Within-family outliers: Segregating alleles or environmental effects? A linkage analysis of height from 5815 sibling pairs

Most information in linkage analysis for quantitative traits comes from pairs of relatives that are phenotypically most discordant or concordant. Confounding this, within-family outliers from non-genetic causes may create false positives and negatives. We investigated the influence of within-family outliers empirically, using one of the largest genome-wide linkage scans for height. The subjects were drawn from Australian twin cohorts consisting of 8447 individuals in 2861 families, providing a total of 5815 possible pairs of siblings in sibships. A variance component linkage analysis was performed, either including or excluding the within-family outliers. Using the entire dataset, the largest LOD scores were on chromosome 15q (LOD 2.3) and 11q (1.5). Excluding within-family outliers increased the LOD score for most regions, but the LOD score on chromosome 15 decreased from 2.3 to 1.2, suggesting that the outliers may create false negatives and false positives, although rare alleles of large effect may also be an explanation. Several regions suggestive of linkage to height were found after removing the outliers, including 1q23.1 (2.0), 3q22.1 (1.9) and 5q32 (2.3). We conclude that the investigation of the effect of within-family outliers, which is usually neglected, should be a standard quality control measure in linkage analysis for complex traits and may reduce the noise for the search of common variants of modest effect size as well as help identify rare variants of large effect and clinical significance. We suggest that the effect of within-family outliers deserves further investigation via theoretical and simulation studies.

Genomewide linkage study in 1,176 affected sister pair families identifies a significant susceptibility locus for endometriosis on chromosome 10q26

Endometriosis is a common gynecological disease that affects up to 10% of women in their reproductive years. It causes pelvic pain, severe dysmenorrhea, and subfertility. The disease is defined as the presence of tissue resembling endometrium in sites outside the uterus. Its cause remains uncertain despite >50 years of hypothesis-driven research, and thus the therapeutic options are limited. Disease predisposition is inherited as a complex genetic trait, which provides an alternative route to understanding the disease. We seek to identify susceptibility loci, using a positional-cloning approach that starts with linkage analysis to identify genomic regions likely to harbor these genes. We conducted a linkage study of 1,176 families (931 from an Australian group and 245 from a U.K. group), each with at least two members--mainly affected sister pairs--with surgically diagnosed disease. We have identified a region of significant linkage on chromosome 10q26 (maximum LOD score [MLS] of 3.09; genomewide P = .047) and another region of suggestive linkage on chromosome 20p13 (MLS = 2.09). Minor peaks (with MLS > 1.0) were found on chromosomes 2, 6, 7, 8, 12, 14, 15, and 17. This is the first report of linkage to a major locus for endometriosis. The findings will facilitate discovery of novel positional genetic variants that influence the risk of developing this debilitating disease. Greater understanding of the aberrant cellular and molecular mechanisms involved in the etiology and pathophysiology of endometriosis should lead to better diagnostic methods and targeted treatments.

Genomewide significant linkage to migrainous headache on chromosome 5q21

Familial typical migraine is a common, complex disorder that shows strong familial aggregation. Using latent-class analysis (LCA), we identified subgroups of people with migraine/severe headache in a community sample of 12,245 Australian twins (60% female), drawn from two cohorts of individuals aged 23-90 years who completed an interview based on International Headache Society criteria. We report results from genomewide linkage analyses involving 756 twin families containing a total of 790 independent sib pairs (130 affected concordant, 324 discordant, and 336 unaffected concordant for LCA-derived migraine). Quantitative-trait linkage analysis produced evidence of significant linkage on chromosome 5q21 and suggestive linkage on chromosomes 8, 10, and 13. In addition, we replicated previously reported typical-migraine susceptibility loci on chromosomes 6p12.2-p21.1 and 1q21-q23, the latter being within 3 cM of the rare autosomal dominant familial hemiplegic migraine gene (ATP1A2), a finding which potentially implicates ATP1A2 in familial typical migraine for the first time. Linkage analyses of individual migraine symptoms for our six most interesting chromosomes provide tantalizing hints of the phenotypic and genetic complexity of migraine. Specifically, the chromosome 1 locus is most associated with phonophobia; the chromosome 5 peak is predominantly associated with pulsating headache; the chromosome 6 locus is associated with activity-prohibiting headache and photophobia; the chromosome 8 locus is associated with nausea/vomiting and moderate/severe headache; the chromosome 10 peak is most associated with phonophobia and photophobia; and the chromosome 13 peak is completely due to association with photophobia. These results will prove to be invaluable in the design and analysis of future linkage and linkage disequilibrium studies of migraine.

