Germinal mosaicism and risk calculation in X-linked diseases.

Germinal mosaicism is a major problem in risk estimation for an X-linked disease. A mutation can happen anytime in germ cell development, and the proportion of germ cells bearing the mutated gene is twice the probability of recurrence of the mutation. This proportion could be either very low in late mutations or very high in germinal and somatic mosaicism. When this heterogeneity is taken into consideration, the distribution of the recurrence risk is conveniently represented as a set of discrete classes that may be derived either from models of gametogenesis or from empirical data. A computer program taking into account germinal mosaicism has been devised to calculate the probability of a possible carrier belonging to any of these classes, in order to settle the origin of the mutation of a given family. Germinal mosaicism increases the probability of inheriting the mutation, but this effect is always lowered by the possibility of heterogeneity. When the mother of a possible carrier is not herself a carrier, the risk of her daughter being a carrier is approximately halved, even under the assumption of a high recurrence risk from mosaicism.     

Mutation carrier testing in Lesch-Nyhan syndrome families: HPRT mutant frequency and mutation analysis with peripheral blood T lymphocytes

Mutations in the X chromosome hypoxanthine-guanine phosphoribosyl transferase (HPRT) gene are responsible for Lesch-Nyhan syndrome and related diseases in humans. Because the gene is on the X chromosome, males are affected and females in the families are at risk of being carriers of the mutation. Because there are so many different mutations that can cause the disease (218 different mutations in 271 families), genetic testing for carrier status of females requires detailed molecular analysis of the familial mutation. This analysis can be complicated by the unavailability of an affected male for study. In addition, when the mutation is a deletion (34 reported instances), molecular analysis in females is difficult because of the two X chromosomes. We have applied a peripheral blood T lymphocyte cloning assay that uses resistance to the purine analogue 6-thioguanine (TG) to measure the frequency of cells in females expressing a mutant HPRT allele to determine mutation carrier status in 123 females in 61 families. In families in which the HPRT mutation was determined and could be easily analyzed in samples from females, we found a mean (+/- SD) mutant frequency of 9.7 (+/- 8.7) x 10(-6) in noncarrier females and 2.9 (+/- 3.0) x 10(-2) in carrier females. The frequency in carrier females is less than the 0.5 expected for nonrandom X inactivation because of in vivo selection against HPRT mutation-expressing T lymphocytes or stem cells during prenatal development. The use of this cloning assay allows determination of the carrier status of females even when the HPRT mutation is not yet known or is difficult to determine in DNA samples from females. This approach provides a rapid assay that yields information on carrier status within 10 days of sample receipt.     

Mutation in the Human HPRT1 Gene and the Lesch-Nyhan Syndrome

Lesch-Nyhan syndrome (LNS) is a rare X-linked inherited neurogenetic disorder of purine metabolism in which the enzyme, hypoxanthine-guanine phosphoribosyltransferase (HGprt) is defective. The authors report a novel mutation which led to HGprt-related neurological dysfunction (HND) in two brothers from the same family with a missense mutation in exon 6 of the coding region of the HPRT1 gene: c.437T>C, p.L146S. Molecular diagnosis discloses the genetic heterogeneity of the HPRT1 gene responsible for HGprt deficiency. It allows fast, accurate carrier detection and genetic counseling.     

High-Resolution Multipoint Linkage-Disequilibrium Mapping in the Context of a Human Genome Sequence

