Systematic exploration of a decade of publications on psychiatric genetics in Latin America.

Psychiatric disorders have a great impact in terms of mortality, morbidity, and disability across the lifespan. Considerable effort has been devoted to understanding their complex and heterogeneous genetic architecture, including diverse ancestry populations. Our aim was to review the psychiatric genetics research published with Latin American populations from 2010 to 2019, and classify it according to country of origin, type of analysis, source of funding, and other variables. We found that most publications came from Brazil, Mexico, and Colombia. Also, local funds are generally not large enough for genome-wide studies in Latin America, with the exception of Brazil and Mexico; larger studies are often done in collaboration with international partners, mostly funded by US agencies. In most of the larger studies, the participants are individuals of Latin American ancestry living in the United States, which limits the potential for exploring the complex gene-environment interaction. Family studies, traditionally strong in Latin America, represent about 30% of the total research publications. Scarce local resources for research in Latin America have probably been an important limitation for conducting bigger and more complex studies, contributing to the reduced representation of these populations in global psychiatric genetics studies. Increasing diversity must be a goal to improve generalizability and applicability in clinical settings.

Frequencies of variants in genes associated with dyslipidemias identified in Costa Rican genomes.

Dyslipidemias are risk factors in diseases of significant importance to public health, such as atherosclerosis, a condition that contributes to the development of cardiovascular disease. Unhealthy lifestyles, the pre-existence of diseases, and the accumulation of genetic variants in some loci contribute to the development of dyslipidemia. The genetic causality behind these diseases has been studied primarily on populations with extensive European ancestry. Only some studies have explored this topic in Costa Rica, and none have focused on identifying variants that can alter blood lipid levels and quantifying their frequency. To fill this gap, this study focused on identifying variants in 69 genes involved in lipid metabolism using genomes from two studies in Costa Rica. We contrasted the allelic frequencies with those of groups reported in the 1000 Genomes Project and gnomAD and identified potential variants that could influence the development of dyslipidemias. In total, we detected 2,600 variants in the evaluated regions. However, after various filtering steps, we obtained 18 variants that have the potential to alter the function of 16 genes, nine variants have pharmacogenomic or protective implications, eight have high risk in Variant Effect Predictor, and eight were found in other Latin American genetic studies of lipid alterations and the development of dyslipidemia. Some of these variants have been linked to changes in blood lipid levels in other global studies and databases. In future studies, we propose to confirm at least 40 variants of interest from 23 genes in a larger cohort from Costa Rica and Latin American populations to determine their relevance regarding the genetic burden for dyslipidemia. Additionally, more complex studies should arise that include diverse clinical, environmental, and genetic data from patients and controls and functional validation of the variants.

Attitudes of Costa Rican individuals towards donation of personal genetic data for research.

Aim: We explore attitudes from the public in Costa Rica regarding willingness to donate DNA data for research. Materials & methods: A total of 224 Costa Rican individuals answered the anonymous online survey 'Your DNA, Your Say'. It covers attitudes toward DNA and medical data donation, trust in research professionals and concerns about consequences of reidentification. Results & conclusion: Most individuals (89%) are willing to donate their information for research purposes. When confronted with different potential uses of their data, participants are significantly less likely to donate data to for-profit researchers (34% willingness to donate). The most frequently cited concerns regarding donation of genetic data relate to possible discrimination by health/life insurance companies and employers. For the participants in the survey, the most trusted professionals are their own medical doctor and nonprofit researchers from their country. This is the first study regarding attitudes toward genetic data donation in Costa Rica.

Underlying domains of anxiety trait in a Costa Rican sample: preliminary results.

