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Journal of Clinical Rheumatology :... Dec 2021
Topics: Humans; Osteochondrodysplasias; Pedigree; Radiography; Spine
PubMed: 31693650
DOI: 10.1097/RHU.0000000000001167 -
Semergen Apr 2022A genogram and a genealogical tree are graphic representations of families that share similarities but have different functionality and meanings. While the first basic...
A genogram and a genealogical tree are graphic representations of families that share similarities but have different functionality and meanings. While the first basic objective is to represent the family structure and the relationships between its members, the second seeks to identify the inheritance pattern and inheritable traits, although its use and applications go much further. Graphic representation is normalized with similar symbols, although some of them have different meanings. Both are used by family doctors, and they must have the necessary skills for their effective management. This work aims to improve these skills by defining the main differences between the two tools, establishing the basic elements for the construction and interpretation of a genealogical tree, and pointing out its clinical utility and its most frequent uses.
Topics: Family Relations; Humans; Pedigree; Phenotype
PubMed: 35172955
DOI: 10.1016/j.semerg.2021.10.005 -
CBE Life Sciences Education Mar 2022Pedigree problems are typical genetics tasks in schools. They are well suited to help students learn scientific reasoning, representing realistic genetic problems....
Pedigree problems are typical genetics tasks in schools. They are well suited to help students learn scientific reasoning, representing realistic genetic problems. However, pedigree problems also pose complex requirements, especially for secondary students. They require a suitable solution strategy and technical knowledge. In this study, we examined the approaches used by = 89 secondary school students when solving two different pedigree problems. In our qualitative analysis of student responses, we examined how two groups of secondary students with varying degrees of experience in genetics constructed arguments to support their decisions. To do so, we categorized = 516 propositions from students' responses using theory- and data-driven codes. Comparison between groups revealed that "advanced genetics" students ( = 44) formulated more arguments, referred more frequently to specific family constellations, and considered superficial pedigree features less often. Conversely, "beginning genetics" students did not use a conclusive approach of step-by-step falsification but argued for the mode of inheritance they believed was correct. Advanced genetics students, in contrast to beginners, to some extent used a falsification strategy. Finally, we demonstrate which family members students used in their decisions and discuss a variety of typical but unreliable arguments.
Topics: Humans; Learning; Pedigree; Problem Solving; Schools; Students
PubMed: 35084933
DOI: 10.1187/cbe.21-01-0009 -
G3 (Bethesda, Md.) Feb 2023This paper proposes a solution to a long-standing problem concerning the joint distribution of allelic identity by descent between two individuals at two linked loci....
This paper proposes a solution to a long-standing problem concerning the joint distribution of allelic identity by descent between two individuals at two linked loci. Such distributions have important applications across various fields of genetics, and detailed formulas for selected relationships appear scattered throughout the literature. However, these results were obtained essentially by brute force, with no efficient method available for general pedigrees. The recursive algorithm described in this paper, and its implementation in R, allow efficient calculation of two-locus identity coefficients in any pedigree. As a result, many existing procedures and techniques may, for the first time, be applied to complex and inbred relationships. Two such applications are discussed, concerning the expected likelihood ratio in forensic kinship testing, and variances in realized relatedness.
Topics: Humans; Pedigree; Algorithms; Alleles; Models, Genetic
PubMed: 36525359
DOI: 10.1093/g3journal/jkac326 -
JAMA Dermatology Apr 2024
Topics: Humans; Keratoderma, Palmoplantar; Pedigree
PubMed: 38477895
DOI: 10.1001/jamadermatol.2024.0117 -
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 -
Fa Yi Xue Za Zhi Oct 2020Complex kinship analysis refers to a kind of special kinship analysis taken for the purpose of personal identification or other issues in civil or criminal cases because... (Review)
Review
Complex kinship analysis refers to a kind of special kinship analysis taken for the purpose of personal identification or other issues in civil or criminal cases because the father or (and) mother is dead, or cannot participate in the analysis for other reasons. Due to the absence of significant appraised persons in this kind of kinship analysis, grandparents, siblings or collateral relatives are required to participate in the analysis. Complex kinship analysis is widely used and the demand is increasing year by year. This paper analyzes the main types of complex kinships, the genetic markers of complex kinship analysis and their advantages and disadvantages and the calculation methods for complex kinship analysis by referring to the relevant literatures at home and abroad in recent years. At the same time, the shortcomings of the present research on complex kinship and its future development are prospected.
Topics: Genetic Markers; Humans; Pedigree; Research; Siblings
PubMed: 33295173
DOI: 10.12116/j.issn.1004-5619.2020.05.016 -
Atherosclerosis May 2020Atherosclerosis and its major clinical manifestations – myocardial infarction, ischemic stroke and peripheral artery disease – remain a leading cause of death...
