In this work we present results on DYS434, DYS437, DYS438 and DYS439 loci studied in three population samples from North Portugal (N: 69), Macao (N: 59) and Mozambique (N: 64). Gene and haplotype diversity values are presented and compared. Gene diversity values ranged from 0.0290 to 0.0620 for DYS434; 0.0615 to 0.5959 for DYS437; 0.4906 to 0.6424 for DYS438; 0.5873 to 0.7038 for DYS439. The highest average gene diversity was found in Macao and the lowest in Mozambique. Haplotype diversity in North Portugal, Macao and Mozambique was calculated to be 0.925, 0.928 and 0.787, respectively.

Allele and haplotype frequency distributions for all markers were compared between the three populations. At the haplotype level all the differences between pairs of samples were significant. Sequencing analysis was performed for all alleles found in the four loci. Identical flanking sequences were observed with most of the alleles differing only by the repeat number. However, two variations were found in allele 10 of DYS438: one in a Macao sample presenting a TTTTA before the last TTTTC repetition and one in a Portuguese sample showing a base substitution (A/C) at position 7 downstream from the tandem repeat. A base substitution (C/T) at position 3 upstream from the repeat motif was also found in allele 14 of DYS437 in a sample from Mozambique.

Congenital erythropoietic porphyria (CEP) results from profoundly deficient activity of the fourth enzyme of the haeme biosynthetic pathway, uroporphyrinogen III synthase (UROIIIS). CEP is a rare, recessively inherited disorder, and mutations in the UROIIIS gene detected in CEP patients are heterogeneous. The notable exception to this rule is a single missense mutation, designated C73R, which represents over 40% of all mutant UROIIIS alleles. In this study, we investigated three separate families with CEP from different ethnic backgrounds. We performed haplotype analysis using two microsatellite markers that closely flank the UROIIIS gene on chromosome 10q24, spanning a region of 4 cM on the GB4 linkage panel. Haplotype analysis revealed the occurrence of C73R on different haplotypes in four out of four disease chromosomes studied. The results are consistent with the hypothesis that C73R is a hotspot mutation for CEP, and does not represent wide dispersion of a single ancestral mutant C73R allele.

Several studies have indicated that additional genes in the major histocompatibility complex (MHC) region, other than the class II genes HLA-DQB1 and -DRB1 (the IDDM1 locus), may contribute to susceptibility and resistance to type 1 diabetes. The relative magnitude of these non- DR/DQ effects is uncertain and their map location is unknown owing to the extraordinary linkage disequilibrium that extends over the 3.5 Mb of the MHC. The homozygous parent test has been proposed as a method for detection of additional risk factors conditional on HLA-DQB1 and -DRB1. However, this method is inefficient since it uses only parents homozygous for the primary disease locus, the DQB1-DRB1 haplotype. To overcome this limitation, Conditional ETDT was used in the present report to test for association conditional on the DQB1-DRB1 haplotype, thereby allowing all parents to be included in the analysis. First, we confirm in UK and Sardinian type 1 diabetic families that allelic variation at HLA-DRB1 has a very significant effect on the association of DQB1 and vice versa. The Conditional ETDT was then applied to the HLA TNF (tumour necrosis factor) region and microsatellite marker D6S273 region, both of which have been reported to contribute to IDDM1 independent of the HLA-DQB1-DRB1 genes. We found no evidence for a major role for either of these two regions in IDDM1.

Linkage analysis and mouse model knockout studies indicate that loci/genes mapping in different chromosome 1 regions are good candidates for nonsyndromic orofacial cleft (OFC) malformation. On this basis, three different regions of the chromosome 1 have been analysed, by linkage analysis, in 38 families with nonsyndromic OFC. Positive scores were obtained by pairwise analysis and a non-parametric linkage approach for the 1p36 region, with markers close to the MTHFR locus. Additional results allowed us to exclude the presence of an OFC susceptibility gene in the 1q21 and 1q32-42·3 regions.

In a study based on 173 individuals drawn from three endogamous, co-resident communities in the province of Punjab, the Awan, Khattar and Rajpoot, an analysis of 10 autosomal single tandem repeats on chromosomes 13 and 15 revealed distinctive genetic profiles in each community. A total of 99 different alleles were detected, with 28 alleles (28.3%) shared by all three communities. The mean private allele frequency was 7.7%. There was a reduction in heterozygosity and high average inbreeding effects (FIS and/or HS), particularly in the Awan, indicating genetic isolation and a high cumulative level of autozygosity. Genotyping with eight Y-chromosome STRs resulted in the construction of six haplotypes, one each for the Awan and the Khattar but four for the Rajpoot, suggesting marked variation in the patterns of male founder effects in the history of each community. The lower than expected levels of homozygosity observed at a number of loci may be indicative of cosegregation of the STRs with nearby early development genes subject to selection.

