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Results for “deleterious mutation”

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PubMed1997

Evidence for a selectively favourable reduction in the mutation rate of the X chromosome.

The equilibrium per-genome mutation rate in sexual species is thought to result from a trade-off between the benefits of reducing the deleterious mutation rate and the costs of increasing fidelity. We propose that selection will often favour a lower mutation rate on the X chromosome than on autosomes, owing to the exposure of deleterious recessive mutations on hemizygous chromosomes. We tested this hypothesis by examining 33 X-linked genes that have been sequenced in both mouse and rat, and compared their rate of evolution against 238 autosomal genes. The X-linked genes were found to have a significantly lower rate of synonymous substitution than the autosomal genes. Neither the supposed higher mutation rate in males nor stronger purifying selection against slightly deleterious mutations on the X chromosome can account for the low value. The most parsimonious explanation is that rodents have a lower mutation rate on the X chromosome than on autosomes. It is therefore likely that previous indirect estimates of the excess male mutation rate are inaccurate. Indeed, after correction we find no evidence for a male-biased mutation rate in rodents. Furthermore, the rate of synonymous substitution in Y-linked genes is not significantly different from that in autosomal ones. The extent to which enhanced male mutation rates are problematic for the mutational deterministic model of the evolution of sex must, in turn, be questioned.

Animals↗

PubMed2000

Androgenetic alopecia in heterozygous carriers of a mutation in the human hairless gene.

BACKGROUND: Androgenetic alopecia is considered to be genetically determined. Recently, a rare autosomal recessive form of hereditary alopecia, termed atrichia with papular lesions (APL), was found to result from mutations in the human hairless gene. OBJECTIVE: Our aim was to assess the pattern of androgenetic alopecia in heterozygous carriers of a deleterious mutation in the human hairless gene. METHODS: Healthy male second-degree relatives (n = 31) of patients affected with APL and belonging to a large consanguineous kindred were interviewed and given a Hamilton score of baldness. DNA was obtained from each subject and analyzed for the presence of a mutation in the human hairless gene known to affect this family. The age at onset and extent of baldness were compared in healthy homozygotes and heterozygous carriers of the mutation. RESULTS: Statistical analysis of the results revealed no differences in age at onset and extent of androgenetic alopecia between the two groups of subjects. CONCLUSION: The present study reports the first attempt to characterize the phenotype of heterozygous carriers of a mutation in the human hairless gene. It indicates that the presence of a deleterious mutation in one allele of the hairless gene does not affect the pattern of androgenetic hair loss.

Adult↗

PubMed2006

On the expected relationship between inbreeding, fitness, and extinction.

We assessed the expected relationship between the level and the cost of inbreeding, measured either in terms of fitness, inbreeding depression or probability of extinction. First, we show that the assumption of frequent, slightly deleterious mutations do agree with observations and experiments, on the contrary to the assumption of few, moderately deleterious mutations. For the same inbreeding coefficient, populations can greatly differ in fitness according to the following: (i) population size; larger populations show higher fitness (ii) the history of population size; in a population that recovers after a bottleneck, higher inbreeding can lead to higher fitness and (iii) population demography; population growth rate and carrying capacity determine the relationship between inbreeding and extinction. With regards to the relationship between inbreeding depression and inbreeding coefficient, the population size that minimizes inbreeding depression depends on the level of inbreeding: inbreeding depression can even decrease when population size increases. It is therefore clear that to infer the costs of inbreeding, one must know both the history of inbreeding (e.g. past bottlenecks) and population demography.

Adaptation, Physiological↗

PubMed1998

The effect of synergistic epistasis on the inbreeding load.

The magnitude of inbreeding depression in Drosophila melanogaster appears too large to be accounted for by mutational load with multiplicative fitness interactions among loci, if current estimates of mutation and selection parameters are valid. One possible explanation for this discrepancy is synergistic epistasis among the fitness effects of deleterious mutations. A simple model of the effect of synergistic epistasis on the inbreeding load is developed. This model is used to show that deleterious mutations could account for the Drosophila data on the effects of inbreeding on components of fitness such as viability.

Animals↗

PubMed1999

Reported in vivo splice-site mutations in the factor IX gene: severity of splicing defects and a hypothesis for predicting deleterious splice donor mutations.

