Nonsyndromic cleft lip and palate (CL/P) is a common craniofacial malformation with a complex genetic component. Attempts at identifying susceptibility loci via family and case-control studies have proved inconsistent. It is likely that initial predictions of the complex interactions involved in facial development were underestimated. The candidate gene list for CL/P is getting longer and the need for an impartial, systematic screening technique, to implicate or refute the inclusion of particular loci, is apparent. Large-scale multi-centre collaborations will also be necessary if we are to pursue the avenues of gene-environment interactions, which have opened up over recent years. So we are faced with the question ‘Can this complex trait be too complex?’

A crucial step beyond the identification of genetic linkage of a disease to a chromosomal region is the production of a physical map that will allow the identification of candidate genes. Although the process of physical map building has been facilitated by the flow of data released by the Human Genome Project, gathering all the information together requires significant effort. In a previous study, we reported linkage between Bipolar Affective Disorder and the chromosomal location 4p15.3–p16.1. In this review we use this example to describe how to collect publicly available sequence, DNA fingerprint, and genetic marker data and integrate these with empirical data to build a large scale high resolution physical map of a region. Methods used to identify new genetic markers and candidate genes within a circumscribed region are also presented.

Compared with other mammals, humans as a species are relatively infertile. Various studies suggest that in young, unselected couples, who are trying to conceive, 20–25% of them should be successful each monthly cycle (Bonde et al. 1998; Edwards & Brody, 1995). This compares with an average of 70% in captive baboons for example (Stevens, 1997). Interestingly, the implantation rate after in vitro fertilisation (IVF) at best averages around 20% per embryo transferred (Edwards & Beard, 1999). Evidence is steadily accumulating to prove that the major cause of implantation failure in humans after both in vivo and in vitro fertilisation is the high incidence of chromosomal abnormality. Combining data from cytogenetic studies of spontaneous abortions with those obtained from preimplantation embryos suggests that meiotically derived aneuploidy occurs in 25% of conceptions, an order of magnitude higher than is found in other well studied species such as the mouse (Hassold & Jacobs, 1984; Jamieson, 1994). Additionally, interphase fluorescent in situ hybridisation (FISH) analysis of three day old human embryos has shown that up to 50% are chromosomally mosaic (Delhanty et al. 1997; Munné et al. 1998), further increasing the chance of implantation failure. This review covers the evidence accumulating from a variety of sources that poor fertility in humans has a chromosomal basis.

Idiopathic Parkinson's disease (IPD), a progressive neurodegenerative disorder, is a common cause of disability. No current therapies modify disease progression. The pathological hallmarks are the presence of Lewy bodies and massive loss of dopaminergic neurons in the pars compacta of the substantia nigra. Two genes (SNCA and parkin) as well as two gene loci have now been implicated in the pathogenesis of familial PD. These represent significant progress in our understanding of the disease, considering the rarity of large families, low heritability in the general population and genetic heterogeneity. Mutations in a further gene, UCHL1, have been described in familial PD although the evidence for its role in PD is less clear. Knowledge of the genes described in PD to date should help to define molecular mechanisms of neurodegeneration in PD, as well as in other diseases where defects in protein handling may be a common feature. Nigral degeneration with Lewy body formation and the resulting clinical picture of PD may represent a final common pathway of a multifactorial disease process in which both environmental and genetic factors have a role. This review discusses the major advances in the field to date and illustrates how the existence of genetic factors has now become firmly established.

The large literature on family-based tests of association and/or linkage is reviewed, concentrating on the underlying principles and on recent methodological developments. We explain the distinction between testing for association and testing for linkage, and give our views on the circumstances in which each is the appropriate null hypothesis.

The nature of polymorphism and molecular sequence variation in the genes of the human major histocompatibility complex (MHC) provides strong support for the idea that these genes are under selection. With the understanding that selection shapes MHC variation new questions have become the focus of study. What is the mode of selection that accounts for MHC polymorphism? Is variation maintained by pathogen pressure or by reproductive mechanisms? Discerning between these requires drawing on information from studies on association between HLA genes and infectious diseases, reproductive success and mating preferences relative to HLA genotypes, and theoretical studies that compare the outcomes of different selection regimes. The pattern that has emerged suggests that several types of selection are plausible for the maintenance of HLA polymorphism.

Smith–Lemli–Opitz syndrome (SLOS) is caused by mutations in the DHCR7 gene leading to deficient activity of 7-dehydrocholesterol reductase (DHCR7; EC 1.3.1.21), the final enzyme of the cholesterol biosynthetic pathway, resulting in low cholesterol and high concentrations of its direct precursor 7-dehydrocholesterol in plasma and tissues. We here report mutations identified in the DHCR7 gene of 13 children diagnosed with SLOS by clinical and biochemical criteria. We found a high frequency of the previously described IVS8–1 G > C splice acceptor site mutation (two homozygotes, eight compound heterozygotes). In addition, 13 missense mutations and one splice acceptor mutation were detected in eleven patients with a mild to moderate SLOS-phenotype. The mutations include three novel missense mutations (W182L, C183Y, F255L) and one novel splice acceptor site mutation (IVS8–1 G > T).

