The use of race, ethnicity and ancestry in human genetic research

Post-Human Genome Project progress has enabled a new wave of population genetic research, and intensified controversy over the use of race/ethnicity in this work. At the same time, the development of methods for inferring genetic ancestry offers more empirical means of assigning group labels. Here, we provide a systematic analysis of the use of race/ethnicity and ancestry in current genetic research. We base our analysis on key published recommendations for the use and reporting of race/ethnicity which advise that researchers: explain why the terms/categories were used and how they were measured, carefully define them, and apply them consistently. We studied 170 population genetic research articles from high impact journals, published 2008-2009. A comparative perspective was obtained by aligning study metrics with similar research from articles published 2001-2004. Our analysis indicates a marked improvement in compliance with some of the recommendations/guidelines for the use of race/ethnicity over time, while showing that important shortfalls still remain: no article using 'race', 'ethnicity' or 'ancestry' defined or discussed the meaning of these concepts in context; a third of articles still do not provide a rationale for their use, with those using 'ancestry' being the least likely to do so. Further, no article discussed potential socio-ethical implications of the reported research. As such, there remains a clear imperative for highlighting the importance of consistent and comprehensive reporting on human populations to the genetics/genomics community globally, to generate explicit guidelines for the uses of ancestry and genetic ancestry, and importantly, to ensure that guidelines are followed.     

Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology

Background

The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container.

Methods

In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server.

Results

The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server database. The internet platform was tested on PC Intel Core2 Duo T9600 2.8GHz 4GB RAM server with 768x576 pixel size, 1.28Mb tiff format images reffering to meningioma tumour (x400, Ki-67/MIB-1). The time consumption was as following: at analysis by CAMI, locally on a server – 3.5 seconds, at remote analysis – 26 seconds, from which 22 seconds were used for data transfer via internet connection. At jpg format image (102 Kb) the consumption time was reduced to 14 seconds.

Conclusions

The results have confirmed that designed remote platform can be useful for pathology image analysis. The time consumption is depended mainly on the image size and speed of the internet connections. The presented implementation can be used for many types of analysis at different staining, tissue, morphometry approaches, etc. The significant problem is the implementation of the JSP page in the multithread form, that can be used parallelly by many users. The presented platform for image analysis in pathology can be especially useful for small laboratory without its own image analysis system.

     

Frequency of lactase persistence genotype in a healthy Polish population

The majority of mammals are unable to digest lactose due to post-weaning deactivation of the LCT gene, which is responsible for encoding the enzyme lactase (i.e., adult-type hypolactasia). A substitution of C with T at position −13910 bp upstream of the LCT gene has been linked to the lactase persistence phenotype in European populations. We investigated the frequency of LCT-13910C>T polymorphism in 223 blood donors from central Poland. All samples were genotyped by polymerase chain reaction and direct sequencing. The LCT-13910 T allele (lactase persistence) was present in 51% of individuals sampled from the Polish population. We did not find any non-European variants associated with lactase persistence (LCT-13907C>G, LCT-13913T>C, LCT-13915T>G), or any new polymorphisms within the sequenced region. Allele frequencies obtained are in agreement with results from other countries and confirm the unique pattern of distribution of the LCT-13910C>T genotype in Europe.     

On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2

The Dnmt2 enzymes show strong amino acid sequence similarity with eukaryotic and prokaryotic DNA-(cytosine C5)-methyltransferases. Yet, Dnmt2 enzymes from several species were shown to methylate tRNA-Asp and had been proposed that eukaryotic DNA methyltransferases evolved from a Dnmt2-like tRNA methyltransferase ancestor [Goll et al., 2006, Science, 311, 395-8]. It was the aim of this study to investigate if this hypothesis could be supported by evidence from sequence alignments. We present phylogenetic analyses based on sequence alignments of the methyltransferase catalytic domains of more than 2300 eukaryotic and prokaryotic DNA-(cytosine C5)-methyltransferases and analyzed the distribution of DNA methyltransferases in eukaryotic species. The Dnmt2 homologues were reliably identified by an additional conserved CFT motif next to motif IX. All DNA methyltransferases and Dnmt2 enzymes were clearly separated from other RNA-(cytosine-C5)-methyltransferases. Our sequence alignments and phylogenetic analyses indicate that the last universal eukaryotic ancestor contained at least one member of the Dnmt1, Dnmt2 and Dnmt3 families of enzymes and additional RNA methyltransferases. The similarity of Dnmt2 enzymes with DNA methyltransferases and absence of similarity with RNA methyltransferases combined with their strong RNA methylation activity suggest that the ancestor of Dnmt2 was a DNA methyltransferase and an early Dnmt2 enzyme changed its substrate preference to tRNA. There is no phylogenetic evidence that Dnmt2 was the precursor of eukaryotic Dnmts. Most likely, the eukaryotic Dnmt1 and Dnmt3 families of DNA methyltransferases had an independent origin in the prokaryotic DNA methyltransferase sequence space.     

