The Human Variome Project country node of Argentina in the first two years of activity: past, present and future / El nodo Argentino del Proyecto Varioma Humano en los primeros dos años de actividad: pasado, presente y futuro

The Human Variome Project (HVP) is an international effort aiming systematically to collect and share information on all human genetic variants. It has been working for years in collaboration with local scientific societies by establishing systems to collect every genetic variant reported in a country and to store these variants within a database repository: LOVD (Argentinian chapter: ar.lovd.org). Formally established in 2017 in the Argentinian Node, up to June 2019 we collected more than 25,000 genetic variants deposited by 17 different laboratories. Nowadays the HVP country nodes represent more than 30 countries. In Latin America there are four country nodes: Argentina, Brazil, Mexico and Venezuela; the first two interacted recently launching the LatinGen database. In the present work we want to share our experience in applying the HVP project focusing on its organization, rules and nomenclature to reach the goal of sharing genetic variants and depositing them in the Leiden Open Variation Database. Contributing laboratories are seeking to share variant data to gain access all over the country. It is one of our goals to stimulate the highest quality by organizing courses, applying current nomenclature rules, sponsoring lectures in national congresses, distributing newsletter to serve the Argentinian genomics community and to stimulate the interaction among Latin America countries.

El Proyecto Varioma Humano (HVP) es un esfuerzo internacional que tiene como objetivo recopilar y compartir sistemáticamente información sobre todas las variantes genéticas humanas. Hemos estado trabajando durante tres años en colaboración con sociedades científicas locales, mediante el establecimiento de sistemas para recolectar todas las variantes genéticas reportadas en el país y almacenarlas dentro de la base de datos LOVD (capítulo argentino: ar.lovd.org). En el año 2017 fue establecido formalmente el Nodo Argentino del HVP, habiéndose recolectado más de 25.000 variantes genéticas depositadas por 17 laboratorios diferentes hasta junio de 2019. Hoy en día existen al menos 30 nodos del HVP, correspondientes a diferentes países. En América Latina hay cuatro nodos: Argentina, Brasil, México y Venezuela; Los dos primeros interactuaron recientemente lanzando la base de datos LatinGen. En el presente trabajo queremos compartir nuestra experiencia en la aplicación del proyecto HVP centrándonos en su organización, reglas y nomenclatura para alcanzar el objetivo de compartir variantes genéticas y depositarlas en la base de datos de variaciones abiertas de Leiden (LOVD). Es uno de nuestros objetivos estimular la más alta calidad mediante la organización de cursos, aplicación de las reglas de nomenclatura actuales, patrocinio de conferencias en congresos nacionales, distribución de boletines informativos para la comunidad de genómica argentina, y estimulación de la interacción entre los países de América Latina.

Donor compensation: an ethical imperative!

The number of living organ donors is increasing worldwide, but donor needs are widely neglected in support of anticommodification policies. This article argues that the warrant of donor autonomy during the decision process to donate is only one requirement of adequate donor care. Another is the donor's protection against the systematic and institutional exploitation of his altruistic dispositions. People with the disposition to support those, who are in desperate need, with a nonrenewable part of their own body, despite a small but unavoidable risk of death or health impairment, do not deserve to be additionally burdened with further disincentives, such as financial risks and uncompensated costs of donation. And although the borderline between a morally required disincentive removal and a more controversial net incentive to boost donation might be vague and open to discussion, to disadvantage living donors by design constitutes a serious barrier to the fairness of living organ donation-a barrier that should be removed.

The role of human demographic history in determining the distribution and frequency of transferase-deficient galactosaemia mutations.

Classical or transferase-deficient galactosaemia is an inherited metabolic disorder caused by mutation in the human Galactose-1-phosphate uridyl transferase (GALT) gene. Of some 170 causative mutations reported, fewer than 10% are observed in more than one geographic region or ethnic group. To better understand the population history of the common GALT mutations, we have established a haplotyping system for the GALT locus incorporating eight single nucleotide polymorphisms and three short tandem repeat markers. We analysed haplotypes associated with the three most frequent GALT gene mutations, Q188R, K285N and Duarte-2 (D2), and estimated their age. Haplotype diversity, in conjunction with measures of genetic diversity and of linkage disequilibrium, indicated that Q188R and K285N are European mutations. The Q188R mutation arose in central Europe within the last 20 000 years, with its observed east-west cline of increasing relative allele frequency possibly being due to population expansion during the re-colonization of Europe by Homo sapiens in the Mesolithic age. K285N was found to be a younger mutation that originated in Eastern Europe and is probably more geographically restricted as it arose after all major European population expansions. The D2 variant was found to be an ancient mutation that originated before the expansion of Homo sapiens out of Africa.

