Population Genetics Identifies Challenges in Analyzing Rare Variants

Geneticists have, for years, understood the nature of genome‐wide association studies using common genomic variants. Recently, however, focus has shifted to the analysis of rare variants. This presents potential problems for researchers, as rare variants do not always behave in the same way common variants do, sometimes rendering decades of solid intuition moot. In this paper, we present examples of the differences between common and rare variants. We show why one must be significantly more careful about the origin of rare variants, and how failing to do so can lead to highly inflated type I error. We then explain how to best avoid such concerns with careful understanding and study design. Additionally, we demonstrate that a seemingly low error rate in next‐generation sequencing can dramatically impact the false‐positive rate for rare variants. This is due to the fact that rare variants are, by definition, seen infrequently, making it hard to distinguish between errors and real variants. Compounding this problem is the fact that the proportion of errors is likely to get worse, not better, with increasing sample size. One cannot simply scale their way up in order to solve this problem. Understanding these potential pitfalls is a key step in successfully identifying true associations between rare variants and diseases.     

New stand magnifiers do not meet rated levels of performance

A new range of stand magnifiers has been released by the COIL company in the United Kingdom. Examination of these magnifiers reveals that they fail to deliver the rated magnifications labelled prominently on the appliances, as a result of the manufacturer's conformance with the requirements of the German DIN standard and the use of back vertex power (F'_v) rather than equivalent dioptric power (F_m) of the magnifier. In this study we provide information on the optometric parameters of these new stand magnifiers that will assist the more accurate specification of improvements in vision expected from their use.     

Poly(methyl methacrylate) synthetic grit formulations sustain the delivery of nicarbazin, a contraceptive agent, in pest waterfowl.

Sixty-three mallards were fed one of ten poly(methyl methacrylate) based synthetic grit formulations containing varying concentrations of a proposed wildlife contraceptive (nicarbazin), plasticizer (acetyl tributylcitrate) and/or cross-linking agent (1,4-butanediol diacrylate). Release characteristics of the contraceptive agent were monitored for the purpose of developing a contraceptive formulation for control of pest waterfowl in urban settings. The addition of plasticizer increased the erosion rate (t(1/2)=0.97-2.85 days), cross-linking the polymer matrix slightly decreased the erosion rate (t(1/2)=4.45-5.05 days) and increasing the concentration of the contraceptive agent increased the erosion rate (t(1/2)=3.3 and 9.9 days at 60% and 7.5% active ingredient, respectively). The larger and smaller grit pieces had longer half lives at 11.0 and 11.6 days, respectively while the mid sized grit had a half life of 4.95 days. Control grit had a half life of 12.7 days based on weight loss. Analysis of blood and feces for monitoring release from the grit and approximate indirect plasma levels of the active ingredient proved feasible.     

HLA-DR typing in identical twins with insulin-dependent diabetes: difference between concordant and discordant pairs

A total of 106 pairs of identical twins, of whom 56 were concordant and 50 discordant for insulin-dependent diabetes, were typed for HLA-DR. In both the concordant and discordant groups there was a high prevalence of the antigens DR3 and DR4, a low prevalence of DR5 and DR7, and a virtual absence of DR2. The heterozygous phenotype DR3,DR4 was more prevalent in concordant than discordant pairs. This was therefore the first demonstration of a genetic difference between concordant and discordant identical twin pairs. These findings suggest that possession of both DR3 and DR4 antigens confers a greater genetic predisposition to insulin-dependent diabetes than does the possession of either antigen alone.     

Papilliferous keratoameloblastoma

A case of papilliferous keratoameloblastoma is reported which is only the second ever documented. The patient was a 76-yr-old black woman with a large expansile multilocular radiolucency of the body, angle and ramus of the mandible. Histologically the lesion consisted of sheets of cystic follicles filled with necrotic debris and sometimes parakeratin. The vast majority of the follicles were lined by a papilliferous epithelium consisting of large rounded cells with centrally placed nuclei. True papillary projections with cores of connective tissue were also present. The remainder of the follicles were lined by a thin parakeratinising stratified squamous epithelium. Histological features characteristic of ameloblastoma were absent. Final classification of these lesions will have to await the reporting of further cases.     

Scintigraphic detection of occult hemorrhage in a patient receiving anticoagulants

The exact location of hemorrhage complicating anticoagulant therapy is sometimes difficult to establish. We present a case in which imaging with 99mTc-labeled red cells had a significant role in the diagnosis of soft-tissue bleeding in a paraplegic patient receiving long-term anticoagulation.     

Color Stability of Dry Earth Pigmented Maxillofacial Silicone A-2186 Subjected to Microwave Energy Exposure

PURPOSE: The purpose of this study was to measure spectrophotometrically the color stability of pigmented A-2186 silicone maxillofacial elastomer with 10% by volume of titanium white dry earth opacifier before and after exposure to microwave energy over a simulated 1.5-year period of microwave sterilization. Materials AND METHODS: A-2186 silicone elastomer opacified with titanium white dry earth pigment, pigmented with 5 cosmetic dry earth pigment colors [no pigment (control) group (Pc), red (Pr), yellow ochre (Py), burnt sienna (Po), and a mixture of Pr + Py + Po color group (P3)], was used in this study. Each of the 5 experimental groups consisted of 5 specimens. All specimens were placed in a 250 ml glass beaker filled with 150 ml of water (replenished for each microwave exposure). An exposure of 6 minutes was used 18 times (simulating 1.5 years of microwave sterilization with one 6 minute exposure monthly). Reflectance values were measured by spectrophotometer. Three- and two-way analyses of variance with repeated measures were performed for the color difference (DeltaE*) with the factors of group/color/months, and group/months, respectively. Means were compared by Tukey Honest Significant Difference (HSD) multiple range test calculated at the 0.05 level of significance using SPSS. RESULTS: The trained human eye can detect color changes (DeltaE*) greater than 1.0. Most DeltaE* values of the red pigment group at all intervals and the mixed pigment group at 15- and 18- month intervals increased significantly greater than 1.0 (p < 0.001) compared with the control group. Yellow and burnt sienna groups remained the most color stable over time with DeltaE* values below 0.35. CONCLUSIONS: Lack of color stability of red dry earth pigmented A-2186 silicone maxillofacial elastomers was clinically significant after 12-month exposure to microwave energy as compared with yellow, burnt sienna, and opacified A-2186 dry earth pigments.