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Results for “deleterious mutation”

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PubMed1999

Molecular biology in radiation oncology. Radiation oncology perspective of BRCA1 and BRCA2.

The breast cancer susceptibility genes, BRCA1 and BRCA2, are used to illustrate the application of molecular biology to clinical radiation oncology. Identified by linkage analysis and cloned, the structure of the genes and the numerous mutations are determined by molecular biology techniques that examine the structure of the DNA and the proteins made by the normal and mutant alleles. Mutations in the non-transcribed portion of the gene will not be found in protein structure assays and may be important in gene function. In addition to potential deleterious mutations, normal polymorphisms of the gene will also be detected, therefore not all differences in gene sequence may represent important mutations, a finding that complicates genetic screening and counseling. The localization of the protein in the nucleus, the expression in relation to cell cycle and the association with RAD51 led to the discovery that the two BRCA genes may be involved in transcriptional regulation and DNA repair. The defect in DNA repair can increase radiosensitivity which might improve local control using breast-conserving treatment in a tumor which is homozygous for the loss of the gene (i.e., BRCA1 and BRCA2 are tumor suppressor genes). This is supported by the early reports of a high rate of local control with breast-conserving therapy. Nonetheless, this radiosensitivity theoretically may also lead to increased susceptibility to carcinogenic effects in surviving cells, a finding that might not be observed for decades. The susceptibility to radiation-induced DNA damage appears also to make the cells more sensitive to chemotherapy. Understanding the role of the normal BRCA genes in DNA repair might help define a novel mechanism for radiation sensitization by interfering with the normal gene function using a variety of molecular or biochemical therapies.

BRCA2 Protein↗

PubMedDate not supplied

Eight novel mutations in the HEXA gene.

PURPOSE: To characterize novel mutations in the HEXA gene (alpha-subunit beta-hexosaminidase A). METHODS: Subjects included participants in the California Tay-Sachs disease prevention program. DNA samples from 49 subjects (47 enzymatically defined carriers and 2 disease afflicted) who were negative for the four common disease-associated and the two pseudodeficient mutations, were subjected to single-strand conformation polymorphism (SSCP) analysis over 14 exons. RESULTS: Targeted sequencing of the 39 electrophoretic variants from SSCP analysis revealed eight novel and deleterious mutations and 31 with previously described mutations. Six novel mutations were found in non-Jewish carriers, and two were found in two patients with infantile Tay-Sachs disease. CONCLUSION: Identification of these eight novel mutations provides additional insight to the mutational spectrum for the HEXA gene. Furthermore, this knowledge should enhance diagnosis and prognosis for Tay-Sachs disease, carrier identification, and fundamental studies in structure/function relationships between this gene and its enzymatic product.

DNA Mutational Analysis↗

PubMed2003

Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses.

Recombination is increasingly seen as an important means of shaping genetic diversity in RNA viruses. However, observed recombination frequencies vary widely among those viruses studied to date, with only sporadic occurrences reported in RNA viruses with negative-sense genomes. To determine the extent of homologous recombination in negative-sense RNA viruses, phylogenetic analyses of 79 gene sequence alignments from 35 negative-sense RNA viruses (a total of 2154 sequences) were carried out. Powerful evidence was found for recombination, in the form of incongruent phylogenetic trees between different gene regions, in only five sequences from Hantaan virus, Mumps virus and Newcastle disease virus. This is the first report of recombination in these viruses. More tentative evidence for recombination, where conflicting phylogenetic trees were observed (but were without strong bootstrap support) and/or where putative recombinant regions were very short, was found in three alignments from La Crosse virus and Puumala virus. Finally, patterns of sequence variation compatible with the action of recombination, but not definitive evidence for this process, were observed in a further ten viruses: Canine distemper virus, Crimean-Congo haemorrhagic fever virus, Influenza A virus, Influenza B virus, Influenza C virus, Lassa virus, Pirital virus, Rabies virus, Rift Valley Fever virus and Vesicular stomatitis virus. The possibility of recombination in these viruses should be investigated further. Overall, this study reveals that rates of homologous recombination in negative-sense RNA viruses are very much lower than those of mutation, with many viruses seemingly clonal on current data. Consequently, recombination rate is unlikely to be a trait that is set by natural selection to create advantageous or purge deleterious mutations.

