Genetic variants associated with fetal hemoglobin levels show the diverse ethnic origin in Colombian patients with sickle cell anemia / Las variantes genéticas asociadas con niveles de hemoglobina fetal señalan diversos orígenes étnicos en pacientes colombianos con anemia falciforme.

Introduction: Fetal hemoglobin is an important factor in modulating the severity of sickle cell anemia. Its level in peripheral blood underlies strong genetic determination. Associated loci with increased levels of fetal hemoglobin display population-specific allele frequencies. Objective: We investigated the presence and effect of known common genetic variants promoting fetal hemoglobin persistence (rs11886868, rs9399137, rs4895441, and rs7482144) in 60 Colombian patients with sickle cell anemia. Materials and methods: Four single nucleotide polymorphisms (SNP) were genotyped by restriction fragment length polymorphisms (RFLP) and the use of the TaqMan procedure. Fetal hemoglobin (HbF) from these patients was quantified using the oxyhemoglobin alkaline denaturation technique. Genotype frequencies were compared with frequencies reported in global reference populations. Results: We detected genetic variants in the four SNPs, reported to be associated with higher HbF levels for all four SNPs in the Colombian patients. Genetic association between SNPs and HbF levels did not reach statistical significance. The frequency of these variants reflected the specific ethnic make-up of our patient population: A high prevalence of rs7482144-'A' reflects the West-African origin of the sickle cell mutation, while high frequencies of rs4895441-'G' and rs11886868-'C' point to a significant influence of an Amerindian ethnic background in the Colombian sickle cell disease population. Conclusion: These results showed that in the sickle cell disease population in Colombia there is not a unique genetic background, but two (African and Amerindian). This unique genetic situation will provide opportunities for a further study of these loci, such as fine-mapping and molecular-biological investigation. Colombian patients are expected to yield a distinctive insight into the effect of modifier loci in sickle cell disease.

Introducción. La hemoglobina fetal es un importante factor modulador de la gravedad de la anemia falciforme, cuya expresión está muy condicionada por el factor genético. Los loci asociados con el incremento de la hemoglobina fetal pueden presentar frecuencias alélicas específicas para cada población. Objetivo. Investigar la presencia y el efecto de las variantes genéticas rs11886868, rs9399137, rs4895441 y rs7482144 asociadas con la persistencia de hemoglobina fetal, en 60 pacientes colombianos con anemia falciforme. Materiales y métodos. Se hizo la genotipificación de los polimorfismos de nucleótido simple ( Single Nucleotide Polymorphisms, SNP) mediante la técnica de polimorfismos de longitud de fragmentos de restricción ( Restriction Fragment Length Polymorphisms, RFLP) y el procedimiento TaqMan. La hemoglobina fetal (HbF) se cuantificó utilizando la técnica de desnaturalización alcalina de la oxihemoglobina. Las frecuencias genotípicas se compararon con las reportadas en poblaciones de referencia global. Resultados. Se observaron variantes genéticas ya reportadas para aumento de HbF en los cuatro SNP. La asociación genética entre los SNP y el incremento de la HbF no alcanzó significancia estadística. La frecuencia de estos alelos reflejó la siguiente composición específica en esta muestra de pacientes colombianos: una gran prevalencia de rs7482144-'A', lo que indica que el origen de la mutación para la anemia falciforme es África occidental, y una gran frecuencia de rs4895441-'G' y rs11886868-'C', lo que denota la influencia significativa del origen genético amerindio. Conclusión. Los resultados evidenciaron que la población con anemia falciforme de Colombia no tiene un único origen genético, sino que existen dos (africano y amerindio). Esta situación genética única ofrece la oportunidad de llevar a cabo un estudio más amplio de estos loci a nivel molecular. Se espera que el estudio de pacientes colombianos permita una visión diferente del efecto de los loci modificadores en esta enfermedad.

Analysis of monotherapy prostate brachytherapy in patients with prostate cancer. Initial PSA and Gleason are important for recurrence?

