Linkage analysis of HSP70 genes and historecognition locus in botryllus schlosseri

The protochordate allorecognition system has long invited comparison with the vertebrate major histocompatibility complex (MHC). In the colonial species Botryllus schlosseri, a rapid fusion or rejection response resembling graft acceptance or rejection in vertebrates is controlled by a single highly polymorphic genetic region. Because linkage between heat shock protein 70 (HSP70) genes and the MHC appears to be conserved within the vertebrate lineage, linkage relationships between two HSP70 genes (HSP70.1 and HSP70.2) and the historecognition locus (FuHC) have been analyzed in B. schlosseri. Segregation patterns of restriction fragment length polymorphisms located in the 3' flanking regions of HSP70.1 and HSP70.2 were determined for progeny of defined crosses. These progeny were also analyzed for fusibility type by an in vivo cut colony assay. No close linkage was detected between any of the three loci. These results do not support the hypothesis that the allorecognition response in B. schlosseri is determined by an MHC homologue. However, it remains a possibility that orthologues of other MHC-linked genes will be linked to the B. schlosseri FuHC.     

Linkage disequilibrium at the human phosphoglucomutase 1 locus

By considering the four common PGM1 alleles as haplotypes, that is, combinations of mutations at two polymorphic intragenic sites (1/2 and A/B), we investigated the levels of linkage disequilibrium in 142 human population samples. These groups showed considerable diversity in their disequilibrium (Drel) and heterogeneity. In all the populations the disequilibrium was found to be due to an excess of 1A and 2B haplotypes, although this direction is the opposite of that expected according to the proposed phylogeny of the system. Natural selection could be one of the major causes for such a disequilibrium direction.     

Genetic locus heterogeneity in Lafora's progressive myoclonus epilepsy

In 1995, we mapped a gene for Lafora's progressive myoclonus epilepsy in chromosome 6q23-25. In 1997 and 1998, we reduced the size of the locus to 300 kb, and an international collaboration identified mutations in the protein tyrosine phosphatase gene. Here, we examine for heterogeneity through the admixture test in 22 families and estimate the proportion of linked families to be 75 to 85%. Extremely low posterior probabilities of linkage (Wi), exclusionary LOD scores, and haplotypes identify 4 families unlikely to be linked to chromosome 6q24.     

Linkage studies in dominant optic atrophy, Kjer type: possible evidence for heterogeneity

Dominant optic atrophy, Kjer type, is an autosomal dominant disorder causing progressive loss of visual acuity and colour vision from early childhood. The gene (OPA1) has variable expressivity, a penetrance of 0.98, and the locus has been localised to 3q28-29. We have genotyped nine British families with the disease using 12 polymorphic microsatellite markers from this region. Linkage and haplotype analysis shows the OPA1 gene to be located in a 2.3 cM interval between markers D3S1601 and D3S2748. One family showed no evidence of linkage with the chromosome 3 markers, suggesting for the first time that locus heterogeneity for this disease may exist, although exclusion for linkage is based on unaffected subjects. In addition, analysis of recombinants has enabled us to order the 12 markers along chromosome 3.     

Autosomal dominant medullary cystic kidney disease: evidence of gene locus heterogeneity

Autosomal dominant medullary cystic kidney disease (ADMCKD; synonym: medullary cystic disease, MCD) is an autosomal dominant kidney disorder, sharing morphological and clinical features with recessive juvenile nephronophthisis (NPH), such as reduced urinary concentration ability and multiple renal cysts at the corticomedullary junction. While in NPH end-stage renal disease (ESRD) occurs in adolescence, ADMCKD leads to ESRD in adulthood. Recently a gene locus for ADMCKD has been localized to chromosome 1q21 in two large Cypriot families. This prompted us to examine linkage in three ADMCKD-families, using the same set of polymorphic microsatellite markers spanning the critical region on chromosome 1q21. Haplotype analysis revealed that none of the three families showed linkage to this locus, thus demonstrating evidence for genetic locus heterogeneity. Additional linkage analysis studies need to be performed in order to identify further gene loci cosegregating with this autosomal dominant kidney disorder.     

