Co-segregation studies based on a selection of intragenic restriction fragment length polymorphisms of the low density lipoprotein receptor (LDLR) gene have been used extensively both for research and diagnostic studies of familial hypercholesterolaemia (FH) families, because direct mutation screening remains complex. Here we describe the development and application of a more efficient approach to co-segregation studies based on highly informative dinucleotide and tetranucleotide repeats flanking the LDLR gene. A series of microsatellites (D19S391, D19S394, D19S221 and D19S179) were selected for study on the basis of linkage analysis in the CEPH families using intragenic polymorphisms for a TA repeat (exon 18) in the LDLR gene, and earlier data for a Pvu II polymorphism (intron 15). A physical map of the region of chromosome 19 also contributed to this selection. One marker in particular, D19S394, sited 150 kilobases telomeric to the gene, was extremely useful, displaying 90% heterozygosity, robust PCR of tetranucleotide repeats without stutter bands, and no recombination with the LDLR gene (θ=0, LOD 68). Use of this marker in the families of twenty-three FH probands from Hampshire demonstrated co-segregation of the hyperlipidaemia phenotype with the LDLR gene region, except in one family with defective apolipoprotein B-100, and a family turning out to display familial combined hyperlipidaemia. This approach should facilitate the search for any families where FH does not co-segregate with the LDLR gene, and will enhance the repertoire of molecular diagnostic tools available for FH.

We addressed the question: Is there evidence that allelic variation in a single unmeasured gene that has a large effect on maximal activity of erythrocyte sodium-lithium countertransport (Na-Li CNT) also has pleiotropic effects on variation in plasma triglyceride levels? Complex segregation analysis models that included plasma triglyceride levels as a covariate were considered as explanations for interindividual variation in Na-Li CNT. A sample of 711 healthy adults from 254 pedigrees enrolled in the Rochester Family Heart Study was selected for this study. The majority of the pedigrees supported the hypothesis that variations in a single unmeasured non-transmitted environmental factor have large effects on the Na-Li CNT distribution. Only gender-specific first-order covariate parameters were necessary in the complex segregation models suggesting that the form of the relationship between Na-Li CNT and plasma triglyceride level was not influenced by variation in the inferred environmental factor with large effects. Stratification of the sample by this inferred environmental factor resulted in three classes of individuals with significant differences in the distributions of coronary heart disease risk factor traits, as well as interindividual variation in both Na-Li CNT and plasma triglyceride levels. These results, along with other observations from the Rochester Family Heart Study sample, emphasize the complex and multifactorial nature of the causes of interindividual variation in Na-Li CNT. Our study further suggests that new research strategies are needed for studying the relationships between genetic and environmental variation and variation in quantitative traits such as Na-Li CNT that have been identified as risk factors for hypertension.

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.

The GM immunoglobulin (Ig) allotype distributions of 49 native Amerindian populations from North to South America were analysed by a new technique called ‘Mobile Sites Method’ (MSM). This allows the global interpretation of genetic diversity in space by means of a distorted geographic map called a ‘genetic similarity map’. This approach has been improved by superimposing in the distorted geographic map both the haplotype set (represented by hypothetical populations having a 100% frequency of the haplotype considered) and the ‘geography-genetics discontinuities’ (i.e. the zones between homogeneous population clusters). This bidimensional representation completes the interpretation of the genetic distances between populations in terms of local genetic diversity and possible migrations. Our results concerning the spatial distribution of the Amerindian populations show: (i) a great interdependence of the geographic locations and the GM haplotype distributions (the importance of the geographic factor was checked with the usual technique of ‘random sampling’ and the percentage of explained distance variability decreases from 78% with the observed data to a level less than 67% with the random data); (ii) a parallelism between genetics and linguistics groups as indicated by the population clusters in the similarity map, and (iii) a complex distorted map revealing the presence of multiple population migrations and admixtures in the course of time. A particular distortion of South America suggests possible migrations by sea along the western and eastern coasts of Central America, or multiple migration waves without population admixture across Central America.

Sjögren–Larsson syndrome (SLS), a rare autosomal disorder characterized by ichthyosis, spastic neurological disorders and oligophrenia, is associated with deficiency of fatty aldehyde dehydrogenase encoded by a gene on chromosome 17q11.2. Mutations of the gene (GDB symbol ALDH10) were recently identified in three SLS patients. Another aldehyde dehydrogenase isozyme, ALDH3, also has a high activity for fatty aldehyde oxidation, and is encoded by a gene in chromosome 17q11.2. Abnormality of the ALDH3 gene could also cause a similar syndrome.

The examination of the ALDH3 locus of three additional SLS patients showed that two are heterozygous with C→G at nt 985 (Pro→Ala at protein position 329). However, the mutation was found to be common (frequency of the atypical allele is about 0·25) in normal subjects, and not related to SLS.

Isoelectric focusing analysis indicated that ALDH3 is hardly expressed in normal as well as patients' fibroblast cells, while ALDH10 expressed in the normal cells is diminished in the three patients' cells. The level of ALDH10 mRNA is also low in the patients' cells.

