Genomic inflation factors under polygenic inheritance

Population structure, including population stratification and cryptic relatedness, can cause spurious associations in genome-wide association studies (GWAS). Usually, the scaled median or mean test statistic for association calculated from multiple single-nucleotide-polymorphisms across the genome is used to assess such effects, and 'genomic control' can be applied subsequently to adjust test statistics at individual loci by a genomic inflation factor. Published GWAS have clearly shown that there are many loci underlying genetic variation for a wide range of complex diseases and traits, implying that a substantial proportion of the genome should show inflation of the test statistic. Here, we show by theory, simulation and analysis of data that in the absence of population structure and other technical artefacts, but in the presence of polygenic inheritance, substantial genomic inflation is expected. Its magnitude depends on sample size, heritability, linkage disequilibrium structure and the number of causal variants. Our predictions are consistent with empirical observations on height in independent samples of ~4000 and ~133,000 individuals.

GWAS of butyrylcholinesterase activity identifies four novel loci, independent effects within BCHE and secondary associations with metabolic risk factors

Serum butyrylcholinesterase (BCHE) activity is associated with obesity, blood pressure and biomarkers of cardiovascular and diabetes risk. We have conducted a genome-wide association scan to discover genetic variants affecting BCHE activity, and to clarify whether the associations between BCHE activity and cardiometabolic risk factors are caused by variation in BCHE or whether BCHE variation is secondary to the metabolic abnormalities. We measured serum BCHE in adolescents and adults from three cohorts of Australian twin and family studies. The genotypes from approximately 2.4 million single-nucleotide polymorphisms (SNPs) were available in 8791 participants with BCHE measurements. We detected significant associations with BCHE activity at three independent groups of SNPs at the BCHE locus (P = 5.8 x 10(-262), 7.8 x 10(-47), 2.9 x 10(-12)) and at four other loci: RNPEP (P = 9.4 x 10(-16)), RAPH1-ABI2 (P = 4.1 x 10(-18)), UGT1A1 (P = 4.0 x 10(-8)) and an intergenic region on chromosome 8 (P = 1.4 x 10(-8)). These loci affecting BCHE activity were not associated with metabolic risk factors. On the other hand, SNPs in genes previously associated with metabolic risk had effects on BCHE activity more often than can be explained by chance. In particular, SNPs within FTO and GCKR were associated with BCHE activity, but their effects were partly mediated by body mass index and triglycerides, respectively. We conclude that variation in BCHE activity is due to multiple variants across the spectrum from uncommon/large effect to common/small effect, and partly results from (rather than causes) metabolic abnormalities.

Novel prognostic factors in chronic myeloid leukemia

Chronic myeloid leukemia (CML) is a malignant clonal blood disease that originates from a pluripotent hematopoietic stem cell. The cytogenetic hallmark of CML, the Philadelphia chromosome (Ph), is formed as a result of reciprocal translocation between chromosomes 9 and 22, which leads to a formation of a chimeric BCR-ABL fusion gene. The BCR-ABL protein is a constitutively active tyrosine kinase that changes the adhesion properties of cells, constitutively activates mitogenic signaling, enhances cell proliferation and reduces apoptosis. This results in leukemic growth and the clinical disease, CML. With the advent of targeted therapies against the BCR-ABL fusion protein, the treatment of CML has changed considerably during the recent decade. In this thesis, the clinical significance of different diagnostic methods and new prognostic factors in CML have been assessed. First, the association between two different methods for measuring CML disease burden (the RQ-PCR and the high mitotic index metaphase FISH) was assessed in bone marrow and peripheral blood samples. The correlation between positive RQ-PCR and metaphase FISH samples was high. However, RQ-PCR was more sensitive and yielded measurable transcripts in 40% of the samples that were negative by metaphase FISH. The study established a laboratory-specific conversion factor for setting up the International Scale when standardizing RQ-PCR measurements. Secondly, the amount of minimal residual disease (MRD) after allogeneic hematopoietic stem cell transplantation (alloHSCT) was determined. For this, metaphase FISH was done for the bone marrow samples of 102 CML patients. Most (68%), had no residual cells during the entire follow-up time. Some (12 %) patients had minor (<1%) MRD which decreased even further with time, whereas 19% had a progressive rise in MRD that exceeded 1% or had more than 1% residual cells when first detected. Residual cells did not become eradicated spontaneously if the frequency of Ph+ cells exceeded 1% during follow-up. Next, the impact of deletions in the derivative chromosome 9, was examined. Deletions were observed in 15% of the CML patients who later received alloHSCT. After alloHSCT, there was no difference in the total relapse rate in patients with or without deletions. Nor did the estimates of overall survival, transplant-related mortality, leukemia-free survival and relapse-free time show any difference between these groups. When conventional treatment regimens are used, the der(9) status could be an important criterion, in conjunction with other prognostic factors, when allogeneic transplantation is considered. The significance of der(9) deletions for patients treated with tyrosine kinase inhibitors is not clear and requires further investigation. In addition to the der(9) status of the patient, the significance of bone marrow lymphocytosis as a prognostic factor in CML was assessed. Bone marrow lymphocytosis during imatinib therapy was a positive predictive factor and heralded optimal response. When combined with major cytogenetic response at three months of treatment, bone marrow lymphocytosis predicted a prognostically important major molecular response at 18 months of imatinib treatment. Although the validation of these findings is warranted, the determination of the bone marrow lymphocyte count could be included in the evaluation of early response to imatinib treatment already now. Finally, BCR-ABL kinase domain mutations were studied in CML patients resistant against imatinib treatment. Point mutations detected in the kinase domain were the same as previously reported, but other sequence variants, e.g. deletions or exon splicing, were also found. The clinical significance of the other variations remains to be determined.