Application of the affected sib-pair method of linkage analysis to sibships with variable numbers of affected and unaffected members requires a scheme for weighting the contributions from the sibships in the calculation of an overall test statistic. Currently accepted weighting schemes are based on the concepts of independent pairs and Shannon information content. Here, we show that the weighting scheme with maximum power to detect linkage can be determined from the theoretical means and variances of the sibship contributions under the null and alternative hypotheses. We derive the theoretical means and variances of the contributions from different types of sibships under a generalized single locus model. We use these theoretical means and variances to obtain the optimal weights for a variety of single locus models, and compare the power of existing weighting schemes relative to the optimum. The results suggest that, under a range of plausible assumptions, optimal power is nearly obtained by weighting to all sibpairs equally, except those occuring in sibships with so many affected siblings (usually five or more) that the probability of parental homozygosity for the disease allele becomes substantial. A corollary is that, in affected sib-pair analysis, the ‘informativeness’ of a sibship is more nearly proportional to the number of affected sib-pairs than to the number of affected siblings, up to about five affected siblings.

Stereocilia of the inner ear play an integral role in the mechanotransduction of sound. Their structural support is derived from actin filaments and actin-binding proteins. We have identified a novel actin-binding protein, 2E4-kaptin (KPTN), which appears to be involved in this structural network. Using double label immunofluorescence, we now show that KPTN extends beyond the barbed ends of actin filaments at the tips of stereocilia, and using cloned human cDNA, we mapped KPTN to chromosome 19q13.4. A combination of FISH, radiation hybrid mapping and YAC screening localized KPTN between markers D19S412 and NIB1805, making this gene an excellent functional and positional candidate for DFNA4, a form of autosomal dominant non-syndromic hearing loss. We identified a second family with inherited deafness that also maps to the DFNA4 region. To screen KPTN for deafness-causing mutations, we first determined its genomic structure and then completed a mutational analysis by direct sequencing and SSCP in affected family members. Although no deafness-causing mutations were identified in the coding region, KPTN remains an excellent candidate gene for hearing loss; by synteny, its murine orthologue also remains a candidate gene for the Nijmegan waltzer (nv) mouse mutant, which has vestibular defects and a variable sensorineural hearing loss.

Molecular variants of individual components of the renin-angiotensin system are thought to contribute to inherited predisposition towards essential hypertension. Using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and sequence analysis, we identified seven polymorphisms in the 5′-flanking region of the angiotensin II type 1 receptor (AGTR1/AT1) gene. We conducted a case-control study in a sample from the Japanese population to determine whether polymorphic markers in the 5′-flanking region of the AT1gene were associated with essential hypertension. The study compared 149 hypertensive subjects to 156 normotensive control subjects. A significantly higher frequency of the AT1(−535)*T allele was observed in hypertensive subjects. Evidence was obtained that the AT1(−535)*T allele showed a synergistic effect on risk of hypertension with angiotensin I converting enzyme D allele (ACE*D).

In order to explore the nature of glucose-6-phosphate dehydrogenase (G6PD) deficiency in south-east Sicily, we have analysed the G6PD gene in 25 unrelated males with abnormal G6PD activity and/or electrophoretic mobility, by using the analysis of the appropriate PCR-amplified fragment of DNA and subsequent digestion by appropriate restriction-enzymes, looking for the presence of certain known G6PD mutations. We amplified the entire G6PD coding sequence into eight fragments, followed by single-strand conformation polymorphism (SSCP) analysis and sequencing of those individual fragments that were found to be abnormal by SSCP. Through these methods we found a total of twelve G6PD Mediterranean variants with the association of a silent mutation 1311 (also known as polymorphic site Bcl I), one G6PD Mediterranean without this association, four G6PD A− Val 68 and two G6PD Santamaria and five G6PD Chatham. In a subject with normal activity a mutation was found in exon 5, designated as G6PD Sao Borja. This is the first report on the molecular analysis of G6PD mutations in Sicily and we have obtained evidence for four distinct classes of variants.

