| Full text | |
| Author(s): Show less - |
Douillard, Venceslas
;
Silva, Nayane dos Santos Brito
;
Bourguiba-Hachemi, Sonia
;
Naslavsky, Michel S.
;
Scliar, Marilia O.
;
Duarte, Yeda A. O.
;
Zatz, Mayana
;
Passos-Bueno, Maria Rita
;
Limou, Sophie
;
Gourraud, Pierre-Antoine
;
Launay, Elise
;
Castelli, Erick C.
;
Vince, Nicolas
Total Authors: 13
|
| Document type: | Journal article |
| Source: | HLA; v. 103, n. 1, p. 14-pg., 2023-11-11. |
| Abstract | |
Human genomics has quickly evolved, powering genome-wide association studies (GWASs). SNP-based GWASs cannot capture the intense polymorphism of HLA genes, highly associated with disease susceptibility. There are methods to statistically impute HLA genotypes from SNP-genotypes data, but lack of diversity in reference panels hinders their performance. We evaluated the accuracy of the 1000 Genomes data as a reference panel for imputing HLA from admixed individuals of African and European ancestries, focusing on (a) the full dataset, (b) 10 replications from 6 populations, and (c) 19 conditions for the custom reference panels. The full dataset outperformed smaller models, with a good F1-score of 0.66 for HLA-B. However, custom models outperformed the multiethnic or population models of similar size (F1-scores up to 0.53, against up to 0.42). We demonstrated the importance of using genetically specific models for imputing populations, which are currently underrepresented in public datasets, opening the door to HLA imputation for every genetic population. (AU) | |
| FAPESP's process: | 12/24731-1 - Retrocopies: origins, polymorphism and somatic variations |
| Grantee: | Pedro Alexandre Favoretto Galante |
| Support Opportunities: | Research Grants - Young Investigators Grants |
| FAPESP's process: | 15/25020-0 - Retroelements in primary and metastatic colorectal tumors. |
| Grantee: | Fernanda Orpinelli Ramos do Rego |
| Support Opportunities: | Scholarships in Brazil - Doctorate |
| FAPESP's process: | 14/50931-3 - Aging and genetic disorders: genomics and metagenomics |
| Grantee: | Mayana Zatz |
| Support Opportunities: | Research Projects - Thematic Grants |
| FAPESP's process: | 13/08028-1 - CEGH-CEL - Human Genome and Stem Cell Research Center |
| Grantee: | Mayana Zatz |
| Support Opportunities: | Research Grants - Research, Innovation and Dissemination Centers - RIDC |
| FAPESP's process: | 17/19223-0 - KIR2DL4, KIR3DL2, KIR3DL3, LILRB1 (ILT2) and LILRB2 (ILT4) variability and haplotypes in a Brazilian population sample from the São Paulo state |
| Grantee: | Erick da Cruz Castelli |
| Support Opportunities: | Regular Research Grants |
| FAPESP's process: | 18/15579-8 - Retroelements: a driving force generating genetic novelties in the human and mouse genome |
| Grantee: | Pedro Alexandre Favoretto Galante |
| Support Opportunities: | Research Grants - Young Investigators Grants - Phase 2 |
| FAPESP's process: | 13/17084-2 - Evaluation of MHC Class I genes variability, regulation and evolutive history |
| Grantee: | Erick da Cruz Castelli |
| Support Opportunities: | Regular Research Grants |
| FAPESP's process: | 20/02413-4 - Intragenic retrocopies as a source of novel protein domains in humans |
| Grantee: | Rafael Luiz Vieira Mercuri |
| Support Opportunities: | Scholarships in Brazil - Doctorate (Direct) |
| FAPESP's process: | 14/50649-6 - SABE study: a longitudinal study of multiple cohorts on the elderly life and health conditions in the municipality of São Paulo - cohort 2015 |
| Grantee: | Yeda Aparecida de Oliveira Duarte |
| Support Opportunities: | Research Projects - Thematic Grants |