Purpose To evaluate the clinical outcome of a cohort of localized prostate cancer patients treate with 125-I permanent brachytherapy at the São José Hospital – CHLC, Lisbon. Materials and Methods A retrospective analysis was carried out on 429 patients with low and intermediate-risk of prostate adenocarcinoma, according to the recommendations of the EORTC, who underwent 125I brachytherapies in intraoperative dosimetry “real-time” system between September 2003 and September 2013. Results The mean follow-up was 71.98 months. Biochemical relapse of disease by rising PSA (Phoenix criterion) was observed in 18 patients (4.2%). Through the application of Kaplan-Meier survival curves in this sample, the rate of survival at 6 years without biochemical relapse was higher than 95%. By Iog rank test comparing biochemical relapse with initial PSA (15-10 and <10) and Gleason values (7 and <7), there was no statistical difference (P=0.830) of the initial PSA in the probability of developing biochemical relapse. In relation to Gleason score, it was noted a statistical difference (P<0.05), demonstrating that patients with Gleason 7 are more likely to develop biochemical relapse. Conclusions Brachytherapy as monotherapy is at present an effective choice in the treatment of localized prostate adenocarcinoma. Biochemical relapses are minimal. The initial PSA showed no statistically difference in the rate of relapses, unlike the value Gleason, where it was demonstrated that patients with Gleason 7 have a higher probability of biochemical relapse. Cases with PSA bounce should be controlled before starting a salvage treatment. .

Comparison of Phenotypic and Genetic Performance of Local Silkworm Groups and Two Commercial Lines

Five Iranian native silkworm groups: Baghdad, Khorasan Orange, Guilan Orange, Khorasan Pink, Khorasan Lemon, and 107 and 110 commercial lines (12 families from each breed) were randomly selected and reared during 2003-2005 (five generations in spring and autumn). In each family, 30 male and 30 female cocoons were individually recorded for weight, shell weight and shell ratio. From among the native groups, the highest average in all three traits belonged to Baghdad and Khorasan Pink, and the lowest to Khorasan Orange and Khorasan Lemon. From among the commercial lines, the highest average in all three traits belonged to 107. In comparing heritabihty for cocoon weight in native groups, the highest heritabihty belonged to Guilan Orange (0.5147) and Khorasan Orange (0.5036) and the lowest heritabihty belonged to Khorasan Pink (0.0967). In the two other traits, the highest heritabihty belonged to Khorasan Orange and Baghdad and the lowest to Khorasan Pink. In the commercial lines, linellO had higher heritabihty than linel07 for cocoon weight and cocoon shell weight. In all the groups, genetic correlations between cocoon weight and cocoon shell weight were high, expect for the Baghdad group. There was médium or low genetic correlation among cocoon weight, cocoon shell weight and cocoon shell ratio.

Analysis of the association between spawning time QTL markers and the biannual spawning behavior in rainbow trout (Oncorhynchus mykiss)

The rainbow trout is a salmonid fish that occasionally exhibits broodstocks with biannual spawning behavior, a phenomenon known as a double annual reproductive cycle (DARC). Spawning time quantitative trait loci (SPT-QTLs) affect the time of the year that female rainbow trout spawn and may influence expression of the DARC trait. In this study, microsatellite markers linked and unlinked to SPT-QTLs were genotyped to investigate the underlying genetics of this trait. SPT-QTLs influenced the DARC trait since in two case-control comparisons three linked markers (OmyFGT12TUF, One3ASC and One19ASC) had significant levels of allelic frequency differentiation and marker-character association. Furthermore, alleles of One3ASC and One19ASC had significantly higher frequencies in populations that carried the DARC trait.

QTL identification of grain protein concentration and its genetic correlation with starch concentration and grain weight using two populations in maize (Zea mays L.).

