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Clinical Genetics Oct 2000Pedigrees are a foundation of genetic counseling and human genetic research. To protect patient/subject and family privacy and confidentiality it is not unusual to find... (Review)
Review
Pedigrees are a foundation of genetic counseling and human genetic research. To protect patient/subject and family privacy and confidentiality it is not unusual to find published pedigrees that have been masked (i.e. a pedigree that has been changed in ways that are obvious to the reader such as diamonds to mask gender) or altered (i.e. changing pedigree information in ways that are not obvious to the reader such as changing gender and birth order or deleting unaffected siblings from the pedigree). Failure to report pedigree data (e.g. omitting ages, ethnicity, etc.) is another measure used to protect subject and family confidentiality. At what point do such practices hinder the recognition of genetic processes? Is there evidence that harm has occurred to subjects who have appeared in published pedigrees? How does the researcher or clinician determine which information is essential to record on the pedigree? The author uses a historical perspective and case examples to illustrate the issues of balancing protection of the genetic subject's privacy with the reporting of unaltered family data. The author presents several critical questions for peer reviewers and investigators to consider when a pedigree is included in a manuscript, or for researchers involved in family studies.
Topics: Eugenics; Female; Genetic Counseling; Genetics; Humans; Male; Pedigree; Publishing
PubMed: 11076049
DOI: 10.1034/j.1399-0004.2000.580401.x -
Yi Chuan = Hereditas Jul 2019Variety pedigree contains a lot of information, including parental origin, breeding methods, genetic relationship, and so on. Studying them could reveal the evolution... (Review)
Review
Variety pedigree contains a lot of information, including parental origin, breeding methods, genetic relationship, and so on. Studying them could reveal the evolution characteristics and rules of breeding and ultimately guide practice. The pedigrees of 326 wheat varieties from 1936 to 2017 in the history of the Sichuan Province was collected and analyzed in terms of breeding methods, parental composition, changes of high frequency parents and backbone parents, genetic contribution, distribution of translocation lines and synthetic germplasms. Over the past 80 years since 1930s, breeders have selected 387 direct parents from a large number of materials, made 256 combinations by means of cross breeding, and have released 314 varieties from them, which contributed directly to wheat breeding and production in Sichuan. Wheat breeding experienced a process from utilizing landraces, introducing foreign germplasm to creating breeding materials independently; high-frequency parents and backbone parents used for breeding gradually changed in different stage of the breeding history. Synthetic germplasms contributed greatly to wheat breeding in recent years. The consistency of breeding objectives will inevitably lead to the loss of genetic diversity and the fragility of genetic basis. In the future, the protection and utilization of genetic resources should be strengthened. In this review, the development of wheat breeding in Sichuan was summarized through pedigree analysis, in order to provide a reference for future research.
Topics: China; Pedigree; Plant Breeding; Triticum
PubMed: 31307969
DOI: 10.16288/j.yczz.19-081 -
BMC Bioinformatics Dec 2020Pedigree files are ubiquitously used within bioinformatics and genetics studies to convey critical information about relatedness, sex and affected status of study...
BACKGROUND
Pedigree files are ubiquitously used within bioinformatics and genetics studies to convey critical information about relatedness, sex and affected status of study samples. While the text based format of ped files is efficient for computational methods, it is not immediately intuitive to a bioinformatician or geneticist trying to understand family structures, many of which encode the affected status of individuals across multiple generations. The visualization of pedigrees into connected nodes with descriptive shapes and shading provides a far more interpretable format to recognize visual patterns and intuit family structures. Despite these advantages of a visual pedigree, it remains difficult to quickly and accurately visualize a pedigree given a pedigree text file.
RESULTS
Here we describe ped_draw a command line and web tool as a simple and easy solution to pedigree visualization. Ped_draw is capable of drawing complex multi-generational pedigrees and conforms to the accepted standards for depicting pedigrees visually. The command line tool can be used as a simple one liner command, utilizing graphviz to generate an image file. The web tool, https://peddraw.github.io , allows the user to either: paste a pedigree file, type to construct a pedigree file in the text box or upload a pedigree file. Users can save the generated image file in various formats.
CONCLUSIONS
We believe ped_draw is a useful pedigree drawing tool that improves on current methods due to its ease of use and approachability. Ped_draw allows users with various levels of expertise to quickly and easily visualize pedigrees.
Topics: Computational Biology; Humans; Pedigree; Software
PubMed: 33297934
DOI: 10.1186/s12859-020-03917-4 -
The Journal of Heredity Jul 2019How successful an individual or cohort is, in terms of their genetic contribution to the future population, is encapsulated in the concept of reproductive value, and is...
