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Nunes N, Carvalho Nunes B, Zamariolli M, Cordeiro de Queiroz Soares D, Caires dos Santos L, Gollo Dantas A, Ayres Meloni V, Iole Belangero S, Gil-Da-Silva-Lopes VL, Ae Kim C, Melaragno MI. Variants in Candidate Genes for Phenotype Heterogeneity in Patients with the 22q11.2 Deletion Syndrome. Genet Res (Camb) 2024; 2024:5549592. [PMID: 38586596 PMCID: PMC10998724 DOI: 10.1155/2024/5549592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/29/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024] Open
Abstract
22q11.2 deletion syndrome (22q11.2DS) is a microdeletion syndrome with a broad and heterogeneous phenotype, even though most of the deletions present similar sizes, involving ∼3 Mb of DNA. In a relatively large population of a Brazilian 22q11.2DS cohort (60 patients), we investigated genetic variants that could act as genetic modifiers and contribute to the phenotypic heterogeneity, using a targeted NGS (Next Generation Sequencing) with a specific Ion AmpliSeq panel to sequence nine candidate genes (CRKL, MAPK1, HIRA, TANGO2, PI4KA, HDAC1, ZDHHC8, ZFPM2, and JAM3), mapped in and outside the 22q11.2 hemizygous deleted region. In silico prediction was performed, and the whole-genome sequencing annotation analysis package (WGSA) was used to predict the possible pathogenic effect of single nucleotide variants (SNVs). For the in silico prediction of the indels, we used the genomic variants filtered by a deep learning model in NGS (GARFIELD-NGS). We identified six variants, 4 SNVs and 2 indels, in MAPK1, JAM3, and ZFPM2 genes with possibly synergistic deleterious effects in the context of the 22q11.2 deletion. Our results provide the opportunity for the discovery of the co-occurrence of genetic variants with 22q11.2 deletions, which may influence the patients´ phenotype.
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Affiliation(s)
- Natalia Nunes
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Beatriz Carvalho Nunes
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Leonardo Caires dos Santos
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Anelisa Gollo Dantas
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vera Ayres Meloni
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Sintia Iole Belangero
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vera Lúcia Gil-Da-Silva-Lopes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Chong Ae Kim
- Genetics Unit, Instituto da Criança, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
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Lu P, Shangguan W, Zhao Q. HIC2 promotes cell cycle transitions by upregulating CDK1 expression in glioblastoma. Asian J Surg 2023; 46:4536-4538. [PMID: 37202257 DOI: 10.1016/j.asjsur.2023.04.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 04/28/2023] [Indexed: 05/20/2023] Open
Affiliation(s)
- Peifen Lu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Wenbing Shangguan
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China.
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Gavril EC, Popescu R, Nucă I, Ciobanu CG, Butnariu LI, Rusu C, Pânzaru MC. Different Types of Deletions Created by Low-Copy Repeats Sequences Location in 22q11.2 Deletion Syndrome: Genotype-Phenotype Correlation. Genes (Basel) 2022; 13:2083. [PMID: 36360320 PMCID: PMC9690028 DOI: 10.3390/genes13112083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/21/2022] [Accepted: 11/08/2022] [Indexed: 09/19/2023] Open
Abstract
The most frequent microdeletion, 22q11.2 deletion syndrome (22q11.2DS), has a wide and variable phenotype that causes difficulties in diagnosis. 22q11.2DS is a contiguous gene syndrome, but due to the existence of several low-copy-number repeat sequences (LCR) it displays a high variety of deletion types: typical deletions LCR A-D-the most common (~90%), proximal deletions LCR A-B, central deletions (LCR B, C-D) and distal deletions (LCR D-E, F). METHODS We conducted a retrospective study of 59 22q11.2SD cases, with the aim of highlighting phenotype-genotype correlations. All cases were tested using MLPA combined kits: SALSA MLPA KIT P245 and P250 (MRC Holland). RESULTS most cases (76%) presented classic deletion LCR A-D with various severity and phenotypic findings. A total of 14 atypical new deletions were identified: 2 proximal deletions LCR A-B, 1 CES (Cat Eye Syndrome region) to LCR B deletion, 4 nested deletions LCR B-D and 1 LCR C-D, 3 LCR A-E deletions, 1 LCR D-E, and 2 small single gene deletions: delDGCR8 and delTOP3B. CONCLUSIONS This study emphasizes the wide phenotypic variety and incomplete penetrance of 22q11.2DS. Our findings contribute to the genotype-phenotype data regarding different types of 22q11.2 deletions and illustrate the usefulness of MLPA combined kits in 22q11.2DS diagnosis.
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Affiliation(s)
- Eva-Cristiana Gavril
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Investigații Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Roxana Popescu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Department of Medical Genetics “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Irina Nucă
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Investigații Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Cristian-Gabriel Ciobanu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
| | - Lăcrămioara Ionela Butnariu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Department of Medical Genetics “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Cristina Rusu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Department of Medical Genetics “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Monica-Cristina Pânzaru
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Department of Medical Genetics “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
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Raje NR, Noel-MacDonnell JR, Shortt KA, Gigliotti NM, Chan MA, Heruth DP. T Cell Transcriptome in Chromosome 22q11.2 Deletion Syndrome. THE JOURNAL OF IMMUNOLOGY 2022; 209:874-885. [DOI: 10.4049/jimmunol.2100346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/23/2022] [Indexed: 11/05/2022]
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Wu X, Huai C, Shen L, Li M, Yang C, Zhang J, Chen L, Zhu W, Fan L, Zhou W, Xing Q, He L, Wan C, Qin S. Genome-wide study of copy number variation implicates multiple novel loci for schizophrenia risk in Han Chinese family trios. iScience 2021; 24:102894. [PMID: 34401673 PMCID: PMC8358640 DOI: 10.1016/j.isci.2021.102894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/17/2021] [Accepted: 07/19/2021] [Indexed: 01/22/2023] Open
Abstract
Schizophrenia (SCZ) is a severe neuropsychiatric disorder that affects 1% of the global population. Copy number variations (CNVs) have been shown to play a critical role in its pathophysiology; however, only case-control studies on SCZ susceptibility CNVs have been conducted in Han Chinese. Here, we performed an array comparative genomic hybridization-based genome-wide CNV analysis in 100 Chinese family trios with SCZ. Burden test suggested that the SCZ probands carried more duplications than their healthy parents and unrelated healthy controls. Besides, five CNV loci were firstly reported to be associated with SCZ here, including both unbalanced transmitted CNVs and enriched de novo CNVs. Moreover, two genes (CTDSPL and MGAM) in these CNVs showed significant SCZ relevance in the expression level. Our findings support the crucial role of CNVs in the etiology of SCZ and provide new insights into the underlying mechanism of SCZ pathogenesis.
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Affiliation(s)
- Xi Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Cong Huai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Lu Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Mo Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Chao Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Juan Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Luan Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wenli Zhu
- The Fourth People's Hospital of Wuhu, Wuhu, Anhui, 241000, China
| | - Lingzi Fan
- Zhumadian Psychiatric Hospital, Zhumadian, Henan, 463000, China
| | - Wei Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Qinghe Xing
- Children's Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
- Corresponding author
| | - Chunling Wan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
- Corresponding author
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
- Corresponding author
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Pineda T, Zarante I, Paredes AC, Rozo JP, Reyes MC, Moreno-Niño OM. CNVs in the 22q11.2 Chromosomal Region Should Be an Early Suspect in Infants with Congenital Cardiac Disease. CLINICAL MEDICINE INSIGHTS-CARDIOLOGY 2021; 15:11795468211016870. [PMID: 34104029 PMCID: PMC8155773 DOI: 10.1177/11795468211016870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 04/19/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Congenital heart disease (CHD) is the most common congenital malformation, it is frequently found as an isolated defect, and the etiology is not completely understood. Although most of the cases have multifactorial causes, they can also be secondary to chromosomal abnormalities, monogenic diseases, microduplications or microdeletions, among others. Copy number variations (CNVs) at 22q11.2 are associated with a variety of symptoms including CHD, thymic aplasia, and developmental and behavioral manifestations. We tested CNVs in the 22q11.2 chromosomal region by MLPA in a cohort of Colombian patients with isolated CHD to establish the frequency of these CNVs in the cohort. METHODS CNVs analysis of 22q11.2 by MLPA were performed in 32 patients with apparently isolate CHD during the neonatal period. Participants were enrolled from different hospitals in Bogotá, and they underwent a clinical assessment by a cardiologist and a clinical geneticist. RESULTS CNVs in the 22q11.2 chromosomal region were found in 7 patients (21.9%). The typical deletion was found in 6 patients (18.75%) and atypical 1.5 Mb duplication was found in 1 patient (3.1%). CONCLUSIONS CNVs in 22q11.2 is a common finding in patients presenting with isolated congenital cardiac disease, therefore these patients should be tested early despite the absence of other clinical manifestations. MLPA is a very useful molecular method and provides an accurate diagnosis.
