A Method for Estimating Penetrance of Pathogenic Mutations in a Mitochondrial Genome

Variation in the age of onset is typical of many mitochondrial diseases. The estimation of penetrance of deleterious mtDNA mutations causing such diseases is usually conducted on samples of individuals whose age exceeds the maximum age of the disease manifestation. In the case of rare diseases, samples of sufficient size sometimes cannot be formed. In this study, we propose a method for estimating penetrance involving individuals of any age. The efficiency of the method is demonstrated using Leber hereditary optic neuropathy as an example. It is shown that the method provides an unbiased estimate of penetrance and considerably reduces the error of this estimate in comparison with a sample including individuals whose age exceeds the maximum age of disease manifestation.     

<Emphasis Type="Italic">HTT</Emphasis> Gene Premutation Allele Frequencies in the Russian Federation

Huntington disease (Huntington chorea, HD) is a severe neurodegenerative disease determined by polyglutamine. Polyglutamine expansion in exon 1 of the HTT gene causes Huntington disease. To date, less than 35 CAG triplets are suggested to be present in normal alleles. Alleles bearing from 27 to 35 CAG repeats are generally considered as intermediate or premutation. Alleles with the number of CAG repeats varying from 36 to 39 demonstrate reduced penetrance and result in late manifestation of the disease. To date, no studies based on representative samples of Russian residents estimating the frequencies of premutation and alleles with reduced penetrance have been published. Meanwhile, this is extremely important for genetic counseling of patients bearing such alleles and for the calculation of risks for their offspring. In the present study, the analysis of samples of Russian patients with incoming diagnoses of Huntington chorea (N = 1092), Wilson–Konovalov disease (N = 333), Hallervorden–Spatz disease (N = 33) and a control group consisting of 230 unexamined individuals from the Russian Federation under 45 years of age was carried out. A spectrum of CAG repeat length in the HTT gene in patients with HD was obtained. Patients with HD were detected in the samples of patients with incoming diagnoses of Wilson–Konovalov disease and Hallervorden–Spatz disease. This observation indicates the complexity of differential diagnosis of these diseases. An assumption was made that an allele with 36 CAG repeats should be classified as premutation. We confirmed the previously observed trend for the increased number of CAG repeats in the case of paternal transmission of the mutant allele. The frequency of premutation allele of 2.6% in Russian residents was established.     

Multipoint linkage analysis using sib pairs: an interval mapping approach for dichotomous outcomes.

I propose an interval mapping approach suitable for a dichotomous outcome, with emphasis on samples of affected sib pairs. The method computes a lod score for each of a set of locations in the interval between two flanking markers and takes as its estimate of trait-locus location the maximum lod score in the interval, provided it exceeds the prespecified critical value. Use of the method depends on prior knowledge of the genetic model for the disease only through available estimates of recurrence risk to relatives of affected individuals. The method gives an unbiased estimate of location, provided the recurrence risk are correctly specified and provided the marker identity-by-descent probabilities are jointly, rather than individually, estimated. I also discuss use of the method for traits determined by two loci and give an approximation that has good power for a wide range of two-locus models.     

The affected sib method. III. Selection and recombination.

The affected sib-pair method has been used to investigate the mode of inheritance, and to estimate the "disease" allele frequency, for a number of HLA-associated diseases. One of the assumptions of the original sib-pair method is that the disease confers no selective disadvantage on affected individuals. This is obviously not the situation for most diseases. We have determined the expected HLA haplotype-sharing distribution among affected sib-pairs when selection against individuals with the disease is taken into account. We have shown that if the mode of inheritance of the selectively disadvantageous disease is recessive or additive, the original affected sib-pair analysis, ignoring selection, still estimates the true mode of inheritance, but usually yields an underestimate of the "disease" allele frequency. For intermediate and dominant models of disease predisposition, both the estimates of the degree of penetrance of the "disease" genotypes, and the "disease" allele frequency, are altered if selection is ignored in the analysis. Similarly, allowing for recombination between the "disease" locus and the HLA region does not affect the determination of the mode of inheritance of the disease if it is recessive or additive; in other cases, however, the estimate of the mode of inheritance is affected. The "disease" allele frequency is overestimated when nonzero recombination is ignored for all the modes of inheritance that have been studied.     