Two patients, homozygous for the IVS8–1 G > C mutation, presented with a severe clinical phenotype and died shortly after birth. Seven patients with a mild to moderate SLOS-phenotype disclosed compound heterozygosity of the IVS8–1 G > C mutation in combination with different novel and known missense mutations.

Rapid prenatal diagnoses of major chromosome aneuploidies have been achieved successfully using quantitative fluoresent PCR (QF–PCR) assays and small tandem repeat (STR) markers. Here we report the results of evaluating the use of previously untested X-linked STRs, (DXS6803) and (DXS6809), together with modified amelogenin (AMXY) sequences and the X22 marker that maps in the pseudoautosomal region PAR2 on the long arm of the X and Y chromosomes. These markers will allow prenatal diagnoses of sex chromosome aneuploidies such as 45,X (pure Turner Syndrome), 47,XXY and 47,XYY, while assessing the sex of the fetuses. Data are also presented concerning the difficulties associated with the evaluation of the frequencies of the various types of sub-populations of cells in amniotic fluid samples collected from fetuses with sex chromosome mosaicism. The results of evaluating the use of new markers for the rapid diagnosis of aneuploidies affecting chromosomes 21,18 and 13 are also presented. Three chromosome 21 specific STRs have been found to produce trisomic triallelic or diallelic patterns from all amniotic samples retrieved from fetuses with Down Syndrome. Since all samples tested were amplified and no false positive or negative results were observed, the present results confirm the diagnostic value of QF–PCR for the prenatal detection of major numerical chromosome disorders.

In this work we focus on a microsatellite-defined Y-chromosomal lineage (network 1.2) identified by us and reported in previous studies, whose geographic distribution and antiquity appear to be compatible with the Neolithic spread of farmers. Here, we set network 1.2 in the Y-chromosomal phylogenetic tree, date it with respect to other lineages associated with the same movements by other authors, examine its diversity by means of tri- and tetranucleotide loci and discuss the implications in reconstructing the spread of this group of chromosomes in the Mediterranean area. Our results define a tripartite phylogeny within HG 9 (Rosser et al. 2000), with the deepest branching defined by alleles T (Haplogroup Eu10) or G (Haplogroup Eu9) at M172 (Semino et al. 2000), and a subsequent branching within Eu9 defined by network 1.2. Population distributions of HG 9 and network 1.2 show that their occurrence in the surveyed area is not due to the spread of people from a single parental population but, rather, to a process punctuated by at least two phases. Our data identify the wide area of the Balkans, Aegean and Anatolia as the possible homeland harbouring the largest variation within network 1.2. The use of recently proposed tests based on the stepwise mutation model suggests that its spread was associated to a population expansion, with a high rate of male gene flow in the Turkish–Greek area.

Distal hereditary motor neuropathies (distal HMNs) are characterised by degeneration of anterior horn cells of the spinal cord resulting in muscle weakness and atrophy. Distal HMN type II is genetically linked to chromosome 12q24.3 and located within a 13 cM region flanked by markers D12S86 and D12S340. We previously excluded the human phospholipase A2 group 1B gene (PLA2G1B) as the disease causing gene. Here, we report the mutation analysis of five other candidate genes localised within the distal HMN II region: the cytoskeletal proteins paxillin (PXN) and restin (RSN); the acidic ribosomal phosphoprotein, large P0 subunit (RPLP0); a nucleoside diphosphate kinase (NME2B); and the β 3 subunit of the voltage-gated calcium channel (CACNB3). DNA sequencing of the coding regions was performed but no disease causing mutations could be identified, hence excluding these five genes for distal HMN type II.

Alpha2-HS glycoprotein (AHSG), which is equivalent to fetuin in other species, is a protein found in human plasma. AHSG is polymorphic with two common alleles and many variants. To examine the intragenic haplotypes and their diversity at this locus, a contiguous genomic DNA sequence (10·3 kb) was analyzed in 20 samples (40 chromosomes), and haplotypes were determined for 309 subjects. Judging from the aligned nucleotide sequences and the conserved amino acid residues comparing human and chimpanzee AHSG, it was concluded that the type 1 allele is probably older and has evolved into four major suballeles. The type 2 allele was generated from one branch of the type 1 allele. AHSG*3 and *5 variants were each found to have a single nucleotide change in exon 7, resulting in the change of an amino acid residue from Arg299 to Cys and from Asp258 to Asn, respectively. It was noted that the AHSG*3 mutation gives rise to an additional cysteine residue, which possibly affects the conformation of the protein. The AHSG gene was found to have a low mutation rate and no apparent recombination events. Furthermore, the detected substitutions were nonhomogeneously distributed at this locus. In particular, four nonsynonymous substitutions were concentrated in the carboxyl-terminal domain.

