Molecular Characterization of Koolen De Vries Syndrome in Two Girls with Idiopathic Intellectual Disability from Central Brazil

Nascimento, Gustavo Rios; Pinto, Irene Plaza; Melo, Aldaires Vieira de; Cruz, Damiana M. da; Ribeiro, Cristiano Luiz; Silva, Cláudio C. da; Cruz, Aparecido D. da; Minasi, Lysa Bernardes

doi:10.1159/000456910

Cited by 9 publications

(10 citation statements)

References 20 publications

(30 reference statements)

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“…LINC00989 and MAPI-IT1 are associated with congenital diseases [ 26 , 27 ], and their relationship with cancer remains unclear. No studies have reported associations between LINC01208, RP5-1-11O1.3, RP11-696F12.1, CTC-297N7.9, CTA-384D8.34, CTC-276P9.4, and cancer, but we speculate that these lncRNA may be involved in BRCA tumorigenesis.…”

Section: Discussionmentioning

confidence: 99%

Development of a Ten-lncRNA Signature Prognostic Model for Breast Cancer Survival: A Study with the TCGA Database

Zhou

Pang

Yao

et al. 2020

Analytical Cellular Pathology

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Long noncoding RNA (lncRNA) plays a critical role in the development of tumors. The aim of our study was construction of a lncRNA signature model to predict breast cancer (BRCA) patient survival. We downloaded RNA-seq data and relevant clinical information from the Cancer Genome Atlas (TCGA) database. Differentially expressed lncRNA were computed using the “edgeR” package and subjected to the univariate and multivariate Cox regression analysis. Corresponding protein-coding genes were used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis. Finally, 521 differentially expression lncRNA were obtained. We constructed a ten-lncRNA signature model (LINC01208, RP5-1011O1.3, LINC01234, LINC00989, RP11-696F12.1, RP11-909N17.2, CTC-297N7.9, CTA-384D8.34, CTC-276P9.4, and MAPT-IT1) to predict BRCA patient survival using the multivariate Cox proportional hazard regression model. The C-index was 0.712, and AUC scores of training, test, and entire sets were 0.746, 0.717, and 0.732, respectively. Univariate Cox regression analysis indicated that age, tumor status, N status, M status, and risk score were significantly related to overall survival in patients with BRCA. Further, the multivariate analysis showed that risk score and M status had outstanding independent prognostic values, both with p<0.001. The Gene Ontology (GO) function and KEEG pathway analysis was primarily enriched in immune response, receptor binding, external surface of plasma membrane, signal transduction, cytokine-cytokine receptor interaction, and cell adhesion molecules (CAMs). Finally, we constructed a ten-lncRNA signature model that can serve as an independent prognostic model to predict BRCA patient survival.

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Section: Discussionmentioning

confidence: 99%

Development of a Ten-lncRNA Signature Prognostic Model for Breast Cancer Survival: A Study with the TCGA Database

Zhou

Pang

Yao

et al. 2020

Analytical Cellular Pathology

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“…Through PhenoScanner [47], we found a proxy SNP for rs11787922, namely rs10512097 (r 2 = 0.85 in Europeans, not included in our GWAS), which was a suggestive expression quantitative trait locus (eQTL) for IMP5 (also called SPPL2C) (P = 7.18 × 10 −6 ) [48]. Deletions of this gene have been reported for some forms of intellectual disability and developmental delay [49,50], although de novo loss-of-function variants in a nearby gene were enough to cause a similar phenotype [51]. Recently, SPPL2C has been highlighted in a G × E study which examined the influence of common variants on language through low-frequency hearing ability [52].…”

Section: Discussionmentioning

confidence: 84%

Quantitative genome-wide association analyses of receptive language in the Danish High Risk and Resilience Study

et al. 2020

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Background: One of the most basic human traits is language. Linguistic ability, and disability, have been shown to have a strong genetic component in family and twin studies, but molecular genetic studies of language phenotypes are scarce, relative to studies of other cognitive traits and neurodevelopmental phenotypes. Moreover, most genetic studies examining such phenotypes do not incorporate parent-of-origin effects, which could account for some of the heritability of the investigated trait. We performed a genome-wide association study of receptive language, examining both child genetic effects and parent-of-origin effects. Results: Using a family-based cohort with 400 children with receptive language scores, we found a genome-wide significant paternal parent-of-origin effect with a SNP, rs11787922, on chromosome 9q21.31, whereby the T allele reduced the mean receptive language score by ~ 23, constituting a reduction of more than 1.5 times the population SD (P = 1.04 × 10 −8). We further confirmed that this association was not driven by broader neurodevelopmental diagnoses in the child or a family history of psychiatric diagnoses by incorporating covariates for the above and repeating the analysis. Conclusions: Our study reports a genome-wide significant association for receptive language skills; to our knowledge, this is the first documented genome-wide significant association for this phenotype. Furthermore, our study illustrates the importance of considering parent-of-origin effects in association studies, particularly in the case of cognitive or neurodevelopmental traits, in which parental genetic data are not always incorporated.

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“…In our study, the use of the CMA allowed the identification of microduplication at 17p11.2 in a boy with intellectual disability, reporting the first case of Potocki-Lupski Syndrome in Central Brazil. Furthermore, our group has applied the CMA to screen for submicroscopic genomic gains and losses in both diagnostic, cancer, and functional scenarios including mutagenesis (PEREIRA et al, 2014;NASCIMENTO et al, 2017;COSTA et al, 2018;LEITE FILHO et al, 2020;RIBEIRO et al, 2021).…”

Section: Resultsmentioning

confidence: 99%

Diagnosis of de novo 17p11.2 microduplication - potocki-lupski syndrome identified by chromosomal microarray analysis: a case report / Diagnóstico de novo 17p11.2 microduplicação - potocki-lupski síndrome identificada por análise de microarray chromosomal: um relatório de caso

Pinto¹,

Minasi²,

Melo³

et al. 2021

BJDV

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Potocki-Lupski Syndrome is a continuous gene syndrome caused by the microduplication of 3.7 Mb segment at 17p11.2 characterized by developmental delay, intellectual disability, the developmental deficit for psychomotor and expressive speech, autistic features, obsessive-compulsive behaviors, and attention deficit. Using CMA, we detected the first de novo 3.7 Mb microduplication at 17p11.2 in a boy with an intellectual disability from Central Brazil.

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Molecular Characterization of Koolen De Vries Syndrome in Two Girls with Idiopathic Intellectual Disability from Central Brazil

Cited by 9 publications

References 20 publications

Development of a Ten-lncRNA Signature Prognostic Model for Breast Cancer Survival: A Study with the TCGA Database

Development of a Ten-lncRNA Signature Prognostic Model for Breast Cancer Survival: A Study with the TCGA Database

Quantitative genome-wide association analyses of receptive language in the Danish High Risk and Resilience Study

Diagnosis of de novo 17p11.2 microduplication - potocki-lupski syndrome identified by chromosomal microarray analysis: a case report / Diagnóstico de novo 17p11.2 microduplicação - potocki-lupski síndrome identificada por análise de microarray chromosomal: um relatório de caso

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