A comparative assessment on gene expression classification methods of RNA-seq data generated using next-generation sequencing (NGS).

Next-generation sequencing or massively parallel sequencing have revolutionized genomic research. RNA sequencing (RNA-Seq) can profile the gene-expression used for molecular diagnosis, disease classification and providing potential markers of diseases. For classification of gene expressions, several methods that have been proposed are based on microarray data which is a continuous scale or require a normal distribution assumption. As the RNA-Seq data do not meet those requirements, these methods cannot be applied directly. In this study, we compare several classifiers including Logistic Regression, Support Vector Machine, Classification and Regression Trees and Random Forest. A simulation study with different parameters such as over dispersion, differential expression rate is conducted and the results are compared with two mRNA experimental datasets. To measure predictive accuracy six performance indicators are used: Percentage Correctly Classified, Area Under Receiver Operating Characteristic (ROC) Curve, Kolmogorov Smirnov Statistics, Partial Gini Index, H-measure and Brier Score. The result shows that Random Forest outperforms the other classification algorithms.

Determinants of cognitive health in Indonesian HIV patients beginning antiretroviral therapy.

Cognitive impairment has been described in people living with HIV and stable on antiretroviral therapy (ART), but has not been monitored in young adults beginning ART with a high burden of cytomegalovirus. We recruited 80 subjects beginning ART with < 200 CD4 T cells/µL in Jakarta, Indonesia. Cognitive function (Z-scores) began low but improved on ART, stabilizing after 6 months with improvements in all domains except memory function. The burden of cytomegalovirus persisting on ART (assessed via antibody levels) correlated inversely with Z-scores (notably memory function) at baseline. In linear mixed models, improvements in Z-scores were influenced by age, education, and CD4 T cell counts.

Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh.

Background: Some Ebola vaccines have been developed and tested in phase III clinical trials. However, assessment of whether public have willingness to purchase or not, especially in unaffected areas, is lacking. The aim of this study was to determine willingness to pay (WTP) for a hypothetical Ebola vaccine in Indonesia. Methods: A cross-sectional study was conducted from 1 August to 30 December 2015 in five cities in Aceh province of Indonesia. Patients' family members who visited outpatient departments were approached and interviewed about their sociodemographic characteristics, knowledge of Ebola, attitude towards vaccination practice and their WTP for a hypothetical Ebola vaccine. A multivariable linear regression model assessed the relationship between these explanatory variables and WTP. Results: During the study, 500 participants were approached and interviewed. There were 424 (84.8%) respondents who completed the interview and 74% (311/424) expressed their acceptance for an Ebola vaccine. There were 288 participants who were willing to pay for an Ebola vaccine (92.6% out of 311). The mean of WTP was US$2.08 (95% CI: 1.75-2.42). The final multivariable model indicated that young age, high educational attainment, working as a private employee, entrepreneur or civil servant (compared to farmers), being unmarried, and residing in a suburb (compared to a city) were associated with higher WTP. Conclusions: Although the proportion of the participants who would accept the Ebola vaccine was relatively high, the amount they were willing to pay for Ebola vaccine was very low. This finding would indicate the need of subsidies for Ebola vaccine in the country.

Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function.

BACKGROUND: Understanding the genetic architecture of cardiac structure and function may help to prevent and treat heart disease. This investigation sought to identify common genetic variations associated with inter-individual variability in cardiac structure and function. METHODS: A GWAS meta-analysis of echocardiographic traits was performed, including 46,533 individuals from 30 studies (EchoGen consortium). The analysis included 16 traits of left ventricular (LV) structure, and systolic and diastolic function. RESULTS: The discovery analysis included 21 cohorts for structural and systolic function traits (n = 32,212) and 17 cohorts for diastolic function traits (n = 21,852). Replication was performed in 5 cohorts (n = 14,321) and 6 cohorts (n = 16,308), respectively. Besides 5 previously reported loci, the combined meta-analysis identified 10 additional genome-wide significant SNPs: rs12541595 near MTSS1 and rs10774625 in ATXN2 for LV end-diastolic internal dimension; rs806322 near KCNRG, rs4765663 in CACNA1C, rs6702619 near PALMD, rs7127129 in TMEM16A, rs11207426 near FGGY, rs17608766 in GOSR2, and rs17696696 in CFDP1 for aortic root diameter; and rs12440869 in IQCH for Doppler transmitral A-wave peak velocity. Findings were in part validated in other cohorts and in GWAS of related disease traits. The genetic loci showed associations with putative signaling pathways, and with gene expression in whole blood, monocytes, and myocardial tissue. CONCLUSION: The additional genetic loci identified in this large meta-analysis of cardiac structure and function provide insights into the underlying genetic architecture of cardiac structure and warrant follow-up in future functional studies. FUNDING: For detailed information per study, see Acknowledgments.

Willingness to pay for a dengue vaccine and its associated determinants in Indonesia: A community-based, cross-sectional survey in Aceh.

