Inferring paternal history of rural african-derived brazilian populations from y chromosomes

About four million Africans were brought to Brazil as slaves during four centuries. Many communities, named \ud quilombos, were founded by runaway or abandoned African slaves. ere are many quilombo remnants in the ‘Vale \ud do Ribeira’ region in the southern part of São Paulo State, Brazil. In order to shed light on their origins, patterns of \ud genetic diversity and to estimate genetic admixture, we used ve biallelic Y chromosome markers (YAP, M3, M242, \ud M168 and M2) and a set of 17 microssatelites (AmpFlSTR Y ler, Applied Biosystems) to de ne haplotypes and \ud haplogroups. e aim of the study was to investigate how Amerindians, Europeans and Africans contributed to \ud the Y chromosome pool in ten African-derived populations (about 300 individuals) from ‘Vale do Ribeira’ region.\ud Allelic and haplotype frequencies were estimated by direct counting using the Arlequin ver 3.5 software (Exco er \ud and Lischer, 2010; Mol Ecol Resour. May; 10(3): 564-7). Haplotype diversity and degrees of interpopulational genetic \ud variation (FST) were inferred using the same software. Y-chromosomal haplogroups predictions based on the set of \ud microsatellites were generated using Haplogroup Predictor (http://www.hprg.com/hapest5/). Admixture analysis \ud based on the biallelic markers indicated that 32.2% of Y chromosomes lineages were African, 60.9% are European and \ud a small proportion, Amerindian (7.0%). Further analysis based on microsatellites allowed identi cation of 99 di erent \ud haplotypes, classi ed into 12 distinct haplogroups. e most frequent were haplogroups R1b (39.5%, European), \ud E1b1a (33.0%, African) and Q (7.8% Amerindian). e remaining haplotypes (19.8%) were classi ed into several \ud di erent European haplogroups. e presence of predominant haplotypes and genealogical data indicate a pattern \ud of origin of quilombos from a limited number of male individuals, some of them having a key role in the foundation \ud of these populations. e genetic distances (FST) analysis indicated that the ten populations studied, geographically \ud close, have a low degree of genetic di erentiation (mean FST = 0.089, p<0.001), indicating that they are genetically \ud very similar, a phenomenon that may be explained by high degree of gene ow between them. is study helped to \ud highlight the history of social interactions during the setting and establishing of the ‘Vale do Ribeira’ populations.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) – CEPID, and Conselho Nacional de Desenvolvimento Cientí co e Tecnológico (CNPq) – PRONEX

Investigating deafness genes as a cause of sudden sensorineural hearing loss

Hearing loss is a very heterogeneous genetic condition, meaning that identical or similar phenotypes result from \ud mutations in many di erent genes, with diverse inheritance mechanisms. Sudden sensorineural hearing loss (SSNHL) \ud is an emergency de ned as sensorineural hearing loss (SNHL) equal to or greater than 30 dB HL, a ecting at least \ud three consecutive tonal frequencies, with sudden onset and occurring within three days. e estimate incidence \ud is 5 to 20 within 100.000 people by year, but despite the extensive list of potentially etiologic factors described, \ud its pathophysiology is poorly understood. Some individuals with deafness due to mitochondrial mutations were \ud described as having SSNHL. In mitochondrial DNA, genes encoding for transporter and ribosome RNA are hot \ud candidates to explain hearing loss due to the large number of mutations associated with deafness already described \ud in them. e main mitochondrial mutations associated with non-syndromic deafness are A1555G, ΔT961insCn, \ud T1095C, C1494T in MTRNR1 gene, that encodes the 12S subunit of rRNA; and A7445G, 7472insC, T7510C and \ud T7511C in MTTS1 gene, that encodes the tRNASer(UCN). Regarding the MTTL1 gene, mutations are more frequently \ud associated to mitochondrial syndroms that can include deafness as a symptom. Besides, mutations c.35delG and \ud c.167delT in the GJB2 gene, del(GJB6-D13S1830) and del(GJB6-D13S1854) deletions near the GJB6 gene and the \ud A1555G mitochondrial mutation in the 12S rRNA gene are described as the most frequently molecular diagnosis \ud among individuals with hearing loss. e aim of this work was to investigate the role of genetic factor in the etiology \ud of SSNHL. In order to achieve this, the screened the mutations in the GJB2 and GJB6 gene and sequenced the \ud mitochondrial genes MTRNR1, MTTS1 and MTTL1 in 53 individuals with SSNHL, associated or not with other \ud symptoms. Mutations c.35delG, c.167delT, the deletions del(GJB6-D13S1830) and del(GJB6-D13S1854) were not \ud found in the sample. Variants in MTTS1 and MTTL1 genes were not detected, either. Regarding the MTRNR1 \ud gene, 15 di erent variants were found, 13 of which were already described as having no phenotypic e ect. Two novel \ud mutations (m.806C>T and m.986G>A) were not reported in SNP database. ey were not found in a Brazilian \ud control sample of 104 normal hearing individuals (Abreu-Silva et al., Ann Hum Biol, 2011, 38(2):210-8), and \ud their meaning still needs to be clari ed through population studies. Although molecular screening did not point \ud to a signi cant role of the tested genes in SSNHL, it is noteworthy that 20 (37,7%) of the 53 subjects reported a \ud positive familial history of hearing loss. while 18% of people in the control sample reported a ected relatives. ese \ud data suggest genetic susceptibility to hearing loss in this group, probably resulting from multifactorial mechanism.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) – CEPID, and Conselho Nacional de Desenvolvimento Cientí co e Tecnológico (CNPQ)