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Affiliation(s)
- Tatiana Pineda
- Institute of Human Genetics, Pontificia
Universidad Javeriana, Bogotá, Colombia
- San Ignacio University Hospital,
Bogotá, Colombia
| | - Ignacio Zarante
- Institute of Human Genetics, Pontificia
Universidad Javeriana, Bogotá, Colombia
- San Ignacio University Hospital,
Bogotá, Colombia
| | - Angela Camila Paredes
- Institute of Human Genetics, Pontificia
Universidad Javeriana, Bogotá, Colombia
- San Ignacio University Hospital,
Bogotá, Colombia
| | | | - Martha C. Reyes
- Cardiopediatrics Intensive Care Unit,
Cardioinfantil Foundation, Bogotá, Colombia
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Screening of 22q11.2DS Using Multiplex Ligation-Dependent Probe Amplification as an Alternative Diagnostic Method. BIOMED RESEARCH INTERNATIONAL 2021; 2020:6945730. [PMID: 33062692 PMCID: PMC7539069 DOI: 10.1155/2020/6945730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/06/2020] [Indexed: 11/18/2022]
Abstract
Background The 22q11.2 deletion syndrome (22q11.2DS) is the most common form of deletion disorder in humans. Low copy repeats flanking the 22q11.2 region confers a substrate for nonallelic homologous recombination (NAHR) events leading to rearrangements which have been reported to be associated with highly variable and expansive phenotypes. The 22q11.2DS is reported as the most common genetic cause of congenital heart defects (CHDs). Methods A total of 42 patients with congenital heart defects, as confirmed by echocardiography, were recruited. Genetic molecular analysis using a fluorescence in situ hybridization (FISH) technique was conducted as part of routine 22q11.2DS screening, followed by multiplex ligation-dependent probe amplification (MLPA), which serves as a confirmatory test. Results Two of the 42 CHD cases (4.76%) indicated the presence of 22q11.2DS, and interestingly, both cases have conotruncal heart defects. In terms of concordance of techniques used, MLPA is superior since it can detect deletions within the 22q11.2 locus and outside of the typically deleted region (TDR) as well as duplications. Conclusion The incidence of 22q11.2DS among patients with CHD in the east coast of Malaysia is 0.047. MLPA is a scalable and affordable alternative molecular diagnostic method in the screening of 22q11.2DS and can be routinely applied for the diagnosis of deletion syndromes.
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Stefekova A, Capkova P, Capkova Z, Curtisova V, Srovnal J, Mracka E, Klaskova E, Prochazka M. MLPA analysis of 32 foetuses with a congenital heart defect and 1 foetus with renal defects - pilot study. The significant frequency rate of presented pathological CNV. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2021; 166:187-194. [PMID: 33824538 DOI: 10.5507/bp.2021.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/17/2021] [Indexed: 11/23/2022] Open
Abstract
AIMS The aim of this retrospective study was to determine the detection rate of the pathogenic copy number variants (CNVs) in a cohort of 33 foetuses - 32 with CHD (congenital heart defects) and 1 with kidney defect, after exclusion of common aneuploidies (trisomy 13, 18, 21, and monosomy X) by karyotyping, Multiplex ligation - dependent probe amplification (MLPA) and chromosomal microarray analysis (CMA). We also assess the effectivity of MLPA as a method of the first tier for quick and inexpensive detection of mutations, causing congenital malformations in foetuses. METHODS MLPA with probe mixes P070, P036 - Telomere 3 and 5, P245 - microdeletions, P250 - DiGeorge syndrome, and P311 - CHD (Congenital heart defects) was performed in 33 samples of amniotic fluid and chorionic villi. CMA was performed in 10 relevant cases. RESULTS Pathogenic CNVs were found in 5 samples: microdeletions in region 22q11.2 (≈2 Mb) in two foetuses, one distal microdeletion of the 22q11.2 region containing genes LZTR1, CRKL, AIFM3 and SNAP29 (≈416 kb) in the foetus with bilateral renal agenesis, 8p23.1 (3.8 Mb) microdeletion syndrome and microdeletion in area 9q34.3 (1.7 Mb, Kleefstra syndrome). MLPA as an initial screening method revealed unambiguously pathogenic CNVs in 15.2 % of samples. CONCLUSION Our study suggests that MLPA and CMA are a reliable and high-resolution technology and should be used as the first-tier test for prenatal diagnosis of congenital heart disease. Determination of the cause of the abnormality is crucial for genetic counselling and further management of the pregnancy.
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Affiliation(s)
- Andrea Stefekova
- Department of Medical Genetics, University Hospital Olomouc, Czech Republic.,Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Pavlina Capkova
- Department of Medical Genetics, University Hospital Olomouc, Czech Republic.,Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Zuzana Capkova
- Department of Medical Genetics, University Hospital Olomouc, Czech Republic.,Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Vaclava Curtisova
- Department of Medical Genetics, University Hospital Olomouc, Czech Republic
| | - Josef Srovnal
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic.,Department of Pediatrics, University Hospital Olomouc, Czech Republic
| | - Enkhjargalan Mracka
- Department of Medical Genetics, University Hospital Olomouc, Czech Republic.,Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Eva Klaskova
- Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic.,Department of Pediatrics, University Hospital Olomouc, Czech Republic
| | - Martin Prochazka
- Department of Medical Genetics, University Hospital Olomouc, Czech Republic.,Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
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Non coding RNAs as the critical factors in chemo resistance of bladder tumor cells. Diagn Pathol 2020; 15:136. [PMID: 33183321 PMCID: PMC7659041 DOI: 10.1186/s13000-020-01054-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/05/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Bladder cancer (BCa) is the ninth frequent and 13th leading cause of cancer related deaths in the world which is mainly observed among men. There is a declining mortality rates in developed countries. Although, the majority of BCa patients present Non-Muscle-Invasive Bladder Cancer (NMIBC) tumors, only 30% of patients suffer from muscle invasion and distant metastases. Radical cystoprostatectomy, radiation, and chemotherapy have proven to be efficient in metastatic tumors. However, tumor relapse is observed in a noticeable ratio of patients following the chemotherapeutic treatment. Non-coding RNAs (ncRNAs) are important factors during tumor progression and chemo resistance which can be used as diagnostic and prognostic biomarkers of BCa. MAIN BODY In present review we summarized all of the lncRNAs and miRNAs associated with chemotherapeutic resistance in bladder tumor cells. CONCLUSIONS This review paves the way of introducing a prognostic panel of ncRNAs for the BCa patients which can be useful to select a proper drug based on the lncRNA profiles of patients to reduce the cytotoxic effects of chemotherapy in such patients.
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Prenatal diagnosis of 22q11.2 copy number abnormalities in fetuses via single nucleotide polymorphism array. Mol Biol Rep 2020; 47:7529-7535. [PMID: 32935260 PMCID: PMC7588391 DOI: 10.1007/s11033-020-05815-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/04/2020] [Indexed: 10/30/2022]
Abstract
The q11.2 region on chromosome 22 contains numerous low-copy repeats that lead to deleted or duplicated regions in the chromosome, thereby resulting in different syndromes characterized by intellectual disabilities or congenital anomalies. The association between patient phenotypes and 22q11.2 copy number abnormalities has been previously described in postnatal cases; however, these features have not been systematically evaluated in prenatal cases because of limitations in phenotypic identification in prenatal testing. In this study, we investigated the detection rate of 22q11.2 copy number abnormalities in 2500 fetuses using single nucleotide polymorphism (SNP) array and determined the common abnormal ultrasound findings in fetuses carrying the 22q11.2 copy number abnormalities. The 22q11.2 copy number abnormalities were identified in 13 fetuses with cardiovascular malformations (6/13), kidney malformations (3/13), isolated ultrasound markers (3/13), or high-risk Down syndrome based on maternal serum screening (1/13). Approximately 0.5% (13/2500) of the fetuses harbored 22q11.2 copy number abnormalities. The most frequent ultrasound findings in fetuses with these abnormalities were cardiovascular malformations, followed by kidney malformations and isolated ultrasound markers. Prenatal diagnosis of these genetic abnormalities allows for the delineation of differential diagnoses, characterization of a wide spectrum of associated malformations, and determination of associations that exist between prenatal diagnosis and obstetrical outcomes.
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Consequences of 22q11.2 Microdeletion on the Genome, Individual and Population Levels. Genes (Basel) 2020; 11:genes11090977. [PMID: 32842603 PMCID: PMC7563277 DOI: 10.3390/genes11090977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 12/27/2022] Open
Abstract
Chromosomal 22q11.2 deletion syndrome (22q11.2DS) (ORPHA: 567) caused by microdeletion in chromosome 22 is the most common chromosomal microdeletion disorder in humans. Despite the same change on the genome level, like in the case of monozygotic twins, phenotypes are expressed differently in 22q11.2 deletion individuals. The rest of the genome, as well as epigenome and environmental factors, are not without influence on the variability of phenotypes. The penetrance seems to be more genotype specific than deleted locus specific. The transcript levels of deleted genes are not usually reduced by 50% as assumed due to haploinsufficiency. 22q11.2DS is often an undiagnosed condition, as each patient may have a different set out of 180 possible clinical manifestations. Diverse dysmorphic traits are present in patients from different ethnicities, which makes diagnosis even more difficult. 22q11.2 deletion syndrome serves as an example of a genetic syndrome that is not easy to manage at all stages: diagnosis, consulting and dealing with.
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12
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Du Q, de la Morena MT, van Oers NSC. The Genetics and Epigenetics of 22q11.2 Deletion Syndrome. Front Genet 2020; 10:1365. [PMID: 32117416 PMCID: PMC7016268 DOI: 10.3389/fgene.2019.01365] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/12/2019] [Indexed: 12/19/2022] Open
Abstract
Chromosome 22q11.2 deletion syndrome (22q11.2del) is a complex, multi-organ disorder noted for its varying severity and penetrance among those affected. The clinical problems comprise congenital malformations; cardiac problems including outflow tract defects, hypoplasia of the thymus, hypoparathyroidism, and/or dysmorphic facial features. Additional clinical issues that can appear over time are autoimmunity, renal insufficiency, developmental delay, malignancy and neurological manifestations such as schizophrenia. The majority of individuals with 22q11.2del have a 3 Mb deletion of DNA on chromosome 22, leading to a haploinsufficiency of ~106 genes, which comprise coding RNAs, noncoding RNAs, and pseudogenes. The consequent haploinsufficiency of many of the coding genes are well described, including the key roles of T-box Transcription Factor 1 (TBX1) and DiGeorge Critical Region 8 (DGCR8) in the clinical phenotypes. However, the haploinsufficiency of these genes alone cannot account for the tremendous variation in the severity and penetrance of the clinical complications among those affected. Recent RNA and DNA sequencing approaches are uncovering novel genetic and epigenetic differences among 22q11.2del patients that can influence disease severity. In this review, the role of coding and non-coding genes, including microRNAs (miRNA) and long noncoding RNAs (lncRNAs), will be discussed in relation to their bearing on 22q11.2del with an emphasis on TBX1.