Animals↗

PubMed2005

Mobile genetic elements and sexual reproduction.

Transposable elements (TE) are prominent components of most eukaryotic genomes. In addition to their possible participation in the origin of sexual reproduction in eukaryotes, they may be also involved in its maintenance as important contributors to the deleterious mutation load. Comparative analyses of transposon content in the genomes of sexually reproducing and anciently asexual species may help to understand the contribution of different TE classes to the deleterious load. The apparent absence of deleterious retrotransposons from the genomes of ancient asexuals is in agreement with the hypothesis that they may play a special role in the maintenance of sexual reproduction and in early extinction for which most species are destined upon the abandonment of sex.

Animals↗

PubMed2001

Germline mutations in BRCA1 and BRCA2 in breast-ovarian families from a breast cancer risk evaluation clinic.

PURPOSE: Data from the Breast Cancer Linkage Consortium suggest that the proportion of familial breast and ovarian cancers linked to BRCA1 or BRCA2 may be as high as 98% depending on the characteristics of the families, suggesting that mutations in BRCA1 or BRCA2 may entirely account for hereditary breast and ovarian cancer families. We sought to determine what proportion of families with both breast and ovarian cancers seen in a breast cancer risk evaluation clinic are accounted for by coding region germline mutations in BRCA1 and BRCA2 as compared to a linkage study group. We also evaluated what clinical parameters were predictive of mutation status. PATIENTS AND METHODS: Affected women from 100 families with at least one case of breast cancer and at least one case of ovarian cancer in the same lineage were screened for germline mutations in the entire coding regions of BRCA1 and BRCA2 by conformation-sensitive gel electrophoresis, a polymerase chain reaction-based heteroduplex analysis, or direct sequencing. RESULTS: Unequivocal deleterious mutations were found in 55% (55 of 100) of the families studied. Mutations in BRCA1 and BRCA2 accounted for 80% and 20% of the mutations overall, respectively. Using multivariate analysis, the strongest predictors of detecting a mutation in BRCA1 or BRCA2 in this study group were the presence of a single family member with both breast and ovarian cancer (P <.0009; odds ratio [OR], 5.68; 95% confidence interval [CI], 2.04 to 15.76) and a young average age at breast cancer diagnosis in the family (P <.0016; OR, 1.69; 95% CI, 1.23 to 2.38). CONCLUSION: These results suggest that at least half of breast/ovarian families evaluated in a high-risk cancer evaluation clinic may have germline mutations in BRCA1 or BRCA2. Whether the remaining families have mutations in noncoding regions in BRCA1, mutations in other, as-yet-unidentified, low-penetrance susceptibility genes, or represent chance clustering remains to be determined.

Adult↗

PubMed1977

Estimation of mutation rate from rare protein variants.

A method for estimating the mutation rate for protein loci from the number of rare alleles in the population is presented. It seems to have a number of advantages compared with Kimura and Ohta's method. Applying this method to Neel's data from American Indians in South America and to Nozawa's data from Japanese macaques, the mutation rate for electrophoretically detectable alleles is estimated to be (2 approximately 3) x 10(-6) per locus per generation. This estimate may not include many severely or substantially deleterious mutations.

Alleles↗

PubMed1987

Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons.

The population dynamics of nearly neutral mutations are studied using a single-site and a multisite model. In the latter model, the nucleotides in a sequence are completely linked and the selection schemes employed are additive, multiplicative, and additive with a threshold. Although the third selection scheme is very different from the first two, the three schemes produce identical results for a wide range of parameter values. Thus the present study provides a general theory for the population dynamics of nearly neutral mutations because the results can also be used to draw inferences about other selection schemes such as stabilizing selection and synergistic selection. It is shown that the number of slightly deleterious mutations accumulated in a sequence can be considerably larger under the multisite model than under the single-site model, particularly if the sequence is long or if the mutation rate per site is high. The results show that even a very slight selective difference between synonymous codons can produce a strong bias in codon usage. Three alternative explanations for the strong bias in codon usage in bacterial and yeast genes are considered. The implications of the present results for molecular evolution are discussed.

Biological Evolution↗

PubMed2006

Hitting HIV where it hurts: an alternative approach to HIV vaccine design.

The ability of HIV-1 to mutate represents a major challenge to current vaccine approaches. However, some individuals achieving control of HIV during natural infection seem unique in their dominant targeting by cellular immune responses of conserved regions of HIV that, if mutated, exact a substantial impact on viral replicative capacity, or fitness. Notably, the partial suppression of HIV in treated individuals harboring viruses with drug-resistant mutations has also been linked to impaired viral fitness. The convergence of these observations suggests that vaccines designed to focus immune responses narrowly against regions of HIV susceptible to highly deleterious mutations might prove effective in controlling viral replication to levels that slow disease progression and reduce transmission. Therefore, it will be crucial to identify these "Achilles heels" of HIV that might represent uniquely susceptible targets, and test whether vaccine constructs enabling specific targeting of CD8(+) T-cell responses against such regions would enable the control of HIV and SIV.

AIDS Vaccines↗

PubMed1996

Spontaneous mutational variances and covariances for fitness-related traits in Drosophila melanogaster.

Starting from a completely homozygous population of Drosophila melanogaster, 176 lines were derived and independently maintained by a single brother-sister mating per generation. Three fitness-related traits were considered (fecundity, egg-to-pupa and pupa-to-adult viabilities). Mutational heritabilities of these traits and genetic correlations between all possible pairs were calculated from the between line divergence (codivergence), after 104-106 generations of mutation accumulation. Mutational heritabilities ranged from 0.60 x 10(-3) to 0.82 x 10(-3) and correlations from -0.11 to 0.25. These values are likely to be underestimates due to selection against deleterious mutations. The distribution of the means of the lines was asymmetric, positive for fecundity and negative for both viability components. The coefficients of asymmetry are also likely to be biased, again due to selection. Extreme lines from the two tails of the distribution were examined in detail. Homozygous line effects were all negative for viability traits but predominantly positive for fecundity, indicating the fixation of mutations with positive effects on the latter. Corresponding heterozygous line effects showed a variable degree of dominance.

Animals↗

PubMed1992

Assessing the underlying pattern of human germline mutations: lessons from the factor IX gene.

Germline mutations cause or predispose to most disease. Hemophilia B is a useful model for studying the underlying pattern of recent germline mutations in humans because the observed pattern of mutation in factor IX more closely reflects the underlying pattern of mutation than the observed pattern for many other genes. In addition, it is possible to identify and correct for biases inherent in ascertaining only those mutations that cause hemophilia. Aspects of the pattern of germline mutation in the factor IX gene are becoming clear: 1) in the United States, two-thirds of mutations causing mild disease arose from three founders whereas almost all the mutations resulting in either moderate or severe disease arose independently, generally within the past 150 years; 2) direct estimates of the rates of mutation in humans indicate that transitions are more frequent than transversions, which in turn are more frequent than deletions and insertions; 3) transitions at CpG are elevated approximately 24-fold relative to transitions at non-CpG dinucleotides; 4) transversions at CpG are elevated approximately eightfold relative to transversions at non-CpG dinucleotides; 5) the sum total of the dinucleotide mutation rates produces a bias against G and C bases that would be sufficient to maintain the G+C content of the factor IX gene at its evolutionarily conserved level of 40%; and 6) the pattern of mutation is similar for Caucasians residing in the United States and for Asians residing in Asia. Two ideas emerge from this and from an analysis of the pattern of recent deleterious mutations compared with ancient neutral mutations that have been fixed during evolution into the factor IX gene. First, the bulk of germline mutations are likely to arise from endogenous processes rather than environmental mutagens. Second, the factor IX protein is composed mostly of two classes of amino acids: critical residues in which all single-base missense changes will disrupt protein function, and "spacer" residues in which the precise nature of the residue is unimportant but the peptide bond is necessary to keep the critical residues in register. More work is necessary to assess the veracity and generality of these ideas.

Amino Acid Sequence↗

PubMed2006

Monogenic hypercholesterolaemias--an evaluation of apolipoprotein B100 and LDL receptor gene polymorphisms.

INTRODUCTION: Normally the N-terminal domain of the LDL receptor (LDLR) binds to low-density lipoprotein through apolipoprotein B100. Mutations within the LDL receptor and/or apolipoprotein B-100 genes compromising this process may lead to congenital monogenic hypercholesterolaemias known as familial hypercholesterolaemia or familial defective apolipoprotein B-100. These diseases are inherited as autosomal dominant traits. AIM: To search for LDLR and apoB100 gene mutations in a Polish population of patients with hypercholesterolaemia and to determine their types and locations. An attempt was also made to evaluate the influence of identified gene mutations on the modification of protein product sequence and the severity of its functional impairment. METHODS: LDLR and apoB100 gene analyses using PCR, SSCP and automated sequencing techniques were performed in 190 hypercholesterolaemic patients. Flow cytometry was used to measure the influence of Cys152Trp mutation in the LDLR gene on ligand binding and internalisation. The OLA method was used for the preparation of adequate genetic markers allowing rapid detection of one of the most deleterious mutations of the apoB100 gene. RESULTS AND CONCLUSIONS: Three brand new mutations, not reported so far, have been detected--Pro2712Leu and Ile3532 in the apoB100 gene, and Cys347Ser in the LDLR gene--and numerous changes in the nucleotide sequence of the LDL receptor gene have been confirmed. The observations of functionality of the mutated receptor gene with flow cytometry suggested the dysfunction of LDLR due to Cys152Trp polymorphism reported in many studies.

Apolipoprotein B-100↗

PubMed2005

Lack of RNA-DNA oligonucleotide (chimeraplast) mutagenic activity in mouse embryos.

There are numerous reports of the use of RNA-DNA oligonucleotides (chimeraplasts) to correct point mutations in vitro and in vivo, including the human apolipoprotein E gene (ApoE). Despite the absence of selection for targeting, high efficiency conversion has been reported. Although mainly used to revert deleterious mutations for gene therapy applications, successful use of this approach would have the potential to greatly facilitate the production of defined mutations in mice and other species. We have attempted to create a point mutation in the mouse ApoE gene by microinjection of chimeraplast into the pronuclei of 1-cell mouse eggs. Following transfer of microinjected eggs we analysed 139 E12.5 embryos, but obtained no evidence for successful conversion.

Animals↗

PubMed2001

Denaturing high-performance liquid chromatography (DHPLC)-based prenatal diagnosis for tuberous sclerosis.

Tuberous sclerosis (TSC) is a frequent autosomal-dominant condition (affecting 1 in 6000 individuals) caused by various mutations in either the hamartin (TSC1) or the tuberin gene (TSC2). This allelic and non-allelic heterogeneity makes genetic counseling and prenatal diagnosis difficult, especially as a significant proportion of TSC cases are due to de novo mutations. For this reason the identification of the disease causing mutation is mandatory for accurate counseling, yet current mutation detection methods such as single-strand conformation polymorphism (SSCP) or denaturing gradient gel electrophoresis (DGGE) are labor intensive with limited detection efficiency. Denaturing high-performance liquid chromatography (DHPLC) is a high-throughput, semi-automated mutation detection system with a reported mutation detection rate close to 100% for PCR fragments of up to 800 bp. We used a recently described DHPLC assay allowing the efficient detection of mutations in TSC1 to analyze the DNA extracted from a chorion villus sample in order to perform a prenatal diagnosis for TSC. The fetus was found not to have inherited the deleterious mutation and the DHPLC diagnosis was confirmed by haplotype analysis. This represents the first DHPLC-based prenatal diagnosis of a genetic disease.

Chorionic Villi↗

PubMed1981

The effect of a change in mutation rate on the incidence of dominant and X-linked recessive disorders in man.

In order to assess the impact on man of a sustained change in mutation rate that might be caused by ionizing radiation or a chemical mutagen in the environment, it is important to determine the current incidence of genetic disease, the rate at which deleterious mutations arise and the number of generations that mutations persist before eliminated by selection. From these data it should be possible to estimate both the increase in genetic disease in the first generation following the increase in mutation rate, and the rate at which a new equilibrium between mutation and selection would occur. In this paper the results of a survey to determine birth frequency, mutation rate and reproductive fitness for each of the important dominant and X-linked recessive disorders are described. It is estimated that these disorders affect about 0.6% of live-born individuals, including 0.1% of live-borns who carry a newly-arising mutation. These figures are approx. 50% lower than those used by the various committees that have assessed the genetic risk to man from ionizing radiation. If the mutation rate were to permanently double, the frequency of these disorders would be expected in increase in the first generation by 15%, to 0.7% of live-births. The increase in the first 2 generations would be 24% and a 50% increase would occur by the 9th generation. A calculation of the possible increase in dominant and X-linked recessive disorders due to exposure of a population to ionizing radiation indicates that the estimate made in 1977 by the United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) may be too high by a factor of 2-6 fold.

Female↗

PubMed2002

Glu274Lys/Gly309Arg mutation of the tissue-nonspecific alkaline phosphatase gene in neonatal hypophosphatasia associated with convulsions.

We describe a patient diagnosed with lethal perinatal hypophosphatasia with a unique clinical presentation of convulsions that responded to vitamin B6. Genomic DNA sequence analysis of the tissue-nonspecific alkaline phosphatase (TNSALP) gene revealed two missense mutations: a G-to-A transition resulting in a Glu to Lys at codon 274 (E274K), and a G-to-C transversion resulting in a Gly to Arg at codon 309 (G309R). The first mutation was maternally transmitted and was previously characterized as a moderate one, whereas the latter was paternally transmitted and has not been previously reported. Phenotype/genotype correlation indicates that G309R is a deleterious mutation that can lead to seizures and a lethal outcome, as was demonstrated in our patient.

Alkaline Phosphatase↗

PubMed1999

The rate of spontaneous mutation for life-history traits in Caenorhabditis elegans.

Spontaneous mutations were accumulated in 100 replicate lines of Caenorhabditis elegans over a period of approximately 50 generations. Periodic assays of these lines and comparison to a frozen control suggest that the deleterious mutation rate for typical life-history characters in this species is at least 0.05 per diploid genome per generation, with the average mutational effect on the order of 14% or less in the homozygous state and the average mutational heritability approximately 0.0034. While the average mutation rate per character and the average mutational heritability for this species are somewhat lower than previous estimates for Drosophila, these differences can be reconciled to a large extent when the biological differences between these species are taken into consideration.

Animals↗

PubMed2001

Inbreeding depression in small populations of self-incompatible plants.

Self-incompatibility (SI) is a widespread mechanism that prevents inbreeding in flowering plants. In many species, SI is controlled by a single locus (the S locus) where numerous alleles are maintained by negative frequency-dependent selection. Inbreeding depression, the decline in fitness of selfed individuals compared to outcrossed ones, is an essential factor in the evolution of SI systems. Conversely, breeding systems influence levels of inbreeding depression. Little is known about the joint effect of SI and drift on inbreeding depression. Here we studied, using a two-locus model, the effect of SI (frequency-dependent selection) on a locus subject to recurrent deleterious mutations causing inbreeding depression. Simulations were performed to assess the effect of population size and linkage between the two loci on the level of inbreeding depression and genetic load. We show that the sheltering of deleterious alleles linked to the S locus strengthens inbreeding depression in small populations. We discuss the implications of our results for the evolution of SI systems.

Alleles↗

PubMed1999

Atrichia with papular lesions resulting from a nonsense mutation within the human hairless gene.

Atrichia with papular lesions is a rare autosomal recessive form of alopecia characterized by hair loss soon after birth and the development during childhood of a diffuse papular rash. We have previously shown that this disorder results from a deleterious mutation in the human hairless gene, a gene also involved in the pathogenesis of a related but clinically distinct form of congenital alopecia, termed alopecia universalis congenita. In this report, we describe a novel nonsense mutation in exon 4 of the human hairless gene in a consanguineous kindred affected with atrichia with papular lesions. This report provides additional evidence for phenotypic heterogeneity among inherited atrichias and for an association between the papular rash of atrichia with papular lesions and nonsense mutations in the human hairless gene.

Alopecia↗