Juan Carlos Alvarez

Genetic analysis of the principal genes related to prostate cancer: A review

Prostate cancer is one of the most common leading causes of cancer death in men. Attributable to many genetic linkage and genome-wide association studies (GWAS) around the world, several high-penetrance genetic variants have been identified. Many polymorphisms in genes, such as ELAC2 (locus HPC2), RNase L (locus hereditary prostate cancer 1 gene [HPC1]), and MSR1 have been recognized as important genetic factors that confer an increased risk of developing prostate cancer in many populations. A review of the literature was then performed analyzing the roles of these and other genes in prostate cancer. Our main challenge is optimizing the role of these genes in prostate cancer development, even trying to use these genes as general biomarkers. The principal aim of this review is to determine the most important variants in the principal genes related to prostate cancer and examine the differences among populations. The concept of individualized or personalized targeted cancer therapy has gained significant attention throughout oncology. In prostate cancer, the creation of a personalized panel of single-nucleotide polymorphisms (SNP) biomarkers may be important for the early and accurate detection of this cancer. As a result, the need for a good biomarker is required to detect prostate cancer earlier and to provide tools to follow patients during the early stages of the cancer. At present, prostate cancer continues to have an unclear etiology, which is a combination of genetic and numerous environmental factors. Among genetic factors, no variants of the RNase L, ELAC2, or MSR1 genes have been detected with similar expression patterns in different populations all around the world.

Dandruff as a Potential Source of DNA in Forensic Casework

Dandruff is a clinical alteration of the skin that consists histologically of orthokeratotic clumps with minute parakeratotic foci found in inflammatory pathologies such as seborrheic dermatitis and psoriasis. Therefore, some nucleated cells should be found in dandruff and hence there is a possibility that forensically typeable DNA could be extracted from dandruff. Because of a particular case in which we were involved, a study was carried out to determine whether or not DNA could be extracted from dandruff, and if the two most widely used extraction techniques (Chelex and organic) would be applicable. Results show that sufficient quantities of DNA (more than 30 to 40 ng) can be obtained from as little as 1.0 to 1.5 mg of dandruff. Both methods yield DNA, although the organic procedure seems to yield more (72.5 ng Chelex vs. 183.3 ng organic). All the DNA samples extracted were typed correctly for the loci HUMTH01 and HUMvWA. Therefore, dandruff can be considered a potential source of DNA for forensic identification.

Genetic Identification of Missing Persons: DNA Analysis of Human Remains and Compromised Samples

Human identification has made great strides over the past 2 decades due to the advent of DNA typing. Forensic DNA typing provides genetic data from a variety of materials and individuals, and is applied to many important issues that confront society. Part of the success of DNA typing is the generation of DNA databases to help identify missing persons and to develop investigative leads to assist law enforcement. DNA databases house DNA profiles from convicted felons (and in some jurisdictions arrestees), forensic evidence, human remains, and direct and family reference samples of missing persons. These databases are essential tools, which are becoming quite large (for example the US Database contains 10 million profiles). The scientific, governmental and private communities continue to work together to standardize genetic markers for more effective worldwide data sharing, to develop and validate robust DNA typing kits that contain the reagents necessary to type core identity genetic markers, to develop technologies that facilitate a number of analytical processes and to develop policies to make human identity testing more effective. Indeed, DNA typing is integral to resolving a number of serious criminal and civil concerns, such as solving missing person cases and identifying victims of mass disasters and children who may have been victims of human trafficking, and provides information for historical studies. As more refined capabilities are still required, novel approaches are being sought, such as genetic testing by next-generation sequencing, mass spectrometry, chip arrays and pyrosequencing. Single nucleotide polymorphisms offer the potential to analyze severely compromised biological samples, to determine the facial phenotype of decomposed human remains and to predict the bioancestry of individuals, a new focus in analyzing this type of markers.