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Affiliation(s)
- Qiumei Du
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - M. Teresa de la Morena
- Department of Pediatrics, The University of Washington and Seattle Children’s Hospital, Seattle, WA, United States
| | - Nicolai S. C. van Oers
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
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Shin G, Greer SU, Xia LC, Lee H, Zhou J, Boles TC, Ji HP. Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes. Nucleic Acids Res 2019; 47:e115. [PMID: 31350896 PMCID: PMC6821272 DOI: 10.1093/nar/gkz661] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 07/02/2019] [Accepted: 07/18/2019] [Indexed: 11/12/2022] Open
Abstract
The human genome is composed of two haplotypes, otherwise called diplotypes, which denote phased polymorphisms and structural variations (SVs) that are derived from both parents. Diplotypes place genetic variants in the context of cis-related variants from a diploid genome. As a result, they provide valuable information about hereditary transmission, context of SV, regulation of gene expression and other features which are informative for understanding human genetics. Successful diplotyping with short read whole genome sequencing generally requires either a large population or parent-child trio samples. To overcome these limitations, we developed a targeted sequencing method for generating megabase (Mb)-scale haplotypes with short reads. One selects specific 0.1-0.2 Mb high molecular weight DNA targets with custom-designed Cas9-guide RNA complexes followed by sequencing with barcoded linked reads. To test this approach, we designed three assays, targeting the BRCA1 gene, the entire 4-Mb major histocompatibility complex locus and 18 well-characterized SVs, respectively. Using an integrated alignment- and assembly-based approach, we generated comprehensive variant diplotypes spanning the entirety of the targeted loci and characterized SVs with exact breakpoints. Our results were comparable in quality to long read sequencing.
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Affiliation(s)
- GiWon Shin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stephanie U Greer
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Li C Xia
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jun Zhou
- Sage Science, Inc., Beverly, MA 01915, USA
| | | | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.,Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
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14
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Rozas MF, Benavides F, León L, Repetto GM. Association between phenotype and deletion size in 22q11.2 microdeletion syndrome: systematic review and meta-analysis. Orphanet J Rare Dis 2019; 14:195. [PMID: 31399107 PMCID: PMC6688301 DOI: 10.1186/s13023-019-1170-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 07/30/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Chromosome 22q11.2 microdeletion syndrome, a disorder caused by heterozygous loss of genetic material in chromosome region 22q11.2, has a broad range of clinical symptoms. The most common congenital anomalies involve the palate in 80% of patients, and the heart in 50-60% of them. The cause of the phenotypic variability is unknown. Patients usually harbor one of three common deletions sizes: 3, 2 and 1.5 Mb, between low copy repeats (LCR) designated A-D, A-C and A-B, respectively. This study aimed to analyze the association between these 3 deletion sizes and the presence of congenital cardiac and/or palatal malformations in individuals with this condition. A systematic review and meta-analysis were conducted, merging relevant published studies with data from Chilean patients to increase statistical power. RESULTS Eight articles out of 432 were included; the data from these studies was merged with our own, achieving a total of 1514 and 487 patients to evaluate cardiac and palate malformations, respectively. None of the compared deleted chromosomal segments were statistically associated with cardiac defects (ORAB v/s AC-AD: 0.654 [0.408-1.046]; OR AD v/s AB-AC: 1.291 [0.860-1.939]) or palate anomalies (ORAB v/s AC-AD: 1.731 [0.708-4.234]; OR AD v/s AB-AC: 0.628 [0.286-1.382]). CONCLUSIONS The lack of association between deletion size and CHD or PA found in this meta-analysis suggests that deletion size does not explain the incomplete penetrance of these 2 major manifestations, and that the critical region for the development of heart and palatal abnormalities is within LCR A-B, the smallest region of overlap among the three deletion sizes.
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Affiliation(s)
- M. Fernanda Rozas
- Programa de Doctorado en Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Avda Las Condes, 12461 Santiago, Chile
| | - Felipe Benavides
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Avda Las Condes, 12438 Santiago, Chile
- Present address: ThermoScientific, Santiago, Chile
| | - Luis León
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Avda Las Condes, 12438 Santiago, Chile
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Pedro de Valdivia, 425 Santiago, Chile
| | - Gabriela M. Repetto
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Avda Las Condes, 12438 Santiago, Chile
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15
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Downregulation of genes outside the deleted region in individuals with 22q11.2 deletion syndrome. Hum Genet 2019; 138:93-103. [PMID: 30627818 DOI: 10.1007/s00439-018-01967-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/22/2018] [Indexed: 12/12/2022]
Abstract
The 22q11.2 deletion syndrome (22q11.2DS) is caused by recurrent hemizygous deletions of chromosome 22q11.2. The phenotype of the syndrome is complex and varies widely among individuals. Little is known about the role of the different genes located in 22q11.2, and we hypothesized that genetic risk factors lying elsewhere in the genome might contribute to the phenotype. Here, we present the whole-genome gene expression data of 11 patients with approximately 3 Mb deletions. Apart from the hemizygous genes mapped to the 22q11.2 region, the TUBA8 and GNAZ genes, neighboring the deleted interval but in normal copy number, showed altered expression. When genes mapped to other chromosomes were considered in the gene expression analysis, a genome-wide dysregulation was observed, with increased or decreased expression levels. The enriched pathways of these genes were related to immune response, a deficiency that is frequently observed in 22q11.2DS patients. We also used the hypothesis-free weighted gene co-expression network analysis (WGCNA), which revealed the co-expression gene network modules with clear connection to mechanisms associated with 22q11.2DS such as immune response and schizophrenia. These findings, combined with the traditional gene expression profile, can be used for the identification of potential pathways and genes not previously considered to be related to the 22q11.2 deletion syndrome.
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16
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Hussein IR, Bader RS, Chaudhary AG, Bassiouni R, Alquaiti M, Ashgan F, Schulten HJ, Al Qahtani MH. Identification of De Novo and Rare Inherited Copy Number Variants in Children with Syndromic Congenital Heart Defects. Pediatr Cardiol 2018. [PMID: 29541814 DOI: 10.1007/s00246-018-1842-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Congenital heart defects (CHDs) are the most common birth defects in neonatal life. CHDs could be presented as isolated defects or associated with developmental delay (DD) and/or other congenital malformations. A small proportion of cardiac defects are caused by chromosomal abnormalities or single gene defects; however, in a large proportion of cases no genetic diagnosis could be achieved by clinical examination and conventional genetic analysis. The development of genome wide array-Comparative Genomic Hybridization technique (array-CGH) allowed for the detection of cryptic chromosomal imbalances and pathogenic copy number variants (CNVs) not detected by conventional techniques. We investigated 94 patients having CHDs associated with other malformations and/or DD. Clinical examination and Echocardiography was done to all patients to evaluate the type of CHD. To investigate for genome defects we applied high-density array-CGH 2 × 400K (41 patients) and CGH/SNP microarray 2 × 400K (Agilent) for 53 patients. Confirmation of results was done using Fluorescent in situ hybridization (FISH) or qPCR techniques in certain cases. Chromosomal abnormalities such as trisomy 18, 13, 21, microdeletions: del22q11.2, del7q11.23, del18 (p11.32; p11.21), tetrasomy 18p, trisomy 9p, del11q24-q25, add 15p, add(18)(q21.3), and der 9, 15 (q34.2; q11.2) were detected in 21/94 patients (22%) using both conventional cytogenetics methods and array-CGH technique. Cryptic chromosomal anomalies and pathogenic variants were detected in 15/73 (20.5%) cases. CNVs were observed in a large proportion of the studied samples (27/56) (48%). Clustering of variants was observed in chromosome 1p36, 1p21.1, 2q37, 3q29, 5p15, 7p22.3, 8p23, 11p15.5, 14q11.2, 15q11.2, 16p13.3, 16p11.2, 18p11, 21q22, and 22q11.2. CGH/SNP array could detect loss of heterozygosity (LOH) in different chromosomal loci in 10/25 patients. Array-CGH technique allowed for detection of cryptic chromosomal imbalances that could not be detected by conventional cytogenetics methods. CHDs associated with DD/congenital malformations presented with a relatively high rate of cryptic chromosomal abnormalities. Clustering of CNVs in certain genome loci needs further analysis to identify candidate genes that may provide clues for understanding the molecular pathway of cardiac development.
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Affiliation(s)
- Ibtessam R Hussein
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, 21589, Kingdom of Saudi Arabia.
| | - Rima S Bader
- Pediatric Cardiology Department, King Abdulaziz University Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Adeel G Chaudhary
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, 21589, Kingdom of Saudi Arabia.,Faculty of Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Randa Bassiouni
- Children Hospital, Ministry of Health, Ta'if, Kingdom of Saudi Arabia
| | - Maha Alquaiti
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, 21589, Kingdom of Saudi Arabia
| | - Fai Ashgan
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, 21589, Kingdom of Saudi Arabia
| | - Hans-Juergen Schulten
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, 21589, Kingdom of Saudi Arabia
| | - Mohammad H Al Qahtani
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, 21589, Kingdom of Saudi Arabia.,Faculty of Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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17
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Raghavan V, Bhomia M, Torres I, Jain S, Wang KK. Hypothesis: Exosomal microRNAs as potential biomarkers for schizophrenia. Med Hypotheses 2017; 103:21-25. [DOI: 10.1016/j.mehy.2017.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/03/2017] [Indexed: 01/27/2023]
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18
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Bertini V, Azzarà A, Legitimo A, Milone R, Battini R, Consolini R, Valetto A. Deletion Extents Are Not the Cause of Clinical Variability in 22q11.2 Deletion Syndrome: Does the Interaction between DGCR8 and miRNA-CNVs Play a Major Role? Front Genet 2017; 8:47. [PMID: 28507561 PMCID: PMC5410573 DOI: 10.3389/fgene.2017.00047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 03/30/2017] [Indexed: 01/14/2023] Open
Abstract
In humans, the most common genomic disorder is the hemizygous deletion of the chromosome 22q11.2 region, that results in the “22q11.2 deletion syndrome” (22q11.2DS). A peculiarity of 22q11.2DS is its great phenotypic variability that makes this pathology a classic example of a syndrome with variable expressivity and incomplete penetrance. The reasons for this variability have not been elucidated yet, and the molecular substrates underlying the different clinical features of 22q11.2DS are still debated. A cohort of 21 patients has been analyzed by array CGH in order to detect some of the genetic differences that may influence this variability. Two aspects have been investigated: (1) the precise localization of the deletion breakpoints within the low copy repeats (LCRs), (2) the additional Copy Number Variations (CNVs) elsewhere in the genome, by analyzing their gene content. Both protein-coding genes and miRNAs were considered, in order to discover possible epistatic interactions between genes of the 22q11.2 region and the rest of the genome. Eighteen out of twenty-one patients had a deletion of ~3 Mb mediated by LCR22-A and D, whereas 3/21 had a smaller deletion. The breakpoints within the LCR22-A and D do not have a major role in the phenotypic variability since they are rather clustered and the small differences concern genes that are not directly related to clinical signs of 22q11.2DS. A detailed analysis of the gene content of 22q11.2 deleted region indicates that this syndrome could be a bioenergetic disorder or consequence of an altered post-transcriptional gene regulation, due to the presence of DGCR8, a major player of the microRNA (miRNA) biogenesis. Only four genes with mitochondrial function are harbored in the additional CNVs, whereas 11 miRNA, all related to biological pathways present in the 22q11.2DS, have been detected in 19/21 patients. CNVs and miRNAs are new entities that have changed the order of complexity at the level of gene expression and regulation, thus CNV-miRNAs (miRNA harbored in the CNVs) are potential functional variants that should be considered high priority candidate variants in genotype-phenotype association studies. Deletion of DGCR8, the main actor in miRNA biogenesis, amplifies this variability. To our knowledge, this is the first report that focus on the miRNA-CNVs in 22q11.2DS, with the aim of trying to better understand their role in the variable expressivity and incomplete penetrance.