Frequency and Origins of Hemoglobin S Mutation in African-Derived Brazilian Populations

Africans arrived in Brazil as slaves in great numbers, mainly after 1550. Before the abolition of slavery in Brazil in 1888, many communities, called quilombos, were formed by runaway or abandoned African slaves. These communities are presently referred to as remnants of quilombos, and many are still partially genetically isolated. These remnants can be regarded as relicts of the original African genetic contribution to the Brazilian population. In this study we assessed frequencies and probable geographic origins of hemoglobin S (HBB*S) mutations in remnants of quilombo populations in the Ribeira River valley, Sao Paulo, Brazil, to reconstruct the history of Africanderived populations in the region. We screened for HBB*S mutations in 11 quilombo populations (1,058 samples) and found HBB*S carrier frequencies that ranged from 0% to 14%. We analyzed β-globin gene cluster haplotypes linked to the HBB*S mutation in 86 chromosomes and found the four known African haplotypes: 70 (81.4%) Bantu (Central Africa Republic), 7 (8.1%) Benin, 7 (8.1%) Senegal, and 2 (2.3%) Cameroon haplotypes. One sickle cell homozygote was Bantu/Bantu and two homozygotes had Bantu/Benin combinations. The high frequency of the sickle cell trait and the diversity of HBB*S linked haplotypes indicate that Brazilian remnants of quilombos are interesting repositories of genetic diversity present in the ancestral African populations

Mutation analysis of SLC26A4 (Pendrin) gene in a Brazilian sample of hearing-impaired subjects

Abstract Background Mutations in the SLC26A4 gene are associated with Pendred syndrome and autosomal recessive non-syndromic deafness (DFNB4). Both disorders have similar audiologic characteristics: bilateral hearing loss, often severe or profound, which may be associated with abnormalities of the inner ear, such as dilatation of the vestibular aqueduct or Mondini dysplasia. But, in Pendred syndrome (OMIM #274600), with autosomal recessive inheritance, besides congenital sensorineural deafness, goiter or thyroid dysfunctions are frequently present. The aim of this study was to determine whether mutations in SLC26A4 are a frequent cause of hereditary deafness in Brazilian patients. Methods Microsatellite haplotypes linked to SLC26A4 were investigated in 68 families presenting autosomal recessive non-syndromic deafness. In the probands of the 16 families presenting segregation consistent with linkage to SLC26A4, Sanger sequencing of the 20 coding exons was performed. In an additional sample of 15 individuals with suspected Pendred syndrome, because of the presence of hypothyroidism or cochleovestibular malformations, the SLC26A4 gene coding region was also sequenced. Results In two of the 16 families with indication of linkage to SLC26A4, the probands were found to be compound heterozygotes for probably pathogenic different mutations: three novel (c.1003 T > G (p. F335 V), c.1553G > A (p.W518X), c.2235 + 2 T > C (IVS19 + 2 T > C), and one already described, c.84C > A (p.S28R). Two of the 15 individuals with suspected Pendred syndrome because of hypothyreoidism or cochleovestibular malformations were monoallelic for likely pathogenic mutations: a splice mutation (IVS7 + 2 T > C) and the previously described c.1246A > C (p.T416P). Pathogenic copy number variations were excluded in the monoallelic cases and in those with normal results after Sanger sequencing. Additional mutations in the SLC26A4 gene or other definite molecular cause for deafness were not identified in the monoallelic patients, after exome sequencing. Conclusions Biallelic pathogenic mutations in SLC26A4 explained ~ 3% of cases selected because of autosomal recessive deafness. Monoallelic mutations were present in ~ 13% of isolated cases of deafness with cochleovestibular malformations or suspected Pendred syndrome. These data reinforce the importance of mutation screening of SLC26A4 in Brazilian subjects and highlight the elevated frequency of monoallelic patients