The number of trinucleotide repeats in the 5′ untranslated regions of the FMR1 and FMR2 genes was determined by PCR in 254 Fragile XA-negative Javanese male children with developmental disabilities. The distribution of FMR1 and FMR2 trinucleotide repeat alleles was found to be significantly different in the Indonesian population with developmental disability compared to that in developmentally disabled populations in North America and Europe (p < 0.021). Sequence analysis was performed on the trinucleotide repeat arrays of the 27 individuals with FMR1 alleles in the ‘grey zone’ (35–54 repeats). A repeat array structure of 9A9A6A9 was found in 16 unrelated individuals with 36 repeats, confirming earlier observations in intellectually normal Japanese. We propose that this FMR1 array pattern is specific for Asian populations and that Javanese and Japanese populations arose from a single progenitor population.

Angiotensin converting enzyme (ACE) gene I/D polymorphism has been associated with high altitude (HA) disorders as well as physical performance. We, however, envisage that the polymorphism may be associated with adaptation to the hypobaric hypoxia of altitude, thus facilitating physical performance. For this purpose, three unrelated adult male groups, namely (1) the Ladakhis (HLs), who reside at and above a height of 3600 m, (2) lowlanders, who migrated to Ladakh (MLLs), and (3) resident lowlanders (LLs), have been investigated. The HLs had significantly (p < 0.001) greater numbers of the II homozygotes and the ID heterozygotes than the DD homozygotes, the genotype distribution being 0.46, 0.43 and 0.11 for II, ID and DD genotypes respectively. The MLLs comprised 60% II homozygotes, which was higher (p < 0.001) than the HLs (46%). In the LLs, the heterozygotes were greater (p < 0.001) in number than the II and DD homozygotes. The I allele frequency was 0.72 in the MLLs, 0.67 in the HLs and 0.55 in the LLs. Polymorphism study suggested that the II genotype could be associated with altitude adaptation, which might influence physical efficiency.

The polymorphic alleles of the human ABO-Secretor locus (FUT2 or Se) show high heterogeneity and overt ethnic specificity. To provide additional data for analysis to elucidate the origins of populations, we have investigated the allelic polymorphism of FUT2 in 40 unrelated Tibetan and 53 Tamang individuals from Nepal, 42 Indonesian individuals from Surabaya, and 55 Uygur individuals from Urumqi, using DNA sequencing. In Tibetan, Tamang and Indonesian populations, the frequency of a nonfunctional allele, se357,385, which is found only in Asian populations, was 0·638, 0·509 and 0·631, respectively. In Uygur, the se428, which is common in Caucasian populations, and the se357,385 consisting of two common nonfunctional FUT2 alleles, had frequencies of 0·3 and 0·145, respectively. The fixation index (FST) based on genetic differentiation was obtained pairwise among the four populations in this study and six populations in our previous studies. The results suggested that genetic differentiation among Tibetan, Tamang, Indonesian and East Asian populations is very low, while the distribution feature of the FUT2 alleles in the Uygur population implied an admixture of European with Asian. The distribution of nonfunctional alleles at the FUT2 locus provided further evidence of human migration among the Asian populations.

Coeliac disease (CD) is a malabsorptive disorder of the small intestine resulting from ingestion of gluten. The HLA risk factors involved in CD are well known but do not explain the whole genetic susceptibility. Several regions of potential linkage on chromosomes 3q, 5q, 10q, 11q, 15q and 19q have already been reported in the literature. These six regions were analyzed with the Maximum Lod Score method on a dense set of markers. A new sample of 89 Italian sibpairs was available for study. There was no evidence for linkage for any of the regions tested, except for chromosome 5q. For this region, our data, as well as a sample of 93 sibpairs from our first genome screen (Greco et al. 1998), are compatible with the presence of a risk factor for CD with a moderate effect.

During recent years the HRAS1 minisatellite has been analysed by several authors because of its putative association with cancer susceptibility. The aim of this report is to test the usefulness of this minisatellite in investigating human population relationships. We have studied 370 chromosomes from two well-differentiated populations: Galicia (North-west Iberia) and South-east Africa, as well as available data on allele length gene frequencies. The fragment analysis results show a strong tendency to differentiate between non-African and African populations. In spite of the usefulness of fragment analysis, the minisatellite variant repeat (MVR) approach of the HRAS1 minisatellite appears to be a more powerful method for use in human population studies, due to the high level of diversity of its interspersion pattern structures. In addition, this approach has allowed us to define some new structural characteristics of this minisatellite. Four different major groups of human HRAS1 minisatellite alleles could be distinguished following a structural criterion based on the MVR code. Furthermore, the characterisation of the HRAS1 minisatellite in chimpanzees revealed clear differences when compared to humans, not only with respect to the allele size but also to the internal structure.

