In this study we report the cloning of four human OCT1 (hOCT1/SLC22A1) isoforms: a long form, hOCT1G/L554, and three shorter forms (hOCT1G/L506, hOCT1G483 and hOCT1G353). All four variants could be identified in the human glioma cell line SK-MG-1, whereas only two isoforms (hOCT1G/L554 and hOCT1G/L506) were found in human liver cDNA. The hOCT1G/L554 represents the full length hOCT1 since the sequence of this clone is more than 99% identical to previously cloned hOCT1 cDNAs. Elucidation of the gene structure of human OCT1 demonstrated that the other isolated isoforms are alternatively spliced variants. The hOCT1 gene consists of 7 exons and 6 introns. When stably expressed in human embryonic kidney (HEK293) cells, only the full length hOCT1 cDNA mediated decynium-22 (D22)-sensitive uptake of tritiated 1-methyl-4-phenylpyridinium ([3H]-MPP+).

Decreased function of the melanocortin-4 receptor (MC4R) was reported to cause late-onset obesity and insulin resistance in rodents. Thus mutations in the MC4R gene drew strong attention as a possible cause of obesity and diabetes. We screened for mutations in the MC4R gene in extremely obese [body mass index (BMI) [ges ] 35 kg/m2] Japanese with diabetes by direct sequencing. A heterozygous mutation (V103I) was detected in one case (2.0 %), however the frequency was not significantly different from that in non-obese (BMI [les ] 24 kg/m2) and non-diabetic subjects (2.7 %). No other mutations were detected. These results suggest that mutations including V103I in the MC4R gene are not a major cause of obesity or diabetes in Japanese.

The mitochondrial haplogroup T, characterized by the nucleotide motif 16126C–16294T in the hypervariable segment I (HVS I), is one of the most frequent among Europeans. It has been shown that this haplogroup includes the only well-resolved subgroup, T1, but that other HVS I sequences cannot be differentiated into subgroups due to possible homoplasies at nucleotide positions 16292, 16296 and 16304, leading to the reticulations in the topology of phylogenetic networks. To study the problem of molecular instability at these positions, we have performed an analysis of 159 previously published West Eurasian HVS I sequences belonging to haplogroup T, together with 12 new HVS I sequences of Eastern Slavs. These 12 sequences represent 16.9% of a total of 71 samples analysed and identified as haplogroup T mtDNAs by RFLP analysis in this study. A search for rare point mutations associated with different combinations of nucleotides 16292T, 16296T and 16304C within the haplogroup T sequences, and specific to certain populations or a group of closely related-by-descent populations, was performed. This analysis revealed 11 marker mutations, each of which was characteristic for a certain group of linguistically or geographically close individuals – the Adygei, Germans, Kazakhs and linguistic isolates of the Eastern Italian Alps. The occurrence of these rare population-specific polymorphisms in association with various combinations of mutations at positions 16292 and 16296 on the haplogroup T background provides evidence of molecular instability at these nucleotide positions. Molecular instability in the haplogroup T HVS I sequences is also suggested by multiple independent losses of the haplogroup T diagnostic nucleotide variants in different populations. The results of the present study suggest that identical haplogroup T HVS I sequence types might have arisen independently in different human populations.

Simultaneously analysing genotype effects at several closely-linked loci may be preferable to analysing them separately, but can be difficult, due to multiple genotype classes, small class sizes, and non-independence induced by associations among loci. Analysis of haplotype effects offers an alternative approach. We studied effects of haplotypes comprising 3 loci (5′ to 3′: PvuII, HindIII, and Ser447-Stop) in the lipoprotein lipase (LPL) gene on plasma lipid levels and LPL activity, in 807 Dutch males with coronary atherosclerosis. We analysed haplotype effects in individuals for whom haplotypes could either be determined unequivocally or inferred with high probability, using contrasts suggested by likely evolutionary relationships among the haplotypes. One haplotype was associated with significantly higher total cholesterol, while another was associated with significantly lower triglyceride levels. Though these two haplotypes had generally opposite effects on lipids, both were associated with significantly higher LPL activity. In genotype analyses, the HindIII (−) allele was associated with higher LPL activity; however, one haplotype bearing it had no significant effect on LPL activity. Haplotypes thus provided more information than genotypes alone would have. The two haplotypes with consistently different effects on lipid levels despite similar effects on LPL activity, provide further evidence that aspects of LPL biology, apart from its catalytic function in lipolysis, may mediate its effects on plasma lipids at least in coronary artery disease patients.