BACKGROUND: Imprecision of the psychiatric phenotype might partially explain the failure of genetic research to identify genes that contribute to susceptibility of anxiety disorders. Previous research concluded two underlying constructs, worry and rumination, might explain anxiety sub-syndromic symptoms in Costa Rican patients with history of mania. The goal of the current study is to explore the presence of latent constructs for quantitative anxiety in a group of subjects with a wide diagnostic phenotype and non-affected individuals. METHODS: We conducted an exploratory factor analysis of anxiety trait in 709 subjects. Our sample was comprised by 419 subjects with psychiatric disorders and 290 non-affected individuals. We used principal factors extraction method with squared multiple correlations of the STAI (trait subscale). RESULTS: We found the following preliminary results: a three-factor solution with a good simple structure and statistical adequacy was obtained with a KMO of 0.92 (>0.6) and Bartlett's Test of Sphericity of 5644,44 (p<0.05). The STAI items were grouped into three factors: anxiety-absent, worry and rumination based on the characteristics of the symptoms. CONCLUSION: Two underlying constructs, worry and rumination may explain anxiety sub-syndromic symptoms in Costa Rican subjects. Our proposed underlying structure of subsyndromal anxiety in individuals should be considered as an important factor in defining better phenotypic characterizations on a broader diagnostic concept. Worry and rumination as a phenotypic characterization may assist in genotyping; however, its predictive value on actual illness outcome still requires more research. The Genome-Wide QTL analysis for anxiety trait in the same sample is ongoing.

Un cuarto de siglo de investigación genética en los trastornos neuropsiquiátricos en Costa Rica

El estudio de la base genética de los trastornos neuropsiquiátricos se inició en Costa Rica hace más de 25 años. En este tiempo se han realizado investigaciones enfocadas en diferentes trastornos: esquizofrenia, trastorno bipolar, demencia de Alzheimer, trastorno obsesivo compulsivo, trastorno obsesivo compulsivo, trastorno por déficit de atención y síndrome de Tourette. Los estudios realizados han tenido una amplia variación en lo que se refiere a diseño (ligamiento/asociación), muestra utilizada (familias/parejas de hermanos afectados/tríos), cobertura genómica (estudios con genes candidatos/tamizajes de todo el genoma) y definición del fenotipo (categoría diagnóstica/clasificación sindrómica/endofenotipo). Presentamos un resumen de los principales hallazgos genómicos obtenidos en estos estudios multidisciplinarios y discutimos la importancia, lecciones y retos de la investigación genética en trastornos psiquiátricos complejos.

In Costa Rica, the study of the genetic basis of neuropsychiatric disorders started more than 25 years ago. During this time, different research efforts have focused on several disorders: schizophrenia, bipolar disorder, Alzheimer's disease, obsessive-compulsive disorder, attention deficit/hyperactivity disorder, and Tourette syndrome. The studies have had a wide scope regarding design (linkage/association), sample used (families/sib pairs/trios), genome coverage (candidate gene studies/genome-wide scans), and phenotype definition (diagnostic category/syndromic classification/endophenotype). Here we present a summary of the main genomic findings of these multidisciplinary studies, and discuss the importance, lessons, and challenges of genetic research of complex psychiatric disorders.

Absolute pitch in Costa Rica: Distribution of pitch identification ability and implications for its genetic basis.

Absolute pitch is the unusual ability to recognize a pitch without an external reference. The current view is that both environmental and genetic factors are involved in the acquisition of the trait. In the present study, 127 adult musicians were subjected to a musical tone identification test. Subjects were university music students and volunteers who responded to a newspaper article. The test consisted of the identification of 40 piano and 40 pure tones. Subjects were classified in three categories according to their pitch naming ability: absolute pitch (AP), high accuracy of tone identification (HA), and non-absolute pitch (non-AP). Both the percentage of correct responses and the mean absolute deviation showed a statistically significant variation between categories. A very clear pattern of higher accuracy for white than for black key notes was observed for the HA and the non-AP groups. Meanwhile, the AP group had an almost perfect pitch naming accuracy for both kinds of tones. Each category presented a very different pattern of deviation around the correct response. The age at the beginning of musical training did not differ between categories. The distribution of pitch identification ability in this study suggests a complex inheritance of the trait.

Heterozygous loss-of-function variants in CYP1B1 predispose to primary open-angle glaucoma.

