No abstract

Nutrigenomics has the potential to tailor diets to optimize health, based on knowledge of key genetic polymorphisms. Identification of candidate genes is often based on a priori knowledge of disease processes. However, genome-wide association methods are not only validating previously identified genes and polymorphisms, but also revealing new gene-disease associations not anticipated from prior knowledge. In Crohn's disease (CD), such studies not only confirm the importance of caspase-activated recruitment domain 15 and major histocompatibility complex II molecules, but also reveal strong associations with the proinflammatory cytokine interleukin-23 receptor and autophagy-related 16-like gene. Genes identified to date in CD can be linked into two interrelated pathways: receptor-mediated cytokine induction or autophagocytosis. New genomic technologies need to be matched with innovative methodologies to characterize the likely impact of foods and to take the field to another dimension of value for human diet development and optimized health.

Myotonic dystrophy type 1 is an autosomal dominant neuromuscular disorder that is caused by the expansion of a CTG trinucleotide repeat in the DMPK gene. The confirmation of a clinical diagnosis of DM-1 usually involves PCR amplification of the CTG repeat-containing region and subsequent sizing of the amplification products in order to deduce the number of CTG repeats. In the case of repeat hyperexpansions, Southern blotting is also used; however, the latter has largely been superseded by triplet repeat-primed PCR (TP-PCR), which does not yield a CTG repeat number but nevertheless provides a means of stratifying patients regarding their disease severity. We report here a combination of forward and reverse TP-PCR primers that allows for the simple and effective scoring of both the size of smaller alleles and the presence or absence of expanded repeat sequences. In addition, the CTG repeat-containing TP-PCR forward primer can target both the DM-1 and Huntington disease genes, thereby streamlining the work flow for confirmation of clinical diagnoses in a diagnostic laboratory.

Crohn's disease (CD) is an Inflammatory Bowel Disease (IBD) that is characterised by destructive inflammation of the intestinal wall. Current methods for determining inflammation of the bowel are costly, time consuming and can cause discomfort to the patients. In order to address these problems, biomarker analysis of more accessible tissues is receiving increasing attention. Oxidative stress has been implicated in the promotion of inflammation. Allantoin has recently been reported as a biomarker for oxidative stress in human serum and urine. This paper investigates allantoin as a biomarker of inflammation in a mouse model of CD. Proton nuclear magnetic resonance ( 1 H NMR) spectroscopy was used to analyse allantoin in urine from the mdr1a -/-mouse which is a model of CD. The data show that the levels of allantoin are strongly correlated with histological injury scores of mouse colonic tissue samples. Allantoin appears to be a useful biomarker of gut inflammation, involving oxidative stress, in a mouse model of CD and may be a potential biomarker in human CD studies.

BackgroundApproximately 75% of clinically definite long QT syndrome (LQTS) cases are caused by mutations in the KCNQ1, KCNH2 and SCN5A genes. Of these mutations, a small proportion (3.2-9.2%) are predicted to affect splicing. These mutations present a particular challenge in ascribing pathogenicity.MethodsHere we report an analysis of the transcriptional consequences of two mutations, one in the KCNQ1 gene (c.781_782delinsTC) and one in the SCN5A gene (c.2437-5C>A), which are predicted to affect splicing. We isolated RNA from lymphocytes and used a directed PCR amplification strategy of cDNA to show mis-spliced transcripts in mutation-positive patients.ResultsThe loss of an exon in each mis-spliced transcript had no deduced effect on the translational reading frame. The clinical phenotype corresponded closely with genotypic status in family members carrying the KCNQ1 splice variant, but not in family members with the SCN5A splice variant. These results are put in the context of a literature review, where only 20% of all splice variants reported in the KCNQ1, KCNH2 and SCN5A gene entries in the HGMDPro 2015.4 database have been evaluated using transcriptional assays.ConclusionsPrediction programmes play a strong role in most diagnostic laboratories in classifying variants located at splice sites; however, transcriptional analysis should be considered critical to confirm mis-splicing. Critically, this study shows that genuine mis- splicing may not always imply clinical significance, and genotype/phenotype cosegregation remains important even when mis-splicing is confirmed.