Genetic variation of 24 STR loci in a Mexican Mestizo population from Mexico D.F

Genetic data from 17 autosomal short tandem repeat (STR) loci found in the Powerplex® ESX 17 System (Promega, Madison, WI, USA) was evaluated in 162 unrelated Mexican Mestizo individuals from Mexico City. Allele frequencies and forensic parameters were estimated for the 17 STRs. All loci analyzed were in Hardy-Weinberg equilibrium in the studied population and showed not any signs of linkage between loci. The combined power of discrimination and the power of exclusion for the 16 aSTRs studied were 1–2.56409·10−19 and 99.999938 %, respectively. Genetic distances reveal a close relationship within different populations of Mexican Mestizos. The obtained data might be useful for population genetics research and for individual identification and paternity testing in forensic science.

Paraguayan population data on the fifteen STR loci included in the PowerPlex 16 kit.

Blood samples were obtained by venipuncture from unrelated individuals (n = 168) living in Paraguay.

Prognostic role of genetic biomarkers in clinical progression of prostate cancer

The aim of this study was to analyze the use of 12 single-nucleotide polymorphisms in genes ELAC2, RNASEL and MSR1 as biomarkers for prostate cancer (PCa) detection and progression, as well as perform a genetic classification of high-risk patients. A cohort of 451 men (235 patients and 216 controls) was studied. We calculated means of regression analysis using clinical values (stage, prostate-specific antigen, Gleason score and progression) in patients and controls at the basal stage and after a follow-up of 72 months. Significantly different allele frequencies between patients and controls were observed for rs1904577 and rs918 (MSR1 gene) and for rs17552022 and rs5030739 (ELAC2). We found evidence of increased risk for PCa in rs486907 and rs2127565 in variants AA and CC, respectively. In addition, rs627928 (TT–GT), rs486907 (AG) and rs3747531 (CG–CC) were associated with low tumor aggressiveness. Some had a weak linkage, such as rs1904577 and rs2127565, rs4792311 and rs17552022, and rs1904577 and rs918. Our study provides the proof-of-principle that some of the genetic variants (such as rs486907, rs627928 and rs2127565) in genes RNASEL, MSR1 and ELAC2 can be used as predictors of aggressiveness and progression of PCa. In the future, clinical use of these biomarkers, in combination with current ones, could potentially reduce the rate of unnecessary biopsies and specific treatments.

Distribution of Y chromosomal STRs loci in Mayan and Mestizo populations from Guatemala

In this study, a sample of 225 Guatemalan males, comprising 115 Mestizo-Guatemalan and 110 Mayan-Guatemalan, was typed for 17 Y-short tandem repeats (STRs) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1 and DYS385a/b). The haplotype diversity (H=1) and discrimination capacity (96.86%) were calculated. Analysis of molecular variance (AMOVA) demonstrated a low but significant interpopulation differentiation when compared with the results obtained when we confront the Mestizo and Mayan populations with the European populations. Furthermore, the genetic variability and differences among the American, African, Asian, and European populations were analyzed with the software Statistica 9.1. In addition, the genetic distances were also calculated using other published data. Reynolds and Slatkińs genetic distance was visualized using the multidimensional scaling (MDS) analysis. All the analysis performed locates the Mayan population next to the Native American population, while Guatemalan-Mestizo population was found to be between these populations and the European population, similar to other Mestizo one. The implementation of the estimation of individual ancestry proportions of the whole population sample showed the presence of two well-differentiated population groups.

Population data on nine STR loci in an El Salvadoran (Central American) sample population.