Atherosclerosis and its major clinical manifestations – myocardial infarction, ischemic stroke and peripheral artery disease – remain a leading cause of death worldwide. The onset of atherosclerosis is driven by the accumulation and expansion of macrophages in the artery wall in response to lipid deposition. Subsequently, the macrophage’s failure to resolve the inflammation and to exit the plaque are key processes in the progression of atherosclerosis. Understanding the underlying causes and pathological mechanisms of this chronic, low grade inflammation that sustains plaque progression has been a major focus of the field in the last decade. In this issue of , Bruikman et al identify a rare variant in the gene encoding the neuroimmune guidance molecule netrin-1 (), in a family with premature atherosclerosis, that alters netrin-1 functions and promotes proatherogenic immune responses.
Topics: Atherosclerosis; Humans; Mutation; Netrin-1; Pedigree
PubMed: 32317107
DOI: 10.1016/j.atherosclerosis.2020.04.003 -
Molecular Ecology Resources Nov 2022Genealogical relationships are fundamental components of genetic studies. However, it is often challenging to infer correct and complete pedigrees even when genome-wide...
Genealogical relationships are fundamental components of genetic studies. However, it is often challenging to infer correct and complete pedigrees even when genome-wide information is available. For example, inbreeding can obscure genetic differences between individuals, making it difficult to even distinguish first-degree relatives such as parent-offspring from full siblings. Similarly, genotyping errors can interfere with the detection of genetic similarity between parents and their offspring. Inbreeding is common in natural, domesticated, and experimental populations and genotyping of these populations often has more errors than in human data sets, so efficient methods for building pedigrees under these conditions are necessary. Here, we present a new method for parent-offspring inference in inbred pedigrees called specific parent-offspring relationship estimation (spore). spore is vastly superior to existing pedigree-inference methods at detecting parent-offspring relationships, in particular when inbreeding is high or in the presence of genotyping errors, or both. spore therefore fills an important void in the arsenal of pedigree inference tools.
Topics: Genome; Humans; Inbreeding; Models, Genetic; Pedigree
PubMed: 35770342
DOI: 10.1111/1755-0998.13680 -
BMC Medical Genomics Sep 2023To report novel pathogenic variants of X-linked genes in five Chinese families with early-onset high myopia (eoHM) by using whole-exome sequencing and analyzing the...
PURPOSE
To report novel pathogenic variants of X-linked genes in five Chinese families with early-onset high myopia (eoHM) by using whole-exome sequencing and analyzing the phenotypic features.
METHODS
5 probands with X-linked recessive related eoHM were collected in Ningxia Eye Hospital from January 2021 to June 2022. The probands and their family members received comprehensive ophthalmic examinations,and DNA was abstracted from patients and family members. Whole-exome sequencing was performed on probands to screen the causative variants, and all suspected pathogenic variants were determined by Sanger sequencing and co-segregation analysis was performed on available family members. The pathogenicity of novel variants was predicted using silico analysis and evaluated according to ACMG guidelines. RT-qPCR was used to detect differences in the relative mRNAs expression of candidate gene in mRNAs available with the proband and family members in the pedigree 2. The relationship between genetic variants and clinical features was analyzed.
RESULTS
All probands were male, and all pedigrees conformed to an X-linked recessive inheritance pattern. They were diagnosed with high myopia at their first visits between 4 and 7 years old. Spherical equivalent ranged between - 6.00D and - 11.00D.The five novel hemizygous variants were found in the probands, containing frameshift deletion variant c.797_801del (p.Val266Alafs*75) of OPN1LW gene in the pedigree 1, nonsense variant c.513G > A (p.Trp171Ter)of RP2 gene in the pedigree 2, missense variant c.98G > T (p.Cys33Phe) of GPR143 gene in the pedigree 3, frameshift deletion variant c.1876_1877del (p.Met626Valfs*22) of FRMD7 gene in the pedigree 4 and inframe deletion variant c.670_ 675del (p.Glu192_ Glu193del) of HMGB3 gene in the pedigree 5. All variants were classified as pathogenic or likely pathogenic by the interpretation principles of HGMD sequence variants and ACMG guidelines. In family 2, RT-qPCR showed that the mRNA expression of RP2 gene was lower in the proband than in other normal family members, indicating that such variant caused an effect on gene function at the mRNA expression level. Further clinical examination showed that pedigrees 1, 2, 3, and 4 were diagnosed as X-linked recessive hereditary eye disease with early-onset high myopia, including quiescent cone dysfunction, retinitis pigmentosa, ocular albinism, and idiopathic congenital nystagmus respectively. The pedigree 5 had eoHM in the right eye and ptosis in both eyes.
CONCLUSION
In this paper,we are the first to report five novel hemizygous variants in OPN1LW, RP2, GPR143, FRMD7, HMGB3 genes are associated with eoHM. Our study extends the genotypic spectrums for eoHM and better assists ophthalmologists in assessing, diagnosing, and conducting genetic screening for eoHM.
Topics: Child; Child, Preschool; Humans; Male; Cytoskeletal Proteins; East Asian People; Genes, X-Linked; Membrane Proteins; Mutation; Myopia; Age of Onset; Exome Sequencing; Pedigree
PubMed: 37749571
DOI: 10.1186/s12920-023-01665-x