Tests for finding complex patterns of differential expression in cancers: towards individualized medicine

BACKGROUND: Microarray studies in cancer compare expression levels between two or more sample groups on thousands of genes. Data analysis follows a population-level approach (e.g., comparison of sample means) to identify differentially expressed genes. This leads to the discovery of 'population-level' markers, i.e., genes with the expression patterns A > B and B > A. We introduce the PPST test that identifies genes where a significantly large subset of cases exhibit expression values beyond upper and lower thresholds observed in the control samples. RESULTS: Interestingly, the test identifies A > B and B < A pattern genes that are missed by population-level approaches, such as the t-test, and many genes that exhibit both significant overexpression and significant underexpression in statistically significantly large subsets of cancer patients (ABA pattern genes). These patterns tend to show distributions that are unique to individual genes, and are aptly visualized in a 'gene expression pattern grid'. The low degree of among-gene correlations in these genes suggests unique underlying genomic pathologies and high degree of unique tumor-specific differential expression. We compare the PPST and the ABA test to the parametric and non-parametric t-test by analyzing two independently published data sets from studies of progression in astrocytoma. CONCLUSIONS: The PPST test resulted findings similar to the nonparametric t-test with higher self-consistency. These tests and the gene expression pattern grid may be useful for the identification of therapeutic targets and diagnostic or prognostic markers that are present only in subsets of cancer patients, and provide a more complete portrait of differential expression in cancer

Quality of life among patients receiving palliative care in South Africa and Uganda: a multi-centred study

<p>Abstract</p> <p>Background</p> <p>Quality of life (QOL) is a core outcome of palliative care, yet in African settings there is a lack of evidence on patients' levels of QOL. We aimed to describe QOL among patients with incurable, progressive disease receiving palliative care in South Africa and Uganda, to compare QOL in cancer and HIV, to determine how domains of QOL correlate with overall QOL, and compare levels of QOL in this population with those in other studies using the same tool.</p> <p>Methods</p> <p>A cross-sectional survey was conducted using the Missoula Vitas Quality of Life Index (MVQOLI), a 26-item QOL questionnaire with five subscales (<it>Function, Symptom, Interpersonal, Well being, Transcendent</it>) covering physical, social, psychological and spiritual domains and one global QOL item. One item in each subscale assesses the subjective importance of the domain on a score from 1 (least important) to 5 (most important), used to weight the contribution of the subscale towards the <it>Total QOL </it>score. The tool was translated into 6 languages and administered to consecutively recruited patients at four facilities in South Africa and one in Uganda.</p> <p>Results</p> <p>285 patients were recruited, with a mean age of 40.1; 197 (69.1%) were female. Patients' primary diagnoses were HIV (80.7%), cancer (17.9%) and other conditions (1.4%). The mean global QOL score was 2.81 (possible range 0 (worst) to 5 (best)); mean <it>Total </it>score 17.32 (possible range 0 to 30). Patients scored most poorly on <it>Function </it>(mean 0.21), followed by <it>Well being </it>(2.59), <it>Symptoms </it>(5.38), <it>Transcendent </it>(5.50), <it>Interpersonal </it>(9.53) (possible range for subscale scores -30 to 30). Most important to patients were: close relationships (mean 4.13), feeling at peace (4.12), sense of meaning in life (4.10), being active (3.84), physical comfort (2.58). Cancer patients were predominantly recruited at three of the sites; hence comparison with HIV-infected patients was restricted to these sites. HIV+ patients (n = 115) scored significantly worse than cancer patients (n = 50) on <it>Well being </it>(<it>Z </it>= -2.778, p = 0.005), <it>Transcendence </it>(<it>Z </it>= -2.693, p = 0.007) and <it>Total QOL </it>(<it>Z </it>= -2.564, p = 0.01). Global QOL score was most weakly correlated with <it>Total QOL </it>(r = 0.37) and the <it>Transcendent </it>subscale was most highly correlated (r = 0.77) (both p < 0.001). Patients receiving palliative care in South Africa and Uganda exhibited significantly poorer QOL compared to similar populations in the USA.</p> <p>Conclusions</p> <p>Feeling at peace and having a sense of meaning in life were more important to patients than being active or physical comfort, and spiritual wellbeing correlated most highly with overall QOL. It is therefore vital to identify and meet the psychological and spiritual care needs of patients, as well as to assess and treat pain and other symptoms. Our finding that patients scored most poorly on the <it>Function </it>domain warrants further research.</p

Photon-Photon and Electron-Photon Colliders with Energies Below a TeV

We investigate the potential for detecting and studying Higgs bosons in $\gamma\gamma$ and $e\gamma$ collisions at future linear colliders with energies below a TeV. Our study incorporates realistic $\gamma\gamma$ spectra based on available laser technology, and NLC and CLIC acceleration techniques. Results include detector simulations. We study the cases of: a) a SM-like Higgs boson based on a devoted low energy machine with $\sqrt{s_{ee}}\le 200$ GeV; b) the heavy MSSM Higgs bosons; and c) charged Higgs bosons in $e\gamma$ collisions.We investigate the potential for detecting and studying Higgs bosons in $\gamma\gamma$ and $e\gamma$ collisions at future linear colliders with energies below a TeV. Our study incorporates realistic $\gamma\gamma$ spectra based on available laser technology, and NLC and CLIC acceleration techniques. Results include detector simulations. We study the cases of: a) a SM-like Higgs boson based on a devoted low energy machine with $\sqrt{s_{ee}}\le 200$ GeV; b) the heavy MSSM Higgs bosons; and c) charged Higgs bosons in $e\gamma$ collisions

