EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow

Magalhães, Wagner C. S.; Araujo, Nathalia Matta; Leal, Thiago P.; Araújo, Gilderlanio Santana de; Viriato, Paula J S; Kehdy, Fernanda S. G.; Costa, Gustavo Nunes de Oliveira; Barreto, Maurício L.; Horta, Bernardo Lessa; Lima‐Costa, Maria Fernanda; Pereira, Alexandre C.; Tarazona‐Santos, Eduardo; Rodrigues, Maíra R.

doi:10.1101/gr.225458.117

Cited by 20 publications

(23 citation statements)

References 30 publications

(34 reference statements)

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“…Similar to BIPMed, other Brazilian initiatives have aimed to make genomic data more transparent and reproducible 35 . However, BIPMed is the first to provide the public with easy access to raw data ( https://bipmed.org/datasharing/ ).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2020

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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.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2020

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“…Genetic differentiation between populations considering only the African gene pool was estimated using the African-ancestry genetic distance (AAGD, SI Appendix , section 4.1). Flowcharts and masterscripts of the analyses are available in the EPIGEN Scientific Workflow (26) web (http://ldgh.com.br/scientificworkflow). Details of Methods are in the SI Appendix.…”

Section: Methodsmentioning

confidence: 99%

Origins, admixture dynamics and homogenization of the African gene pool in the Americas

Gouveia

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Leal

et al. 2019

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53 4169-007, Portugal. 54 21 CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, Vairão, 4485-55 661, Portugal. 56 Abstract 76 The Transatlantic Slave Trade transported more than 9 million Africans to the Americas 77 between the early 16th and the mid-19th centuries. We performed genome-wide 78 analysis of 6,267 individuals from 22 populations and observed an enrichment in West-79 African ancestry in northern latitudes of the Americas, whereas South/East African 80 ancestry is more prevalent in southern South-America. This pattern results from distinct 81 geographic and geopolitical factors leading to population differentiation. However, we 82 observed a decrease of 68% in the African gene pool between-population diversity 83 within the Americas when compared to the regions of origin from Africa, underscoring 84 the importance of historical factors favoring admixture between individuals with 85 different African origins in the New World. This is consistent with the excess of West-86 Central Africa ancestry (the most prevalent in the Americas) in the US and Southeast-87 Brazil, respect to historical-demography expectations. Also, in most of the Americas, 88 admixture intensification occurred between 1,750 and 1,850, which correlates strongly 89 with the peak of arrivals from Africa. This study contributes with a population genetics 90 perspective to the ongoing social, cultural and political debate regarding ancestry, race, 91 and admixture in the Americas.92 93 Significance Statement 94 Differently from most genetic studies, that have estimated the overall African ancestry 95 in the Americas, we perform a finer geographic analysis and infer how different African 96 groups contributed to North-, South-American and Caribbean populations, in the 97 context of geographic and geopolitical factors. We also perform a formal comparison of 98 information from demographic history records of the Transatlantic Slave Trade with 99 inferences based on genomic diversity of current populations. Our approach reveals the 100 6 distinct regional African ancestry roots of different populations from North-, South-101 America and the Caribe and other important aspects of the historical process of 102 mestizaje and its dynamics in the American continent. 103 104 157(from Ghana, mean: 18%) ( Fig. 2A and B, SI Appendix, Table S3). 158The Western Africa-associated ancestry cluster has its highest proportions in Puerto 159 Ricans (38% of African ancestry), Colombians (27%) and US African-Americans (19-160 20%, purple in Fig. 1, SI Appendix, Table S1), while Brazilians have the lowest 161 proportion (<9%), limited to a Mandinka-like (Gambia) contribution and with no 162

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“…[28][29][30][31] Fortunately, current funding and resource development efforts, as well as ongoing international collaborations, aim to improve our knowledge of the basis of health/disease in diverse populations. 19,[32][33][34][35][36][37][38][39][40] Additional and continuous investments will be necessary to support studies that capture multidimensional and multilevel data, and allow a deeper understanding of how different factors interact to contribute to the observed cancer health disparities.…”

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confidence: 99%

Cancer health disparities in racial/ethnic minorities in the United States

et al. 2020

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There are well-established disparities in cancer incidence and outcomes by race/ethnicity that result from the interplay between structural, socioeconomic, socio-environmental, behavioural and biological factors. However, large research studies designed to investigate factors contributing to cancer aetiology and progression have mainly focused on populations of European origin. The limitations in clinicopathological and genetic data, as well as the reduced availability of biospecimens from diverse populations, contribute to the knowledge gap and have the potential to widen cancer health disparities. In this review, we summarise reported disparities and associated factors in the United States of America (USA) for the most common cancers (breast, prostate, lung and colon), and for a subset of other cancers that highlight the complexity of disparities (gastric, liver, pancreas and leukaemia). We focus on populations commonly identified and referred to as racial/ethnic minorities in the USA—African Americans/Blacks, American Indians and Alaska Natives, Asians, Native Hawaiians/other Pacific Islanders and Hispanics/Latinos. We conclude that even though substantial progress has been made in understanding the factors underlying cancer health disparities, marked inequities persist. Additional efforts are needed to include participants from diverse populations in the research of cancer aetiology, biology and treatment. Furthermore, to eliminate cancer health disparities, it will be necessary to facilitate access to, and utilisation of, health services to all individuals, and to address structural inequities, including racism, that disproportionally affect racial/ethnic minorities in the USA.

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EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow

Cited by 20 publications

References 30 publications

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

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

Origins, admixture dynamics and homogenization of the African gene pool in the Americas

Cancer health disparities in racial/ethnic minorities in the United States

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