Alessandro Clayton Souza Ferreira

The Ancestry of Brazilian mtDNA Lineages

We have analyzed 247 Brazilian mtDNAs for hypervariable segment (HVS)-I and selected restriction fragment-length-polymorphism sites, to assess their ancestry in different continents. The total sample showed nearly equal amounts of Native American, African, and European matrilineal genetic contribution but with regional differences within Brazil. The mtDNA pool of present-day Brazilians clearly reflects the imprints of the early Portuguese colonization process (involving directional mating), as well as the recent immigrant waves (from Europe) of the last century. The subset of 99 mtDNAs from the southeastern region encompasses nearly all mtDNA haplogroups observed in the total Brazilian sample; for this regional subset, HVS-II was analyzed, providing, in particular, some novel details of the African mtDNA phylogeny.

Updated Brazilian STR allele frequency data using over 100,000 individuals: An analysis of CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPOX and vWA loci

The Brazilian population is one of the most heterogeneous populations of the world, formed mainly by an admixture of European, African and Native American populations. Brazil is the fifth largest country in the world (8,511,960 km(2)), being divided into five geographical regions. This study provides population genetic data of up to 137,161 unrelated individuals representing the entire Brazilian territory. Allelic frequencies and other population data analysis are reported for the 15 autosomal STR loci included in the PowerPlex®16 kit (Promega Corporation, Madison, WI, USA). In order to guarantee that individuals were not related, we have considered only F1 data from couples undergoing paternity testing. The number of individuals genotyped for each locus was: CSF1PO (113,526); D3S1358 (135,133); D5S818 (135,181); D7S820 (137,136); D8S1179 (134,211); D13S317 (137,161); D16S539 (136,942); D18S51 (136,739); D21S11 (130,014); FGA (135,839); Penta D (110,333); Penta E (128,055); TH01 (112,695); TPOX (123,102); vWA (127,415). Allele sizes ranged from 1 to 48.2. Statistic parameters (PD, PIC and Ho; considering values ≥0.75) suggest that markers D13S317, D16S539, D18S51, D21S11, D7S820, D8S1179, Penta D, Penta E, TH01, FGA and vWA were more informative for genetic identification purposes in the Brazilian population.

Prevalence of C282Y and H63D mutations in the HFE gene of Brazilian individuals with clinical suspicion of hereditary hemochromatosis

A hemocromatose hereditaria classica (HH) e uma doenca autossomica recessiva caracterizada por uma sobrecarga sistemica de ferro, a qual esta frequentemente relacionada as mutacoes C282Y e H63D no gene HFE. No Brasil, registros das frequencias das mutacoes no gene HFE sao raros, principalmente envolvendo uma amostra representativa da populacao. Este estudo teve como objetivo a determinacao da prevalencia das mutacoes C282Y e H63D em individuos com suspeita clinica de HH. Para isto, foram estudados 1955 pacientes para os quais as mutacoes C282Y e H63D foram pesquisadas pela tecnica de Reacao em Cadeia da Polimerase seguida de digestao enzimatica. A amostra consistiu de 76,6% homens e 23,4% de mulheres. A maioria dos individuos analisados (56,9%) estava concentrada no grupo de 41 a 60 anos. Embora nao tenham sido observadas diferencas genicas e genotipicas entre os generos, foi observado um maior numero de mulheres na faixa etaria acima dos 60 anos A mutacao C282Y estava presente em homozigose em 2,9% dos individuos e em heterozigose em 10,1%, enquanto H63D estava presente em homozigose em 4,3% e em heterozigose em 30,6% dos individuos estudados. As frequencias dos alelos mutantes C282Y e H63D foram de 0,079 e 0,196, respectivamente. Alem de mais frequente entre a populacao estudada, a mutacao H63D mostrou equilibrio genetico, ao contrario da mutacao C282Y. Este trabalho tem como importância a determinacao do perfil genetico da populacao acometida pela HH no Brasil.

New CODIS core loci allele frequencies for 96,400 Brazilian individuals.

