Quantification of 3-dimensional structure and properties of flocculated natural suspended sediment

Natural sediment flocs are fragile and highly heterogeneous aggregates of biogenic and minerogenic material typically with high porosity and low density. In aquatic environments dominated by fine, cohesive or mixed sediments they can dominate suspended sediment flux. Consequently, monitoring and modelling the behaviour, transport and distribution of flocs is very important for many aquatic industries, maintenance of waterways and conservation and management of aquatic waterbodies. Mathematical models that predict the behaviour of flocs rely on the accurate assessments of the size, shape, density, porosity and fractal dimension of flocs. These inherently 3-dimensional (3D) characteristics are typically derived from 2-dimensional (2D) data, largely due to the challenges associated with sampling, capturing, imaging and quantifying these fragile aggregates. We have developed new volumetric microscopy techniques which can quantify 3D internal and external structures and characteristics of sediment flocs. Here, these techniques were applied to quantify the 3D size (volume), shape and fractal dimension of natural and artificial sediment flocs and compare them to standard 2D approaches. Our study demonstrates that 2D approaches are under-estimating shape complexity and over-estimating the size and mass settling flux of flocs by up to two orders of magnitude, and the discrepancy between 2D and 3D is most marked for natural, organic rich macroflocs. Our study has significant implications for estimations of sediment flux at local to global scales within in aquatic environments. These new data and approaches offer the potential to improve the current parameterisation of sediment transport models and to improve the accuracy of current field-monitoring techniques.

Time to Surgery Following Short-Course Radiotherapy in Rectal Cancer and its Impact on Postoperative Outcomes. A Population-Based Study Across the English National Health Service, 2009-2014

AIMS

Preoperative short-course radiotherapy (SCRT) is an important treatment option for rectal cancer. The length of time between completing SCRT and surgery may influence postoperative outcomes, but the evidence available to determine the optimal interval is limited and often conflicting.

MATERIALS AND METHODS

Information was extracted from a colorectal cancer data repository (CORECT-R) on all surgically treated rectal cancer patients who received SCRT in the English National Health Service between April 2009 and December 2014. The time from radiotherapy to surgery was described across the population. Thirty-day postoperative mortality, returns to theatre, length of stay and 1-year survival were investigated in relation to the interval between radiotherapy and surgery.

RESULTS

Within the cohort of 3469 patients, the time to surgery was 0-7 days for 76% of patients, 8-14 days for 19% of patients and 15-27 days for 5% of patients. There was a clear variation in relation to different patient characteristics. There was, however, no evidence of differences in postoperative outcomes in relation to interval length.

CONCLUSIONS

This study suggests that the time interval between SCRT and surgery does not influence postoperative outcomes up to a year after surgery. The study provides population-level, real-world evidence to complement that from clinical trials.

Genetic determinants of age-related macular degeneration in diverse populations from the PAGE study

PURPOSE

Substantial progress has been made in identifying susceptibility variants for AMD in European populations; however, few studies have been conducted to understand the role these variants play in AMD risk in diverse populations. The present study aims to examine AMD risk across diverse populations in known and suspected AMD complement factor and lipid-related loci.

METHODS

Targeted genotyping was performed across study sites for AMD and lipid trait-associated single nucleotide polymorphism (SNPs). Genetic association tests were performed at individual sites and then meta-analyzed using logistic regression assuming an additive genetic model stratified by self-described race/ethnicity. Participants included cases with early or late AMD and controls with no signs of AMD as determined by fundus photography. Populations included in this study were European Americans, African Americans, Mexican Americans, and Singaporeans from the Population Architecture using Genomics and Epidemiology (PAGE) study.

RESULTS

Index variants of AMD, rs1061170 (CFH) and rs10490924 (ARMS2), were associated with AMD at P=3.05×10(-8) and P=6.36×10(-6), respectively, in European Americans. In general, none of the major AMD index variants generalized to our non-European populations with the exception of rs10490924 in Mexican Americans at an uncorrected P value<0.05. Four lipid-associated SNPS (LPL rs328, TRIB1 rs6987702, CETP rs1800775, and KCTD10/MVK rs2338104) were associated with AMD in African Americans and Mexican Americans (P<0.05), but these associations did not survive strict corrections for multiple testing.

CONCLUSIONS

While most associations did not generalize in the non-European populations, variants within lipid-related genes were found to be associated with AMD. This study highlights the need for larger well-powered studies in non-European populations.