PURPOSE: Although primary congenital glaucoma (PCG)-associated CYP1B1 mutations in the heterozygous state have been evaluated for association with primary open-angle glaucoma (POAG) in several small studies, their contribution to the occurrence of POAG is still controversial. The present study was conducted to determine whether heterozygous functionally characterized CYP1B1 mutations are associated with the disease in a large cohort of German patients with POAG. METHODS: The frequency of CYP1B1 variants on direct sequencing of the entire coding region was compared in 399 unrelated German patients with POAG (270, POAG; 47, JOAG; and 82, NTG) and 376 control subjects without any signs of glaucoma on ophthalmic examination. In vitro functional assays were performed and relative enzymatic activity of the CYP1B1 variants embedded in their respective background haplotypes and not previously unambiguously classified were determined, to assess their possible causative role. RESULTS: Apart from known polymorphic variants, 11 amino acid substitutions in CYP1B1 reported before, both in PCG and POAG cases, were identified. After in vitro functional assay, variants P52L and R368H showed marked reduction of activity, confirming their role as loss-of-function mutations similar to previously determined variants G61E, N203S, and G329V. In contrast, variants G168D, A443G, and A465V showed no relevant effects and were thus classified as polymorphisms. Overall, seven functionally impaired variants were present in 13 (3.6%) patients and in 1 (0.2%) control subject (P = 0.002, OR = 5.4). Reanalysis of previous studies reporting CYP1B1 mutations in patients with POAG based on updated functional validation showed a significant excess of carriers among patients compared to controls (OR = 3.85; P = 2.3 x 10(-7)). CONCLUSIONS: Heterozygous CYP1B1 mutations with absent or reduced relative enzymatic activity can be considered a risk factor for POAG.

Molecular analysis of CYP1B1 in Omani patients with primary congenital glaucoma: a pilot study.

PURPOSE: To screen cytochrome P4501B1 (CYP1B1) for causative mutations in Omani patients with a clinical diagnosis of primary congenital glaucoma (PCG) METHODS: Nine PCG families were recruited for the study. All patients underwent detailed clinical examinations to confirm the diagnosis of PCG. The families of index patients were also examined. Genealogical information was obtained by pedigree analysis. The primary candidate gene, CYP1B1, was amplified from genomic DNA, sequenced, and analyzed in patients to identify the disease-causing mutations. RESULTS: Eight of the nine PCG families were consanguineous (89%). Molecular analysis of CYP1B1 showed three distinct mutations, p.G61E, p.D374N, and p.R368H, in seven of nine unrelated PCG index patients (78%). Six patients had homozygous mutations and one had a compound heterozygous mutation. Causative mutations were not identified in two families. In family 4, the index patient was found to be heterozygous for the p.E229K variant. In family 6, although affected individuals were found to be homozygous in the CYP1B1 region, no mutation could be identified. CONCLUSIONS: This study indicates that CYP1B1 could be the predominant cause of PCG in the Omani population (78%). Omani PCG patients show allelic heterogeneity. Further studies are needed to delineate the spectrum of CYP1B1mutations in Omani PCG families and to identify new or modifier genes contributing to the manifestations of PCG in this region.

Mutations in CYP1B1 cause primary congenital glaucoma by reduction of either activity or abundance of the enzyme.

Primary congenital glaucoma (PCG) is an autosomal recessive disorder caused predominantly by mutations in the CYP1B1 gene. A total of five frequent single nucleotide polymorphisms (SNPs) have been identified in the coding sequence of CYP1B1: rs10012C>G (p.R48G), rs1056827G>T (p.A119S), rs1056836C>G (p.V432L), rs1056837C>T (p.D449D), and rs1800440A>G (p.N453S). We performed a functional characterization of four common CYP1B1 variants presenting different coding SNP haplotypes (RAVDN, GSLDN, RALDS, and RALDN) and five CYP1B1 mutations reported for PCG patients: c.182G>A (p.G61E), c.608A>G (p.N203S), c.1033_1035del (p.L343del), c.241 T>A (p.Y81N), and c.685G>A (p.E229 K). Each mutation was embedded in its corresponding background SNP haplotype. The common variants revealed variation in enzymatic activity; among them, RAVDN showed the highest activity. Mutants p.G61E, p.N203S, and p.L343del each revealed a residual activity (<10%) of their respective haplotype. The microsomal CYP1B1 abundance relative to total protein also showed variation in common variants and a significant reduction in p.L343del, p.Y81N, and p.E229 K. The free energy of folding (DeltaDeltaG) values suggest that the lower stability of the mutants is one key property leading to the experimentally observed lower protein abundance. Our new measure of relative enzymatic activity (U/mg total protein), which combines activity and abundance values, was significantly lower for all five mutations compared to the corresponding background haplotype. We classified p.Y81N and p.E229 K not as mutations but as hypomorphic alleles, since their relative activity values are intermediate between bona fide mutations and the common variant with the lowest activity (RALDS). We propose that CYP1B1 mutations can act by either reducing enzymatic activity (p.G61E and p.N203S), reducing the abundance of the enzyme (p.Y81N and p.E229 K), or both (p.L343del).

Profiling of WDR36 missense variants in German patients with glaucoma.

PURPOSE: Mutations in WDR36 were recently reported in patients with adult-onset primary open-angle glaucoma (POAG). In this study, the prevalence of WDR36 variants was investigated in patients with glaucoma who were of German descent with diverse age of onset and intraocular pressure levels. METHODS: Recruited were 399 unrelated patients with glaucoma and 376 healthy subjects of comparable age and origin, who had had repeated normal findings in ophthalmic examinations. The frequency of observed variants was obtained by direct sequencing of the entire WDR36 coding region. RESULTS: A total of 44 WDR36 allelic variants were detected, including 14 nonsynonymous amino acid alterations, of which 7 are novel (P31T, Y97C, D126N, T403A, H411Y, H411L, and P487R) and 7 have been reported (L25P, D33E, A163V, H212P, A449T, D658G and I264V). Of these 14 variants, 6 were classified as polymorphisms as they were detected in patients and control individuals at similar frequencies. Eight variants present in 15 patients (3.7%) but only 1 control individual (0.2%) were defined as putative disease-causing variants (P = 0.0005). Within this patient group, 12 (80%) presented with high and 3 (20%) with low intraocular pressure. Disease severity and age of onset showed a broad range. CONCLUSIONS: The occurrence of several rare putative disease-causing variants in patients with glaucoma suggests that WDR36 may be a minor disease-causing gene in glaucoma, at least in the German population. The large variability in WDR36, though, requires functional validation of these variants, once its function is characterized.

Novel CYP1B1 and known PAX6 mutations in anterior segment dysgenesis (ASD).

PURPOSE: The study intended to define the underlying genetic defects for 21 index patients affected with different forms of anterior segment dysgenesis. Sequence analysis for the PAX6, PITX2, FOXC1, and CYP1B1 genes has been implemented for this purpose. METHODS: Ten patients affected with Peters anomaly, 8 with Rieger anomaly, and 3 with aniridia were included in this study. All patients underwent a complete eye examination, including anterior segment evaluation, with slit-lamp microsocopy, fundoscopy, tonography, and gonioscopy. Twenty-one intronic primer pairs were used to amplify the coding exons of the FOXC1, CYP1B1, PITX2, and PAX6 genes for sequence analysis on an automated sequencer (ABI 3730). RESULTS: We were able to detect mutations in 5 of 21 patients with anterior segment malformations. We found mutations in individuals suffering from Rieger anomaly and aniridia, in CYP1B1 and PAX6, respectively. None of the 10 Peters anomaly patients had causative mutations in any of the 4 genes we screened. CONCLUSIONS: Our results suggest primary congenital glaucoma and the anterior segment dysgenesis disorders may share a common molecular pathophysiology in the CYP1B1 pathway.

Primary congenital glaucoma and Rieger's anomaly: extended haplotypes reveal founder effects for eight distinct CYP1B1 mutations.

