Qizhai Li

A Genome-wide Association Study of Lung Cancer Identifies a Region of Chromosome 5p15 Associated with Risk for Adenocarcinoma

Three genetic loci for lung cancer risk have been identified by genome-wide association studies (GWAS), but inherited susceptibility to specific histologic types of lung cancer is not well established. We conducted a GWAS of lung cancer and its major histologic types, genotyping 515,922 single-nucleotide polymorphisms (SNPs) in 5739 lung cancer cases and 5848 controls from one population-based case-control study and three cohort studies. Results were combined with summary data from ten additional studies, for a total of 13,300 cases and 19,666 controls of European descent. Four studies also provided histology data for replication, resulting in 3333 adenocarcinomas (AD), 2589 squamous cell carcinomas (SQ), and 1418 small cell carcinomas (SC). In analyses by histology, rs2736100 (TERT), on chromosome 5p15.33, was associated with risk of adenocarcinoma (odds ratio [OR]=1.23, 95% confidence interval [CI]=1.13-1.33, p=3.02x10(-7)), but not with other histologic types (OR=1.01, p=0.84 and OR=1.00, p=0.93 for SQ and SC, respectively). This finding was confirmed in each replication study and overall meta-analysis (OR=1.24, 95% CI=1.17-1.31, p=3.74x10(-14) for AD; OR=0.99, p=0.69 and OR=0.97, p=0.48 for SQ and SC, respectively). Other previously reported association signals on 15q25 and 6p21 were also refined, but no additional loci reached genome-wide significance. In conclusion, a lung cancer GWAS identified a distinct hereditary contribution to adenocarcinoma.

Genome-wide association study of circulating vitamin D levels

The primary circulating form of vitamin D, 25-hydroxy-vitamin D [25(OH)D], is associated with multiple medical outcomes, including rickets, osteoporosis, multiple sclerosis and cancer. In a genome-wide association study (GWAS) of 4501 persons of European ancestry drawn from five cohorts, we identified single-nucleotide polymorphisms (SNPs) in the gene encoding group-specific component (vitamin D binding) protein, GC, on chromosome 4q12-13 that were associated with 25(OH)D concentrations: rs2282679 (P = 2.0 × 10−30), in linkage disequilibrium (LD) with rs7041, a non-synonymous SNP (D432E; P = 4.1 × 10−22) and rs1155563 (P = 3.8 × 10−25). Suggestive signals for association with 25(OH)D were also observed for SNPs in or near three other genes involved in vitamin D synthesis or activation: rs3829251 on chromosome 11q13.4 in NADSYN1 [encoding nicotinamide adenine dinucleotide (NAD) synthetase; P = 8.8 × 10−7], which was in high LD with rs1790349, located in DHCR7, the gene encoding 7-dehydrocholesterol reductase that synthesizes cholesterol from 7-dehydrocholesterol; rs6599638 in the region harboring the open-reading frame 88 (C10orf88) on chromosome 10q26.13 in the vicinity of ACADSB (acyl-Coenzyme A dehydrogenase), involved in cholesterol and vitamin D synthesis (P = 3.3 × 10−7); and rs2060793 on chromosome 11p15.2 in CYP2R1 (cytochrome P450, family 2, subfamily R, polypeptide 1, encoding a key C-25 hydroxylase that converts vitamin D3 to an active vitamin D receptor ligand; P = 1.4 × 10−5). We genotyped SNPs in these four regions in 2221 additional samples and confirmed strong genome-wide significant associations with 25(OH)D through meta-analysis with the GWAS data for GC (P = 1.8 × 10−49), NADSYN1/DHCR7 (P = 3.4 × 10−9) and CYP2R1 (P = 2.9 × 10−17), but not C10orf88 (P = 2.4 × 10−5).

Pathway analysis by adaptive combination of P-values†

It is increasingly recognized that pathway analyses—a joint test of association between the outcome and a group of single nucleotide polymorphisms (SNPs) within a biological pathway—could potentially complement single‐SNP analysis and provide additional insights for the genetic architecture of complex diseases. Building upon existing P‐value combining methods, we propose a class of highly flexible pathway analysis approaches based on an adaptive rank truncated product statistic that can effectively combine evidence of associations over different SNPs and genes within a pathway. The statistical significance of the pathway‐level test statistics is evaluated using a highly efficient permutation algorithm that remains computationally feasible irrespective of the size of the pathway and complexity of the underlying test statistics for summarizing SNP‐ and gene‐level associations. We demonstrate through simulation studies that a gene‐based analysis that treats the underlying genes, as opposed to the underlying SNPs, as the basic units for hypothesis testing, is a very robust and powerful approach to pathway‐based association testing. We also illustrate the advantage of the proposed methods using a study of the association between the nicotinic receptor pathway and cigarette smoking behaviors. Genet. Epidemiol. 33:700–709, 2009. Published 2009 Wiley‐Liss, Inc.