An important design issue in allelic association studies for mapping disease genes is the choice of markers. We have used a simple model of a founder population, similar to those of Ott & Rabinowitz (1997) and Chapman & Wijsman (1998), to explore the effect of the number of alleles at a marker polymorphism on the power to detect linkage disequilibrium due to single or multiple ancestral disease mutations. We show that the optimal number of alleles is more than 2 even in the case of a single ancestral disease mutation, and much higher still if multiple ancestral mutations are present. In large samples, much power is lost by using too few alleles, but relatively little power is lost by using too many alleles. These results confirm the desirability of using highly polymorphic markers or multi-locus haplotypes for association analysis. They also show that multiple ancestral disease mutations do not necessarily preclude linkage disequilibrium mapping, if highly polymorphic markers or multi-locus haplotypes are used.

To examine the possible internal heterogeneity within the Basque population, nine samples typed for several HLA loci were compiled and HLA-A, B, C and DR loci were analysed. First, the shared features of HLA in Basques were analysed by principal component analysis and genetic distances. Two major Basque dialect groups (‘French’ and ‘Spanish’) were considered. FST statistics were computed and corrected for sampling intensity. The dialectal and political division did not seem to differentiate these two groups genetically. Analysis of Molecular Variance also failed to show consistently significant genetic variance components between French and Spanish Basques. Thus, in this particular example, linguistic diversity does not seem to correlate with a genetic stratification.

We report an analysis of allelic diversity at short tandem repeat polymorphisms within the fragile XA locus in 1069 male volunteers from twelve Indonesian sub-populations. An odd numbered allele of DXS548 was found at high frequency in all Indonesian populations. Greater allelic diversity was identified at the loci under study than has been previously reported for an Asian population. These differences distinguish the Indonesian population from all previously reported Asian, European and African populations. A high frequency of small premutation alleles, 4/120 (3.3%, 95% CI 0.9–8.3%), was identified in the Moluccan population of Hiri Island.

The proportions of affected sibs sharing 2, 1 or 0 identical by descent parental marker alleles have been shown to conform to the ‘triangle constraints’ (Suarez, 1978; Holmans, 1993). It has also been shown (Dudoit & Speed, 1999) that the constraints are verified provided certain assumptions hold. In this study we explore a realistic situation in which the constraints fail due to the presence of a factor in which the sibs differ, a factor on which penetrance depends. This factor may be a characteristic of the trait (severe vs. mild form), or the presence/absence of an associated trait or an environmental factor. We show that under such situations, using the triangle constraints may lead to important loss of power to detect linkage by the MLS test. We propose here an alternative approach in order to detect both linkage and heterogeneity.

A likelihood ratio test of disease-marker association is proposed, based on the observation of marker alleles transmitted from parents to affected children. The proposed association test has the advantage of identifying the population pattern of disease-marker association, differentiating between marker alleles that are positively and negatively associated with the disease. The power of the test for detecting association is evaluated and compared with three existing multi-allelic tests for some specific disease-marker association patterns. The power of the parametric tests depends crucially on the pattern of disease-marker association. An over-parameterised association model is less detrimental in terms of power than an under parameterised model.

We have localized the gene encoding the fast skeletal muscle isoform of troponin I (TNNI2) to 11p15.5 by PCR-based analysis of somatic cell hybrid panels: based on the Genebridge4 radiation hybrid panel, TNNI2 is coincident with the marker D11S922. The gene encoding the fast skeletal muscle troponin T gene (TNNT3) has been previously assigned to 11p15.5 suggesting that TNNI2 and TNNT3 may be closely linked. The overall location of genes encoding troponin I and T isoforms now reveals that they are organized at three loci each containing a troponin I/troponin T gene pair. This organization contrasts with all other sarcomeric protein genes and has implications for the evolution of these two gene families, for their regulation and for the analysis of mutations suspected to result in cardiomyopathy.

