Irina Dinu

Improving gene set analysis of microarray data by SAM-GS

BackgroundGene-set analysis evaluates the expression of biological pathways, or a priori defined gene sets, rather than that of individual genes, in association with a binary phenotype, and is of great biologic interest in many DNA microarray studies. Gene Set Enrichment Analysis (GSEA) has been applied widely as a tool for gene-set analyses. We describe here some critical problems with GSEA and propose an alternative method by extending the individual-gene analysis method, Significance Analysis of Microarray (SAM), to gene-set analyses (SAM-GS).ResultsUsing a mouse microarray dataset with simulated gene sets, we illustrate that GSEA gives statistical significance to gene sets that have no gene associated with the phenotype (null gene sets), and has very low power to detect gene sets in which half the genes are moderately or strongly associated with the phenotype (truly-associated gene sets). SAM-GS, on the other hand, performs very well. The two methods are also compared in the analyses of three real microarray datasets and relevant pathways, the diverging results of which clearly show advantages of SAM-GS over GSEA, both statistically and biologically. In a microarray study for identifying biological pathways whose gene expressions are associated with p53 mutation in cancer cell lines, we found biologically relevant performance differences between the two methods. Specifically, there are 31 additional pathways identified as significant by SAM-GS over GSEA, that are associated with the presence vs. absence of p53. Of the 31 gene sets, 11 actually involve p53 directly as a member. A further 6 gene sets directly involve the extrinsic and intrinsic apoptosis pathways, 3 involve the cell-cycle machinery, and 3 involve cytokines and/or JAK/STAT signaling. Each of these 12 gene sets, then, is in a direct, well-established relationship with aspects of p53 signaling. Of the remaining 8 gene sets, 6 have plausible, if less well established, links with p53.ConclusionWe conclude that GSEA has important limitations as a gene-set analysis approach for microarray experiments for identifying biological pathways associated with a binary phenotype. As an alternative statistically-sound method, we propose SAM-GS. A free Excel Add-In for performing SAM-GS is available for public use.

Permanent Bilateral Sensory and Neural Hearing Loss of Children After Neonatal Intensive Care Because of Extreme Prematurity: A Thirty-Year Study

OBJECTIVE. We present population-based, childhood prevalence rates of and neonatal risk factors for permanent hearing loss among extremely premature infants. METHODS. By using an inception-cohort, longitudinal study design for 1974–2003, we studied permanent hearing loss among 1279 survivors with gestational age of ≤28 weeks and birth weight of <1250 g (mortality rate: 42.7%; lost to follow-up monitoring: 4.7%) Newborn hearing screening, performed by experienced pediatric audiologists, used click-evoked auditory brainstem response testing after 1975. Survivors underwent repeated behavioral audiologic testing and multidisciplinary follow-up monitoring. Permanent hearing loss was defined as mild/moderate (26–70 dB hearing level), severe/profound (71 to >90 dB hearing level), delayed-onset (diagnosed after previously normal hearing), or progressive (increase in loss of ≥15 dB hearing level). Permanent hearing loss rates were established at 3 years of age, with newborn, infant, and >5-year final hearing outcomes being recorded. Risk factors were compared for children with and without hearing loss, odds ratios were calculated, and prediction performance was determined through area under the curve analysis. RESULTS. Forty (3.1%) of 1279 survivors 3 years of age had permanent hearing loss and 24 (1.9%) had severe/profound loss, with no changes over time. Bilateral delayed-onset loss occurred for 4 children (10%) and progressive loss for 11 children (28%). One child had auditory neuropathy, and 29 (73%) had multiple disabilities. Prolonged oxygen use, gastrointestinal surgery, patent ductus arteriosus ligation, and low socioeconomic index yielded good prediction of permanent hearing loss; oxygen use was the most significant predictor of severe/profound loss. CONCLUSIONS. Permanent hearing loss remains an adverse outcome of extreme prematurity, complicated by significant delayed-onset and progressive loss. Prolonged supplemental oxygen use is a marker for predicting permanent hearing loss; this requires detailed analysis of the pathophysiologic features, to reduce the prevalence of permanent hearing loss.

Osteonecrosis in Adult Survivors of Childhood Cancer: A Report From the Childhood Cancer Survivor Study

