Zuoheng Wang

Standard Outcome Measures for Thymic Malignancies

Thymic malignancies present particular issues due to the pace of disease progression, patterns of recurrence, and causes of death that make nuances of how outcomes are reported particularly important. The relatively limited number of patients also creates a challenge to glean as much as possible from the available experience, but risks over-interpretation and potentially misleading conclusions. Therefore the International Thymic Malignancy Interest Group has developed a set of standards for reporting of outcome measures of clinical studies, which have been adopted for collaborative projects undertaken by the organization. Widespread adoption of this baseline will enhance the ability to compare results from different series.

A Genome-Wide Association Study on Obesity and Obesity-Related Traits

Large-scale genome-wide association studies (GWAS) have identified many loci associated with body mass index (BMI), but few studies focused on obesity as a binary trait. Here we report the results of a GWAS and candidate SNP genotyping study of obesity, including extremely obese cases and never overweight controls as well as families segregating extreme obesity and thinness. We first performed a GWAS on 520 cases (BMI>35 kg/m2) and 540 control subjects (BMI<25 kg/m2), on measures of obesity and obesity-related traits. We subsequently followed up obesity-associated signals by genotyping the top ∼500 SNPs from GWAS in the combined sample of cases, controls and family members totaling 2,256 individuals. For the binary trait of obesity, we found 16 genome-wide significant signals within the FTO gene (strongest signal at rs17817449, P = 2.5×10−12). We next examined obesity-related quantitative traits (such as total body weight, waist circumference and waist to hip ratio), and detected genome-wide significant signals between waist to hip ratio and NRXN3 (rs11624704, P = 2.67×10−9), previously associated with body weight and fat distribution. Our study demonstrated how a relatively small sample ascertained through extreme phenotypes can detect genuine associations in a GWAS.

Variant Callers for Next-Generation Sequencing Data: A Comparison Study

Next generation sequencing (NGS) has been leading the genetic study of human disease into an era of unprecedented productivity. Many bioinformatics pipelines have been developed to call variants from NGS data. The performance of these pipelines depends crucially on the variant caller used and on the calling strategies implemented. We studied the performance of four prevailing callers, SAMtools, GATK, glftools and Atlas2, using single-sample and multiple-sample variant-calling strategies. Using the same aligner, BWA, we built four single-sample and three multiple-sample calling pipelines and applied the pipelines to whole exome sequencing data taken from 20 individuals. We obtained genotypes generated by Illumina Infinium HumanExome v1.1 Beadchip for validation analysis and then used Sanger sequencing as a “gold-standard” method to resolve discrepancies for selected regions of high discordance. Finally, we compared the sensitivity of three of the single-sample calling pipelines using known simulated whole genome sequence data as a gold standard. Overall, for single-sample calling, the called variants were highly consistent across callers and the pairwise overlapping rate was about 0.9. Compared with other callers, GATK had the highest rediscovery rate (0.9969) and specificity (0.99996), and the Ti/Tv ratio out of GATK was closest to the expected value of 3.02. Multiple-sample calling increased the sensitivity. Results from the simulated data suggested that GATK outperformed SAMtools and glfSingle in sensitivity, especially for low coverage data. Further, for the selected discrepant regions evaluated by Sanger sequencing, variant genotypes called by exome sequencing versus the exome array were more accurate, although the average variant sensitivity and overall genotype consistency rate were as high as 95.87% and 99.82%, respectively. In conclusion, GATK showed several advantages over other variant callers for general purpose NGS analyses. The GATK pipelines we developed perform very well.

The Role and Challenges of Exome Sequencing in Studies of Human Diseases

Recent advances in next-generation sequencing technologies have transformed the genetics study of human diseases; this is an era of unprecedented productivity. Exome sequencing, the targeted sequencing of the protein-coding portion of the human genome, has been shown to be a powerful and cost-effective method for detection of disease variants underlying Mendelian disorders. Increasing effort has been made in the interest of the identification of rare variants associated with complex traits in sequencing studies. Here we provided an overview of the application fields for exome sequencing in human diseases. We describe a general framework of computation and bioinformatics for handling sequencing data. We then demonstrate data quality and agreement between exome sequencing and exome microarray (chip) genotypes using data collected on the same set of subjects in a genetic study of panic disorder. Our results show that, in sequencing data, the data quality was generally higher for variants within the exonic target regions, compared to that outside the target regions, due to the target enrichment. We also compared genotype concordance for variant calls obtained by exome sequencing vs. exome genotyping microarrays. The overall consistency rate was >99.83% and the heterozygous consistency rate was >97.55%. The two platforms share a large amount of agreement over low frequency variants in the exonic regions, while exome sequencing provides much more information on variants not included on exome genotyping microarrays. The results demonstrate that exome sequencing data are of high quality and can be used to investigate the role of rare coding variants in human diseases.

A comparison of association methods correcting for population stratification in case-control studies.