Microsomal triglyceride transfer protein (MTP) plays a central role in the synthesis of lipoproteins by shuttling lipids between phospholipid membranes to apoB. We have examined the effect of three MTP gene variants, −493G > T, Q95H and H297Q, in 2831 healthy UK middle-aged men. The rare allele frequencies were: 0.25 (95% CI 0.24–0.26) for −493T, 0.054 (95% CI 0.05–0.06) for 95H and 0.32 (95% CI 0.31–0.33) for 297Q. The three variants were in strong allelic association in all pairwise combinations (p < 0.001). None of the variant sites were associated with significant differences in cholesterol, triglyceride, apoB or apoAI levels. When stratified by tertiles of triglycerides for the H297Q variant alone there was a significant effect on apoB levels in men in the top tertile (p = 0.01). Considering the −493G > T and H297Q genotype in combination on baseline levels, individuals with three or four rare alleles had 6.6% higher mean apoB levels compared to the rest (p = 0.007). Therefore, homozygosity for 297Q at higher triglyceride (Tg) levels, or in combination with −493G > T, is associated with a raising effect on apoB levels, suggesting the importance of modest differences in MTP activity in determining hepatic secretion of lipoproteins in healthy men.

When searching for trait loci along the genome, properly incorporating prior genomic information into the analysis will almost certainly increase the chance of success. Recently, we devised a method that utilizes such prior information in the mapping of trait genes for complex disorders (Vieland, 1998; Wang et al. 1999; Vieland et al. 2000). This method uses the posterior probability of linkage (PPL) based on the admixture model as a measure of linkage information. In this paper, we study the consistency of the PPL. It is shown that, as the number of pedigrees increases, the PPL converges in probability to 1 when there is linkage between the marker and a trait locus, and converges to 0 otherwise. This conclusion is shown to be true for general pedigrees and trait models, even when the likelihood functions are based on misspecified trait models. As part of the effort to prove this conclusion, it is shown that when there is no linkage, the maximum likelihood estimator of the recombination fraction in the admixture model is asymptotically 0.5, even when the admixture model misrepresents the true model.

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterised by the development of benign tumors in multiple organs often causing serious neurologic impairment. To develop a reliable genetic test for TSC, two-dimensional electrophoresis with denaturing gradient gel electrophoresis (2D DGGE) has been developed to detect mutations in TSC1. The 23 exons of TSC1 were amplified using two rounds of PCR. In the first round, all coding regions of TSC1 were amplified in four fragments ranging in size from 7.4 kb to 9.9 kb. In the second round, 32 fragments representing 23 exons were amplified using primers designed to avoid overlapping fragments and with a GC clamp on one end to optimise melting characteristics. These exon fragments were then separated by size in the first dimension using a polyacrylamide gel, and by melting characteristics in the second dimension using a urea/formamide gradient to yield 32 distinct bands. If a mutation is present, four bands instead of one, are typically observed. During the development of this assay, we analysed 63 patient samples with known TSC1 mutations from prior studies. These 63 patients had 68 known mutations or polymorphisms. With DGGE, all 68 of these were identified (45 point mutations, 3 small insertions, 20 small deletions) and an additional 27 single base variants were discovered. To evaluate the assay, we analysed 19 of these samples in a blinded study. In the blinded analysis, 19/20 (95%) known mutations or polymorphisms were detected. The single missed mutation in the blinded analysis could be identified in retrospect and the assay was modified accordingly. During this study, we identified 2 new mutations (exon 8 and exon 15), a new polymorphism (intron 4), and the first variant identified in a non-coding exon (exon 2).

In recent years variance components models have been developed for localising genes that contribute to human quantitative variation. In typical applications one assumes a multivariate normal model for phenotypes and estimates model parameters by maximum likelihood. For the joint analysis of several correlated phenotypes, however, finding the maximum likelihood estimates for an appropriate multivariate normal model can be a difficult computational task due to complex constraints among the model parameters. We propose an algorithm for computing maximum likelihood estimates in a multi-phenotype variance components linkage model that readily accommodates these parameter constraints. Data simulated for Genetic Analysis Workshop 10 are used to demonstrate the potential increase in power to detect linkage that can be obtained if correlated phenotypes are analysed jointly rather than individually.

We and others have shown that a family history of squamous cell carcinoma of the head and neck (SCCHN) is a risk factor for this disease. We performed a segregation analysis on a dataset comprised of 1429 first-degree relatives of 242 unselected cases of SCCHN and 934 first-degree relatives of 156 spouse controls. Using the SAGE software, we demonstrated that a Mendelian model was favored and a model postulating a purely environmental cause of SCCHN was rejected. The model suggests that 18% of the population who smoke and drink are susceptible. The lifetime risk for non-smokers and non-drinkers who are heterozygotes for the susceptible allele is close to zero, but for those heterozygotes who smoke and drink the risk is 14% by age 70. These findings suggest that specific genetic factors account for a significant fraction of the risk of SCCHN associated with a family history of SCCHN.