Observation of a transition in the water-nanoparticle formation process at 167 K.

Rapid-scan Fourier transform infrared spectroscopy of the vapor/solid formation process of water nanoparticles in the 180-140 K temperature range at thermal-equilibrium conditions is reported. At 167 K a transition in the formation process was observed: the particle volume quintuples and the particle formation time triples within a temperature interval of +/-0.4 K caused by the temperature control. The authors interpret this behavior by an abrupt change in the nucleation rate of the H2O monomers in He buffer gas kept at 167 K and 200 mbar. A size and shape analysis of the particles during the formation process was carried out by application of the discrete dipole approximation method which delivers excellent accordance between experimental and calculated mid-IR spectra. Compared to other compact shapes (cube, prolate ellipsoid, and hexagonal prism) the ideal spherical shape fits the experimental spectra best. A distinct change in shape by particle conversion or agglomeration could be excluded to be involved in the formation process. As a possible explanation of the observed phenomenon, a transition from vapor/liquid/solid to vapor/solid nucleation with decreasing temperature is considered which was recently theoretically predicted by van Dongen and co-workers [J. Chem. Phys. 117, 5647 (2002); private communication; J. Chem. Phys. 120, 6314 (2004)].

Insulin growth factor-binding protein 2 is a candidate biomarker for PTEN status and PI3K/Akt pathway activation in glioblastoma and prostate cancer.

PTEN is an important tumor-suppressor gene associated with many cancers. Through expression profiling of glioblastoma tissue samples and prostate cancer xenografts, we identified a molecular signature for loss of the PTEN tumor suppressor in glioblastoma and prostate tumors. The PTEN signature consists of a minimum of nine genes, several of which are involved in various pathways already implicated in tumor formation. Among these signature genes, the most significant was an increase in insulin growth factor-binding protein 2 (IGFBP-2) mRNA. Up-regulation of IGFBP-2 was confirmed at the protein level by Western blot analysis and validated in samples not included in the microarray analysis. The link between IGFBP-2 and PTEN was of particular interest because elevated serum IGFBP-2 levels have been reported in patients with prostate and brain tumors. To further investigate this link, we determined that IGFBP-2 expression is negatively regulated by PTEN and positively regulated by phosphatidylinositol 3-kinase (PI3K) and Akt activation. In addition, Akt-driven transformation is impaired in IGFBP2(-/-) mouse embryo fibroblasts, implicating a functional role for IGFBP-2 in PTEN signaling. Collectively, these studies establish that PTEN and IGFBP-2 expression are inversely correlated in human brain and prostate cancers and implicate serum IGFBP-2 levels as a potential serum biomarker of PTEN status and PI3K Akt pathway activation in cancer patients.

Spectroscopic investigation of the deeply buried Cu(In,Ga)(S,Se)2/Mo interface in thin-film solar cells.

The Cu(In,Ga)(S,Se)(2)Mo interface in thin-film solar cells has been investigated by surface-sensitive photoelectron spectroscopy, bulk-sensitive x-ray emission spectroscopy, and atomic force microscopy. It is possible to access this deeply buried interface by using a suitable lift-off technique, which allows us to investigate the back side of the absorber layer as well as the front side of the Mo back contact. We find a layer of Mo(S,Se)(2) on the surface of the Mo back contact and a copper-poor stoichiometry at the back side of the Cu(In,Ga)(S,Se)(2) absorber. Furthermore, we observe that the Na content at the Cu(In,Ga)(S,Se)(2)Mo interface as well as at the inner grain boundaries in the back contact region is significantly lower than at the absorber front surface.

YY1 binding within the human HSD3B2 gene intron 1 is required for maximal basal promoter activity: identification of YY1 as the 3beta1-A factor.