Genome-wide association study identifies a susceptibility locus for schizophrenia in Han Chinese at 11p11.2

To identify susceptibility loci for schizophrenia, we performed a two-stage genome-wide association study (GWAS) of schizophrenia in the Han Chinese population (GWAS: 746 individuals with schizophrenia and 1,599 healthy controls; validation: 4,027 individuals with schizophrenia and 5,603 healthy controls). We identified two susceptibility loci for schizophrenia at 6p21-p22.1 (rs1233710 in an intron of ZKSCAN4, Pcombined = 4.76 × 10−11, odds ratio (OR) = 0.79; rs1635 in an exon of NKAPL, Pcombined = 6.91 × 10−12, OR = 0.78; rs2142731 in an intron of PGBD1, Pcombined = 5.14 × 10−10, OR = 0.79) and 11p11.2 (rs11038167 near the 5′ UTR of TSPAN18, Pcombined = 1.09 × 10−11, OR = 1.29; rs11038172, Pcombined = 7.21 × 10−10, OR = 1.25; rs835784, Pcombined = 2.73 × 10−11, OR = 1.27). These results add to previous evidence of susceptibility loci for schizophrenia at 6p21-p22.1 in the Han Chinese population. We found that NKAPL and ZKSCAN4 were expressed in postnatal day 0 (P0) mouse brain. These findings may lead to new insights into the pathogenesis of schizophrenia.

Population substructure and control selection in genome-wide association studies.

Determination of the relevance of both demanding classical epidemiologic criteria for control selection and robust handling of population stratification (PS) represents a major challenge in the design and analysis of genome-wide association studies (GWAS). Empirical data from two GWAS in European Americans of the Cancer Genetic Markers of Susceptibility (CGEMS) project were used to evaluate the impact of PS in studies with different control selection strategies. In each of the two original case-control studies nested in corresponding prospective cohorts, a minor confounding effect due to PS (inflation factor λ of 1.025 and 1.005) was observed. In contrast, when the control groups were exchanged to mimic a cost-effective but theoretically less desirable control selection strategy, the confounding effects were larger (λ of 1.090 and 1.062). A panel of 12,898 autosomal SNPs common to both the Illumina and Affymetrix commercial platforms and with low local background linkage disequilibrium (pair-wise r 2<0.004) was selected to infer population substructure with principal component analysis. A novel permutation procedure was developed for the correction of PS that identified a smaller set of principal components and achieved a better control of type I error (to λ of 1.032 and 1.006, respectively) than currently used methods. The overlap between sets of SNPs in the bottom 5% of p-values based on the new test and the test without PS correction was about 80%, with the majority of discordant SNPs having both ranks close to the threshold. Thus, for the CGEMS GWAS of prostate and breast cancer conducted in European Americans, PS does not appear to be a major problem in well-designed studies. A study using suboptimal controls can have acceptable type I error when an effective strategy for the correction of PS is employed.

Common Genetic Variants and Risk for HPV Persistence and Progression to Cervical Cancer

HPV infrequently persists and progresses to cervical cancer. We examined host genetic factors hypothesized to play a role in determining which subset of individuals infected with oncogenic human papillomavirus (HPV) have persistent infection and further develop cervical pre-cancer/cancer compared to the majority of infected individuals who will clear infection. We evaluated 7140 tag single nucleotide polymorphisms (SNPs) from 305 candidate genes hypothesized to be involved in DNA repair, viral infection and cell entry in 416 cervical intraepithelial neoplasia 3 (CIN3)/cancer cases, 356 HPV persistent women (median: 25 months), and 425 random controls (RC) from the 10,049 women Guanacaste Costa Rica Natural History study. We used logistic regression to compute odds ratios and p-trend for CIN3/cancer and HPV persistence in relation to SNP genotypes and haplotypes (adjusted for age). We obtained pathway and gene-level summary of associations by computing the adaptive combination of p-values. Genes/regions statistically significantly associated with CIN3/cancer included the viral infection and cell entry genes 2′,5′ oligoadenylate synthetase gene 3 (OAS3), sulfatase 1 (SULF1), and interferon gamma (IFNG); the DNA repair genes deoxyuridine triphosphate (DUT), dosage suppressor of mck 1 homolog (DMC1), and general transcription factor IIH, polypeptide 3 (GTF2H4); and the EVER1 and EVER2 genes (p<0.01). From each region, the single most significant SNPs associated with CIN3/cancer were OAS3 rs12302655, SULF1 rs4737999, IFNG rs11177074, DUT rs3784621, DMC1 rs5757133, GTF2H4 rs2894054, EVER1/EVER2 rs9893818 (p-trends≤0.001). SNPs for OAS3, SULF1, DUT, and GTF2H4 were associated with HPV persistence whereas IFNG and EVER1/EVER2 SNPs were associated with progression to CIN3/cancer. We note that the associations observed were less than two-fold. We identified variations DNA repair and viral binding and cell entry genes associated with CIN3/cancer. Our results require replication but suggest that different genes may be responsible for modulating risk in the two critical transition steps important for cervical carcinogenesis: HPV persistence and disease progression.