We have reported the allele frequencies of 15 STR loci, including the original 13 CODIS core loci, in over 100,000 Brazilian individuals. A new CODIS core loci has been proposed, but the recently established Brazilian Integrated Network of DNA Databases made a decision in 2010 to postpone the implementation of this new set of loci due to the lack of allele frequency data for the Brazilian population. We aimed to report allele frequencies of 20 loci, estimated from 96,400 Brazilian individuals undergoing paternity testing during 2011-2013. The percentage of missing data was less than 0.6% for all loci, except for CSF1PO (3.15%) and D7S820 (2.5%). The dropout rates estimated by the MicroDrop software were 0.013 for CSF1PO, 0.000037 for D7S820 and less than 0.000001 for other loci. Small missing data percentages and dropout rates reflect the high quality of the data.

Assessment of microsatellite instability in colorectal cancer patients from Brazil

The replication error status analysis of DNA, through microsatellite instability detection, has become an indispensable tool for hereditary non-polyposis colorectal cancer screening. This study investigated the microsatellite instability in Brazilian individuals presenting colorectal cancer. In this study, 66 patients were clinically analyzed according to Amsterdam II and Bethesda guidelines. Normal and tumour tissues were collected and analyzed for MSI degree according to molecular markers BAT25, BAT26, BAT40, APC–D5S346, D2S123, and D17S250. Eight patients (12.1%) fulfilled the Amsterdam II guidelines, and 15 (22.7%) met the Bethesda guidelines. BAT25 was the most sensitive marker (86.7%), while BAT26 was the least sensitive (66.7%). The specificity of both markers was 100%, but all of the markers must be used since the contribution of each marker to the sensitivity and specificity of the test is complementary. Proximal tumours were significantly predominant among RER+ patients. Conclusions: Patients with a family history of colorectal cancer with the tumour in the proximal colon must be screened to replication error status as early as possible in order to avoid the progression of the disease.

Mutações predisponentes à trombofilia em indivíduos de Minas Gerais - Brasil com suspeita clínica de trombose

A trombose e reconhecidamente uma doenca de carater multifatorial. Sua ocorrencia esta intimamente relacionada a presenca de fatores geneticos e adquiridos que concorrem isoladamente ou em associacao para o seu desencadeamento. No entanto, a frequencia dos fatores geneticos pode variar de acordo com a origem etnica e com outros aspectos epidemiologicos dos grupos de individuos e populacoes estudadas. No Brasil, dados referentes a individuos brasileiros e em especial do estado de Minas Gerais sao escassos. O objetivo do presente estudo foi investigar a frequencia das mutacoes fator V Leiden e G20210A no gene protrombina em 1.103 individuos com suspeita clinica de trombofilia, empregando a tecnica da reacao em cadeia da polimerase seguida de restricao enzimatica (PCR-RFLP). Os dados foram analisados usando-se o programa Epi Info versao 6.04. A amostra consistiu de 76,16% mulheres e 23,84% homens, com media de idade de 43,06± 14,65. A mutacao fator V Leiden foi observada em heterozigose em 7,52% dos individuos e em 0,36% em homozigose. A mutacao G20210A no gene da protrombina apresentou-se em heterozigose em 5,90% dos individuos e em homozigose em 0,18%. O presente trabalho mostra a importância dos testes geneticos conforme o perfil da populacao analisada, ressaltando informacoes epidemiologicas da populacao brasileira e beneficios clinicos.

Fitting the Balding-Nichols model to forensic databases.

Large forensic databases provide an opportunity to compare observed empirical rates of genotype matching with those expected under forensic genetic models. A number of researchers have taken advantage of this opportunity to validate some forensic genetic approaches, particularly to ensure that estimated rates of genotype matching between unrelated individuals are indeed slight overestimates of those observed. However, these studies have also revealed systematic error trends in genotype probability estimates. In this analysis, we investigate these error trends and show how they result from inappropriate implementation of the Balding-Nichols model in the context of database-wide matching. Specifically, we show that in addition to accounting for increased allelic matching between individuals with recent shared ancestry, studies must account for relatively decreased allelic matching between individuals with more ancient shared ancestry.