Significant Difference In Mutation Rates Research Articles

Sanger sequencing in routine KRAS testing: a review of 1720 cases from a pathologist's perspective

BackgroundSanger sequencing (SS) of PCR products is still the most frequent method to test colorectal cancer for KRAS mutations in routine practice.MethodsAn audit of SS on 1720 routine cases was...

Hepatitis B virus X mutations occurring naturally associated with clinical severity of liver disease among Korean patients with chronic genotype C infection

Few reports have detailed mutation frequencies and mutation patterns in the entire X region according to clinical status. The aims of this study were to elucidate the relationships between mutation patterns and their frequencies in the X region and clinical status in a Korean cohort and determine specific X mutation types, related closely with liver disease progression. All X mutations were determined by direct sequencing in 184 patients with different clinical features. Mutation rates in the X region in patients with more severe liver disease, hepatocellular carcinoma (HCC) (3.6%) or liver cirrhosis (4%) were always significantly higher than in patients with corresponding less severe forms, chronic hepatitis (2.9%) or asymptomatic carriers (2.1%), but no significant difference in mutation rates was found in terms of HBeAg serostatus. All five mutation types (V5M/L, P38S, H94Y, I127T/N, and K130M and V131I) affecting the six codons were found to be related significantly to clinical severity. Among these, two mutation types (V5M/L and K130M and V131I) were observed more frequently in HBeAg negative patients than in HBeAg positive patients. In conclusion, the results suggest that an accumulation of mutations in the X region contributes to disease progression in chronic patients, at least Korean patients with genotype C. Specific mutation types appears to be related more to severe liver diseases such as HCC or liver cirrhosis. In particular, a novel mutation type (V5M/L) discovered firstly during the present study was found to be associated significantly with HCC.

A mutational analysis of Caenorhabditis elegans in space

The International Caenorhabditis elegans Experiment First Flight (ICE-First) was a project using C. elegans as a model organism to study the biological effects of short duration spaceflight (11 days in the International Space Station). As a member of the ICE-First research team, our group focused on the mutational effects of spaceflight. Several approaches were taken to measure mutational changes that occurred during the spaceflight including measurement of the integrity of poly-G/poly-C tracts, determination of the mutation frequency in the unc-22 gene, analysis of lethal mutations captured by the genetic balancer eT1( III; V), and identification of alterations in telomere length. By comparing the efficiency, sensitivity, and convenience of these methods, we deduced that the eT1 balancer system is well-suited for capturing, maintaining and recovering mutational events that occur over several generations during spaceflight. In the course of this experiment, we have extended the usefulness of the eT1 balancer system by identifying the physical breakpoints of the eT1 translocation and have developed a PCR assay to follow the eT1 chromosomes. C. elegans animals were grown in a defined liquid media during the spaceflight. This is the first analysis of genetic changes in C. elegans grown in the defined media. Although no significant difference in mutation rate was detected between spaceflight and control samples, which is not surprising given the short duration of the spaceflight, we demonstrate here the utility of worms as an integrating biological dosimeter for spaceflight.

Mutation in the Tyrosine Kinase Domain of Epidermal Growth Factor Receptor Is a Predictive and Prognostic Factor for Gefitinib Treatment in Patients with Non–Small Cell Lung Cancer

