Replication error (RER) is defined as mutation events in repetitive DNA segments. To investigate further the RER phenomenon and reveal any differences in mutation outcome between different short tandem repeat (STR) loci, we have investigated the somatic mutation rate and the size distribution of new tumour alleles in four tetranucleotide STRs in a large material of unselected colorectal adenocarcinomas. DNA was extracted from the blood and carcinomas of 217 patients. All blood/tumour pairs were analysed using the STRs HUMTHO1, HUMFES/FPS, HUMVWA31/A and HUMF13A1. Mutations are detected at all four loci. There are substantial differences in mutation rate and mutation direction (i.e. expansion versus contraction) between different STR loci. In all four STRs, the majority of events represent gain or loss of a single repeat. Almost all new tumour alleles correspond to known alleles in a population database, indicating that these are also composed of integers of the four base pair repeat. There is no statistically significant size bias in the mutating alleles as compared to the allelic distribution in the population database.

We have refined polymerase chain reaction (PCR) assays for the detection of sickle cell anaemia, the delta F 508 deletion causing cystic fibrosis, and the IVS1–110 mutation leading to beta-thalassaemia, allowing them to be successfully performed upon single cells using fluorescent primers. We have also assessed the possibility of detecting aneuploidies of chromosomes 13, 18 and 21 using a quantitative fluorescent polymerase chain reaction (QF-PCR) with primers flanking polymorphic short tandem repeat (STR) markers. Trisomies were readily diagnosed by the detection of tri-allelic patterns. However some heterozygote normal and trisomic diallelic patterns did not produce the expected ratios of amplified PCR products due to preferential DNA sequence amplification. Total allelic drop out (ADO) did not occur with any of the cells tested. Multiplex QF-PCR assays can be performed on a single cell in under 6 h and simultaneously provide diagnosis of single gene defects, sex determination and an indication of selected chromosome aneuploidy.

Coeliac Disease (CD) is a gluten sensitive enteropathy characterised by villous atrophy and crypt cell hyperplasia. There is a tight HLA association between CD and the HLA DQ alleles DQA1∗0501, DQB1∗0201 (DQ2), arranged in either cis- or trans- configuration, are found in 98.9% of cases in Northern European populations and 80% in Greeks and Ashkenazi Jews resident in Israel. We have previously shown that the HLA alleles and CD do not co-segregate in families multiply affected with CD, suggesting that the HLA association is entirely due to the necessity to have these normal DQ alleles for CD to manifest, and that the main genetic predisposition lies at a locus other than the MHC. It is therefore possible to conduct genetic linkage studies in order to isolate the non HLA genes which predispose to CD. Recently a group conducted a genome screen for the non HLA genes in an affected sib-pair analysis and identified four non HLA loci with positive lod scores. We examined these loci using a pedigree based linkage study. Our pedigree sample consisted of a cohort of 21 families with 60 affected individuals and 125 unaffected family members. We used 11 microsatellite markers at the loci implicated and analysed the genotype data using both MLINK and MFLINK to detect linkage. The MLINK and MFLINK analyses did not provide any evidence to support the earlier findings, although the difficulties involved in analysing complex diseases mean that one cannot be certain that these regions do not harbour susceptibility loci, at least in some families.

Data on the GM and KM haplotypes and RFLPs in the immunoglobulin IGHG loci are reported intending to evaluate the genetic contribution of the different populations (Europeans and Africans) who settled Tenerife Island. The GM and KM allotypic systems reveal an estimated European genetic admixture of 88%. The only possible African contribution is the presence of the GM*1,17;..;5* haplotype (2.5%), but no other traces of Black African characteristic haplotypes are found. Although new RFLP haplotypes are described, DNA variation is similar to that reported in Caucasoids with a marked absence of restriction fragments characteristic of Black Africans.

We have studied the impact of natural selection on the Italian population, analysing the relationship between stillbirth and three related variables: birth weight, birth order and maternal age. A progressive relaxation of selection with time has been demonstrated by the reduction of the Haldane index calculated with respect to the three variables.

The genetic basis of many human diseases, especially those with substantial genetic determinants, has been identified. Notable amongst others are cystic fibrosis, Huntington's disease and some forms of cancer. However, the detection of genetic factors with more modest effects such as in bipolar disorders and a majority of the cancers, has been more complicated. Standard linkage analysis procedures may not only have little power to detect such genes but they do, at best, only narrow the location of the disease susceptibility gene to a rather large region. Association studies are therefore necessary to further unveil the aetiological relevance of these factors to disease. However, the number of tests required if such procedures were used in extended genome-wide screens, is prohibitive and as such association studies have seen limited application, except in the investigation of candidate genes. In this paper, we discuss a logistic regression approach as a generalization of this procedure so that it can accommodate clusters of linked markers or candidate genes. Furthermore, we introduce an expectation maximization (E–M) algorithm with which to estimate haplotype frequencies for multiple locus systems with incomplete information on phase.

Scenarios, such as populations experiencing a bottleneck or an exponential growth, have been suggested as candidates for explaining the observed differences among mitochondrial DNA sequences in a sample of a given population closed to migrations. Here, population size is considered as capable of varying, and the set of the at least 95% most probable population paths capable of producing the observed mean number of pairwise nucleotide differences is delineated. To do this, the mean and the variance of coalescence times of two genes taken in an n-genes sample with varying population size are expressed. The observed mean coalescence time already echoed a set of population paths due to the variance associated to the coalescent process, but only specific scenarios have been studied, such as the bottleneck or the exponential function. However, mitochondrial DNA data does not reflect a single scenario, after the effect of the variance. These scenarios implied by pairwise nucleotide differences are described through a set-valued function, the ‘regulation map’, a convenient way to represent temporal population paths.

Risch and Zhang recently proposed to use extreme discordant sib pairs for mapping quantitative trait loci. Here, it is shown that the set of genetically possible distributions of the number of marker alleles in such sib-pairs is described by two inequalities. Thus, a likelihood ratio test analogous to Holmans's possible triangle test for affected sib pairs can be defined. The performance of this test is compared to the mean test considered by Risch and Zhang. For most of the genetic models considered, the mean test is slightly more powerful than the restricted likelihood ratio test. However, for models with a rare recessive gene (or equivalently a common dominant gene), the restricted likelihood ratio test is much more powerful.

Ann. Hum. Genet. (1997), 61, 319–333

Correction and additional citation

The author has noticed two errors he failed to correct in this paper, as follows:

(i) Page 329: ‘Thus if the case has genotype AA and the control is BC one adds 0.5 to TAB and 0.5 to TAC’ should read ‘Thus if the case has genotype AD and the control is BC one adds 0.5 to each of TAB, TAC, TDB and TDC.’

(ii) Table 3, first ‘Score’ line: ‘0.25tAB, 0.5tAC, 0.5tCB’ should read ‘0.5tAB, 0.5tAC, 0.5tCB.’

Since the paper was published the author has learned that the use of siblings as controls was proposed by L. S. Penrose, and a method of analysis devised by C. A. B. Smith, for application to studies of blood groups and duodenal ulcer (Clarke et al. 1956). The author is grateful to C. A. Clarke for making him aware of this previous work.

Clarke, C. A., Wyn Edwards, J., Haddock, D. R. W., Howel-Evans, A. W., McConnell, R. B. & Sheppard, P. M. ABO blood groups and secretor character in duodenal ulcer. Br. Med. J. (1956), 725–731.