Statistical issues and approaches in endophenotype research

This special topic comprises 9 papers which were presented at the Symposium. (Chinese Science Bulletin, 2011, v. 56 n. 32 Editorial. doi: 10.1007/s11434-011-4716-4)This journal issue entitled: SPECIAL TOPIC Endophenotype Strategies for the Study of Neuropsychiatric DisordersThe endophenotype concept was initially proposed to enhance the power of genetic studies of complex disorders. It is closely related to the genetic component in a liability-threshold model; a perfect endophenotype should have a correlation of 1 with the genetic component of the liability to disease. In reality, a putative endophenotype is unlikely to be a perfect representation of the genetic component of disease liability. The magnitude of the correlation between a putative endophenotype and the genetic component of disease liability can be estimated by fitting multivariate genetic models to twin data. A number of statistical methods have been developed for incorporating endophenotypes in genetic linkage and association analyses with the aim of improving statistical power. The most recent of such methods can handle multiple endophenotypes simultaneously for the greatest increase in power. In addition to increasing statistical power, endophenotype research plays an important role in helping to understand the mechanisms which connect the associated genetic variants with disease occurrence. Novel statistical approaches may be required for the analysis of the complex relationships between endophenotypes at different levels and how they converge to cause the occurrence of disease. © 2011 Science China Press and Springer-Verlag Berlin Heidelberg.published_or_final_versio

A knowledge-based weighting framework to boost the power of genome-wide association studies

Background: We are moving to second-wave analysis of genome-wide association studies (GWAS), characterized by comprehensive bioinformatical and statistical evaluation of genetic associations. Existing biological knowledge is very valuable for GWAS, which may help improve their detection power particularly for disease susceptibility loci of moderate effect size. However, a challenging question is how to utilize available resources that are very heterogeneous to quantitatively evaluate the statistic significances. Methodology/Principal Findings: We present a novel knowledge-based weighting framework to boost power of the GWAS and insightfully strengthen their explorative performance for follow-up replication and deep sequencing. Built upon diverse integrated biological knowledge, this framework directly models both the prior functional information and the association significances emerging from GWAS to optimally highlight single nucleotide polymorphisms (SNPs) for subsequent replication. In the theoretical calculation and computer simulation, it shows great potential to achieve extra over 15% power to identify an association signal of moderate strength or to use hundreds of whole-genome subjects fewer to approach similar power. In a case study on late-onset Alzheimer disease (LOAD) for a proof of principle, it highlighted some genes, which showed positive association with LOAD in previous independent studies, and two important LOAD related pathways. These genes and pathways could be originally ignored due to involved SNPs only having moderate association significance. Conclusions/Significance: With user-friendly implementation in an open-source Java package, this powerful framework will provide an important complementary solution to identify more true susceptibility loci with modest or even small effect size in current GWAS for complex diseases. © 2010 Li et al.published_or_final_versio

Host genetic factors as determinants of immunologic and adverse responses on influenza vaccination in humans

