QuickPed: an online tool for drawing pedigrees and analysing relatedness

Vigeland, Magnus Dehli

doi:10.1186/s12859-022-04759-y

Cited by 9 publications

(5 citation statements)

References 22 publications

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“…Therefore, the unification of LR can be divided into two problems: the calculation of the ratio of conditional probabilities under each state according to the participants’ genotypes (as discussed in section 2.3 ); and the Δ/ κ distribution according to the alleged relationship ( Pinto et al, 2010 ), which remains unchanged if the identification purpose is set (e.g.,

for full-sibling identification) and can be obtained from the pedigree tree using existing tools ( Vigeland, 2022 ). Thus, it is not necessary to infer the distribution of the two types of coefficients per case if there is a recognized result for the target identification.…”

Section: Methods and Resultsmentioning

confidence: 99%

An approach to unified formulae for likelihood ratio calculation in pairwise kinship analysis

Ma,

Wang,

Cong

et al. 2024

Front. Genet.

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Introduction: The likelihood ratio (LR) can be an efficient means of distinguishing various relationships in forensic fields. However, traditional list-based methods for derivation and presentation of LRs in distant or complex relationships hinder code editing and software programming. This paper proposes an approach for a unified formula for LRs, in which differences in participants’ genotype combinations can be ignored for specific identification. This formula could reduce the difficulty of by-hand coding, as well as running time of large-sample-size simulation.Methods: The approach is first applied to a problem of kinship identification in which at least one of the participants is alleged to be inbred. This can be divided into two parts: i) the probability of different identical by descent (IBD) states according to the alleged kinship; and ii) the ratio of the probability that specific genotype combination can be detected assuming the alleged kinship exists between the two participants to the similar probability assuming that they are unrelated, for each state. For the probability, there are usually recognized results for common identification purposes. For the ratio, subscript letters representing IBD alleles of individual A’s alleles are used to eliminate differences in genotype combinations between the two individuals and to obtain a unified formula for the ratio in each state. The unification is further simplified for identification cases in which it is alleged that both of the participants are outbred. Verification is performed to show that the results obtained with the unified and list-form formulae are equivalent.Results: A series of unified formulae are derived for different identification purposes, based on which an R package named KINSIMU has been developed and evaluated for use in large-size simulations for kinship analysis. Comparison between the package with two existing tools indicated that the unified approach presented here is more convenient and time-saving with respect to the coding process for computer applications compared with the list-based approach, despite appearing more complicated. Moreover, the method of derivation could be extended to other identification problems, such as those with different hypothesis sets or those involving multiple individuals.Conclusion: The unified approach of LR calculation can be beneficial in kinship identification field.

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Section: Methods and Resultsmentioning

confidence: 99%

An approach to unified formulae for likelihood ratio calculation in pairwise kinship analysis

Ma,

Wang,

Cong

et al. 2024

Front. Genet.

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“…The arrows indicate the patients (P1 and P2) described in this case report. The pedigree chart was created in the program QuickPed ( 28 ).…”

Section: Case Reportmentioning

confidence: 99%

Identification of a novel RPGR mutation associated with retinitis pigmentosa and primary ciliary dyskinesia in a Slovak family: a case report

Kolkova,

Durdik,

Holubekova

et al. 2024

Front. Pediatr.

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BackgroundThe mutations in the RPGR (retinitis pigmentosa GTPase regulator) gene are the most common cause of X-linked retinitis pigmentosa (XLRP), a rare genetic disorder affecting the photoreceptor cells in the retina. Several reported cases identified this gene as a genetic link between retinitis pigmentosa (RP) and primary ciliary dyskinesia (PCD), characterised by impaired ciliary function predominantly in the respiratory tract. Since different mutations in the same gene can result in various clinical manifestations, it is important to describe a correlation between the gene variant and the observed phenotype.MethodsTwo young brothers from a non-consanguineous Slovak family with diagnosed retinal dystrophy and recurrent respiratory infections were examined. Suspected PCD was diagnosed based on a PICADAR questionnaire, nasal nitric oxide analysis, transmission electron microscopy, high-speed video microscopy analysis, and genetic testing.ResultsWe identified a novel frameshift RPGR mutation NM_001034853: c.309_310insA, p.Glu104Argfs*12, resulting in a complex X-linked phenotype combining PCD and RP. In our patients, this mutation was associated with normal ultrastructure of respiratory cilia, reduced ciliary epithelium, more aciliary respiratory epithelium, shorter cilia, and uncoordinated beating with a frequency at a lower limit of normal beating, explaining the clinical manifestation of PCD in our patients.ConclusionThe identified novel pathogenic mutation in the RPGR gene expands the spectrum of genetic variants associated with the X-linked PCD phenotype overlapping with RP, highlighting the diversity of mutations contributing to the disorder. The described genotype–phenotype correlation can be useful in clinical practice to recognise a broader spectrum of PCD phenotypes as well as for future research focused on the genetic basis of PCD, gene interactions, the pathways implicated in PCD pathogenesis, and the role of RPGR protein for the proper functioning of cilia in various tissues throughout the body.

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“…Pedigree chart showing the distribution of chronic kidney disease in the family 11. Prepared by Soumita Bagchi.…”

Section: Case Presentationmentioning

confidence: 99%

Significance of genetic analysis in adult patients with inherited chronic kidney disease

Maity,

Barwad,

Bhowmik

et al. 2024

BMJ Case Rep

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Genetic focal segmental glomerulosclerosis (FSGS) is an important but underestimated cause of inherited proteinuric chronic kidney disease (CKD) in adults. We discuss a case of familial CKD due to inverted formin 2 (INF2) gene mutation, where three siblings had disparate phenotypic presentations ranging from CKD with subnephrotic proteinuria to nephrotic-range proteinuria with collapsing FSGS on kidney biopsy over a period of 8 years. The youngest sibling was the index case. The family agreed to undergo genetic testing only after two more siblings were diagnosed with kidney disease. This case highlights how clinical heterogeneity, absence of family history in the index case, initial lack of specific biopsy-proven diagnosis and reluctance to undergo genetic testing can delay the diagnosis of genetic kidney disease in adults.

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QuickPed: an online tool for drawing pedigrees and analysing relatedness

Cited by 9 publications

References 22 publications

An approach to unified formulae for likelihood ratio calculation in pairwise kinship analysis

An approach to unified formulae for likelihood ratio calculation in pairwise kinship analysis

Identification of a novel RPGR mutation associated with retinitis pigmentosa and primary ciliary dyskinesia in a Slovak family: a case report

Significance of genetic analysis in adult patients with inherited chronic kidney disease

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