Whole-exome sequencing (WES) has been widely used for analysis of human genetic diseases, but its value for the pharmacogenomic profiling of individuals is not well studied. Initially, we performed an in-depth evaluation of the accuracy of WES variant calling in the pharmacogenes CYP2D6 and CYP2C19 by comparison with MiSeq® amplicon sequencing data (n = 36). This analysis revealed that the concordance rate between WES and MiSeq® was high, achieving 99.60% for variants that were called without exceeding the truth-sensitivity threshold (99%), defined during variant quality score recalibration (VQSR). Beyond this threshold, the proportion of discordant calls increased markedly. Subsequently, we expanded our findings beyond CYP2D6 and CYP2C19 to include more genes genotyped by the iPLEX® ADME PGx Panel in the subset of twelve samples. WES performed well, agreeing with the genotyping panel in approximately 99% of the selected pass-filter variant calls. Overall, our results have demonstrated WES to be a promising approach for pharmacogenomic profiling, with an estimated error rate of lower than 1%. Quality filters, particularly VQSR, are important for reducing the number of false variants. Future studies may benefit from examining the role of WES in the clinical setting for guiding drug therapy.

Distinction of basal and squamous cell carcinomas of the skin can be readily achieved with routine immunohistochemistry using Ber EP4 and EMA. Identification of basosquamous carcinoma is also facilitated with this method.

Proteases of Porphyromonas gingivalis are considered to be important virulence determinants of this periodontal bacterium. Several biochemical isoforms of arginine-specific proteases are derived from rgpA and rgpB. HRgpA is a heterodimer composed of the catalytic α chain noncovalently associated with a β adhesin chain derived from the C terminus of the initial full-length translation product. The catalytic α chain is also present as a monomer (RgpA) either free in solution or associated with membranes.rgpB lacks the coding region for the adhesin domain present in rgpA and yields only monomeric forms (RgpB) which again may be soluble or membrane associated. In this study, the catalytic chains of this unusual group of enzymes are shown to be differentially modified by the posttranslational addition of carbohydrate. A monoclonal antibody (MAb 1B5) raised to the monomeric RgpA did not react with the corresponding recombinant RgpA α chain expressed inEscherichia coli but was immunoreactive with P. gingivalis lipopolysaccharide. MAb 1B5 also reacted with the membrane-associated forms of RgpA and RgpB but not with the heterodimeric HRgpA and the soluble form of RgpB. RgpA treated with denaturants was capable of binding to MAb 1B5 whereas treatment with periodate abolished this binding, suggesting the presence of carbohydrate residues within the epitope. Chemical deglycosylation abolished immunoreactivity with MAb 1B5 and caused a ∼30% reduction in the size of the membrane-associated enzymes. Monosaccharide analysis of HRgpA and RgpA demonstrated 2.1 and 14.4%, respectively, carbohydrate by weight of protein. Furthermore, distinct differences were detected in their monosaccharide compositions, indicating that these protease isoforms are modified not only to different extents but also with different sugars. The variable nature of these additions may have a significant effect on the structure, stability, and immune recognition of these protease glycoproteins.

Objective. To determine rates of human papillomavirus (HPV) infections, abnormal cervical smears, and squamous intraepithelial lesions (SIL) among women with systemic lupus erythematosus (SLE). Methods. We investigated 30 women with SLE, 67 with abnormal smears from colposcopy clinics, and 15 community subjects with normal smears. Polymerase chain reaction results for viral DNA and HPV-16 sequencing data were correlated to cytology and colposcopic findings. . SLE patients were also more likely to be HPV-16 DNA positive than colposcopy patients (P < 0.05). SLE patients with a high HPV-16 viral load more frequently had SIL (n ‫؍‬ 6) than those with a low HPV-16 viral load (n ‫؍‬ 1; P < 0.05). HPV and HPV-16 DNA positivity were not associated with previous or current drug therapy for SLE patients. All HPV-16 DNA sequences from 6 SLE and 5 colposcopy patients were the European-type variant. Eighteen (60%) SLE patients had a previous or current cervical abnormality. At the time of study, 5 (17%) SLE patients had an abnormal cervical smear and 8 (27%) had SIL. For those diagnosed with SLE for >10 years, the rate of SIL was 44% lower than those with SLE for <5 years (odds ratio 0.56, 95% confidence interval 0.1-3.5). Conclusion. UK women with a recent SLE diagnosis had disturbingly elevated levels of HPV infections (particularly with European HPV-16 variants at a high viral load), abnormal cervical cytology, and SIL. KEY WORDS. Systemic lupus erythematosus; Human papillomavirus infection; Cervical squamous intraepithelial lesions.