Protein is one of the three main storage chemical components in maize grains, and is negatively correlated with starch concentration (SC). Our objective was to analyse the influence of genetic backgrounds on QTL detection for protein concentration (PC) and to reveal the molecular genetic associations between PC and both SC and grain weight (GWP). Two hundred and eighty-four (Pop1) and 265 (Pop2) F(2:3) families were developed from two crosses between one high-oil maize inbred GY220 and two normal maize inbreds 8984 and 8622 respectively, and were genotyped with 185 and 173 pairs of SSR markers. PC, SC and GWP were evaluated under two environments. Composite interval mapping (CIM) and multiple interval mapping (MIM) methods were used to detect single-trait QTL for PC, and multiple-trait QTL for PC with both SC and GWP. No common QTL were shared between the two populations for their four and one PC QTL. Common QTL with opposite signs of effects for PC and SCGWP were detected on three marker intervals at bins 6.07-6.08, 8.03 and 8.03-8.04. Multiple-traits QTL mapping showed that tightly-linked QTL, pleiotropic QTL and QTL having effects with opposite directions for PC and SCGWP were all observed in Pop1, while all QTL reflected opposite effects in Pop2.

Analysis of genetic and non-genetic factors that affect the QTc interval in a Mongolian population: the GENDISCAN study

The QTc interval is a complex quantitative trait and a strong prognostic indicator of cardiovascular mortality in general, healthy people. The aim of this study was to identify non-genetic factors and quantitative trait loci that govern the QTc interval in an isolated Mongolian population. We used multiple regression analysis to determine the relationship between the QTc interval and non-genetic factors including height, blood pressure, and the plasma lipid level. Whole genome linkage analyses were performed to reveal quantitative trait loci for the QTc interval with 349 microsatellite markers from 1,080 Mongolian subjects. Among many factors previously known for association with the QTc interval, age, sex, heart rate, QRS duration of electrocardiogram and systolic blood pressure were also found to have influence on the QTc interval. A genetic effect for the QTc interval was identified based on familial correlation with a heritability value of 0.31. In a whole genome linkage analysis, we identified the four potential linkage regions 7q31-34, 5q21, 4q28, and 2q36.

Mapping quantitative trait loci for binary trait in the F2:3 design.

In the analysis of inheritance of quantitative traits with low heritability, an F(2:3) design that genotypes plants in F(2) and phenotypes plants in F(2:3) progeny is often used in plant genetics. Although statistical approaches for mapping quantitative trait loci (QTL) in the F(2:3) design have been well developed, those for binary traits of biological interest and economic importance are seldom addressed. In this study, an attempt was made to map binary trait loci (BTL) in the F(2:3) design. The fundamental idea was: the F(2) plants were genotyped, all phenotypic values of each F(2:3) progeny were measured for binary trait, and these binary trait values and the marker genotype informations were used to detect BTL under the penetrance and liability models. The proposed method was verified by a series of Monte-Carlo simulation experiments. These results showed that maximum likelihood approaches under the penetrance and liability models provide accurate estimates for the effects and the locations of BTL with high statistical power, even under of low heritability. Moreover, the penetrance model is as efficient as the liability model, and the F(2:3) design is more efficient than classical F(2) design, even though only a single progeny is collected from each F(2:3) family. With the maximum likelihood approaches under the penetrance and the liability models developed in this study, we can map binary traits as we can do for quantitative trait in the F(2:3) design.

Quantitative trait loci for carcass, internal organ and meat quality traits on porcine chromosomes 16, 17 and 18

The objective of this study was to map quantitative trait loci (QTL) on porcine chromosomes 16, 17 and 18 and to determine their association with carcass, organ and meat quality traits. An F2 population was produced by crossing two boars of the naturalized Brazilian Piau breed with 18 commercial females (Landrace x Large White x Pietrain). The population was genotyped for 11 microsatellite markers distributed over the three chromosomes and the results were used to construct a marker-specific linkage map for the population. Analysis of the polymorphic information content showed that the microsatellite markers were adequate for the study of quantitative traits. QTL were identified by regression interval mapping using QTL Express software. QTL not previously described in the literature were detected on chromosome 16, whereas QTL described in other populations were detected on chromosomes 17 and 18. The information from the significant QTL identified here will be useful for future fine-mapping studies and should provide a better understanding of productive phenotypes in pigs.

Segregation distortion at a microsatellite marker in the olive flounder, Paralichtys olivaceus.