Design and analysis of drug combination experiments

In this paper we present and discuss a novel, simple and easy to implement parametric modeling approach to assess synergy. An extended three parameter log-logistic model is used to analyse the data and calculate confidence intervals of the interaction indices. In addition the model corrects for the bias due to plate-location effects. The analysis is performed with PROC NLMIXED and SAS-code is provided. The approach is illustrated using data coming from an oncology study in which the inhibition effect of a combination of two compounds is studied using 96-well plates and a fixed-ratio design.     

Duration of alpha 1-antichymotrypsin gene activation by interleukin-1 is determined by efficiency of inhibitor of nuclear factor kappa B alpha resynthesis in primary human astrocytes

Expression of alpha1antichymotrypsin (ACT) is significantly activated by interleukin-1 (IL-1) in human astrocytes; however, it is barely affected by IL-1 in hepatocytes. This tissue-specific regulation depends upon an enhancer that contains both nuclear factor kappaB (NF-kappaB) and activating protein 1 (AP-1) elements, and is also observed for an NF-kappaB reporter but not for an AP-1 reporter. We found efficient activation of NF-kappaB binding in both cell types; however, this binding was persistent in glial cells and only transient in hepatocytes. IL-1-activated NF-kappaB complexes consisted of p65 and p50, with p65 transiently phosphorylated on serine 536 in glial cells whereas more persistently in hepatic cells. Overexpression of p65 or constitutively active IKKbeta (inhibitor of NF-kappaB kinase beta) resulted in an efficient activation of the ACT reporter in hepatic cells, indicating that a specific mechanism exists in these cells terminating IL-1 signaling. IL-1 effectively induced the degradation of inhibitor of NF-kappaBalpha (IkBalpha) and IkBepsilon in both cell types but IkBbeta was not affected. However, IkBalpha was resynthesized much more rapidly in hepatic cells in comparison to glial cells. In addition, the initial levels of IkBalpha were much lower in glial cells. We propose that the tissue-specific regulation of the ACT gene expression by IL-1 is determined by different efficiencies of IkBalpha resynthesis in glial and hepatic cells.     

Astrocyte- and hepatocyte-specific expression of genes from the distal serpin subcluster at 14q32.1 associates with tissue-specific chromatin structures

The distal serpin subcluster contains genes encoding alpha1-antichymotrypsin (ACT), protein C inhibitor (PCI), kallistatin (KAL) and the KAL-like protein, which are expressed in hepatocytes, but only the act gene is expressed in astrocytes. We show here that the tissue-specific expression of these genes associates with astrocyte- and hepatocyte-specific chromatin structures. In hepatocytes, we identified 12 Dnase I-hypersensitive sites (DHSs) that were distributed throughout the entire subcluster, with the promoters of expressed genes accessible to restriction enzyme digestion. In astrocytes, only six DHSs were located exclusively in the 5' flanking region of the act gene, with its promoter also accessible to restriction enzyme digestion. The acetylation of histone H3 and H4 was found throughout the subcluster in both cell types but this acetylation did not correlate with the expression pattern of these serpin genes. Analysis of histone modifications at the promoters of the act and pci genes revealed that methylation of histone H3 on lysine 4 correlated with their expression pattern in both cell types. In addition, inhibition of methyltransferase activity resulted in suppression of ACT and PCI mRNA expression. We propose that lysine 4 methylation of histone H3 correlates with the tissue-specific expression pattern of these serpin genes.     