The examination of the ALDH10 locus revealed the existence of a 3 base deletion coupled with a 21 base insertion at intron 6/exon 7 junction in one patient. This abnormality is the same as that found in the patient previously reported by other investigators. One patient is associated with a 2 base deletion at nt 1297 and consequent premature chain termination at protein position 434. Another patient is a compound heterozygote for the same 2 base deletion at nt 1297 and a 5 base insertion at nt 1311 and premature chain termination at protein position 457. Unique characteristics of the SLS mutations are pointed out.

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.

A powerful test for population association of a disease with alleles at a bi-allelic marker locus is the transmission/disequilibrium test (TDT). A generalization of the test to multi-allelic marker locus is proposed which utilizes the maximal association of individual alleles with the disease, given by the maximum TDT statistic, TDT(max). To overcome the multiple testing problem encountered when using the maximal association to test the null hypothesis of no disease-marker association, a randomization procedure is developed. An investigation of the power of the test suggests that the randomization procedure performs almost as well as a recently proposed likelihood based test of linkage disequilibrium. The advantage of the new test is that it can be applied sequentially, based on a one-sided version of the TDT statistic, for investigating patterns of association of several individual alleles with the disease.

We have studied the impact of natural selection through stillbirth on the Italian population, taking into account the socio-economic heterogeneity of the country. The results suggest that older age at delivery and lower cultural level of the mothers, indicators of critical biological and socio-economic conditions, even at present increase stillbirth risk. Moreover, in the less favourable environment of the southern regions, selection is still sex-specific.

The hypervariable segment I of the control region of the mtDNA was sequenced in 45 unrelated individuals from Bioko and 50 from São Tomé, two islands in the Gulf of Guinea that have had very different settlement patterns: Bioko was colonized around 10000 BP, while São Tomé was first settled by the Portuguese, who brought African slaves to the island. Two different patterns of sequence variation are evident and are also clearly a consequence of their very different demographic histories. The Bubi present a low genetic diversity and it is likely that the island was colonized by a small number of individuals with small later migration. São Tomeans might be considered a subset of a mainland African population relocated to the island. They present high genetic diversity with a high number of sequences being shared with many continental populations. This study, with knowledge of the population history in island populations, strengthens the genetic approach to unravel past demographic events.

The polymorphisms of nine loci containing reiterated CAG repeats were examined in four populations from three continents. Their normal variation was analysed across populations or in subsets of loci grouped according to either the presence/absence of disease-associated expansions or CAG interruptions. A unifying feature of the allele distributions of all loci in all populations was the marked non-normality. Significantly larger numbers of alleles, average lengths, length ranges and variances in repeat number were observed in loci with vs. without known expansions. Significantly longer alleles were found at loci with vs. without interruption of the (CAG)n motif. The nine loci detected levels of inter-population variability comparable to other loci. Altogether the data are at odds with a model assuming that autosomal expressed trinucleotides accumulate variation exclusively by insertion/deletion of a single unit.

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.

Despite the recent cloning of BRCA1, BRCA2 and the mismatch repair genes, it will still be a long time before it is possible to specify any individual's risk for ovarian cancer based on her genotype. Most women concerned about their risk on the basis of one or two affected relatives do not belong to extensive ovarian cancer families. Risk calculations depend on a reliable genetic model for ovarian cancer derived, ideally, from the population from which an individual is drawn. We have carried out a segregation analysis using data collected from consecutive ovarian cancer patients in two different centres in the UK. Complex segregation analysis was carried out with the addition of diathesis as a separate parameter allowing other cancers, associated with ovarian cancer, to be taken into account. The use of diathesis in the derivation of this alternative model is described. Analysed under joint likelihood without diathesis, the gene frequency is 0·0028 and penetrance to age 70 years is 50%. This is in agreement with other published models. Incorporating diathesis into the model under joint likelihood gives similar parameters for a single locus model but gives the best fit with a two locus model where both genes are rare.

As part of the 1990/1991 Pakistan Demographic and Health Survey, data were collected on the outcome of 26408 births to 6611 women, with mortality rates investigated at specific age intervals during the first 5 years of life. Bivariate and multivariate logistic regression analyses were employed to examine the comparative roles of consanguineous marriage and a number of demographic and socioeconomic factors, including the sex of the child, maternal age, maternal education, birth interval and birth order, as determinants of early death. The results indicate that, even after controlling for these non-genetic variables, inbreeding at the level of first cousin exerted a significant adverse effect on survival in four of the five age intervals examined, neonatal, post-neonatal, infant and under 5 years.

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.