The oxidation and isomerization of 3beta-hydroxy-5-ene steroids into keto-4-ene steroids, a pivotal step in the synthesis of all hormonal steroids, is catalyzed by several isoforms of 3beta-hydroxysteroid dehydrogenase. In humans, two highly homologous isoforms exist, type I expressed by the HSD3B1 gene in peripheral tissues, and type II expressed by the HSD3B2 gene in steroidogenic organs. Previously, it was shown that the HSD3B1 gene 3beta1-A element, encompassing 24 nucleotides of intron 1 not perfectly conserved between the two genes and overlapping with a conserved TG box, contributes to maximal basal promoter activity by binding the ubiquitous and unidentified 3beta1-A transcription factor. In this study for the first time we report that similarly, the HSD3B2 gene intron 1 is required for maximal basal promoter activity in reporter gene analyses, as lack of intron 1 results in a 4- to 10-fold reduction in promoter activity. Mutational analysis in gel shift assays revealed that the 3beta1-A factor binds both the HSD3B2 and HSD3B1 gene intron 1 by requiring only seven nucleotides of a conserved segment within the 3beta1-A element. By competition analysis and use of anti-YY1 antibody in both gel shift and Western blot experiments, we identified the 3beta1-A protein as the ubiquitous transcription factor YY1. In addition, we have characterized another similar YY1 binding site differently located with respect to the 3beta1-A element in both genes. Deletion and mutational analysis in transient transfections experiments revealed that contrarily to as previously shown for the HSD3B1 gene, lack of YY1 binding to the type II 3beta1-A element only results in a marginal reduction of basal promoter activity. Instead, YY1 binding to the second site, placed 35 bp downstream from the 3beta1-A element, strongly activates the HSD3B2 gene basal promoter activity, as preventing YY1 binding to this region caused a 50% decrease of basal transcription. Complete abrogation of YY1 binding within type II intron 1 resulted in a gene reporter activity identical to a reporter construct lacking the whole intron 1. These results designate YY1 as the factor responsible for the intron 1-mediated boost of the HSD3B2 gene basal promoter activity. Similarities and dissimilarities between YY1 binding within the HSD3B1 and HSD3B2 gene intron 1 are discussed involving the conserved intron 1 TG box, that suggests different mechanisms are implicated in the YY1-mediated stimulation of these two genes basal promoter activity.

Polymorphic markers in the SRD5A2 gene and prostate cancer risk: a population-based case-control study.

It has been suggested that the activity of the steroid 5alpha-reductase type II enzyme (encoded by the SRD5A2 gene) may be associated with prostate cancer risk and that population differences in this enzyme's activity may account for part of the substantial racial/ethnic disparity in prostate cancer risk. To provide etiological clues, we evaluated the relationships of four polymorphic markers in the SRD5A2 gene, specifically, A49T (a substitution of threonine for alanine at codon 49), V89L (a substitution of leucine for valine at codon 89), R227Q (a substitution of glutamine for arginine at codon 227), and a (TA)n dinucleotide repeat, with prostate cancer risk in a population-based case-control study in China, a population with the lowest reported prostate cancer incidence rate in the world. Genotypes of these four markers were determined from genomic DNA of 191 incident cases of prostate cancer and 304 healthy controls using PCR-based assays, and serum androgen levels were measured in relation to these genotypes. All study subjects had the wild-type AA genotype of the A49T marker, and 99% had the RR genotype of the R227Q marker. For the V89L marker, prevalences of the LL, VV, and VL genotypes among controls were 35%, 21%, and 45%, respectively. Compared with men with the VV genotype, those with the LL genotype had a statistically nonsignificant 12% reduced risk (odds ratio = 0.88, 95% confidence interval, 0.53-1.47). In addition, men with the LL genotype had significantly higher serum levels of testosterone and significantly lower serum levels of 5alpha-androstane-3alpha,17beta-diol glucuronide than men with other genotypes. Men heterozygous for the (TA)0 allele of the (TA)n marker had a modest, statistically nonsignificant risk reduction (odds ratio = 0.67; 95% confidence interval, 0.39-1.12) compared with men homozygous for the (TA)0 allele, along with significantly higher serum dihydrotestosterone levels. The observed V89L genotype prevalences and the association between V89L genotypes and serum androgen levels support the hypothesis that genotypes associated with lower levels of 5alpha-reductase activity are more common in low-risk populations. Although we found no statistically significant associations of these SRD5A2 polymorphisms with prostate cancer risk, a small effect of these markers cannot be ruled out because of the rarity of certain marker genotypes. Larger studies are needed to further clarify the role of these markers and to elucidate whether genetic diversity of the SRD5A2 gene, alone or in combination with other susceptibility genes, can help explain the large racial/ethnic differences in prostate cancer risk.

Pharmacogenetics of human androgens and prostatic diseases.

