Global Biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts.

Polygenic risk scores (PRSs) have been widely explored in precision medicine. However, few studies have thoroughly investigated their best practices in global populations across different diseases. We here utilized data from Global Biobank Meta-analysis Initiative (GBMI) to explore methodological considerations and PRS performance in 9 different biobanks for 14 disease endpoints. Specifically, we constructed PRSs using pruning and thresholding (P + T) and PRS-continuous shrinkage (CS). For both methods, using a European-based linkage disequilibrium (LD) reference panel resulted in comparable or higher prediction accuracy compared with several other non-European-based panels. PRS-CS overall outperformed the classic P + T method, especially for endpoints with higher SNP-based heritability. Notably, prediction accuracy is heterogeneous across endpoints, biobanks, and ancestries, especially for asthma, which has known variation in disease prevalence across populations. Overall, we provide lessons for PRS construction, evaluation, and interpretation using GBMI resources and highlight the importance of best practices for PRS in the biobank-scale genomics era.

Unexpected inverse correlation between Native American ancestry and Asian American variants of HPV16 in admixed Colombian cervical cancer cases.

BACKGROUND: European (E) variants of HPV 16 are evenly distributed among world regions, meanwhile Non-European variants such as European-Asian (EAs), Asian American (AA) and African (Af) are mostly confined to Eastern Asia, The Americas and African regions respectively. Several studies have shown that genetic variation of HPV 16 is associated with the risk of cervical cancer, which also seems to be dependent on the population. This relationship between ethnicity and variants have led to the suggestion that there is co-evolution of variants with humankind. Our aim was to evaluate the relationship between the individual ancestry proportion and infection with HPV 16 variants in cervical cancer. METHODS: We examined the association between ancestry and HPV 16 variants in samples of 82 cervical cancer cases from different regions of Colombia. Individual ancestry proportions (European, African and Native American) were estimated by genotyping 106 ancestry informative markers. Variants were identified by PCR amplification of the E6 gene, followed by reverse line blot hybridization (RLB) with variants specific probes. RESULTS: Overall European (E) and Asian American (AA) variants frequency was 66.5% and 33.5% respectively. Similar distribution was observed in cases with higher proportions of European or African ancestry. A higher Native American ancestry was significantly associated with higher frequency of E variants (median ancestry>23.6%, Age and place of birth adjusted OR: 3.55, 95% CI: 1.26-10.03, p=0.01). Even further, an inverse geographic correlation between Native American ancestry and frequency of infections with AA variants was observed (ρ=-0.825, p=0.008). Regions with higher proportion of Native American ancestry had a lower frequency of AA variants of HPV 16. CONCLUSIONS: This study suggests replacement of AA variants by E variants of human papillomavirus 16 in cervical cancer cases with high Native American ancestry.

Distribución de variantes del virus del papiloma humano 16 (VPH 16) en mujeres con y sin neoplasia intraepitelial cervical grado 3 y cáncer cervical / Distribution of variants of the human papilloma virus 16 (HPV 16) in Women with and without grade 3 cervical intraepithelial neoplasia and cervical cancer

Objetivos: Describir la distribución de variantes del virus del papiloma humano 16 en mujeres con y sin neoplasia intraepitelial cervical grado 3 y cáncer cervical. Métodos: Se determinaron las variantes moleculares en casos de carcinoma escamocelular, adenocarcinoma cervical y en mujeres sin anormalidades citológicas de alto grado y positivas para el virus del papiloma humano 16. Para la detección de las variantes moleculares se amplificó el marco abierto de lectura del gen E6 del virus del papiloma humano 16 y se utilizó una técnica de hibridación reversa para la detección de los principales cambios de nucleótidos que identifican las ramas filogenéticas y las clases de variantes. Resultados:Hubo diferencias estadísticamente significativas en la distribución de variantes de virus del papiloma humano 16. Los controles no presentaron infecciones con variantes no europeas, mientras que ellas estuvieron presentes en el 30% de los casos de carcinoma escamocelular o neoplasia intraepitelial cervical grado tres. En adenocarcinoma, el 65% de las infecciones fueron del tipo no europeo. Conclusiones: La prevalencia de variantes no europeas de virus de papiloma humano 16 fue de 31,2% en neoplasia intraepitelial cervical grado 3 y cáncer escamocelular, y de 64,1% en adenocarcinoma de cérvix, mientras que estas no se observaron en mujeres sin cáncer.

Objectives: To describe the distribution of the variants of the human papilloma virus 16 in women with and without grade 3 cervical intraepithelial neoplasia and cervical cancer. Methods: Molecular variants were established in cases of squamous cell carcinoma, cervical adenocarcinoma and in women with high grade Pap smear abnormalities who tested positive for human papilloma virus 16. For the detection of molecular variants the open reading framework for the E6 gene of the human papilloma virus 16 was amplified and a reverse hybridization technique was utilized for the detection of major changes in the nucleotides which identify the phylogenetic branches and classes of variants. Results: There were statistically significant results in the distribution of the variants of the human papilloma virus 16. Control cases showed no infections with non European variants, but they were present in 30% of squamous cell carcinoma or grade three cervical intraepithelial neoplasia. For adenocarcinoma, 65% of infections were of non European type. Conclusions: The prevalence of non European variants of the human papilloma virus 16 was 31.2% in grade 3 cervical intraepithelial neoplasia and squamous cell cancer, and 64.1% in cervical adenocarcinoma; however, these were not observed among women without cancer.

The interaction of an antiparasitic peptide active against African sleeping sickness with cell membrane models.

Zwitterionic peptides with trypanocidal activity are promising lead compounds for the treatment of African Sleeping Sickness, and have motivated research into the design of compounds capable of disrupting the protozoan membrane. In this study, we use the Langmuir monolayer technique to investigate the surface properties of an antiparasitic peptide, namely S-(2,4-dinitrophenyl)glutathione di-2-propyl ester, and its interaction with a model membrane comprising a phospholipid monolayer. The drug formed stable Langmuir monolayers, whose main feature was a phase transition accompanied by a negative surface elasticity. This was attributed to aggregation upon compression due to intermolecular bond associations of the molecules, inferred from surface pressure and surface potential isotherms, Brewster angle microscopy (BAM) images, infrared spectroscopy and dynamic elasticity measurements. When co-spread with dipalmitoyl phosphatidyl choline (DPPC), the drug affected both the surface pressure and the monolayer morphology, even at high surface pressures and with low amounts of the drug. The results were interpreted by assuming a repulsive, cooperative interaction between the drug and DPPC molecules. Such repulsive interaction and the large changes in fluidity arising from drug aggregation may be related to the disruption of the membrane, which is key for the parasite killing property.