CEP104 gene may involve in the pathogenesis of a new developmental disorder other than joubert syndrome

Badv, Reza Shervin; Mahdiannasser, Mojdeh; Rasoulinezhad, Maryam; Habibi, Laleh; Rashidi-Nezhad, Ali

doi:10.1007/s11033-022-07353-w

Cited by 4 publications

(3 citation statements)

References 30 publications

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“…Evaluation and analysis of raw data generated using the GenAP Genome Analysis Platform (Cimorgh Medical IT solutions Inc.) 12,13 . For maximum sensitivity and reducing the number of variants that require labor‐intensive specialized investigation, genotype‐driven and phenotype‐driven analyses were used in filtering.…”

Section: Methodsmentioning

confidence: 99%

“…Evaluation and analysis of raw data generated using the GenAP Genome Analysis Platform (Cimorgh Medical IT solutions Inc.). 12,13 For maximum sensitivity and reducing the number of variants that require labor-intensive specialized investigation, genotype-driven and phenotype-driven analyses were used in filtering. With the genotype-driven analysis strategy, almost all variants that may have sufficient evidence to be classified as pathogenic or likely pathogenic, including quality control (QBase <20), candidate gene identification, previously reported pathogenic variants, and Loss of function variants, were captured.…”

Section: F I G U R Ementioning

confidence: 99%

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The challenges in the interpretation of genetic variants detected by genomics techniques in patients with congenital anomalies

Vaseghi,

Akrami,

Rashidi‐Nezhad

2023

Clinical Laboratory Analysis

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BackgroundDespite the efforts that have been made to standardize the interpretation of variants, in some cases, their pathogenicity remains vague and confusing, and sometimes their interpretation does not help clinicians to establish clinical correlation using genetic test results. This study aims to shed more lights on these challenging variants.MethodsIn a clinical setting, the variants found from 81 array CGH and 79 whole exome sequencing (WES) in patients with congenital anomalies were interpreted based on American College of Medical Genetics and Genomics guidelines.ResultsIn this study, the interpretation of the disease‐causing variants and the variants with uncertain clinical significance detected by WES was far more challenging than the variants detected by array CGH. The presence of unreported clinical symptoms, incomplete penetrance, variable expressivity, parents' reluctance to analyze segregation in the family, and the limitations of prenatal tests, were among the challenging factors in the interpretation of variants in this study.ConclusionA careful study of the pedigree and disease mode of inheritance, as well as a careful clinical examination of the carrier parents in diseases with autosomal dominant inheritance, are among the primary strategies for determining the clinical significance of the variants. Continued efforts to mitigate these challenges are needed to improve the interpretation of variants.

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Section: Methodsmentioning

confidence: 99%

Section: F I G U R Ementioning

confidence: 99%

The challenges in the interpretation of genetic variants detected by genomics techniques in patients with congenital anomalies

Vaseghi,

Akrami,

Rashidi‐Nezhad

2023

Clinical Laboratory Analysis

View full text Add to dashboard Cite

show abstract

“…We found that an editing site within the 3'UTR of CEP104 gene in neurons was positively correlated with the number of cells expressing a neuronal marker TUJ1 (Figure 2E, Table S2). CEP104 gene encodes a ciliary protein and lossof-function mutations on CEP104 were found in individuals with a neurodevelopmental condition, Joubert syndrome [80][81][82] . These results indicate that RNA-editing can influence fate decisions even without having an effect on the amino acid sequence of the protein.…”

Section: Cell-type-specific Rna-editing During Human Neocortical Diff...mentioning

confidence: 99%

Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis

Aygün,

Krupa,

Mory

et al. 2023

Preprint

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The function of some genetic variants associated with brain-relevant traits has been explained through colocalization with expression quantitative trait loci (eQTL) conducted in bulk post-mortem adult brain tissue. However, many brain-trait associated loci have unknown cellular or molecular function. These genetic variants may exert context-specific function on different molecular phenotypes including post-transcriptional changes. Here, we identified genetic regulation of RNA-editing and alternative polyadenylation (APA), within a cell-type-specific population of human neural progenitors and neurons. More RNA-editing and isoforms utilizing longer polyadenylation sequences were observed in neurons, likely due to higher expression of genes encoding the proteins mediating these post-transcriptional events. We also detected hundreds of cell-type-specific editing quantitative trait loci (edQTLs) and alternative polyadenylation QTLs (apaQTLs). We found colocalizations of a neuron edQTL in CCDC88A with educational attainment and a progenitor apaQTL in EP300 with schizophrenia, suggesting genetically mediated post-transcriptional regulation during brain development lead to differences in brain function.

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Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis

Aygün,

Vuong,

Krupa

et al. 2024

The American Journal of Human Genetics

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CEP104 gene may involve in the pathogenesis of a new developmental disorder other than joubert syndrome

Cited by 4 publications

References 30 publications

The challenges in the interpretation of genetic variants detected by genomics techniques in patients with congenital anomalies

The challenges in the interpretation of genetic variants detected by genomics techniques in patients with congenital anomalies

Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis

Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis

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