Most studies of the pathogenesis of coronary heart disease occur between gene variants and biochemical or physiological variables known to be atherogenic. In many situations, however, the gene products are not necessarily known. We studied 17 families (n = 122) with mutations in the low density lipoprotein (LDL) receptor gene as a model in which to test formally for linkage directly between an atherogenic genotype and ischemic heart disease (IHD) or aorto-coronary calcified atherosclerosis. In each family one of three different mutations was found: the Trp66–Gly mutation, the Trp23–Stop mutation, or a ten kilobase deletion removing exons 3–6 of the LDL receptor gene. Genomic DNA was used to determine these mutations by either enzymatic cleavage assays or Southern blotting. Aorto-coronary calcification was significantly associated with age and plasma cholesterol. Sex, hypertension, BMI and smoking were not associated with aorto-coronary calcification. Nonparametric analysis indicated significant linkage of the LDL receptor gene locus to aortic (p < 0.00005) and to aorto-coronary calcified atherosclerosis (p < 0.00001). Assuming a dominant mode of inheritance, significant linkage was detected for aortic (LOD = 3.89) and aorto-coronary calcified atherosclerosis (LOD = 4.10). We suggest that the atherogenicity of variations in other genes could be assessed by a similar approach.

Carriers of X-linked juvenile retinoschisis (RS) were previously suggested to give birth to an excess of boys. We determined the carrier status for the 214G > A mutation of the RS1 gene in 202 females belonging to a large RS founder pedigree. The secondary sex ratio (SSR) in the offspring of 149 carriers was 129.8 (z = 2.25), which differed significantly from that of the Finnish population (SSR 106) but not from that of 53 non-carrier females belonging to the same pedigree (SSR 116.7; z = 0.51). Since possible causes for the skewed SSR include factors affecting fertilisation, implantation and embryonic death, we searched for expression of RS1 in various placental and uterine cells and found that, in addition to the retina, RS1 is expressed in the uterus. We hypothesize that the RS1 protein has a role in implantation or embryonic survival.

An efficient test of deviation from Hardy–Weinberg frequencies with one degree of freedom was applied to 44 marker loci in a genome scan, and 7 loci had a significant excess of apparent homozygotes (χ2(1) > 6) suggestive of typing error. In this example evidence for linkage did not increase when outliers were censored. Statistical quality control is an essential part of genotyping, and the effect of mistyping and map error should be considered in evaluating any genome scan.

In its usual form, the multifactorial model of disease transmission assumes that the liabilities to disease have a multivariate normal distribution. This paper studies how sensitive to this assumption are the quantitative results from the model. Accordingly, bounds are established for the probability of a child having a disease, given that both parents have it and taking the heritability of the disease to be known. Unfortunately, these bounds turn out to be wide. For example, a probability that is 0.38 under the trivariate normal model may be as low as 0.12 or as high as 0.78 under other trivariate models, even if attention is restricted to those of variables-in-common form. The broader statistical issue of the meaning of trivariate dependence, as distinct from bivariate dependence, is also discussed.

Expressions are derived for the sample size required to achieve a given power in variance component linkage analysis of a quantitative trait in unascertained samples. For simplicity an additive model, comprising effects due to a single QTL, residual additive genetic factors, and individual-specific random environmental variation, is considered. Equations are given relating sample size to trait heritability for sibpairs, sib trios, nuclear families having two and three sibs, and arbitrary relative pairs. The effects of nonzero residual additive genetic variance and parental information are discussed, and a scale relationship for sample sizes with sibships and nuclear families is derived. For larger sampling structures such as extended pedigrees the inheritance space is randomly sampled and the relevant equations are solved numerically. Comparative power curves are presented for sibships of size 2–4 and for an extended pedigree of 48 individuals. Simulation results for sibpairs confirm the validity of the theoretical results.