A new susceptibility locus for autosomal dominant pancreatic cancer maps to chromosome 4q32-34

Pancreatic cancer is the fifth leading cause of cancer death in the United States. Nearly every person diagnosed with pancreatic cancer will die from it, usually in <6 mo. Familial clustering of pancreatic cancers is commonly recognized, with an autosomal dominant inheritance pattern in approximately 10% of all cases. However, the late age at disease onset and rapid demise of affected individuals markedly hamper collection of biological samples. We report a genetic linkage scan of family X with an autosomal dominant pancreatic cancer with early onset and high penetrance. For the study of this family, we have developed an endoscopic surveillance program that allows the early detection of cancer and its precursor, before family members have died of the disease. In a genomewide screening of 373 microsatellite markers, we found significant linkage (maximum LOD score 4.56 in two-point analysis and 5.36 in three-point analysis) on chromosome 4q32-34, providing evidence for a major locus for pancreatic cancer.     

Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease

Some individuals with a particular disease-causing mutation or genotype fail to express most if not all features of the disease in question, a phenomenon that is known as ‘reduced (or incomplete) penetrance’. Reduced penetrance is not uncommon; indeed, there are many known examples of ‘disease-causing mutations’ that fail to cause disease in at least a proportion of the individuals who carry them. Reduced penetrance may therefore explain not only why genetic diseases are occasionally transmitted through unaffected parents, but also why healthy individuals can harbour quite large numbers of potentially disadvantageous variants in their genomes without suffering any obvious ill effects. Reduced penetrance can be a function of the specific mutation(s) involved or of allele dosage. It may also result from differential allelic expression, copy number variation or the modulating influence of additional genetic variants in cis or in trans. The penetrance of some pathogenic genotypes is known to be age- and/or sex-dependent. Variable penetrance may also reflect the action of unlinked modifier genes, epigenetic changes or environmental factors. At least in some cases, complete penetrance appears to require the presence of one or more genetic variants at other loci. In this review, we summarize the evidence for reduced penetrance being a widespread phenomenon in human genetics and explore some of the molecular mechanisms that may help to explain this enigmatic characteristic of human inherited disease.     

Linkage study of a large family with autosomal dominant polycystic kidney disease with reduced expression

Summary We describe a large three generation family with autosomal dominant polycystic kidney disease (PKD). Ultrasonographic screening of 60 family members revealed 20 individuals, whose age ranged from ten to eighty years, with one or several cysts in only one kidney and 7 individuals with cysts in both kidneys. Transmission of unilateral cysts seems to be autosomal dominant, although there are some generation gaps. Linkage studies with several markers of the PKD1 locus on the short arm of chromosome 16 showed no linkage with the disease. Lod scores for linkage between the disease and the most informative marker 3HVR were computed using different penetrance models and several hypotheses concerning the clinical status of individuals with unilateral renal cysts. Results varied from Z = 1.31 to Z =-21.47 ( = 0). Smith's test of heterogeneity gave a conditional probability of non-linkage between 0.9 and 1.0. We conclude that this family presents a form of autosomal dominant PKD with reduced penetrance and no linkage to the PKD1 locus on the short arm of chromosome 16. Other hypotheses, such as the existence of two distinct hereditary diseases in this large family, or neomutation in one branch of the family associated with a high frequency of isolated renal cysts, are also considered.     

Genetic linkage analysis in familial breast and ovarian cancer: results from 214 families. The Breast Cancer Linkage Consortium.