Vascular growth factors and progenitor cells in cardiac allograft arteriosclerosis

Heart transplantation is the only therapeutic modality for many end-stage heart diseases but poor long-term survival remains a challenging problem. This is mainly due to the development of cardiac allograft arteriosclerosis (TxCAD) that is an accelerated form of coronary artery disease. Both traditional cardiovascular and transplantation-related risk factors for TxCAD have been identified but options for therapy are limited. TxCAD involves dysfunction of cardiac allograft vascular cells. Activated endothelial cells (EC) regulate allograft inflammation and secrete smooth muscle cell (SMC) growth factors. In turn, SMC and their progenitors invade the intima of the injured vessels and occlude the affected coronary arteries. Different vascular growth factors have to be delicately regulated in normal vascular development. In the present study, experimental heterotopic transplantation models were used to study the role of angiogenic and pro-inflammatory vascular endothelial growth factor (VEGF), EC growth factor angiopoietin (Ang), and SMC mitogen platelet-derived growth factor (PDGF) in the development of TxCAD. Pharmacological and gene transfer approaches were used to target these growth factors and to assess their therapeutic potential. This study shows that alloimmune response in heart transplants upregulates VEGF expression, and induces allograft angiogenesis that involves donor-derived primitive EC. Intracoronary adenoviral VEGF gene transfer increased macrophage infiltration, intimal angiogenesis and TxCAD. VEGF inhibition with PTK787 decreased allograft inflammation and TxCAD, and simultaneous PDGF inhibition with imatinib further decreased TxCAD. Specific inhibition of two VEGF-receptors (VEGFR) decreased allograft inflammation and TxCAD, and VEGFR-2 inhibition normalized the density of primitive and mature capillaries in the allografts. Adenovirus-mediated transient Ang1 expression in the allograft had anti-inflammatory and anti-arteriosclerotic effects. Adeno-associated virus (AAV)-mediated prolonged Ang1 or Ang2 expression had similar anti-inflammatory effects. However, AAV-Ang1 activated allograft SMC whereas AAV-Ang2 had no effects on SMC activation and decreased the development of TxCAD. These studies indicate an interplay of inflammation, angiogenesis and arteriosclerosis in cardiac allografts, and show that vascular growth factors are important regulators in the process. Also, VEGF inhibition, PDGF inhibition and angiopoietin therapy with clinically-relevant pharmacological agents or novel gene therapy approaches may counteract vascular dysfunction in cardiac allografts, and have beneficial effects on the survival of heart transplant patients in the future.

Measuring route passenger load diversity for capacity and quality of service assessment

This paper develops theory that quantifies transit route passenger-relative load factor and distinguishes it from occupancy load factor. The ratio between these measures is defined as the load diversity coefficient, which as a single measure characterizes the diversity of passenger load factor between route segments according to the origin-destination profile. The relationship between load diversity coefficient and route coefficient of variation in occupancy load factor is quantified. Two tables are provided that enhance passenger capacity and quality of service (QoS) assessment regarding onboard passenger load. The first expresses the transit operator’s perspective of load diversity and the passengers’ perspective of load factor relative to the operator’s, across six service levels corresponding to ranges of coefficient of variation in occupancy load factor. The second interprets the relationships between passenger average travel time and each of passenger-relative load factor and occupancy load factor. The application of this methodology is illustrated using a case study of a premium radial bus route in Brisbane, Australia. The methodology can assist in benchmarking and decision making regarding route and schedule design. Future research will apply value of time to QoS measurement, reflecting perceived passenger comfort through crowding and average time spent aboard. This would also assist in transit service quality econometric modeling.

