Distribution of local ancestry and evidence of adaptation in admixed populations.

Admixed American populations have different global proportions of European, Sub-Saharan African, and Native-American ancestry. However, individuals who display the same global ancestry could exhibit remarkable differences in the distribution of local ancestry blocks. We studied for the first time the distribution of local ancestry across the genome of 264 Brazilian admixed individuals, ascertained within the scope of the Brazilian Initiative on Precision Medicine. We found a decreased proportion of European ancestry together with an excess of Native-American ancestry on chromosome 8p23.1 and showed that this is due to haplotypes created by chromosomal inversion events. Furthermore, Brazilian non-inverted haplotypes were more similar to Native-American haplotypes than to European haplotypes, in contrast to what was found in other American admixed populations. We also identified signals of recent positive selection on chromosome 8p23.1, and one gene within this locus, PPP1R3B, is related to glycogenesis and has been associated with an increased risk of type 2 diabetes and obesity. These findings point to a selection event after admixture, which is still not entirely understood in recent admixture events.

MicroRNA hsa-miR-134 is a circulating biomarker for mesial temporal lobe epilepsy.

Epilepsy is misdiagnosed in up to 25% of patients, leading to serious and long-lasting consequences. Recently, circulating microRNAs have emerged as potential biomarkers in a number of clinical scenarios. The purpose of this study was to identify and to validate circulating microRNAs that could be used as biomarkers in the diagnosis of epilepsy. Quantitative real-time PCR was used to measure plasma levels of three candidate microRNAs in two phases of study: an initial discovery phase with 14 patients with mesial temporal lobe epilepsy (MTLE), 13 with focal cortical dysplasia (FCD) and 16 controls; and a validation cohort constituted of an independent cohort of 65 patients with MTLE and 83 controls. We found hsa-miR-134 downregulated in patients with MTLE (p = 0.018) but not in patients with FCD, when compared to controls. Furthermore, hsa-miR-134 expression could be used to discriminate MTLE patients with an area under the curve (AUC) of 0.75. To further assess the robustness of hsa-miR-134 as a biomarker for MTLE, we studied an independent cohort of 65 patients with MTLE, 27 of whom MTLE patients were responsive to pharmacotherapy, and 38 patients were pharmacoresistant and 83 controls. We confirmed that hsa-miR-134 was significantly downregulated in the plasma of patients with MTLE when compared with controls (p < 0.001). In addition, hsa-miR-134 identified patients with MTLE regardless of their response to pharmacotherapy or the presence of MRI signs of hippocampal sclerosis. We revealed that decreased expression of hsa-miR-134 could be a potential non-invasive biomarker to support the diagnosis of patients with MTLE.

Refinement of chromosome 3p22.3 region and identification of a susceptibility gene for bipolar affective disorder.

Genome-wide association studies and meta-analysis, as well as our own previous family-based association results, have pointed to chromosome (ch) 3p22.3 and 3p21.1 as candidate regions to contain a susceptibility gene for bipolar affective disorder (BPAD). In the present study, we further refined the region of interest on ch 3p22.3. We genotyped 94 SNPs within the candidate region in 74 families and performed family-based association analysis using a transmission disequilibrium test. One single SNP (rs166508) was associated with the BPAD phenotype (P = 0.0187). This SNP is located within intron 15 of the integrin alpha 9 (ITGA9) gene. ITGA9 encodes the α9 subunit of the α9ß1 integrin, a membrane glycoprotein receptor for neurotrophins, such as nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF). Quantification of ITGA9 transcripts in the peripheral blood of patients with BPAD and controls showed an upregulation of ITGA9 (Kruskal-Wallis P = 0.0339) in patients with the disease-associated genotype (rs166508*A/A), compared to those with rs166508*G/G and rs166508*G/A genotypes. Sequencing of the ITGA9 cDNA revealed a sequence variant (r.1689_1839del) in rs166508*A carriers, which leads to loss of the entire exon 16. In silico analysis revealed that the deleted region contains three putative microRNA binding sites, which may be involved in the negative regulation of ITGA9. In conclusion, our results confirm previous evidence pointing to a candidate region for BPAD on ch 3p.22.3. In addition, we suggest a molecular substrate that could explain the increase of ITGA9 mRNA levels in probands with BPAD, proposing a new mechanism that could be involved in the genetic susceptibility to the disease.

Family-based association study for bipolar affective disorder.

In this study we aimed to evaluate 21 candidate loci for bipolar affective disorder (BPAD) identified earlier in a large genome-wide association study. We evaluated 74 pedigrees with BPAD, with a total of 411 individuals, including 96 patients who fulfilled clinical criteria for BPAD according to Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition classification. Family-based association analysis was performed using the UNPHASED software. We identified a single nucleotide polymorphism (rs9834970) localized on chromosome 3p22.3, showing statistically significant association with BPAD after the Bonferroni correction for multiple comparisons (P(corrected)=0.0025) with an odds ratio=2.64 (95% confidence interval: 1.30-5.35). Single nucleotide polymorphism rs9834970 is located in an intergenic region and is not known to be associated to regulatory genomic sequences.

LINKGEN: a new algorithm to process data in genetic linkage studies.

Genetic linkage studies using whole genome scans are useful approaches for identifying genes related to human diseases. In general, these studies require genotyping of a large number of markers, which are used in statistical analysis. Recent technology has allowed easy genotyping of a large number of markers in less time; therefore, interface programs are required for manipulation of these large data sets. We present a new algorithm, which processes input data in LINKAGE format from data analyzed by automated genotyping systems. The algorithm was implemented in PERL script and R environment. Validation was performed with genotyped data from 127 individuals and 720 microsatellite markers of two whole genome scans. Our results showed a significant decrease in data processing time. In addition, this algorithm provides unbiased allele frequency estimation used for linkage analysis. LINKGEN is a freely available online tool and allows easier, faster, and reliable manipulation of large genotyping data sets.