Breast cancer is known to have an inherited component, consistent in some families with autosomal dominant inheritance; in such families the disease often occurs in association with ovarian cancer. Previous genetic linkage studies have established that in some such families disease occurrence is linked to markers on chromosome 17q. This paper reports the results of a collaborative linkage study involving 214 breast cancer families, including 57 breast-ovarian cancer families; this represents almost all the known families with 17q linkage data. Six markers on 17q, spanning approximately 30 cM, were typed in the families. The aims of the study were to define more precisely the localization of the disease gene, the extent of genetic heterogeneity and the characteristics of linked families and to estimate the penetrance of the 17q gene. Under the assumption of no genetic heterogeneity, the strongest linkage evidence was obtained with D17S588 (maximum LOD score [Zmax] = 21.68 at female recombination fraction [theta f] = .13) and D17S579 (Zmax = 13.02 at theta f = .16). Multipoint linkage analysis allowing for genetic heterogeneity provided evidence that the predisposing gene lies between the markers D17S588 and D17S250, an interval whose genetic length is estimated to be 8.3 cM in males and 18.0 cM in females. This position was supported over other intervals by odds of 66:1. The location of the gene with respect to D17S579 could not be determined unequivocally. Under the genetic model used in the analysis, the best estimate of the proportion of linked breast-ovarian cancer families was 1.0 (lower LOD-1 limit 0.79). In contrast, there was significant evidence of genetic heterogeneity among the families without ovarian cancer, with an estimated 45% being linked. These results suggest that a gene(s) on chromosome 17q accounts for the majority of families in which both early-onset breast cancer and ovarian cancer occur but that other genes predisposing to breast cancer exist. By examining the fit of the linkage data to different penetrance functions, the cumulative risk associated with the 17q gene was estimated to be 59% by age 50 years and 82% by age 70 years. The corresponding estimates for the breast-ovary families were 67% and 76%, and those for the families without ovarian cancer were 49% and 90%; these penetrance functions did not differ significantly from one another.     

Clinical penetrance of C282Y homozygous HFE haemochromatosis

The prevalence of the C282Y homozygous HFE genotype is high, approximately 1 in 200 in populations of Anglo-Celtic descent, and most authorities assumed this mutation would have a high clinical penetrance. Recent studies report the clinical penetrance of C282Y homozygous hereditary haemochromatosis is much lower than its prevalence, with possibly less than 5% developing clinical disease, although there is lack of consensus on a precise estimate. This review discusses reasons for this paradigm shift, including controversy on various definitions of clinical penetrance.It is inescapable that there are pronounced variations in clinical penetrance, and that certain C282Y homozygous individuals will not develop the clinical phenotype. This has prompted a search for modifier gene mutations amongst iron-metabolism genes, especially the known non- HFE haemochromatosis genes, and for possible environmental factors which might explain the observed variation in clinical penetrance.     

Effects of misspecifying genetic parameters in lod score analysis

The lod score method is widely used to test linkage and to estimate the recombination fraction between a disease locus and a marker locus. The parameters (gene frequency, penetrance, and degree of dominance) are assumed to be known at each locus. This condition may not be fulfilled at the disease locus. In this paper, we evaluate the errors due to the use of wrong parameters. The power of the linkage test is sensitive to the degree of dominance, and slightly to the penetrance, but not to the gene frequency. In contrast, the estimation of the recombination fraction may be strongly affected by an error on any genetic parameter.     

A Novel Statistical Model to Estimate Host Genetic Effects Affecting Disease Transmission

There is increasing recognition that genetic diversity can affect the spread of diseases, potentially affecting plant and livestock disease control as well as the emergence of human disease outbreaks. Nevertheless, even though computational tools can guide the control of infectious diseases, few epidemiological models can simultaneously accommodate the inherent individual heterogeneity in multiple infectious disease traits influencing disease transmission, such as the frequently modeled propensity to become infected and infectivity, which describes the host ability to transmit the infection to susceptible individuals. Furthermore, current quantitative genetic models fail to fully capture the heritable variation in host infectivity, mainly because they cannot accommodate the nonlinear infection dynamics underlying epidemiological data. We present in this article a novel statistical model and an inference method to estimate genetic parameters associated with both host susceptibility and infectivity. Our methodology combines quantitative genetic models of social interactions with stochastic processes to model the random, nonlinear, and dynamic nature of infections and uses adaptive Bayesian computational techniques to estimate the model parameters. Results using simulated epidemic data show that our model can accurately estimate heritabilities and genetic risks not only of susceptibility but also of infectivity, therefore exploring a trait whose heritable variation is currently ignored in disease genetics and can greatly influence the spread of infectious diseases. Our proposed methodology offers potential impacts in areas such as livestock disease control through selective breeding and also in predicting and controlling the emergence of disease outbreaks in human populations.     

MLEP: an R package for exploring the maximum likelihood estimates of penetrance parameters

ABSTRACT: BACKGROUND: Linkage analysis is a useful tool for detecting genetic variants that regulate a trait of interest, especially genes associated with a given disease. Although penetrance parameters play an important role in determining gene location, they are assigned arbitrary values according to the researcher's intuition or as estimated by the maximum likelihood principle. Several methods exist by which to evaluate the maximum likelihood estimates of penetrance, although not all of these are supported by software packages and some are biased by marker genotype information, even when disease development is due solely to the genotype of a single allele. FINDINGS: Programs for exploring the maximum likelihood estimates of penetrance parameters were developed using the R statistical programming language supplemented by external C functions. The software returns a vector of polynomial coefficients of penetrance parameters, representing the likelihood of pedigree data. From the likelihood polynomial supplied by the proposed method, the likelihood value and its gradient can be precisely computed. To reduce the effect of the supplied dataset on the likelihood function, feasible parameter constraints can be introduced into maximum likelihood estimates, thus enabling flexible exploration of the penetrance estimates. An auxiliary program generates a perspective plot allowing visual validation of the model's convergence. The functions are collectively available as the MLEP R package. CONCLUSIONS: Linkage analysis using penetrance parameters estimated by the MLEP package enables feasible localization of a disease locus. This is shown through a simulation study and by demonstrating how the package is used to explore maximum likelihood estimates. Although the input dataset tends to bias the likelihood estimates, the method yields accurate results superior to the analysis using intuitive penetrance values for disease with low allele frequencies. MLEP is part of the Comprehensive R Archive Network and is freely available at http://cran.r-project.org/web/packages/MLEP/index.html.     

An immune defect causing dominant chronic mucocutaneous candidiasis and thyroid disease maps to chromosome 2p in a single family

We describe a large family in which a combination of chronic mucocutaneous candidiasis (fungal infections of the skin, nails, and mucous membranes) and thyroid disease segregate as an autosomal dominant trait with reduced penetrance. The family includes (a) four members with both candidiasis and thyroid disease, (b) five members, including one pair of phenotype-concordant MZ twins, with candidiasis only, and (c) three members with thyroid disease only. A whole-genome scan using DNA samples from 20 members of the family identified a candidate linkage region on chromosome 2p. By sampling additional individuals and genotyping supplementary markers, we established linkage to a region of approximately 15 cM bounded by D2S367 and D2S2240 and including seven adjacent markers consistent with linkage. With a penetrance estimate of.8, which was based on pedigree and affected status, the peak two-point LOD score was 3.70 with marker D2S2328, and the peak three-point LOD score was 3.82. This is the first linkage assignment of a dominant locus for mucocutaneous candidiasis.     

Risks of manifestation of Huntington chorea.

