Nonsense mutation in the homeobox region of the aniridia gene.
Explore the source record for details and available documents.
Aniridia↗
Biomedical subjects
R E Ferrell
Publications and source records attributed to R E Ferrell.
Population genetic characteristics of the D1S80 locus in seven human populations.
We have analyzed the allele frequency distribution at the highly polymorphic variable number of tandem repeat (VNTR) locus D1S80 (pMCT118) in seven ethnic populations (namely, New Guinea Highlanders of Papua New Guinea, Dogrib Indians of Canada, Pehuenche Indians of Chile, American and Western Samoans, Kacharis of Northeast India, and German Caucasians) using the polymerase chain reaction (PCR) technique. In the pooled sample of 443 unrelated individuals 20 segregating alleles were detected. A trimodal pattern of allelic distribution is present in the majority of populations and is indicative of the evolutionary antiquity of the polymorphism at this locus. In spite of the observed high degree of polymorphism (expected heterozygosity 56%-86%), with a single exception--the marginally significant P value (0.04) of the exact test in American Samoans--the genotype distributions in all populations conform to their respective Hardy-Weinberg expectations. Summary statistics indicate that, in general, the allele frequency distribution at this locus may be approximated by the infinite allele model. The data also demonstrate that alleles that are shared by all populations have the highest average frequency within populations. Furthermore, the kinship bioassay analysis demonstrates that the extensive variation observed at the D1S80 locus is at the interindividual within population level, which dwarfs any interpopulation allele frequency variation, consistent with the population dynamics of hypervariable polymorphisms. These characteristics of the D1S80 locus make it a very useful marker for population genetic research, genetic linkage studies, forensic identification of individuals, and for determination of biological relatedness of individuals.
Alleles↗
Hypervariable polymorphism of APO(a) in blacks and whites as reflected by phenotyping.
Genetic polymorphism at the apolipoprotein(a) structural locus was investigated in 203 American blacks using a high-resolution SDS-agarose electrophoresis method followed by immunoblotting, and the gene frequency data were compared with a previously screened American white sample using the same method. Between the two samples, a total of 27 discrete APO(a) allelic isoforms have been documented; of these, 24 were common to both groups. Of the 203 blacks screened, APO(a) immunoreactive isoforms were detected in 201, with a total of 101 distinct phenotypes (67 (33%) single-banded and 134 (67%) double-banded). A similar level of gene diversity was observed at the APO(a) locus in blacks (93%) and whites (94%). Despite having a similar number of alleles and a similar level of gene diversity, the frequencies of some APO(a) alleles were significantly different between blacks and whites. Overall, the frequencies of large-size APO(a) alleles, associated with lower LP(a) levels, were significantly lower (P < 0.0001), while the frequencies of medium-size APO(a) alleles, associated with intermediate LP(a) levels, were significantly higher (P < 0.0001) in blacks than in whites. However, the frequencies of small-size alleles, associated with higher LP(a) levels, were comparable between the two race groups. These data indicate that the observed differences in mean LP(a) levels between whites and blacks may be accounted for by the size variation at the APO(a) structural locus.
Adolescent↗
A gene for Crouzon craniofacial dysostosis maps to the long arm of chromosome 10.
Crouzon craniofacial dysostosis (CFD) is an autosomal dominant craniofacial disorder characterized by premature craniosynostosis, shallow orbits and hypoplastic maxilla. To map the gene responsible, we have used a mapping strategy of testing for linkage to known developmental genes. Analysis of a large kindred established linkage between CFD and three loci (D10S190, D10S209 and D10S216) that span a 13 cM region on chromosome 10q. A maximum pairwise lod score of 4.42 (theta = 0) at D10S190 was obtained and the addition of a second kindred produced a combined pairwise lod score of 5.32 (theta = 0) at the same locus. The developmental gene, PAX2, located within this region, is an attractive candidate gene.
Chromosome Mapping↗
Chromosome 13 and chromosome 2 (CA)n polymorphisms.
Explore the source record for details and available documents.
