PIMA: A population informative multiplex for the Americas.

We describe an ancestry-informative autosomal SNP multiplex designed to be a small-scale, flexible panel that can complement uniparental markers in assessing the American variability (i.e. pre-Colombian) found in contemporary indigenous American populations. This study centered on choosing SNPs with the specific characteristics of: 1) extreme allele frequency differences between indigenous Americans and the African, European and East Asian population groups that contribute to present-day population variation in the Americas; 2) high informativeness-for-assignment In values; and 3) well-spaced genomic distribution and chromosomal separation from existing small-scale forensic ancestry marker sets. The resulting capillary electrophoresis SNaPshot single base extension test was named: PIMA (Population Informative Multiplex for the Americas), comprising 26 autosomal SNPs, a single X-chromosome SNP plus the amelogenin sex marker adapted for SNaPshot. PIMA complements the established 34plex forensic ancestry panel to provide a powerful and simple tool for the analysis of American populations, including those with admixed histories, commonly encountered in America. Comparing the results obtained with the combined marker panels of PIMA and 34plex to SNP data from a much larger ancestry panel allowed us to gauge their relative efficiency. PIMA+34plex gives equivalent power to the 314-SNP 'LACE' genomic ancestry control panel, while requiring a much smaller genotyping effort. The ancestry profiles and genetic structure of 22 populations spread across the American continent were estimated using PIMA+34plex data, and those estimates were contrasted with information provided by uniparental markers (mtDNA and Y-chromosome loci) for a small set of admixed individuals from Venezuela. Our results indicate that an American genetic component is efficiently detected in contemporary American populations using a small set of ancestry informative SNPs, and these co-ancestry estimates are consistent with the known history and demography of the Americas. The small scale and high population differentiation power of PIMA, particularly when combined with 34plex, provides a practical and powerful tool for genetic studies of American populations as well as forensic DNA analyses.

Analysis of the SNPforID 52-plex markers in four Native American populations from Venezuela.

The SNPforID 52-plex single nucleotide polymorphisms (SNPs) were analyzed in four native Venezuelan populations: Bari, Pemon, Panare and Warao. None of the population-locus combinations showed significant departure from Hardy-Weinberg equilibrium. Calculation of forensic and statistical parameters showed lower values of genetic diversity in comparison with African and European populations, as well as other, admixed populations of neighboring regions of Caribbean, Central and South America. Significant levels of divergence were observed between the four Native Venezuelan populations as well as with other previously studied populations. Analysis of the 52-plex SNP loci with Structure provided an optimum number of population clusters of three, corresponding to Africans, Europeans and Native Americans. Analysis of admixed populations indicated a range of membership proportions for ancestral populations consisting of Native American, African and European components. The genetic differences observed in the Native American groups suggested by the 52 SNPs typed in our study are in agreement with current knowledge of the demographic history of the Americas.

Molecular analysis of SRY gene in patients with mixed gonadal dysgenesis.

Mixed gonadal dysgenesis (MGD) includes a group of heterogeneous conditions consisting of a dysgenetic testis with a streak gonad. MGD is probably due to a disturbance in testicular determination/differentiation. The objective of this study is to analyze the SRY gene in MGD patients. A molecular investigation was undertaken in sixteen patients with this disorder in an attempt to determine mutations in SRY through polymerase chain reaction, single strand conformational polymorphism and direct sequencing. Eleven patients showed 45,X/46,XY and five 46,XY karyotype. Mutations in SRY gene were shown to be absent in these patients. This study confirms the findings of other studies. The etiology of MGD is heterogeneous, and cytogenetics mosaicism typically seen in these patients may be a cause of this condition, although, the presence of mutations in testicular organizing genes downstream of SRY is still to rule out.

CFTR mutations in three Latin American countries.

We analyzed 192 cystic fibrosis (CF) alleles in three Latin American countries: Mexico, Colombia, and Venezuela. Mutation screening was performed by polymerase chain reaction (PCR) and a reverse dot blot detection kit that enables determination of 16 of the most common CF mutations worldwide. Mutations were detected in 47.9% of the screened CF alleles. The most prevalent CF allele was DeltaF508 (39. 6%). The remaining 16 non-DeltaF508 detectable mutations represented 8.3% of the CF alleles. Among them, the G542X, N1303K, and 3849+10kb C>T were the most common. Although the frequency of DeltaF508 described here is lower than that reported for Caucasian populations, including in Spain, it is remarkable that mutation prevalences found in this study resemble those observed in Spain. Two of these mutations, G542X and 3849+10kb C>T, that were relevant in this analysis, have a particularly high incidence in Spanish communities. The low frequency of DeltaF508 described here may be explained by the Amerindian, Caucasian, and Black admixture that occurred in Latin America after the discovery of the New World, and also by the probable occurrence of mutations contributed by the original natives, which were undetectable in this analysis.

