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PubMed2005

Concepts to elucidate the pattern-associated analysis of tooth marks in court.

Increased awareness by crime scene detectives has led to a rise in number of bite mark associated cases appearing before the South African courts. This has led to an increased number of dentists being subpoenaed to give forensic evidence. The purpose of this paper was to elucidate the presentation of evidence in pattern associated tooth mark analysis. Three aspects are discussed. They are the basic principle of pattern association, the effects of limited shrinkage and distortion on the pattern of the tooth marks, and finally how to overcome the difficulties that court personnel experience in visualising bite marks. The author has applied these basic concepts over the past six years. Judges and defence advocates have been able to understand the simple concepts and apply them to the more complex issues before them. The concepts described should be familiar to all dentists and forensic odontologists giving tooth mark evidence in the high court. They will assist in explaining all aspects of pattern association to the legal fraternity and aid in the presentation of the evidence. Their strength is in their simplicity.

Bites, Human↗
PubMed2004

Association analysis between interleukin-1 family polymorphisms and generalized aggressive periodontitis in a Chinese population.

BACKGROUND: It has been suggested that aggressive periodontitis (AgP) has a genetic basis, but this theory has not been confirmed. The intent of this investigation was to study whether specific interleukin (IL)-1 genotypes and/or alleles could be used to predict susceptibility to generalized AgP (GAgP) in Chinese. METHODS: The GAgP group consisted of 122 patients, and the control group included 95 healthy subjects. Single nucleotide polymorphisms at IL-1A (+4845) and IL-1B (-511, +3954) were analyzed by standard polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. The polymorphism of a variable number tandem repeat (VNTR) in intron 2 of IL-1RN was detected by PCR amplification and fragment size analysis. RESULTS: There was no significant association of IL-1 polymorphisms with GAgP in the unstratified subjects. However, when cases were stratified by gender, the frequencies of A2+ genotype and allele 2 at IL-1A +4845 were significantly increased in male patients compared to male controls (genotype: odds ratio [OR] 5.58, 95% confidence interval [CI]: 1.09 to 28.68, P = 0.039; allele: OR 4.97, 95% CI: 1.01 to 24.50, P = 0.049; adjusted for age and smoking status). The frequency of IL-1B -511 A1/A2 heterozygote was significantly increased in male GAgP group compared to male controls (adjusted OR 3.16, 95% CI: 1.01 to 9.89, P = 0.048). In females, no significant differences were found between patients and controls in corresponding analyses at all polymorphic loci. A possible combined effect of IL-1B -511 polymorphism and smoking on the elevated risk to GAgP was observed. The OR of GAgP for combined A2+ genotype and smoking was 12.45 (95% CI: 1.43 to 108.06, P = 0.022), and for combined allele 2 and smoking was 18.25 (95% CI: 2.32 to 143.86, P = 0.006). CONCLUSIONS: The polymorphisms of IL-1A +4845 and IL-1B -511 may play an important role in determining GAgP susceptibility in Chinese males. Furthermore, a possible combined effect of the polymorphism of IL-1B -511 and smoking on GAgP susceptibility was suggested.

Acute Disease↗
PubMed2002

Association analysis of candidate genes for neuropsychiatric disease: the perpetual campaign.

Association studies have been proposed to identify the genetic determinants of complex neuropsychiatric traits. Although such studies of candidate genes offer great potential to identify genetic variants that contribute to the expression of psychiatric disease, no consistent associations have been identified. Studies to date have focused on candidate genes that are selected for analysis on the basis of incomplete information about gene function in the brain, therefore the majority of genes expressed in the brain have been ignored. Additionally, most genetic determinants of psychiatric disease will probably be of modest effect and therefore require association studies of large samples. As genomic technologies advance, massive genotyping of large samples should allow identification of alleles that contribute to psychopathology.

Data Interpretation, Statistical↗
PubMed2004

Haplotype-based association analysis in cohort studies of unrelated individuals.