Population stratification is an important issue in case–control studies of disease‐marker association. Failure to properly account for population structure can lead to spurious association or reduced power. In this article, we compare the performance of six methods correcting for population stratification in case–control association studies. These methods include genomic control (GC), EIGENSTRAT, principal component‐based logistic regression (PCA‐L), LAPSTRUCT, ROADTRIPS, and EMMAX. We also include the uncorrected Armitage test for comparison. In the simulation studies, we consider a wide range of population structure models for unrelated samples, including admixture. Our simulation results suggest that PCA‐L and LAPSTRUCT perform well over all the scenarios studied, whereas GC, ROADTRIPS, and EMMAX fail to correct for population structure at single nucleotide polymorphisms (SNPs) that show strong differentiation across ancestral populations. The Armitage test does not adjust for confounding due to stratification thus has inflated type I error. Among all correction methods, EMMAX has the greatest power, based on the population structure settings considered for samples with unrelated individuals. The three methods, EIGENSTRAT, PCA‐L, and LAPSTRUCT, are comparable, and outperform both GC and ROADTRIPS in almost all situations.

An analysis, systematic review, and meta-analysis of the perioperative mortality after neoadjuvant therapy and pneumonectomy for non–small cell lung cancer

OBJECTIVE Pneumonectomy after neoadjuvant therapy remains controversial. METHODS A systematic PubMed search was performed for original articles from 1990 through 2010 describing pneumonectomy after neoadjuvant therapy. Specific data on 30-day and 90-day perioperative mortalities were abstracted from these articles. Meta-analysis compared 30-day mortality between right and left pneumonectomy with a fixed-effects model. Comparison between 30-day and 90-day mortalities was also performed. RESULTS The search strategy yielded 27 studies. Overall, 30-day and 90-day perioperative mortalities were 7% and 12%, respectively. Among 15 studies providing side-specific 30-day mortality, cumulative mortalities were 11% and 5% for right and left pneumonectomies, respectively. In the meta-analysis that included 10 studies, 30-day mortality for right pneumonectomy remained greater than for left pneumonectomy (odds ratio, 1.97; 95% confidence interval, 1.11-3.49; P = .02). Among 6 studies providing side-specific 90-day mortality, cumulative mortalities were 20% and 9% for right and left pneumonectomies, respectively. In the meta-analysis that included 4 studies, 90-day mortality for right pneumonectomy was greater than for left pneumonectomy (odds ratio, 2.01; 95% confidence interval, 1.09-3.72; P = .03). Among 11 studies providing both 30-day and 90-day mortalities, mortality difference was 5% (95% confidence interval, 4%-7%, P < .0001). Pulmonary complications were the most common cause of 30-day and 90-day deaths. CONCLUSIONS Right pneumonectomy is associated with significantly higher 30-day and 90-day mortalities after neoadjuvant therapy than left pneumonectomy. Also, 90-day mortality for all pneumonectomies appears to be greater than expected, suggesting that the 30-day mortality figure may inadequately assess the perioperative mortality.

Genome-wide association study of N370S homozygous Gaucher disease reveals the candidacy of CLN8 gene as a genetic modifier contributing to extreme phenotypic variation†

Mutations in GBA1 gene result in defective acid β‐glucosidase and the complex phenotype of Gaucher disease (GD) related to the accumulation of glucosylceramide‐laden macrophages. The phenotype is highly variable even among patients harboring identical GBA1 mutations. We hypothesize that modifier gene(s) underlie phenotypic diversity in GD and performed a GWAS study in Ashkenazi Jewish patients with type 1 GD (GD1), homozygous for N370S mutation. Patients were assigned to mild, moderate, or severe disease categories using composite disease severity scoring systems. Whole‐genome genotyping for >500,000 SNPs was performed to search for association signals using OQLS algorithm in 139 eligible patients. Several SNPs in linkage disequilibrium within the CLN8 gene locus were associated with the GD1 severity: SNP rs11986414 was associated with GD1 severity at P value 1.26 × 10−6. Compared to mild disease, risk allele A at rs11986414 conferred an odds ratio of 3.72 for moderate/severe disease. Loss of function mutations in CLN8 causes neuronal ceroid‐lipofuscinosis, but our results indicate that its increased expression may protect against severe GD1. In cultured skin fibroblasts, the relative expression of CLN8 was higher in mild GD compared to severely affected patients, in whom CLN8 risk alleles were overrepresented. In an in vitro cell model of GD, CLN8 expression was increased, which was further enhanced in the presence of bioactive substrate, glucosylsphingosine. Taken together, CLN8 is a candidate modifier gene for GD1 that may function as a protective sphingolipid sensor and/or in glycosphingolipid trafficking. Future studies should explore the role of CLN8 in pathophysiology of GD. Am. J. Hematol., 2012.