Poster Session: VaccinesBackground: Seasonal influenza epidemics cause a great burden of illnesses, hospitalizations, and deaths worldwide. Although influenza vaccination has generally been regarded as safe and effective in preventing influenza infection, some people do develop poor immune responses or occasional serious adverse events on receiving the vaccination. Little is known about how host genetic determinants are affecting responses to influenza vaccination in humans. Materials and Methods: We used a genetic association study with a candidate gene approach based on a randomized placebocontrolled trial on influenza vaccination to examine the role of host genetic variation on immune years were randomized to receive either an inactivated trivalent seasonal influenza vaccine (TIV) (Vaxigrip, Sanofi Pasteur) or placebo in phases from 2009 to 2010. Vaccine response was defined by a post-vaccination antibody titer of 1:40 or ≥ 4-fold rise in all TIV components. An adverse vaccine responder was defined by an aggregated symptom score ≥ 2 on day 1 post-vaccination, based on 10 symptoms each on a scale of 0 (absent), 1 (mild), 2 (moderate, or 3 (severe), thus having at least 2 mild or 1 moderate symptoms. All participants kept a daily symptom dairy. Whole blood samples from 535 participants receiving TIV were collected for genetic analysis in this study. DNA was extracted and genotyped for single nucleotide polymorphisms for IL-1B-511G>A (rs16944), IL-6-5843A/G (rs1818879), IL-8-251T/A (rs4073), IL-10-082A/G (rs1800896), -819T/C (rs1800871), -592A/C (rs1800872), MBL-2-5232G>A (rs1800451), 221C/G (rs7096206), -34C>T (rs5030737), -550G>C (rs11003125), MxA-88G/T (rs2071430), OSA1-347A/G (rs2660), RIG1 G/C (rs9695310), TLR3- 1377T/G (rs3755290), -7G/T (rs3775296), TLR4 G/A (rs5030718), Asp299Gly (rs4986790), TLR7 Gln11Leu (rs179008), 1817G/T (rs5741880), TLR8-129G/C (rs3764879), Met1Val (rs3764880), and (rs11003131)G/T. Logistic regression models were used to evaluate the relationship of polymorphisms with various outcomes and to compute the ORs and 95% confidence interval (CIs) in relation to vaccination response and adverse vaccination reaction. The heterozygous and homozygous variant genotypes were analyzed both as a nominal and an ordinal variable as consisting, respectively, of one and two variant alleles and compared with the wild-type homozygous genotype. The heterozygous genotype was also grouped with either of the two homozygous genotypes to analyze in a dominant or recessive model. Two-sided P values are reported and P ≤ .05 was considered to indicate statistical significance. Results: Among 535 subjects receiving TIV, 295 were classified as vaccine responders. Polymorphisms IL-6 rs1818879 G mutation in an ordinal model (OR = 1.56, CI = 1.054-2.31), AG (OR = 1.667, CI = 1.109-2.504), and combined AG/GG (OR = 1.637, CI = 1.093-2.454) in a dominant model were associated with increased odds of response. TLR7 rs5741880 GT (OR = 0.161, CI = 0.046-0.566), combined GT/TT (OR = 0.371, CI = 0.159- 0.866) in a dominant model, and TLR3 rs3755290 GG (OR = 0.572, CI = 0.335-0.976) in a recessive model compared with GT/TT were associated with lower odds of response. No serious vaccine response, including anaphylaxis or shock, was reported by any recipient. With a symptom score ≥ 2, 26.1% were classified as adverse responders for TIV. IL-6 rs1818879 AG (OR = 1.833, CI = 1.14- 2.945) and combined AG/GG (OR = 1.778, CI = 1.108-2.854) were associated with a higher risk, while CCL1 rs2282691 AT (OR = 0.578, CI = 0.347-0.963) was associated with a lower risk of adverse response. All these effects of polymorphisms in relation to vaccination response are compatible with the current understanding regarding the role played by those genes in either the pathogenesis or immunological response to influenza infection. Conclusions: Our findings suggest the potential role of host genetic variation and identified genetic determinants that affect the immunological and adverse responses to seasonal influenza vaccination in humans. These findings may help to explain the great variability in protection achieved by influenza vaccination.published_or_final_versio

Using glycosylated haemoglobin to define the metabolic syndrome in adults in the United States

Introduction: Recently, the American Diabetes Association has proposed the use of glycosylated haemoglobin (GHb) in the definition of diabetes and the category of increased diabetes risk. We therefore investigated whether GHb can be used instead of fasting plasma glucose in identifying individuals with the metabolic syndrome, which is associated with increased risk of cardiovascular diseases. Methods: Participants of the US National Health and Nutrition Examination Survey (NHANES) 1999-2006 who had fasting blood glucose were included (n=3551 in 1999-2002 and n=3412 in 2003-2006). The metabolic syndrome was defined using International Diabetes Federation criteria in 2009. Raised blood glucose was defined either as fasting glucose ≥100 mg/dL (5.6 mmol/L), or as GHb ≥5.7%. Results: In 2003-2006, there was 91.3% agreement between GHb and fasting glucose when either is used to define the metabolic syndrome, although the use of GHb slightly lowered the syndrome’s prevalence (34.8% vs 38.8%, P=0.012). The agreement was good (≥87%) irrespective of age, sex, race/ethnicity and body mass index. Only 2.3% of the sample population had the metabolic syndrome defined using GHb but not using fasting glucose. The syndrome, defined using GHb alone, was associated with cardiovascular diseases (ischaemic heart disease, heart failure or stroke) [OR=1.95, P=0.002]. Similar results were found in 1999-2002. Conclusions: Using GHb instead of fasting glucose to define the metabolic syndrome is feasible. The syndrome defined in this way also identifies individuals with increased cardiovascular risk.published_or_final_versio

Does Dysbiosis Play a Role in Age-Related Hearing Impairment?