A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other

In this report, we describe a simple correction for multiple testing of single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of pairwise LD between SNPs. This method provides a useful alternative to more computationally intensive permutation tests. Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor "loadings" after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.

Further evidence for linkage of Gilles de la Tourette syndrome (GTS) susceptibility loci on chromosomes 2p11, 8q22 and 11q23-24 in South African Afrikaners

Utilizing DNA samples from 91 Afrikaner nuclear families with one or more affected children, five genomic regions on chromosomes 2p, 8q, 11q, 20q, and 21q that gave evidence for association with GTS in previous case-control association studies were investigated for linkage and association with GTS. Highly polymorphic markers with mean heterozygosity of 0.77 were typed and resulting genotypes evaluated using single marker transmission disequilibrium (TDT), single marker haplotype relative risk (HRR), and multi-marker "extended" TDT and HRR methods. Single marker TDT analysis showed evidence for linkage or association, with p-values near 0.05, for markers D2S139, GATA28F12, and D11S1377 on chromosomes 2p11, 8q22 and 11q23-24, respectively. Extended, two-locus TDT and HRR analysis provided further evidence for linkage or association on chromosome 2 with p-values of 0.007 and 0.025, and chromosome 8 with p-values of 0.059 and 0.013, respectively. These results provide important additional evidence for the location of GTS susceptibility loci.

Exclusion of angiotensinogen gene in molecular basis of human hypertension: Sibpair linkage and association analyses in Australian anglo-caucasians

Linkage with essential hypertension has been claimed for a microsatellite marker near the angiotensinogen gene (AGT; chromosome 1q42), as has association for the AGT variants M235T, G(-6)A and A(-20)C. To more rigorously evaluate AGT as a candidate gene for hypertension we performed sibpair analysis with multiple microsatellite markers surrounding this locus and using more sophisticated analysis programs. We also performed an association study of the AGT variants in unrelated subjects with a strong family history (two affected parents). For the linkage study, single and multiplex polymerase chain reaction (PCRs) and automated genescan analysis were conducted on DNA from 175 Australian Anglo-Celtic Caucasian hypertensives for the following markers: D1S2880-(2.1 cM)-D1S213-(2.8 cM)-D1S251-(6.5 cM)-AGT-(2.0 cM) -D1S235. Statistical evaluation of genotype data by nonparametric methods resulted in the following scores: Single-point analysis - SPLINK, P > 0.18; APM method, P > 0.25; ASPEX, MLOD < 0.28; SIB-PAIR, P > 0. 24; Multipoint analysis - MAPMAKER/SIBS, MLOD < 0.24; GENEHUNTER, P > 0.35. Exclusion scores of Lod -4.1 to -5.1 were obtained for these markers using MAPMAKER/SIBS for a lambda(s) of 1.6. The association study of G(-6)A, A(-20)C and M235T variants in 111 hypertensives with strong family history and 190 normotensives with no family history showed significant linkage disequilibrium between particular haplotypes, but we could find no association with hypertension. The present study therefore excludes AGT in the etiology of hypertension, at least in the population of Australian Anglo-Celtic Caucasians studied.

