Different Allele Frequency between Males and Females of a SNP of the Human Beta T Cell Receptor

We studied a single nucleotide polymorphism (SNP) located in the human beta T-cell receptor, in association studies and different allele frequency in the two sexes. Here we report a new series of 200 subjects (100 males and 100 females) in a restricted age range, 20-30 years. We found the following results: in males 57/100 (57%) were heterozygous, 26/100 (26%) were homozygous for the two digestion fragments and 17/100 (17%) were homozygous for the 603bp fragment. Females were 44/100 (44%) heterozygous, 24/100 (24%) homozygous for the two digestion fragments and 32/100 (32%) homozygous for the 603bp fragment. The allele frequency was significantly different according to chi square analysis (X square statistic (df = 2) = 7.412; p = 0.025). Our study shows that in females, but not in males , there is a significant increase of CC homozygous status and a proportionate decrease of heterozygous status compared with Hardy-Weinberg expectations. This study could explain the controversial results obtained by association studies between this SNP (rs1800907) and autoimmune diseases made in the ninety and uncorfirmed in more recent papers. Moreover it could be a starting point to search for other autosomical DNAs diffences between the two sexes

A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database

BACKGROUND: Many of the most popular pre-processing methods for Affymetrix expression arrays, such as RMA, gcRMA, and PLIER, simultaneously analyze data across a set of predetermined arrays to improve precision of the final measures of expression. One problem associated with these algorithms is that expression measurements for a particular sample are highly dependent on the set of samples used for normalization and results obtained by normalization with a different set may not be comparable. A related problem is that an organization producing and/or storing large amounts of data in a sequential fashion will need to either re-run the pre-processing algorithm every time an array is added or store them in batches that are pre-processed together. Furthermore, pre-processing of large numbers of arrays requires loading all the feature-level data into memory which is a difficult task even with modern computers. We utilize a scheme that produces all the information necessary for pre-processing using a very large training set that can be used for summarization of samples outside of the training set. All subsequent pre-processing tasks can be done on an individual array basis. We demonstrate the utility of this approach by defining a new version of the Robust Multi-chip Averaging (RMA) algorithm which we refer to as refRMA. RESULTS: We assess performance based on multiple sets of samples processed over HG U133A Affymetrix GeneChip(® )arrays. We show that the refRMA workflow, when used in conjunction with a large, biologically diverse training set, results in the same general characteristics as that of RMA in its classic form when comparing overall data structure, sample-to-sample correlation, and variation. Further, we demonstrate that the refRMA workflow and reference set can be robustly applied to naïve organ types and to benchmark data where its performance indicates respectable results. CONCLUSION: Our results indicate that a biologically diverse reference database can be used to train a model for estimating probe set intensities of exclusive test sets, while retaining the overall characteristics of the base algorithm. Although the results we present are specific for RMA, similar versions of other multi-array normalization and summarization schemes can be developed

T-cell receptor polymorphism in primary biliary cirrhosis

T-cell receptor (TCR) plays a key role in immune regulation and polymorphisms of its genes have been found in association with several autoimmune diseases. No data are available for primary biliary cirrhosis, an autoimmune liver disease the natural history of which is highly variable. We studied a TCR constant beta-2 chain polymorphism in 70 patients affected by primary biliary cirrhosis and in 70 healthy controls. The DNA chains of patients and controls were amplified by means of polymerase chain reaction using primers designed around a Bgl II polymorphic restriction site and digested for restriction fragment length polymorphism analysis. We found a slight increase of the heterozygous genotype in patients compared with controls (49 vs 40%), which became higher if only patients with early disease were considered (60 vs 40%). Heterozygous patients had less severe disease as indicated by a lower Mayo score (5.1 +/- 1.2 vs 5.7 +/- 1.2 in non-heterozygous). Our data suggest that TCR constant beta-2 polymorphism does not play a key role in modulating the multifactorial etiopathogenesis of primary biliary cirrhosis

Chromosome 7 monosomy and deletions in myeloproliferative diseases

We studied deletion and monosomy of chromosome 7 in 150 patients with myeloproliferative diseases. We found 8/150 patients with monosomy 7 by cytogenetics and 4/150 with deletions of the long arm of chromosome 7 by restriction fragment length polymorphism (RFLP) analysis performed with Southern and polymerase chain reaction. To overcome limitation of RFLP analysis, we restricted loss of heterozygosity study with microsatellites to 45 patients, observing deletion 7q31.1 in 7/45 patients. In all patients with molecular alterations the deletion was observed only in myeloid cells, while the monosomy was detected in both myeloid precursor and lymphocytes. This finding suggests a CD34-totipotent stem cell origin for the monosomy and a colony forming unit - granulocyte, erythrocyte, monocyte, megakaryocytes (CFU-GEMM) stem cell origin for the deletions

Towards a consensus-based classification of childhood arterial ischemic stroke.

Background and purposeThe implementation of uniform nomenclature and classification in adult arterial ischemic stroke (AIS) has been critical for defining outcomes and recurrence risks according to etiology and in developing risk-stratified treatments. In contrast, current classification and nomenclature in childhood AIS are often overlapping or contradictory. Our purpose was to develop a comprehensive consensus-based classification system for childhood AIS.MethodsUsing a modified-Delphi method, members of the International Pediatric Stroke Study (IPSS) developed the Childhood AIS Standardized Classification And Diagnostic Evaluation (CASCADE) criteria. Two groups of pediatric stroke specialists from the IPSS classified 7 test cases using 2 methods each: (1) classification typical of the individual clinician's current clinical practice; and (2) classification based on the CASCADE criteria. Group 1 underwent in-person training in the utilization of the CASCADE criteria. Group 2 classified the same cases via an online survey, including definitions but without training. Inter-rater reliability (IRR) was assessed via multi-rater unweighted κ-statistic.ResultsIn Group 1 (with training), IRR was improved using CASCADE criteria (κ=0.78, 95% CI=[0.49, 0.94]), compared with typical clinical practice (κ=0.40, 95% CI=[0.11, 0.60]). In Group 2 (without training), IRR was lower than among trained raters (κ=0.61, 95% CI=[0.29, 0.77]), but higher than current practice (κ=0.23, 95% CI=[0.03, 0.36]).ConclusionsA new, consensus-based classification system for childhood AIS, the CASCADE criteria, can be used to classify cases with good IRR. These preliminary findings suggest that the CASCADE criteria may be particularity useful in the setting of prospective multicenter studies in childhood-onset AIS, where standardized training of investigators is feasible