A new method is presented for fine-scale linkage disequilibrium (LD) mapping of a disease mutation; it uses multiple linked single-nucleotide polymorphisms, restriction-fragment-length polymorphisms, or microsatellite markers and incorporates information from an annotated human genome sequence (HGS) and from a human mutation database. The method takes account of population demographic effects, using Markov chain Monte Carlo methods to integrate over the unknown gene genealogy and gene coalescence times. Information about the relative frequency of disease mutations in exons, introns, and other regions, from mutational databases, as well as assumptions about the completeness of the gene annotation, are used with an annotated HGS, to generate a prior probability that a mutation lies at any particular position in a specified region of the genome. This information is updated with information about mutation location, from LD at a set of linked markers in the region, to generate the posterior probability density of the mutation location. The performance of the method is evaluated by simulation and by analysis of a data set for diastrophic dysplasia (DTD) in Finland. The DTD disease gene has been positionally cloned, so the actual location of the mutation is known and can be compared with the position predicted by our method. For the DTD data, the addition of information from an HGS results in disease-gene localization at a resolution that is much higher than that which would be possible by LD mapping alone. In this case, the gene would be found by sequencing a region < or =7 kb in size.     

Genetik und Klinik der Hämophilie A und B

Haemophilia A and B are caused by various mutations in the factor VIII (FVIII) and factor IX (FIX) genes, respectively. The clinical course of the disease is variable, dependent on the severity of the molecular defect. Nowadays, haemophilia patients can excellently be treated by plasma-derived or recombinant clotting factor concentrates. Thus, bleeding and its consequences can be almost completely prevented with nearly normal quality of life and life expectancy. The most severe complication of this treatment is the formation of antibodies (inhibitors) against the substituted clotting factor. The risk of inhibitor formation correlates significantly with specific mutation types that preclude endogenous factor VIII/IX protein synthesis and can be as high as 20–50%. The information on the expected clinical course is at present the most important indication for FVIII/IX gene analysis. Knowledge of the underlying FVIII/IX gene mutation further allows a reliable and fast carrier diagnosis in female relatives of patients with haemophilia.     

Angiotensinogen gene M235T variant and pre-eclampsia in Romanian pregnant women

Background. Association between the human angiotensinogen gene and essential hypertension has been confirmed in recent studies. Pre-eclampsia is a complication of pregnancy characterised by increased vascular resistance, high blood pressure, proteinuria and oedema, that appears in the second and third trimester of pregnancy. The aim of our study was the analysis of M235T mutation in the gene encoding angiotensinogen in Romanian women with different forms of hypertension during pregnancy. Methods. Fourteen women with obstetric complications were tested for M235T angiotensinogen gene mutation. Indications for testing were: severe or mild pre-eclampsia and pre-eclampsia associated with chronic hypertension. We also tested for control 6 healthy women. The M235T angiotensinogen gene mutation was analysed by polymerase chain reaction followed by enzymatic digestion with Tth 111I restriction endonuclease enzyme and agarose gel electrophoresis of the products. Results. Eleven (78.57%) of the 14 women with complications of pregnancy had M235T mutation: 9 (64.28%) were found to be heterozygous carriers of the M235T variant of the angiotensinogen gene and 2(14.28%) were found to be homozygous carriers. In the group of women with normal pregnancy, 3 (50%) of the 6 women had M235T mutation: 2 (33.33%) were found to be heterozygous carriers of the M235T variant of the angiotensinogen gene and 1 (16.66%) was found to be homozygous carrier. Conclusions. Our study shows that the M235T variant in the gene encoding angiotensinogen could be a risk factor in mild and severe pre-eclampsia.     

Sex-specific mutation rates for x-linked disorders: estimation and application

Emerging human molecular data are adding to our knowledge about the frequency and pattern of genetic mutations. This not only gives important insight into the biological processes underlying mutation, but also provides data which must be incorporated in the clinical setting. An example is the assumption of equal mutation probability in the male and female germ lines. This is a key assumption in Bayesian risk calculation for families segregating an X-linked recessive disorder. For some disorders, data are now available that demonstrate that the mutation probability in males differs from that in females. In this paper, we review the estimation of the male-female mutation rate ratio, including the construction of confidence intervals, and apply sex-specific mutation rates to carrier risk calculation in a variety of pedigree structures. In several instances, the difference in risk is substantial.     