A methodology allowing the estimate of risks heterozygosity and manifestation of Huntington's chorea (HC) within preestablished periods for individuals of any age was developed. For this, the procedure was the following: 1. The variables which could influence the distribution of age frequencies were studied. 2. The error due to the exclusion of the heterozygotes dying before the manifestation of the disease from the distribution of Wendt et al. (1959) of affected persons was corrected separately for each sex. 3. The frequency of non-affected heterozygotes in each age group was calculated separately for each sex, from the corrected distribution. From those data estimates of the following parameters could be reached: a) the probability of heterozygosity for consultants of any age; b) the risks of manifestation for the gene in a given individual within a determined period, taking into account his probability of heterozygosity and survival. 4. The risks of manifestation were tabulated for making easier their use in concrete cases. Simplified tables with approximate risks are also presented for the more common cases in genetic counseling. 5. The methodology presented allows a discrimination between the probability of heterozygostiy and the risk of manifestation. This makes possible the estimate of risks of becoming affected, taking into account not only the age of the consultant at the moment, but also the period of time starting with the consultation, to which the risk applies. This is essential for adequate genetic counseling.     

Effect of Some Honeybee Diseases on Seasonal Mortality of <Emphasis Type="Italic">Apis mellifera intermissa</Emphasis> in Algeria Apiaries

With a view to identify the pathogens and to establish the role of these pathogens in regulation of the density of honey bee population occurring in the apiaries of the area concerned samples of honeybee were collected from the beekeepers in some parts of central Algeria It is revealed that Nosema sp., Varroa destrutor, Peanibacillus larvae are associated with the disease manifestation in honey bees. The presence of Nosema sp., Varroa destrutor, Peanibacillus larvae was analyzed using standard OIE methods. Spores of Paenibacillus larvae were detected in 56.6 % in winter 52.32 % in spring. 29.33 % in autumn and 11.25 % in summer. Nosema infestation was recorded in 47.91 % bee individuals during spring. Varroa infestation rate was maximum 12.57 % in summer and lowest 3.44 % in spring. Analysis of data indicates that Boumerdes and Tipaza, diseases induced mortality exceeds 10 % in honeybee. There exists a significant correlation between Nosema disease and mortalities in honeybees. Seasons play significant role, irrespective of pathogens, in disease manifestation.     

Body mass prediction from stature and bi-iliac breadth in two high latitude populations, with application to earlier higher latitude humans

Previous studies have indicated that body mass can be estimated from stature and bi-iliac (maximum pelvic) breadth with reasonable accuracy in modern humans, supporting the use of this method to estimate body mass in earlier human skeletal samples. However, to date the method has not been tested specifically on high latitude individuals, whose body form in some ways more closely approximates that of earlier higher latitude humans (i.e., large and broad-bodied). In this study, anthropometric data for 67 Alaskan Inupiat and 54 Finnish adults were used to test the stature/bi-iliac body mass estimation method. Both samples are very broad-bodied, and the Finnish sample is very tall as well. The method generally works well in these individuals, with average directional biases in body mass estimates of 3% or less, except in male Finns, whose body masses are systematically underestimated by an average of almost 9%. A majority of individuals in the total pooled sample have estimates to within +/-10% of their true body masses, and more than three-quarters have estimates to within +/-15%. The major factor found to affect directional bias is shoulder to hip breadth (biacromial/bi-iliac breadth). Male Finns have particularly wide shoulders, which may in part explain their systematic underestimation. New body mass estimation equations are developed that include the new data from this study. When applied to a sample of earlier (late middle Pleistocene to early Upper Paleolithic) higher latitude skeletal specimens, differences between previous and new body estimates are small (less than 2%). However, because the Finns significantly extend the range of morphological variation beyond that represented in the original world-wide reference sample used in developing the method, thereby increasing its generality, it is recommended that these new formulas be used in subsequent body mass estimations.     

Polymorphisms of pro-inflammatory genes and prostate cancer risk: a pharmacogenomic approach

In this paper, we consider the role of the genetics of inflammation in the pathophysiology of prostate cancer (PCa). This paper is not an extensive review of the literature, rather it is an expert opinion based on data from authors’ laboratories on age-related diseases and inflammation. The aim is the detection of a risk profile that potentially allows both the early identification of individuals at risk for disease and the possible discovery of potential targets for medication. In fact, a major goal of clinical research is to improve early detection of age-related diseases, cancer included, by developing tools to move diagnosis backward in disease temporal course, i.e., before the clinical manifestation of the malady, where treatment might play a decisive role in preventing or significantly retarding the manifestation of the disease. The better understanding of the function and the regulation of inflammatory pathway in PCa may help to know the mechanisms of its formation and progression, as well as to identify new targets for the refinement of new treatment such as the pharmacogenomics approach.     