Self-report measurement of pain & symptoms in palliative care patients: a comparison of verbal, visual and hand scoring methods in Sub-Saharan Africa

Background: Despite a high incidence of life-limiting disease, there is a deficit of palliative care outcome evidence in sub-Saharan Africa. Providers of end of life care call for appropriate measurement tools. The objective is to compare four approaches to self-report pain and symptom measurement among African palliative care patients completing the African Palliative Care Association African Palliative Outcome Scale (APCA African POS). Methods: Patients were recruited from five services (4 in South Africa and 1 in Uganda). Research nurses cross-sectionally administered POS pain and symptom items in local languages. Both questions were scored from 0 to 5 using 4 methods: verbal rating, demonstrating the score using the hand (H), selecting a face on a visual scale (F), and indicating a point on the Jerrycan visual scale (J). H, F and J scores were correlated with verbal scores as reference using Spearman’s rank and weighted Kappa. A Receiver Operating Characteristic (ROC) analysis was performed. Results: 315 patients participated (mean age 43.5 years, 69.8% female), 71.1% were HIV positive and 35.6% had cancer, 49.2% lived in rural areas. Spearman’s rank correlations for pain scores were: H: 0.879, F: 0.823, J: 0.728 (all p  F > J (0.96–0.89) in ROC analysis. Conclusions: Hands and faces scoring methods correlate highly with verbal scoring. The Jerrycan method had only moderate weighted Kappa. POS scores can be reliably measured using hand or face score

A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci.

We conducted a multi-stage, genome-wide association study of bladder cancer with a primary scan of 591,637 SNPs in 3,532 affected individuals (cases) and 5,120 controls of European descent from five studies followed by a replication strategy, which included 8,382 cases and 48,275 controls from 16 studies. In a combined analysis, we identified three new regions associated with bladder cancer on chromosomes 22q13.1, 19q12 and 2q37.1: rs1014971, (P = 8 × 10⁻¹²) maps to a non-genic region of chromosome 22q13.1, rs8102137 (P = 2 × 10⁻¹¹) on 19q12 maps to CCNE1 and rs11892031 (P = 1 × 10⁻⁷) maps to the UGT1A cluster on 2q37.1. We confirmed four previously identified genome-wide associations on chromosomes 3q28, 4p16.3, 8q24.21 and 8q24.3, validated previous candidate associations for the GSTM1 deletion (P = 4 × 10⁻¹¹) and a tag SNP for NAT2 acetylation status (P = 4 × 10⁻¹¹), and found interactions with smoking in both regions. Our findings on common variants associated with bladder cancer risk should provide new insights into the mechanisms of carcinogenesis

Exome and whole genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity

The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. With a five-year survival rate of 15%, identification of new therapeutic targets for EAC is greatly important. We analyze the mutation spectra from whole exome sequencing of 149 EAC tumors/normal pairs, 15 of which have also been subjected to whole genome sequencing. We identify a mutational signature defined by a high prevalence of A to C transversions at AA dinucleotides. Statistical analysis of exome data identified significantly mutated 26 genes. Of these genes, four (TP53, CDKN2A, SMAD4, and PIK3CA) have been previously implicated in EAC. The novel significantly mutated genes include chromatin modifying factors and candidate contributors: SPG20, TLR4, ELMO1, and DOCK2. Functional analyses of EAC-derived mutations in ELMO1 reveal increased cellular invasion. Therefore, we suggest a new hypothesis about the potential activation of the RAC1 pathway to be a contributor to EAC tumorigenesis

A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci.

We conducted a multi-stage, genome-wide association study of bladder cancer with a primary scan of 591,637 SNPs in 3,532 affected individuals (cases) and 5,120 controls of European descent from five studies followed by a replication strategy, which included 8,382 cases and 48,275 controls from 16 studies. In a combined analysis, we identified three new regions associated with bladder cancer on chromosomes 22q13.1, 19q12 and 2q37.1: rs1014971, (P = 8 × 10⁻¹²) maps to a non-genic region of chromosome 22q13.1, rs8102137 (P = 2 × 10⁻¹¹) on 19q12 maps to CCNE1 and rs11892031 (P = 1 × 10⁻⁷) maps to the UGT1A cluster on 2q37.1. We confirmed four previously identified genome-wide associations on chromosomes 3q28, 4p16.3, 8q24.21 and 8q24.3, validated previous candidate associations for the GSTM1 deletion (P = 4 × 10⁻¹¹) and a tag SNP for NAT2 acetylation status (P = 4 × 10⁻¹¹), and found interactions with smoking in both regions. Our findings on common variants associated with bladder cancer risk should provide new insights into the mechanisms of carcinogenesis