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1.  A rigorous approach for selection of optimal variant sets for carrier screening with demonstration of clinical utility 
Carrier screening for certain diseases is recommended by major medical and Ashkenazi Jewish (AJ) societies. Most carrier screening panels test only for common, ethnic-specific variants. However, with formerly isolated ethnic groups becoming increasingly intermixed, this approach is becoming inadequate. Our objective was to develop a rigorous process to curate all variants, for relevant genes, into a database and then apply stringent clinical validity classification criteria to each in order to retain only those with clear evidence for pathogenicity. The resulting variant set, in conjunction with next-generation DNA sequencing (NGS), then affords the capability for an ethnically diverse, comprehensive, highly specific carrier-screening assay. The clinical utility of our approach was demonstrated by screening a pan-ethnic population of 22,864 individuals for Bloom syndrome carrier status using a BLM variant panel comprised of 50 pathogenic variants. In addition to carriers of the common AJ founder variant, we identified 57 carriers of other pathogenic BLM variants. All variants reported had previously been curated and their clinical validity documented, or were of a type that met our stringent, preassigned validity criteria. Thus, it was possible to confidently report an increased number of Bloom’s syndrome carriers compared to traditional, ethnicity-based screening, while not reducing the specificity of the screening due to reporting variants of unknown clinical significance.
doi:10.1002/mgg3.148
PMCID: PMC4521971  PMID: 26247052
BLM; bloom syndrome; carrier screening; next-generation DNA sequencing; recessive disorders; variant classification
2.  OpenHelix: bioinformatics education outside of a different box 
Briefings in Bioinformatics  2010;11(6):598-609.
The amount of biological data is increasing rapidly, and will continue to increase as new rapid technologies are developed. Professionals in every area of bioscience will have data management needs that require publicly available bioinformatics resources. Not all scientists desire a formal bioinformatics education but would benefit from more informal educational sources of learning. Effective bioinformatics education formats will address a broad range of scientific needs, will be aimed at a variety of user skill levels, and will be delivered in a number of different formats to address different learning styles. Informal sources of bioinformatics education that are effective are available, and will be explored in this review.
doi:10.1093/bib/bbq026
PMCID: PMC2984537  PMID: 20798181
bioinformatics education; training and learning; outreach; genomics; data management; computational biology resources
3.  Chronic treatment with Carvedilol improves ventricular function and reduces myocyte apoptosis in an animal model of heart failure 
BMC Physiology  2003;3:6.
Background
β-blocker treatment has emerged as an effective treatment modality for heart failure. Interestingly, β-blockers can activate both pro-apoptotic and anti-apoptotic pathways. Nevertheless, the mechanism for improved cardiac function seen with β-blocker treatment remains largely unknown. Carvedilol is a non-selective β-blocker with α-receptor blockade and antioxidant properties. We therefore studied the impact of the effects of carvedilol in an animal model of end-stage heart failure.
Results
To test whether chronic treatment with β-blockade decreases apoptosis, we treated myopathic turkeys with two dosages of carvedilol, 1 mg/kg (DCM1) and 20 mg/kg (DCM20), for four weeks and compared them to non-treated DCM animals (DCM0) and to control turkeys (CON). Echocardiographic measurements showed that non-treated DCM animals had a significantly lower fractional shortening (FS) when compared to CON (68.73 ± 1.37 vs. 18.76 ± 0.59%, p < 0.001). Both doses of carvedilol significantly improved FS (33.83 ± 10.11 and 27.73 ± 6.18% vs. 18.76 ± 0.59 % for untreated DCM, p < 0.001). DCM left ventricles were characterized by a higher percentage of apoptotic nuclei when compared to CON (5.64 ± 0.49 vs. 1.72 ± 0.12%, respectively p < 0.001). Both doses of carvedilol significantly reduced the number of apoptotic nuclei (2.32 ± 0.23% and 2.36 ± 0.26% 1 mg and 20 mg/kg respectively).
Conclusions
Carvedilol improves ventricular function. Furthermore, treatment with carvedilol decreased the incidence of apoptosis in cardiac myocytes from failing hearts at both doses. These data suggest that the inhibition of apoptosis with carvedilol may lead to improvement in ventricular function and may underlie a beneficial effect of β-blockade independent of heart rate lowering effects.
doi:10.1186/1472-6793-3-6
PMCID: PMC212709  PMID: 12873352
Heart failure; carvedilol myocyte; β-blocker

Results 1-3 (3)