FISH and PCR analysis of the presence of Y-chromosome sequences in a patient with Xq-isochromosome and testicular tissue.

Mixed gonadal dysgenesis includes a heterogeneous group of different chromosomal, gonadal, and phenotypic abnormalities, characterized by the presence of a testis on one side and streak or an absent gonad on the other, persistence of müllerian duct structures and/or wolffian derivatives, and a variable degree of genital ambiguity. Here, we describe a patient with virilized external genitalia and phenotypic features of Turner syndrome, whose blood karyotype was 45,X/46,X,i(Xq). The presence of a unilateral dysgenetic testis was confirmed by histopathology. Using fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR)-based analysis to detect Y-specific sequences, Y-chromosome material was not detected. To date, this is the first case reported of Xq-isochromosome associated with the presence of testicular tissue.

Plasma excitatory amino acids in autism.

Plasma amino acid levels were measured by high pressure liquid chromatography (HPLC) in fourteen autistic children, all below 10 years of age. Mean glutamic and aspartic acid valued were elevated (169 +/- 142 uM and 22.1 +/- 13 uM respectively) together with taurine (90.1 +/- 78.7 uM) (p > 0.1). All affected children had low levels of glutamine (241 +/- 166 uM; p < 0.01) and asparagine (22.9 +/- 12.9 uM; p < 0.01) as compared to normal values (585 +/- 25 and 59.2 +/- 4.2 uM respectively); eleven children had increased aspartic acid and eight children had high levels of glutamate; seven of these children had a concomitant increment of taurine. The increment of the three above mentioned compounds was observed at the same time only in five children. These findings demonstrate that abnormal plasmatic levels of neurotransmitter amino acids may be found in some autistic children. Increased glutamatemia may be dietary in origin or may arise endogenously for several reasons, among others, metabolic derrangements in glutamate metabolism perhaps involving vitamin B6, defects or blockage of the glutamate receptor at the neuronal compartment, or alterations in the function of the neurotransmitters transporters. Increments of taurine, an inhibitor, is likely compensatory and calcium dependent.

[Molecular diagnosis of Duchenne/Becker muscular dystrophy in Venezuelan patients with the polymerase chain reaction]. / Diagnóstico molecular en pacientes venezolanos con distrofia muscular de Duchenne/Becker mediante la reacción en cadena de la polimerasa.

Duchenne and Becker muscular dystrophy (DMD/BMD) are recessive X-linked neuromuscular diseases produced by allelic mutations in the human dystrophin gen. In the present study we determined the 14-deletion prone exons by multiplex PCR in 24 no related venezuelan patients with clinical diagnosis of DMD/BMD. We found 37% of intragenic deletions of which 77% were located at the "hot spot" deletion region that includes exons 44 to 55. The present study show that deletion frequency observed in venezuelan patients resembles some Asian populations and is lower than that observed in Europe and North America. The explanation of the low frequency detected in our patients is beyond the present study, but it is likely that different mutations, ocurring at other regions of the gene is determining a molecular heterogeneity of the DMD/BMD disease in Venezuela.

[Clinical heterogeneity of the autistic syndrome: a study of 60 families]. / Heterogeneidad clínica del síndrome autista: un estudio en sesenta familias.

Sixty families ascertained through a single proband, has helped to better define infantile autism as a heterogeneous group of disorders. Forty four patients showed a characteristic facio- auricular dysplasia. Twenty four of these, showed increased pyruvate and lactate and laboratory findings of metabolic acidosis i.e., anion gap above 18 mEq/L or serum bicarbonate below 21 mEq/L but only nine of these probands demonstrated reduction of plasma bicarbonate below 18 mEq/lt. Plasma amino acids in 17 probands and matched controls showed increased taurine with the rest of amino acids significantly (p less than 0.05) below the control level. Glutamate and aspartate were also significantly elevated (p less than 0.05; Student t-test). Segregation analysis in thirty four of these families which linked through at least one ancestral family name, suggested autosomal recessive inheritance (p = 0.20). Three out of eight probands who received megadoses of pyridoxine (Vitamin B6), subjectively gained in language abilities, affectivity and response to behavior modification therapy. Five autistic patients proved to have clinically defined syndromes: two with the Martin-Bell syndrome, and three girls affected respectively with the Rett syndrome, phenylketonuria and dicarboxylic aciduria.