Exploring the associations between haplotypes and disease phenotypes is an important step toward the discovery of genes that influence complex human diseases. When unrelated subjects are sampled, haplotypes are often ambiguous because of the unknown gametic phase of the measured sites along a chromosome. We consider cohort studies of unrelated subjects which collect data on potentially censored ages of onset of disease along with unphased genotypes and possibly time-varying environmental factors. We formulate the effects of haplotypes and environmental variables on the time to disease occurrence through a semiparametric Cox proportional hazards model, which can accommodate a variety of genetic mechanisms as well as gene-environment interactions. We develop a simple and fast expectation-maximization algorithm to maximize the likelihood for the relative risks and other parameters based on the observable data of unphased genotypes and potentially censored ages of onset. The resultant estimators are consistent, efficient, and asymptotically normal. Simulation studies show that, for practical situations, the parameter estimators are virtually unbiased, the association tests maintain type I errors near nominal levels, the confidence intervals have proper coverage probabilities, and the efficiency loss due to unknown gametic phase is small.

Algorithms↗
PubMed2001

Combined linkage and association analysis in pedigrees.

We applied a combined linkage and association model for quantitative traits in pedigrees to identify possible functional polymorphisms and to test for association resulting from population stratification and admixture. Functional polymorphisms are identified as variants that are significantly associated with a trait (high chi 2 value) and showing no residual evidence of linkage (low lod score). Applying our model to the simulated data in the population isolate (replicate 1) we correctly identified the polymorphism in gene 6 (MG1) that affects Q1. Without modeling association the lod score for Q1 was 5.4. At the site of the functional variant (5782 bp) the association chi 2 was 88.1 on 1 df (p < 0.001) and the lod score was 0.003. We estimated a 3.7-unit increase in the average Q1 for each extra copy of the polymorphism (95% CI = 2.95-4.41) and there was no evidence of population stratification or admixture (chi 2 = 0.08 on 2 df). For Q5 and gene 2, modeling the sequence variants at 11 loci simultaneously identified multiple functional variants. Including the main effect of 11 marker genotypes reduced the lod score at gene 2 from 8.7 to 0.9. Again, no evidence of population stratification or admixture was found (all chi 2 < 4.9 on 2 df; p > 0.05).

Adult↗
PubMed2005

Case-control single-marker and haplotypic association analysis of pedigree data.

Related individuals collected for use in linkage studies may be used in case-control linkage disequilibrium analysis, provided one takes into account correlations between individuals due to identity-by-descent (IBD) sharing. We account for these correlations by calculating a weight for each individual. The weights are used in constructing a composite likelihood, which is maximized iteratively to form likelihood ratio tests for single-marker and haplotypic associations. The method scales well with increasing pedigree size and complexity, and is applicable to both autosomal and X chromosomes. We apply the approach to an analysis of association between type 2 diabetes and single-nucleotide polymorphism markers in the PPAR-gamma gene. Simulated data are used to check validity of the test and examine power. Analysis of related cases has better power than analysis of population-based cases because of the increased frequencies of disease-susceptibility alleles in pedigrees with multiple cases compared to the frequencies of these alleles in population-based cases. Also, utilizing all cases in a pedigree rather than just one per pedigree improves power by increasing the effective sample size. We demonstrate that our method has power at least as great as that of several competing methods, while offering advantages in the ability to handle missing data and perform haplotypic analysis.

Alleles↗
PubMed2000

Association analysis of GABAAbeta2 and gamma2 gene polymorphisms with event-related prefrontal activity in man.

Gamma-aminobutyric acid (GABA)A-receptors play a crucial role in the generation of electroencephalogram (EEG) oscillations and evoked potentials (ERPs). The present association study was designed to test whether EEG and ERPs are modulated by genetic variations of the human GABAA beta2 (GABRB2) and gamma2 (GABRG2) genes on chromosome 5q33. The genotypes of two nucleotide substitution polymorphisms of the GABRB2 and GABRG2 genes were assessed in 95 psychiatrically healthy subjects of German descent. Neurophysiological phenotyping was performed with four factorized EEG/ERP parameters: EEG activation, anterior and posterior EEG synchronization, and event-related activity (N100/ P200-complex). No genotypic association was found for the GABRB2 nucleotide exchange polymorphism with any electrophysiological parameter. A significant association was found between the genotype of the intronic GABRG2 G-->A nucleotide exchange and the event-related N100/P200 (ANOVA: F=3.81; df=2; P=0.026). A comparison of homozygous subjects carrying either the G/G or A/A genotype of the GABRG2 polymorphism consistently revealed an even stronger difference in the effect-size (ANOVA: F=11.13; df=1; P=0.002). Post hoc analysis of this association with current density analysis in three-dimensional neuroanatomic Talairach space-time showed a reduction in the event-related signal power after 120 ms in the right dorsolateral prefrontal cortex. Taking into account the risk of false-positive association findings attributable to multiple testing, our results encourage further replication studies to examine the phenotype-genotype relationship of GABRG2 gene variants and event-related prefrontal activity.