Age-related hearing impairment (ARHI) is prevalent in older adults, affecting at least 60% of people by the time they reach 71 to 80 years of age.1 The number of people with ARHI will necessarily increase as humans live longer and a greater proportion of the population is older.2 Hearing loss does not just impact communication; it is associated with loneliness and depression, cognitive decline and dementia, as well as reduced physical well-being.3-6 A decade ago, an international report calculated that hearing loss cost Europe £213 billion annually.7 There is currently no effective drug treatment for hearing loss. Hearing aids (average cost £2,300/pair) are the most commonly prescribed ameliorative therapy, but uptake is low; and among those who obtain hearing aids, a high proportion do not use them or are dissatisfied with them. Hearing loss prevention is therefore of compelling necessity, and genetic studies will help us understand how and why people lose their hearing ability and will inform prevention strategies

Gamma-glutamyl transferase level predicts the development of hypertension in Hong Kong Chinese

Introduction: Liver enzymes are elevated in cardiometabolic diseases, particularly when there is non-alcoholic fatty liver disease. We therefore investigated if hypertension is associated with elevated levels of alkaline phosphatase (ALP), alanine aminotransferase (ALT), aspartate aminotransferase and γ-glutamyl transferase (GGT). Methods: We included 235 hypertensive and 708 normotensive subjects from the Hong Kong Cardiovascular Risk Factor Prevalence Study-2 (CRISPS-2) in 2000-2004 who had fewer than one alcoholic drink a week. In the follow-up study in 2005-2008 (CRISPS-3), 126 out of the 708 subjects had developed hypertension. Results: In CRISPS-2, plasma ALT (OR=1.31 per SD of log-transformed level, P=0.005) and GGT (OR=1.52 per SD of log-transformed level, P<0.001) were significantly associated with prevalent hypertension after adjusting for age, sex and body mass index (BMI). Among subjects not on anti-hypertensive medication, plasma ALP and GGT were significantly associated with both systolic blood pressure (beta=0.141, P<0.001 for ALP and beta=0.096, P=0.004 for GGT) and diastolic blood pressure (beta=0.131, P<0.001 for ALP and beta=0.102, P=0.004 for GGT). In forward stepwise logistic regression analysis of subjects normotensive at CRISPS-2, the highest tertile of plasma GGT level was an independent predictor of the development of hypertension in CRISPS-3 (OR=2.40, P=0.010), together with age, BMI, systolic blood pressure and plasma CRP at baseline, and change in BMI. The other liver enzymes were not significantly predictors of new-onset hypertension. Conclusions: Among the four liver enzymes, elevated GGT level is the strongest risk factor for hypertension in Hong Kong Chinese. Acknowledgement: This study was funded by Hong Kong Research Grant Council grants (HKU7229/01M and HKU7626/07M) and the Sun Chieh Yeh Heart Foundation.published_or_final_versio

Relationship of genetic variants in gene encoding adrenomedullin with hypertension and dysglycaemia in Hong Kong Chinese

published_or_final_versionThe 15th Annual Research Conference of the Department of Medicine, The University of Hong Kong, Hong Kong, 16 January 2010. In Hong Kong Medical Journal, 2010, v. 16, suppl. 1, p. 50, abstract no. 8

Role of genetic variants in gene encoding lipocalin-2 in the development of elevated blood pressure