Alleles↗
A common deletion polymorphism in the apolipoprotein A4 gene and its significance in lipid metabolism.
Apolipoprotein A-IV (apoA-IV, protein; APOA4, gene) is a major constituent of high-density lipoprotein (HDL) and triglyceride-rich lipoprotein particles, but its precise function in lipid metabolism is still uncertain. We have determined APOA4 genetic polymorphism in 285 randomly selected Melanesians from the Solomon Islands and have evaluated its significance in lipid metabolism. By using isoelectric focusing and immunoblotting techniques, a variant pattern, indistinguishable from the APOA4*2 allele uniquely found in white populations at a frequency of about 8%, was detected at a relatively high frequency (19%) in the Melanesian sample. Polymerase chain reaction (PCR) amplification and DNA sequencing of the 3' end of the APOA4 gene revealed that the Melanesian mutation is distinct from the known APOA4*2 mutation and that it involves a four-amino acid deletion in the evolutionarily conserved carboxyl-terminal region in the apoA-IV protein, which consists of four repeats of four amino acids each. After adjustment for concomitant variables, we investigated the impact of the deletion polymorphism on plasma levels of cholesterol, triglycerides, apoA-I, apoA-II, and apoE. A significant (P = .02) and gene-dosage effect was observed on the plasma levels of apoA-I and apoA-II: these levels were lowest in individuals homozygous for the deletion allele (D), intermediate in heterozygotes (ND), and highest in homozygous individuals for the normal allele (N). The average effect of the APOA4*D allele was to lower apoA-I and apoA-II by 8 mg/dL and 2 mg/dL, respectively, and the APOA4 polymorphism accounted for about 3% of the phenotypic variance in both cases.(ABSTRACT TRUNCATED AT 250 WORDS)
Alleles↗
Role of common genetic polymorphisms in the LDL receptor gene in affecting plasma cholesterol levels in the general population.
A large number of rare mutations in the low-density lipoprotein (LDL) receptor gene cause the autosomal dominant disorder familial hypercholesterolemia. In addition, a number of common DNA polymorphisms have been identified in the LDL receptor gene, but their significance in affecting plasma cholesterol levels in the general population has not been studied widely. We investigated the role of two common DNA polymorphisms, Ava II (exon 13) and Nco I (exon 18), at the LDL receptor locus in affecting plasma lipid profiles in normolipidemic Hispanics (n = 385) and non-Hispanic whites (NHWs; n = 543) from the San Luis Valley, Colorado. While the distribution of the Nco I polymorphism was comparable between Hispanics and NHWs, the allele frequencies at the Ava II restriction site differed significantly between the two ethnic groups (P < .001). The Ava II and Nco I polymorphisms were in linkage disequilibrium (P < .05) in both Hispanics and NHWs. Both polymorphisms revealed a gender-specific effect on total and LDL cholesterol (LDL-C) confined to women only in both ethnic groups. The AVA II polymorphism was associated significantly with total cholesterol and LDL-C in NHW women (P = .001 and P = .014) and in Hispanic women (P = .011 and P = .057). The effect of the Nco I polymorphism was significant on total cholesterol and LDL-C (P = .019 and P = .035) in Hispanic women only. Although a similar trend was observed in NHW women, the effect was not significant at the 5% level.(ABSTRACT TRUNCATED AT 250 WORDS)
Alleles↗
Preliminary localization of a gene for autosomal dominant hypoparathyroidism to chromosome 3q13.
