DNA polymorphisms and linkage disequilibrium in the angiotensinogen gene

A number of recent studies have implicated the angiotensinogen gene in the aetiology of essential hypertension in Caucasian, Japanese and African Caribbean subjects. We have genotyped 153 healthy white Caucasian subjects at a dinucleotide repeat polymorphism and seven diallelic sites in the coding or flanking regions of the angiotensinogen gene, including one polymorphism not previously studied. We have also documented patterns of linkage disequilibrium between polymorphisms. There is evidence of variation in the frequency of several mutations when compared with published results from other Caucasian control populations, possibly due to cryptic ethnic differences between these groups. This should be considered in the design and interpretation of studies of the angiotensinogen gene. Received: 10 November 1995 / Revised: 25 March 1996     

Genotyping HapSTR loci: phase determination from direct sequencing of PCR products

HapSTRs combine information from a microsatellite (or simple tandem repeat, STR) with one or more single nucleotide polymorphisms in the DNA sequence immediately flanking the STR. These loci may offer increased power for the estimation of demographic parameters, but also present some challenges for data collection and analysis. We describe a process for inferring HapSTR alleles, including the flanking haplotypes, STR alleles and their phase relative to each other, directly from DNA sequence electropherograms of PCR products from heterozygous individuals. Our approach eliminates the need for more costly and time-consuming processes, such as cloning or acrylamide gel electrophoresis to separate alleles prior to sequencing.     

Identification of Hb D-Punjab gene: application of DNA amplification in the study of abnormal hemoglobins.

Hemoglobin D-Punjab (or D-Los Angeles) is a common variant worldwide. It is also the most frequent abnormal hemoglobin in Xinjiang Uygur Autonomous Region of China. A large survey of hemoglobinopathy, including 142,171 people and 21 national/ethnic groups, was carried out in Xinjiang and indicated Hb D-Punjab accounted for 55.6% of the total hemoglobin variants there. Here we describe a simple way--EcoRI mapping of the amplified beta-globin DNA sampling from dried blood spots on filter paper blotters--of identifying the Hb D-Punjab gene. The primers were designed and synthesized to emzymatically amplify a 144-bp fragment of beta-globin gene which included codons beta 121 (GAA) and 122 (TTC) representing an EcoRI recognition site. The Hb D-Punjab gene could be easily detected by EcoRI digestion of the amplified DNA sequence on agarose gel because of a single base change at codon 121. The analysis of amplified DNA sampling from dried blood provides a very useful method for population study of Hb D-Punjab and will be of significance for demonstration of the occurrence of the Hb D-Punjab gene and for understanding of the relations among various nationalities.     

Inheritance and linkage of isozyme loci in almond

The segregation of seven isozyme marker genes was investigated using eight controlled crosses in almond. The cultivar Nonpareil was the maternal parent in all crosses. Pollination was achieved using eight different cultivars, and a total of 3200 individual kernels were assessed. For each isozyme the goodness-of-fit test was used to test for departure from the expected frequencies assuming Mendelian inheritance. Given a higher than expected number of significant results for individual isozymes, independent segregation between pairs of isozymes was tested using the chi-square statistic on the resulting two-way contingency tables. In all crosses a highly significant association (P value< 0.001) was observed between (1) the AAT- 1 and IDH isozymes loci and (2) the LAP-1 and PGM-2 isozymes loci, which leads to the conclusion that the respective isozyme pairs are linked.In addition, a significant association (P value < 0.001) was observed between LAP-1 and GPI-2 when the pollen sources were Fritz, Mission, or Price, but this could not be tested for the remaining five pollen sources, Carmel, Grant, Keane, Ne plus Ultra, Peerless, because they are homozygous at these loci. If LAP-1 is linked with GPI-2 and PGM-2, it might be expected that we should find evidence of linkage between GPI-2 and PGM-2. The lack of a significant association between these two isozymes suggests that LAP-1 is located centrally on the chromosome. These three pairs of linked loci are the first to be reported in almond.     