Adult↗
PubMed2006

Genetic linkage and association analysis in type 1 von Willebrand disease: results from the Canadian type 1 VWD study.

BACKGROUND: von Willebrand disease (VWD) is the most common bleeding disorder known in humans, with type 1 VWD representing the majority of cases. Unlike the other variant forms of VWD, type 1 disease represents a complex genetic trait, influenced by both genetic and environmental factors. AIM: To evaluate the contribution of the von Willebrand factor (VWF) and ABO blood group loci to the type 1 VWD phenotype, and to assess the potential for locus heterogeneity in this condition, we have performed genetic linkage and association studies on a large, unselected type 1 VWD population. METHOD: We initially collected samples from 194 Canadian type 1 VWD families for analysis. After the exclusion of families found to have either type 2 or type 3 VWD, and pedigrees with samples from single generations, linkage and association analysis was performed on 155 type 1 VWD families. RESULTS AND CONCLUSION: The linkage study has shown a low heterogeneity LOD score of 2.13 with the proportion of families linked to the VWF gene estimated to be 0.41. Linkage was not detected to the ABO locus in this type 1 VWD population. In the family-based association test, significant association was found between the type 1 VWD phenotype, the quantitative traits, VWF:Ag, VWF:RCo, and FVIII:C and the ABO 'O' and 'A' alleles and the VWF codon 1584 variant. There was also weak association with the -1185 promoter polymorphism and VWF:Ag, VWF:RCo, and FVIII:C plasma levels. These studies provide further evidence to support the role for genetic loci other than VWF and ABO in the pathogenesis of type 1 VWD.

ABO Blood-Group System↗
PubMed2005

Association analysis of common variants of STAT6, GATA3, and STAT4 to asthma and high serum IgE phenotypes.

BACKGROUND: Immune responses characterized by T H 2 type cells and IgE are important for the development of asthma and atopy. The transcription factors STAT6, GATA3, and STAT4 mediate the cytokine-induced development of naive CD4 + T cells into either T H 1 or T H 2 type. OBJECTIVE: We studied genetic variation of the STAT6, GATA3, and STAT4 genes and examined whether single nucleotide polymorphisms (SNPs) in these loci were associated with asthma or serum high IgE levels in the Finnish asthmatic families. METHODS: With denaturing high-performance liquid chromatography we screened all exons and exon-intron boundaries of the genes in 14 to 22 patients. All identified SNPs were genotyped in 120 nuclear families, and the haplotypes were analyzed by Haplotype Pattern Mining based statistical analysis. When potential association was observed, the analysis was replicated among 245 asthmatic patients and 405 population-based control subjects. RESULTS: A total of 23 SNPs were identified, of which 8 were not previously listed in the SNP database. Interestingly, a haplotype analysis of GATA3 showed 3 related haplotypes that associated with different asthma and atopy related phenotypes among both the family and case-control data sets. For STAT6 and STAT4, no significant association to asthma or serum total IgE levels was observed. CONCLUSIONS: We identified a panel of novel SNPs in genes coding for proteins important in the T H 1/T H 2 cell differentiation. SNPs of the GATA3 gene showed an initial association to asthma-related phenotypes. Elucidation of the importance of the identified panel of SNPs in other T H 1/T H 2 mediated diseases will be of great interest.

Adult↗
PubMed2003

Association analysis of MAOA and COMT with neuroticism assessed by peers.