A large family in which hypoparathyroidism was observed to segregate as an autosomal dominant trait in three generations was identified. Mutation in the PTH gene was excluded by linkage and single-stranded conformational analysis. The hypocalcemic phenotype in this family was mapped by linkage analysis using short, tandem-repeat polymorphisms to the region of chromosome 3q13. A maximum lod score of 2.71 at theta = 0.0 was observed with marker D3S1303. Positive lod scores were observed at theta = 0.0 with markers flanking D3S1303. Multipoint linkage analysis gave a lod score of 2.71 for the region flanking D3S1303. Simulation using the computer program SLINK showed that a lod score of 2.71 at theta = 0.0 was the maximum lod score possible given the pedigree structure. The simulation also showed that given the structure of the pedigree the probability of observing a lod score of 2.71 at theta = 0.0 by chance was 1 in 1000. The data presented above provide important preliminary evidence supporting linkage to chromosome 3q13. This region contains a Ca(2+)-sensing receptor gene that is proposed as a key signal transduction element for changes in extracellular Ca2+ concentrations in mechanisms of regulation of PTH secretion from parathyroid cells. The mutation in this family may activate the Ca(2+)-sensing receptor suppressing PTH secretion and lowering the "set point" for serum calcium levels.
Chromosome Mapping↗
ApoA-IV polymorphism associated with myocardial infarction in obese NIDDM patients. The San Luis Valley Diabetes Study.
Non-insulin-dependent diabetes mellitus (NIDDM) confers myocardial infarction (MI) risk unexplained by known factors. In 356 NIDDM patients and 1,087 people with normal glucose tolerance, we investigated the association between MI risk and polymorphism at codon 360 in the apolipoprotein A-IV (apoA-IV) gene. During 1984-1992, MI was diagnosed in 84 diabetic and in 106 nondiabetic people. The risk of MI did not differ by apoA-IV phenotype in nondiabetic people; however, in NIDDM patients, those with the apoA-IV 1-2 phenotype had 2.8 (95% confidence interval: 1.4-5.6) higher MI risk than those with the 1-1 phenotype, adjusting for age, gender, ethnicity, hypertension, smoking, body mass index, fat centrality, and low-density lipoprotein and high-density lipoprotein cholesterol. The risk of MI was particularly high in obese NIDDM patients with the apoA-IV 1-2 phenotype: 5.1 (2.4-11.2) times that in obese apoA-IV 1-1 NIDDM patients and 7.7 (3.6-16.7) times that in lean nondiabetic people. The effect of apoA-IV 1-2 did not appear to be a part of the insulin-resistance syndrome nor was it dependent on diabetes duration or control. One half of the excess MI risk in the diabetic population studied was explained by the apoA-IV 1-2 phenotype. These results indicate that approximately 17% of NIDDM patients have a high MI risk apoA-IV phenotype that is particularly deleterious in obese patients.
Adult↗
An improved method for pouring DNA sequencing gels.
Explore the source record for details and available documents.
Acrylic Resins↗
Dinucleotide repeat polymorphism at the HPR locus.
Explore the source record for details and available documents.
Base Sequence↗
Paired box mutations in familial and sporadic aniridia predicts truncated aniridia proteins.
Aniridia, an autosomal dominant ocular disorder characterized by iris hypoplasia, results from mutations in the PAX6 gene, which encodes paired box and homeobox motifs. In this report we describe five new mutations in the paired box region of the human PAX6 gene that are associated with aniridia. The paired box mutations that we detected were in both familial (three) and sporadic (two) cases. All five mutations predict truncated PAX6 proteins. Our study indicates that early premature translational termination mutations in the PAX6 gene result in haploinsufficiency and generate the aniridia phenotype.
Amino Acid Sequence↗
The gender-specific apolipoprotein E genotype influence on the distribution of plasma lipids and apolipoproteins in the population of Rochester, MN. III. Correlations and covariances.
The gender-specific influence that the apolipoprotein E (ApoE) polymorphism has on the correlations and covariances between pairs of nine plasma lipid and apolipoprotein traits (total cholesterol; in triglycerides; high-density-lipoprotein cholesterol; apolipoproteins AI, AII, B, CII, lnCIII, and lnE) was studied in 507 unrelated individuals representative of the adult population of Rochester, MN. Analyses are presented separately for females and males. The Apo E polymorphism had a significant influence on a large number (10 of 36) of correlations and covariances in females and on a small number (3 of 36) in males. The contribution of allelic variation in the Apo E gene to the definition of multivariate measures of the 36-dimensional correlation structure was evaluated. The influence of Apo E genotype on correlation structure was gender dependent. These findings were used to demonstrate how heterogeneity of risk-factor correlations and covariances among genotype-gender subgroups of the population at large may influence the evaluation of risk of coronary artery disease.