17beta-estradiol regulation of human growth hormone (hGH), insulin-like growth factor-I (IGF-I) and insulin-like growth factor binding protein-3 (IGFBP-3) axis in hypoestrogenic, hypergonadotropic women

OBJECTIVE: Ovarian hormonal function may be as important contributing factor to hGH-IGF-I-IGFBP-3 axis as age. AIM: To examine plasma hGH, IGF-1 and IGFBP-3 levels in women with premature ovarian failure compared to healthy normal controls and postmenopausal ones. PATIENTS: Group A-15 women with premature ovarian failure (POF) (mean: age 38.9+/-5.2 years, FSH 101.4+/-29.0 IU/l; 17beta-estradiol 22.5+/-14.6 ng/l). Group B consisted of 15 menopausal women (mean: age 54.7+/-2.7 years; FSH 81.9+/-32.1 IU/l; 17beta-estradiol 17.1+/- 8.0 ng/l). Group C - controls - 15 normally menstruating women (mean: age 37.1+/-9.0 years; FSH 6.2+/-1.0 IU/l; 17beta-estradiol 144.8+/-117.1 ng/l). METHODS: Body mass and BMI were measured. Basic fasting plasma hGH, IGF-I, IGFBP-3, insulin, testosterone and LH as well as prolactin (PRL), FSH and estradiol were assessed by RIA kits. Statistical analysis. Shapiro-Wilk test, Mann-Whitney u-test, Spearman rang correlation coefficient, stepwise multiple regression. RESULTS: Mean serum IGF-I level was the lowest (p<0.005) in group B (172.0+/-54.6 microg/l) and the highest in group C (273.6+/-109.0 microg/l). The mean plasma IGF-I level in group A was similar (NS) (208.3+/-66.5 microg/l) to that found in group B and lower (p<0.02) compared with that in group C. The lowest (p<0.005) serum IGFBP-3 level was found in group B (3.1+/-0.7 microg/l) compared to group C (4.4+/-0.3 microg/l). The mean plasma IGFBP-3 level (3.1+/-1.0 microg/l) in group A was lower than in group C (p<0.005) but identical as in group B. No statistically significant differences between groups were observed in mean hGH levels. Women in group A and C were younger (p<0.001) than those in group B. The lowest mean estradiol level was found in groups A and B. The highest was in group C (p<0.001). Mean plasma LH and FSH levels were higher (p<0.001) in groups A and B vs group C. In group C there were links between IGF-I and age (r=-0.60; p=0.014) The IGF-I/age relation disappeared in the groups A and B (rA=-0.26; rB=0.10; NS). The same regards IGFBP-3/ age link (rA=-0.44, NS; rB=0,31;NS). Estradiol level was related to hGH levels in group C (r=-0.54; p<0.05). In none of groups hGH/IGF-1 as well as IGFBP-3/hGH relations were found. Prolactin accounted for 69% of the variance in IGF-I level in the group B (p=0.003) and for 24% in group A (NS). Testosterone accounted for 88% (p=0.004) of the variance in IGF-I level in group B and IGFBP-3 was responsible for 86% (p=0.038) of the variance in IGF-I level in group C. Again IGFBP-3 was responsible for 47% (p=0.023) in group A and for 49% (p=0.04) in group B of the hGH variance. CONCLUSIONS: 17b-estradiol may be as important contributor to insulin-like growth factor-I (IGF-I) plasma level as age in hypoestrogenic, hypogonadotropic women.     

Influence of hormonal therapy on growth rate and bone age progression in patients with Turner syndrome

The efficacy of growth promoting hormonal therapy is assessed on the basis of growth rate as well as bone age progression until the patients reach their final height. The aim of our study was to investigate which hormonal therapy influences in most appropriate way height velocity and bone age progression in patients with Turner syndrome (TS) and to establish the optimal age to initiate treatment. Patients were divided into five groups according to the type of hormonal therapy: 1) 11 patients treated with growth hormone (GH); 2) 18 patients treated with GH and oxandrolone (Ox); 3) 7 patients treated with GH, Ox and estrogens (E); 4) 6 patients treated with OX and E; and the control group (Group 0) of 62 untreated patients. The patients height was expressed in hSDS calculated on the basis of growth chart for patients with TS (hSDST). Bone age (BA) was assessed according to Greulich-Pyle method. Results: The mean values of deltahSDST in the first and second year of therapy in individual groups were significantly different. The difference resulted from significantly higher value of deltahSDST in group treated with GH+Ox. Analysis of regression between deltaCA and deltaBA revealed regression coefficients alpha of equation deltaBA= alpha x deltaCA: in group 0: 0.817; group GH: 1.233; group GH+Ox: 0.861; group GH+Ox+E: 0.997; group Ox+E: 1.141. There was significant difference between regression coefficients in studied groups. It resulted from significantly higher value of alpha in group treated with GH than in a group 0 and treated with GH+Ox. Only group treated with GH+Ox showed a significant negative correlation between baseline CA and deltaBA during the therapy. We can conclude that all regimens of hormonal therapy improved height in our patients but the highest increase of height during the therapy and the smallest progression of the bone age in the same time were observed in patients treated with GH+Ox.