We defined the Y-chromosome haplotypes on the basis of six polymorphic sites: an Alu-element insertion (YAP), a single-base change (C→T at DYS199), one trinucleotide repeat (DYS392) and three tetranucleotide repeats (DYS393, DYS390 and DYS19). Among 140 Y chromosomes from Whites, Blacks, Japanese and Amerindians we identified 67 different haplotypes, the majority of them population-specific; only seven haplotypes were shared by three different racial groups, mostly owing to admixture. Overall, three main lineages can be defined on the basis of the YAP/DYS199/DYS392 markers: (a) a predominant /−/C/10/13/22 (or) 23/ lineage, observed among all racial groups; (b) a/+/C/ lineage which predominates among Blacks (comprising mainly the sublineage /+/C/10/13/), although it is eventually found among Japanese and Whites; and (c) a /−/T/ lineage observed only among Amerindians (comprising mainly the sublineage /−/T/13/13/). The decreasing haplotype diversity of the three lineages agrees with the idea that the first is the most ancient, while the last is the more recent. The data also indicate that the YAP insertion occurred in a /−/C/10/13/ chromosome and the C→T mutation occurred in a /−/C/13/13/ chromosome. Finally, the data suggest that at least two Y-chromosome lineages (/−/C/13/ and /−/T/13/) contributed to the early peopling of the Americas, and supports the hypothesis that /−/T/13/ could be derived from /−/C/13/ and that both haplotypes could be present in the ancestral populations that peopled the continent.

Affected sib pairs with typed but unaffected parents, conveniently termed foursomes, have become a major source of information on genetic susceptibility to common disease. So far most methods of analysis have been based on extensions of the single locus analyses developed, and successfully applied, to the mendelian disorders. However, unifactorial methods are not suited to multifactorial disorders. The power of methods of detecting linkage in the presence of more than one locus with one or more susceptibility alleles is considered.

The relevance of familial clustering to predicting the presence of loci with susceptibility or resistance alleles sufficiently frequent and effective to have an appreciable influence on population incidence is discussed. The mathematical problem of clustering due to numerous alleles of small effect was resolved by Pearson in 1901 in relation to claims that the mendelian model of an allele at a single locus determining a distinct phenotype was necessary to explain the familial concentrations that had been observed in several species. The apparent inconsistency between the mendelian and polygenic models was resolved by Fisher's demonstration in 1918 that there was no essential difference between these two extreme forms of phenotypic determination. Although constant penetrance models are unrealistic, and no longer necessary since Pearson's analysis, the assumption is implicit in most recent analyses and has the advantage of simplicity in providing a lower limit on the sample sizes necessary.

Nonrandom associations between DNA polymorphisms are commonly tested by Fisher's exact test in spite of it is seriously conservative. Theoretical statistical studies have shown that the exact test with Tocher's correction does not present this problem but Tocher's correction is never used by experimentalists for detecting gametic associations. We have examined the practical consequences of using these two alternative tests for the detection of nonrandom associations in populations. A total of 1566 pairs of RFLPs of eleven gene regions and sixteen populations from previously published human and Drosophila disequilibrium data were examined. The analysis reveals remarkable differences between the two tests for detecting gametic associations. In some gene regions, the exact test with Tocher's correction detects a percentage of significant associations between RFLPS which is twice or three times higher than that detected by the exact test without correction. Therefore, the widely used exact test can be seriously underestimating disequilibrium in populations. In addition, the study shows that the standard chi-square test for independence in 2 × 2 tables detects a similar percentage of significant associations between RFLPs than Tocher's test.

LCN1 gene encodes the tear lipocalin; the lipocalins are a large and growing family of proteins characterized by their ability to bind small hydrophobic molecules. We report here the location of a dinucleotide repeat microsatellite marker (D9S1826) close to LCN1 gene. Using the CEPH reference families, the position of LCN1 is located within the 9q34 genetic map between D9S23 and D9S158.

Defects in the AGXT gene mapped to chromosome 2q37.3 cause primary hyperoxaluria type 1 (PH1), one of the inherited disorders of endogenous oxalate overproduction. In order to identify diagnostically useful linkage markers in this region of chromosome 2 we have typed three microsatellite loci mapping to the q37 region of chromosome 2 in 192 individuals from 30 families. They were additionally studied for mutations and polymorphisms in the AGXT gene. Maximum lod scores of 29·1, 22·8 and 15·8 were obtained for D2S140, D2S125 and D2S395 respectively at recombination fractions (theta) of 0·001, 0·015 and 0·02. Confidence intervals for recombination as determined by the ‘lod-1 rule’ were 0·015, 0·05 and 0·06. Three recombinants were identified between AGXT and D2S125/D2S395, whereas no recombination between AGXT and D2S140 was observed. These data allow the calculation of the risk of incorrect prenatal diagnosis of PH1 based solely on linkage analysis with these extragenic markers.

Haseman & Elston (1972) introduced a sib pair method using classical regression analysis to detect linkage between a polymorphic marker locus and any quantitative trait locus. Most of the diseases mapped to date follow simple Mendelian, single locus transmission. But there are many familial diseases that do not follow simple Mendelian segregation, for example diabetes, several forms of cancer, etc. In this paper, we extend Haseman and Elston's sib pair method to two unlinked quantitative trait loci each linked to one of two unlinked polymorphic marker loci. For the two-locus epistatic model, we give a general formulation of the complete regression model and details of the regression coefficients in terms of variance components.