High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach

Background

Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data.

Methods

In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads.

Results

Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found.

Conclusions

Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.

Importance of nonsynonymous OCA2 variants in human eye color prediction

Background

The color of the eyes is one of the most prominent phenotypes in humans and it is often used to describe the appearance of an individual. The intensity of pigmentation in the iris is strongly associated with one single‐nucleotide polymorphism (SNP), rs12913832:A>G that is located in the promotor region of OCA2 (OMIM #611409). Nevertheless, many eye colors cannot be explained by only considering rs12913832:A>G.

Methods

In this study, we searched for additional variants in OCA2 to explain human eye color by sequencing a 500 kbp region, encompassing OCA2 and its promotor region.

Results

We identified three nonsynonymous OCA2 variants as important for eye color, including rs1800407:G>A (p.Arg419Gln) and two variants, rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile), not previously described as important for eye color variation. It was shown that estimated haplotypes consisting of four variants (rs12913832:A>G, rs1800407:G>A (p.Arg419Gln), rs74653330:A>T (p.Ala481Thr), and rs121918166:G>A (p.Val443Ile)) explained 75.6% (adjusted R² = 0.76) of normal eye color variation, whereas rs12913832:A>G alone explained 68.8% (adjusted R² = 0.69). Moreover, rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile) had a measurable effect on quantitative skin color (P = 0.008).

Conclusion

Our data showed that rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile) have a measurable effect on normal pigmentation variation.

Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis

The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72 individuals using only 24 barcoded libraries.

Unilateral proliferative diabetic retinopathy and uveitis in the fellow eye: report of a case

We report the case of a young man with a 20-year history of insulin-dependent diabetes mellitus, proliferative diabetic retinopathy OD, and uveitis OS. None of the common reported causes contributing to this difference between eyes was present. No features of diabetic retinopathy appeared OS after a follow-up of 36 months. This is the first case, to our knowledge, in which uveitis appeared to be associated with an asymmetric presentation in diabetes.

Argon versus krypton panretinal photocoagulation side effects on the anterior segment

The modification of corneal sensitivity, accommodation, pupillary diameter and endothelial cell density after argon versus krypton panretinal photocoagulation were studied prospectively in 88 eyes of 64 diabetic patients with proliferative diabetic retinopathy, randomized for one of the two laser treatments. In both groups a marked internal ophthalmoplegia and reduction of corneal sensitivity occurred after laser photocoagulation. At no time, 2, 90 and 180 days after PRP, were these parameters significantly different. Endothelial cell loss was non significantly greater in the krypton group. The results indicated that the side effects commonly observed on the anterior segment after PRP are comparable using argon or krypton lasers.

Contact transscleral cyclophotocoagulation with Nd:YAG laser in uncontrolled glaucoma

To evaluate the effectiveness of contact delivery systems, we treated 23 eyes with uncontrolled intraocular pressure using a continuous wave Nd:YAG laser delivered by a fiber optic. With the fiber's tip perpendicular to the surface of the conjunctiva, 1.5 mm from the corneal limbus, we applied 16 laser spots of 2 J/second energy. Patients were followed for at least 6 months (mean, 8.6 +/- 2.4 months). The mean pressure decreased from a pretreatment value of 43.7 mm Hg to a posttreatment value of 24.7 mm Hg (P = 0.000). A total of 66.6% of the treated eyes achieved a pressure on last follow-up visit of 25 mm Hg or less. Pain decreased in all the patients treated (P less than .005). Complications were minimal.