Germ-line and somatic DICER1 mutations in pineoblastoma.
Acta Neuropathol. 2014 Jul 15;
Authors: de Kock L, Sabbaghian N, Druker H, Weber E, Hamel N, Miller S, Choong CS, Gottardo NG, Kees UR, Rednam SP, van Hest LP, Jongmans MC, Jhangiani S, Lupski JR, Zacharin M, Bouron-Dal Soglio D, Huang A, Priest JR, Perry A, Mueller S, Albrecht S, Malkin D, Grundy RG, Foulkes WD
Germ-line RB-1 mutations predispose to pineoblastoma (PinB), but other predisposing genetic factors are not well established. We recently identified a germ-line DICER1 mutation in a child with a PinB. This was accompanied by loss of heterozygosity (LOH) of the wild-type allele within the tumour. We set out to establish the prevalence of DICER1 mutations in an opportunistically ascertained series of PinBs. Twenty-one PinB cases were studied: Eighteen cases had not undergone previous testing for DICER1 mutations; three patients were known carriers of germ-line DICER1 mutations. The eighteen PinBs were sequenced by Sanger and/or Fluidigm-based next-generation sequencing to identify DICER1 mutations in blood gDNA and/or tumour gDNA. Testing for somatic DICER1 mutations was also conducted on one case with a known germ-line DICER1 mutation. From the eighteen PinBs, we identified four deleterious DICER1 mutations, three of which were germ line in origin, and one for which a germ line versus somatic origin could not be determined; in all four, the second allele was also inactivated leading to complete loss of DICER1 protein. No somatic DICER1 RNase IIIb mutations were identified. One PinB arising in a germ-line DICER1 mutation carrier was found to have LOH. This study suggests that germ-line DICER1 mutations make a clinically significant contribution to PinB, establishing DICER1 as an important susceptibility gene for PinB and demonstrates PinB to be a manifestation of a germ-line DICER1 mutation. The means by which the second allele is inactivated may differ from other DICER1-related tumours.
PMID: 25022261 [PubMed - as supplied by publisher]
Clostridium difficile infection in diabetes.
Diabetes Res Clin Pract. 2014 Jun 21;
Authors: Qu HQ, Jiang ZD
Diabetes-related hospitalization and hospital utilization is a serious challenge to the health care system, a situation which may be further aggravated by nosocomial Clostridium difficile (C. difficile) infection (CDI). Studies have demonstrated that diabetes increases the risk of recurrent CDI with OR (95% CI) 2.99 (1.88, 4.76). C. difficile is a gram-positive, spore-forming anaerobic bacterium which is widely distributed in the environment. Up to 7% of healthy adults and up to 45% of infants may have asymptomatic intestinal carriage of C. difficile. A large number of strains of C. difficile have been identified. A number of PCR or sequence-based molecular typing methods are available for typing C. difficile isolates. C. difficile virulence evolved independently in the highly epidemic lineages, associated with the expression of toxin genes and other virulence factors. This article briefly reviews recent progresses in the bateriology of C. difficile and highlights the limited knowledge of potential mechanisms for the increased risk of CDI in diabetes which warrants further research.
PMID: 25015315 [PubMed - as supplied by publisher]
How important are rare variants in common disease?
Brief Funct Genomics. 2014 Jul 8;
Authors: Saint Pierre A, Génin E
Genome-wide association studies have uncovered hundreds of common genetic variants involved in complex diseases. However, for most complex diseases, these common genetic variants only marginally contribute to disease susceptibility. It is now argued that rare variants located in different genes could in fact play a more important role in disease susceptibility than common variants. These rare genetic variants were not captured by genome-wide association studies using single nucleotide polymorphism-chips but with the advent of next-generation sequencing technologies, they have become detectable. It is now possible to study their contribution to common disease by resequencing samples of cases and controls or by using new genotyping exome arrays that cover rare alleles. In this review, we address the question of the contribution of rare variants in common disease by taking the examples of different diseases for which some resequencing studies have already been performed, and by summarizing the results of simulation studies conducted so far to investigate the genetic architecture of complex traits in human. So far, empirical data have not allowed the exclusion of many models except the most extreme ones involving only a small number of rare variants with large effects contributing to complex disease. To unravel the genetic architecture of complex disease, case-control data will not be sufficient, and alternative study designs need to be proposed together with methodological developments.
PMID: 25005607 [PubMed - as supplied by publisher]
An effective method based on real time fluorescence quenching for single nucleotide polymorphism detection.
J Biotechnol. 2014 Jul 3;
Authors: Xu Y, Han S, Huang X, Zhuo S, Dai H, Li Z, Wang K, Liu J
In the Human Genome Project, the most common type of these variations is single nucleotide polymorphisms (SNPs). A large number of different SNP typing technologies have been developed in recent years. Enhancement and innovation for genotyping technologies are currently in progress. We described a rapid and effective method based on real time fluorescence quenching for SNP detection. The new method, Quenching-PCR, offering a single base extension method fully integrated with PCR which used a probe with quencher to eliminate fluorophor of the terminal base according to dideoxy sequencing method. In this platform, dideoxy sequencing reaction and obtaining values of real-time fluorescence occur simultaneously. The assay was validated by 106 DNA templates comparing with Sanger's sequencing and TaqMan assay. Compared with the results of DNA sequencing, the results of Quenching-PCR showed a high concordance rate of 93.40%, while the results of TaqMan platform showed a concordance rate of 92.45%, indicating that Quenching PCR and TaqMan assay were similar in accuracy. Therefore, Quenching PCR will be easily applicable and greatly accelerate the role of SNP detection in physiological processes of human health.
PMID: 24998766 [PubMed - as supplied by publisher]