I compare the transmission/disequilibrium test (TDT) and affected sib pair (ASP) test under a general algebraic model describing a bi-allelic disease locus. Assuming linkage to a bi-allelic marker, I derive two binomial probabilities, one for parental allele ‘transmission’ (Pt ) which determines the magnitude of the TDT χ2 statistic (χ2tdt), and a second for identity-by-descent (ibd) marker allele ‘sharing’ (Ps) which determines the magnitude of the ASP test statistic (χ2asp). I also consider the ASP test applied to a completely polymorphic marker and demonstrate that the probability of ASP marker allele sharing (Ps) is identical to Ps observed for a bi-allelic marker in equilibrium with the disease locus. I present a general framework for determining the power of the TDT and ASP test based on expressions for Pt, Ps and the proportion (H/F) of ascertained parents who are informative at the marker. Two previous analytic investigations of TDT power based on the work of Ott (1989), and Risch & Merikangas (1996) are shown to be special cases of this general framework. In addition, I show the relationship between the framework I present and a third analytic investigation of TDT power for multi-allelic markers based on the work of Sham & Curtis (1995).

The original transmission disequilibrium test (TDT), was introduced to test for linkage between a marker and a disease-susceptibility locus (Spielman et al. 1993). Allison (1997) extended the TDT procedure to quantitative traits. Allison's test, however, is restrictive in that it requires family trios consisting of one heterozygous parent, one homozygous parent and one child, and considers only the situation where the marker locus is analogous to the quantitative trait locus itself. In this paper, we propose, investigate and apply a general TDT for quantitative traits that permits more than one child per family, does not require only one parent to be heterozygous, and allows for the fact that the various alleles at the marker and trait loci may be at varying degree of linkage disequilibrium. We also show that this TDT for quantitative traits is still a valid test of linkage in the presence of population substructure. To provide guidelines for study design, we develop analytic formulae for calculation of the power of the TDT for mapping quantitative trait loci and investigate the impact of various factors on the power. Power calculations show that the proposed TDT for quantitative traits is more powerful than Allison's basic test statistic and the extreme discordant sib pair linkage method. The proposed TDT statistic for quantitative traits is applied to systolic blood pressure variation in the Rochester Family Heart Study using an extremely discordant sibling pair design.

Genetic studies have emphasized the contrast between North African and sub-Saharan populations, but the particular affinities of the North African mtDNA pool to that of Europe, the Near East, and sub-Saharan Africa have not previously been investigated. We have analysed 268 mtDNA control-region sequences from various Northwest African populations including several Senegalese groups and compared these with the mtDNA database. We have identified a few mitochondrial motifs that are geographically specific and likely predate the distribution and diversification of modern language families in North and West Africa. A certain mtDNA motif (16172C, 16219G), previously found in Algerian Berbers at high frequency, is apparently omnipresent in Northwest Africa and may reflect regional continuity of more than 20 000 years. The majority of the maternal ancestors of the Berbers must have come from Europe and the Near East since the Neolithic. The Mauritanians and West-Saharans, in contrast, bear substantial though not dominant mtDNA affinity with sub-Saharans.

Four sequence variants in the 11β-hydroxylase (CYP11B1) gene are reported. One of the sequence changes occurs in exon 1 and is in linkage disequilibrium with a second variant in intron 3. The other two changes occur at adjacent nucleotides in intron 1. The finding of easily demonstrable, intragenic variants will be beneficial to the study of the role of the CYP11B1 and the adjacent aldosterone synthase (CYP11B2) gene in hypertensive disease.

Many traits that distinguish one individual from another, such as height or weight, are clearly heritable and yet vary continuously in populations. Continuous, heritable variation in trait levels presumably reflects the segregation of multiple genes, but elucidation of the genetic architecture of quantitative traits has been limited. Haseman & Elston (1972) developed a genetically robust method (HE) for detecting linkage to quantitative trait loci using sib-pairs. The method is based on a simple linear regression of the squared sib-pairs trait difference on the proportion of alleles shared identical by descent at a marker locus. Linkage is detected by a negative slope which has been traditionally assessed by a standard t-test. Wan, Cohen & Guerra (1997) have shown that the standard t-test is robust to the violations of the stochastic assumptions underlying the test. In practice, however, the standard t-test, based on least-squares regression, is sensitive to outliers. The presence of outliers in the data can lead to false positive and false negative linkage results. Accordingly we have developed and evaluated a statistically robust procedure for the HE approach to linkage. The procedure is based on robust regression. Simulation studies show that this robust procedure has greater power than the standard t-test in the presence of outliers, and has similar power to the standard t-test in the absence of outliers. This robust procedure also shows greater power than rank-based approaches either in the absence or presence of outliers. To illustrate the methods using real data we reanalyse data from two lipoprotein systems that motivated this work.

For most of the past century, prehistorians have had to rely on the fossil and archaeological records in order to reconstruct the past. In the last few decades, this evidence has been substantially supplemented from classical human genetics. More recently, phylogenetic analyses of DNA sequences that incorporate geographical information have provided a high-resolution tool for the investigation of prehistoric demographic events, such as founder effects and population expansions. These events can be dated using a molecular clock when the mutation rate and founder haplotypes are known. We have previously applied such methods to sequence data from the mitochondrial DNA control region, to suggest that most extant mitochondrial sequences in western Europe have a local ancestry in the Early Upper Palaeolithic, with a smaller proportion arriving from the Near East in the Neolithic. Here, we describe a cladistic notation for mitochondrial variation and expand upon our earlier analysis to present a more detailed portrait of the European mitochondrial record.

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.

Population samples from Liguria, Piacenza and Pavia provinces, and North Lombardy are compared for surnames and HLA gene frequencies. The genetic structure inferred from the principal coordinate analysis of surname frequencies is different from that inferred from HLA gene frequencies. The latter may represent ancient migrations, since surnames are relatively recent genetic markers dating from a.d. 1500. Ligurian and Celts were the ancient inhabitants of this northern Italy geographic area. Genetic distances, derived from HLA gene frequencies, and represented with an unrooted tree show the presence of a Ligurian and a Celtic pole. The aggregation of the subpopulations to each pole accords with the history and the archaeological findings in the area.

We have prepared a transferrin (TF) cDNA from total RNA of peripheral blood cells of an individual with a TF B variant (TF Bv) phenotype to analyze the molecular basis for the TF Bv. The TF B variant allele (TF Bv) was found to contain an A to G transition at nucleotide 1879 in the coding region that may result in substitution of glutamic acid for lysine at codon 627 located in exon 16. In addition, a transient expression study by transfection of each plasmid containing TF C1, TF C2 or TF Bv cDNA into monkey kidney (COS7) cells indicated that the products from specific TF alleles were able to be identified respective phenotypes by isoelectrofocusing electrophoresis and immunoblotting analyses. Based on this nucleotide substitution, we also established a PCR–RFLP method to detect the TF Bv allele from genomic DNA. Thus, peripheral blood cells were useful as an alternative source for preparation of cDNA from human liver for the molecular analysis of TF polymorphism.