How successful an individual or cohort is, in terms of their genetic contribution to the future population, is encapsulated in the concept of reproductive value, and is crucial for understanding selection and evolution. Long-term studies of pedigreed populations offer the opportunity to estimate reproductive values directly. However, the degree to which genetic contributions, as defined by a pedigree, may converge on their long-run values within the time frames of available data sets, such that they may be interpreted as estimates of reproductive value, is unclear. We develop a system for pedigree-based calculation of the expected genetic representation that both individuals and cohorts make to the population in the years following their birth. We apply this system to inference of individual and cohort reproductive values in Soay sheep (Ovis aries) from St Kilda, Outer Hebrides. We observe that these genetic contributions appear to become relatively stable within modest time frames. As such, it may be reasonable to consider pedigree-based calculations of genetic contributions to future generations as estimates of reproductive value. This approach and the knowledge that the estimates can stabilize within decades should offer new opportunities to analyze data from pedigreed wild populations, which will be of value to many fields within evolutionary biology and demography.
Topics: Algorithms; Animals; Female; Genetics, Population; Genome; Male; Models, Genetic; Pedigree; Reproduction; Sheep; Sheep, Domestic
PubMed: 31259373
DOI: 10.1093/jhered/esz033 -
Journal of Computational Biology : a... Sep 2012Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent... (Comparative Study)
Comparative Study
Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent and child. New methods to automate this process take as input genetic data from a set of extant individuals and reconstruct ancestral individuals. There is a great need to evaluate the quality of these methods by comparing the estimated pedigree to the true pedigree. In this article, we consider two main pedigree comparison problems. The first is the pedigree isomorphism problem, for which we present a linear-time algorithm for leaf-labeled pedigrees. The second is the pedigree edit distance problem, for which we present (1) several algorithms that are fast and exact in various special cases, and (2) a general, randomized heuristic algorithm. In the negative direction, we first prove that the pedigree isomorphism problem is as hard as the general graph isomorphism problem, and that the sub-pedigree isomorphism problem is NP-hard. We then show that the pedigree edit distance problem is APX-hard in general and NP-hard on leaf-labeled pedigrees. We use simulated pedigrees to compare our edit-distance algorithms to each other as well as to a branch-and-bound algorithm that always finds an optimal solution.
Topics: Algorithms; Artificial Intelligence; Computer Simulation; Humans; Models, Genetic; Pedigree
PubMed: 22897201
DOI: 10.1089/cmb.2011.0254 -
IEEE/ACM Transactions on Computational... 2018Reconstruction of ancestral relationships among genera, species, and populations is a core task in evolutionary biology. At the population level, pedigrees have been...
Reconstruction of ancestral relationships among genera, species, and populations is a core task in evolutionary biology. At the population level, pedigrees have been commonly used. Reconstruction of pedigree is required in practice due to legal or medical reasons. Pedigrees are very important to geneticists for inferring haplotype segments, recombination, and allele sharing status with which disease loci can be identified. Evaluating reconstruction methods requires comparing the inferred pedigree and the known pedigrees. Moreover, comparison of pedigrees is required in studying relationships among crops such as maize, wheat and barley, etc. In this paper, we discuss three models for comparison of pedigrees, the maximum pedigree isomorphism problem, the maximum paternal-path-preserved mapping problem, and the minimum edge-cutting mapping problem. For the maximum pedigree isomorphism problem, we prove that the problem is NP-hard and give a fixed-parameter algorithm for the problem. For the maximum paternal-path-preserved mapping problem, we give a dynamic-programming algorithm to find the mapping that preserves the maximum number of paternal paths between the two input pedigrees. For the minimum edge-cutting mapping problem, we prove that the problem is NP-hard and give a fixed-parameter algorithm with running time , where is the number of vertices in the two input pedigrees and is the number of edges to be cut. This algorithm is useful in practice when comparing two similar pedigrees.
Topics: Algorithms; Animals; Computational Biology; Computer Simulation; Female; Male; Models, Genetic; Pedigree
PubMed: 27076461
DOI: 10.1109/TCBB.2016.2550434 -
American Journal of Human Genetics Jul 2016Accurate estimation of shared ancestry is an important component of many genetic studies; current prediction tools accurately estimate pairwise genetic relationships up...
