition.

SUBMITTER: Rocha CS

PROVIDER: S-EPMC7532430 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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The Brazilian Initiative on Precision Medicine (BIPMed): fostering genomic data-sharing of underrepresented populations.

Rocha Cristiane S CS Secolin Rodrigo R Rodrigues Maíra R MR Carvalho Benilton S BS Lopes-Cendes Iscia I

NPJ genomic medicine 20201002

The development of precision medicine strategies requires prior knowledge of the genetic background of the target population. However, despite the availability of data from admixed Americans within large reference population databases, we cannot use these data as a surrogate for that of the Brazilian population. This lack of transferability is mainly due to differences between ancestry proportions of Brazilian and other admixed American populations. To address the issue, a coalition of research ...[more]

PMID: 33083011

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Project description:Precision medicine (PM) programs typically use broad consent. This approach requires maintenance of the social license and public trust. The ultimate success of PM programs will thus likely be contingent upon understanding public expectations about data sharing and establishing appropriate governance structures. There is a lack of data on public attitudes towards PM in Asia. The aim of the research was to measure the priorities and preferences of Singaporeans for sharing health-related data for PM. We used adaptive choice-based conjoint analysis (ACBC) with four attributes: uses, users, data sensitivity and consent. We recruited a representative sample of n = 1000 respondents for an in-person household survey. Of the 1000 respondents, 52% were female and majority were in the age range of 40-59 years (40%), followed by 21-39 years (33%) and 60 years and above (27%). A total of 64% were generally willing to share de-identified health data for IRB-approved research without re-consent for each study. Government agencies and public institutions were the most trusted users of data. The importance of the four attributes on respondents' willingness to share data were: users (39.5%), uses (28.5%), data sensitivity (19.5%), consent (12.6%). Most respondents found it acceptable for government agencies and hospitals to use de-identified data for health research with broad consent. Our sample was consistent with official government data on the target population with 52% being female and majority in the age range of 40-59 years (40%), followed by 21-39 years (33%) and 60 years and above (27%). While a significant body of prior research focuses on preferences for consent, our conjoint analysis found consent was the least important attribute for sharing data. Our findings suggest the social license for PM data sharing in Singapore currently supports linking health and genomic data, sharing with public institutions for health research and quality improvement; but does not support sharing with private health insurers or for private commercial use.

Project description:BackgroundThe diversity of clinical tumor profiling approaches (small panels to whole exomes with matched or unmatched germline analysis) may engender uncertainty about their benefits and liabilities, particularly in light of reported germline false positives in tumor-only profiling and use of global mutational and/or neoantigen data. The goal of this study was to determine the impact of genomic analysis strategies on error rates and data interpretation across contexts and ancestries.MethodsWe modeled common tumor profiling modalities-large (n = 300 genes), medium (n = 48 genes), and small (n = 15 genes) panels-using clinical whole exomes (WES) from 157 patients with lung or colon adenocarcinoma. We created a tumor-only analysis algorithm to assess germline false positive rates, the impact of patient ancestry on tumor-only results, and neoantigen detection.ResultsAfter optimizing a germline filtering strategy, the germline false positive rate with tumor-only large panel sequencing was 14 % (144/1012 variants). For patients whose tumor-only results underwent molecular pathologist review (n = 91), 50/54 (93 %) false positives were correctly interpreted as uncertain variants. Increased germline false positives were observed in tumor-only sequencing of non-European compared with European ancestry patients (p < 0.001; Fisher's exact) when basic germline filtering approaches were used; however, the ExAC database (60,706 germline exomes) mitigated this disparity (p = 0.53). Matched and unmatched large panel mutational load correlated with WES mutational load (r(2) = 0.99 and 0.93, respectively; p < 0.001). Neoantigen load also correlated (r(2) = 0.80; p < 0.001), though WES identified a broader spectrum of neoantigens. Small panels did not predict mutational or neoantigen load.ConclusionsLarge tumor-only targeted panels are sufficient for most somatic variant identification and mutational load prediction if paired with expanded germline analysis strategies and molecular pathologist review. Paired germline sequencing reduced overall false positive mutation calls and WES provided the most neoantigens. Without patient-matched germline data, large germline databases are needed to minimize false positive mutation calling and mitigate ethnic disparities.

Dataset Information

The Brazilian Initiative on Precision Medicine (BIPMed): fostering genomic data-sharing of underrepresented populations.

Publications

The Brazilian Initiative on Precision Medicine (BIPMed): fostering genomic data-sharing of underrepresented populations.

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