A new HLA-C∗02 null allele described in quilombo remnants samples from southern brazil

Abstract

The present study describes a new HLA-C null allele in African-derived Quilombo communities from the Ribeira River Valley in the state of São Paulo, Brazil. Quilombo are small communities founded by runway, abandoned and freed African-descendent slaves, in the late seventeen century. In the São Paulo state, Quilombo remnants are confined to a small area, on the southern border along the Ribeira River Valley. In the present study, 146 individuals from 12 Quilombo communities from the Ribeira River Valley (Abobral, André Lopes, Galvão, São Pedro, Pedro Cubas, Pilões, Nhunguara, Sapatu, Ivaporanduva, Maria Rosa, Poças and Reginaldo) were typed for HLA-A, -B, -C and DRB1 by PCR-SBT (Thermo Fisher). We identified a new HLA-C∗02 null in three individuals: an 84 yo female (sample 20), a 38 yo female (sample 75) and an 18 yo male (sample 137), from Galvão, São Pedro and Pedro Cubas communities respectively. This new allele presented an insertion of seven nucleotides (TCGCCGT) in exon 2 at codon 50, leading to a frame shift and generating a subsequent stop at codon 76. In all the three cases the HLA-C∗02 null allele was associated with the following haplotype: A∗80:01∼C∗02N∼B∗18:01:01G∼DRB1∗07:01. To further characterize this allele and verify if it was exclusively found in this Quilombo communities, we performed a parallel study, typing the HLA-C locus by PCR-SBT in six unrelated urban Brazilian Afro-descendants individuals from São Paulo state. They were selected based on the HLA-A, -B, -C, -DRB1 haplotype and were previously typed as HLA-A∗80, B∗18, C∗02, DRB1∗07 (Intermediate resolution, PCR-SSO). The new HLA-C∗02 null was not observed in any of them. The kinship coefficient, estimated by Moment method based on 600K genomewide SNPs, between the 3 individuals are: θ Samples 20–75 = 0.0271, θ Samples 20–137 = 0.0278 and θ Samples 75–137 = 0.0170. This result shows that the individuals have some kinship degree and suggests that the shared null allele/haplotype is derived from a unique common ancestor. This new allele was submitted to the GenBank (accession numbers: KR698080, KR698081 and KR698082 for samples 20, 75 and 137 respectively) and IMGT for official nomenclature.