Genetic variants associated with fasting glucose and insulin concentrations in an ethnically diverse population: results from the Population Architecture using Genomics and Epidemiology (PAGE) study

BACKGROUND

Multiple genome-wide association studies (GWAS) within European populations have implicated common genetic variants associated with insulin and glucose concentrations. In contrast, few studies have been conducted within minority groups, which carry the highest burden of impaired glucose homeostasis and type 2 diabetes in the U.S.

METHODS

As part of the 'Population Architecture using Genomics and Epidemiology (PAGE) Consortium, we investigated the association of up to 10 GWAS-identified single nucleotide polymorphisms (SNPs) in 8 genetic regions with glucose or insulin concentrations in up to 36,579 non-diabetic subjects including 23,323 European Americans (EA) and 7,526 African Americans (AA), 3,140 Hispanics, 1,779 American Indians (AI), and 811 Asians. We estimated the association between each SNP and fasting glucose or log-transformed fasting insulin, followed by meta-analysis to combine results across PAGE sites.

RESULTS

Overall, our results show that 9/9 GWAS SNPs are associated with glucose in EA (p = 0.04 to 9 × 10-15), versus 3/9 in AA (p= 0.03 to 6 × 10-5), 3/4 SNPs in Hispanics, 2/4 SNPs in AI, and 1/2 SNPs in Asians. For insulin we observed a significant association with rs780094/GCKR in EA, Hispanics and AI only.

CONCLUSIONS

Generalization of results across multiple racial/ethnic groups helps confirm the relevance of some of these loci for glucose and insulin metabolism. Lack of association in non-EA groups may be due to insufficient power, or to unique patterns of linkage disequilibrium.

Generalization and dilution of association results from European GWAS in populations of non-European ancestry: the PAGE study

The vast majority of genome-wide association study (GWAS) findings reported to date are from populations with European Ancestry (EA), and it is not yet clear how broadly the genetic associations described will generalize to populations of diverse ancestry. The Population Architecture Using Genomics and Epidemiology (PAGE) study is a consortium of multi-ancestry, population-based studies formed with the objective of refining our understanding of the genetic architecture of common traits emerging from GWAS. In the present analysis of five common diseases and traits, including body mass index, type 2 diabetes, and lipid levels, we compare direction and magnitude of effects for GWAS-identified variants in multiple non-EA populations against EA findings. We demonstrate that, in all populations analyzed, a significant majority of GWAS-identified variants have allelic associations in the same direction as in EA, with none showing a statistically significant effect in the opposite direction, after adjustment for multiple testing. However, 25% of tagSNPs identified in EA GWAS have significantly different effect sizes in at least one non-EA population, and these differential effects were most frequent in African Americans where all differential effects were diluted toward the null. We demonstrate that differential LD between tagSNPs and functional variants within populations contributes significantly to dilute effect sizes in this population. Although most variants identified from GWAS in EA populations generalize to all non-EA populations assessed, genetic models derived from GWAS findings in EA may generate spurious results in non-EA populations due to differential effect sizes. Regardless of the origin of the differential effects, caution should be exercised in applying any genetic risk prediction model based on tagSNPs outside of the ancestry group in which it was derived. Models based directly on functional variation may generalize more robustly, but the identification of functional variants remains challenging.

Association of functional polymorphism rs2231142 (Q141K) in the ABCG2 gene with serum uric acid and gout in 4 US populations: the PAGE Study

A loss-of-function mutation (Q141K, rs2231142) in the ATP-binding cassette, subfamily G, member 2 gene (ABCG2) has been shown to be associated with serum uric acid levels and gout in Asians, Europeans, and European and African Americans; however, less is known about these associations in other populations. Rs2231142 was genotyped in 22,734 European Americans, 9,720 African Americans, 3,849 Mexican Americans, and 3,550 American Indians in the Population Architecture using Genomics and Epidemiology (PAGE) Study (2008-2012). Rs2231142 was significantly associated with serum uric acid levels (P = 2.37 × 10(-67), P = 3.98 × 10(-5), P = 6.97 × 10(-9), and P = 5.33 × 10(-4) in European Americans, African Americans, Mexican Americans, and American Indians, respectively) and gout (P = 2.83 × 10(-10), P = 0.01, and P = 0.01 in European Americans, African Americans, and Mexican Americans, respectively). Overall, the T allele was associated with a 0.24-mg/dL increase in serum uric acid level (P = 1.37 × 10(-80)) and a 1.75-fold increase in the odds of gout (P = 1.09 × 10(-12)). The association between rs2231142 and serum uric acid was significantly stronger in men, postmenopausal women, and hormone therapy users compared with their counterparts. The association with gout was also significantly stronger in men than in women. These results highlight a possible role of sex hormones in the regulation of ABCG2 urate transporter and its potential implications for the prevention, diagnosis, and treatment of hyperuricemia and gout.