Long-term survival after lung resection for non–small cell lung cancer with circulatory bypass: A systematic review

OBJECTIVE Resection of locally advanced non-small cell lung cancer using circulatory bypass is not frequently performed. The objective of this study was to systematically review the long-term survival associated with the published studies dealing with the performance of lung resections for non-small cell lung cancer using circulatory bypass. METHODS A systematic review of publications dealing with lung resections for non-small cell lung cancer under circulatory bypass spanning from January 1, 1990, to December, 31 2010, was performed using a PubMed search with specific inclusion and exclusion criteria. The primary end point collected was survival. Several other clinical variables were also collected and analyzed. Survival curves were calculated using the Kaplan-Meier method. Univariate comparisons of survival were performed using a Cox proportional hazard model. Multivariate analysis was carried out using a Cox regression model. RESULTS The search algorithm yielded 20 articles for the analysis. The overall 5-year survival was 37% (median, 36 ± 6 months). Survival was significantly higher when placement on bypass was planned (54%; median, 67 ± 19 months) as opposed to unplanned or emergency placement (11%; median, 19 ± 6 months; P = .006). Multivariate analysis demonstrated that the use of unplanned bypass was prognostic for a worse long-term survival (hazard ratio = 0.28; 95% confidence interval, 0.09-0.90; P = .033). The 30-day and 90-day perioperative mortalities were 0% and 1%, respectively. CONCLUSIONS The literature over the past 2 decades demonstrates that favorable long-term survival for extended resections of locally advanced non-small cell lung cancer using circulatory bypass can be achieved. The use of unplanned cardiopulmonary bypass, though, seems to be prognostic of unfavorable long-term survival.

Preliminary analysis of positive and negative syndrome scale in ketamine-associated psychosis in comparison with schizophrenia.

OBJECTIVE Studies of the effects of the N-methyl-d-aspartate (NMDA) glutamate receptor antagonist, ketamine, have suggested similarities to the symptoms of schizophrenia. Our primary goal was to evaluate the dimensions of the Positive and Negative Syndrome Scale (PANSS) in ketamine users (acute and chronic) compared to schizophrenia patients (early and chronic stages). METHOD We conducted exploratory factor analysis for the PANSS from four groups: 135 healthy subject administrated ketamine or saline, 187 inpatients of ketamine abuse; 154 inpatients of early course schizophrenia and 522 inpatients of chronic schizophrenia. Principal component factor analyses were conducted to identify the factor structure of the PANSS. RESULTS Factor analysis yielded five factors for each group: positive, negative, cognitive, depressed, excitement or dissociation symptoms. The symptom dimensions in two schizophrenia groups were consistent with the established five-factor model (Wallwork et al., 2012). The factor structures across four groups were similar, with 19 of 30 symptoms loading on the same factor in at least 3 of 4 groups. The factors in the chronic ketamine group were more similar to the factors in the two schizophrenia groups rather than to the factors in the acute ketamine group. Symptom severities were significantly different across the groups (Kruskal-Wallis χ(2)(4) = 540.6, p < 0.0001). Symptoms in the two ketamine groups were milder than in the two schizophrenia groups (Cohens d = 0.7). CONCLUSION Our results provide the evidence of similarity in symptom dimensions between ketamine psychosis and schizophrenia psychosis. The interpretations should be cautious because of potential confounding factors.

Hospital Readmission After Pulmonary Lobectomy Is Not Affected by Surgical Approach

BACKGROUND The aim of this study is to identify the predictors of hospital readmission or early unplanned return to clinic within 30 days of discharge after pulmonary lobectomy. METHODS The medical records of patients undergoing lobectomy by the thoracic surgery service between January 2009 and July 2012 were reviewed. All lobectomies were included irrespective of the etiology of disease. Multivariate logistic regression methods were used to identify predictors of readmission and or early unplanned return to clinic. RESULTS Two hundred thirteen patients underwent a pulmonary lobectomy during the study period (median age, 67 years). Pathologic diagnosis was malignant in 94% of the patients and benign in 6%. Minimally invasive approaches were used in 69% of the patients, whereas open thoracotomy was used in 31%. Median hospital length of stay was 4 days, and postoperative mortality occurred in 1 patient (0.5%). The Charlson comorbidity index was 1 ± 1. Predicted postoperative forced expiratory volume in 1 second and diffusing capacity of the lung for carbon monoxide were 68% ± 18% and 64% ± 17%, respectively. Postoperative complications occurred in 31% of patients; 13% required readmission to the hospital within 30 days of discharge or early unplanned return to clinic. Predictors of readmission or early unplanned return to clinic were unplanned transfer to the intensive care unit (odds ratio, 10.4; 95% confidence interval, 1.1 to 103.5; p = 0.04) and Charlson comorbidity index greater than 0 (odds ratio, 1.5; 95% confidence interval, 1.04 to 2.03; p = 0.03). Readmission or early unplanned return to clinic was independent of surgical approach (p = 0.32). CONCLUSIONS Patients who require a postoperative transfer to the intensive care unit or with higher Charlson comorbidity index are at higher risk for hospital readmission after pulmonary lobectomy. Readmission was not affected by the surgical approach. Whether a different strategy to follow-up for these high-risk patients can prevent readmission remains to be determined.