Phosphorus retention in forest soils and the functioning of buffer zones used in forestry

Phosphorus (P) retention properties of soils typical for boreal forest, i.e. podzolic soil and peat soils, vary significantly, but the range of this variation has not been sufficiently documented. To assess the usefulness of buffer zones used in forestry in removing P from the discharge by chemical sorption in soil, and to estimate the risk of P leaching after forestry operations, more data is needed on soil P retention properties. P retention properties of soils were studied at clear-cut areas, unharvested buffer zones adjoining the clear-cut and at peatland buffer zone areas. Desorption-sorption isotherms were determined for the humus layer, the mineral soil horizons E, B and C of the Podzol profile and for the surface layer peat (0-15 cm) and the subsurface layer peat (15-30 cm). The efficiency of buffer zones in retaining P was studied at six peatland buffer zone areas by adding P-containing solute in the inflow. A tracer study was conducted at one of the buffer zone areas to determine the allocation of the added P in soil and vegetation. Measured sorption or desorption rather than parameter values of fitted sorption equations described P desorption and sorption behaviour in soil. The highest P retention efficiency was in the B horizon and consequently, if contact occurred or was established between the soluble P in the water and the soil B horizon, the risk of P leaching was low. Humus layer was completely incapable of retaining P after clear-cutting. In the buffer zones, the decrease in P retention properties in the humus layer and the low amount of P sorbed by it indicated that the importance of the layer in the functioning of buffer zones is low. The peatland buffer zone areas were efficient in retaining soluble P from inflow. P sorption properties of the peat soil at the buffer zone areas varied largely but the contribution of P sorption in the peat was particularly important during high flow in spring, when the vegetation was not fully developed. Factors contributing to efficient P retention were large buffer size and low hydrological load whereas high hydrological load combined with the formation of preferential flow paths, especially during early spring or late autumn was disadvantageous. However, small buffer zone areas, too, may be efficient in reducing P load.

Risk factors associated with corneal nerve alteration in type 1 diabetes in the absence of neuropathy: A longitudinal in vivo corneal confocal microscopy study

Purpose The aim of this study was to determine alterations to the corneal subbasal nerve plexus (SNP) over four years using in vivo corneal confocal microscopy (IVCM) in participants with type 1 diabetes and to identify significant risk factors associated with these alterations. Methods A cohort of 108 individuals with type 1 diabetes and no evidence of peripheral neuropathy at enrollment underwent laser-scanning IVCM, ocular screening, and health and metabolic assessment at baseline and the examinations continued for four subsequent annual visits. At each annual visit, eight central corneal images of the SNP were selected and analyzed to quantify corneal nerve fiber density (CNFD), branch density (CNBD) and fiber length (CNFL). Linear mixed model approaches were fitted to examine the relationship between risk factors and corneal nerve parameters. Results A total of 96 participants completed the final visit and 91 participants completed all visits. No significant relationships were found between corneal nerve parameters and time, sex, duration of diabetes, smoking, alcohol consumption, blood pressure or BMI. However, CNFD was negatively associated with HbA1c (β=-0.76, P<0.01) and age (β=-0.13, P<0.01) and positively related to high density lipids (HDL) (β=2.01, P=0.03). Higher HbA1c (β=-1.58, P=0.04) and age (β=-0.23, P<0.01) also negatively impacted CNBD. CNFL was only affected by higher age (β=-0.06, P<0.01). Conclusions Glycemic control, HDL and age have significant effects on SNP structure. These findings highlight the importance of diabetic management to prevent corneal nerve damage as well as the capability of IVCM for monitoring subclinical alterations in the corneal SNP in diabetes.

Anisochrony of O-methylene protons of ethyl ester functions and structural factors in the connected chiral entities

(i) Incistrans pairs of cyclic 1,3-dicarboxylic acid ethyl esters thecis-foms exhibit higher O-methylene proton (HA, HB) anisochrony than thetrans-forms; (ii) anisochrony, easily observed in certain decalin-10-carboxylic ethyl esters, ‘disappears’ on one of the rings attaining the possibility of transforming into a ‘twist’ form; (iii) in certain pairs of chiralsecethyl esters and theirtert-methylated analogues anisochrony is higher in the latter, contrary to expectation, while, in certain others, the reverse is observed. Attempted explanations are based on assessments whether H A and H B are or are not in highly different magnetic environments in confomers regarded as preferred. This subsumes the possibility thatXYZC-CO2H A H B Me chiral ethyl acetates differ fromXYZC-CH A H B Me ethanes because intervention by the carboxyl group insulates the prochiral centre and allows anisotropic effects to gain somewhat in importance among mechanisms that discriminate between H A and H B so long as rotamerpopulation inequalities persist. Background information on why rotamer-population inequalities will always persist and on a heuristic that attempts to generalize the effects ofXYZ inXYZC - CU AUB V is provided. Possible effects when connectivity exists between a pair amongX, Y, Z or when specific interactions occur betweenV andX, Y orZ are considered. An interpretation in terms of ‘increasing conformational mobility’ has been suggested for the observed increase in the rate of temperature-dependence of O-methylene anisochrony down a series of chiral ethyl esters.