Non-C282Y familial iron overload: evidence for locus heterogeneity in haemochromatosis

Haemochromatosis (HC) is an autosomal recessive disease with progressive iron overload leading to midlife onset of clinical complications. The causal gene (HFE) maps to 6p, in close linkage with the HLA class I genes. An HFE candidate gene recently identified has two missense mutations (C282Y and H63D) associated with the disease. Here we document the phenotypic and genetic analysis of a nuclear family comprising two sibs with symptomatic and massive iron overload before the age of 25. The disease seemed to be recessively transmitted and fitted the agreed criteria for haemochromatosis, but was neither associated with the C282Y and H63D mutations nor linked with HLA markers. Our data strongly support locus heterogeneity in haemochromatosis by showing evidence that the gene responsible for juvenile haemochromatosis (JH) does not map to 6p. In the absence of clear cut phenotypic distinction from typical haemochromatosis, patients below 30 years of age and C282Y negative should be considered as putative juvenile cases. This has practical implications in genetic counselling and family management.     

Linkage analysis of complex traits using affected sibpairs: effects of single-locus approximations on estimates of the required sample size

We investigated the power of the affected sibpair method for detecting a disease locus when the disease is inherited through two bi-allelic loci. The power was computed for all possible values of the gene frequencies and penetrances that lead to a given population prevalence and a given sibling relative risk. A method to generate rapidly all possible models that give a specific population prevalence and relative risk is provided. We applied it to the case of a two-locus disease with a prevalence of 10% and a low sibling relative risk of 1.5. For this particular example, regardless of the true underlying model, a sample size (N = 450 for alpha = 0.05, N = 1,500 for alpha = 0.0001) may be determined such that one would expect enough power (0.80) to detect at least one of the two disease genes. In addition to the general case, we examined a special class of models in which the marginal penetrances at each locus are either recessive or dominant. In this instance, the gene frequencies were excellent predictors of the power afforded by a particular sample size. These methods have been implemented in a C program called SIBPOWER which is freely available from the first author. With this program, investigators can perform their own power calculations for any two-locus model of their choice thus avoiding the need to use single-locus approximations that may grossly underestimate the necessary sample size.     

Linkage disequilibrium mapping of complex disease: fantasy or reality?

In the past year, data about the level and nature of linkage disequilibrium between alleles of tightly linked SNPs have started to become available. Furthermore, increasing evidence of allelic heterogeneity at the loci predisposing to complex disease has been observed, which has lead to initial attempts to develop methods of linkage disequilibrium detection allowing for this difficulty. It has also become more obvious that we will need to think carefully about the types of populations we need to analyze in an attempt to identify these elusive genes, and it is becoming clear that we need to carefully re-evaluate the prognosis of the current paradigm with regard to its robustness to the types of problems that are likely to exist.     

Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium

The contribution of BRCA1 and BRCA2 to inherited breast cancer was assessed by linkage and mutation analysis in 237 families, each with at least four cases of breast cancer, collected by the Breast Cancer Linkage Consortium. Families were included without regard to the occurrence of ovarian or other cancers. Overall, disease was linked to BRCA1 in an estimated 52% of families, to BRCA2 in 32% of families, and to neither gene in 16% (95% confidence interval [CI] 6%-28%), suggesting other predisposition genes. The majority (81%) of the breast-ovarian cancer families were due to BRCA1, with most others (14%) due to BRCA2. Conversely, the majority of families with male and female breast cancer were due to BRCA2 (76%). The largest proportion (67%) of families due to other genes was found in families with four or five cases of female breast cancer only. These estimates were not substantially affected either by changing the assumed penetrance model for BRCA1 or by including or excluding BRCA1 mutation data. Among those families with disease due to BRCA1 that were tested by one of the standard screening methods, mutations were detected in the coding sequence or splice sites in an estimated 63% (95% CI 51%-77%). The estimated sensitivity was identical for direct sequencing and other techniques. The penetrance of BRCA2 was estimated by maximizing the LOD score in BRCA2-mutation families, over all possible penetrance functions. The estimated cumulative risk of breast cancer reached 28% (95% CI 9%-44%) by age 50 years and 84% (95% CI 43%-95%) by age 70 years. The corresponding ovarian cancer risks were 0.4% (95% CI 0%-1%) by age 50 years and 27% (95% CI 0%-47%) by age 70 years. The lifetime risk of breast cancer appears similar to the risk in BRCA1 carriers, but there was some suggestion of a lower risk in BRCA2 carriers <50 years of age.     