Novel mutation in the human HPRT1 gene and the Lesch-Nyhan disease

Lesch-Nyhan disease (LND) is a rare X-linked inherited neurogenetic disorder of purine metabolism in which the enzyme, hypoxanthine-guanine phosphoribosyltransferase (HGprt) is defective. The authors report a novel point mutation that led to HGprt-related neurological dysfunction (HND) in a family in which there was a missense mutation in exon 6 of the coding region of the HPRT1 gene: g.34938G>T, c.403G>T, p.D135Y. Molecular diagnosis is consistent with the genetic heterogeneity of the HPRT1 gene responsible for HGprt deficiency. It allows fast, accurate carrier detection and genetic counseling.     

Lesch–Nyhan Syndrome in a Family with a Deletion Followed by an Insertion within the HPRT1 Gene

Lesch–Nyhan syndrome (LNS) is a rare X-linked inherited neurogenetic disorder of purine metabolism in which the enzyme, hypoxanthine-guanine phosphoribosyltransferase(HGprt) is defective. The authors report a novel mutation which led to LNS in a family with a deletion followed by an insertion (INDELS) via the serial replication slippage mechanism: c.428_432delTGCAGinsAGCAAA, p.Met143Lysfs*12 in exon 6 of HPRT1 gene. Molecular diagnosis discloses the genetic heterogeneity of HPRT1 gene responsible for HGprt deficiency. It allows fast, accurate carrier detection and genetic counseling.     

Preferential mutation of the neurofibromatosis type 1 gene in paternally derived chromosomes

Summary An interesting feature of neurofibromatosis type 1 (NF1) is its high mutation rate of 1×10^–4 per gamete per generation. The molecular basis for frequent NF1 mutation in unknown; the gene is not deletion prone. We have found that in all ten families examined, the apparent new NF1 mutation occurred on the paternally-derived chromosome. The probability of observing this result by chance is less than 0.001 assuming an equal frequency of mutation of paternal and maternal NF1 genes. We hypothesize a role for genomic imprinting that may either enhance mutation of the paternal NF1 gene or confer protection from mutation to the maternal NF1 gene.     

Prevalence of ΔF508 cystic fibrosis carriers in The Netherlands: logistic regression on sex,age, region of residence and number of offspring

An average cystic fibrosis (CF) carrier frequency of 1 in 25 in Europe is cited in numerous reports, although a great variability in estimated prevalences has been found in different European populations. The estimates of these frequencies were based on numbers of CF patients before identification of the gene in 1989. Here we report the results of a study to determine the carrier frequency of the ΔF508 mutation in The Netherlands by analyzing mouthwashes and matched blood samples from 11 654 blood donors all over the country. We analyzed possible relationships between a number of theoretically explanatory variables and the ΔF508 carrier frequency by means of univariate and multivariate logistic regression. These variables were: distance of the blood banks from the northeastern part of the country (distance); whether the blood donors knew that we were looking for a CF mutation; sex and age of the donor; and number of children of the donor (family size). We detected a ΔF508 carrier frequency of 1 in 42 (95% CI 1/37–1/47) in The Netherlands. If we assume that the relative frequency of the ΔF508 mutation among carriers and patients is comparable in The Netherlands, this gives an estimated overall CF carrier frequency of 1 in 32 (95% CI 1/28–1/36), significantly less than 1 in 25. The univariate logistic regression analysis of the effects of the explanatory variables on the carrier frequency revealed no significant relationships, except for an increase in carrier frequency with increasing distance from the northeastern region. In the multivariate analysis with all five independent variables, distance, age and family size were significantly related to the carrier frequency, but sex and CF information were not. There was a significant interaction between age and family size. In our final model, distance, age and family size were positively related to the carrier frequency, while the interaction of age with family size showed a negative relation. These results confirm that there is a gradient in gene frequency with low frequencies in the northeastern part of the country and high frequencies in the southern part. They also suggest a relation of age and family size with carrier frequency. This relation, however, is too complex to be explained by heterozygote advantage. Received: 10 May 1996     