Membrane associated transporter protein gene (SLC45A2) and the genetic basis of normal human pigmentation variation

This work is concerned with the genetic basis of normal human pigmentation variation. Specifically, the role of polymorphisms within the solute carrier family 45 member 2 (SLC45A2 or membrane associated transporter protein; MATP) gene were investigated with respect to variation in hair, skin and eye colour ― both between and within populations. SLC45A2 is an important regulator of melanin production and mutations in the gene underly the most recently identified form of oculocutaneous albinism. There is evidence to suggest that non-synonymous polymorphisms in SLC45A2 are associated with normal pigmentation variation between populations. Therefore, the underlying hypothesis of this thesis is that polymorphisms in SLC45A2 will alter the function or regulation of the protein, thereby altering the important role it plays in melanogenesis and providing a mechanism for normal pigmentation variation. In order to investigate the role that SLC45A2 polymorphisms play in human pigmentation variation, a DNA database was established which collected pigmentation phenotypic information and blood samples of more than 700 individuals. This database was used as the foundation for two association studies outlined in this thesis, the first of which involved genotyping two previously-described non-synonymous polymorphisms, p.Glu272Lys and p.Phe374Leu, in four different population groups. For both polymorphisms, allele frequencies were significantly different between population groups and the 272Lys and 374Leu alleles were strongly associated with black hair, brown eyes and olive skin colour in Caucasians. This was the first report to show that SLC45A2 polymorphisms were associated with normal human intra-population pigmentation variation. The second association study involved genotyping several SLC45A2 promoter polymorphisms to determine if they also played a role in pigmentation variation. Firstly, the transcription start site (TSS), and hence putative proximal promoter region, was identified using 5' RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE). Two alternate TSSs were identified and the putative promoter region was screened for novel polymorphisms using denaturing high performance liquid chromatography (dHPLC). A novel duplication (c.–1176_–1174dupAAT) was identified along with other previously described single nucleotide polymorphisms (c.–1721C>G and c.–1169G>A). Strong linkage disequilibrium ensured that all three polymorphisms were associated with skin colour such that the –1721G, +dup and –1169A alleles were associated with olive skin in Caucasians. No linkage disequilibrium was observed between the promoter and coding region polymorphisms, suggesting independent effects. The association analyses were complemented with functional data, showing that the –1721G, +dup and –1169A alleles significantly decreased SLC45A2 transcriptional activity. Based on in silico bioinformatic analysis that showed these alleles remove a microphthalmia-associated transcription factor (MITF) binding site, and that MITF is a known regulator of SLC45A2 (Baxter and Pavan, 2002; Du and Fisher, 2002), it was postulated that SLC45A2 promoter polymorphisms could contribute to the regulation of pigmentation by altering MITF binding affinity. Further characterisation of the SLC45A2 promoter was carried out using luciferase reporter assays to determine the transcriptional activity of different regions of the promoter. Five constructs were designed of increasing length and their promoter activity evaluated. Constitutive promoter activity was observed within the first ~200 bp and promoter activity increased as the construct size increased. The functional impact of the –1721G, +dup and –1169A alleles, which removed a MITF consensus binding site, were assessed using electrophoretic mobility shift assays (EMSA) and expression analysis of genotyped melanoblast and melanocyte cell lines. EMSA results confirmed that the promoter polymorphisms affected DNA-protein binding. Interestingly, however, the protein/s involved were not MITF, or at least MITF was not the protein directly binding to the DNA. In an effort to more thoroughly characterise the functional consequences of SLC45A2 promoter polymorphisms, the mRNA expression levels of SLC45A2 and MITF were determined in melanocyte/melanoblast cell lines. Based on SLC45A2’s role in processing and trafficking TYRP1 from the trans-Golgi network to stage 2 melanosmes, the mRNA expression of TYRP1 was also investigated. Expression results suggested a coordinated expression of pigmentation genes. This thesis has substantially contributed to the field of pigmentation by showing that SLC45A2 polymorphisms not only show allele frequency differences between population groups, but also contribute to normal pigmentation variation within a Caucasian population. In addition, promoter polymorphisms have been shown to have functional consequences for SLC45A2 transcription and the expression of other pigmentation genes. Combined, the data presented in this work supports the notion that SLC45A2 is an important contributor to normal pigmentation variation and should be the target of further research to elucidate its role in determining pigmentation phenotypes. Understanding SLC45A2’s function may lead to the development of therapeutic interventions for oculocutaneous albinism and other disorders of pigmentation. It may also help in our understanding of skin cancer susceptibility and evolutionary adaptation to different UV environments, and contribute to the forensic application of pigmentation phenotype prediction.