Linkage of Wolfram syndrome to chromosome 4p16.1 and evidence for heterogeneity

Wolfram syndrome (DIDMOAD syndrome; MIM 222300) is an autosomal recessive neurodegenerative disorder characterized by juvenile-onset diabetes mellitus and bilateral optic atrophy. Previous linkage analysis of multiply affected families indicated that the gene for Wolfram syndrome is on chromosome 4p, and it produced no evidence for locus heterogeneity. We have investigated 12 U.K. families with Wolfram syndrome, and we report confirmation of linkage to chromosome 4p, with a maximum two-point LOD score of 4.6 with DRD5, assuming homogeneity, and of 5.1, assuming heterogeneity. Overlapping multipoint analysis using six markers at a time produced definite evidence for locus heterogeneity: the maximum multipoint LOD score under homogeneity was <2, whereas when heterogeneity was allowed for an admixture a LOD of 6.2 was obtained in the interval between D4S432 and D4S431, with the peak close to the marker D4S3023. One family with an atypical phenotype was definitely unlinked to the region. Haplotype inspection of the remaining 11 families, which appear linked to chromosome 4p and had typical phenotypes, revealed crossover events during meiosis, which also placed the gene in the interval D4S432 and D4S431. In these families no recombinants were detected with the marker D4S3023, which maps within the same interval.     

Linkage disequilibrium within the HLA complex does not extend into HLA-DP

It is well known that certain alleles from different loci within the Human Leucocyte Antigen (HLA) complex are in linkage disequilibrium. This linkage phenomenon is relatively well characterized for haplotypes that include specific class I and class II alleles such as HLA-B8 and HLA-DR3. However, the HLA-DP genes are located at the centromeric end of the HLA complex and are less well characterized with regard to linkage disequilibrium. The availability of a large population of healthy subjects and sequence-specific oligonucleotide (SSO) typing enabled us to assess the degree of linkage between HLA-DPB1 and HLA-DQB1 genes. Using the polymerase chain reaction and a series of oligonucleotide probes which define seven DQ beta alleles and twenty DP beta alleles, we studied 180 unrelated, normal Caucasian individuals and found only weak or negative associations between HLA-DPB1 and HLA-DQB1. These data demonstrate that the association between HLA-DQ and DP is weak and also imply that DP extended haplotypes related to particular diseases may not reflect normal associations. Implications of these results might impact on the concept of linkage disequilibrium in general as well as the evolution of the HLA complex. In addition, extensions of this work may have clinical ramifications with regard to bone marrow transplantation and founder effects in certain diseases.     

Linkage analysis in familial Alzheimer disease: description of the Duke and Boston data sets

Familial Alzheimer diseases is a neurological disorder of adult onset. Three research centers have each contributed their families and genetic linkage data for combined analyses. The data from the Duke and Boston centers, comprising 73 pedigrees for whom numerous markers on chromosomes 19 and 21 were typed are described.     

Examining the locus of age effects on complex span tasks.

To investigate the locus of age effects on complex span tasks, the authors evaluated the contributions of working memory functions and processing speed. Age differences were found in measures of storage capacity, language processing speed, and lower level speed. Statistically controlling for each of these in hierarchical regressions substantially reduced, but did not eliminate, the complex span age effect. Accounting for lower level speed and storage, however, removed essentially the entire age effect, suggesting that both functions play important and independent roles. Additional evidence for the role of storage capacity was the absence of complex span age differences with span size calibrated to individual word span performance. Explanations for age differences based on inhibition and concurrent task performance were not supported. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Enzyme variation at the aspartate aminotransferase locus in members of the Anopheles gambiae complex (Diptera: Culicidae)