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Affiliation(s)
- Veronica Bertini
- Cytogenetics and Molecular Genetics Unit, Department of Laboratory Medicine, Azienda Ospedaliera Univeristaria PisanaPisa, Italy
| | - Alessia Azzarà
- Cytogenetics and Molecular Genetics Unit, Department of Laboratory Medicine, Azienda Ospedaliera Univeristaria PisanaPisa, Italy
| | - Annalisa Legitimo
- Laboratory of Immunology, Department of Clinical and Experimental Medicine, University of PisaPisa, Italy
| | - Roberta Milone
- Department of Developmental Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico Stella MarisPisa, Italy
| | - Roberta Battini
- Department of Developmental Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico Stella MarisPisa, Italy
| | - Rita Consolini
- Laboratory of Immunology, Department of Clinical and Experimental Medicine, University of PisaPisa, Italy
| | - Angelo Valetto
- Cytogenetics and Molecular Genetics Unit, Department of Laboratory Medicine, Azienda Ospedaliera Univeristaria PisanaPisa, Italy
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19
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An exploratory study of predisposing genetic factors for DiGeorge/velocardiofacial syndrome. Sci Rep 2017; 7:40031. [PMID: 28059126 PMCID: PMC5216377 DOI: 10.1038/srep40031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/01/2016] [Indexed: 12/13/2022] Open
Abstract
DiGeorge/velocardiofacial syndrome (DGS/VCFS) is a disorder caused by a 22q11.2 deletion mediated by non-allelic homologous recombination (NAHR) between low-copy repeats (LCRs). We have evaluated the role of LCR22 genomic architecture and PRDM9 variants as DGS/VCFS predisposing factors. We applied FISH using fosmid probes on chromatin fibers to analyze the number of tandem repeat blocks in LCR22 in two DGS/VCFS fathers-of-origin with proven 22q11.2 NAHR susceptibility. Results revealed copy number variations (CNVs) of L9 and K3 fosmids in these individuals compared to controls. The total number of L9 and K3 copies was also characterized using droplet digital PCR (ddPCR). Although we were unable to confirm variations, we detected an additional L9 amplicon corresponding to a pseudogene. Moreover, none of the eight DGS/VCFS parents-of-origin was heterozygote for the inv(22)(q11.2) haplotype. PRDM9 sequencing showed equivalent allelic distributions between DGS/VCFS parents-of-origin and controls, although a new PRDM9 allele (L50) was identified in one case. Our results support the hypothesis that LCR22s variations influences 22q11.2 NAHR events, however further studies are needed to confirm this association and clarify the contribution of pseudogenes and rare PDRM9 alleles to NAHR susceptibility.
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20
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Do C, Xing Z, Yu YE, Tycko B. Trans-acting epigenetic effects of chromosomal aneuploidies: lessons from Down syndrome and mouse models. Epigenomics 2016; 9:189-207. [PMID: 27911079 PMCID: PMC5549717 DOI: 10.2217/epi-2016-0138] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
An important line of postgenomic research seeks to understand how genetic factors can influence epigenetic patterning. Here we review epigenetic effects of chromosomal aneuploidies, focusing on findings in Down syndrome (DS, trisomy 21). Recent work in human DS and mouse models has shown that the extra chromosome 21 acts in trans to produce epigenetic changes, including differential CpG methylation (DS-DM), in specific sets of downstream target genes, mostly on other chromosomes. Mechanistic hypotheses emerging from these data include roles of chromosome 21-linked methylation pathway genes (DNMT3L and others) and transcription factor genes (RUNX1, OLIG2, GABPA, ERG and ETS2) in shaping the patterns of DS-DM. The findings may have broader implications for trans-acting epigenetic effects of chromosomal and subchromosomal aneuploidies in other human developmental and neuropsychiatric disorders, and in cancers.
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Affiliation(s)
- Catherine Do
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program & Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program & Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Taub Institute for Research on Alzheimer's disease & the Aging Brain, Columbia University, New York, NY 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
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21
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Kaufman CS, Genovese A, Butler MG. Deletion of TOP3B Is Associated with Cognitive Impairment and Facial Dysmorphism. Cytogenet Genome Res 2016; 150:106-111. [PMID: 27880953 DOI: 10.1159/000452815] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2016] [Indexed: 11/19/2022] Open
Abstract
Deletions of different regions of chromosome 22q11 have been extensively characterized in the literature, with a recent review outlining common deletions with a standardized system proposed for classification and nomenclature. The genotype-phenotype relationships have not been sufficiently elucidated for these deletions, and it remains unclear which specific genes play the dominant roles in producing associated clinical features. Several deletions involve entirely distinct regions of chromosome 22q11 but do not overlap, suggesting that a number of different genes contribute to the clinical features. Studies of patients with small deletions involving only 1 or 2 genes may provide more convincing evidence for the impact of individual genes on the observed phenotype. In this case report, we present a 12-year-old female with autism, cognitive impairment, dysmorphic features, and behavioral concerns and a 268-kb deletion of chromosome 22q11.22 including TOP3B, the only recognized disease-causing gene in the deletion. The mechanism of pathogenesis contributing significantly to our patient's clinical findings may relate to interaction between TOP3B and fragile X mental retardation protein (FMRP), an mRNA-binding protein that regulates translation and is altered in fragile X syndrome, a condition involving developmental delay, learning disability, and autism. All these features are recognized in our patient.
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Affiliation(s)
- Carolyn S Kaufman
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS, USA
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22
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Analysis of induced pluripotent stem cells carrying 22q11.2 deletion. Transl Psychiatry 2016; 6:e934. [PMID: 27801899 PMCID: PMC5314118 DOI: 10.1038/tp.2016.206] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 12/18/2022] Open
Abstract
Given the complexity and heterogeneity of the genomic architecture underlying schizophrenia, molecular analyses of these patients with defined and large effect-size genomic defects could provide valuable clues. We established human-induced pluripotent stem cells from two schizophrenia patients with the 22q11.2 deletion (two cell lines from each subject, total of four cell lines) and three controls (total of four cell lines). Neurosphere size, neural differentiation efficiency, neurite outgrowth, cellular migration and the neurogenic-to-gliogenic competence ratio were significantly reduced in patient-derived cells. As an underlying mechanism, we focused on the role of DGCR8, a key gene for microRNA (miRNA) processing and mapped in the deleted region. In mice, Dgcr8 hetero-knockout is known to show a similar phenotype of reduced neurosphere size (Ouchi et al., 2013). The miRNA profiling detected reduced expression levels of miRNAs belonging to miR-17/92 cluster and miR-106a/b in the patient-derived neurospheres. Those miRNAs are reported to target p38α, and conformingly the levels of p38α were upregulated in the patient-derived cells. p38α is known to drive gliogenic differentiation. The inhibition of p38 activity by SB203580 in patient-derived neurospheres partially restored neurogenic competence. Furthermore, we detected elevated expression of GFAP, a gliogenic (astrocyte) marker, in postmortem brains from schizophrenia patients without the 22q11.2 deletion, whereas inflammation markers (IL1B and IL6) remained unchanged. In contrast, a neuronal marker, MAP2 expressions were decreased in schizophrenia brains. These results suggest that a dysregulated balance of neurogenic-to-gliogenic competence may underlie neurodevelopmental disorders such as schizophrenia.
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23
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Síndrome de deleción 22q11: bases embriológicas y algoritmo diagnóstico. REVISTA COLOMBIANA DE CARDIOLOGÍA 2016. [DOI: 10.1016/j.rccar.2016.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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24
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Richard AC, Rovelet-Lecrux A, Delaby E, Charbonnier C, Thiruvahindrapuram B, Hatchwell E, Eis PS, Afenjar A, Gilbert Dussardier B, Scherer SW, Betancur C, Campion D. The 22q11 PRODH/DGCR6 deletion is frequent in hyperprolinemic subjects but is not a strong risk factor for ASD. Am J Med Genet B Neuropsychiatr Genet 2016; 171B:377-82. [PMID: 26978485 DOI: 10.1002/ajmg.b.32416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 12/23/2015] [Indexed: 12/11/2022]
Abstract
The proline dehydrogenase (PRODH) gene maps to 22q11.2 in the region deleted in the velo-cardio-facial syndrome (VCFS). A moderate to severe reduction (>50%) in PRODH activity resulting from recessive deletions and/or missense mutations has been shown to cause type 1 hyperprolinemia (HPI). Autistic features have been reported as a common clinical manifestation of HPI. Here we studied the frequency of a recurrent small 22q11.2 deletion encompassing PRODH and the neighboring DGCR6 gene in three case-control studies, one comprising HPI patients (n = 83), and the other two comprising autism spectrum disorder (ASD) patients (total of n = 2800), analyzed with high-resolution microarrays. We found that the PRODH deletion is a strong risk factor for HPI (OR = 50.7; 95%CI = 7.5-2147) but not for ASD (P = 0.4, OR = 0.6-3.3). This result indicates either that the suggested association between ASD and HPI is spurious and results from a bias leading to the preferential inclusion of patients with autistic features in HPI series, or that HPI is present in only a very small subset of ASD patients. In this latter case, a very large sample size would be required to detect an association between the PRODH deletion and ASD in a case-control study.