X-linked hypohidrotic ectodermal dysplasia: DNA probe linkage analysis and gene localization

Summary A linkage study of 24 families with hypohidrotic (anhidrotic) ectodermal dysplasia (HED) has been performed. The previously suggested linkage to DXYS1 has been confirmed, and linkage to probes DXS14 and DXS3 has been established. We suggest that the HED locus lies in the centromeric region between DXYS1 on the long arm and DXS14 on the short arm of the X chromosome, probably on proximal Xq.     

Equine gene mapping: Close linkage between the loci for soluble malic enzyme and Xk (Pa)

Resolution of equine soluble malic enzyme phenotypes is greatly improved by isoelectric focusing as compared with starch gel electrophoresis. Phenotype differences can be recognized in plasma as well as haemolysates. The locus for soluble malic enzyme (ME1) is closely linked to the locus for Xk.     

Joint linkage and linkage disequilibrium mapping of quantitative trait loci in natural populations

Linkage analysis and allelic association (also referred to as linkage disequilibrium) studies are two major approaches for mapping genes that control simple or complex traits in plants, animals, and humans. But these two approaches have limited utility when used alone, because they use only part of the information that is available for a mapping population. More recently, a new mapping strategy has been designed to integrate the advantages of linkage analysis and linkage disequilibrium analysis for genome mapping in outcrossing populations. The new strategy makes use of a random sample from a panmictic population and the open-pollinated progeny of the sample. In this article, we extend the new strategy to map quantitative trait loci (QTL), using molecular markers within the EM-implemented maximum-likelihood framework. The most significant advantage of this extension is that both linkage and linkage disequilibrium between a marker and QTL can be estimated simultaneously, thus increasing the efficiency and effectiveness of genome mapping for recalcitrant outcrossing species. Simulation studies are performed to test the statistical properties of the MLEs of genetic and genomic parameters including QTL allele frequency, QTL effects, QTL position, and the linkage disequilibrium of the QTL and a marker. The potential utility of our mapping strategy is discussed.     

A DNA polymorphism in close physical linkage with the proopiomelanocortin gene

Cellular DNAs from a panel of 20 unrelated individuals were screened for restriction fragment length polymorphisms (RFLP) with a DNA probe containing the first exon of the proopiomelanocortin gene (POMC), which has been assigned to chromosome 2p23-25. Digestion with the restriction endonuclease Sst 1 revealed a high frequency RFLP. The two alleles that were found are fragments of 10- and 15-kilobase (kb) length and are in Hardy-Weinberg equilibrium with frequencies of 72.6% and 27.4%, respectively. Informative families were tested for linkage between POMC/Sst 1 RFLP and other polymorphic markers of chromosome 2. Linkage was excluded to AcP-1 (2p23-25) at 15% recombination, which is still consistent with the chromosomal assignments for these genes. The close physical linkage (10 kb) of the polymorphic locus to the POMC gene makes this RFLP a suitable marker for future linkage studies involving the POMC gene.     

Concerning the linkage relationships of the Gc and MNSs loci

Summary Human liver alcohol dehydrogenase isozyme patterns were studied using prolonged high voltage starch-gel electrophoresis and gel-slab isoelectric focusing. Homo- and heterodimers of ADH₂ locus were easily distinguished from each other. The gene frequencies of ADH₂²and ADH₃²in 46 random liver samples from Germany were found to be 0.044 and 0.424 respectively.Alexander von Humboldt-Foundation Fellow     

Analysis of the HLA-ABC linkage disequilibrium: Decreasing strength of gametic association with increasing map distance

Summary 1242 HLA-ABC haplotypes of the North German population (Hamburg) as deduced by family analyses are described. They are in perfect agreement with recently published data by Mayr (1977) from Austria (Vienna) in all parameters tested: frequency of the single HLA-alleles, haplotype distribution and linkage disequilibrium values. Gametic association studies revealed that 69.4% of the B and C genes (map distance 0.2 cM) 36.9% of the A and C genes (0.6 cM), but only 23.2% of the A and B genes (0.8 cM) were significantly more often combined than expected due to their frequencies. From these findings it seems likely that the linkage disequilibrium within the MHC is rather due to a short evolutionary period than to selective forces. Some observations as to the most common European haplotype A1,B8 are discussed.     

Close linkage between the albumin and Gc loci in the horse

Evidence for close linkage between the structural loci for albumin and Gc protein in the horse was presented. A recombination frequency (c) of 0.009 ± 0.006 (95 % confidence limits: 0.001 < c < 0.032) was estimated. These results were based on a study of a large sire family comprising 223 offspring from informative matings. No evidence of linkage disequilibrium was observed in one horse population studied.     

Hb D Los Angeles (D-Punjab) and Hb Presbyterian: analysis of the defect at the DNA level

Summary Amplification of the -globin gene by the polymerase chain reaction (PCR) and direct sequencing were used for a fast and reliable identification of the -globin variant Hb D Los Angeles and revealed the predicted GC substitution in codon 121. The same method showed the molecular defect in Hb Presbyterian to be a CG substitution in codon 108; this eliminates a MaeII restriction site.     

Genetic linkage study between the loci for Duchenne and Becker muscular dystrophy and nine X-chromosomal DNA markers

Summary A set of nine polymorphic loci defined by DNA probes was studied for linkage with the disease locus in ten families with a history of Duchenne muscular dystrophy (DMD), and three families with a history of Becker muscular dystrophy (BMD). The results confirm DMD and BMD linkage to all marker loci and suggest closer linkage of several probes than hitherto detected. This will be of practical interest for risk calculations in affected families.     

A composite-conditional-likelihood approach for gene mapping based on linkage disequilibrium in windows of marker loci

A composite-conditional-likelihood (CCL) approach is proposed to map the position of a trait-influencing mutation (TIM) using the ancestral recombination graph (ARG) and importance sampling to reconstruct the genealogy of DNA sequences with respect to windows of marker loci and predict the linkage disequilibrium pattern observed in a sample of cases and controls. The method is designed to fine-map the location of a disease mutation, not as an association study. The CCL function proposed for the position of the TIM is a weighted product of conditional likelihood functions for windows of a given number of marker loci that encompass the TIM locus, given the sample configuration at the marker loci in those windows. A rare recessive allele is assumed for the TIM and single nucleotide polymorphisms (SNPs) are considered as markers. The method is applied to a range of simulated data sets. Not only do the CCL profiles converge more rapidly with smaller window sizes as the number of simulated histories of the sampled sequences increases, but the maximum-likelihood estimates for the position of the TIM remain as satisfactory, while requiring significantly less computing time. The simulations also suggest that non-random samples, more precisely, a non-proportional number of controls versus the number of cases, has little effect on the estimation procedure as well as sample size and marker density beyond some threshold values. Moreover, when compared with some other recent methods under the same assumptions, the CCL approach proves to be competitive.     

DNA haplotype analysis suggests linkage disequilibrium in the human insulin receptor gene

Summary Haplotypes of the insulin receptor gene were resolved in parents from Scandinavian nuclear families by studying the segregation of seven restriction fragment length polymorphisms (RFLPs). Of 97 unrelated parents, 41 had non-insulin-dependent diabetes mellitus (NIDDM). Considerable linkage disequilibrium in the region of the insulin receptor gene was found. Pairwise non-random associations were found between proximate RFLP sites, indicating the absence of recombinational hot spots between these sites. Thus, association studies between DNA polymorphisms at this locus and disease susceptibility genes could well be feasible in this population. Differences in the distribution of insulin receptor haplotypes were examined between NIDDM patients and healthy subjects. However, the differences observed were not statistically significant.     