HotSpotter: efficient visualization of driver mutations

Background

Driver mutations are positively selected during the evolution of cancers. The relative frequency of a particular mutation within a gene is typically used as a criterion for identifying a driver mutation. However, driver mutations may occur with relative infrequency at a particular site, but cluster within a region of the gene. When analyzing across different cancers, particular mutation sites or mutations within a particular region of the gene may be of relatively low frequency in some cancers, but still provide selective growth advantage.

Results

This paper presents a method that allows rapid and easy visualization of mutation data sets and identification of potential gene mutation hotspot sites and/or regions. As an example, we identified hotspot regions in the NFE2L2 gene that are potentially functionally relevant in endometrial cancer, but would be missed using other analyses.

Conclusions

HotSpotter is a quick, easy-to-use visualization tool that delivers gene identities with associated mutation locations and frequencies overlaid upon a large cancer mutation reference set. This allows the user to identify potential driver mutations that are less frequent in a cancer or are localized in a hotspot region of relatively infrequent mutations.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1044) contains supplementary material, which is available to authorized users.     

Progeny testing for recessive genes: procedures and interpretations

Summary Methods for calculating the probability of detecting a carrier of a recessive gene by utilizing matings among related individuals are presented for single and litter bearing species. The confidence level for detection of heterozygosity depends upon: (1) the genetic relationship between mates, (2) the number of mates per male and the number of offspring per mate, (3) whether an estimate of recessive gene frequency before selection is available and (4) the magnitude of that frequency. Methods of computing probability of heterozygosity vs homozygosity utilizing Bayes theorem also are presented. In the conventional progeny test method, a sire initially is assumed heterozygous before calculations are made, but no prior information concerning his probable genotype is utilized. In the method using Bayes theorem, prior sources of information from relatives or from estimates of population allele frequency are utilized. This method gives the exact probability that a sire is not a carrier, given prior information and that he produces all normal offspring. These methods could be used in any sexually reproducing species to identify not only detrimental genes but beneficial genes as well.     

Identification and rapid detection of three Tay-Sachs mutations in the Moroccan Jewish population.

Infantile Tay-Sachs disease (TSD) is caused by mutations in the HEXA gene that result in the complete absence of beta-hexosaminidase A activity. It is well known that an elevated frequency of TSD mutations exists among Ashkenazi Jews. More recently it has become apparent that elevated carrier frequencies for TSD also occur in several other ethnic groups, including Moroccan Jews, a subgroup of Sephardic Jews. Elsewhere we reported an in-frame deletion of one of the two adjacent phenylalanine codons at position 304 or 305 (delta F304/305) in one HEXA allele of a Moroccan Jewish TSD patient and in three obligate carriers from six unrelated Moroccan Jewish families. We have now identified two additional mutations within exon 5 of the HEXA gene that account for the remaining TSD alleles in the patient and carriers. One of the mutations is a novel C-to-G transversion, resulting in a replacement of Tyr180 by a stop codon. The other mutation is a G-to-A transition resulting in an Arg170-to-Gln substitution. This mutation is at a CpG site in a Japanese infant with Tay-Sachs disease and was described elsewhere. Analysis of nine obligate carriers from seven unrelated families showed that four harbor the delta F304/305 mutation, two the Arg170----Gln mutation, and one the Tyr180----Stop mutation. We also have developed rapid, nonradioactive assays for the detection of each mutation, which should be helpful for carrier screening.     

Pre-counseling education materials for BRCA testing: does tailoring make a difference?