PURPOSE Osteonecrosis (ON) is a potentially serious complication of therapy in survivors of childhood cancer. Our goals were to describe the incidence of ON and identify patient and treatment characteristics associated with elevated risk. PATIENTS AND METHODS The rate of self-reported ON was determined for 9,261 patients enrolled onto the Childhood Cancer Survivor Study, a cohort of 5-year survivors of childhood cancer diagnosed from 1970 to 1986, and compared with the rate in a random sample of 2,872 siblings of survivors. Survivors with positive responses were reinterviewed to confirm the diagnosis. RESULTS Fifty-two cancer survivors reported ON in 78 joints, yielding 20-year cumulative incidence of 0.43% and a rate ratio (RR) of 6.2 (95% CI, 2.3 to 17.2) compared with siblings, adjusted for age and sex; 44% developed ON in a previous radiation field. The RR was greatest among survivors of stem-cell transplantation for acute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML), and chronic myelogenous leukemia (RR = 26.9, 66.5, and 93.1, respectively). Nontransplantation patients with ALL (RR = 6.5; 95% CI, 2.2 to 19.4), AML (RR = 11.2; 95% CI, 2.1 to 61.2), and bone sarcoma (RR = 7.3; 95% CI, 2.0 to 26.2) were at higher risk for ON. Older age at diagnosis, shorter elapsed time, older treatment era, exposure to dexamethasone (+/- prednisone), and gonadal and nongonadal radiation were independently associated with ON. CONCLUSION ON among long-term survivors of childhood cancer is rare. However, compared with siblings, childhood cancer survivors have a significantly increased relative rate of ON, particularly those who were older at diagnosis and who received dexamethasone or radiation therapy. Future studies are needed to better delineate our findings, particularly the increased risk after gonadal radiation.

Two-Year Survival and Mental and Psychomotor Outcomes After the Norwood Procedure An Analysis of the Modified Blalock-Taussig Shunt and Right Ventricle–to–Pulmonary Artery Shunt Surgical Eras

Background— The Norwood procedure for stage 1 palliation of hypoplastic left heart syndrome is performed with either the modified Blalock-Taussig (MBTS) or the right ventricle–to–pulmonary artery (RVPA) shunt. In our institution, surgical practice changed from use of the MBTS to use of the RVPA shunt in 2002. We analyzed survival and mental and psychomotor outcomes of the 2 consecutive surgical eras. Methods and Results— Between September 1996 and July 2005, 94 neonates with hypoplastic left heart syndrome underwent the Norwood procedure. Patients were recruited as neonates and followed up prospectively. Health, mental, and psychomotor outcomes (Bayley Scales of Infant Development-II) were assessed at 2 years. The study subjects were from the Norwood-MBTS era (n=62; 1996 to 2002) or the Norwood-RVPA era (n=32; 2002 to 2005). In the MBTS era, early and 2-year mortality rates were 23% (14/62) and 52% (32/62); the mean (SD) mental and psychomotor developmental indices were 79 (18) and 67 (19). In the RVPA era, early and 2-year mortality rates were 6% (2/32) and 19% (6/32); the mean (SD) mental and psychomotor developmental indices were 85 (18) and 78 (18). The 2-year mortality rate (P=0.002) and the psychomotor developmental index (P=0.029) were improved in the more recent surgical era. On multivariable Cox regression analysis, postoperative highest serum lactate independently predicted 2-year mortality in the MBTS and RVPA eras. Conclusions— Analysis of 2 consecutive surgical eras of hypoplastic left heart syndrome patients undergoing the Norwood procedure showed a significant improvement in 2-year survival and psychomotor development in the more recent era. Adverse neurodevelopmental outcome in this patient population remains a concern.

Neurodevelopmental outcome following exposure to sedative and analgesic drugs for complex cardiac surgery in infancy

Objectives/Aim:  To determine whether sedation/analgesia drugs used before, during, and after infant cardiac surgery are associated with neurodevelopmental outcome.

SNP-SNP Interactions Discovered by Logic Regression Explain Crohn's Disease Genetics

In genome-wide association studies (GWAS), the association between each single nucleotide polymorphism (SNP) and a phenotype is assessed statistically. To further explore genetic associations in GWAS, we considered two specific forms of biologically plausible SNP-SNP interactions, ‘SNP intersection’ and ‘SNP union,’ and analyzed the Crohns Disease (CD) GWAS data of the Wellcome Trust Case Control Consortium for these interactions using a limited form of logic regression. We found strong evidence of CD-association for 195 genes, identifying novel susceptibility genes (e.g., ISX, SLCO6A1, TMEM183A) as well as confirming many previously identified susceptibility genes in CD GWAS (e.g., IL23R, NOD2, CYLD, NKX2-3, IL12RB2, ATG16L1). Notably, 37 of the 59 chromosomal locations indicated for CD-association by a meta-analysis of CD GWAS, involving over 22,000 cases and 29,000 controls, were represented in the 195 genes, as well as some chromosomal locations previously indicated only in linkage studies, but not in GWAS. We repeated the analysis with two smaller GWASs from the Database of Genotype and Phenotype (dbGaP): in spite of differences of populations and study power across the three datasets, we observed some consistencies across the three datasets. Notable examples included TMEM183A and SLCO6A1 which exhibited strong evidence consistently in our WTCCC and both of the dbGaP SNP-SNP interaction analyses. Examining these specific forms of SNP interactions could identify additional genetic associations from GWAS. R codes, data examples, and a ReadMe file are available for download from our website: http://www.ualberta.ca/~yyasui/homepage.html.