Anthropometric predictors of coronary heart disease in Chinese women

OBJECTIVE: To evaluate the associations of body size and fat distribution with incidence of coronary heart disease (CHD) in Chinese women.DESIGN: Population-based, prospective cohort study.SUBJECTS: A total of 67 334 women aged 40–70 y, who had no prior history of CHD, stroke, and cancer at study recruitment.MEASUREMENTS: Weight, standing and sitting heights, circumferences of waist and hip, and ratios of the anthropometric measurements. Outcome: incidence of CHD (non-fatal myocardial infarction (MI) or fatal CHD).RESULTS: After a mean follow-up of 2.5 y (168 164 person-years), there were 70 incident cases of CHD (49 non-fatal MIs and 21 CHD deaths). Body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), waist-to-standing height ratio (WHtR), waist-to-sitting height ratio (WsHtR), and conicity index were all positively associated with the risk of CHD. With the exception of WHR, all other anthropometric indexes only predicted the risk of CHD among women ≤55 y of age at enrollment. The relative risks (RRs) between extreme tertiles of BMI were 9.0 (95% CI, 2.0–41.5; P for trend=0.002) for younger women vs 1.3 (0.6–3.0; P for trend=0.83) for older women. Similarly, the RRs for WC, WHtR, WsHtR, and conicity index were 6.1 (1.8–21.4) vs 1.9 (0.6–5.4), 9.4 (2.6–33.8) vs 1.2 (0.5–3.1), 15.2 (3.3–69.1) vs 1.0 (0.4–2.5), and 7.8 (2.2–28.0) vs 0.9 (0.4–2.3) for the young and elderly, respectively. In contrast, the RR for WHR was 3.2 (1.1–9.1) for the young and 2.9 (1.0–8.4) for the elderly.CONCLUSIONS: WHR was positively associated with the risk of CHD in both younger and older women, while other anthropometrics, including BMI, were related to CHD risk primarily among younger women.

Identification of Bacteria in Water by a Fluorescent Array

We report a method for the rapid and efficient identification of bacteria making use of five probes having fluorescent characteristics (F-array) and subsequent statistical analysis. Eight kinds of bacteria, including normal and multidrug-resistant bacteria, are differentiated successfully. Our easy-to-perform and time-saving method consists of mixing bacteria and probes, recording fluorescent intensity data by automated flow cytometry, and statistical analysis. No washing steps are required in order to identify the different bacteria simultaneously.

Efficient Approximation of P‐value of the Maximum of Correlated Tests, with Applications to Genome‐Wide Association Studies

Genome‐wide association study (GWAS), typically involving 100,000 to 500,000 single‐nucleotide polymorphisms (SNPs), is a powerful approach to identify disease susceptibility loci. In a GWAS, single‐marker analysis, which tests one SNP at a time, is usually used as the first stage to screen SNPs across the genome in order to identify a small fraction of promising SNPs with relatively low p‐values for further and more focused studies. For single‐marker analysis, the trend test derived for an additive genetic model is often used. This may not be robust when the additive assumption is not appropriate for the true underlying disease model. A robust test, MAX, based on the maximum of three trend test statistics derived for recessive, additive, and dominant models, has been proposed recently for GWAS. But its p‐value has to be evaluated through a resampling‐based procedure, which is computationally challenging for the analysis of GWAS. Obtaining the p‐value for MAX with adjustment for the covariates can be even more time‐consuming. In this article, we provide a simple approximation for the p‐value of the MAX test with or without adjusting for the covariates. The new method avoids resampling steps and thus makes the MAX test readily applicable to GWAS. We use simulation studies as well as real datasets on 17 confirmed disease‐associated SNPs to assess the accuracy of the proposed method. We also apply the method to the GWAS of coronary artery disease.

Body fat distribution and risk of diabetes among Chinese women

OBJECTIVE: To assess the relationship between measures of central and overall obesity and risk of diabetes.DESIGN: Nested case–control study.SETTING: Shanghai, China.PARTICIPANTS: A total of 57 130 women were screened for diabetes at enrollment for the Shanghai Womens Health Study (SWHS), a population-based cohort study of Chinese women aged 40–70 y. In this study, 345 women diagnosed with diabetes and 2760 age-matched controls (eight controls per case), randomly selected from women who tested negative for urine glucose, were included.RESULTS: Risk of diabetes increased significantly with increasing levels of obesity, particularly with measures of central obesity. Compared to those in the lowest quartile, women in the highest quartile of body mass index (BMI) (≥26.57) and waist to hip ratio (WHR) (≥0.855) had a 2.57-fold (95% CI 1.75–3.77) and a 6.05-fold (95% CI 4.05–9.04) increased risk of diabetes, respectively. The risk of diabetes was elevated with increasing WHR at all levels of BMI, while the positive association between BMI and diabetes was observed primarily among women with a low WHR. However, test for multiplicative interaction was not statistically significant.CONCLUSIONS: Our data indicated that central obesity is a stronger risk factor for diabetes than overall obesity, suggesting that WHR may be a better indicator of risk of diabetes than BMI among Chinese women.