Analysis of Variance↗
Clinical diversity and chromosomal localization of X-linked cone dystrophy (COD1).
X-linked progressive cone dystrophy (COD1) causes progressive deterioration of visual acuity, deepening of central scotomas, macular changes, and bull's-eye lesions. The cone electroretinography (ERG) is variably abnormal in affected males, and the rod ERG may also be abnormal. The clinical picture of heterozygous females ranges from asymptomatic to a widespread spectrum of cone-mediated dysfunction. A prior linkage study demonstrated linkage between the COD1 locus and the marker locus DXS84, assigned to Xp21.1, with no recombination. In the present study, we have clinically characterized a large four-generation family with COD1 and have performed a linkage analysis using seven polymorphic markers on the short arm of the X chromosome. No recombination was observed between the disease and the marker loci DXS7 and MAOA, suggesting that the location of COD1 is in the region Xp11.3, distal to DXS84 and proximal to ARAF1.
Child↗
Genetic characterization of American and Western Samoans.
The Samoan islands were politically separated into American Samoa and Western Samoa in the early 1900s. Economic modernization is far more extensive in American Samoa. However, the Samoan archipelago has maintained a remarkable degree of sociocultural homogeneity, including intermarriage. The sociocultural exchanges presumably led to genetic homogeneity between the two Samoas. Detailed genetic comparisons and characterizations of Samoans are scanty, however. As part of a multidisciplinary study of modernization and cardiovascular risk factors in adults, we analyzed nine hypervariable nuclear DNA (HVR) and four serum protein polymorphisms in the two Samoan groups. The average heterozygosities at both DNA and serum protein loci are comparable in the two groups. As expected, the HVR loci reveal a high degree of variability (heterozygosity 30-87%) compared with the serum protein loci (heterozygosity 1-52%). A large proportion of alleles at the HVR loci, ranging from 50% to 100%, are shared between American and Western Samoa. With the exceptions of the D1S80 locus in American Samoa and the D13S118 locus in Western Samoa, the genotype distributions at all loci conform to their respective Hardy-Weinberg expectations. Sporadic occurrence of the F13B*2 allele at the F13B locus in Samoans indicates a low level of European admixture because this allele is unique to Europeans. The calculated zero values of kinship coefficients and standard genetic distances indicate minimal population differentiation between the two Samoan groups.
Alleles↗
Genetic polymorphism of apolipoprotein A-IV in the chimpanzee: common deletion of a conserved 12-nucleotide tandem repeat.
Apolipoprotein A-IV (apoA-IV protein; APOA4 gene) is structurally polymorphic in various mammalian species, including human, baboon, dog, horse, and mouse. To analyze the extent of genetic variation in the chimpanzee APOA4 gene, we screened 115 common chimpanzees (Pan troglodytes) (86 unrelated wild captured parents and 29 captive-born offspring) using isoelectric focusing followed by immunoblotting for protein polymorphism and using polymerase chain reaction (PCR) assay for DNA polymorphism. At the protein level the unrelated sample of chimpanzees is highly variable, having four alleles, APOA4*1, APOA4*2, APOA4*3, and APOA4*4, with frequencies of 0.192, 0.430, 0.331, and 0.047, respectively. The chimpanzee APOA4 locus, with four common alleles and a gene diversity of 67%, is more variable than previously reported variations in baboons (five alleles with 52% gene diversity) and humans (two alleles with 15% gene diversity). PCR amplification of chimpanzee DNAs, using a pair of human oligonucleotide primers covering a region of 300 nucleotides in the third exon, revealed a common 12-nucleotide deletion (allele frequency = 0.192) that correlates exactly with the APOA4*1 allele detected by isoelectric focusing and immunoblotting. DNA sequencing of the 300-nucleotide PCR amplified product revealed the deletion of 12 nucleotides near the carboxyl terminal region of the mature apoA-IV protein. This in-frame deletion, which codes for and eliminates four amino acids [glutamic acid (GAG), glutamine (CAG), glutamine (CAG), and glutamine (CAG)], occurs in a region that is evolutionarily conserved among rats, mice, chimpanzees, and humans. The partial DNA sequencing of the 3' end of the chimpanzee APOA4 gene revealed 99% identity with the human APOA4 gene.