Introduction: Lipocalin-2 is recently recognised as a biomarker of obesity and inflammation, which are both risk factors for hypertension. We therefore investigated the association of common single nucleotide polymorphisms (SNPs) in the gene encoding lipocalin-2 (LCN2) with elevated blood pressure in Hong Kong Chinese. Methods: Five tagging SNPs were genotyped in 1936 subjects from the Hong Kong Cardiovascular Risk Factor Prevalence Study-2 (CRISPS-2) with a median follow-up period of 6.4 years. Elevated blood pressure was defined as ≥130/85 mm Hg or taking anti-hypertensive medication. Results: There were only two haplotypes with frequency of >5%, namely AGATC (45.5%) and GGTCC (41.2%). Haplotype GGTCC was associated with elevated blood pressure at follow-up (OR=1.17 compared to haplotype AGATC, P=0.031 after adjusting for age and sex). Among 1381 subjects without elevated blood pressure at baseline, 321 subjects developed elevated blood pressure at follow-up. Haplotype GGTCC was associated with the development of elevated blood pressure at follow-up (OR=1.30 compared to haplotype AGATC, P=0.011 after adjusting for age, sex, systolic blood pressure, and follow-up duration; OR=1.44, P=0.0015 after further adjusting for other covariates). Among subjects not taking anti-hypertensive medication, carriers of the haplotype GGTCC had higher systolic blood pressure than non-carriers (119.7±16.4 mm Hg vs 117.9±17.3 mm Hg, P=0.043). Conclusion: Our findings suggest, for the first time, that genetic variants in LCN2 may affect blood pressure. Further studies on the role of lipocalin-2 in blood pressure regulation are warranted. Acknowledgement: This study was funded by Hong Kong Research Grant Council grants (HKU7229/01M and HKU7626/07M) and the Sun Chieh Yeh Heart Foundation.published_or_final_versio

Gamma-glutamyl transferase level predicts the development of hypertension in Hong Kong Chinese

Background: Plasma activities of alkaline phosphatase, alanine aminotransferase (ALT), aspartate aminotransferase, and γ-glutamyl transferase (GGT) are often increased in cardiometabolic diseases. We investigated if hypertension is associated with increased activities of these plasma markers. Methods: We included 235 hypertensive and 708 normotensive subjects (mean age 47.3 ± 9.6 and 58.0 ± 10.2. years respectively) from the Hong Kong Cardiovascular Risk Factor Prevalence Study-2 (CRISPS-2) in 2000-2004 who had drank < 1/week. In the follow-up study in 2005-2008 (CRISPS-3), 126 out of the 708 subjects had developed hypertension. Results: Raised plasma ALT (OR = 1.22 per SD of log-transformed level, P=0.045) and GGT (OR = 1.38 per SD of log-transformed level, P=0.001) levels were associated with hypertension at baseline in CRISPS-2 after adjusting for covariates. Among subjects not on anti-hypertensive medications, plasma ALP, ALT and GGT were related to blood pressure (P< 0.01). In subjects normotensive at CRISPS-2, plasma GGT, but not ALP, ALT and AST, was an independent predictor of new-onset hypertension at CRISPS-3 (OR = 1.38 per SD of log-transformed level, P=0.020 and OR = 2.68 for 3rd tertile vs. 1st tertile, P=0.004) after adjusting for covariates. Conclusions: Among the 4 plasma markers, increased GGT activity is the strongest predictor for existing and new-onset hypertension in Hong Kong Chinese. © 2011 Elsevier B.V.postprin

Self-reported hearing loss questions provide a good measure for genetic studies: a polygenic risk score analysis from UK Biobank

Age-related hearing impairment (ARHI) is very common in older adults and has major impact on quality of life. The heritability of ARHI has been estimated to be around 50%. The present study aimed to estimate heritability and environmental contributions to liability of ARHI and the extent to which a polygenic risk score (PRS) derived from a recent genome-wide association study of questionnaire items regarding hearing loss using the UK Biobank is predictive of hearing loss in other samples. We examined (1) a sample from TwinsUK who have had hearing ability measured by pure-tone audiogram and the speech-to-noise ratio test as well as questionnaire measures that are comparable with the UK Biobank questionnaire items and (2) European and non-European samples from the UK Biobank which were not part of the original GWAS. Results indicated that the questionnaire items were over 50% heritable in TwinsUK and comparable with the objective hearing measures. In addition, we found very high genetic correlation (0.30–0.84) between the questionnaire responses and objective hearing measures in the TwinsUK sample. Finally, PRS computed from weighted UK Biobank GWAS results were predictive of both questionnaire and objective measures of hearing loss in the TwinsUK sample, as well as questionnaire-measured hearing loss in Europeans but not non-European subpopulations. These results demonstrate the utility of questionnaire-based methods in genetic association studies of hearing loss in adults and highlight the differences in genetic predisposition to ARHI by ethnic background