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At least 19 recordsLinked to original sources
PubMed1983

Evaluating pedigree data. I. The estimation of pedigree error in the presence of marker mistyping.

Pedigrees used in the analysis of genetic or medical data are usually ascertained from sources subject to a variety of errors including misidentification of individuals, faults in historical documents or record linkage, nonpaternity, and unidentified adoption. Genetic markers can be used to verify putative family and pedigree data through the search for inconsistencies, or genetic exclusions, between putative parents and offspring. The probability of observing an exclusion given the occurrence of an error depends upon the gene frequencies at the loci under study and the forms of error. In addition, inconsistencies can arise from laboratory errors in marker determination. Together, these problems make the proper statistical analysis of such data desirable. Here we give a model that specifies the combined effects of various kinds of pedigree error along with genetic marker error. This model allows the maximum-likelihood estimation of the rates of various forms of pedigree error and laboratory error from genetic marker data collected on putative families. The method is illustrated by applying it to data obtained from a South Pacific island population, Tokelau. From the observed distribution of genetic marker inconsistencies between the parents and offspring of putative families, derived from the extensive genealogy of this population, we are able to estimate that the error of a paternal link is 4%, the error of a maternal link is zero, and the overall system typing error is 1%.

Alleles↗
PubMed1975

Extensions to pedigree analysis I. Likehood calculations for simple and complex pedigrees.

A graph theoretic definition of pedigrees is given and a distinction drawn between simple and complex pedigrees. Algorithms are presented to calculate the likeihood of any kind of pedigree, assuming only segregation at a finite set of loci, nonassortative mating and no environmental correlations; multiple births and consanguineous marriages are explicity allowed for. The formulation given can lead to more powerful genetic counselling, segregation analysis and linkage analysis.

Genetic Linkage↗
PubMed1987

PEDIGREE-PLOT: a computer program for plotting pedigrees.

PEDIGREE-PLOT is a FORTRAN program which can be used for the drawing of pedigrees in either a horizontal or a circular shape. Eight different symbols are available for characterizing a person. Special symbols for stillbirth, abortion, unspecified sex, twins and half sibships exist.

Humans↗
PubMed1991

Insulin and glucose levels and prevalence of glucose intolerance in pedigrees with multiple diabetic siblings.

Hyperinsulinemia may be an early inherited marker for a defect in insulin action that subsequently results in glucose intolerance and non-insulin-dependent diabetes mellitus (NIDDM). To examine the role of hyperinsulinemia in individuals at high genetic risk for NIDDM and determine the prevalence of impaired glucose tolerance (IGT) and newly diagnosed diabetes in members of NIDDM pedigrees, we studied 310 members of 16 pedigrees ascertained for greater than or equal to 2 NIDDM siblings. Nondiabetic members of all pedigrees were examined by 75-g oral glucose tolerance test with fasting and 1-h insulin levels. Participants had height and weight recorded. Spouses of pedigree members (n = 88) served as control subjects. The spouse control subjects were older and slightly more obese than the undiagnosed pedigree members. The prevalence of IGT was 14.8% in spouses and 7.7% in pedigree members, and NIDDM was present in 11.3% of spouses and 2.3% of previously undiagnosed pedigree members. However, neither spouses nor pedigree members differed significantly from published age-specific prevalence rates for IGT or newly diagnosed NIDDM. Insulin and glucose levels were examined in pedigree members with normal glucose tolerance (NGT). Fasting insulin levels were not significantly different between spouses and NGT pedigree members. However, after adjustment for age, weight (body mass index), and sex, NGT pedigree members had higher 1-h insulin levels and higher fasting and 1-h glucose levels than spouses. These differences were also evident when pedigree members with at least 1 affected (NIDDM or IGT) parent were compared with spouses with no family history of diabetes.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed2026

Fault-tolerant pedigree reconstruction from pairwise kinship relations.

MOTIVATION: Pedigrees reconstructed from biologically related ancient genomes have revealed many insights into (pre)history. To our knowledge, all reported ancient pedigrees have been primarily manually reconstructed, as existing pedigree reconstruction methods are ill-suited for the quality and nature of ancient DNA data. RESULTS: We introduce repare, an open-source software method to automatically reconstruct pedigrees from inferred pairwise kinship relations, which are readily obtainable from ancient genomes. This method reconstructs pedigrees by iteratively incorporating pairwise kinship relations into a set of candidate pedigrees, with pruning and sampling to reduce its search space. It optionally considers supporting information such as haplogroups and skeletal age-at-death estimates. We evaluate this method on a variety of simulated pedigrees with varying error rates and missingness. We also use this method to reconstruct several published pedigrees that were originally manually reconstructed; for one, we present a potential alternative topology. repare optionally incorporates user-inferred pedigree constraints, enabling "human-in-the-loop" reconstruction workflows. Especially when used with these user-inferred constraints, we find that repare represents a powerful and flexible tool for ancient pedigree reconstruction. AVAILABILITY AND IMPLEMENTATION: repare is freely available at https://github.com/Narasimhan-Lab/repare. In addition, source code, benchmark scripts, and benchmark results used in this work are archived at https://doi.org/10.5281/zenodo.19716772.

Pedigree↗
PubMed1989

Identifying pedigrees segregating at a major locus for a quantitative trait: an efficient strategy for linkage analysis.

Having found evidence for segregation at a major locus for a quantitative trait, a logical next step is to identify those pedigrees in which major-locus segregation is occurring. If the quantitative trait is a risk factor for an associated disease, identifying such segregating pedigrees can be important in classifying families by etiology, in risk assessment, and in suggesting treatment modalities. Identifying segregating pedigrees can also be helpful in selecting pedigrees to include in a subsequent linkage study to map the major locus. Here, we describe a strategy to identify pedigrees segregating at a major locus for a quantitative trait. We apply this pedigree selection strategy to simulated data generated under a major-locus or mixed model with a rare dominant allele and sampled according to one of several fixed-structure or sequential sampling designs. We demonstrate that for the situations considered, the pedigree selection strategy is sensitive and specific and that a linkage study based only on the pedigrees classified as segregating extracts essentially all the linkage information in the entire sample of pedigrees. Our results suggest that for large-scale linkage studies involving many genetic markers, the savings from this strategy can be substantial and that, compared with fixed-structure sampling, sequential sampling of pedigrees can greatly improve the efficiency for linkage analysis of a quantitative trait.

Genetic Linkage↗
PubMed1991

Genetic variation in insulin receptor beta-chain exons among members of familial type 2 (non-insulin-dependent) diabetic pedigrees.

Insulin resistance appears to be an essential component of Type 2 (non-insulin-dependent) diabetes mellitus. Both hyperinsulinaemia and insulin resistance are inherited and may precede the onset of Type 2 diabetes. To determine whether insulin receptor gene mutations, and specifically whether mutations of the beta-chain could account for the observed insulin resistance, we studied members of 16 pedigrees ascertained for two or more Type 2 diabetic siblings and members of four additional pedigrees ascertained for a mixture of Type 1 and Type 2 diabetes. We previously demonstrated insulin resistance among unaffected members of these pedigrees. Each pedigree was initially examined with insulin receptor restriction fragment length polymorphisms to determine whether any allele segregated with Type 2 diabetes in these pedigrees. Of the 16 pedigrees ascertained for Type 2 diabetes, at least one recombinant event between diabetes and the insulin receptor locus was present in seven pedigrees. An additional two pedigrees showed no linkage if individuals with impaired glucose tolerance were also considered affected. In all but one of the remaining pedigrees, apparent sharing of haplotypes may have resulted from insufficient polymorphism to distinguish all parental alleles. Subsequently, exons 13-21 of each allele which appeared in a Type 2 diabetic individual were examined by single strand conformation polymorphisms to detect any mutations in this region. A total of five mutations were detected, but DNA sequence analysis showed each mutation to be silent and thus not likely to result in defective insulin receptor function. No mutation detected in this fashion was present on an allele which appeared to segregate with Type 2 diabetes.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1988

Insulin gene in familial NIDDM. Lack of linkage in Utah Mormon pedigrees.

Although non-insulin-dependent diabetes mellitus (NIDDM) is well recognized to be an inherited disease, the genetic lesion responsible remains to be determined. Several pedigrees have been reported in which defects of the insulin gene result in glucose intolerance or diabetes in affected members, but the role of insulin gene mutations in NIDDM is unknown. To evaluate this role, we ascertained 23 Caucasian pedigrees for a diabetic individual with at least one diabetic family member, sampled the unaffected individuals by a 75-g glucose tolerance test, and prepared leukocyte DNA on all family members. Included in the pedigrees ascertained were those with both predominantly lean and predominantly obese diabetic members and four pedigrees included as insulin-dependent diabetic individual. Insulin gene involvement was evaluated via previously described restriction-fragment-length polymorphisms (RFLPs) for the insulin gene and the nearby c-Ha-Ras oncogene (HRAS). Combination of these RFLPs resulted in the ability to trace the insulin alleles in all pedigrees studied. Analysis of individual pedigrees for sharing of insulin alleles was possible in 12 pedigrees, and lack of linkage was demonstrated in 6 of them. Neither linkage nor lack of linkage could be proved in the remaining pedigrees. Analysis of the pooled pedigree data failed to demonstrate linkage under several models, including autosomal-dominant and -recessive inheritance with different sporadic frequencies of diabetes and different prevalence figures. These results show that mutations of the insulin gene and the immediately surrounding area, including regulatory regions of the insulin gene, are unlikely to account for a significant subset of NIDDM in Caucasian individuals.

Diabetes Mellitus, Type 2↗
PubMed1988

Hypertension and sodium-lithium countertransport in Utah pedigrees: evidence for major-locus inheritance.

Likelihood analysis was used to test for evidence that an allele at a major locus elevates rates of sodium-lithium countertransport (SLC) in a sample of 1,989 members of 89 Utah pedigrees. The pedigrees were ascertained through two or three sibs who died of stroke before age 74 years (stroke pedigrees), through hypertensive and normotensive probands of the Salt Lake Center of the Hypertension Detection and Followup Program (HDFP pedigrees), or through men who suffered a myocardial infarction before age 55 years (coronary pedigrees). Major-locus inheritance could be rejected in the total sample; transmission probability estimates of tau1 = .972, tau2 = .520, tau3 = .185 differed significantly from Mendelian transmission specified by tau1 = 1, tau2 = 1/2, tau3 = 0. However, heterogeneity between ascertainment groups was significant (chi2(18) = 40.06, P less than .01) and justified analysis within subsets of the sample. In the stroke pedigrees, evidence of major-locus inheritance was not found; polygenic heritability was estimated as .647. In the HDFP pedigrees, estimates of tau1 = .987, tau2 = .430, tau3 = .506 differed significantly from Mendelian transmission; the inferred model consisted of a mixture of two distributions incompatible with both Mendelian and environmental transmission but compatible with polygenic inheritance within distributions. In the coronary pedigrees, the hypothesis of Mendelian transmission could not be rejected. In the coronary pedigrees, the evidence supported an incompletely recessive allele with a frequency of .227 which elevated the level of SLC to a mean of .530 mmol/liter RBC/h.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗
PubMed1990

Selecting pedigrees for linkage analysis of a quantitative trait: the expected number of informative meioses.

With evidence of segregation at a major locus for a quantitative trait having been found, a logical next step is to select a subset of the pedigrees to include in a linkage study to map the major locus. Ideally this subset should include much of the linkage information in the sample but include only a fraction of the pedigrees. We previously described a strategy for selecting pedigrees for linkage analysis of a quantitative trait on the basis of a pedigree likelihood-ratio statistic. For quantitative traits controlled by a major locus with a rare dominant allele, the likelihood-ratio strategy extracted nearly all the information for linkage while typically requiring marker data on only about one-third of the pedigrees. Here, we describe a new strategy to select pedigrees for linkage analysis on the basis of the expected number of potentially informative meioses in each pedigree. We demonstrate that this informative-meioses strategy provides an efficient and more general means to select pedigrees for a linkage study of a quantitative trait.

Female↗
PubMed1984

Ascertainment and goodness of fit of variance component models for pedigree data.

The multivariate normal parameterization of the polygenic model (Lange et al., 1976) provides a great deal of flexibility for analyzing quantitative data on pedigrees. The likelihood approach employed ensures statistical efficiency and allows for hypothesis testing using the likelihood ratio criterion. The parameterization also facilitates ascertainment correction and goodness-of-fit testing (Spence et al., 1977; Ott, 1979; Hopper and Mathews, 1982; Boehnke, 1983). We reviewed these results and then described a simulation study undertaken to determine their utility when applied to data. Pedigree data were generated under polygenic and mixed models and sampled either randomly or via probands. We found that the variance components of the model were accurately estimated for random sampling, but less so for ascertained data analyzed by conditioning on probands. Goodness-of-fit tests employing test statistics corresponding to individual phenotypes and entire pedigrees were conservative, but pedigree tests did demonstrate reasonable power to reject a variety of mixed model alternatives. In addition, we found that the pedigree test statistics could be used to enrich a sample of pedigrees for those pedigrees segregating at a major locus, providing an objective criterion for choosing pedigrees to be included in a linkage analysis.

Chromosome Mapping↗
PubMed2026

X chromosome-wide association studies for quantitative trait loci based on the mixture of general pedigrees and additional unrelated individuals.

Genome-wide association studies have successfully identified many genetic variants associated with complex traits. However, most existing methods target autosomes rather than X chromosome, and several existing X chromosome-wide association studies (XWAS) at quantitative trait loci (QTL) largely focus on unrelated individuals, with limited attention to general pedigrees or mixture of general pedigrees and additional unrelated individuals (called the mixed data for brevity). In this study, we propose nine novel methods for XWAS at QTL in the mixed data (${\mathrm{MQX}}_{\mathrm{cat}}$, ${\mathrm{MQZ}}_{\mathrm{max}}$, ${\mathrm{MT}}_{\mathrm{plinkw}}$, ${\mathrm{MT}}_{\mathrm{chenw}}$, $\mathrm{MwM}3\mathrm{VNA}$, ${\mathrm{MQMVX}}_{\mathrm{cat}}$, ${\mathrm{MQMVZ}}_{\mathrm{max}}$, $\mathrm{MpMV}$, and $\mathrm{McMV}$), also applicable to general pedigrees alone. The first four methods test for mean differences across genotypes; the latter four test for differences in both means and variances; $\mathrm{MwM}3\mathrm{VNA}$ tests for variance differences only. All mean-based and mean-variance-based methods incorporate X chromosome inactivation information, and all nine methods consider genetic relatedness in pedigrees. Simulation studies confirm well-controlled type I error rates, and inclusion of pedigrees significantly improves statistical power. Note that there has been no study focusing on X chromosome for the mixed data or general pedigrees from UK Biobank database, so we apply our proposed methods to this dataset, which identify five total cholesterol (TC)-associated and 13 low-density lipoprotein cholesterol (LDL-C)-associated single nucleotide polymorphisms (SNPs). Linkage disequilibrium (LD) analysis reveals that these SNPs fall into three distinct LD blocks. Functional annotation and gene ontology enrichment analysis reveal 16 and 28 enriched pathways for TC-associated and LDL-C-associated genes, respectively. These methods provide robust and powerful tools for XWAS at QTL in both mixed data and general pedigrees.

Quantitative Trait Loci↗
PubMed1983

Evaluating pedigree data. II. Identifying the cause of error in families with inconsistencies.

Pedigree data can be evaluated, and subsequently corrected, by analysis of the distribution of genetic markers, taking account of the possibility of mistyping . Using a model of pedigree error developed previously, we obtained the maximum likelihood estimates of error parameters in pedigree data from Tokelau. Posterior probabilities for the possible true relationships in each family are conditional on the putative relationships and the marker data are calculated using the parameter estimates. These probabilities are used as a basis for discriminating between pedigree error and genetic marker errors in families where inconsistencies have been observed. When applied to the Tokelau data and compared with the results of retyping inconsistent families, these statistical procedures are able to discriminate between pedigree and marker error, with approximately 90% accuracy, for families with two or more offspring. The large proportion of inconsistencies inferred to be due to marker error (61%) indicates the importance of discriminating between error sources when judging the reliability of putative relationship data. Application of our model of pedigree error has proved to be an efficient way of determining and subsequently correcting sources of error in extensive pedigree data collected in large surveys.

Female↗
PubMed1986

Description of a large pedigree with an adverse lipoprotein cholesterol phenotype: the Bogalusa Heart Study.

A large pedigree (N = 356) with a high prevalence of heart disease and associated adverse lipoprotein phenotype was studied. The adverse lipoprotein phenotype is characterized by both low levels of high-density-lipoprotein cholesterol (HDL-C) alone (16.3%) and in combination with other adverse lipoprotein levels (12.8%). In all, 44.2% of all pedigree members had at least one adverse lipoprotein level. Analysis of mating types showed that all lipids and lipoproteins possess familial clustering with 25-36% of offspring above median levels when both parents had levels below the median, while 67-83% had levels above the median when both parents had levels above the median. Using adjusted lipid and lipoprotein levels, a statistically significant linear trend was found between the degree of relationship to pedigree members with heart disease, and both the low-density-lipoprotein cholesterol/high-density-lipoprotein cholesterol (LDL-C/HDL-C) ratio (P less than .05), and the very-low-density-lipoprotein cholesterol (VLDL-C; P less than .01) level. A similar analysis using the prevalence of adverse lipoprotein levels as the dependent variable and degree of relationship to heart diseased pedigree numbers as the independent variable showed significant (P less than .05) relationships with VLDL-C and the LDL-C/HDL-C ratio. Further genetic analyses of this pedigree may reveal genetic mechanisms responsible for the familiality of lipoprotein levels in this pedigree.

Adolescent↗
PubMed1992

Coronary risk factors and the severity of angiographic coronary artery disease in members of high-risk pedigrees.

Affected members of early coronary pedigrees in Utah are at markedly increased risk for the development of clinical coronary heart disease (CHD). The relationship between the presence of coronary risk factors and the severity of angiographic coronary artery disease (CAD) in 53 members of high-risk Utah pedigrees was examined. Mean angiographic severity scores were higher in familial hypercholesterolemia or familial low high-density lipoprotein cholesterol (HDL-C) pedigrees than in type III hyperlipidemia or familial combined hyperlipidemia pedigrees. One sibling pair with hyperhomocyst(e)inemia had the highest mean angiographic severity scores. Clinical CHD (p less than 0.0001), increasing low-density lipoprotein cholesterol (LDL-C) (p = 0.0107), and decreasing HDL-C (p = 0.0068) were significant predictors of angiographic CAD severity. There appeared to be an interaction between gender and body mass index but not between gender and serum lipids in the prediction of angiographic CAD severity. Results of the present study in members of high-risk Utah pedigrees are consistent with results from other angiographic studies in non-high-risk persons. Of particular interest is the suggested independent predictive value of low HDL-C for angiographic CAD severity in members of high-risk pedigrees.

Coronary Angiography↗
PubMed1977

Ascertainment in the sequential sampling of pedigrees.

One aim in the analysis of pedigree data may be to infer the mode of inheritance of a characteristic. If only "interesting" pedigrees are analysed, the ascertainment bias may lead to some modes of inheritance being unintentionally preferred. Also, it is clearly most efficient in attempting to make such inferences, if a decision on whether to continue sampling a pedigree is made conditional on the types of individuals who have been observed; an a priori decision to examine 500 members of a pedigree may lead to much wasted effort, since the pedigree may prove to be largely uninformative. The present paper shows that provided all observed families are included in the analysis, even those which appeared "uninteresting" or "sporadic" and were not sampled further, and provided a decision to continue sampling is made conditional on types observed up to that point, the correct likelihood for the mode of inheritance may be easily computed. This opens the way for a more detailed study of the wider problem of optimal samplings rules on pedigrees.

Computers↗
PubMed2026

[Pathogenicity analysis and prenatal genetic counseling for five Chinese pedigrees harboring a hemizygous c.-32C>G variant of FGF13 gene].

OBJECTIVE: To explore the pathogenicity and prenatal counseling strategies for five Chinese pedigrees harboring a hemizygous c.-32C>G (NM_001139500.2) variant of fibroblast growth factor 13 (FGF13) gene. METHODS: Five Chinese pedigrees found to carry a hemizygous c.-32C>G variant of the FGF13 gene at the Prenatal Diagnosis Center of Henan Provincial People's Hospital between January 2024 and January 2025 were selected as study subjects. The pedigrees had undergone prenatal diagnosis for a family history of genetic disorders, abnormal fetal ultrasound findings, or advanced maternal age. A retrospective analysis was carried out, wherein clinical data for all members of the pedigrees were obtained through the medical records system and outpatient visit system. Peripheral blood samples were collected from all pedigree members, and amniotic fluid samples were obtained from the probands. Following extraction of genomic DNA, prenatal diagnosis was performed using chromosomal microarray analysis (CMA) and trio whole-exome sequencing (trio-WES). Sanger sequencing was used to determine the carrier status for the candidate variant, and Mini-Mental State Examination (MMSE) was used to assess the cognitive function of hemizygous individuals carrying the FGF13 gene c.-32C>G variant. Pathogenicity of candidate variant was assessed based on guidelines from the American College of Medical Genetics and Genomics (ACMG). This study was approved by the Medical Ethics Committee of the hospital (Ethics No.: 2021-171). RESULTS: CMA and trio-WES revealed no pathogenic variants in all probands, whilst trio-WES and Sanger sequencing had identified 11 male individuals carrying a hemizygous c.-32C>G variant of the FGF13 gene from the five pedigrees, which included six adult males, a young boy, and four fetuses. One fetus had undergone termination of pregnancy due to hydrocephalus, one was born pre-term at 34+1 weeks of gestation owing to maternal hypertension, and other two were delivered at full term. Follow-up of the survived males revealed no phenotypic manifestations related to language or intellectual impairment. Among these, three adult males underwent the MMSE assessment, all of whom showed normal cognitive function. Search of the gnomAD database suggested the carrier frequency of FGF13 c.-32C>G variant in the East Asian population to be 0.125%, with 11 hemizygous males documented. Three male patients harboring the variant showed severe intellectual disability. Both in vitro and in vivo studies suggested that it could reduce the translation levels of FGF13 protein. Based on the ACMG guidelines, it was classified as variant of uncertain significance (BS4+PS3_Supporting). CONCLUSION: There is insufficient evidence to classify the FGF13 c.-32C>G as a pathogenic variant in clinical practice, and its presence should not be considered an indication for pregnancy termination due to major birth defects.

Adult↗
PubMed1989

Genetic heritability and common environmental components of resting and stressed blood pressures, lipids, and body mass index in Utah pedigrees and twins.

The relative contributions of genes and shared environment to cardiovascular risk factors were studied in twins and pedigrees in 1983-1985. Sitting, standing, isometric hand grip, bicycling, and mentally stressed (serial subtraction) blood pressures were obtained from 146 male monozygous twins, 162 male dizygous twins, and 1,102 healthy adults in 67 Utah pedigrees. Fasting total plasma cholesterol, triglycerides, high density lipoprotein cholesterol (HDL), and body mass index were also measured. Heritability was estimated before and after adjusting for 12 environmental variables (measures of socioeconomic status; personality types; exercise levels; use of tobacco, alcohol, coffee, etc.) by using age-adjusted twin intraclass correlations. These heritabilities were compared with those obtained from a variance components analysis of the pedigree data separating genetic and common household effects. Sitting and standing blood pressure heritability estimates were much higher from twin than from pedigree data (39-63% in twins vs. 16-22% in pedigrees), as were those for cholesterol and triglycerides (65 and 75% from twins vs. 42 and 37% from pedigrees) and body mass index (51 vs. 21%). Estimates were similar for heritability of HDL cholesterol (51 vs. 45%). Most of the stressed blood pressure heritabilities were similar to sitting blood pressure estimates. No common household effect (except for adjusted HDL cholesterol (24%), p less than 0.01) was statistically significant for the lipids, blood pressures, or body mass index. Environmental variables correlated much better in monozygous twins and spouses than in dizygous twins, brothers, or sisters. Spouse correlations for lipids, blood pressures, and body mass index were low, with a maximum of 0.12 (p less than 0.05) for HDL cholesterol. We conclude that genes contribute much more than shared environment to the well-recognized familial correlation of blood pressures, lipids, and body mass index.

Adult↗