Small consensus sequences have been defined for RNA splicing, but questions about splicing in humans remain unanswered. Analysis of germline mutations in the factor IX gene offers a highly advantageous system for studying the mutational process in humans. In a sample of 860 families with hemophilia B, 9% of independent mutations are likely to disrupt splicing as their primary mode of action. This includes 26 splicing mutations reported herein. When combined with the factor IX splice mutations reported by others, at least 104 independent mutations have been observed, 80 of which are single base substitutions within the splice donor and splice acceptor consensus sequences. After analysis of these mutations, the following inferences emerge: (1) the susceptibility of a splice donor sequence to deleterious mutation depends on the degree of similarity with the donor consensus sequence, suggesting a simple "5-6 hypothesis" for predicting deleterious vs. neutral mutations; (2) the great majority of mutations that disrupt the splice donor or splice acceptor sequences result in at least a 100-fold decrement in factor IX coagulant activity, indicating that the mutations at these sites generally function as an on/off switch; (3) mutations that create cryptic splice junctions or that shorten but do not interrupt the polypyrimidine tract in the splice acceptor sequence can reduce splicing by a variable amount; and (4) there are thousands of potential donor-acceptor consensus sequence combinations in the 38-kb factor IX gene region apparently not reduced by evolutionary selective pressure, presenting an apparent paradox; i.e., mutations in the donor and acceptor consensus sequences at intron/exon splice junctions can dramatically alter normal splicing, yet, appropriately spaced, good matches to the consensus sequences do not predispose to significant amounts of alternative splicing.

Computer Simulation↗

PubMed2003

A phylogenetic approach to assessing the significance of missense mutations in disease genes.

The identification of deleterious mutations within candidate genes is a crucial step in the elucidation of the genetic bases of human disease. However, the significance of any base or amino acid change within a gene is unknown until detailed structural and functional analysis has been carried out. A potentially rapid way of identifying functionally important sites within a gene is to identify evolutionarily conserved regions. Mutations affecting such sites are assumed to be deleterious for the carrier. In this communication we generalize this approach and present a formal framework to assess whether a specific mutation is deleterious given sequence data from a set of homologues. We propose a score that takes into account the nature of the mutation, the conservation of the affected residue among the different species, and their phylogenetic relationships. Its performance is examined using published TP53 mutations and frequent polymorphic variants.

Computational Biology↗

PubMed2001

Frequency of BRCA1 and BRCA2 germline mutations in Japanese breast cancer families.

The purpose of this investigation is to study the frequency of BRCA1 and BRCA2 germline mutations in Japanese breast cancer families. Mutation analysis of BRCA1 and BRCA2 by SSCP was conducted on the 113 breast cancer patients (probands) with at least 1 breast cancer (site-specific breast cancer families, n = 101) or 1 ovarian cancer (breast/ovarian cancer families, n = 12) patient in their first-degree relatives. Fifteen deleterious mutations (13.3%), including 8 nonsense and 7 frameshift mutations, were identified in BRCA1, and 21 deleterious mutations (18.6%), including 8 nonsense, 12 frameshift and 1 splice-site mutations, were identified in BRCA2. In site-specific breast cancer families, mutation frequency of BRCA1 or BRCA2 was high in families with 3 or more breast cancer patients (36%, 9/25), early onset (40 < or = years old) breast cancer patients (38%, 19/50) or bilateral breast cancer patients (40%, 6/15). In breast/ovarian cancer families, mutations of BRCA1 (58.3%, n = 7), but not BRCA2 (0%, n = 0), were observed. BRCA1 codon 63 (TTA to TAA) nonsense mutation and BRCA2 frameshift mutation (5802 del AATT) were observed in 4 and 7 independent families, respectively. Haplotype analysis has suggested that carriers of each of these mutations have common ancestors. These results demonstrate that family profiles are important determinants of risk for carrying a BRCA1 or BRCA2 mutation and that cumulative frequency of BRCA1 and BRCA2 mutations in Japanese breast cancer families (31.9%) is within the range observed in Caucasian breast cancer families. Presence of Japanese founder mutations has also been suggested.

Adult↗

PubMed2005

[Mutational analysis of BRCA1 and BRCA2 genes in early-onset breast cancer patients in Shanghai].

OBJECTIVE: To investigate the prevalence of BRCA1 and BRCA2 mutations among early-onset breast cancer patients in Shanghai. METHODS: Fifty patients unselected for family history, who were diagnosed with breast cancer before the age of 40 years were analyzed. Among them, 13 patients have at least one first-degree relative affected with breast cancer. Mutation screening of BRCA1 and BRCA2 was performed in the whole coding sequence through Denaturing High Performance Liquid Chromatography (DHPLC) and subsequent DNA direct sequencing. RESULTS: Six deleterious mutations, including 2 novel frameshift mutations (3449insA, 5587-1del8) and 2 novel splice-site mutations (IVS17-1G > T, IVS21 + 1G > C) in BRCA1 were identified. Two deleterious mutations detected in BRCA2, including one frameshift mutation (5950delCT) and one novel missense mutation (5911G > C), all occurring on exon 11 adjacently. Additional 12 novel sequence variants were also detected including one unclassified variant and 7 intronic variants in BRCA1, and 4 novel intronic variants in BRCA2, all causing no alteration of amino acid coding. The prevalence of BRCA1 and BRCA2 mutations in the patients with early-onset breast cancer was 12% and 4%, respectively. CONCLUSION: Four novel mutations in BRCA1 and one novel mutation in BRCA2 may be mutations characterized of early-onset breast cancer in Chinese population. Germline mutations in BRCA2 may contribute less than mutations in BRCA1 to early-onset breast cancer in Shanghai. These data contribute to information on spectrum of BRCA gene in Chinese population and also offer a recommended screening mode for clinical genetic testing programme in China.

BRCA1 Protein↗

PubMed1997

The evolution of bacterial transformation: sex with poor relations.

Bacteria are the only organisms known to actively take up DNA and recombine it into their genomes. While such natural transformation systems may provide many of the same benefits that sexual reproduction provides eukaryotes, there are important differences that critically alter the consequences, especially when recombination's main benefit is reducing the mutation load. Here, analytical and numerical methods are used to study the selection of transformation genes in populations undergoing deleterious mutation. Selection for transformability depends on the shape of the fitness function against mutation. If the fitness function is linear, then transformation would be selectively neutral were it not for the possibility that transforming cells may take up DNA that converts them into nontransformable cells. If the selection includes strong positive (synergistic) epistasis, then transformation can be advantageous in spite of this risk. The effect of low quality DNA (from selectively killed cells) on selection is then studied analytically and found to impose an additional cost. The limited data available for real bacterial populations suggest that the conditions necessary for the evolution of transformation are unlikely to be met, and thus that DNA uptake may have some function other than recombination of deleterious mutations.

Bacteria↗

PubMed2004

BRCA mutations and risk of prostate cancer in Ashkenazi Jews.

PURPOSE: The Breast Cancer Linkage Consortium and other family-based ascertainments have suggested that male carriers of BRCA mutations are at increased risk of prostate cancer. Several series looking at the frequency of BRCA mutations in unselected patients with prostate cancer have not confirmed this finding. To clarify this issue, we conducted a large case-control study. EXPERIMENTAL DESIGN: Blood specimens from 251 unselected Ashkenazi men with prostate cancer were screened for the presence of one of the three common Ashkenazi founder mutations in BRCA1 and BRCA2. The incidence of founder mutations was compared with the incidence of founder mutations in 1472 male Ashkenazi volunteers without prostate cancer using logistic regression analysis after adjusting for age. RESULTS: Thirteen (5.2%) cases had a deleterious mutation in BRCA1 or BRCA2 compared with 28 (1.9%) controls. After adjusting for age, the presence of a BRCA1 or BRCA2 mutation was associated with the development of prostate cancer (odds ratio, 3.41; 95% confidence interval, 1.64-7.06; P = 0.001). When results were stratified by gene, BRCA2 mutation carriers demonstrated an increased risk of prostate cancer (odds ratio, 4.78; 95% confidence interval, 1.87-12.25; P = 0.001), whereas the risk in BRCA1 mutation carriers was not significantly increased. CONCLUSIONS: BRCA2 mutations are more likely to be found in unselected individuals with prostate cancer than age-matched controls. These results support the hypothesis that deleterious mutations in BRCA2 are associated with an increased risk of prostate cancer.

Adult↗

PubMed2003

The advantages of segregation and the evolution of sex.

In diploids, sexual reproduction promotes both the segregation of alleles at the same locus and the recombination of alleles at different loci. This article is the first to investigate the possibility that sex might have evolved and been maintained to promote segregation, using a model that incorporates both a general selection regime and modifier alleles that alter an individual's allocation to sexual vs. asexual reproduction. The fate of different modifier alleles was found to depend strongly on the strength of selection at fitness loci and on the presence of inbreeding among individuals undergoing sexual reproduction. When selection is weak and mating occurs randomly among sexually produced gametes, reductions in the occurrence of sex are favored, but the genome-wide strength of selection is extremely small. In contrast, when selection is weak and some inbreeding occurs among gametes, increased allocation to sexual reproduction is expected as long as deleterious mutations are partially recessive and/or beneficial mutations are partially dominant. Under strong selection, the conditions under which increased allocation to sex evolves are reversed. Because deleterious mutations are typically considered to be partially recessive and weakly selected and because most populations exhibit some degree of inbreeding, this model predicts that higher frequencies of sex would evolve and be maintained as a consequence of the effects of segregation. Even with low levels of inbreeding, selection is stronger on a modifier that promotes segregation than on a modifier that promotes recombination, suggesting that the benefits of segregation are more likely than the benefits of recombination to have driven the evolution of sexual reproduction in diploids.

Alleles↗

PubMed1997

The advantage of sex in evolving yeast populations.

Sex is a general feature of the life cycle of eukaryotes. It is not universal, however, as many organisms seem to lack sex entirely. The widespread occurrence of sex is puzzling, both because meiotic recombination can disrupt co-adapted combinations of genes, and because it halves the potential rate of reproduction in organisms with strongly differentiated male and female gametes. Most attempts to explain the maintenance of sexuality invoke differences between parents and sexual offspring. These differences may be advantageous in novel or changing environments if new gene combinations are favoured from time to time. Sex would then serve to concentrate beneficial mutations that have arisen independently into the same line of descent. But in a stable environment sex might serve to concentrate deleterious mutations, so that they will be more effectively purged from the population by selection. We have studied the effect of sex on mean fitness in experimental populations of the budding yeast Saccharomyces cerevisiae. Our results show that sex increases mean fitness in an environment to which the populations were well adapted, but not in an environment to which new adaptation occurred, supporting the hypothesis that the advantage of sexuality lay in the removal of deleterious mutations.

Adaptation, Physiological↗

PubMed2005

Evidence for widespread degradation of gene control regions in hominid genomes.

Although sequences containing regulatory elements located close to protein-coding genes are often only weakly conserved during evolution, comparisons of rodent genomes have implied that these sequences are subject to some selective constraints. Evolutionary conservation is particularly apparent upstream of coding sequences and in first introns, regions that are enriched for regulatory elements. By comparing the human and chimpanzee genomes, we show here that there is almost no evidence for conservation in these regions in hominids. Furthermore, we show that gene expression is diverging more rapidly in hominids than in murids per unit of neutral sequence divergence. By combining data on polymorphism levels in human noncoding DNA and the corresponding human-chimpanzee divergence, we show that the proportion of adaptive substitutions in these regions in hominids is very low. It therefore seems likely that the lack of conservation and increased rate of gene expression divergence are caused by a reduction in the effectiveness of natural selection against deleterious mutations because of the low effective population sizes of hominids. This has resulted in the accumulation of a large number of deleterious mutations in sequences containing gene control elements and hence a widespread degradation of the genome during the evolution of humans and chimpanzees.

Animals↗

PubMedDate not supplied

Double heterozygotes for non-Caucasian families with mutations in BRCA-1 and BRCA-2 genes.

The recent discovery of the BRCA-1 and BRCA-2 genes as contributing factors to hereditary breast cancer has significantly improved our understanding of familial breast cancer. Deleterious mutations in both BRCA-1 and BRCA-2 in an individual patient is exceedingly rare, with few case reports in the literature, particularly among non-Caucasian, non-Jewish families. We describe here two cases of deleterious mutations in both genes in a cohort of Korean women with early onset breast cancer.

Adult↗

PubMed2004

Evidence that positive selection drives Y-chromosome degeneration in Drosophila miranda.

