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Tang X, Yi S, Qin Z, Yi S, Chen J, Yang Q, Li S, Luo J. Compound heterozygous WDR19 variants associated with nephronophthisis, Caroli disease, refractory epilepsy and congenital bilateral central blindness: Case report. Heliyon 2024; 10:e23257. [PMID: 38163131 PMCID: PMC10754840 DOI: 10.1016/j.heliyon.2023.e23257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
The WDR19 gene has been reported to be involved in nephronophthisis-related ciliopathies such as isolated nephronophthisis 13 (NPHP13), Sensenbrenner syndrome, Jeune syndrome, Senior-Loken syndrome, Caroli disease, retinitis pigmentosa and Asthenoteratospermia. In the present study, we provided the detailed clinical characteristics and genetic analysis of a patient with four variants in WDR19 and TG, reviewed a comprehensive mutation analysis in the WDR19-related ciliopathies, discussed the relationship between genotype and phenotype, and compared the allele frequencies (AFs) of WDR19 variants depending on the ethnic background. We used whole-exome sequencing (WES) combined with bioinformatics analysis to investigate the genetic variants of a 3-year-old boy with common features of WDR19-associated NPHP13 and Caroli disease, bilateral central blindness, refractory epilepsy, and elevated thyroid stimulating hormone. A novel splice-donor variant, c.98+1G > C, and a recurrent missense variant, c.3533G > A, were identified in the WDR19 gene. We used effective mRNA analysis to verify the effects on pre-mRNA processing and to assess the pathogenicity of the splice-site variant. The patient also harbored compound heterozygous variants of the TG gene (c.4889A > G, c.274+2T > G). Of note, using a review of an in-house database, we identified four additional likely pathogenic WDR19 variants and estimated the overall AF of WDR19 mutations to be 0.0025 in the southern Chinese population. Our findings have expanded the allelic spectrum of mutations in the WDR19 gene and broadened the clinical phenotype spectrum of WDR19-related ciliopathies. The results have also provided new insights into the clinical heterogeneity of the disorder, which would be useful in accurate genetic counseling for affected individuals and carrier screening in a general population.
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Affiliation(s)
- Xianglian Tang
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Sheng Yi
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zailong Qin
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shang Yi
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Junjie Chen
- Department of Radiology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qi Yang
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shanshan Li
- Department of Radiology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jingsi Luo
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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Cao C, Kossinna P, Kwok D, Li Q, He J, Su L, Guo X, Zhang Q, Long Q. Disentangling genetic feature selection and aggregation in transcriptome-wide association studies. Genetics 2021; 220:6444993. [PMID: 34849857 DOI: 10.1093/genetics/iyab216] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/04/2021] [Indexed: 12/14/2022] Open
Abstract
The success of transcriptome-wide association studies (TWAS) has led to substantial research towards improving the predictive accuracy of its core component of Genetically Regulated eXpression (GReX). GReX links expression information with genotype and phenotype by playing two roles simultaneously: it acts as both the outcome of the genotype-based predictive models (for predicting expressions) and the linear combination of genotypes (as the predicted expressions) for association tests. From the perspective of machine learning (considering SNPs as features), these are actually two separable steps-feature selection and feature aggregation-which can be independently conducted. In this work, we show that the single approach of GReX limits the adaptability of TWAS methodology and practice. By conducting simulations and real data analysis, we demonstrate that disentangled protocols adapting straightforward approaches for feature selection (e.g., simple marker test) and aggregation (e.g., kernel machines) outperform the standard TWAS protocols that rely on GReX. Our development provides more powerful novel tools for conducting TWAS. More importantly, our characterization of the exact nature of TWAS suggests that, instead of questionably binding two distinct steps into the same statistical form (GReX), methodological research focusing on optimal combinations of feature selection and aggregation approaches will bring higher power to TWAS protocols.
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Affiliation(s)
- Chen Cao
- Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Pathum Kossinna
- Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Devin Kwok
- Department of Mathematics & Statistics, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Qing Li
- Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jingni He
- Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Liya Su
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Qingrun Zhang
- Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.,Department of Mathematics & Statistics, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Quan Long
- Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.,Department of Mathematics & Statistics, University of Calgary, Calgary, AB T2N 1N4, Canada.,Department of Medical Genetics, University of Calgary, Calgary, AB T2N 4N1, Canada.,Hotchkiss Brain Institute, O'Brien Institute for Public Health, University of Calgary, Calgary, AB T2N 4N1, Canada
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Ramachandran D, Dörk T. Genomic Risk Factors for Cervical Cancer. Cancers (Basel) 2021; 13:5137. [PMID: 34680286 PMCID: PMC8533931 DOI: 10.3390/cancers13205137] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/04/2021] [Accepted: 10/11/2021] [Indexed: 12/28/2022] Open
Abstract
Cervical cancer is the fourth common cancer amongst women worldwide. Infection by high-risk human papilloma virus is necessary in most cases, but not sufficient to develop invasive cervical cancer. Despite a predicted genetic heritability in the range of other gynaecological cancers, only few genomic susceptibility loci have been identified thus far. Various case-control association studies have found corroborative evidence for several independent risk variants at the 6p21.3 locus (HLA), while many reports of associations with variants outside the HLA region remain to be validated in other cohorts. Here, we review cervical cancer susceptibility variants arising from recent genome-wide association studies and meta-analysis in large cohorts and propose 2q14 (PAX8), 17q12 (GSDMB), and 5p15.33 (CLPTM1L) as consistently replicated non-HLA cervical cancer susceptibility loci. We further discuss the available evidence for these loci, knowledge gaps, future perspectives, and the potential impact of these findings on precision medicine strategies to combat cervical cancer.
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Affiliation(s)
| | - Thilo Dörk
- Gynaecology Research Unit, Department of Gynaecology and Obstetrics, Comprehensive Cancer Center, Hannover Medical School, D-30625 Hannover, Germany;
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