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Affiliation(s)
- Anne Claire Richard
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, France
| | - Anne Rovelet-Lecrux
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, France
| | - Elsa Delaby
- Inserm U1130, Neuroscience Paris Seine, Paris, France.,CNRS UMR 8246, Neuroscience Paris Seine, Paris, France.,Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, Paris, France
| | - Camille Charbonnier
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, France
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, and Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Peggy S Eis
- Population Diagnostics, Inc., Melville, New York
| | - Alexandra Afenjar
- Unité de neuropédiatrie et pathologie du développement, CHU Paris Est-Hôpital d'Enfants Armand-Trousseau, Paris, France
| | | | - Stephen W Scherer
- The Centre for Applied Genomics, and Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Ontario, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Catalina Betancur
- Inserm U1130, Neuroscience Paris Seine, Paris, France.,CNRS UMR 8246, Neuroscience Paris Seine, Paris, France.,Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, Paris, France
| | - Dominique Campion
- Inserm U1079, Institute for Research and Innovation in Biomedicine, University of Rouen, France.,Centre Hospitalier du Rouvray, Sotteville-lès-Rouen, France
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25
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Evers LJM, Engelen JJM, Houben LMH, Curfs LMG, van Amelsvoort TAMJ. The use of two different MLPA kits in 22q11.2 deletion syndrome. Eur J Med Genet 2016; 59:183-8. [PMID: 26921528 DOI: 10.1016/j.ejmg.2016.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 02/15/2016] [Accepted: 02/21/2016] [Indexed: 11/30/2022]
Abstract
22q11.2 deletion syndrome (22q11DS) is one of the most common recurrent copy-number variant disorder, caused by a microdeletion in chromosome band 22q11.2 and occurring with a population prevalence of 1 in 2000. Until today there has been no evidence that the size of the deletion has an influence on the clinical phenotype. Most studies report that 22q11DS is associated with mild or borderline intellectual disability. There are a limited number of reports on 22q11DS subjects with moderate or severe intellectual disability. In this study we describe 63 adult patients with 22q11DS, including 22q11DS patients functioning at a moderate to severe intellectual disabled level. Deletion size was established with an experimental Multiplex ligation-dependent probe amplification (MLPA) mixture (P324) in addition to the commonly used MLPA kit (P250). We compared deletion size with intellectual functioning and presence of psychotic symptoms during life. The use of the experimental MLPA kit gives extra information on deletion size, only when combined with the common MLPA kit. We were able to detect eleven atypical deletions and in two cases the deletion size was shorter than all other "typical ones". We conclude that the use of the experimental kit P324 gives extra information about the deletion size, but only when used together with the standard P250 kit. We did not found any relation of deletion size with intelligence or presence of psychosis.
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Affiliation(s)
- L J M Evers
- Koraalgroup, MFCG, Heel, The Netherlands; Governor Kremers Centre, Maastricht University Medical Centre, Maastricht, The Netherlands.
| | - J J M Engelen
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - L M H Houben
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - L M G Curfs
- Governor Kremers Centre, Maastricht University Medical Centre, Maastricht, The Netherlands; Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands; GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands; CAPHRI, School for Public Health and Primary Care, Maastricht University, Maastricht, The Netherlands
| | - T A M J van Amelsvoort
- Department of Psychiatry and Psychology, Maastricht University, Maastricht, The Netherlands; Mondriaan Mental Healthcare, Heerlen, The Netherlands; Virenze Mental Healthcare, Gronsveld, The Netherlands
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Poirsier C, Besseau-Ayasse J, Schluth-Bolard C, Toutain J, Missirian C, Le Caignec C, Bazin A, de Blois MC, Kuentz P, Catty M, Choiset A, Plessis G, Basinko A, Letard P, Flori E, Jimenez M, Valduga M, Landais E, Lallaoui H, Cartault F, Lespinasse J, Martin-Coignard D, Callier P, Pebrel-Richard C, Portnoi MF, Busa T, Receveur A, Amblard F, Yardin C, Harbuz R, Prieur F, Le Meur N, Pipiras E, Kleinfinger P, Vialard F, Doco-Fenzy M. A French multicenter study of over 700 patients with 22q11 deletions diagnosed using FISH or aCGH. Eur J Hum Genet 2015; 24:844-51. [PMID: 26508576 DOI: 10.1038/ejhg.2015.219] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 09/02/2015] [Accepted: 09/08/2015] [Indexed: 12/31/2022] Open
Abstract
Although 22q11.2 deletion syndrome (22q11.2DS) is the most recurrent human microdeletion syndrome associated with a highly variable phenotype, little is known about the condition's true incidence and the phenotype at diagnosis. We performed a multicenter, retrospective analysis of postnatally diagnosed patients recruited by members of the Association des Cytogénéticiens de Langue Française (the French-Speaking Cytogeneticists Association). Clinical and cytogenetic data on 749 cases diagnosed between 1995 and 2013 were collected by 31 French cytogenetics laboratories. The most frequent reasons for referral of postnatally diagnosed cases were a congenital heart defect (CHD, 48.6%), facial dysmorphism (49.7%) and developmental delay (40.7%). Since 2007 (the year in which array comparative genomic hybridization (aCGH) was introduced for the routine screening of patients with intellectual disability), almost all cases have been diagnosed using FISH (96.1%). Only 15 cases (all with an atypical phenotype) were diagnosed with aCGH; the deletion size ranged from 745 to 2904 kb. The deletion was inherited in 15.0% of cases and was of maternal origin in 85.5% of the latter. This is the largest yet documented cohort of patients with 22q11.2DS (the most commonly diagnosed microdeletion) from the same population. French cytogenetics laboratories diagnosed at least 108 affected patients (including fetuses) per year from among a national population of ∼66 million. As observed for prenatal diagnoses, CHDs were the most frequently detected malformation in postnatal diagnoses. The most common CHD in postnatal diagnoses was an isolated septal defect.
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Affiliation(s)
| | | | | | | | | | - Cédric Le Caignec
- CHU Nantes, Service de Génétique Médicale, Inserm UMR957, Faculté de Médecine, Nantes, France
| | - Anne Bazin
- Laboratoire de Cytogénétique Pasteur-Cerba, Saint-Ouen l'Aumône, France
| | - Marie Christine de Blois
- Service de Cytogénétique, CHU de Necker, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Paul Kuentz
- Service de Cytogénétique, CHU de Besançon, Besançon, France
| | - Marie Catty
- Service de Cytogénétique, Biolille, Lille, France
| | - Agnès Choiset
- Service de Cytogénétique, Hôpital Saint Vincent de Paul, Paris, France
| | - Ghislaine Plessis
- Laboratoire de Cytogénétique Postnatal, CHU Clemenceau, Caen, France
| | - Audrey Basinko
- Service de Cytogénétique et Biologie de la Reproduction, CHRU de Brest, Brest, France
| | | | - Elisabeth Flori
- Service de Cytogénétique, CHU de Strasbourg, Strasbourg, France
| | | | | | | | | | - François Cartault
- Service de Cytogénétique, Hôpital de Saint-Denis, Saint-Denis de la Réunion, France
| | | | | | | | - Céline Pebrel-Richard
- Univ Clermont 1, UFR Médecine, Histologie Embryologie Cytogénétique, Clermont-Ferrand, France.,CHU-Estaing Clermont-Ferrand, Cytogénétique Médicale, Clermont-Ferrand, France.,EA 4677 ERTICA, Univ Clermont 1, UFR Médecine, Clermont-Ferrand, France
| | | | - Tiffany Busa
- Departement de Genétique Medicale, Hopital de la Timone, CHU de Marseille, Marseille, France
| | | | | | | | - Radu Harbuz
- Service de Génétique, CHU de Poitiers, Poitiers, France
| | - Fabienne Prieur
- Service de Cytogénétique, CHU de Saint-Etienne, Saint-Etienne, France
| | - Nathalie Le Meur
- Service de Cytogénétique, Etablissement Français du Sang de Normandie, Rouen, France
| | - Eva Pipiras
- Hôpital Jean Verdier, UF de Cytogénétique, CHU Paris, Paris, France.,Université Paris 13, Sorbonne Paris Cité, INSERM 1141, Paris, France
| | - Pascale Kleinfinger
- Laboratoire de Cytogénétique Pasteur-Cerba, Saint-Ouen l'Aumône, France.,Association des Cytogénéticiens de Langue Française (French-Speaking Cytogeneticists Association), Paris, France
| | - François Vialard
- Service de Cytogénétique, Hôpital Poissy/Saint-Germain-en-Laye, Poissy, France.,Association des Cytogénéticiens de Langue Française (French-Speaking Cytogeneticists Association), Paris, France.,GIG, UVSQ, Versailles, Paris, France
| | - Martine Doco-Fenzy
- Département de Génétique, CHU de Reims, Reims, France.,Association des Cytogénéticiens de Langue Française (French-Speaking Cytogeneticists Association), Paris, France.,EA3801, SFR-CAP Santé, Reims, France
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27
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Jalbrzikowski M, Lazaro MT, Gao F, Huang A, Chow C, Geschwind DH, Coppola G, Bearden CE. Transcriptome Profiling of Peripheral Blood in 22q11.2 Deletion Syndrome Reveals Functional Pathways Related to Psychosis and Autism Spectrum Disorder. PLoS One 2015. [PMID: 26201030 PMCID: PMC4511766 DOI: 10.1371/journal.pone.0132542] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background 22q11.2 Deletion Syndrome (22q11DS) represents one of the greatest known genetic risk factors for the development of psychotic illness, and is also associated with high rates of autistic spectrum disorders (ASD) in childhood. We performed integrated genomic analyses of 22q11DS to identify genes and pathways related to specific phenotypes. Methods We used a high-resolution aCGH array to precisely characterize deletion breakpoints. Using peripheral blood, we examined differential expression (DE) and networks of co-expressed genes related to phenotypic variation within 22q11DS patients. Whole-genome transcriptional profiling was performed using Illumina Human HT-12 microarrays. Data mining techniques were used to validate our results against independent samples of both peripheral blood and brain tissue from idiopathic psychosis and ASD cases. Results Eighty-five percent of 22q11DS individuals (N = 39) carried the typical 3 Mb deletion, with significant variability in deletion characteristics in the remainder of the sample (N = 7). DE analysis and weighted gene co-expression network analysis (WGCNA) identified expression changes related to psychotic symptoms in patients, including a module of co-expressed genes which was associated with psychosis in 22q11DS and involved in pathways associated with transcriptional regulation. This module was enriched for brain-expressed genes, was not related to antipsychotic medication use, and significantly overlapped with transcriptional changes in idiopathic schizophrenia. In 22q11DS-ASD, both DE and WGCNA analyses implicated dysregulation of immune response pathways. The ASD-associated module showed significant overlap with genes previously associated with idiopathic ASD. Conclusion These findings further support the use of peripheral tissue in the study of major mutational models of diseases affecting the brain, and point towards specific pathways dysregulated in 22q11DS carriers with psychosis and ASD.
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Affiliation(s)
- Maria Jalbrzikowski
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, United States of America
| | - Maria T. Lazaro
- Interdepartmental Neuroscience Program, University of California Los Angeles, Los Angeles, United States of America
| | - Fuying Gao
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, United States of America
| | - Alden Huang
- Interdepartmental Neuroscience Program, University of California Los Angeles, Los Angeles, United States of America
| | - Carolyn Chow
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, United States of America
| | - Daniel H. Geschwind
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, United States of America
- Department of Neurology, University of California Los Angeles, Los Angeles, United States of America
| | - Giovanni Coppola
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, United States of America
- Department of Neurology, University of California Los Angeles, Los Angeles, United States of America
| | - Carrie E. Bearden
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, United States of America
- Department of Psychology, University of California Los Angeles, Los Angeles, United States of America
- * E-mail:
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28
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Tang S, Lv J, Chen X, Bai L, Li H, Chen C, Wang P, Xu X, Lu J. Prenatal Diagnosis of DNA Copy Number Variations by Genomic Single-Nucleotide Polymorphism Array in Fetuses with Congenital Heart Defects. Fetal Diagn Ther 2015; 39:64-73. [DOI: 10.1159/000431320] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 05/07/2015] [Indexed: 11/19/2022]
Abstract
Objectives: To evaluate the usefulness of single-nucleotide polymorphism (SNP) array for prenatal genetic diagnosis of congenital heart defect (CHD), we used this approach to detect clinically significant copy number variants (CNVs) in fetuses with CHDs. Methods: A HumanCytoSNP-12 array was used to detect genomic samples obtained from 39 fetuses that exhibited cardiovascular abnormalities on ultrasound and had a normal karyotype. The relationship between CNVs and CHDs was identified by using genotype-phenotype comparisons and searching of chromosomal databases. All clinically significant CNVs were confirmed by real-time PCR. Results: CNVs were detected in 38/39 (97.4%) fetuses: variants of unknown significance were detected in 2/39 (5.1%), and clinically significant CNVs were identified in 7/39 (17.9%). In 3 of the 7 fetuses with clinically significant CNVs, 3 rare and previously undescribed CNVs were detected, and these CNVs encompassed the CHD candidate genes FLNA (Xq28 dup), BCOR (Xp11.4 dup), and RBL2 (16q12.2 del). Conclusion: Compared with conventional cytogenetic genomics, SNP array analysis provides significantly improved detection of submicroscopic genomic aberrations in pregnancies with CHDs. Based on these results, we propose that genomic SNP array is an effective method which could be used in the prenatal diagnostic test to assist genetic counseling for pregnancies with CHDs.
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29
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Chung JH, Cai J, Suskin BG, Zhang Z, Coleman K, Morrow BE. Whole-Genome Sequencing and Integrative Genomic Analysis Approach on Two 22q11.2 Deletion Syndrome Family Trios for Genotype to Phenotype Correlations. Hum Mutat 2015; 36:797-807. [PMID: 25981510 DOI: 10.1002/humu.22814] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 05/01/2015] [Indexed: 12/20/2022]
Abstract
The 22q11.2 deletion syndrome (22q11DS) affects 1:4,000 live births and presents with highly variable phenotype expressivity. In this study, we developed an analytical approach utilizing whole-genome sequencing (WGS) and integrative analysis to discover genetic modifiers. Our pipeline combined available tools in order to prioritize rare, predicted deleterious, coding and noncoding single-nucleotide variants (SNVs), and insertion/deletions from WGS. We sequenced two unrelated probands with 22q11DS, with contrasting clinical findings, and their unaffected parents. Proband P1 had cognitive impairment, psychotic episodes, anxiety, and tetralogy of Fallot (TOF), whereas proband P2 had juvenile rheumatoid arthritis but no other major clinical findings. In P1, we identified common variants in COMT and PRODH on 22q11.2 as well as rare potentially deleterious DNA variants in other behavioral/neurocognitive genes. We also identified a de novo SNV in ADNP2 (NM_014913.3:c.2243G>C), encoding a neuroprotective protein that may be involved in behavioral disorders. In P2, we identified a novel nonsynonymous SNV in ZFPM2 (NM_012082.3:c.1576C>T), a known causative gene for TOF, which may act as a protective variant downstream of TBX1, haploinsufficiency of which is responsible for congenital heart disease in individuals with 22q11DS.
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Affiliation(s)
- Jonathan H Chung
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Jinlu Cai
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Barrie G Suskin
- Department of Obstetrics & Gynecology and Women's Health, Montefiore Medical Center, Bronx, New York
| | - Zhengdong Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Karlene Coleman
- Children's Healthcare of Atlanta at Egleston, Atlanta, Georgia
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
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30
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Cytogenomic Evaluation of Subjects with Syndromic and Nonsyndromic Conotruncal Heart Defects. BIOMED RESEARCH INTERNATIONAL 2015; 2015:401941. [PMID: 26137477 PMCID: PMC4475533 DOI: 10.1155/2015/401941] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 05/01/2015] [Accepted: 05/03/2015] [Indexed: 02/07/2023]
Abstract
Despite considerable advances in the detection of genomic abnormalities in congenital heart disease (CHD), the etiology of CHD remains largely unknown. CHD is the most common birth defect and is a major cause of infant morbidity and mortality, and conotruncal defects constitute 20% of all CHD cases. We used array comparative genomic hybridization (array-CGH) to retrospectively study 60 subjects with conotruncal defects and identify genomic imbalances. The DNA copy number variations (CNVs) detected were matched with data from genomic databases, and their clinical significance was evaluated. We found that 38.3% (23/60) of CHD cases possessed genomic imbalances. In 8.3% (5/60) of these cases, the imbalances were causal or potentially causal CNVs; in 8.3% (5/60), unclassified CNVs were identified; and in 21.6% (13/60), common variants were detected. Although the interpretation of the results must be refined and there is not yet a consensus regarding the types of CHD cases in which array-CGH should be used as a first-line test, the identification of these CNVs can assist in the evaluation and management of CHD. The results of such studies emphasize the growing importance of the use of genome-wide assays in subjects with CHD to increase the number of genomic data sets associated with this condition.
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31
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DGCR6 at the proximal part of the DiGeorge critical region is involved in conotruncal heart defects. Hum Genome Var 2015; 2:15004. [PMID: 27081520 PMCID: PMC4785558 DOI: 10.1038/hgv.2015.4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/12/2014] [Accepted: 12/17/2014] [Indexed: 02/06/2023] Open
Abstract
Cardiac anomaly is one of the hallmarks of DiGeorge syndrome (DGS), observed in approximately 80% of patients. It often shows a characteristic morphology, termed as conotruncal heart defects. In many cases showing only the conotruncal heart defect, deletion of 22q11.2 region cannot be detected by fluorescence in situ hybridization (FISH), which is used to detect deletion in DGS. We investigated the presence of genomic aberrations in six patients with congenital conotruncal heart defects, who show no deletion at 22q11.2 in an initial screening by FISH. In these patients, no abnormalities were identified in the coding region of the TBX1 gene, one of the key genes responsible for the phenotype of DGS. However, when copy number alteration was analyzed by high-resolution array analysis, a small deletion or duplication in the proximal end of DiGeorge critical region was detected in two patients. The affected region contains the DGCR6 and PRODH genes. DGCR6 has been reported to affect the expression of the TBX1 gene. Our results suggest that altered dosage of gene(s) other than TBX1, possibly DGCR6, may also be responsible for the development of conotruncal heart defects observed in patients with DGS and, in particular, in those with stand-alone conotruncal heart defects.