Modelling ideal turbulent vortex breakdown

In this computational study we investigate the role of turbulence in ideal axisymmetric vortex breakdown. A pipe geometry with a slight constriction near the inlet is used to stabilise the location of the breakdown within the computed domain. Eddy-viscosity and differential Reynolds stress models are used to model the turbulence. Changes in upstream turbulence levels, flow Reynolds and Swirl numbers are considered. The different computed solutions are monitored for indications of different breakdown flow configurations. Trends in vortex breakdown due to turbulent flow conditions are identified and discussed.

Incorporating an economic model in the health impact assessment approach

The current policy decision making in Australia regarding non-health public investments (for example, transport/housing/social welfare programmes) does not quantify health benefits and costs systematically. To address this knowledge gap, this study proposes an economic model for quantifying health impacts of public policies in terms of dollar value. The intention is to enable policy-makers in conducting economic evaluation of health effects of non-health policies and in implementing policies those reduce health inequalities as well as enhance positive health gains of the target population. Health Impact Assessment (HIA) provides an appropriate framework for this study since HIA assesses the beneficial and adverse effects of a programme/policy on public health and on health inequalities through the distribution of those effects. However, HIA usually tries to influence the decision making process using its scientific findings, mostly epidemiological and toxicological evidence. In reality, this evidence can not establish causal links between policy and health impacts since it can not explain how an individual or a community reacts to changing circumstances. The proposed economic model addresses this health-policy linkage using a consumer choice approach that can explain changes in group and individual behaviour in a given economic set up. The economic model suggested in this paper links epidemiological findings with economic analysis to estimate the health costs and benefits of public investment policies. That is, estimating dollar impacts when health status of the exposed population group changes by public programmes – for example, transport initiatives to reduce congestion by building new roads/ highways/ tunnels etc. or by imposing congestion taxes. For policy evaluation purposes, the model is incorporated in the HIA framework by establishing association among identified factors, which drive changes in the behaviour of target population group and in turn, in the health outcomes. The economic variables identified to estimate the health inequality and health costs are levels of income, unemployment, education, age groups, disadvantaged population groups, mortality/morbidity etc. However, though the model validation using case studies and/or available database from Australian non-health policy (say, transport) arena is in the future tasks agenda, it is beyond the scope of this current paper.

An exploration of knowledge management and intellectual capital in a nonprofit organisation context