Prostate cancer (PCa) and benign prostatic hypertrophy (BPH) are two common and growing public health problems in the Western world. We review here the recent biochemical and pharmacogenetic literature related to these two prostatic disorders. We focus first on constitutional ('germline') single nucleotide polymorphism (SNPs) at the steroid 5 alpha-reductase (SRD5A2) locus, which encodes the human prostatic (or Type II) steroid 5 alpha-reductase enzyme. The investigations reviewed point to several uses of personalised medicine at the SRD5A2 locus. In addition, we report on recent identification of somatic pharmacogenetic alterations at the androgen receptor (AR) locus, which encodes the human androgen receptor, suggesting that this also may be a fruitful field of investigation, with important clinical applications. Pharmacogenomic investigation of constitutional and somatic DNA changes in human genes predisposing to cancer may lead to significant advances in chemoprevention, presymptomatic diagnosis and improved treatment of PCa.

A genetic factor for age-related cataract: identification and characterization of a novel galactokinase variant, "Osaka," in Asians.

Galactokinase (GALK) deficiency is an autosomal recessive disorder characterized by hypergalactosemia and cataract formation. Through mass screening of newborn infants, we identified a novel and prevalent GALK variant (designated here as the "Osaka" variant) associated with an A198V mutation in three infants with mild GALK deficiency. GALK activity and the amount of immunoreactive protein in the mutant were both 20% of normal construct in expression analysis. The K(m) values for galactose and ATP-Mg(2+) in erythrocytes with homozygous A198V were similar to those of the healthy adult control subjects. A population study for A198V revealed prevalences of 4.1% in Japanese and 2.8% in Koreans, lower incidence in Taiwanese and Chinese, no incidence in blacks and whites from the United States, and a significantly high frequency (7.8%; P < .023) in Japanese individuals with bilateral cataract. This variant probably originated in Japanese and Korean ancestors and is one of the genetic factors that causes cataract in elderly individuals.

Multiplex automated primer extension analysis: simultaneous genotyping of several polymorphisms.

Accurate and fast genotyping of single nucleotide polymorphisms (SNPs) is of significant scientific importance for linkage and association studies. We report here an automated fluorescent method we call multiplex automated primer extension analysis (MAPA) that can accurately genotype multiple known SNPs simultaneously. This is achieved by substantially improving a commercially available protocol (SNaPshot). This protocol relies on the extension of a primer that ends one nucleotide 5'of a given SNP with fluorescent dideoxy-NTPs (minisequencing), followed by analysis on an ABI PRisMS 377 Semi-Automated DNA Sequencer Our modification works by multiplexing the initial reaction that produces the DNA template for primer extension and/or multiplexing several primers (corresponding to several SNPs) in the same primer extension reaction. Then, we run each multiplexed reaction on a single gel lane. We demonstrate that MAPA can be used to genotype up to four SNPs simultaneously, even in compound heterozygote samples, with complete accuracy (based on concordance with sequencing results). We also show that primer design, unlike the DNA template purification method, can significantly affect genotyping accuracy, and we suggest useful guidelines for quick optimization.

Molecular basis of disorders of human galactose metabolism: past, present, and future.

Molecular cloning and characterization of all three human galactose-metabolic genes have led to the identification of a number of mutations which result in three forms of galactosemia which are caused by kinase (GALK), transferase (GALT), or epimerase (GALE) deficiency. We review here recent developments in the molecular characterization of all three disorders of human galactose metabolism. Recent progress in the biochemical and/or structural analyses of the GALT and GALE proteins has complemented human mutational studies. Interestingly, genotype/phenotype correlations have been modest as in some other Mendelian disorders. We discuss possible reasons for this apparent paradox. Finally, we note the panethnic nature of galactosemia and suggest a hypothesis for it.

Prostatic steroid 5 alpha-reductase, an androgen metabolic gene.

Prostate cancer risk is highest in African Americans, lowest in Asians, and intermediate in Caucasians and Latinos. The data clearly suggest that environmental and genetic factors are involved. Investigation of the genetic factors suggests that allelic variation in the SRD5A2 gene is partially responsible for the striking racial and ethnic variations in risk.

Biochemical and pharmacogenetic dissection of human steroid 5 alpha-reductase type II.