Although tailored print materials (TPMs) have been assessed for a variety of behavioral targets, their effectiveness as decision aids for genetic testing had not been evaluated at the time this study began. We compared TPMs and non-tailored print material (NPMs) that included similar content about genetic testing for breast and ovarian cancer susceptibility. TPMs were prepared especially for an individual based on information from and about her. We mailed baseline surveys to 461 women referred by physicians or identified through a tumor registry. All had personal and family histories of breast and/or ovarian cancer and, on the basis of these histories, an estimated > or =10% probability of carrying a mutation in the breast/ovarian cancer genes BRCA1 or BRCA2. The 325 (70%) who responded were randomly assigned to receive TPM or NPM. Followup surveys, mailed 2 weeks following receipt of print materials, were returned by 262 women (81% of baseline responders). Participants were predominately white (94%) and well-educated (50% college graduates). The mean age was 49 years. At follow-up, TPM recipients exhibited significantly greater improvement in percent of correct responses for the 13-item true/false measure of knowledge (24% increase for TPM vs. 16% for NPM; p < 0.0001) and significantly less over-estimation of risk of being a mutation carrier (40% TPM group overestimated vs. 70% NPM; p < 0.0001). Anxiety did not differ significantly between groups. Reactions to materials differed on two items: "seemed to be prepared just for me" (76% TPM vs. 52% NPM; p < 0.001) and "told me what I wanted to know about BRCA1 and 2 testing" (98% TPM vs. 91% NPM; p < 0.05). TPMs showed an advantage in increasing knowledge and enhancing accuracy of perceived risk. Both are critical components of informed decision making.     

Human HPRT1 gene and the Lesch–Nyhan disease: Substitution of alanine for glycine and inversely in the HGprt enzyme protein

Lesch–Nyhan disease (LND) is a rare X-linked inherited neurogenetic disorder of purine metabolism in which the enzyme, hypoxanthine-guanine phosphoribosyltransferase (HGprt) is defective. The authors report three novel independent mutations in the coding region of the HPRT1 gene from genomic DNA of (a) a carrier sister of two male patients with LND: c.569G>C, p.G190A in exon 8; and (b) two LND affected male patients unrelated to her who had two mutations: c.648delC, p.Y216X, and c.653C>G, p.A218G in exon 9. Molecular analysis reveals the heterogeneity of genetic mutation of the HPRT1 gene responsible for the HGprt deficiency. It allows fast, accurate detection of carriers and genetic counseling.     

Fixation probability favors increased fecundity over reduced generation time

The cornerstone of population genetics is a probabilistic understanding of the ultimate fate--survival or extinction--of rare mutations. If a mutation is beneficial, it enables its carrier to reproduce faster than native wild-type individuals. In classic derivations and in the considerable body of research that has followed, "faster" has been defined mathematically to mean "able to produce more surviving offspring per generation." Many organisms, however, may increase their reproductive rate by producing the same number of offspring in a shorter generation time: a mutant bacterium, for example, may complete the cell cycle and produce two offspring more quickly than the wild type. We find that the ultimate fixation probability of a mutation conferring a shorter generation time differs from that of a mutation conferring more offspring by a factor of 2 ln(2)-nearly 40%. This predicts a reduction in the overall substitution rate for any mutation that decreases the generation time: fixation probability is biased toward increased offspring number.     

Presymptomatic detection or exclusion of prion protein gene defects in families with inherited prion diseases.

The identification of defects in the prion protein (PrP) gene in families with inherited Creutzfeldt-Jakob disease or Gerstmann-Straussler syndrome allows presymptomatic diagnosis or exclusion of these disorders in subjects at risk. After counseling, PrP gene analysis was performed in three such individuals: two from families with a 144-bp insert and one with a point mutation at codon 102 in the PrP gene. The presence of a PrP gene defect was confirmed in one and excluded in two. Despite the potential problems of using PrP gene analysis in genetic prediction - specifically, uncertainty about penetrance and, generally, problems of presymptomatic testing in any inherited late-onset neurodegenerative disorder - we conclude that it has a role to play in improved genetic counseling for families with inherited prion diseases.