Replication of genetic loci for ages at menarche and menopause in the multi-ethnic Population Architecture using Genomics and Epidemiology (PAGE) study

STUDY QUESTION

Do genetic associations identified in genome-wide association studies (GWAS) of age at menarche (AM) and age at natural menopause (ANM) replicate in women of diverse race/ancestry from the Population Architecture using Genomics and Epidemiology (PAGE) Study?

SUMMARY ANSWER

We replicated GWAS reproductive trait single nucleotide polymorphisms (SNPs) in our European descent population and found that many SNPs were also associated with AM and ANM in populations of diverse ancestry.

WHAT IS KNOWN ALREADY

Menarche and menopause mark the reproductive lifespan in women and are important risk factors for chronic diseases including obesity, cardiovascular disease and cancer. Both events are believed to be influenced by environmental and genetic factors, and vary in populations differing by genetic ancestry and geography. Most genetic variants associated with these traits have been identified in GWAS of European-descent populations.

STUDY DESIGN, SIZE, DURATION

A total of 42 251 women of diverse ancestry from PAGE were included in cross-sectional analyses of AM and ANM.

MATERIALS, SETTING, METHODS

SNPs previously associated with ANM (n = 5 SNPs) and AM (n = 3 SNPs) in GWAS were genotyped in American Indians, African Americans, Asians, European Americans, Hispanics and Native Hawaiians. To test SNP associations with ANM or AM, we used linear regression models stratified by race/ethnicity and PAGE sub-study. Results were then combined in race-specific fixed effect meta-analyses for each outcome. For replication and generalization analyses, significance was defined at P < 0.01 for ANM analyses and P < 0.017 for AM analyses.

MAIN RESULTS AND THE ROLE OF CHANCE

We replicated findings for AM SNPs in the LIN28B locus and an intergenic region on 9q31 in European Americans. The LIN28B SNPs (rs314277 and rs314280) were also significantly associated with AM in Asians, but not in other race/ethnicity groups. Linkage disequilibrium (LD) patterns at this locus varied widely among the ancestral groups. With the exception of an intergenic SNP at 13q34, all ANM SNPs replicated in European Americans. Three were significantly associated with ANM in other race/ethnicity populations: rs2153157 (6p24.2/SYCP2L), rs365132 (5q35/UIMC1) and rs16991615 (20p12.3/MCM8). While rs1172822 (19q13/BRSK1) was not significant in the populations of non-European descent, effect sizes showed similar trends.

LIMITATIONS, REASONS FOR CAUTION

Lack of association for the GWAS SNPs in the non-European American groups may be due to differences in locus LD patterns between these groups and the European-descent populations included in the GWAS discovery studies; and in some cases, lower power may also contribute to non-significant findings.

WIDER IMPLICATIONS OF THE FINDINGS

The discovery of genetic variants associated with the reproductive traits provides an important opportunity to elucidate the biological mechanisms involved with normal variation and disorders of menarche and menopause. In this study we replicated most, but not all reported SNPs in European descent populations and examined the epidemiologic architecture of these early reported variants, describing their generalizability and effect size across differing ancestral populations. Such data will be increasingly important for prioritizing GWAS SNPs for follow-up in fine-mapping and resequencing studies, as well as in translational research.

Genetic variation and reproductive timing: African American women from the Population Architecture using Genomics and Epidemiology (PAGE) Study