Accurate estimation of shared ancestry is an important component of many genetic studies; current prediction tools accurately estimate pairwise genetic relationships up to the ninth degree. Pedigree-aware distant-relationship estimation (PADRE) combines relationship likelihoods generated by estimation of recent shared ancestry (ERSA) with likelihoods from family networks reconstructed by pedigree reconstruction and identification of a maximum unrelated set (PRIMUS), improving the power to detect distant relationships between pedigrees. Using PADRE, we estimated relationships from simulated pedigrees and three extended pedigrees, correctly predicting 20% more fourth- through ninth-degree simulated relationships than when using ERSA alone. By leveraging pedigree information, PADRE can even identify genealogical relationships between individuals who are genetically unrelated. For example, although 95% of 13(th)-degree relatives are genetically unrelated, in simulations, PADRE correctly predicted 50% of 13(th)-degree relationships to within one degree of relatedness. The improvement in prediction accuracy was consistent between simulated and actual pedigrees. We also applied PADRE to the HapMap3 CEU samples and report new cryptic relationships and validation of previously described relationships between families. PADRE greatly expands the range of relationships that can be estimated by using genetic data in pedigrees.
Topics: Algorithms; Female; Haplotypes; Humans; Male; Models, Genetic; Pedigree; Reproducibility of Results
PubMed: 27374771
DOI: 10.1016/j.ajhg.2016.05.020 -
American Family Physician Aug 2005The collection of a family history ranges from simply asking patients if family members have the same presenting illness to diagramming complex medical and psychosocial... (Review)
Review
The collection of a family history ranges from simply asking patients if family members have the same presenting illness to diagramming complex medical and psychosocial relationships as part of a family genogram. The three-generation pedigree provides a pictorial representation of diseases within a family and is the most efficient way to assess hereditary influences on disease. Two recent events have made family history assessment more important than ever: the completion of the Human Genome Project with resultant identification of the inherited causes of many diseases, and the establishment of national clinical practice guidelines based on systematic reviews of preventive interventions. The family history is useful in stratifying a patient's risk for rare single-gene disorders and more common diseases with multiple genetic and environmental contributions. Major organizations have endorsed using standardized symbols in pedigrees to identify inherited contributions to disease.
Topics: Genetic Predisposition to Disease; Genetic Testing; Humans; Medical History Taking; Pedigree
PubMed: 16100858
DOI: No ID Found -
American Journal of Medical Genetics Apr 1995To determine consistency in usage of pedigree symbols by genetics professionals, we reviewed pedigrees printed in 10 human genetic and medical journals and 24 medical... (Review)
Review
To determine consistency in usage of pedigree symbols by genetics professionals, we reviewed pedigrees printed in 10 human genetic and medical journals and 24 medical genetics textbooks. We found no consistent symbolization for common situations such as pregnancy, spontaneous abortion, death, or test results. Inconsistency in pedigree design can create difficulties in the interpretation of family studies and detract from the pedigree's basic strength of simple and accurate communication of medical information. We recommend the development of standard pedigree symbols, and their incorporation into genetic publications, professional genetics training programs, pedigree software programs, and genetic board examinations.
Topics: Genetics, Medical; Humans; Pedigree; Publishing
PubMed: 7778593
DOI: 10.1002/ajmg.1320560314 -
Bioinformatics (Oxford, England) Nov 2021The use and functionality of Electronic Health Records (EHR) have increased rapidly in the past few decades. EHRs are becoming an important depository of patient health...
MOTIVATION
The use and functionality of Electronic Health Records (EHR) have increased rapidly in the past few decades. EHRs are becoming an important depository of patient health information and can capture family data. Pedigree analysis is a longstanding and powerful approach that can gain insight into the underlying genetic and environmental factors in human health, but traditional approaches to identifying and recruiting families are low-throughput and labor-intensive. Therefore, high-throughput methods to automatically construct family pedigrees are needed.
RESULTS
We developed a stand-alone application: Electronic Pedigrees, or E-Pedigrees, which combines two validated family prediction algorithms into a single software package for high throughput pedigrees construction. The convenient platform considers patients' basic demographic information and/or emergency contact data to infer high-accuracy parent-child relationship. Importantly, E-Pedigrees allows users to layer in additional pedigree data when available and provides options for applying different logical rules to improve accuracy of inferred family relationships. This software is fast and easy to use, is compatible with different EHR data sources, and its output is a standard PED file appropriate for multiple downstream analyses.
AVAILABILITY AND IMPLEMENTATION
The Python 3.3+ version E-Pedigrees application is freely available on: https://github.com/xiayuan-huang/E-pedigrees.
Topics: Humans; Pedigree; Software; Algorithms; Electronic Health Records
PubMed: 34086863
DOI: 10.1093/bioinformatics/btab419