Human prostatic steroid 5alpha-reductase, encoded by the SRD5A2 gene on chromosome band 2p23, catalyses the irreversible conversion of testosterone to dihydrotestosterone (DHT), the most active androgen in the prostate, with NADPH as its cofactor. This enzyme has never been purified but a number of competitive inhibitors have been developed for this enzyme since increased steroid 5alpha-reductase activity may cause benign prostatic hypertrophy and prostate cancer. We report here the detailed biochemical and pharmacogenetic dissection of the human enzyme by analysing 10 missense substitutions and three double mutants which are all naturally found in humans. Nine of these 13 mutants reduce activity (measured as Vmax) by 20% or more, three increase steroid 5alpha-reductase by more than 15% and one results in essentially unaltered kinetic properties suggesting that it is a truly neutral ('polymorphic') amino acid substitution. Substantial pharmacogenetic variation among the mutants was also observed when three competitive inhibitors, finasteride, GG745 (dutasteride) and PNU157706, were investigated. Our studies not only define the substrate and cofactor binding sites of human steroid 5alpha-reductase, but also have significant consequences for the pharmacological usage of steroid 5alpha-reductase inhibitors in human patients treated for prostatic conditions.

Evidence for an association between the SRD5A2 (type II steroid 5 alpha-reductase) locus and prostate cancer in Italian patients.

We have investigated the contributions of three polymorphic markers in the SRD5A2 gene to prostate cancer in a group of Italian patients. We have genotyped cases and controls for a polymorphic (TA)n dinucleotide repeat and two functional substitutions, A49T and V89L, substituting respectively alanine with threonine at codon 49, and valine to leucine at codon 89. We found a substantially increased but not significant risk associated with the 49T mutation and a reduction of risk for the V89L substitution. In conclusion, we report on preliminary evidence for both increased and decreased risk associated with separate markers at this locus.

Atmospheric temperature profiling in the presence of clouds with a pure rotational Raman lidar by use of an interference-filter-based polychromator.

A lidar polychromator design for the measurement of atmospheric temperature profiles in the presence of clouds with the rotational Raman method is presented. The design utilizes multicavity interference filters mounted sequentially at small angles of incidence. Characteristics of this design are high signal efficiency and adjustable center wavelengths of the filters combined with a stable and relatively simple experimental setup. High suppression of the elastic backscatter signal in the rotational Raman detection channels allows temperature measurements independent of the presence of thin clouds or aerosol layers; no influence of particle scattering on the lidar temperature profile was observed in clouds with a backscatter ratio of at least 45. The minimum integration time needed for temperature profiling with a statistical temperature error of +/-1 K at, e.g., 20-km height and 960-m height resolution is 1.5 h.

Lidar inelastic multiple-scattering parameters of cirrus particle ensembles determined with geometrical-optics crystal phase functions.

Multiple-scattering correction factors for cirrus particle extinction coefficients measured with Raman and high spectral resolution lidars are calculated with a radiative-transfer model. Cirrus particle-ensemble phase functions are computed from single-crystal phase functions derived in a geometrical-optics approximation. Seven crystal types are considered. In cirrus clouds with height-independent particle extinction coefficients the general pattern of the multiple-scattering parameters has a steep onset at cloud base with values of 0.5-0.7 followed by a gradual and monotonic decrease to 0.1-0.2 at cloud top. The larger the scattering particles are, the more gradual is the rate of decrease. Multiple-scattering parameters of complex crystals and of imperfect hexagonal columns and plates can be well approximated by those of projected-area equivalent ice spheres, whereas perfect hexagonal crystals show values as much as 70% higher than those of spheres. The dependencies of the multiple-scattering parameters on cirrus particle spectrum, base height, and geometric depth and on the lidar parameters laser wavelength and receiver field of view, are discussed, and a set of multiple-scattering parameter profiles for the correction of extinction measurements in homogeneous cirrus is provided.

Error analysis of Raman differential absorption lidar ozone measurements in ice clouds.

A formalism for the error treatment of lidar ozone measurements with the Raman differential absorption lidar technique is presented. In the presence of clouds wavelength-dependent multiple scattering and cloud-particle extinction are the main sources of systematic errors in ozone measurements and necessitate a correction of the measured ozone profiles. Model calculations are performed to describe the influence of cirrus and polar stratospheric clouds on the ozone. It is found that it is sufficient to account for cloud-particle scattering and Rayleigh scattering in and above the cloud; boundary-layer aerosols and the atmospheric column below the cloud can be neglected for the ozone correction. Furthermore, if the extinction coefficient of the cloud is ?0.1 km(-1), the effect in the cloud is proportional to the effective particle extinction and to a particle correction function determined in the limit of negligible molecular scattering. The particle correction function depends on the scattering behavior of the cloud particles, the cloud geometric structure, and the lidar system parameters. Because of the differential extinction of light that has undergone one or more small-angle scattering processes within the cloud, the cloud effect on ozone extends to altitudes above the cloud. The various influencing parameters imply that the particle-related ozone correction has to be calculated for each individual measurement. Examples of ozone measurements in cirrus clouds are discussed.