Blood samples were obtained by venipuncture from unrelated individuals (n = 323) living in El Salvador. Approximately 1–3 ng of DNA were used in each PCR. The samples were amplified using the Profiler Plus™ kit (PE) and the alleles were separated and detected using an Applied Biosystems ABI310 genetic analyzer. The frequency of each allele for each locus was calculated from the numbers of each genotype in the sample set (i.e., the gene count method). Unbiased estimates of expected heterozygosity were computed as described by Edwards et al. (1). Possible divergence from Hardy-Weinberg expectations (HWE) was tested by calculating the unbiased estimate of the expected homozygote/heterozygote frequencies (1–4) and the exact test (5), based on 2000 shufflings experiments. An interclass correlation criterion (6) for two-locus associations was used for detecting disequilibrium between the STR loci. The program for this analysis was kindly provided by R. Chakraborty (University of Texas, School of Biomedical Sciences, Houston, TX).

Sequential Multiplex Amplification: Utility in Forensic Casework with Minimal Amounts of DNA and Partially Degraded Samples

Since its introduction, PCR has become a widely-used, routine technique in forensic laboratories. A number of PCR protocols that were developed originally are now being replaced by more powerful approaches, particularly those based on multiplex amplification of short tandem repeat (STR) loci. One alternative from of multiplex PCR amplification, called Sequential Multiplex Amplification (SMA), was designed to amplify a single locus and then recover and reuse the remaining genomic DNA as a template for subsequent PCR. The SMA process could be repeated several times. SMA has proven to be useful in typing genomic DNA contained in stored PCR samples and analyzing samples of limited quality and/or quantity for multiple loci. The efficacy of the use of SMA for actual typing of casework samples permitted typing for a second locus 98.11% of the samples considered; 70.75% were typeable for a third locus, and 16.98% for a fourth locus.

Population genetic data of 38 insertion-deletion markers in South East Spanish population.

Insertion–deletion polymorphisms (INDELs) are usually diallelic markers derived from a single mutation event. INDELs can combine characteristics of both SNPs and STRs, as an extended distribution throughout the genome [1,2]; the possibility of the use of reduced amplicon sizes improving amplification success of compromised samples [3–5]; origination from a single mutation event occurring at a low frequency and unlikely to present recurrent mutations; and the effortlessness of analysis through PCR and capillary electrophoresis, as STRs [6–8]. These beneficial characteristics make them suitable for forensic and parentage testing [6,8–10]. Furthermore, the significant differences in allele frequencies among geographically separated population groups [11,12] make some INDELs good ancestry informative markers. According to the Spanish Statistics Office 2011 census, the South East Spanish population consists of 3,205,644 inhabitants, of which 28.76% are found in the province of Granada, 49.75% in the province of Málaga and 21.48% in the province of Almerı́a (http:// www.ine.es/). These three provinces occupy an area of 28,613 km, 5.67% of the Spanish territory. The purpose of this study was to characterize the diversity of 38 INDEL markers in the South East Spanish population, provinces of Granada, Málaga and Almerı́a; and to assess their usefulness both in forensic casework and population genetics. Buccal cell swabs from a total of 143 unrelated adults from the South East Spanish population, [Almerı́a (45), Granada (53), Málaga (45)] were collected under informed consent and the study was approved by the ethics committee of the University of Granada. Genomic DNA was isolated using an organic extraction procedure by phenol/chloroform/isoamyl alcohol and proteinase K. It was purificated by Amicon 100 (Millipore). Quantification of extracted DNA was performed by 0.8% agarose gel. The samples were amplified using a 38 INDELs multiplex, according to Pereira et al. [13]. PCR was carried out in a GeneAmp PCR System 2720 thermal cycler (Applied Biosystems, California) under the following conditions: initial incubation at 95 8C for 15 min; 10 cycles at 94 8C for 30 s, 60 8C for 90 s and 72 8C for 60 s; 20 cycles at 94 8C for 30 s, 58 8C for 90 s and 72 8C for 60 s; with a final extension at 72 8C for 60 min. Amplification products were separated by electrophoresis in an Applied Biosystems ABI 3130 genetic analyzer and allele calls were determined automatically with GeneMapperX v1.1 software (Applied Biosystems) using the bin sets for INDELs provided by Pereira et al. [13]. Typing quality and allele designation were warranted by simultaneous electrophoretic analysis of a control