Why does the Y chromosome harbor so few functional loci? Evolutionary theory predicts that Y chromosomes degenerate because they lack genetic recombination. Both positive and negative selection models have been invoked to explain this degeneration, as both can result in the recurrent fixation of linked deleterious mutations on a nonrecombining Y chromosome. To distinguish between these models, I investigated patterns of nucleotide variability along 37 kb of the recently formed neo-Y chromosome in Drosophila miranda. Levels of nucleotide variability on this chromosome are 30 times lower than in highly recombining portions of the genome. Both positive and negative selection models can result in reduced variability levels, but their effects on the frequency spectrum of mutations differ. Using coalescent simulations, I show that the patterns of nucleotide variability on the neo-Y chromosome are unlikely under deleterious mutation models (including background selection and Muller's ratchet) but are expected under recent positive selection. These results implicate positive selection as an important force driving the degeneration of Y chromosomes; adaptation at a few loci, possibly increasing male fitness, occurs at the cost of most other genes on this chromosome.

Animals↗

PubMed2004

Incidence of BRCA1 and BRCA2 mutations in young Korean breast cancer patients.

PURPOSE: The prevalence of BRCA-associated breast carcinoma in the Korean population has not been evaluated extensively. METHODS: Sixty Korean women who developed breast cancer by age 40 years were studied. Lymphocyte specimens from peripheral blood were processed for BRCA1 and BRCA2 by complete sequencing. Family history through three generations was obtained. Available paraffin-embedded tissue blocks were processed for immunohistochemical staining. RESULTS: In the cohort of 60 patients, nine patients with 11 deleterious mutations (six in BRCA1 and five in BRCA2) and seven missense mutations of unknown significance were found. Two patients had deleterious mutations in both BRCA1 and BRCA2 (double mutant). One half of the mutations were novel, and no founder mutations were observed in this cohort. Most of the BRCA-associated patients had no family history of breast and/or ovarian cancer. The expression of HER-2/neu, cyclin D1, and hormone receptors was less common, and p53 overexpression was more common in BRCA-associated tumors. CONCLUSION: The prevalence of BRCA1 and BRCA2 mutations in Korean women with breast cancer at a young age was high. However, the penetrance, as evidenced by the low frequency of breast and ovarian cancers in family members, appears to be low. These data suggest that there may be different genetic and etiologic factors affecting transmission and penetrance of the BRCA genes in Korean patients with breast cancer diagnosed at a young age.

Adult↗

PubMed2003

Patterns of epistasis in RNA viruses: a review of the evidence from vaccine design.

Epistasis results when the fitness effects of a mutation change depending on the presence or absence of other mutations in the genome. The predictions of many influential evolutionary hypotheses are determined by the existence and form of epistasis. One rich source of data on the interactions among deleterious mutations that has gone untapped by evolutionary biologists is the literature on the design of live, attenuated vaccine viruses. Rational vaccine design depends upon the measurement of individual and combined effects of deleterious mutations. In the current study, we have reviewed data from 29 vaccine-oriented studies using 14 different RNA viruses. Our analyses indicate that (1) no consistent tendency towards a particular form of epistasis exists across RNA viruses and (2) significant interactions among groups of mutations within individual viruses occur but are not common. RNA viruses are significant pathogens of human disease, and are tractable model systems for evolutionary studies--we discuss the relevance of our findings in both contexts.

Drug Design↗

PubMed1991

Haploidy or diploidy: which is better?

Although the evolutionary advantages of sexual reproduction have been extensively discussed, much less attention has been paid to haploid and diploid phases of the sexual life cycle. The relative lengths of these phases differ greatly in various taxa, including as extremes those with one or the other phase reduced to a single cell. Here we consider the efficiency of elimination of deleterious mutations as an evolutionary force and compare the mutation loads under haploid and diploid selection, Ln and L2n. With truncation-like selection, partial dominance, and heterozygous effect of a mutation less than about 1/4 its hemizygous effect, L2n less than Ln; otherwise L2n greater than Ln. The difference becomes important when the genomic deleterious mutation rate exceeds about 1 per genome. This suggests that the mutation rate, degree of dominance and mode of selection can be important in life-cycle evolution.

Biological Evolution↗