Role of the Mitochondrial Mutations, m. 827A > G and the Novel m. 7462C > T, in the Origin of Hearing Loss

Samples from 30 deaf probands exhibiting features suggestive of syndromic mitochondrial deafness or from families with maternal transmission of deafness were selected for investigation of mutations in the mitochondrial genes MT-RNR1 and MT-TS1. Patients with mutation m. 1555A>G had been previously excluded from this sample. In the MT-RNR1 gene, five probands presented the m. 827A>G sequence variant, of uncertain pathogenicity. This change was also detected in 66 subjects of an unaffected control sample of 306 Brazilian individuals from various ethnic backgrounds. Given its high frequency, we consider it unlikely to have a pathogenic role on hereditary deafness. As to the MT-TS1 gene, one proband presented the previously known pathogenic m. 7472insC mutation and three probands presented a novel variant, m. 7462C>T, which was absent from the same control sample of 306 individuals. Because of its absence in control samples and association with a family history of hearing impairment, we suggest it might be a novel pathogenic mutation.CEPID-FAPESPFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)CNPqConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Aberrant transcript produced by a splice donor site deletion in the TECTA gene is associated with autosomal dominant deafness in a Brazilian family

We ascertained a Brazilian family with nine individuals affected by autosomal dominant nonsyndromic sensorineural hearing loss. The bilateral hearing loss affected mainly mid-high frequencies, was apparently stable with an early onset. Microsatellites close to the DFNA8/DFNA12 locus, which harbors the TECTA gene, showed significant multipoint lod scores (32) close to marker D11S4107. Sequencing of the exons and exon-intron boundaries of the TECTA gene in one affected subject revealed the deletion c.5383 + 5delGTGA in the 5' end of intron 16, that includes the last two bases of the donor splice site consensus sequence. This mutation segregates with deafness within the family. To date, 33 different TECTA mutations associated with autossomal dominant hearing loss have been described. Among them is the mutation reported herein, first described by Hildebrand et al. (2011) in a UK family. The audioprofiles from the UK and Brazilian families were similar. In order to investigate the transcripts produced by the mutated allele, we performed cDNA analysis of a lymphoblastoid cell line from an affected heterozygote with the c.5383 + 5delGTGA and a noncarrier from the same family. The analysis allowed us to identify an aberrant transcript with skipping of exon 16, without affecting the reading frame. One of the dominant TECTA mutations already described, a synonymous substitution in exon 16 (c.5331 G&lt;A), was also shown to affect splicing resulting in an aberrant transcript lacking exon 16. Despite the difference in the DNA level, both the synonymous substitution in exon 16 (c.5331 G&lt;A) and the mutation described herein affect splicing of exon 16, leading to its skipping. At the protein level they would have the same effect, an in-frame deletion of 37 amino-acids (p.S1758Y/G1759_N1795del) probably leading to an impaired function of the ZP domain. Thus, like the TECTA missense mutations associated with dominant hearing loss, the c5383 + 5delGTGA mutation does not have an inactivating effect on the protein. (C) 2012 Elsevier B.V. All rights reserved.Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES

Novel OTOF mutations in Brazilian patients with auditory neuropathy

The OTOF gene encoding otoferlin is associated with auditory neuropathy (AN), a type of non-syndromic deafness. We investigated the contribution of OTOF mutations to AN and to non-syndromic recessive deafness in Brazil. A test for the Q829X mutation was carried out on a sample of 342 unrelated individuals with non-syndromic hearing loss, but none presented this mutation. We selected 48 cases suggestive of autosomal recessive inheritance, plus four familial and seven isolated cases of AN, for genotyping of five microsatellite markers linked to the OTOF gene. The haplotype analysis showed compatibility with linkage in 11 families (including the four families with AN). Samples of the 11 probands from these families and from seven isolated cases of AN were selected for an exon-by-exon screening for mutations in the OTOF gene. Ten different pathogenic variants were detected, among which six are novel. Among the 52 pedigrees with autosomal recessive inheritance (including four familial cases of AN), mutations were identified in 4 (7.7%). Among the 11 probands with AN, seven had at least one pathogenic mutation in the OTOF gene. Mutations in the OTOF gene are frequent causes of AN in Brazil and our results confirm that they are spread worldwide. Journal of Human Genetics (2009) 54, 382-385; doi: 10.1038/jhg.2009.45; published online 22 May 2009CNPqConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FAPESPCEPID-Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)PRONEX Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq