Correction For Ascertainment Bias Research Articles

Lifestyle Factors and Breast Cancer in Females with PTEN Hamartoma Tumor Syndrome (PHTS).

Females with PTEN Hamartoma Tumor Syndrome (PHTS) have breast cancer risks up to 76%. This study assessed associations between breast cancer and lifestyle in European female adult PHTS patients. Data were collected via patient questionnaires (July 2020-March 2023) and genetic diagnoses from medical files. Associations between lifestyle and breast cancer were calculated using logistic regression corrected for age. Index patients with breast cancer before PHTS diagnosis (breast cancer index) were excluded for ascertainment bias correction. In total, 125 patients were included who completed the questionnaire at a mean age of 44 years (SD = 13). This included 21 breast cancer indexes (17%) and 39 females who developed breast cancer at 43 years (SD = 9). Breast cancer patients performed about 1.1 times less often 0-1 times/week physical activity than ≥2 times (ORtotal-adj = 0.9 (95%CI 0.3-2.6); consumed daily about 1.2-1.8 times more often ≥1 than 0-1 glasses of alcohol (ORtotal-adj = 1.2 (95%CI 0.4-4.0); ORnon-breastcancer-index-adj = 1.8 (95%CI 0.4-6.9); were about 1.04-1.3 times more often smokers than non-smokers (ORtotal-adj = 1.04 (95%CI 0.4-2.8); ORnon-breastcancer-index-adj = 1.3 (95%CI 0.4-4.2)); and overweight or obesity (72%) was about 1.02-1.3 times less common (ORtotal-adj = 0.98 (95%CI 0.4-2.6); ORnon-breastcancer-index-adj = 0.8 (95%CI 0.3-2.7)). Similar associations between lifestyle and breast cancer are suggested for PHTS and the general population. Despite not being statistically significant, results are clinically relevant and suggest that awareness of the effects of lifestyle on patients' breast cancer risk is important.

Smith-Lemli-Opitz syndrome: what is the actual risk for couples carriers of the DHCR7:c.964-1G>C variant?

The founder variant DHCR7:c.964-1G>C causing autosomal recessive Smith-Lemli-Opitz (SLOS) was introduced into the Israeli preconception carrier program for Ashkenazi Jews in 2017 because of the high carrier frequency in this population (2.3%). Other disease-causing variants in DHCR7 are relatively rare in Israeli population. Discrepancy between the carrier frequency and disease prevalence raises the question of the actual risks for affected offspring for couples detected by the screening program. We performed a literature review of all relevant publications regarding homozygous DHCR7:c.964-1G>C fetuses/patients. We also collected clinical data about couples identified in the national screening program, including reproductive history. Out of 32 homozygous fetuses, six died in utero, 11 pregnancies were terminated during second trimester, and 15 children were born. All died between first days of life till 3 months of age. Reproductive history of SLOS-at-risk couples showed that after correction for ascertainment bias, out of 61 pregnancies, there was an absence of affected fetuses/children and an excess of miscarriages even if assumed that all the homozygous fetuses were miscarried. Out of these, eight families were Israelis, they had a total of one sick child, 21 healthy children, and 21 miscarriages. Our observations support the previous knowledge that homozygosity for c.964-1G>C in DHCR7 leads to a severe phenotype or early miscarriage. An unexpected observation was the excess of early miscarriages. This phenomenon is unclear and awaits further studies.

Data partitioning and correction for ascertainment bias reduce the uncertainty of placental mammal divergence times inferred from the morphological clock.

Bayesian estimates of divergence times based on the molecular clock yield uncertainty of parameter estimates measured by the width of posterior distributions of node ages. For the relaxed molecular clock, previous works have reported that some of the uncertainty inherent to the variation of rates among lineages may be reduced by partitioning data. Here we test this effect for the purely morphological clock, using placental mammals as a case study. We applied the uncorrelated lognormal relaxed clock to morphological data of 40 extant mammalian taxa and 4,533 characters, taken from the largest published matrix of discrete phenotypic characters. The morphologically derived timescale was compared to divergence times inferred from molecular and combined data. We show that partitioning data into anatomical units significantly reduced the uncertainty of divergence time estimates for morphological data. For the first time, we demonstrate that ascertainment bias has an impact on the precision of morphological clock estimates. While analyses including molecular data suggested most divergences between placental orders occurred near the K‐Pg boundary, the partitioned morphological clock recovered older interordinal splits and some younger intraordinal ones, including significantly later dates for the radiation of bats and rodents, which accord to the short‐fuse hypothesis.

Including autapomorphies is important for paleontological tip-dating with clocklike data, but not with non-clock data.

Tip-dating, where fossils are included as dated terminal taxa in Bayesian dating inference, is an increasingly popular method. Data for these studies often come from morphological character matrices originally developed for non-dated, and usually parsimony, analyses. In parsimony, only shared derived characters (synapomorphies) provide grouping information, so many character matrices have an ascertainment bias: they omit autapomorphies (unique derived character states), which are considered uninformative. There has been no study of the effect of this ascertainment bias in tip-dating, but autapomorphies can be informative in model-based inference. We expected that excluding autapomorphies would shorten the morphological branchlengths of terminal branches, and thus bias downwards the time branchlengths inferred in tip-dating. We tested for this effect using a matrix for Carboniferous-Permian eureptiles where all autapomorphies had been deliberately coded. Surprisingly, date estimates are virtually unchanged when autapomorphies are excluded, although we find large changes in morphological rate estimates and small effects on topological and dating confidence. We hypothesized that the puzzling lack of effect on dating was caused by the non-clock nature of the eureptile data. We confirm this explanation by simulating strict clock and non-clock datasets, showing that autapomorphy exclusion biases dating only for the clocklike case. A theoretical solution to ascertainment bias is computing the ascertainment bias correction (Mkparsinf), but we explore this correction in detail, and show that it is computationally impractical for typical datasets with many character states and taxa. Therefore we recommend that palaeontologists collect autapomorphies whenever possible when assembling character matrices.

Low penetrance of paraganglioma and pheochromocytoma in an extended kindred with a germline SDHB exon 3 deletion.

In the Netherlands, the majority of hereditary paragangliomas (PGL) is caused by SDHD, SDHB and SDHAF2 mutations. Founder mutations in SDHD are particularly prevalent, but several SDHB founder mutations have also been described. Here, we describe an extended PGL family with a Dutch founder mutation in SDHB, c.201-4429_287-933del. The proband presented with apparently sporadic head and neck paraganglioma at advanced age. Subsequently, evaluation of the family identified several unaffected mutation carriers, asymptomatic and symptomatic PGL patients, and patients presenting with early-onset malignant pheochromocytoma. The calculated penetrance of the SDHB mutation in this kindred is lower than the risk suggested for SDHB mutations in the literature. This may represent a characteristic of this particular SDHB mutation, but may also be a reflection of the inclusion of relatively large numbers of asymptomatic mutation carriers in this family and adequate statistical correction for ascertainment bias. The low penetrance of SDHB mutations may obscure the hereditary nature of SDHB-linked disease and is important in the counseling of SDHB-linked patients. Risk estimates should preferably be based on the specific mutation involved.

Statistical analysis of binary data generated from multilocus dominant DNA markers

The use of methodologies such as RAPD and AFLP for studying genetic variation in natural populations is widespread in the ecology community. Because data generated using these methods exhibit dominance, their statistical treatment is less straightforward. Several estimators have been proposed for estimating population genetic parameters, assuming simple random sampling and the Hardy-Weinberg (HW) law. The merits of these estimators remain unclear because no comparative studies of their theoretical properties have been carried out. Furthermore, ascertainment bias has not been explicitly modelled. Here, we present a comparison of a set of candidate estimators of null allele frequency (q), locus-specific heterozygosity (h) and average heterozygosity () in terms of their bias, standard error, and root mean square error (RMSE). For estimating q and h, we show that none of the estimators considered has the least RMSE over the parameter space. Our proposed zero-correction procedure, however, generally leads to estimators with improved RMSE. Assuming a beta model for the distribution of null homozygote proportions, we show how correction for ascertainment bias can be carried out using a linear transform of the sample average of h and the truncated beta-binomial likelihood. Simulation results indicate that the maximum likelihood and empirical Bayes estimator of have negligible bias and similar RMSE. Ascertainment bias in estimators of is most pronounced when the beta distribution is J-shaped and negligible when the latter is inverse J-shaped. The validity of the current findings depends importantly on the HW assumption-a point that we illustrate using data from two published studies.

Initial human transmission dynamics of the pandemic (H1N1) 2009 virus in North America.

Background Between 5 and 25 April 2009, pandemic (H1N1) 2009 caused a substantial, severe outbreak in Mexico, and subsequently developed into the first global pandemic in 41 years. We determined the reproduction number of pandemic (H1N1) 2009 by analyzing the dynamics of the complete case series in Mexico City during this early period. Methods We analyzed three mutually exclusive datasets from Mexico City Distrito Federal which constituted all suspect cases from 15 March to 25 April: confirmed pandemic (H1N1) 2009 infections, non‐pandemic influenza A infections and patients who tested negative for influenza. We estimated the initial reproduction number from 497 suspect cases identified prior to 20 April, using a novel contact network methodology incorporating dates of symptom onset and hospitalization, variation in contact rates, extrinsic sociological factors, and uncertainties in underreporting and disease progression. We tested the robustness of this estimate using both the subset of laboratory‐confirmed pandemic (H1N1) 2009 infections and an extended case series through 25 April, adjusted for suspected ascertainment bias. Results The initial reproduction number (95% confidence interval range) for this novel virus is 1·51 (1·32–1·71) based on suspected cases and 1·43 (1·29–1·57) based on confirmed cases before 20 April. The longer time series (through 25 April) yielded a higher estimate of 2·04 (1·84–2·25), which reduced to 1·44 (1·38–1·51) after correction for ascertainment bias. Conclusions The estimated transmission characteristics of pandemic (H1N1) 2009 suggest that pharmaceutical and non‐pharmaceutical mitigation measures may appreciably limit its spread prior the development of an effective vaccine.

Correcting Estimators of θ and Tajima's D for Ascertainment Biases Caused by the Single-Nucleotide Polymorphism Discovery Process

Most single-nucleotide polymorphism (SNP) data suffer from an ascertainment bias caused by the process of SNP discovery followed by SNP genotyping. The final genotyped data are biased toward an excess of common alleles compared to directly sequenced data, making standard genetic methods of analysis inapplicable to this type of data. We here derive corrected estimators of the fundamental population genetic parameter = 4N(e)mu (N(e), effective population size; mu, mutation rate) on the basis of the average number of pairwise differences and on the basis of the number of segregating sites. We also derive the variances and covariances of these estimators and provide a corrected version of Tajima's D statistic. We reanalyze a human genomewide SNP data set and find substantial differences in the results with or without ascertainment bias correction.

A Correction for Ascertainment Bias in Estimating Rates of Onset of Highly Penetrant Genetic Disorders

Estimation of rates of onset of rare, late-onset dominantly inherited genetic disorders is complicated by: (a) probable ascertainment bias resulting from the ‘recruitment’ of strongly affected families into studies; and (b) inability to identify the true ‘at risk’ population of mutation carriers. To deal with the latter, Gui & Macdonald (2002a) proposed a non-parametric (Nelson-Aalen) estimate (x) of a simple function Λ(x) of the rate of onset at age x. The function Λ(x) had a finite bound, which was an increasing function of the probability p that a child of an affected parent inherits the mutation and σ the life-time penetrance. However if (x) exceeds this bound, it explodes to infinity, and this can happen at quite low ages. We show that such ‘failure’ may in fact be a useful measure of ascertainment bias. Gui & Macdonald assumed that p = 1/2 and σ = 1, but ascertainment bias means that p > 1/2 and σ ≠ 1 in the sample. The maximum attained by (x) allows us to estimate a range for the product pσ, and therefore the degree of ascertainment bias that may be present, leading to bias-corrected estimates of rates of onset. However, we find that even classical independent censoring, prior to ascertainment, can introduce new bias. We apply these results to early-onset Alzheimer’s disease associated with mutations in the Presenilin-1 gene.

A Correction for Ascertainment Bias in Estimating Rates of Onset of Highly Penetrant Genetic Disorders

Estimation of rates of onset of rare, late-onset dominantly inherited genetic disorders is complicated by: (a) probable ascertainment bias resulting from the ‘recruitment’ of strongly affected families into studies; and (b) inability to identify the true ‘at risk’ population of mutation carriers. To deal with the latter, Gui & Macdonald (2002a) proposed a non-parametric (Nelson-Aalen) estimate (x) of a simple function Λ(x) of the rate of onset at age x. The function Λ(x) had a finite bound, which was an increasing function of the probability p that a child of an affected parent inherits the mutation and σ the life-time penetrance. However if (x) exceeds this bound, it explodes to infinity, and this can happen at quite low ages. We show that such ‘failure’ may in fact be a useful measure of ascertainment bias. Gui & Macdonald assumed that p = 1/2 and σ = 1, but ascertainment bias means that p > 1/2 and σ ≠ 1 in the sample. The maximum attained by (x) allows us to estimate a range for the product pσ, and therefore the degree of ascertainment bias that may be present, leading to bias-corrected estimates of rates of onset. However, we find that even classical independent censoring, prior to ascertainment, can introduce new bias. We apply these results to early-onset Alzheimer’s disease associated with mutations in the Presenilin-1 gene.

Ascertainment Bias in Spatially Structured Populations: A Case Study in the Eastern Fence Lizard

Despite increased interest in applying single nucleotide polymorphism (SNP) data to questions in natural systems, one unresolved issue is to what extent the ascertainment bias induced during the SNP discovery phase will impact available analysis methods. Although most studies addressing ascertainment bias have focused on human populations, it is not clear whether existing methods will work when applied to other species with more complex demographic histories and more significant levels of population structure. Here we present findings from an empirical approach to exploring the effect of population structure on issues of ascertainment bias in the Eastern Fence Lizard, Sceloporus undulatus. We find that frequency spectra and summary statistics were highly sensitive to SNP discovery strategy, necessitating careful selection of the initial ascertainment panel. Randomly selected ascertainment panels performed equally well as ascertainment panels chosen to jointly sample geographic, phenotypic, and genetic diversity. Geographically restricted panels resulted in larger biases. Additionally, we found existing ascertainment bias correction methods, which were not developed for geographically structured data sets, were largely effective at reducing the impact of ascertainment bias. Because bias correction methods performed well even when underlying assumptions were violated, our results suggest tools are currently available to analyze SNP data in structured populations.

A Two‐Stage Approach to the Correction of Ascertainment Bias in Complex Genetic Studies Involving Variance Components

Correction for ascertainment bias is a vital part of the analysis of genetic epidemiology studies that needs to be undertaken whenever subjects are not recruited at random. Adjustment often requires extensive numerical integration, which can be very slow or even computationally infeasible, especially if the model includes many fixed and random effects. In this paper we propose a two-stage method for ascertainment bias correction. In the first stage we estimate parameters that pertain to the ascertained population, that is the population that would be selected into the sample if the ascertainment criterion were applied to everyone. In the second stage we convert the estimates for the ascertained population into general population parameter estimates. We illustrate the method with simulations based on a simple model and then describe how the method can be used with complex models. The two-stage approach avoids some of the integration required in direct adjustment, hence speeding up the process of model fitting.

Myotonic dystrophy--no evidence for preferential transmission of the mutated allele: a prenatal analysis.

Myotonic dystrophy is the commonest autosomal dominant type of muscular dystrophy in adults. It is one of the trinucleotide repeat expansion disorders, and its severity correlates with the number of CTG repeats in the myotonic dystrophy gene. It has been suggested that myotonic dystrophy exhibits the phenomenon of preferential transmission of the larger mutated alleles that has been described in other trinucleotide repeat disorders. Several authors have reported that the frequency of transmission of the mutated alleles is higher than 50%--a finding that, if true, does not comply with the Mendelian laws of segregation. However, these studies were based on data from the analysis of pedigrees with ascertainment bias. In our study, we determined the frequency of transmission of mutated alleles using data from prenatal molecular studies, which are not subject to ascertainment bias. This is the first study to examine the segregation of the mutated alleles in myotonic dystrophy in pregnancy. Eighty-three fetuses were examined, 30 of 62 mothers (48.38%) and 8 of 21 fathers (38.09%) transmitted the mutated allele, giving an overall transmission rate of 45.78%. We found no evidence of statistically significant deviation of the frequency of transmission of the mutated alleles from the 50% expected in autosomal dominant disorders. This study, unlike previous ones, excludes preferential transmission in myotonic dystrophy, a finding that may be attributable to the lack of correction for ascertainment bias in previous studies and to the use of prenatal data in this study.

Correcting for ascertainment bias in the COGA data set.

The effects of several corrections for ascertainment bias on a linkage result in the COGA data are examined. A correction that models the complete ascertainment protocol markedly reduces the evidence for linkage. Different partial corrections increase the linkage signal and recover good estimates of the population trait prevalence, but do not represent adequately the complexity of the COGA ascertainment scheme. Evidently the present size of the COGA data set cannot support a complete correction for ascertainment bias, but an effective partial correction can and should be implemented.

Anticipation in Crohn's disease may be influenced by gender and ethnicity of the transmitting parent.

We sought to examine whether anticipation (an earlier age of onset in succeeding generations) is observed in Crohn's disease (CD) patients within the New York metropolitan area, and whether there are differences in the degree of anticipation with respect to gender and ethnicity of the affected parent. Sixty-one parent-child pairs both affected by CD were identified; about half of the pairs were of Ashkenazi Jewish descent. An additional 17 pairs of second-degree relatives with CD were also identified. The intergenerational difference in age at diagnosis (AAD) was used to perform regression analysis and the degree of anticipation among subsets of patients separated on the basis of gender and ethnicity of the transmitting parent was determined. The AAD was consistently (90% of the time) lower in the younger member of the 61 parent-child pairs (35.3+/-1.6 yr vs 20.8+/-1.1 yr, p = 0.0001). Furthermore, the degree of anticipation was significantly greater for father-child pairs (20.6+/-3.2 yr) than for mother-child pairs (11.7+/-2.1 yr). However, when the patient population where the parent had an AAD of < 28 was analyzed separately, there was a lack of clear-cut evidence of anticipation in the population as a whole. Only when the population was subdivided by ethnicity was there convincing evidence of anticipation in the Jewish population. Ascertainment bias may be responsible for the apparent anticipation observed in the CD population as a whole or in the nonJewish CD subgroup. However, the Jewish CD population displays strong evidence of anticipation even after correction for ascertainment bias.

Anticipation in Crohn’s disease may be influenced by gender and ethnicity of the transmitting parent

Objective: We sought to examine whether anticipation (an earlier age of onset in succeeding generations) is observed in Crohn’s disease (CD) patients within the New York metropolitan area, and whether there are differences in the degree of anticipation with respect to gender and ethnicity of the affected parent. Methods: Sixty-one parent-child pairs both affected by CD were identified; about half of the pairs were of Ashkenazi Jewish descent. An additional 17 pairs of second-degree relatives with CD were also identified. The intergenerational difference in age at diagnosis (AAD) was used to perform regression analysis and the degree of anticipation among subsets of patients separated on the basis of gender and ethnicity of the transmitting parent was determined. Results: The AAD was consistently (90% of the time) lower in the younger member of the 61 parent-child pairs (35.3 ± 1.6 yr vs 20.8 ± 1.1 yr, p = 0.0001). Furthermore, the degree of anticipation was significantly greater for father-child pairs (20.6 ± 3.2 yr) than for mother-child pairs (11.7 ± 2.1 yr). However, when the patient population where the parent had an AAD of < 28 was analyzed separately, there was a lack of clear-cut evidence of anticipation in the population as a whole. Only when the population was subdivided by ethnicity was there convincing evidence of anticipation in the Jewish population. Conclusion: Ascertainment bias may be responsible for the apparent anticipation observed in the CD population as a whole or in the nonJewish CD subgroup. However, the Jewish CD population displays strong evidence of anticipation even after correction for ascertainment bias.

A pedigree analysis with minimised ascertainment bias shows anticipation in Met30-transthyretin related familial amyloid polyneuropathy.

In type I familial amyloid polyneuropathy (FAP) caused by a variant Met30-transthyretin (TTR), genetic anticipation has been reported. To determine whether anticipation of the disease is a true biological phenomenon...

MODED: Microcephaly‐oculo‐digito‐esophageal‐duodenal syndrome

We report on 4 families with microcephaly, type A brachydactyly, variable learning disabilities, short stature, duodenal atresia, patent ductus arteriosus (PDA), hallux valgus, restricted elbow and finger movements, and amesophalangy and syndactyly of toes. Three previous families manifested all signs of the syndrome, and in another four reports the phenotype was incomplete. These cases are reviewed. Penetrance of digital and toe anomalies is almost complete and microcephaly is present in 78% of known cases. Short stature was present in 70% of our cases, but this is probably an overestimation. Esophageal and duodenal atresias were present in 25% of known cases. Correction for ascertainment bias gave a lower estimate of 16.6%. Learning disabilities were present in 31% of all patients. Longitudinal follow-up suggested that hypoplasia or absence of the diaphyseal ossification centers is the primary cause of the phalangeal changes. Observations in a 9-year-old girl, followed since age 3.3, suggest that the eventual absence of the middle phalanges of the toes may be caused by fusion. Am. J. Med. Genet. 71:251–257, 1997. © 1997 Wiley-Liss, Inc.

Between-generation differences in ascertainment and penetrance: relevance to genetic hypotheses in fragile X

Between-generation differences in ascertainment were examined in 54 extended fragile X pedigrees, where all available members were clinically, psychometrically, and cytogenetically investigated. In 24 families a diagnosis was verified by molecular characterization using the pfxa3 fragile X-specific probe. We found considerable differences between generations in relative proportions of affected fragile X subjects versus 'non-penetrant' carriers. We also found deviation in the segregation ratio in unbiased samples of relatives in pedigrees. We claim that these irregularities are influenced by different rates of ascertainment, depending on the clinical expression of the condition (penetrance) and the fertility of fragile X individuals in a pedigree, as well as by the thoroughness of clinical investigation in individual families. Penetrance and fertility were estimated in fragile X females assessed by psychometric tests, and they were compared with earlier estimates based on a subjective judgement of their intellectual status. We suggest that the standard correction for ascertainment bias, such as has been applied in segregation analysis of this condition, is not sufficient to adjust for all types of bias.

No Female Preponderance in Juvenile Periodontitis After Correction for Ascertainment Bias

Juvenile periodontitis (JP) is generally recognized to exist in 2 clinical forms: localized and generalized. Historically, females have been reported to be affected by both forms of JP at rates of 2 to 10 times greater than males. However, evidence suggests that females are more likely than males to seek dental care. If this is true, females will be diagnosed with JP more often than males even if juvenile periodontitis is equally prevalent among males and females in the general population. Thus, previous reports of a female predominance for JP may simply reflect this selection bias. The purpose of this study was to test our hypothesis that juvenile periodontitis occurs with equal frequency in males and females after correcting for selection bias. Twenty-four juvenile periodontitis probands were ascertained from the VCU/MCV dental clinics. The families of these individuals were examined to determine the relative prevalence of JP among male and female relatives of these probands. Our results indicate that while females are 3 times more likely than males to be initially ascertained as juvenile periodontitis probands, among relatives of probands the proportion of affected males and females is equal.