Vaccination strategies are being considered as a part of dengue prevention programs in endemic countries. To accelerate the introduction of dengue vaccine into the public sector program and private markets, understanding the private economic benefits of a dengue vaccine is therefore essential. The aim of this study was to assess the willingness to pay (WTP) for a dengue vaccine among community members in Indonesia and its associated explanatory variables. A community-based, cross-sectional survey was conducted in nine regencies of Aceh province, Indonesia, from November 2014 to March 2015. A pre-tested validated questionnaire was used to facilitate the interviews. To assess the explanatory variables influencing participants' WTP for a dengue vaccine, a linear regression analysis was employed. We interviewed 677 healthy community members; 476 participants (87.5% of the total) were included in the final analysis. An average individual was willing to pay around US-$ 4 (mean: US-$ 4.04; median: US-$ 3.97) for a dengue vaccine. Our final multivariate model revealed that working as a civil servant, living in the city, and having good knowledge on dengue viruses, a good attitude towards dengue, and good preventive practice against dengue virus infection were associated with a higher WTP (P<0.05). Our model suggests that marketing efforts should be directed to community members who are working in the suburbs especially as farmers. In addition, the results of our study underscore the need for low-cost quality vaccines, public sector subsidies for vaccinations, and intensifying efforts to further educate and encourage households regarding other dengue preventive measures, using trusted individuals as facilitators.

Comprehensive landscape of subtype-specific coding and non-coding RNA transcripts in breast cancer.

Molecular classification of breast cancer into clinically relevant subtypes helps improve prognosis and adjuvant-treatment decisions. The aim of this study is to provide a better characterization of the molecular subtypes by providing a comprehensive landscape of subtype-specific isoforms including coding, long non-coding RNA and microRNA transcripts. Isoform-level expression of all coding and non-coding RNAs is estimated from RNA-sequence data of 1168 breast samples obtained from The Cancer Genome Atlas (TCGA) project. We then search the whole transcriptome systematically for subtype-specific isoforms using a novel algorithm based on a robust quasi-Poisson model. We discover 5451 isoforms specific to single subtypes. A total of 27% of the subtype-specific isoforms have better accuracy in classifying the intrinsic subtypes than that of their corresponding genes. We find three subtype-specific miRNA and 707 subtype-specific long non-coding RNAs. The isoforms from long non-coding RNAs also show high performance for separation between Luminal A and Luminal B subtypes with an AUC of 0.97 in the discovery set and 0.90 in the validation set. In addition, we discover 1500 isoforms preferentially co-expressed in two subtypes, including 369 isoforms co-expressed in both Normal-like and Basal subtypes, which are commonly considered to have distinct ER-receptor status. Finally, analyses at protein level reveal four subtype-specific proteins and two subtype co-expression proteins that successfully validate results from the isoform level.

One CNV Discordance in NRXN1 Observed Upon Genome-wide Screening in 38 Pairs of Adult Healthy Monozygotic Twins.

Monozygotic (MZ) twins stem from the same single fertilized egg and therefore share all their inherited genetic variation. This is one of the unequivocal facts on which genetic epidemiology and twin studies are based. To what extent this also implies that MZ twins share genotypes in adult tissues is not precisely established, but a common pragmatic assumption is that MZ twins are 100% genetically identical also in adult tissues. During the past decade, this view has been challenged by several reports, with observations of differences in post-zygotic copy number variations (CNVs) between members of the same MZ pair. In this study, we performed a systematic search for differences of CNVs within 38 adult MZ pairs who had been misclassified as dizygotic (DZ) twins by questionnaire-based assessment. Initial scoring by PennCNV suggested a total of 967 CNV discordances. The within-pair correlation in number of CNVs detected was strongly dependent on confidence score filtering and reached a plateau of r = 0.8 when restricting to CNVs detected with confidence score larger than 50. The top-ranked discordances were subsequently selected for validation by quantitative polymerase chain reaction (qPCR), from which one single ~120kb deletion in NRXN1 on chromosome 2 (bp 51017111-51136802) was validated. Despite involving an exon, no sign of cognitive/mental consequences was apparent in the affected twin pair, potentially reflecting limited or lack of expression of the transcripts containing this exon in nerve/brain.

Improving the Prediction of Prostate Cancer Overall Survival by Supplementing Readily Available Clinical Data with Gene Expression Levels of IGFBP3 and F3 in Formalin-Fixed Paraffin Embedded Core Needle Biopsy Material.