PURPOSE: Mutations in the cytochrome P450 1B1 (CYP1B1) gene are a frequent cause of primary congenital glaucoma (PCG) in different ethnic groups. Cytochrome P450 proteins are monooxygenases, which catalyze many reactions involved in the metabolism of drugs as well as steroids and other lipids. The repeated occurence of several mutations in various ethnic groups raises the question if founder effects or mutation-prone sites in CYP1B1 are the cause for this observation. METHODS: A total of 30 individuals (26 PCG patients, three Rieger's anomaly patients, and one variant carrier), presenting 17 variants in CYP1B1 (15 mutations and two variations) were included in our study. We sequenced the entire genomic region of CYP1B1 and analyzed microsatellites flanking the gene in all individuals and constructed haplotypes for all variations using a combination of single nucleotide polymorphisms and microsatellites. RESULTS: For the CYP1B1 genomic region, we identified five extended haplotypes associated with 17 variations. These haplotypes were complemented with microsatellite information from the region surrounding this gene. A total of eight CYP1B1 mutations were found more than once, each of them presenting one identical haplotype in different individuals. Six mutations were represented in different ethnic groups. CONCLUSIONS: Our results confirm founder effects for most of CYP1B1 mutations. Most of these mutations must have occurred as unique events in the past.

Glaucoma in Costa Rica. Initial approaches: [minireview]

Glaucoma is the second most frequent cause of irreversible blindness worldwide. Genetic factors have been implicated in the development of the disease. So far six loci (GLC1A-GLC1F) and two genes (TIGR/MYOC and OPTN) are involved in the development of juvenile (JOAG) and adult onset or chronic primary open angle glaucoma (COAG), while two loci (GLC3A,GLC3B) and one gene (CYP1B1) are known for primary congenital glaucoma (PCG). Here we summarize the results of the first genetic studies of glaucoma in Costa Rica. Nine families: 1 with JOAG, 1 with PCG and 7 with COAG were screened for mutations at the known genes. A 10 bp duplication, 1546-1555dupTCATGCCACC, at the CYP1B1 gene, causes, in homozygous state, glaucoma in the consanguineous PCG family. This mutation has been found in different countries and generates an early stop codon that termitates protein synthesis 140 amino acids earlier than the normal allele. In exon 1 of the T1GR/MYOC the innocuous Arg76Lys variant was found in two of the COAG families. In the OPTN gene two variants in the coding region (Thr34Thr, Met 98Lys) and 7 intronic changes were found in other Costa Rican glaucoma patients. One of the COAG families was chosen for a genome scan with 379 microsatellite markers and linkage analysis. LOD scores [quot ]suggestive[quot ] of linkage were obtained for several chromosomal regions. Evidence indicates that hereditary glaucoma in Costa Rica is highly heterogeneous and that further studies in the country will probably disclose some up to now unknown genes responsible for the disease.

Glaucoma in Costa Rica. Initial approaches.

Glaucoma is the second most frequent cause of irreversible blindness worldwide. Genetic factors have been implicated in the development of the disease. So far six loci (GLC1A-GLC1F) and two genes (TIGR/MYOC and OPTN) are involved in the development of juvenile (JOAG) and adult onset or chronic primary open angle glaucoma (COAG), while two loci (GLC3A,GLC3B) and one gene (CYP1B1) are known for primary congenital glaucoma (PCG). Here we summarize the results of the first genetic studies of glaucoma in Costa Rica. Nine families: 1 with JOAG, 1 with PCG and 7 with COAG were screened for mutations at the known genes. A 10 bp duplication, 1546-1555dupTCATGCCACC, at the CYP1B1 gene, causes, in homozygous state, glaucoma in the consanguineous PCG family. This mutation has been found in different countries and generates an early stop codon that termitates protein synthesis 140 amino acids earlier than the normal allele. In exon 1 of the T1GR/MYOC the innocuous Arg76Lys variant was found in two of the COAG families. In the OPTN gene two variants in the coding region (Thr34Thr, Met 98Lys) and 7 intronic changes were found in other Costa Rican glaucoma patients. One of the COAG families was chosen for a genome scan with 379 microsatellite markers and linkage analysis. LOD scores "suggestive" of linkage were obtained for several chromosomal regions. Evidence indicates that hereditary glaucoma in Costa Rica is highly heterogeneous and that further studies in the country will probably disclose some up to now unknown genes responsible for the disease.