In recent years, practitioners and researchers alike have turned their attention to knowledge management (KM) in order to increase organisational performance (OP). As a result, many different approaches and strategies have been investigated and suggested for how knowledge should be managed to make organisations more effective and efficient. However, most research has been undertaken in the for-profit sector, with only a few studies focusing on the benefits nonprofit organisations might gain by managing knowledge. This study broadly investigates the impact of knowledge management on the organisational performance of nonprofit organisations. Organisational performance can be evaluated through either financial or non-financial measurements. In order to evaluate knowledge management and organisational performance, non-financial measurements are argued to be more suitable given that knowledge is an intangible asset which often cannot be expressed through financial indicators. Non-financial measurement concepts of performance such as the balanced scorecard or the concept of Intellectual Capital (IC) are well accepted and used within the for-profit and nonprofit sectors to evaluate organisational performance. This study utilised the concept of IC as the method to evaluate KM and OP in the context of nonprofit organisations due to the close link between KM and IC: Indeed, KM is concerned with managing the KM processes of creating, storing, sharing and applying knowledge and the organisational KM infrastructure such as organisational culture or organisational structure to support these processes. On the other hand, IC measures the knowledge stocks in different ontological levels: at the individual level (human capital), at the group level (relational capital) and at the organisational level (structural capital). In other words, IC measures the value of the knowledge which has been managed through KM. As KM encompasses the different KM processes and the KM infrastructure facilitating these processes, previous research has investigated the relationship between KM infrastructure and KM processes. Organisational culture, organisational structure and the level of IT support have been identified as the main factors of the KM infrastructure influencing the KM processes of creating, storing, sharing and applying knowledge. Other research has focused on the link between KM and OP or organisational effectiveness. Based on existing literature, a theoretical model was developed to enable the investigation of the relation between KM (encompassing KM infrastructure and KM processes) and IC. The model assumes an association between KM infrastructure and KM processes, as well as an association between KM processes and the various levels of IC (human capital, structural capital and relational capital). As a result, five research questions (RQ) with respect to the various factors of the KM infrastructure as well as with respect to the relationship between KM infrastructure and IC were raised and included into the research model: RQ 1 Do nonprofit organisations which have a Hierarchy culture have a stronger IT support than nonprofit organisations which have an Adhocracy culture? RQ 2 Do nonprofit organisations which have a centralised organisational structure have a stronger IT support than nonprofit organisations which have decentralised organisational structure? RQ 3 Do nonprofit organisations which have a stronger IT support have a higher value of Human Capital than nonprofit organisations which have a less strong IT support? RQ 4 Do nonprofit organisations which have a stronger IT support have a higher value of Structural Capital than nonprofit organisations which have a less strong IT support? RQ 5 Do nonprofit organisations which have a stronger IT support have a higher value of Relational Capital than nonprofit organisations which have a less strong IT support? In order to investigate the research questions, measurements for IC were developed which were linked to the main KM processes. The final KM/IC model contained four items for evaluating human capital, five items for evaluating structural capital and four items for evaluating relational capital. The research questions were investigated through empirical research using a case study approach with the focus on two nonprofit organisations providing trade promotions services through local offices worldwide. Data for the investigation of the assumptions were collected via qualitative as well as quantitative research methods. The qualitative study included interviews with representatives of the two participating organisations as well as in-depth document research. The purpose of the qualitative study was to investigate the factors of the KM infrastructure (organisational culture, organisational structure, IT support) of the organisations and how these factors were related to each other. On the other hand, the quantitative study was carried out through an online-survey amongst staff of the various local offices. The purpose of the quantitative study was to investigate which impact the level of IT support, as the main instrument of the KM infrastructure, had on IC. Overall several key themes were found as a result of the study: • Knowledge Management and Intellectual Capital were complementary with each other, which should be expressed through measurements of IC based on KM processes. • The various factors of the KM infrastructure (organisational culture, organisational structure and level of IT support) are interdependent. • IT was a primary instrument through which the different KM processes (creating, storing, sharing and applying knowledge) were performed. • A high level of IT support was evident when participants reported higher level of IC (human capital, structural capital and relational capital). The study supported previous research in the field of KM and replicated the findings from other case studies in this area. The study also contributed to theory by placing the KM research within the nonprofit context and analysing the linkage between KM and IC. From the managerial perspective, the findings gave clear indications that would allow interested parties, such as nonprofit managers or consultants to understand more about the implications of KM on OP and to use this knowledge for implementing efficient and effective KM strategies within their organisations.

Measuring quality : how does this improve construction performance?

The paper charts the history and development of the Hong Kong Housing Department (HKHD) Performance Assessment Scoring System (PASS) from 1990 to the present day and examines its effect on facilitating change to the quality of construction work of building contractors engaged in the production of public sector housing projects Hong Kong. The paper builds partly on empirical research carried out by the author as part of a doctoral thesis from 2000 to 2005, on experiential knowledge and also on some relevant case studies. The outcomes from this earlier research and validation of PASS based on results derived from the system since the research was originally undertaken are of benefit to practitioners and academics working and studying in the areas of performance assessment and organisational culture and change. The conclusions presented in the paper further underpin the connection established in previous research between strong organisational culture and project and corporate success. Organisational culture was measured using a survey instrument originally developed by Denison and Neale (1994), adapted for the environment of the study, and corporate success was measured by the PASS system mentioned above. The major results of the original study indicate that there is significant linkage between strong organisational cultures and business success and the detailed findings were that, (1) strong organisational culture was positively associated a high level of company effectiveness, (2) a high level of company effectiveness was positively associated with the cultural traits of ‘consistency’, ‘adaptability’ and ‘mission’, and (3) a high level of company effectiveness was positively associated with the combined cultural traits represented by the dimensions of ‘external focus’ and ‘stable culture’. Several opportunities to take forward this research have been identified, including extending the study to other countries and also longitudinally re-evaluating some of the original case studies to ascertain how organisational cultures have changed or further developed in relation to the changing construction climate in Hong Kong.