The enzyme aspartate aminotransferase (AAT) currently is used to identify Anopheles quadriannulatus Theobald, the animal-biting, nonmalaria vector species of the Anopheles gambiae complex. Samples of An. quadriannulatus from South Africa and An. gambiae Giles s.str. from the island of Grand Comoros and the People's Republic of Congo have shown variation in electromorph frequencies that indicate that AAT has five alleles. The three slowest alleles are found in An. quadriannulatus and the three fastest in An. gambiae, An. arabiensis Patton and An. merus D?nitz. One of these is common to both An. quadriannulatus and An. gambiae. This overlap indicates a potential misidentification of 0.3% of unknown females with a further 2.1% being unidentifiable. However, all of the specimens in the overlap area were classified correctly using octanol dehydrogenase (ODH). Variation at the ODH locus in An. quadriannulatus is recorded for the first time, with four of 157 specimens being heterozygous for the fast allele. The probability of both AAT and ODH giving an incorrect or indecisive identification is 0.0005. The slowest AAT alleles were present in samples from a single locality, indicating the lack of gene flow between subpopulations of An. quadriannulatus in close geographic proximity in the Shingwedzi area, South Africa. A modified method for multiple gel casting is given.     

Linkage of familial hemophagocytic lymphohistiocytosis to 10q21-22 and evidence for heterogeneity

An interleukin-6 (IL-6) response was detected in 81 patients with febrile urinary tract infections (UTIs). Bacteremic patients (n=24) had higher serum IL-6 at inclusion and throughout the first 24 h (P<. 01) and higher urine IL-6 from 6 h after start of therapy (P<.01) than did nonbacteremic patients (n=57). The serum and urine IL-6 responses remained elevated longer in the bacteremic group. Patients with clinical signs of pyelonephritis had higher serum and urine IL-6 concentrations than did other patients in the study population (P=.058, P<.01, respectively). IL-6 high responders had higher temperatures (P<.05) and C-reactive protein levels (P<.05, P<.01) than did low responders. The results demonstrate that IL-6 responses accompany febrile UTIs regardless of bacteremia and that the response reflects disease severity. The results suggest that IL-6 produced in the urinary tract can trigger the systemic host response in the absence of bacteremia.     

Identification of a complex congenital heart defect susceptibility locus by using DNA pooling and shared segment analysis

The isotope dilution technique of [6-3H]glucose, [U-14C]lactate and [l-14C]propionate was used to evaluate the effect of dietary chromium (Cr) supplementation on whole-body kinetics of glucose, lactate, and propionate in rams. Rams were fed a high grain diet at 2% of body weight with or without 0.5 ppm of supplemental Cr from chelated Cr for the initial 14 days, and then intake was increased to 2.5% at body weight for the last 9 days. Weight gain was enhanced (P < 0.01) with Cr supplementation. Plasma concentrations of glucose, lactate, and propionate were not influenced by Cr supplementation. Turnover rates of glucose and lactate, and their interconversion were also not influenced. Propionate turnover rate tended to increase (P = 0.11) and the conversion of propionate to glucose increased (P < 0.05) with Cr supplementation, leading the increased proportional contribution of propionate to glucose turnover rate (P < 0.05). Chromium supplementation may influence the contribution of each glucogenic substrate for glucose production in rams fed a high grain diet.     

Linkage relationships of the loci of the major histocompatibility complex in families with a recombination in the HLA region

A number of families with an established recombination in the major histocompatibility complex has been investigated for markers known to be coded by genes of this linkage group. The results provide further data on the relative position of the loci for HLA-A, HLA-B, HLA-C, HLA-D, Bf, Chido, Rodgers and PGM3 on chromosome 6. A positive lodscore for linkage between HLA and blood group P was found; lodscores between HLA and nineteen other markers were negative.     

Genetics of mouse antibodies. I. Linkage of the dextran response locus, VH-DEX, to allotype

The antibody response of mice to alpha-1,3 linked dextran is shown to be controlled by a heavy chain variable region gene, VH-DEX. The map distance between this gene and the heavy chain allotype locus is estimated to be 0.3 recombination units.