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32
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Hwang VJ, Maar D, Regan J, Angkustsiri K, Simon TJ, Tassone F. Mapping the deletion endpoints in individuals with 22q11.2 deletion syndrome by droplet digital PCR. BMC MEDICAL GENETICS 2014; 15:106. [PMID: 25312060 PMCID: PMC4258952 DOI: 10.1186/s12881-014-0106-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/09/2014] [Indexed: 01/25/2023]
Abstract
Background Chromosome 22q11.2 deletion syndrome (22q11DS) is the most common human microdeletion syndrome and is associated with many cognitive, neurological and psychiatric disorders. The majority of individuals have a 3 Mb deletion while others have a nested 1.5 Mb deletion, but rare atypical deletions have also been described. To date, a study using droplet digital PCR (ddPCR) has not been conducted to systematically map the chromosomal breakpoints in individuals with 22q11DS, which would provide important genotypic insight into the various phenotypes observed in this syndrome. Methods This study uses ddPCR to assess copy number (CN) changes within the chromosome 22q11 deletion region and allows the mapping of the deletion endpoints. We used eight TaqMan assays interspersed throughout the deleted region of 22q11.2 to characterize the deleted region of chromosome 22 in 80 individuals known to have 22q11DS by FISH. Ten EvaGreen assays were used for finer mapping of the six identified individuals with 22q11DS atypical deletions and covering different regions of chromosome 22. Results ddPCR provided non-ambiguous CN measurements across the region, confirmed the presence of the deletion in the individuals screened, and led to the identification of five differently sized and located deletions. The majority of the participants (n = 74) had the large 3 Mb deletions, whereas three had the smaller 1.5 Mb deletions, and the remaining three had an interstitial deletion of different size. Conclusions The lower cost, rapid execution and high reliability and specificity provided by ddPCR for CN measurements in the 22q11 region constitutes a significant improvement over the variable CN values generated by other technologies. The ability of the ddPCR approach, to provide a high resolution mapping of deletion endpoints may result in the identification of genes that are haplo-insufficient and play a role in the pathogenesis of 22q11DS. Finally, this methodology can be applied to the characterization of other microdeletions throughout the genome.
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Affiliation(s)
| | | | | | | | | | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, UC Davis, 2700 Stockton Blvd, Suite 2102, Sacramento 95817, CA, USA.
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33
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Lv L, Deng H, Li Y, Zhang C, Liu X, Liu Q, Zhang D, Wang L, Pu Y, Zhang H, He Y, Wang Y, Yu Y, Yu T, Zhu J. The DNA methylation-regulated miR-193a-3p dictates the multi-chemoresistance of bladder cancer via repression of SRSF2/PLAU/HIC2 expression. Cell Death Dis 2014; 5:e1402. [PMID: 25188512 PMCID: PMC4540198 DOI: 10.1038/cddis.2014.367] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 06/30/2014] [Accepted: 07/24/2014] [Indexed: 01/18/2023]
Abstract
Chemoresistance hinders the curative cancer chemotherapy. To define the role of the DNA methylation-regulated microRNA (miR) genes in the chemoresistance of bladder cancer, we performed both DNA methylomic and miRomic analyses of a multi-chemosensitive (5637) versus a multi-chemoresistant (H-bc) cell line and found that miR-193a-3p is hypermethylated/silenced in 5637 and hypomethylated/expressed in H-bc cells. A forced reversal of its level turned around the chemoresistance in the cultured cells and the tumor xenografts in nude mice. Three of its targets: SRSF2, PLAU and HIC2, work in concert to relay the miR-193a-3p's impact on the bladder cancer chemoresistance by modulating the activities of the following five signaling pathways: DNA damage, Notch, NF-κB, Myc/Max, and Oxidative Stress. In addition to the mechanistic insights in how the newly identified miR-193a-3p/SRSF2,PLAU,HIC2/five signaling pathway axis regulates the chemoresistance of bladder cancer cells, our study provides a new set of diagnostic targets for the guided personalized chemotherapy of bladder cancer.
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MESH Headings
- 3' Untranslated Regions
- Animals
- Antineoplastic Agents, Phytogenic/therapeutic use
- Antineoplastic Agents, Phytogenic/toxicity
- Base Sequence
- Cell Line, Tumor
- Cell Survival/drug effects
- DNA Damage
- DNA Methylation
- Drug Resistance, Neoplasm
- Gene Expression Regulation, Neoplastic
- Humans
- Kruppel-Like Transcription Factors/antagonists & inhibitors
- Kruppel-Like Transcription Factors/genetics
- Kruppel-Like Transcription Factors/metabolism
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- MicroRNAs/antagonists & inhibitors
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Molecular Sequence Data
- NF-kappa B/metabolism
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/metabolism
- Oxidative Stress
- Plasminogen Activators/antagonists & inhibitors
- Plasminogen Activators/genetics
- Plasminogen Activators/metabolism
- Proto-Oncogene Proteins c-myc/metabolism
- RNA Interference
- RNA, Small Interfering/metabolism
- Receptors, Notch/metabolism
- Ribonucleoproteins/antagonists & inhibitors
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- Serine-Arginine Splicing Factors
- Signal Transduction
- Transplantation, Heterologous
- Tumor Suppressor Proteins/antagonists & inhibitors
- Tumor Suppressor Proteins/genetics
- Tumor Suppressor Proteins/metabolism
- Urinary Bladder Neoplasms/drug therapy
- Urinary Bladder Neoplasms/metabolism
- Urinary Bladder Neoplasms/pathology
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Affiliation(s)
- L Lv
- Cancer Epigenetics Program, Anhui Cancer Hospital, Hefei, Anhui 230031, China
| | - H Deng
- Cancer Epigenetics Program, Anhui Cancer Hospital, Hefei, Anhui 230031, China
| | - Y Li
- Department of Biology, School of Life Science, Anhui Medical University, Hefei, Anhui 230031, China
| | - C Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - X Liu
- Department of Bioinformatics, MHBI (Shanghai) Biotech Inc., GuiPing Road 333, Building 4/104, Shanghai Juke Biotech Park, Shanghai, China
| | - Q Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - D Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - L Wang
- Cancer Epigenetics Program, Anhui Cancer Hospital, Hefei, Anhui 230031, China
| | - Y Pu
- Cancer Epigenetics Program, Anhui Cancer Hospital, Hefei, Anhui 230031, China
| | - H Zhang
- Cancer Epigenetics Program, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University, Shanghai 200032, China
| | - Y He
- Cancer Epigenetics Program, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University, Shanghai 200032, China
| | - Y Wang
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Y Yu
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - T Yu
- Cancer Epigenetics Program, Anhui Cancer Hospital, Hefei, Anhui 230031, China
| | - J Zhu
- Cancer Epigenetics Program, Anhui Cancer Hospital, Hefei, Anhui 230031, China
- Cancer Epigenetics Program, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University, Shanghai 200032, China
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34
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Abstract
The 22q11 deletion syndrome (22q11DS) is the most common microdeletion syndrome in humans and presents with a complex and variable psychiatric phenotype. Patients show cognitive impairment and have a higher probability of psychiatric disorders. As much as 30% of patients with 22q11DS suffer from schizophrenia, the strongest association between any mutation and the disease. Schizophrenia is a complex psychiatric disease that affects multiple brain regions, giving rise to a constellation of seemingly unrelated symptoms including hallucinations, social withdrawal, and memory deficits. Synaptic or neuronal malfunctions within certain physiological circuits appear to be at the core of these symptoms. Understanding disease at the synaptic level requires genetic model systems where intact neural circuits can be interrogated for functional deficits. Because of the overlap between 22q11DS and schizophrenia, models of 22q11DS may be key genetic tools for investigating both diseases. Here we discuss the advantages of using a synaptic function approach to studying mouse models of 22q11DS, review recent findings, and discuss them in the broader context of 22q11DS and schizophrenia.
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Affiliation(s)
- Laurie R Earls
- Department of Development Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanislav S Zakharenko
- Department of Development Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
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35
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Dykes IM, van Bueren KL, Ashmore RJ, Floss T, Wurst W, Szumska D, Bhattacharya S, Scambler PJ. HIC2 is a novel dosage-dependent regulator of cardiac development located within the distal 22q11 deletion syndrome region. Circ Res 2014; 115:23-31. [PMID: 24748541 DOI: 10.1161/circresaha.115.303300] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE 22q11 deletion syndrome arises from recombination between low-copy repeats on chromosome 22. Typical deletions result in hemizygosity for TBX1 associated with congenital cardiovascular disease. Deletions distal to the typically deleted region result in a similar cardiac phenotype but lack in extracardiac features of the syndrome, suggesting that a second haploinsufficient gene maps to this interval. OBJECTIVE The transcription factor HIC2 is lost in most distal deletions, as well as in a minority of typical deletions. We used mouse models to test the hypothesis that HIC2 hemizygosity causes congenital heart disease. METHODS AND RESULTS We created a genetrap mouse allele of Hic2. The genetrap reporter was expressed in the heart throughout the key stages of cardiac morphogenesis. Homozygosity for the genetrap allele was embryonic lethal before embryonic day E10.5, whereas the heterozygous condition exhibited a partially penetrant late lethality. One third of heterozygous embryos had a cardiac phenotype. MRI demonstrated a ventricular septal defect with over-riding aorta. Conditional targeting indicated a requirement for Hic2 within the Nkx2.5+ and Mesp1+ cardiovascular progenitor lineages. Microarray analysis revealed increased expression of Bmp10. CONCLUSIONS Our results demonstrate a novel role for Hic2 in cardiac development. Hic2 is the first gene within the distal 22q11 interval to have a demonstrated haploinsufficient cardiac phenotype in mice. Together our data suggest that HIC2 haploinsufficiency likely contributes to the cardiac defects seen in distal 22q11 deletion syndrome.
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Affiliation(s)
- Iain M Dykes
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Kelly Lammerts van Bueren
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Rebekah J Ashmore
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Thomas Floss
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Wolfgang Wurst
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Dorota Szumska
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Shoumo Bhattacharya
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Peter J Scambler
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom.