Age at menarche (AM) and age at natural menopause (ANM) define the boundaries of the reproductive lifespan in women. Their timing is associated with various diseases, including cancer and cardiovascular disease. Genome-wide association studies have identified several genetic variants associated with either AM or ANM in populations of largely European or Asian descent women. The extent to which these associations generalize to diverse populations remains unknown. Therefore, we sought to replicate previously reported AM and ANM findings and to identify novel AM and ANM variants using the Metabochip (n = 161,098 SNPs) in 4,159 and 1,860 African American women, respectively, in the Women's Health Initiative (WHI) and Atherosclerosis Risk in Communities (ARIC) studies, as part of the Population Architecture using Genomics and Epidemiology (PAGE) Study. We replicated or generalized one previously identified variant for AM, rs1361108/CENPW, and two variants for ANM, rs897798/BRSK1 and rs769450/APOE, to our African American cohort. Overall, generalization of the majority of previously-identified variants for AM and ANM, including LIN28B and MCM8, was not observed in this African American sample. We identified three novel loci associated with ANM that reached significance after multiple testing correction (LDLR rs189596789, p = 5×10⁻⁰⁸; KCNQ1 rs79972789, p = 1.9×10⁻⁰⁷; COL4A3BP rs181686584, p = 2.9×10⁻⁰⁷). Our most significant AM association was upstream of RSF1, a gene implicated in ovarian and breast cancers (rs11604207, p = 1.6×10⁻⁰⁶). While most associations were identified in either AM or ANM, we did identify genes suggestively associated with both: PHACTR1 and ARHGAP42. The lack of generalization coupled with the potentially novel associations identified here emphasize the need for additional genetic discovery efforts for AM and ANM in diverse populations.

Consistent directions of effect for established type 2 diabetes risk variants across populations: the population architecture using Genomics and Epidemiology (PAGE) Consortium

Common genetic risk variants for type 2 diabetes (T2D) have primarily been identified in populations of European and Asian ancestry. We tested whether the direction of association with 20 T2D risk variants generalizes across six major racial/ethnic groups in the U.S. as part of the Population Architecture using Genomics and Epidemiology Consortium (16,235 diabetes case and 46,122 control subjects of European American, African American, Hispanic, East Asian, American Indian, and Native Hawaiian ancestry). The percentage of positive (odds ratio [OR] >1 for putative risk allele) associations ranged from 69% in American Indians to 100% in European Americans. Of the nine variants where we observed significant heterogeneity of effect by racial/ethnic group (P(heterogeneity) < 0.05), eight were positively associated with risk (OR >1) in at least five groups. The marked directional consistency of association observed for most genetic variants across populations implies a shared functional common variant in each region. Fine-mapping of all loci will be required to reveal markers of risk that are important within and across populations.

A novel tracer technique for the assessment of fine sediment dynamics in urban water management systems

Urban storm water run off can reduce the quality of receiving waters due to high sediment load and associated sediment-bound contaminants. Consequently, urban water management systems, such as detention ponds, that both modify water quantity through storage and improve water quality through sediment retention are frequently-used best management practices. To manage such systems effectively and to improve their efficiency, there is a need to understand the dynamics (transport and settling) of sediment, and in particular the fine sediment fraction (<63 μm) and its associated contaminants within urban storm water management systems. This can be difficult to achieve, as modelling the transport behaviour of fine-grained and cohesive sediment is problematic and field-based measurements can be costly, time-consuming and unrepresentative. The aim of this study was to test the application of a novel cohesive sediment tracer and to determine fine sediment transport dynamics within a storm water detention pond. The cohesive sediment tracer used was a holmium labelled montmorillonite clay which flocculated and had similar size and settling velocity to the natural pond sediment it was intended to mimic. The tracer demonstrated that fine sediment was deposited across the entire pond, with the presence of reed beds and water depth being important factors for maximising sediment retention. The results of the sediment tracer experiment were in good agreement with those of a mathematical sediment transport model. Here, the deposited sediment tracer was sampled by collecting and analysing surface pond sediments for holmium. However, analysis and sampling of the three dimensional suspended tracer 'cloud' may provide more accurate information regarding internal pond sediment dynamics.

Dissection of chromosome 16p12 linkage peak suggests a possible role for CACNG3 variants in age-related macular degeneration susceptibility

PURPOSE

Age-related macular degeneration (AMD) is a complex disorder of the retina, characterized by drusen, geographic atrophy, and choroidal neovascularization. Cigarette smoking and the genetic variants CFH Y402H, ARMS2 A69S, CFB R32Q, and C3 R102G have been strongly and consistently associated with AMD. Multiple linkage studies have found evidence suggestive of another AMD locus on chromosome 16p12 but the gene responsible has yet to be identified.

METHODS

In the initial phase of the study, single-nucleotide polymorphisms (SNPs) across chromosome 16 were examined for linkage and/or association in 575 Caucasian individuals from 148 multiplex and 77 singleton families. Additional variants were tested in an independent dataset of unrelated cases and controls. According to these results, in combination with gene expression data and biological knowledge, five genes were selected for further study: CACNG3, HS3ST4, IL4R, Q7Z6F8, and ITGAM.