BACKGROUND: A previously reported expression signature of three genes (IGFBP3, F3 and VGLL3) was shown to have potential prognostic value in estimating overall and cancer-specific survivals at diagnosis of prostate cancer in a pilot cohort study using freshly frozen Fine Needle Aspiration (FNA) samples. METHODS: We carried out a new cohort study with 241 prostate cancer patients diagnosed from 2004-2007 with a follow-up exceeding 6 years in order to verify the prognostic value of gene expression signature in formalin fixed paraffin embedded (FFPE) prostate core needle biopsy tissue samples. The cohort consisted of four patient groups with different survival times and death causes. A four multiplex one-step RT-qPCR test kit, designed and optimized for measuring the expression signature in FFPE core needle biopsy samples, was used. In archive FFPE biopsy samples the expression differences of two genes (IGFBP3 and F3) were measured. The survival time predictions using the current clinical parameters only, such as age at diagnosis, Gleason score, PSA value and tumor stage, and clinical parameters supplemented with the expression levels of IGFBP3 and F3, were compared. RESULTS: When combined with currently used clinical parameters, the gene expression levels of IGFBP3 and F3 are improving the prediction of survival time as compared to using clinical parameters alone. CONCLUSION: The assessment of IGFBP3 and F3 gene expression levels in FFPE prostate cancer tissue would provide an improved survival prediction for prostate cancer patients at the time of diagnosis.

Integration of somatic mutation, expression and functional data reveals potential driver genes predictive of breast cancer survival.

MOTIVATION: Genome and transcriptome analyses can be used to explore cancers comprehensively, and it is increasingly common to have multiple omics data measured from each individual. Furthermore, there are rich functional data such as predicted impact of mutations on protein coding and gene/protein networks. However, integration of the complex information across the different omics and functional data is still challenging. Clinical validation, particularly based on patient outcomes such as survival, is important for assessing the relevance of the integrated information and for comparing different procedures. RESULTS: An analysis pipeline is built for integrating genomic and transcriptomic alterations from whole-exome and RNA sequence data and functional data from protein function prediction and gene interaction networks. The method accumulates evidence for the functional implications of mutated potential driver genes found within and across patients. A driver-gene score (DGscore) is developed to capture the cumulative effect of such genes. To contribute to the score, a gene has to be frequently mutated, with high or moderate mutational impact at protein level, exhibiting an extreme expression and functionally linked to many differentially expressed neighbors in the functional gene network. The pipeline is applied to 60 matched tumor and normal samples of the same patient from The Cancer Genome Atlas breast-cancer project. In clinical validation, patients with high DGscores have worse survival than those with low scores (P = 0.001). Furthermore, the DGscore outperforms the established expression-based signatures MammaPrint and PAM50 in predicting patient survival. In conclusion, integration of mutation, expression and functional data allows identification of clinically relevant potential driver genes in cancer. AVAILABILITY AND IMPLEMENTATION: The documented pipeline including annotated sample scripts can be found in http://fafner.meb.ki.se/biostatwiki/driver-genes/. CONTACT: yudi.pawitan@ki.se SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Operator dependent choice of prostate cancer biopsy has limited impact on a gene signature analysis for the highly expressed genes IGFBP3 and F3 in prostate cancer epithelial cells.

BACKGROUND: Predicting the prognosis of prostate cancer disease through gene expression analysis is receiving increasing interest. In many cases, such analyses are based on formalin-fixed, paraffin embedded (FFPE) core needle biopsy material on which Gleason grading for diagnosis has been conducted. Since each patient typically has multiple biopsy samples, and since Gleason grading is an operator dependent procedure known to be difficult, the impact of the operator's choice of biopsy was evaluated. METHODS: Multiple biopsy samples from 43 patients were evaluated using a previously reported gene signature of IGFBP3, F3 and VGLL3 with potential prognostic value in estimating overall survival at diagnosis of prostate cancer. A four multiplex one-step qRT-PCR test kit, designed and optimized for measuring the signature in FFPE core needle biopsy samples was used. Concordance of gene expression levels between primary and secondary Gleason tumor patterns, as well as benign tissue specimens, was analyzed. RESULTS: The gene expression levels of IGFBP3 and F3 in prostate cancer epithelial cell-containing tissue representing the primary and secondary Gleason patterns were high and consistent, while the low expressed VGLL3 showed more variation in its expression levels. CONCLUSION: The assessment of IGFBP3 and F3 gene expression levels in prostate cancer tissue is independent of Gleason patterns, meaning that the impact of operator's choice of biopsy is low.

Affinity proteomics reveals elevated muscle proteins in plasma of children with cerebral malaria.

Systemic inflammation and sequestration of parasitized erythrocytes are central processes in the pathophysiology of severe Plasmodium falciparum childhood malaria. However, it is still not understood why some children are more at risks to develop malaria complications than others. To identify human proteins in plasma related to childhood malaria syndromes, multiplex antibody suspension bead arrays were employed. Out of the 1,015 proteins analyzed in plasma from more than 700 children, 41 differed between malaria infected children and community controls, whereas 13 discriminated uncomplicated malaria from severe malaria syndromes. Markers of oxidative stress were found related to severe malaria anemia while markers of endothelial activation, platelet adhesion and muscular damage were identified in relation to children with cerebral malaria. These findings suggest the presence of generalized vascular inflammation, vascular wall modulations, activation of endothelium and unbalanced glucose metabolism in severe malaria. The increased levels of specific muscle proteins in plasma implicate potential muscle damage and microvasculature lesions during the course of cerebral malaria.