Alleles↗
Impact of apolipoprotein E polymorphism in determining interindividual variation in total cholesterol and low density lipoprotein cholesterol in Hispanics and non-Hispanic whites.
The extent of apolipoprotein E (apo E) polymorphism and its effect on eight quantitative risk factors for coronary heart disease (total cholesterol; low density lipoprotein (LDL) cholesterol; total high density lipoprotein and its subfractions, HDL2 and HDL3; triglycerides; fasting glucose and fasting insulin) has been determined in 238 randomly selected Hispanics (120 males and 118 females) and 201 non-Hispanic whites (NHWs) (105 males and 96 females) from the San Luis Valley, Colorado. The frequencies for the E * 2, E * 3 and E * 4 alleles were 0.048, 0.853 and 0.099, respectively, in Hispanics and 0.080, 0.783 and 0.137, respectively, in NHWs. Relatively low frequency of the E * 2 and E * 4 alleles in Hispanics compared with NHWs is consistent with the genetic and anthropologic data that Hispanics have substantial Amerindian admixture. The impact of apo E polymorphism on each quantitative trait was estimated after adjusting for concomitant variables including age, cigarette smoking and body mass index in both genders and pre- or post-menopause status in females. The distribution of eight quantitative traits was analyzed among three common apo E phenotypes, 3-2, 3-3 and 4-3. In Hispanics, significant variability among apo E phenotypes was observed for total cholesterol (P = 0.001) in females only and the apo E polymorphism accounts for 12.4% variation in total cholesterol and 15.2% variation in LDL-cholesterol. In NHWs, significant mean differences among apo E phenotypes were observed for total cholesterol in both males (P = 0.007) and females (P = 0.0004). In NHW males and females, the apo E polymorphism explained 9.2% and 12.4%, respectively, of the variation in total cholesterol, and 15.1% and 6.6%, respectively, of the variation in LDL-cholesterol. In NHWs, borderline significance levels were also noted for phenotype specific differences in HDL2-cholesterol in males (P = 0.04) and females (P = 0.05), for total HDL cholesterol in females (P = 0.02) and HDL3-cholesterol in females (P = 0.06). While the estimated effects of the apo E polymorphism on quantitative traits differ somewhat between Hispanics and non-Hispanic whites, this probably reflects the overall difference in frequencies of the less common alleles in the Hispanics rather than a biological difference in the effects of these alleles on lipid metabolism.
Alleles↗
Relation of apolipoprotein E phenotype to myocardial infarction and mortality from coronary artery disease.
The apolipoprotein E polymorphism is a genetic determinant of low-density lipoprotein (LDL) cholesterol. Its status as a risk factor for coronary artery disease (CAD), either through a causal relation with LDL cholesterol level or independently, is less clearly established. Data from the Multiple Risk Factor Intervention Trial were used to examine the influence of apolipoprotein E phenotype on risk of coronary events. Of the 12,866 randomized participants, 619 were studied in a nested case-control design. CAD deaths (93) and nonfatal myocardial infarctions (113) were matched to 412 controls. The allele frequencies of apolipoprotein E in the white subset (epsilon 2 = 0.06, epsilon 3 = 0.79, and epsilon 4 = 0.15) were very similar to other nonselected white American populations, and the relation of apolipoprotein E on total and LDL cholesterol was generally similar to that seen in other studies, with the epsilon 2 allele being associated with lower and the epsilon 4 allele with higher total and LDL cholesterol. Allele frequencies were not the same for patients and control subjects. The presence of epsilon 4 was associated with an increased risk of CAD that was most evident for fatal cases. There was no relation between changes in LDL cholesterol over time during the trial and apolipoprotein E phenotypes.
Alleles↗