Both hepatic lipase (HL) and apolipoprotein C-III (apoC-III) influence lipid metabolism. Common variation in promoters of both genes, LIPC -514C > T and APOC3 -482C > T, respectively, have been shown to affect plasma lipids and lipoproteins and glucose tolerance. We studied the interaction between both variants on parameters of glucose tolerance and lipid metabolism in 714 healthy young males participating in the second European Atherosclerosis Research Study (EARS-II). Approximately 18% of the subjects were carriers of at least one rare LIPC and APOC3 allele. These subjects exhibited, after fasting and oral fat loading, the highest values of triglyceride-rich lipoproteins, but there was no significant interactive effect on any lipid variable. However, interaction occurred on basal diastolic blood pressure (p =0.036) and, during oral glucose tolerance testing, on peak (p = 0.0065) and area under the curve for glucose (p =0.049), and insulin (p = 0.035). This resulted in the highest diastolic blood pressure and lowest glucose tolerance in carriers of at least one rare allele of both genes. Thus gene:gene interaction between LIPC and APOC3, even in these healthy young males, leads to changes in parameters that are typically characteristic of Syndrome-X.

Tainos and Caribs were the inhabitants of the Caribbean when Columbus reached the Americas; both human groups became extinct soon after contact, decimated by the Spaniards and the diseases they brought. Samples belonging to pre-Columbian Taino Indians from the La Caleta site (Dominican Republic) have been analyzed, in order to ascertain the genetic affinities of these groups in relation to present-day Amerinds, and to reconstruct the genetic and demographic events that took place during the peopling of the Caribbean.

Twenty-seven bone samples were extracted and analyzed for mtDNA variation. The four major Amerindian mtDNA lineages were screened through amplification of the specific marker regions and restriction enzymatic digestion, when needed. The HVRI of the control region was amplified with four sets of overlapping primers and sequenced in 19 of the samples. Both restriction enzyme and sequencing results suggest that only two (C and D) of the major mtDNA lineages were present in the sample: 18 individuals (75%) belonged to the C haplogroup, and 6 (25%) to the D haplogroup. Sequences display specific substitutions that are known to correlate with each haplogroup, a fact that helped to reject the possibility of European DNA contamination. A low rate of Taq misincorporations due to template damage was estimated from the cloning and sequencing of different PCR products of one of the samples. High frequencies of C and D haplogroups are more common in South American populations, a fact that points to that sub-continent as the homeland of the Taino ancestors, as previously suggested by linguistic and archaeological evidence. Sequence and haplogroup data show that the Tainos had a substantially reduced mtDNA diversity, which is indicative of an important founder effect during the colonization of the Caribbean Islands, assumed to have been a linear migratory movement from mainland South America following the chain configuration of the Antilles.

Two Spanish eastern Pyrenean populations, Andorra and Pallars Sobirà, have been tested for G1m(1,2,3,17), G2m(23), G3m(5,6,10,11,13,14,15,16,21,24,28) and Km(1) immunoglobulin allotypes. Km allele and Gm haplotype frequencies in both samples fit well into the Western Mediterranean and, more strictly, Pyrenean ranges with some peculiarities: Andorra showed an elevated frequency (14.7%) of the typical Asian and European Gm21,28;1,2,17;.. haplotype, while Pallars Sobirà was characterized by high values (3.7%) of Gm5*;1,17;.., a typical sub-Saharan Gm haplotype. Gm diversity assessed through genetic distance and variance analyses revealed a significant geographic partition (4.3%) of Mediterraneans among south, north-east, and north-west groups. It is interesting to note the relatively low genetic variance (2.1%) found between south and north-western Mediterraneans that could reflect ancient population relationships. More locally, genetic boundaries and diversity analyses failed to indicate any geographic pattern and/or genetic differentiation related with the political border in the Pyrenees. The present pattern of variation in this area is probably the result of genetic isolation processes, in addition to some specific demographic phenomena, in the Pyrenean valleys.

Although frequencies of mitochondrial DNA (mtDNA) haplogroups in the different European populations are rather homogenous, there are a few European populations or linguistic isolates that show different mtDNA haplogroup distributions; examples are the Saami and Ladin speakers from the eastern Italian Alps.

MtDNA sequence diversity was analysed from subjects from two villages in Veneto. The first, Posina, is situated in the Venetian Alps near Vicenza. The second, Barco di Pravisdomini is a village on the plains near Venice. In spite of their common Veneto dialect, the two group populations have not preserved a genetic homogeneity; particularly, they show differences in T and J haplogroups frequencies. MtDNA diversity in these two groups seems to depend more on their geographic situation.