In the course of quantitative trait loci (QTL) analysis of the back cross (BC1) families of olive flounder (Paralichtys olivaceus), we observed significant segregation distortion at a microsatellite marker Poli9-58TUF in two crosses of informative progenies. The family 1 of the random BC1 progenies derived from a cross between a F1 male genotype (A/B) and a F1's female parent genotype (A/C) and the family 2 (A/C x A/C) displayed a strong bias in the locus from the Mendelian inheritance by the elimination of homozygous A/A genotype. The deleterious roles of the AA genotypes are suggested during the metamorphosis and it implies that the parents of these families carried a recessive gene or genes hampering development at an early stage because the offspring of the double heterozygote parents show the reduction in frequency or elimination of one homozygous class, which is an evidence for linkage between the genetic marker and gene(s) with recessive deleterious alleles. This data support a hypothesis that the region contains a recessive lethal gene or genes.

Heritability and linkage study on heart rates in a Mongolian population

Elevated heart rate has been proposed as an independent risk factor for cardiovascular diseases, but their interrelationships are not well understood. In this study, we performed a genome-wide linkage scan in 1,026 individuals (mean age 30.6 years, 54.5% women) from 73 extended families of Mongolia and determined quantitative trait loci that influence heart rate. The DNA samples were genotyped using deCODE 1,039 microsatellite markers for 3 cM density genome-wide linkage scan. Correlation analysis was carried out to evaluate the correlation of the covariates and the heart rate. T-tests of the heart rate were also performed on sex, smoking and alcohol intake. Consequently, this model was used in a nonparametric genome-wide linkage analysis using variance component model to create a multipoint logarithm of odds (LOD) score and a corresponding P value. In the adjusted model, the heritability of heart rate was estimated as 0.32 (P<.0001) and a maximum multipoint LOD score of 2.03 was observed in 77 cM region at chromosome 18. The second largest LOD score of 1.52 was seen on chromosome 5 at 216 cM. Genes located on the specified locations in chromosomes 5 and 18 may be involved in the regulation of heart rate.

Methylation Profiles of CpG Island Loci in Major Types of Human Cancers

Several reports have described aberrant methylation in various types of human cancers. However, the interpretation of methylation frequency in various human cancers has some limitations because of the different materials and methods used for methylation analysis. To gain an insight into the role of DNA hypermethylation in human cancers and allow direct comparison of tissue specific methylation, we generated methylation profiles in 328 human cancers, including 24 breast, 48 colon, 61 stomach, 48 liver, 37 larynx, 24 lung, 40 prostate, and 46 uterine cervical cancer samples by analyzing CpG island hypermethylation of 13 genes using methylation-specific PCR. The mean numbers of methylated genes were 6.5, 4.4, 3.6, 3.4, 3.1, 3.1, 3.1, and 2.1 in gastric, liver, prostate, larynx, colon, lung, uterine cervix, and in breast cancer samples, respectively. The number of genes that were methylated at a frequency of more than 40% in each tumor type ranged from nine (stomach) to one (breast). Generally genes frequently methylated in a specific cancer type differed from those methylated in other cancer types. The findings indicate that aberrant CpG island hypermethylation is a frequent finding in human cancers of various tissue types, and each tissue type has its own distinct methylation pattern.

A critical evaluation of the effect of population size and phenotypic measurement on QTL detection and localization using a large F2 murine mapping population

Population size and phenotypic measurement are two key factors determining the detection power of quantitative trait loci (QTL) mapping. We evaluated how these two controllable factors quantitatively affect the detection of QTL and their localization using a large F2 murine mapping population and found that three main points emerged from this study. One finding was that the sensitivity of QTL detection significantly decreased as the population size decreased. The decrease in the percentage logarithm of the odd score (LOD score, which is a statistical measure of the likelihood of two loci being lied near each other on a chromosome) can be estimated using the formula 1 - n/N, where n is the smaller and N the larger population size. This empirical formula has several practical implications in QTL mapping. We also found that a population size of 300 seems to be a threshold for the detection of QTL and their localization, which challenges the small population sizes commonly-used in published studies, in excess of 60 percent of which cite population sizes <300. In addition, it seems that the precision of phenotypic measurement has a limited capacity to affect detection power, which means that quantitative traits that cannot be measured precisely can also be used in QTL mapping for the detection of major QTL.

