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Nature Communications Apr 2023Craniofacial microsomia (CFM; also known as Goldenhar syndrome), is a craniofacial developmental disorder of variable expressivity and severity with a recognizable set...
Craniofacial microsomia (CFM; also known as Goldenhar syndrome), is a craniofacial developmental disorder of variable expressivity and severity with a recognizable set of abnormalities. These birth defects are associated with structures derived from the first and second pharyngeal arches, can occur unilaterally and include ear dysplasia, microtia, preauricular tags and pits, facial asymmetry and other malformations. The inheritance pattern is controversial, and the molecular etiology of this syndrome is largely unknown. A total of 670 patients belonging to unrelated pedigrees with European and Chinese ancestry with CFM, are investigated. We identify 18 likely pathogenic variants in 21 probands (3.1%) in FOXI3. Biochemical experiments on transcriptional activity and subcellular localization of the likely pathogenic FOXI3 variants, and knock-in mouse studies strongly support the involvement of FOXI3 in CFM. Our findings indicate autosomal dominant inheritance with reduced penetrance, and/or autosomal recessive inheritance. The phenotypic expression of the FOXI3 variants is variable. The penetrance of the likely pathogenic variants in the seemingly dominant form is reduced, since a considerable number of such variants in affected individuals were inherited from non-affected parents. Here we provide suggestive evidence that common variation in the FOXI3 allele in trans with the pathogenic variant could modify the phenotypic severity and accounts for the incomplete penetrance.
Topics: Animals; Mice; Goldenhar Syndrome; Facial Asymmetry; Pedigree; Forkhead Transcription Factors
PubMed: 37041148
DOI: 10.1038/s41467-023-37703-6 -
Taiwanese Journal of Obstetrics &... Mar 2022To investigate the phenotypes, biochemical features and genotypes for 244 pedigrees with methylmalonic aciduria (MMA) in China, and to perform the prenatal genetic...
OBJECTIVES
To investigate the phenotypes, biochemical features and genotypes for 244 pedigrees with methylmalonic aciduria (MMA) in China, and to perform the prenatal genetic diagnosis by chorionic villus for these pedigrees.
MATERIALS AND METHODS
Gene analyses were performed for 244 pedigrees. There are 130 pedigrees, chorionic villus sampling was performed on the pregnant women to conduct the prenatal diagnosis.
RESULTS
Among 244 patients, 168 (68.9%) cases were combined methylmalonic aciduria and homocystinuria, 76 (31.1%) cases were isolated methylmalonic aciduria. All the patients were diagnosed with MMA by their clinical manifestation, elevated blood propionylcarnitine, propionylcarnitine to acetylcarnitine ratio, and/or urine/blood methylmalonic acid with or without homocysteine. MMACHC, MMUT, SUCLG1 and LMBRD1 gene variants were found in 236 (96.7%) pedigrees included 6 probands with only one heterozygous variant out of 244 cases. For the 130 pedigrees who received a prenatal diagnosis, 22 fetuses were normal, 69 foetuses were carriers of heterozygous variants, and the remaining 39 foetuses harboured compound heterozygous variants or homozygous variants. The follow-up results were consistent with the prenatal diagnosis.
CONCLUSION
The present study indicates genetic heterogeneity in MMA patients. Genetic analysis is a convenient method for prenatal diagnosis that will aid in avoiding the delivery of MMA patients.
Topics: Amino Acid Metabolism, Inborn Errors; China; Female; Genotype; Humans; Nucleocytoplasmic Transport Proteins; Oxidoreductases; Pedigree; Pregnancy; Prenatal Diagnosis
PubMed: 35361390
DOI: 10.1016/j.tjog.2022.02.017 -
Molecular Ecology Oct 2018The concept of kinship permeates many domains of fundamental and applied biology ranging from social evolution to conservation science to quantitative and human...
The concept of kinship permeates many domains of fundamental and applied biology ranging from social evolution to conservation science to quantitative and human genetics. Until recently, pedigrees were the gold standard to infer kinship, but the advent of next-generation sequencing and the availability of dense genetic markers in many species make it a good time to (re)evaluate the usefulness of genetic markers in this context. Using three published data sets where both pedigrees and markers are available, we evaluate two common and a new genetic estimator of kinship. We show discrepancies between pedigree values and marker estimates of kinship and explore via simulations the possible reasons for these. We find these discrepancies are attributable to two main sources: pedigree errors and heterogeneity in the origin of founders. We also show that our new marker-based kinship estimator has very good statistical properties and behaviour and is particularly well suited for situations where the source population is of small size, as will often be the case in conservation biology, and where high levels of kinship are expected, as is typical in social evolution studies.
Topics: Genetic Markers; Genetics, Population; Humans; Models, Genetic; Pedigree
PubMed: 30107060
DOI: 10.1111/mec.14833 -
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 -
Bioinformatics (Oxford, England) Jul 2023The resemble between relatives computed from pedigree and genomic data is an important resource for geneticists and ecologists, who are interested in understanding how...
MOTIVATION
The resemble between relatives computed from pedigree and genomic data is an important resource for geneticists and ecologists, who are interested in understanding how genes influence phenotypic variation, fitness adaptation, and population dynamics.
RESULTS
The AGHmatrix software is an R package focused on the construction of pedigree (A matrix) and/or molecular markers (G matrix), with the possibility of building a combined matrix of pedigree corrected by molecular markers (H matrix). Designed to estimate the relationships for any ploidy level, the software also includes auxiliary functions related to filtering molecular markers, and checks pedigree errors in large data sets. After computing the relationship matrices, results from the AGHmatrix can be used in different contexts, including on prediction of (genomic) estimated breeding values and genome-wide association studies.
AVAILABILITY AND IMPLEMENTATION
AGHmatrix v2.1.0 is available under GPL-3 license in CRAN at https://cran.r-project.org/web/packages/AGHmatrix/index.html and also in GitHub at https://github.com/rramadeu/AGHmatrix. It has a comprehensive tutorial, and it follows with real data examples.
Topics: Genome-Wide Association Study; Software; Genomics; Ploidies; Pedigree
PubMed: 37471595
DOI: 10.1093/bioinformatics/btad445 -
American Journal of Medical Genetics.... May 2023Exome sequencing is a powerful tool in prenatal and postnatal genetics and can help identify novel candidate genes critical to human development. We describe seven... (Review)
Review
Exome sequencing is a powerful tool in prenatal and postnatal genetics and can help identify novel candidate genes critical to human development. We describe seven unpublished probands with rare likely pathogenic variants or variants of uncertain significance that segregate with recessive disease in TBC1D32, including four fetal probands in three unrelated pedigrees and three pediatric probands in unrelated pedigrees. We also report clinical comparisons with seven previously published patients. Index probands were identified through an ongoing prenatal exome sequencing study and through an online data sharing platform (Gene Matcher™). A literature review was also completed. TBC1D32 is involved in the development and function of cilia and is expressed in the developing hypothalamus and pituitary gland. We provide additional data to expand the phenotype correlated with TBC1D32 variants, including a severe prenatal phenotype associated with life-limiting congenital anomalies.
Topics: Pregnancy; Female; Humans; Child; Phenotype; Ciliopathies; Pedigree; Adaptor Proteins, Signal Transducing
PubMed: 36826837
DOI: 10.1002/ajmg.a.63150 -
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 -
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 -
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