Determining the linkage of disease-resistance genes to molecular markers: the LOD-SCORE method revisited with regard to necessary sample sizes

Some approaches to molecular marker-assisted linkage detection for a dominant disease-resistance trait based on a segregating F₂ population are discussed. Analysis of two-point linkage is carried out by the traditional measure of maximum lod score. It depends on (1) the maximum-likelihood estimate of the recombination fraction between the marker and the disease-resistance gene locus, (2) the observed absolute frequencies, and (3) the unknown number of tested individuals. If one replaces the absolute frequencies by expressions depending on the unknown sample size and the maximum-likelihood estimate of recombination value, the conventional rule for significant linkage (maximum lod score exceeds a given linkage threshold) can be resolved for the sample size. For each sub-population used for linkage analysis [susceptible (= recessive) individuals, resistant (= dominant) individuals, complete F₂] this approach gives a lower bound for the necessary number of individuals required for the detection of significant two-point linkage by the lod-score method.     

Inter- and intrafamilial heterogeneity: effective sampling strategies and comparison of analysis methods.

Heterogeneity, both inter- and intrafamilial, represents a serious problem in linkage studies of common complex diseases. In this study we simulated different scenarios with families who phenotypically have identical diseases but who genotypically have two different forms of the disease (both forms genetic). We examined the proportion of families displaying intrafamilial heterogeneity, as a function of mode of inheritance, gene frequency, penetrance, and sampling strategies. Furthermore, we compared two different ways of analyzing linkage in these data sets: a two-locus (2L) analysis versus a one-locus (SL) analysis combined with an admixture test. Data were simulated with tight linkage between one disease locus and a marker locus; the other disease locus was not linked to a marker. Our findings are as follows: (1) In contrast to what has been proposed elsewhere to minimize heterogeneity, sampling only "high-density" pedigrees will increase the proportion of families with intrafamilial heterogeneity, especially when the two forms are relatively close in frequency. (2) When one form is dominant and one is recessive, this sampling strategy will greatly decrease the proportions of families with a recessive form and may therefore make it more difficult to detect linkage to the recessive form. (3) An SL analysis combined with an admixture test achieves about the same lod scores and estimate of the recombination fraction as does a 2L analysis. Also, a 2L analysis of a sample of families with intrafamilial heterogeneity does not perform significantly better than an SL analysis. (4) Bilineal pedigrees have little effect on the mean maximum lod score and mean maximum recombination fraction, and therefore there is little danger that including these families will lead to a false exclusion of linkage.     

Non-parametric estimation of the age-at-onset distribution from a cross-sectional sample

We propose and study a simple and innovative non-parametric approach to estimate the age-of-onset distribution for a disease from a cross-sectional sample of the population that includes individuals with prevalent disease. First, we estimate the joint distribution of two event times, the age of disease onset and the survival time after disease onset. We accommodate that individuals had to be alive at the time of the study by conditioning on their survival until the age at sampling. We propose a computationally efficient expectation–maximization (EM) algorithm and derive the asymptotic properties of the resulting estimates. From these joint probabilities we then obtain non-parametric estimates of the age-at-onset distribution by marginalizing over the survival time after disease onset to death. The method accommodates categorical covariates and can be used to obtain unbiased estimates of the covariate distribution in the source population. We show in simulations that our method performs well in finite samples even under large amounts of truncation for prevalent cases. We apply the proposed method to data from female participants in the Washington Ashkenazi Study to estimate the age-at-onset distribution of breast cancer associated with carrying BRCA1 or BRCA2 mutations.