Recommendations for clinical interpretation of variants found in non-coding regions of the genome

Background The majority of clinical genetic testing focuses almost exclusively on regions of the genome that directly encode proteins. The important role of variants in non-coding regions in penetrant disease is, however, increasingly being demonstrated, and the use of whole genome sequencing in clinical diagnostic settings is rising across a large range of genetic disorders. Despite this, there is no existing guidance on how current guidelines designed primarily for variants in protein-coding regions should be adapted for variants identified in other genomic contexts. Methods We convened a panel of nine clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups. Results We discuss considerations specifically for variants in non-coding regions of the genome. We outline how to define candidate regulatory elements, highlight examples of mechanisms through which non-coding region variants can lead to penetrant monogenic disease, and outline how existing guidelines can be adapted for the interpretation of these variants. Conclusions These recommendations aim to increase the number and range of non-coding region variants that can be clinically interpreted, which, together with a compatible phenotype, can lead to new diagnoses and catalyse the discovery of novel disease mechanisms

Automated Atlas-Based Clustering of White Matter Fiber Tracts from DTMRI

A new framework is presented for clustering fiber tracts into anatomically known bundles. This work is motivated by medical applications in which variation analysis of known bundles of fiber tracts in the human brain is desired. To include the anatomical knowledge in the clustering, we invoke an atlas of fiber tracts, labeled by the number of bundles of interest. In this work, we construct such an atlas and use it to cluster all fiber tracts in the white matter. To build the atlas, we start with a set of labeled ROIs specified by an expert and extract the fiber tracts initiating from each ROI. Affine registration is used to project the extracted fiber tracts of each subject to the atlas, whereas their B-spline representation is used to efficiently compare them to the fiber tracts in the atlas and assign cluster labels. Expert visual inspection of the result confirms that the proposed method is very promising and efficient in clustering of the known bundles of fiber tracts

Antitumor effects of human interferon-alpha 2b secreted by recombinant bacillus Calmette-Guérin vaccine on bladder cancer cells*

Objective: Our objective was to construct a recombinant bacillus Calmette-Guérin vaccine (rBCG) that secretes human interferon-alpha 2b (IFNα-2b) and to study its immunogenicity and in vitro antitumor activity against human bladder cancer cell lines T24 and T5637. Methods: The signal sequence BCG Ag85B and the gene IFNα-2b were amplified from the genome of BCG and human peripheral blood, respectively, by polymerase chain reaction (PCR). The two genes were cloned in Escherichia coli-BCG shuttle-vector pMV261 to obtain a new recombinant plasmid pMV261-Ag85B-IFNα-2b. BCG was transformed with the recombinant plasmid by electroporation and designated rBCG-IFNα-2b. Mononuclear cells were isolated from human peripheral blood (PBMCs) and stimulated with rBCG-IFNα-2b or wild type BCG for 3 d, and then cultured with human bladder cancer cell lines T24 and T5637. Their cytotoxicities were measured by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Results: BCG was successfully transformed with the recombinant plasmid pMV261-Ag85B-IFNα-2b by electroporation and the recombinant BCG (rBCG-IFNα-2b) was capable of synthesizing and secreting cytokine IFNα-2b. PBMC proliferation was enhanced significantly by rBCG-IFNα-2b, and the cytotoxicity of PBMCs stimulated by rBCG-IFNα-2b to T24 and T5627 was significantly stronger in comparison to wild type BCG. Conclusions: A recombinant BCG, secreting human IFNα-2b (rBCG-IFNα-2b), was constructed successfully and was superior to control wild type BCG in inducing immune responses and enhancing cytotoxicity to human bladder cancer cell lines T24 and T5637. This suggests that rBCG-IFNα-2b could be a promising agent for bladder cancer patients in terms of possible reductions in both clinical dosage and side effects of BCG immunotherapy