RESULTS

After genotyping additional tagging SNPs across each gene, the strongest evidence for linkage and association was found within CACNG3 (rs757200 nonparametric LOD* = 3.3, APL (association in the presence of linkage) P = 0.06, and rs2238498 MQLS (modified quasi-likelihood score) P = 0.006 in the families; rs2283550 P = 1.3 × 10(-6), and rs4787924 P = 0.002 in the case-control dataset). After adjusting for known AMD risk factors, rs2283550 remained strongly associated (P = 2.4 × 10(-4)). Furthermore, the association signal at rs4787924 was replicated in an independent dataset (P = 0.035) and in a joint analysis of all the data (P = 0.001).

CONCLUSIONS

These results suggest that CACNG3 is the best candidate for an AMD risk gene within the 16p12 linkage peak. More studies are needed to confirm this association and clarify the role of the gene in AMD pathogenesis.

Using genetic variation and environmental risk factor data to identify individuals at high risk for age-related macular degeneration

A major goal of personalized medicine is to pre-symptomatically identify individuals at high risk for disease using knowledge of each individual's particular genetic profile and constellation of environmental risk factors. With the identification of several well-replicated risk factors for age-related macular degeneration (AMD), the leading cause of legal blindness in older adults, this previously unreachable goal is beginning to seem less elusive. However, recently developed algorithms have either been much less accurate than expected, given the strong effects of the identified risk factors, or have not been applied to independent datasets, leaving unknown how well they would perform in the population at large. We sought to increase accuracy by using novel modeling strategies, including multifactor dimensionality reduction (MDR) and grammatical evolution of neural networks (GENN), in addition to the traditional logistic regression approach. Furthermore, we rigorously designed and tested our models in three distinct datasets: a Vanderbilt-Miami (VM) clinic-based case-control dataset, a VM family dataset, and the population-based Age-related Maculopathy Ancillary (ARMA) Study cohort. Using a consensus approach to combine the results from logistic regression and GENN models, our algorithm was successful in differentiating between high- and low-risk groups (sensitivity 77.0%, specificity 74.1%). In the ARMA cohort, the positive and negative predictive values were 63.3% and 70.7%, respectively. We expect that future efforts to refine this algorithm by increasing the sample size available for model building, including novel susceptibility factors as they are discovered, and by calibrating the model for diverse populations will improve accuracy.

Analysis of the indel at the ARMS2 3'UTR in age-related macular degeneration

Controversy remains as to which gene at the chromosome 10q26 locus confers risk for age-related macular degeneration (AMD) and statistical genetic analysis is confounded by the strong linkage disequilibrium (LD) across the region. Functional analysis of related genetic variations could solve this puzzle. Recently, Fritsche et al. reported that AMD is associated with unstable ARMS2 transcripts possibly caused by a complex insertion/deletion (indel; consisting of a 443 bp deletion and an adjacent 54 bp insertion) in its 3'UTR (untranslated region). To validate this indel, we sequenced our samples. We found that this indel is even more complex and is composed of two side-by-side indels separated by 17 bp: (1) 9 bp deletion with 10 bp insertion; (2) 417 bp deletion with 27 bp insertion. The indel is significantly associated with the risk of AMD, but is also in strong LD with the non-synonymous single nucleotide polymorphism rs10490924 (A69S). We also found that ARMS2 is expressed not only in placenta and retina but also in multiple human tissues. Using quantitative PCR, we found no correlation between the indel and ARMS2 mRNA level in human retina and blood samples. The lack of functional effects of the 3'UTR indel, the amino acid substitution of rs10490924 (A69S), and strong LD between them suggest that A69S, not the indel, is the variant that confers risk of AMD. To our knowledge, it is the first time it has been shown that ARMS2 is widely expressed in human tissues. Conclusively, the indel at 3'UTR of ARMS2 actually contains two side-by-side indels. The indels are associated with risk of AMD, but not correlated with ARMS2 mRNA level.

Use of principal components analysis (PCA) on estuarine sediment datasets: the effect of data pre-treatment

Principal components analysis (PCA) is a multivariate statistical technique capable of discerning patterns in large environmental datasets. Although widely used, there is disparity in the literature with respect to data pre-treatment prior to PCA. This research examines the influence of commonly reported data pre-treatment methods on PCA outputs, and hence data interpretation, using a typical environmental dataset comprising sediment geochemical data from an estuary in SE England. This study demonstrated that applying the routinely used log (x + 1) transformation skewed the data and masked important trends. Removing outlying samples and correcting for the influence of grain size had the most significant effect on PCA outputs and data interpretation. Reducing the influence of grain size using granulometric normalisation meant that other factors affecting metal variability, including mineralogy, anthropogenic sources and distance along the salinity transect could be identified and interpreted more clearly.