DGAT1 K232A polymorphism in Brazilian cattle breeds

Recent reports identified DGAT1 (EC 2.3.1.20) harboring a lysine to alanine substitution (K232A) as a candidate gene with a strong effect on milk production traits. Our objective was to estimate the frequency of the DGAT1 K232A polymorphism in the main Zebu and Taurine breeds in Brazil as well as in Zebu x Taurine crossbreds as a potential QTL for marker-assisted selection. Samples of 331 animals from the main Brazilian breeds, Nellore, Guzerat, Red Sindhi, Gyr, Holstein, and Gyr x Holstein F1 were genotyped for DGAT1 K232A polymorphism (A and K alleles) using the PCR-RFLP technique. The highest frequency of the A allele was found in the Holstein sample (73%) followed by Gyr x Holstein F1 (39%). Gyr and Red Sindhi showed low frequencies of A alleles (4 and 2.5%, respectively). The A allele was not found in the Nellore and Guzerat samples. Our results could be used to guide association studies between this locus and milk traits in these breeds.

Quantitative trait loci mapping for meat quality traits in swine chromosome 6

Realizou-se o mapeamento de QTL no cromossomo 6 suíno (SSC6), associado às características de qualidade da carne. Um total de 557 animais de uma populacão F2 foi obtido do cruzamento entre dois machos da raca nativa brasileira Piau e 18 fêmeas comerciais, cujos genótipos foram obtidos para 13 marcadores microssatélites. As características avaliadas na F2 foram pH, medido 45 minutos e 24 horas post-mortem (pH45 e pH24, respectivamente); perda por gotejamento (DL); perda por cozimento (CL); perda total (TL); gordura intramuscular (IMF); maciez objetiva (OT); luminosidade (L); índice de vermelho (A); índice de amarelo (B); tonalidade de cor (h); e índice de saturacão (c). Utilizou-se o método de regressão por intervalo de mapeamento, por meio do programa QTL Express. Foram detectados QTLs significativos para pH45 e DL, sugestivos para DL, e não foram encontrados QTLs para as demais características. Constatou-se que grupos gênicos, localizados em torno de 76, 88 e 97cM, podem atuar no pH45 e no DL. Nas regiões dos picos da estatística F, onde se verificaram QTLs sugestivos para DL, devem ser incluídos mais marcadores, para confirmar a presenca de QTLs.

Genetic trends of abdominal fat content in a male broiler chicken line

Data of chickens from a broiler-breeding program were collected and used to determine the genetic trends of absolute and relative abdominal fat content. The genetic trends were estimated by the regression of trait genetic value averages on hatch-years. Genetic values from 32,485 individuals were used for regression analysis. The genetic trend estimate for absolute abdominal fat content was +0.39 g per year, indicating that abdominal fat deposition in the analyzed line, in absolute terms, tended to increase, making the existing excess fat deposition in the broilers even worse. However, the genetic trend of relative abdominal fat content was not significant, indicating that there is no increase on abdominal fat content when it is corrected for body weight.

Integrating genomics into Eucalyptus breeding

The advent of high throughput genomic technologies has opened new perspectives in the speed, scale and detail with which one can investigate genes, genomes and complex traits in Eucalyptus species. A genomic approach to a more detailed understanding of important metabolic and physiological processes, which affect tree growth and stress resistance, and the identification of genes and their allelic variants, which determine the major chemical and physical features of wood properties, should eventually lead to new opportunities for directed genetic modifications of far-reaching economic impact in forest industry. It should be kept in mind, however, that basic breeding strategies, coupled with sophisticated quantitative methods, breeder's experience and breeder's intuition, will continue to generate significant genetic gains and have a clear measurable impact on production forestry. Even with a much more global view of genetic processes, genomics will only succeed in contributing to the development of improved industrial forests if it is strongly interconnected with intensive fieldwork and creative breeding. Integrated genomic projects involving multi-species expressed sequence tag sequencing and quantitative trait locus detection, single nucleotide polymorphism discovery for association mapping, and the development of a gene-rich physical map for the Eucalyptus genome will quickly move toward linking phenotypes to genes that control the wood formation processes that define industrial-level traits. Exploiting the full power of the superior natural phenotypic variation in wood properties found in Eucalyptus genetic resources will undoubtedly be a key factor to reach this goal.