DOI: 10.5061/dryad.x3ffbg7rc
title: HLA class I Sanger sequences data of Honduras HIV cohort

description: HLA polymorphisms represent the strongest genetic modifier of HIV disease
 progression. Diverse HLA distribution can lead to distinct HIV control
 landscapes at the population level. We aimed to describe HLA allele and
 haplotype frequencies (linkage disequilibrium, LD), CCR5-Δ32 frequency and
 the impact of these variants on HIV disease outcome. HLA class I (cI) loci
 were typed at 4-digit resolution, and CCR5 variants were determined in 402
 HIV clade B-infected, ART-naïve individuals from Honduras. HLA LD were
 assessed using Fisher’s exact test. Using univariable and multivariable
 analyses we evaluated HLA associations with HIV pVL and CD4 counts. We did
 not find any effect on HIV control between CCR5 genotypes. Previously
 defined HLA associations were found: B*57:01/03, B*42:01, A*25:01 and
 C*12:03 (protective), and B*53:01 and A*68:01 (risk). Being consistent
 with our previous research in a Mesoamerican HIV cohort, Amerindian
 B*35:12 was associated to poor HIV control. Other HLA-HIV associations not
 previously described were C*03:04 and B*08:01 that were associated with
 higher pVL. Overall, this first report highlights the immunogenetic
 uniqueness admixture of the Honduras population that express Amerindian,
 Caucasian and African HLA subtypes. These findings not only support this
 cohort as ideal for identifying HLA correlates of HIV control but also may
 improve future research regarding allotransplantation and disease
 association.
description: HLA class I loci
 <em>(HLA-A</em>, <em>HLA-C</em> and
 <em>HLA-B)</em> were resolved at second field resolution
 (i.e., subtype or protein level) using a previously described protocol.
 Briefly, a nested PCR with locus-specific primers were used to amplify a
 ~1000 bp region spanning exons 2 and 3. These PCR products were directly
 sequenced using a set of sequencing primers as previously described
 (Cotton LA, et al. 2012. HLA class I sequence-based typing using DNA
 recovered from frozen plasma. J Immunol Methods 382:40–47) on a 3730xl
 Genetic Analyzer (Applied Biosystems, Foster City). HLA subtypes were
 assigned using UType v7.1 RUO (Applied Biosystems) using the IPD-IMGT/HLA
 Database (release 3.31.0, 2018-01). Primer (allelic) and phase resolution
 ambiguities were resolved as previously explained (Valenzuela-Ponce H, et
 al. 2018. Novel HLA class I associations with HIV-1 control in a unique
 genetically admixed population. Sci Rep 8:17.).
description: # HLA class I Sanger sequences data of Honduras HIV cohort
 [https://doi.org/10.5061/dryad.x3ffbg7rc](https://doi.org/10.5061/dryad.x3ffbg7rc) HLA Sanger sequences encompassing exons 2 and 3 of HLA-A, HLA-B and HLA-C loci of Honduras HIV cohort ## Description of the data and file structure HLA class I loci *(HLA-A*, *HLA-C* and *HLA-B)* were resolved at second field resolution (i.e., subtype or protein level) using a previously described protocol (Valenzuela-Ponce H., et al. 2018. Novel HLA class I associations with HIV-1 control in a unique genetically admixed population. Sci Rep 8:17.). Briefly, a nested PCR with locus-specific primers were used to amplify a \~1000 bp region spanning exons 2 and 3. These PCR products were directly sequenced using a set of sequencing primers as previously described (Cotton LA, et al. 2012. HLA class I sequence-based typing using DNA recovered from frozen plasma. J Immunol Methods 382:40–47.) on a 3730xl Genetic Analyzer (Applied Biosystems, Foster City). HLA subtypes were assigned using UType v7.1 RUO (Applied Biosystems) using the IPD-IMGT/HLA Database (release 3.31.0, 2018-01). Primer (allelic) and phase resolution ambiguities were resolved as previously explained (Valenzuela-Ponce H., et al. 2018. Novel HLA class I associations with HIV-1 control in a unique genetically admixed population. Sci Rep 8:17.). Each folder contains the Sanger sequences (ab1 files and related files) of the 3 amplified genes (exons 2 and 3 of HLA-A, B and C loci) where the files were properly anonymized and randomized. Folders and files were renamed as donor-1, donor-2, and so on. Files were compressed into a zip file. ## Sharing/Access information Data was derived from the following sources: * Article named "Honduras HIV cohort: HLA class I and CCR5-Δ32 profile and their associations with HIV disease outcome" to be publish in Microbiology Spectrum (American Society of Microbiology)