Localization of age-related macular degeneration-associated ARMS2 in cytosol, not mitochondria

PURPOSE

To analyze the relationship between ARMS2 and HTRA1 in the association with age-related macular degeneration (AMD) in an independent case-control dataset and to investigate the subcellular localization of the ARMS2 protein in an in vitro system.

METHODS

Two SNPs in ARMS2 and HTRA1 were genotyped in 685 cases and 269 controls by a genotyping assay. Allelic association was tested by a chi(2) test. A likelihood ratio test (LRT) of full versus reduced models was used to analyze the interaction between ARMS2 and smoking and HTRA1 and smoking, after adjustment for CFH and age. Immunofluorescence and immunoblot were applied to localize ARMS2 in retinal epithelial ARPE-19 cells and COS7 cell transfected by ARMS2 constructs.

RESULTS

Both significantly associated SNP rs10490924 and rs11200638 (P < 0.0001) are in strong linkage disequilibrium (LD; D' = 0.97, r(2) = 0.93) that generates virtually identical association test and odds ratios. In separate logistic regression models, the interaction effect for both smoking with ARMS2 and with HTRA1 was not statistically significant. Immunofluorescence and immunoblot show that both endogenous and exogenous ARMS2 are mainly distributed in the cytosol, not the mitochondria. Compared with the wild-type, ARMS2 A69S is more likely to be associated with the cytoskeleton in COS7 cells.

CONCLUSIONS

The significant associations in ARMS2 and HTRA1 are with polymorphisms in strong LD that confer virtually identical risks, preventing differentiation at the statistical level. ARMS2 was mainly distributed in the cytosol, not in the mitochondrial outer membrane as previously reported, suggesting that ARMS2 may not confer risk to AMD through the mitochondrial pathway.

C3 R102G polymorphism increases risk of age-related macular degeneration

Inflammation has long been suspected to play a role in the pathogenesis of age-related macular degeneration (AMD). Association of variants in the complement factor H (CFH) and complement factor B (CFB) genes has targeted the search for additional loci to the alternative complement cascade, of which C3 is a major component. Two non-synonymous coding polymorphisms within C3, R102G and L314P, have previously been strongly associated with increased risk. These variants are in strong linkage disequilibrium (LD), making the contribution of this locus to AMD even more difficult to ascertain. We sought to determine whether the C3 association resulted primarily from only one of these two variants or from a combined effect of both in 223 families and an independent dataset of 701 cases and 286 unrelated controls. The C3 polymorphisms were in strong LD (r(2) = 0.85), and both were associated in the family-based and case-control datasets (R102G genoPDT P = 0.02, case-control genotypic P = 0.004; L314P genoPDT P = 0.001, case-control genotypic P = 0.04). In conditional analyses in the case-control dataset, R102G remained associated with disease in the L314P risk allele carriers (P = 0.01), but there was no effect of L314P in the R102G risk allele carriers (P = 0.2). After adjusting for age, smoking, CFH Y402H, LOC387715 A69S, and CFB R32Q, the effect of R102G remained strong [P = 0.015, odds ratio = 1.55, 95% confidence interval 1.09 to 2.21, adjusted PAR(population attributable risk) = 0.17]. Therefore, while the strong LD between R102G and L314P makes it difficult to disentangle their individual effects on disease risk, the R102G polymorphism acting alone provides the best model for disease in our data.