Silylation of layered double hydroxides via a calcination−rehydration route

Silylated layered double hydroxides (LDHs) were synthesized through a surfactant-free method involving an in situ condensation of silane with the surface hydroxyl group of LDHs during its reconstruction in carbonate solution. X-ray diffraction (XRD) patterns showed the silylation reaction occurred on the external surfaces of LDHs layers. The successful silylation was evidenced by 29Si cross-polarization magic-angle spinning nuclear magnetic resonance (29Si CP/MAS NMR) spectroscopy, attenuated total reflection Fourier transform infrared (ATR FTIR) spectroscopy, and infrared emission spectroscopy (IES). The ribbon shaped crystallites with a “rodlike” aggregation were observed through transmission electron microscopy (TEM) images. The aggregation was explained by the T2 and T3 types of linkage between adjacent silane molecules as indicated in the 29Si NMR spectrum. In addition, the silylated products show high thermal stability by maintained Si related bands even when the temperature was increased to 1000 °C as observed in IES spectra.

The utility and challenges of using ICD codes in child maltreatment research : a review of existing literature

Objective: The objectives of this article are to explore the extent to which the International Statistical Classification of Diseases and Related Health Problems (ICD) has been used in child abuse research, to describe how the ICD system has been applied and to assess factors affecting the reliability of ICD coded data in child abuse research.----- Methods: PubMed, CINAHL, PsychInfo and Google Scholar were searched for peer reviewed articles written since 1989 that used ICD as the classification system to identify cases and research child abuse using health databases. Snowballing strategies were also employed by searching the bibliographies of retrieved references to identify relevant associated articles. The papers identified through the search were independently screened by two authors for inclusion, resulting in 47 studies selected for the review. Due to heterogeneity of studies metaanalysis was not performed.----- Results: This paper highlights both utility and limitations of ICD coded data. ICD codes have been widely used to conduct research into child maltreatment in health data systems. The codes appear to be used primarily to determine child maltreatment patterns within identified diagnoses or to identify child maltreatment cases for research.----- Conclusions: A significant impediment to the use of ICD codes in child maltreatment research is the under-ascertainment of child maltreatment by using coded data alone. This is most clearly identified and, to some degree, quantified, in research where data linkage is used. Practice Implications: The importance of improved child maltreatment identification will assist in identifying risk factors and creating programs that can prevent and treat child maltreatment and assist in meeting reporting obligations under the CRC.

Bayesian latent trait modeling of migraine symptom data

Definition of disease phenotype is a necessary preliminary to research into genetic causes of a complex disease. Clinical diagnosis of migraine is currently based on diagnostic criteria developed by the International Headache Society. Previously, we examined the natural clustering of these diagnostic symptoms using latent class analysis (LCA) and found that a four-class model was preferred. However, the classes can be ordered such that all symptoms progressively intensify, suggesting that a single continuous variable representing disease severity may provide a better model. Here, we compare two models: item response theory and LCA, each constructed within a Bayesian context. A deviance information criterion is used to assess model fit. We phenotyped our population sample using these models, estimated heritability and conducted genome-wide linkage analysis using Merlin-qtl. LCA with four classes was again preferred. After transformation, phenotypic trait values derived from both models are highly correlated (correlation = 0.99) and consequently results from subsequent genetic analyses were similar. Heritability was estimated at 0.37, while multipoint linkage analysis produced genome-wide significant linkage to chromosome 7q31-q33 and suggestive linkage to chromosomes 1 and 2. We argue that such continuous measures are a powerful tool for identifying genes contributing to migraine susceptibility.