Browsing by Subject "Principal Component Analysis"

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    Glycosyltransferase gene expression profiles classify cancer types and propose prognostic subtypes
    (2016) Ashkani, Jahanshah; Naidoo, Kevin J
    Aberrant glycosylation in tumours stem from altered glycosyltransferase (GT) gene expression but can the expression profiles of these signature genes be used to classify cancer types and lead to cancer subtype discovery? The differential structural changes to cellular glycan structures are predominantly regulated by the expression patterns of GT genes and are a hallmark of neoplastic cell metamorphoses. We found that the expression of 210 GT genes taken from 1893 cancer patient samples in The Cancer Genome Atlas (TCGA) microarray data are able to classify six cancers; breast, ovarian, glioblastoma, kidney, colon and lung. The GT gene expression profiles are used to develop cancer classifiers and propose subtypes. The subclassification of breast cancer solid tumour samples illustrates the discovery of subgroups from GT genes that match well against basal-like and HER2-enriched subtypes and correlates to clinical, mutation and survival data. This cancer type glycosyltransferase gene signature finding provides foundational evidence for the centrality of glycosylation in cancer.
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    Open Access
    Socioeconomic status and dietary patterns in children from around the world: different associations by levels of country human development?
    (2017) Manyanga, Taru; Tremblay, Mark S; Chaput, Jean-Philippe; Katzmarzyk, Peter T; Fogelholm, Mikael; Hu, Gang; Kuriyan, Rebecca; Kurpad, Anura; Lambert, Estelle V; Maher, Carol; Maia, José; Matsudo, Victor; Olds, Timothy; Onywera, Vincent; Sarmiento, Olga L; Standage, Martyn; Tudor-Locke, Catrine; Zhao, Pei; Mikkila, Vera; Broyles, Stephanie T
    Abstract Background Although ‘unhealthy’ diet is a well-known risk factor for non-communicable diseases, its relationship with socio-economic status (SES) has not been fully investigated. Moreover, the available research has largely been conducted in countries at high levels of human development. This is the first study to examine relationships among dietary patterns and SES of children from countries spanning a wide range of human development. Methods This was a multinational cross-sectional study among 9–11 year-old children (n = 6808) from urban/peri-urban sites across 12 countries. Self-reported food frequency questionnaires were used to determine the children’s dietary patterns. Principal Components Analysis was employed to create two component scores representing ‘unhealthy’ and ‘healthy’ dietary patterns. Multilevel models accounting for clustering at the school and site level were used to examine the relationships among dietary patterns and SES. Results The mean age of participants in this study (53.7% girls) was 10.4 years. Largest proportions of total variance in dietary patterns occurred at the individual, site, and school levels (individual, school, site: 62.8%; 10.8%; 26.4% for unhealthy diet pattern (UDP) and 88.9%; 3.7%; 7.4%) for healthy diet pattern (HDP) respectively. There were significant negative ‘unhealthy’ diet-SES gradients in 7 countries and positive ‘healthy’ diet-SES gradients in 5. Within country diet-SES gradients did not significantly differ by HDI. Compared to participants in the highest SES groups, unhealthy diet pattern scores were significantly higher among those in the lowest within-country SES groups in 8 countries: odds ratios for Australia (2.69; 95% CI: 1.33–5.42), Canada (4.09; 95% CI: 2.02–8.27), Finland (2.82; 95% CI: 1.27–6.22), USA (4.31; 95% CI: 2.20–8.45), Portugal (2.09; 95% CI: 1.06–4.11), South Africa (2.77; 95% CI: 1.22–6.28), India (1.88; 95% CI: 1.12–3.15) and Kenya (3.35; 95% CI: 1.91–5.87). Conclusions This study provides evidence of diet-SES gradients across all levels of human development and that lower within-country SES is strongly related to unhealthy dietary patterns. Consistency in within-country diet-SES gradients suggest that interventions and public health strategies aimed at improving dietary patterns among children may be similarly employed globally. However, future studies should seek to replicate these findings in more representative samples extended to more rural representation.