The registry and follow-up of complex pediatric therapies program of Western Canada: a mechanism for service, audit, and research after life-saving therapies for young children.

Newly emerging health technologies are being developed to care for children with complex cardiac defects. Neurodevelopmental and childhood school-related outcomes are of great interest to parents of children receiving this care, care providers, and healthcare administrators. Since the 1970s, neonatal follow-up clinics have provided service, audit, and research for preterm infants as care for these at-risk children evolved. We have chosen to present for this issue the mechanism for longitudinal follow-up of survivors that we have developed for western Canada patterned after neonatal follow-up. Our program provides registration for young children receiving complex cardiac surgery, heart transplantation, ventricular assist device support, and extracorporeal life support among others. The program includes multidisciplinary assessments with appropriate neurodevelopmental intervention, active quality improvement evaluations, and outcomes research. Through this mechanism, consistently high (96%) follow-up over two years is maintained.

Five-year neurocognitive and health outcomes after the neonatal arterial switch operation

OBJECTIVES We sought to assess the 5-year neurocognition and health of an interprovincial inception cohort undergoing the arterial switch operation for transposition of the great arteries. METHODS Sixty-nine consecutive neonates had operations from 1996-2003 with full-flow cardiopulmonary bypass and selective deep hypothermic circulatory arrest. Outcomes were recorded at 58 +/- 9 months of age. Univariate and multivariate analyses were used to identify outcome predictors, including surgical subtype and preoperative, operative, and postoperative variables. RESULTS There was 1 (1.5%) operative death. Two children were lost to follow-up, and 1 was excluded because of postdischarge meningitis. Outcomes are reported for 65 survivors. Two (3%) children have cerebral palsy, and 7 (11%) have language disorders, 4 of whom also meet the criteria for autism spectrum disorder. Two of the 4 children with autism have an affected older sibling. Of the 61 children without autism, scores approach those of peers, with a full-scale intelligence quotient of 97 +/- 16, a verbal intelligence quotient of 97 +/- 18, a performance intelligence quotient of 96 +/- 15, and a visual-motor integration score of 95 +/- 16. Mothers education, birth gestation or weight, and postoperative plasma lactate values account for 21% to 32% of the variance of these scores. Septostomy adds 7% to the variance of visual-motor integration scores. CONCLUSIONS Most preschool children do well after surgical correction for transposition of the great arteries, including complex forms. Potentially modifiable variables include high preoperative plasma lactate levels and septostomy. A minority of children were given diagnoses of language disorders, including autism, in which familial factors likely contribute to outcome.

Early childhood outcomes of infants born with gastroschisis

PURPOSE To describe neonatal and childhood outcomes of a contemporary cohort of infants with gastroschisis. METHODS Observational, single center, inception cohort of children born with gastroschisis from January 2005 to December 2008. RESULTS Of 63 infants, 61 survived to hospital discharge and 39 were seen for follow-up. Complications included sepsis (37%), necrotizing enterocolitis (10%), parenteral nutrition related cholestasis (25%), and short bowel syndrome (13%). Of survivors, 5% had visual impairment and 10% had hearing loss. No child tested had mental delay or cerebral palsy. Early gestational age predicted death or disability (OR 0.60, 95% CI 0.38, 0.96; p=0.033). There was a high incidence of prescription medications for presumed gastroesophageal reflux (90%). Some infants continued to require tube feeds (15%). There were improvements in longitudinal growth reflected in increasing z-scores. CONCLUSIONS Although children with gastroschisis are at risk for disability, childhood outcomes are encouraging.

A prospective outcome study on the effects of facet joint radiofrequency denervation on pain, analgesic intake, disability, satisfaction, cost, and employment.

OBJECTIVE To assess the effect of radiofrequency denervation (RFD) on patients with chronic low back pain (LBP) of facet joint origin. DESIGN Prospective cohort study. SETTING Interventional pain management program. PARTICIPANTS Consecutive subjects (N=44; 101 facet joints) over 2 years with chronic refractory mechanical LBP of facet origin established by 2 local anesthetic blocks (medial branch +/- intra-articular) resulting in more than 50% pain relief. INTERVENTION RFD of the symptomatic lumbar facet joints. MAIN OUTCOME MEASURES Self-reported pain intensity, frequency, bothersomeness, analgesic intake, satisfaction, disability, back pain-related costs, and employment twice prior to and at 1, 3, 6, 9, and 12 months post-RFD. RESULTS Post-RFD, significant improvements in pain, analgesic requirement, satisfaction, disability, and direct costs occurred. They peaked at 3 to 6 months and gradually diminished thereafter. Satisfaction with medical care and living with current symptoms improved similarly. Overall, satisfaction with the RFD procedure was high, and no complications were reported. CONCLUSIONS RFD provides safe and significant short-term improvement in pain, analgesic requirements, function, satisfaction, and direct costs in patients with chronic LBP of facet origin.