There are several reported associations between depressive disorders, panic disorder, and obsessive-compulsive disorder (OCD) and a variety of polymorphisms in the monoamine oxidase A (MAOA) gene. Associations have also been reported between the catechol-O-methyltransferase (COMT) gene and both OCD and bipolar depression. However, the role of these markers has not been explored for the personality trait of neuroticism (N), a normally distributed quantitative trait, which is highly genetically correlated with anxiety and depression and may be a vulnerability to either type of disorder. We explored the possible role of MAOA, COMT, and their interaction on N using a selected extremes design. From a sample of 2,085 individuals, each assessed for N by two independent peers rather than using self-report questionnaires, we selected 57 individuals from the top 10% of scores, and 62 individuals from the bottom 10%. Using selected extreme low subjects as the controls, rather than an unselected control group gives roughly twice the power of a standard case-control design. We typed a functional variable number tandem repeat (VNTR) in the MAOA gene promoter, and a functional polymorphism in the coding region of the COMT gene. Two novel alleles in the MAOA VNTR were identified on the basis of their size, and their structure examined by sequencing analysis. We found weak evidence for association with COMT genotype, when the females and males were considered separately, and for MAOA genotype in males only. There was no significant interaction between COMT and MAOA.

Adolescent↗
PubMed2005

Mutation screening and association analysis of six candidate genes for autism on chromosome 7q.

Genetic studies have provided evidence for an autism susceptibility locus (AUTS1) on chromosome 7q. Screening for mutations in six genes mapping to 7q, CUTL1, SRPK2, SYPL, LAMB1, NRCAM and PTPRZ1 in 48 unrelated individuals with autism led to the identification of several new coding variants in the genes CUTL1, LAMB1 and PTPRZ1. Analysis of genetic variants provided evidence for association with autism for one of the new missense changes identified in LAMB1; this effect was stronger in a subgroup of affected male sibling pair families, implying a possible specific sex-related effect for this variant. Association was also detected for several polymorphisms in the promoter and untranslated region of NRCAM, suggesting that alterations in expression of this gene may be linked to autism susceptibility.

Autistic Disorder↗
PubMed1996

Genetic polymorphisms in the keratin-like S gene within the human major histocompatibility complex and association analysis on the susceptibility to psoriasis vulgaris.

Psoriasis vulgaris is associated with the HLA-Cw6 and Cw7 antigens. However, it has not yet been clarified if the HLA-Cw6 and Cw7 genes themselves are the susceptible gene related to this disease or if it is some other non-HLA gene in a linkage disequilibrium with these HLA-C alleles. The S gene, recently identified in the HLA class I region 160 kb telomeric of HLA-C, encodes a keratin-like protein and is expressed specifically in the granular layer of the epidermis. Therefore, it is tempting to speculate that the S gene is one of the strong candidate genes responsible for the pathogenesis of psoriasis vulgaris. Direct sequencing of the first and second exon of the S gene after polymerase chain reaction (PCR) amplification has allowed the identification of two diallelic polymorphic sites in exon I and seven diallelic polymorphic sites in exon 2, three among which result in amino acid exchanges, a Ser-Phe substitution at amino acid position 186, a Gly-Val substitution at position 393 and a Ser-Leu substitution at position 394. No significant difference in the dimorphic distributions of the S gene was observed between the patients with psoriasis vulgaris and healthy controls, suggesting that the susceptible gene for psoriasis is not the S gene itself.

Disease Susceptibility↗
PubMed2001

[Myelopathy - Sjogren's syndrome association: analysis of clinical and radiological findings and clinical course].

Myelopathies associated with Sjögren's syndrome has been rarely described especially concerning magnetic resonance imaging (MRI) and treatment aspects. The aim of this study was to determine the clinical, laboratory and radiological features of myelopathies occurring in Sjögren's syndrome. Eleven patients were studied, 7 with an acute myelopathy and 4 with a chronic form. Acute myelopathy were clinically severe with a feature of transverse myelitis necessitating immunosuppressive drugs. On the other hand, chronic forms were closely similar to progressive multiple sclerosis (MS), for clinical and laboratory data. In 7 cases optic neuritis was found associated with myelopathy and fulfilled the diagnostic criteria of Devic's syndrome in 4 cases. The diagnosis of myelopathy associated with Sjögren's syndrome may be difficult especially compared with MS, HTLV1 or HIV myelopathy and sarcoidosis, in the chronic form but also with other vasculitis, MS or viral infection in the acute forms. However, in this last form, magnetic resonance imaging and cerebrospinal fluid data should bring to the diagnosis of Sjögren syndrome and confirmed by appropriate tests. This diagnosis will have direct consequences for an early treatment by immunosuppressive drugs.