Deletion of CFHR3 and CFHR1 genes in age-related macular degeneration

Age-related macular degeneration (AMD) impairs vision for approximately 7.5 million Americans. Both susceptibility variants and protective haplotypes in the complement factor H (CFH) gene modulate risk for AMD. Recently, deletion of the 'CFH-related' genes CFHR1 and CFHR3 was found to be segregating with a particular CFH haplotype, which reduced the risk of AMD. We tested the deletion for association in a Caucasian population of 780 cases and 265 controls and examined its effect in the context of known AMD risk factors. The deletion did not segregate perfectly with any one SNP, as previously suggested. CFH haplotype P2 was the most frequent haplotype in deletion homozygotes (47%), and the majority (14/16) of these individuals were homozygous for the non-risk allele of Y402H. Overall, deletion homozygosity was significantly more frequent in controls than cases (2.6% controls, 0.8% cases, P = 0.025, OR = 0.29, 95% CI = 0.10-0.86). After controlling for age, Y402H, smoking and LOC387715 A69S, the protective effect of the deletion was no longer statistically significant (P = 0.27). However, using a CFH haplotype that all deletion homozygotes share as a surrogate for the deletion, this marker remained modestly associated with AMD after adjustment for known risk factors (OR = 0.63, 95% CI 0.39-1.04, P = 0.07). Therefore, deletion of CFHR1 and CFHR3 may account for a small portion of the protection from AMD associated with particular haplotypes in CFH. The presence of protective haplotypes in CFH that do not carry the deletion, suggests that other protective variants in this region have yet to be discovered.

Haplotypes spanning the complement factor H gene are protective against age-related macular degeneration

PURPOSE

Age-related macular degeneration (AMD) is a devastating disorder that adversely affects the quality of life of nearly 2 million Americans who have advanced forms of the disease. Besides the well-known risk imparted by carrying the Y402H variant in the complement factor H (CFH) gene on chromosome 1, recent evidence of the existence of protective haplotypes spanning CFH has been reported.

METHODS

The haplo.stats program was used to test for association of the protective haplotypes after adjusting for age in the dataset of 584 sporadic cases and 248 control samples. Logistic regression modeling and likelihood ratio tests were used to investigate an interaction between a particular haplotype and smoking status. The HBAT option of FBAT was used to confirm the associations in an independent dataset of 201 families.

RESULTS

Two protective (P) haplotypes in a family-based dataset (P1 = CAATTTAG, P = 0.021; and P2 = CGGCTTAG, P = 0.018) were identified for the first time. Age-adjusted score statistics provided support for these protective haplotypes in the case-control dataset (P1 frequency in cases approximately 13%, in controls approximately 20%, P = 0.001; P2 frequency in cases approximately 5%, in controls approximately 8%, P = 0.077). There was also tentative evidence of an interaction between one of the protective haplotypes and cigarette smoking (P = 0.04 likelihood ratio test for P2-smoking interaction).

CONCLUSIONS

Replication of the association between the protective haplotypes and decreased AMD susceptibility provides increased evidence that these associations have biological meaning. The suggestion of a haplotype-smoking interaction adds to the growing body of evidence that smoking is an important environmental covariate in AMD that should be considered in genetic studies. Identification of the protective variant(s) carried within these haplotypes is critical for understanding the etiology of AMD.

Protective effect of complement factor B and complement component 2 variants in age-related macular degeneration

Age-related macular degeneration (AMD) is a devastating disorder of the central retina, causing significant visual impairment for 7.5 million elderly Americans. Abnormal regulation of the complement system likely caused by the Y402H polymorphism in the complement factor H gene is a recognized risk factor for AMD, as is the A69S variant in the poorly characterized LOC387715 gene. Recently, polymorphisms in the factor B (CFB) and complement component 2 (CC2) genes were associated with decreased susceptibility to AMD. To validate this association in independent family-based and case-control Caucasian data sets, we genotyped two single-nucleotide polymorphisms (SNPs) in CC2 and four SNPs in CFB. The R32Q variant of CFB was significantly associated with protection from AMD in the family-based data set (P = 0.025). Three SNPs in CC2 and CFB were strongly associated with decreased risk of AMD in the case-control data set (CC2 E318D: P = 0.02; CC2 rs547154: P = 9 x 10(-6); and CFB R32Q P = 2 x 10(-5)). The minor alleles at CC2 rs547154 and CFB R32Q are present in 4% of cases versus 10% of controls, and as these SNPs are in strong linkage disequilibrium (r(2)=0.92), these results likely represent the same protective signal. After controlling for age, Y402H, A69S and smoking, the effect of CFB R32Q remained quite strong (OR 0.21, 95% confidence interval 0.11-0.39; P < 10(-4)). Likelihood ratio testing and conditional analyses in the case-control data set suggest that a weaker, independent protective effect exists for CC2 E318D.

Independent Effects of Complement Factor H Y402H Polymorphism and Cigarette Smoking on Risk of Age-Related Macular Degeneration

OBJECTIVE

To examine the potential gene-environment interaction between cigarette smoking and the complement factor H (CFH) T1277C polymorphism, 2 strong risk factors for age-related macular degeneration (AMD).

DESIGN

Retrospective case-control study.