Mutations in epidermal growth factor receptor (EGFR) can be used to predict the tumor response of patients receiving gefitinib for non-small cell lung cancer (NSCLC). We investigated the association between mutations in EGFR tyrosine kinase domain and tumor response and survival in gefitinib-treated NSCLC patients. EGFR mutations in exons 18 to 21 were analyzed by DNA sequencing of paraffin-embedded tumor tissues from gefitinib-treated NSCLC patients. The results were correlated with clinical variables. EGFR mutations were found in 61.1% (33 of 54) of cases; response rate and disease control rate were 56.8% and 68.5%, respectively. There was no significant difference in mutation rates between adenocarcinoma (29 of 43) and nonadenocarcinoma (4 of 11; P = 0.085). However, all four nonadenocarcinomas with EGFR mutations had no response to gefitinib. Presence of EGFR mutations was the only independent predictor for disease control (P = 0.003) and tumor response (P = 0.017) in multivariate analysis; positive predictive values were 87.9% and 70.8% and negative predictive values were 61.9% and 69.2%, respectively. In comparison with patients whose tumor was negative for EGFR mutations, patients with EGFR mutations had better progression-free survival (median, 7.6 versus 1.7 months; P = 0.011) and overall survival (median, 14.7 versus 4.7 months; P = 0.046). Mutations in EGFR tyrosine kinase correlate with treatment response and survival in gefitinib-treated NSCLC patients and can be used as a predictive and prognostic factor. Thus, analysis of EGFR tyrosine kinase mutations in lung adenocarcinoma is of clinical significance, as it can permit the customization of treatment with EGFR tyrosine kinase inhibitors.

Comparison of drug resistance genotypes between Beijing and non-Beijing family strains of Mycobacterium tuberculosis in Korea

The frequency of resistance genotypes among Beijing and non-Beijing strains was compared using a reverse blot hybridization assay to detect mutations within genes associated with rifampicin ( rpoB) and isoniazid ( katG, inhA, and ahpC) resistance. Of the 743 Mycobacterium tuberculosis isolates, 569 (77%) belonged to Beijing family. The proportion of Beijing strains was significantly higher among MDR-TB isolates than among drug-susceptible strains (82% vs. 72%, p < 0.01). Genotype analysis of the rpoB gene revealed significantly lower rates of the Ser531Leu mutation rate among Beijing vs. non-Beijing MDR-TB strains (41% vs. 66%, p < 0.005). While the mutation for Ser315Thr in the katG gene was more common among Beijing vs. non-Beijing family strains (65% vs. 50%, p < 0.01), the mutation rate of promoter region of the inhA gene was lower among Beijing strains compared with non-Beijing strains (14% vs. 25%, p < 0.05). Reverse hybridization successfully detected over 80% of isoniazid-resistant strains and over 92% of rifampicin-resistant strains among Korean isolates. Significant differences in mutation rates in the rpoB, katG, and inhA genes between Beijing strains and non-Beijing strains could explain discrepancies in mutation rates of genotypes in different countries. Reverse hybridization was useful for rapid detection of isoniazid and rifampicin resistant strains.

Y-chromosomal microsatellite mutation rates: differences in mutation rate between and within loci

We have studied 1766 father–son pairs of confirmed paternity (a total of 15 894 meioses) in nine Y-STR loci. The fathers were also analysed in five biallelic markers defining haplogroups (Hg) 1, 2, 3, 4, 9 and 16. A total of 36 fragment length mutations were observed. Our data demonstrate a significant surplus of gains and a bias towards increase in allele length upon mutational events. Overall, the mutation rate is correlated to STR repeat length, and there is a significant excess of losses in long alleles and gains in short alleles. Significant differences in mutation rate between and within loci are verified as is differences in mutation rates between haplogroups. Our findings clearly demonstrate the necessity of not only locus-specific but even allele-specific mutation rate estimates for forensic and population genetic purposes.

Messages through Bottlenecks: On the Combined Use of Slow and Fast Evolving Polymorphic Markers on the Human Y Chromosome

In 1995, much to the delight of mitochondrial Eve (Cann et al. 1987), the search for a suitable partner resulted in the discovery of Y-chromosomal Adam (Dorit et al. 1995; Paabo 1995). Like Eve, he was traced back to sub-Saharan Africa, although with a date of 270,000 years ago, he seems a bit older than she. On the basis of the absence of sequence variation in a part of the ZFY gene in 38 globally dispersed male subjects, this date was not undisputed (Donnelly et al. 1996; Fu and Li 1996; Rogers et al. 1996; Weiss and von Haeseler 1996). Later in the same year, two additional studies did reveal a limited number of sequence variants on other parts of the Y chromosome. Because of these variants, estimates were obtained of the times back to our most recent common (male) ancestor of 37,000–49,000 years ago (Whitfield et al. 1995) and of 51,000–411,000 years ago (Hammer 1994). Now, just 5 years later, with simple PCR strategies, ⩾250 polymorphic loci scattered over the entire nonrecombining part of the human Y chromosome can be identified. Among these polymorphisms are (1) biallelic markers with a low mutation rate representing unique (or near-unique) mutation events (UMEs) in human evolution, such as single base-pair substitutions (Underhill et al. 1997), an ALU insertion/deletion polymorphism (Hammer 1994), or a LINE insertion (Santos et al. 2000); (2) moderately fast-evolving microsatellites or simple-tandem repeats (STRs), with an average mutation frequency of ∼.2% per generation (Heyer et al. 1997; Jobling et al. 1999; Kayser et al. 2000); and (3) fast-evolving loci, such as the minisatellite locus MSY1 (Jobling et al. 1998) with a mutation frequency of 6%–11% per generation. With the exception of the two pseudoautosomal regions, the almost 60–Mb nonrecombining part of the Y chromosome is transmitted strictly from father to son without recombination (Jobling and Tyler-Smith 1995). This renders the Y chromosome probably the most versatile haplotypic genotyping system of the human genome. It is thus not surprising that chromosome-Y polymorphisms have been used to follow the migration patterns of our male ancestors from the recent past (Heyer et al. 1997; Foster et al. 1998) through historical times (Skorecki et al. 1997; Hammer et al. 2000), to the origins of modern humans (Hammer et al. 1998). Recently, two excellent review articles featuring the Y chromosome were published. The first (Bertranpetit 2000) addresses the difficulties of reliably tracing back human origins solely on the basis of Y-chromosomal UMEs. The second (Jobling and Tyler-Smith 2000) gives a detailed discussion of many genetic aspects of the Y chromosome in the context of disease and selection. This editorial will be restricted to the combined use of UMEs and STRs on the Y chromosome to reconstruct our genetic history. This application has received considerable attention in recent articles published in this journal and elsewhere (see, e.g., Zerjal et al. 1997; Bianchi et al. 1998; Hurles et al. 1998, 1999; Kittles et al. 1998; Bosch et al. 1999; Karafet et al. 1999; Lahermo et al. 1999; Ruiz-Linares et al. 1999; Helgason et al. 2000b; Hill et al. 2000; Santos et al. 2000). That the combined use of Y-chromosomal UMEs and STRs is not without any caveats will be explained below.

Molecular reconstruction and homology modelling of the catalytic domain of the common ancestor of the haemostatic vitamin-K-dependent serine proteinases.

The vitamin-K-dependent serine proteinases of coagulation have evolved by a process of gene duplication and divergence, acquiring along the way a considerable degree of functional diversity that has equipped them for their different roles in haemostasis. The cDNA sequences encoding the catalytic domains of the early mammalian ancestors of five vitamin-K-dependent factors (factors VII, IX and X, protein C and prothrombin) were reconstructed by employing cDNA sequence data from a range of extant mammals and by using established phylogenies. The cDNA sequence of the putative common ancestor of these early mammalian proteins was then reconstructed from the five sequences by using a deduced phylogeny that was different in a number of respects from those previously proposed. Factor IX is proposed to have branched off early on, followed by protein C and prothrombin and finally factors VII and X. Significant differences in mutation rates were observed between proteins within a species; factor IX exhibited a lower mutation rate than the other proteins, consistent with its early emergence. Differences in mutation rates were also observed between species for a given protein and these exhibited an inverse correlation with generation time. A biophysically plausible structure for the ancestral vitamin-K-dependent factor protein was constructed by comparative methods. Studies of the functional architecture of this model provide new insights into the evolution of protein-binding specificity in this family of proteins.

Recent observations in human DNA-minisatellite mutations.

We report maternal and paternal mutation rates at loci D1S7 (MS1), D7S21 (MS31), D12S11 (MS43A), and D7S22 (G3). The respective mutation rates were as follows: [table: see text] At loci D7S21, D12S11, and D7S22 statistically significant differences in mutation rates exist between the sexes. No such difference was observed at locus D1S7. However inspection of the latter data reveals that by mutation at spermiogenesis approximately two-thirds of the fragments showed an addition of repetitive units, while a 50: 50 ratio was encountered in the series of maternal mutations. We also report the observation of naturally occurring 3-fragment patterns.

Biological effects of background radiation: mutagenicity of 40K.

The naturally occurring radioactive isotope 40K is the single largest contributor to the internal background radiation dose in living organisms. We examined cell growth and mutation rate or frequency in several strains of Escherichia coli in (i) media containing the natural content of 40K, (ii) media containing potassium from which essentially all of the 40K had been removed by isotope separation, and (iii) media highly enriched in 40K. Growth rates (doubling times) were identical in the present or absence of 40K. In more than 40 chemostat experiments, we were unable to detect any significant differences in mutation rate to bacteriophage T5 resistance or in mutation frequency to valine resistance or tryptophan prototrophy attributable to 40K. We conclude that, in the bacterial systems we have studied, 40K does not make a significant contribution to spontaneous mutation.

EMS- and relation-induced mutation frequencies at individual loci in Arabidopsis thaliana (L.) Heynh

Average mutation frequencies per locus per dose of mutagen — EMS, X-rays and fast neutrons — were estimated from 15 different loci of Arabidopsis thaliana. These loci related to clearly distinguishable phenotypic mutant groups, each affected by a limited number of loci. There were significant differences in mutation rate between individual loci. The proposition of a linear relationship between DNA content and mutation frequency per locus is rejected.

Untersuchungen �ber Die Bedeutung Von Temperatur Und Genetischer Konstitution F�r Die Mutabilit�t Von Bakteriophagen

The relation between mutation rate and the environmental temperature was studied for theh (host range) locus of the bacteriophages T 2r and T 7. No significant difference in mutation rate occurred between 19° C and 36° C.

Spontaneous Mutation at the R Locus in Maize. II. Race Differences in Mutation Rate

1. The frequency of seed-color mutation differs widely in different races. The highest rate found was 18.2 x 10-4 in an inbred race designated "Cornell stock." Other stocks gave lower rates, including several with no mutations in populations of 10,000 to 20,000 tested gametes. 2. Plant-color mutation rates, determined on a smaller scale, also vary rather widely. There appears to be no correlation between frequency of plant-color mutation and frequency of seed-color mutation in the same alleles. 3. Differences in seed-color mutation frequency are due in part to intrinsic differences in mutability of the various R alleles. R alleles which yield seed-color mutants distinguishable by their plant-color effects may be compared in mutation rate under strictly comparable conditions in heterozygotes. In these trials significant differences in mutation rate for the two alleles compared are found in some cases. 4. Seed-color mutations in such heterozygotes marked also at the g locus (proximal to R at about 14 cross-over units) are not associated with crossing over in the R-g segment. Among the 14 rr and rg mutants tested, only two showed crossing over in this segment. 5. Differences in mutation rate between different races are also due in large part to the effects of modifying factors. In F1 hybrids produced by crossing the Cornell stock with various other stocks, the Rr: Cornell gametes of the F1 commonly yield mutations at a rate much lower than that found in the Cornell stock. 6. Homozygous Rr: Cornell derivatives of lowered mutation frequency are readily extracted from crosses of the Cornell stock with strains carrying distinguishable R alleles. Among extracted stocks of various Rr alleles, Rr: Cornell stocks are not outstanding in mutation frequency. 7. The varying modifier genotypes occurring in different homozygous Rr: Cornell extractions also sharply modify plant-color mutation rate, apparently independently of their effect upon seed-color mutation rate.