Adult↗
PubMed2006

Two-stage designs in case-control association analysis.

DNA pooling is a cost-effective approach for collecting information on marker allele frequency in genetic studies. It is often suggested as a screening tool to identify a subset of candidate markers from a very large number of markers to be followed up by more accurate and informative individual genotyping. In this article, we investigate several statistical properties and design issues related to this two-stage design, including the selection of the candidate markers for second-stage analysis, statistical power of this design, and the probability that truly disease-associated markers are ranked among the top after second-stage analysis. We have derived analytical results on the proportion of markers to be selected for second-stage analysis. For example, to detect disease-associated markers with an allele frequency difference of 0.05 between the cases and controls through an initial sample of 1000 cases and 1000 controls, our results suggest that when the measurement errors are small (0.005), approximately 3% of the markers should be selected. For the statistical power to identify disease-associated markers, we find that the measurement errors associated with DNA pooling have little effect on its power. This is in contrast to the one-stage pooling scheme where measurement errors may have large effect on statistical power. As for the probability that the disease-associated markers are ranked among the top in the second stage, we show that there is a high probability that at least one disease-associated marker is ranked among the top when the allele frequency differences between the cases and controls are not <0.05 for reasonably large sample sizes, even though the errors associated with DNA pooling in the first stage are not small. Therefore, the two-stage design with DNA pooling as a screening tool offers an efficient strategy in genomewide association studies, even when the measurement errors associated with DNA pooling are nonnegligible. For any disease model, we find that all the statistical results essentially depend on the population allele frequency and the allele frequency differences between the cases and controls at the disease-associated markers. The general conclusions hold whether the second stage uses an entirely independent sample or includes both the samples used in the first stage and an independent set of samples.

Algorithms↗
PubMed1986

The VATER association. Analysis of 46 patients.

Evaluation of 46 patients with the VATER association indicates that in addition to the major defects seen in this association, numerous other abnormalities occur at lesser frequency. Four of the defects that are not usually associated with the VATER association, namely, inguinal hernias, small intestinal malformations, choanal atresia, and cleft lip and/or palate, were seen at a relatively high frequency in this patient population. Two children possessed defects found in both the VATER and CHARGE associations. The spectrum of defects in the 46 patients in this study also is compared with that in 186 cases derived from the literature.

Abnormalities, Multiple↗
PubMed2006

Genetic association analysis of LRCH1 as an osteoarthritis susceptibility locus.

OBJECTIVE: A genetic association with knee osteoarthritis (OA) of a single nucleotide polymorphism (SNP) in intron 1 of the LRCH1 gene was recently reported in a UK Caucasian case-control sample and confirmed in a Newfoundland Caucasian sample. Our objective was to assess whether the SNP was associated with OA in our large UK Caucasian sample. METHODS: The SNP was genotyped in 1521 cases that had undergone elective joint replacement of the hip (1098 cases), of the knee (340 cases) or of the hip and knee (83 cases) due to end-stage primary OA. The SNP was also genotyped in 736 controls of similar ages in the cases. RESULTS: There was no significant difference (all P-values >0.05) in genotype or allele frequencies between our cases and our controls. There was also no significant difference when the cases were stratified by sex, by joint replaced or by sex combined with joint replaced. CONCLUSION: Our data on 2257 individuals implies that the LRCH1 intron 1 SNP is not a risk factor for OA aetiology of the knee or of the hip in our UK Caucasian sample.

Aged↗
PubMed2005

Locally weighted transmission/disequilibrium test for genetic association analysis.

The transmission/disequilibrium test statistic has been used for assessing genetic association in affected-parent trios. In the presence of multiple tightly linked marker loci where local dependency may exist, haplotypes are reconstructed statistically to estimate the joint effects of these markers. In this manuscript, we propose an alternative to the haplotype approach by taking a weighted average of multiple loci, where the weight is proportional to the product of (1-2X recombination fraction) and the linkage disequilibrium between markers. As an illustration, we applied the method to the simulated Aipotu data.

Genome-Wide Association Study↗