PARTICIPANTS

A university clinic-based sample of 599 people with AMD and 242 controls.

METHODS

Standard criteria were used to rate disease severity (grades 1-5) from fundus photographs. Individuals were classified as "ever smokers" or "never smokers" based on self-reported lifetime smoking of at least 100 cigarettes. Intensity of smoking was evaluated by calculating pack-years of smoking, which was analyzed as a continuous variable, and by categorizing individuals as smoking more or less than the median 30 pack-years. T1277C genotypes were determined by sequencing the polymorphic site. Generalized estimating equations were used to analyze the effects of smoking and genotype, controlling for age and gender and adjusting for correlations among related subjects.

MAIN OUTCOME MEASURE

Age-related macular degeneration affection status.

RESULTS

Interaction terms between T1277C genotype and smoking variables were not statistically significant, indicating a multiplicative relationship between risk factors. Effects of both T1277C genotype and cigarette smoking were stronger when comparing neovascular (grade 5) AMD with grade 1 controls than when comparing all cases (grades 3-5) with grades 1 to 2 controls.

CONCLUSION

These results suggest that cigarette smoking and T1277C are independent risk factors for AMD and that both risk factors are associated more strongly with neovascular AMD than all forms of AMD combined.

Potential impacts of water injection dredging on water quality and ecotoxicity in Limehouse Basin, River Thames, SE England, UK

The use of water injection dredging (WID) is increasing in the UK's inland waterways and marinas. Jets of water are injected under low pressure directly into bottom sediment creating a turbulent water-sediment mixture that flows under the influence of gravity. Many of these sediments are highly contaminated and little is known of the effects of contaminant release on water quality or the risk to biota living in both the sediment and the water column. Sediment cores were collected from Limehouse Basin, a proposed WID site in SE England and current sediment toxicity was assessed using a number of techniques. Comparison of metal data to US sediment quality guidelines indicated intermediate levels of toxicity while, calculation of acid volatile sulphide to simultaneously extracted metal ratios underestimated the potential toxicity to sediment dwelling organisms. In contrast, porewater ammonia concentrations were in excess of all published ecotoxicological guidelines and indicate serious risk to biota. Re-suspension experiments were used to mimic the effects of WID on overlying water quality and ecotoxicity tests were carried out on elutriates using Daphnia magna to examine the impacts on biota. Concentrations of a range of metals in the elutriates predict that adverse biological effects would be observed during WID, however only 10% of the elutriate samples caused an adverse effect on Daphnia. Limehouse Basin is a complex aquatic environment receiving predominantly fresh waters while the sediments have high porewater chloride concentrations reminiscent of previous tidal inputs to the basin, making the choice of test organism problematic.

Complement factor H variant increases the risk of age-related macular degeneration

Age-related macular degeneration (AMD) is a leading cause of visual impairment and blindness in the elderly whose etiology remains largely unknown. Previous studies identified chromosome 1q32 as harboring a susceptibility locus for AMD. We used single-nucleotide polymorphisms to interrogate this region and identified a strongly associated haplotype in two independent data sets. DNA resequencing of the complement factor H gene within this haplotype revealed a common coding variant, Y402H, that significantly increases the risk for AMD with odds ratios between 2.45 and 5.57. This common variant likely explains approximately 43% of AMD in older adults.

Clinical Chemical Studies in Aleutian Disease of Mink

Clinical chemical determinations were carried out on blood removed by cardiac puncture from 49 mink affected with Aleutian disease and 25 normal animals and the respective differences tested for statistical significance. Blood urea nitrogen, serum total protein and globulin, thymol turbidity, glutamic oxalacetic and glutamic pyruvic transaminases and amylase were definitely elevated in the affected animals whereas serum calcium, albumin and A/G ratio were depressed. No statistically significant difference was apparent between the two groups in the comparison of inorganic phosphorus, alkaline and acid phosphatases, bilirubin, total cholesterol and esters, cephalin-cholesterol flocculation (3+ in each case), sodium, potassium, chloride, CO(2)-combining power, leucine aminopeptidase and lactic dehydrogenase (means: over 2,000 u./ml.). For both the control and affected mink, the distribution of serum lactic dehydrogenase isozymes resembled that of human homologous serum hepatitis. Electrophoresis of serum proteins confirmed earlier findings of hypergammaglobulinemia in the diseased animals but a fast-moving or pre-albumin component, averaging 4% of the total protein, occurred in both the diseased and normal mink.