Identification and replication of three novel myopia common susceptibility gene loci on chromosome 3q26 using linkage and linkage disequilibrium mapping

Refractive error is a highly heritable quantitative trait responsible for considerable morbidity. Following an initial genome-wide linkage study using microsatellite markers, we confirmed evidence for linkage to chromosome 3q26 and then conducted fine-scale association mapping using high-resolution linkage disequilibrium unit (LDU) maps. We used a preliminary discovery marker set across the 30-Mb region with an average SNP density of 1 SNP/15 kb (Map 1). Map 1 was divided into 51 LDU windows and additional SNPs were genotyped for six regions (Map 2) that showed preliminary evidence of multi-marker association using composite likelihood. A total of 575 cases and controls selected from the tails of the trait distribution were genotyped for the discovery sample. Malecot model estimates indicate three loci with putative common functional variants centred on MFN1 (180,566 kb; 95% confidence interval 180,505–180, 655 kb), approximately 156 kb upstream from alternate-splicing SOX2OT (182,595 kb; 95% CI 182,533–182,688 kb) and PSARL (184,386 kb; 95% CI 184,356–184,411 kb), with the loci showing modest to strong evidence of association for the Map 2 discovery samples (p<10⁻⁷, p<10⁻¹⁰, and p=0.01, respectively). Using an unselected independent sample of 1,430 individuals, results replicated for the MFN1 (p=0.006), SOX2OT (p=0.0002), and PSARL (p=0.0005) gene regions. MFN1 and PSARL both interact with OPA1 to regulate mitochondrial fusion and the inhibition of mitochondrial-led apoptosis, respectively. That two mitochondrial regulatory processes in the retina are implicated in the aetiology of myopia is surprising and is likely to provide novel insight into the molecular genetic basis of common myopia.     

Mapping of the hooded,Gc protein,and albumin gene loci in linkage group VI of the laboratory rat

Crosses to determine the position of the three gene loci, h, Gc, and Alb, in the sixth linkage group of the rat used three strains, the TM strain, the ACI-alb analbuminemic congenic strain, and the abh-alb tester strain established by crossing the abh coat color tester strain and analbuminemic rats. Their genotypes were [C/C, h/h, GcB/GcB, Alb/Alb], [C/C, hi/hi, GcA/GcA, alb/alb] and [C/C, h/h, GcA/GcA, alb/alb], respectively. Determination of genotypes was performed by coat color and polyacrylamide gel electrophoresis (PAGE of serum protein for the Gc and albumin genes. The positions of the three gene loci in the VI linkage group were calculated from the recombination values from the phenotypes of progenies. According to this data, the three gene loci were in h-Gc-Alb tandem and the distances were 15.5 +/- 1.0% in h-Gc, 15.8 +/- 1.0% in h-Alb, and 0.32 +/- 0.16% in Gc-Alb. These data confirmed the relationship among the Gc, Alb, and Afp genes in the rat as well as in humans.     

DNA fingerprinting analysis of Booroola pedigrees: a search for linkage to the Booroola gene

Seven minisatellite probes from a variety of sources were used to analyse 11 paternal half-sib families in which the Booroola gene was segregating. A total of 402 bands that showed segregation in the pedigrees were examined for linkage to the Booroola gene. None of the bands showed segregation with the Booroola gene. The most likely evidence for a linked band was produced by the HaRas HVR probe in Family 902 (=0.0; LOD 2.3). The conclusion, however, is that the minisatellite probes used in this study could not be used as markers for the Booroola gene. The study highlighted problems associated with the use of minisatellite probes in linkage studies in half-sib families. The complex banding patterns found on fingerprinting gels was a major source of scoring error. In a few cases both of the sire's alleles could be identified at a particular locus, but in most cases only one of the alleles could be identified. For the most part, the bands had to be treated as dominant alleles. The contribution of dam alleles to the banding pattern could only be estimated. There was an indication that minisatellite loci in sheep are clustered in particular regions of the sheep genome as the rate at which bands segregated with each other was higher than one would expect from loci randomly distributed throughout the genome.