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Roberts JL, Hovanes K, Dasouki M, Manzardo AM, Butler MG. Chromosomal microarray analysis of consecutive individuals with autism spectrum disorders or learning disability presenting for genetic services. Gene 2014; 535:70-8. [PMID: 24188901 PMCID: PMC4423794 DOI: 10.1016/j.gene.2013.10.020] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/26/2013] [Accepted: 10/10/2013] [Indexed: 01/15/2023]
Abstract
Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105 K and 180K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum disorders (ASD) or developmental delay/learning disability for genetic services at the University of Kansas Medical Center during the past 4 years (2009-2012). Of the 215 patients [140 males and 75 females (male/female ratio=1.87); 65 with ASD and 150 with learning disability], abnormal microarray results were seen in 45 individuals (21%) with a total of 49 CNVs. Of these findings, 32 represented a known diagnostic CNV contributing to the clinical presentation and 17 represented non-diagnostic CNVs (variants of unknown significance). Thirteen patients with ASD had a total of 14 CNVs, 6 CNVs recognized as diagnostic and 8 as non-diagnostic. The most common chromosome involved in the ASD group was chromosome 15. For those with a learning disability, 32 patients had a total of 35 CNVs. Twenty-six of the 35 CNVs were classified as a known diagnostic CNV, usually a deletion (n=20). Nine CNVs were classified as an unknown non-diagnostic CNV, usually a duplication (n=8). For the learning disability subgroup, chromosomes 2 and 22 were most involved. Thirteen out of 65 patients (20%) with ASD had a CNV compared with 32 out of 150 patients (21%) with a learning disability. The frequency of chromosomal microarray abnormalities compared by subject group or gender was not statistically different. A higher percentage of individuals with a learning disability had clinical findings of seizures, dysmorphic features and microcephaly, but not statistically significant. While both groups contained more males than females, a significantly higher percentage of males were present in the ASD group.
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Key Words
- A2BP1
- ACADL
- ACOXL
- ADIPOQ
- ALS2 chromosome region gene 8
- ALS2CR8
- ANKRD11
- ANOVA
- ASD
- Autism spectrum disorders (ASD)
- BAC
- BCL2-like 11 gene
- BCL2L11
- CACNA1C
- CHRNA7
- CNV
- COBL
- CT
- Chromosomal microarray analysis
- Copy number variant (CNV)
- DLG1
- DLG4
- DNA
- Developmental delay
- EEF1B2
- EEG
- F-box only 45 gene
- FAM117B
- FAT tumor suppressor 1 gene
- FAT1
- FBXO45
- FISH
- FXR2
- FZD5
- GALR1
- GATA zinc finger domain-containing protein 2B gene
- GATAD2B
- GDNF-inducible zinc finger protein 1 gene
- GZF1
- HAX1
- HCLS1-associated protein X1 gene
- HDAC
- IDH1
- IL1RAPL1
- ITPR1
- KLF7
- KNG1
- LINS
- LMNA
- Learning disability
- MAP2
- MBP
- MRPL19
- MYL1
- NADH-ubiquinone oxidoreductase Fe-S protein 1 gene
- NDUFS1
- NLGN2
- NPHP1
- NRXN1
- PAK2
- PARK2
- PMP22
- POLG
- PRPF8
- PTEN
- PTH2R
- RPE
- SACS
- SD
- SH2B adaptor protein 1 gene
- SH2B1
- SH3 and multiple ankyrin repeat domains 3 gene
- SHANK3
- SHOX
- SMARCA4
- STAG2
- SUMF1
- SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member gene
- TRAPPC2
- UCSC
- USP6
- University of California, Santa Cruz
- X-linked inhibitor of apoptosis gene
- XIAP
- YWHAE
- ZNF407
- aCGH
- acyl-coA dehydrogenase, long chain gene
- acyl-coA oxidase-like gene
- adipocyte-, C1q-, and collagen domain containing gene
- analysis of variance
- ankyrin repeat domain-containing protein 11 gene
- array comparative genomic hybridization
- ataxin 2-binding protein 1 gene
- autism spectrum disorder
- bacterial artificial chromosome
- calcium channel, voltage dependent, L-type, alpha 1C subunit gene
- cholinergic receptor, neuronal nicotinic, alpha polypeptide 7 gene
- computed tomography
- copy number variant
- cordon-bleu gene
- deoxyribonucleic acid
- discs, large homolog 1 gene
- discs, large homolog 4 gene
- electroencephalogram
- eukaryotic translation elongation factor 1, beta-2 gene
- family with sequence similarity 117, member B gene
- fluorescence in situ hybridization
- fragile X mental retardation, autosomal homolog 2 gene
- frizzled 5 gene
- galanin receptor 1 gene
- histone deacetylase gene
- inositol 1,4,5-triphosphate receptor, type 1 gene
- interleukin 1 receptor accessory protein-like 1 gene
- isocitrate dehydrogenase 1 gene
- kininogen 1 gene
- kruppel-like factor 7 gene
- lamin A gene
- lines homolog gene
- microtubule-associated protein 2 gene
- mitochondrial ribosomal protein L19 gene
- myelin basic protein gene
- myosin, light peptide 1 gene
- nephrocystin 1 gene
- neurexin 1 gene
- neuroligin 2 gene
- parathyroid hormone receptor 2 gene
- parkin gene
- peripheral myelin protein 22 gene
- phosphatase and tensin homolog gene
- polymerase gamma gene
- precursor mRNA-processing factor 8 gene
- protein-activated kinase 2 gene
- ribulose 5-phosphate 3-epimerase gene
- sacsin gene
- short stature homeobox gene
- standard deviation
- stromal antigen 2 gene
- sulfatase-modifying factor 1 gene
- tracking protein particle complex, subunit 2 gene
- tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon isoform gene
- ubiquitin-specific protease 6 gene
- zinc finger protein 407 gene
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Affiliation(s)
- Jennifer L Roberts
- Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas, Medical Center, Kansas City, KS, USA
| | | | - Majed Dasouki
- Department of Neurology, The University of Kansas Medical Center, Kansas City, KS, USA; King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ann M Manzardo
- Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas, Medical Center, Kansas City, KS, USA
| | - Merlin G Butler
- Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas, Medical Center, Kansas City, KS, USA.
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Xu F, Li L, Schulz VP, Gallagher PG, Xiang B, Zhao H, Li P. Cytogenomic mapping and bioinformatic mining reveal interacting brain expressed genes for intellectual disability. Mol Cytogenet 2014; 7:4. [PMID: 24410907 PMCID: PMC3905969 DOI: 10.1186/1755-8166-7-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/16/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Microarray analysis has been used as the first-tier genetic testing to detect chromosomal imbalances and copy number variants (CNVs) for pediatric patients with intellectual and developmental disabilities (ID/DD). To further investigate the candidate genes and underlying dosage-sensitive mechanisms related to ID, cytogenomic mapping of critical regions and bioinformatic mining of candidate brain-expressed genes (BEGs) and their functional interactions were performed. Critical regions of chromosomal imbalances and pathogenic CNVs were mapped by subtracting known benign CNVs from the Databases of Genomic Variants (DGV) and extracting smallest overlap regions with cases from DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources (DECIPHER). BEGs from these critical regions were revealed by functional annotation using Database for Annotation, Visualization, and Integrated Discovery (DAVID) and by tissue expression pattern from Uniprot. Cross-region interrelations and functional networks of the BEGs were analyzed using Gene Relationships Across Implicated Loci (GRAIL) and Ingenuity Pathway Analysis (IPA). RESULTS Of the 1,354 patients analyzed by oligonucleotide array comparative genomic hybridization (aCGH), pathogenic abnormalities were detected in 176 patients including genomic disorders in 66 patients (37.5%), subtelomeric rearrangements in 45 patients (25.6%), interstitial imbalances in 33 patients (18.8%), chromosomal structural rearrangements in 17 patients (9.7%) and aneuploidies in 15 patients (8.5%). Subtractive and extractive mapping defined 82 disjointed critical regions from the detected abnormalities. A total of 461 BEGs was generated from 73 disjointed critical regions. Enrichment of central nervous system specific genes in these regions was noted. The number of BEGs increased with the size of the regions. A list of 108 candidate BEGs with significant cross region interrelation was identified by GRAIL and five significant gene networks involving cell cycle, cell-to-cell signaling, cellular assembly, cell morphology, and gene expression regulations were denoted by IPA. CONCLUSIONS These results characterized ID related cross-region interrelations and multiple networks of candidate BEGs from the detected genomic imbalances. Further experimental study of these BEGs and their interactions will lead to a better understanding of dosage-sensitive mechanisms and modifying effects of human mental development.
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Affiliation(s)
- Fang Xu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Lun Li
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA.,Hubei Bioinformatics and Molecular Imaging Key Laboratory, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Vincent P Schulz
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Patrick G Gallagher
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Bixia Xiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
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38
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Gong X, Wu X, Ma X, Wu D, Zhang T, He L, Qin S, Li X. Microdeletion and microduplication analysis of chinese conotruncal defects patients with targeted array comparative genomic hybridization. PLoS One 2013; 8:e76314. [PMID: 24098474 PMCID: PMC3788710 DOI: 10.1371/journal.pone.0076314] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/23/2013] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVE The current study aimed to develop a reliable targeted array comparative genomic hybridization (aCGH) to detect microdeletions and microduplications in congenital conotruncal defects (CTDs), especially on 22q11.2 region, and for some other chromosomal aberrations, such as 5p15-5p, 7q11.23 and 4p16.3. METHODS Twenty-seven patients with CTDs, including 12 pulmonary atresia (PA), 10 double-outlet right ventricle (DORV), 3 transposition of great arteries (TGA), 1 tetralogy of Fallot (TOF) and one ventricular septal defect (VSD), were enrolled in this study and screened for pathogenic copy number variations (CNVs), using Agilent 8 x 15K targeted aCGH. Real-time quantitative polymerase chain reaction (qPCR) was performed to test the molecular results of targeted aCGH. RESULTS Four of 27 patients (14.8%) had 22q11.2 CNVs, 1 microdeletion and 3 microduplications. qPCR test confirmed the microdeletion and microduplication detected by the targeted aCGH. CONCLUSION Chromosomal abnormalities were a well-known cause of multiple congenital anomalies (MCA). This aCGH using arrays with high-density coverage in the targeted regions can detect genomic imbalances including 22q11.2 and other 10 kinds CNVs effectively and quickly. This approach has the potential to be applied to detect aneuploidy and common microdeletion/microduplication syndromes on a single microarray.
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Affiliation(s)
- Xiaohui Gong
- Obstetrics and Gynecology Hospital of Shanghai Fudan University, the Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
| | - Xi Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojing Ma
- Pediatric Hospital, Shanghai Fudan University, Shanghai, China
| | - Dandan Wu
- Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Zhang
- Capital Institute of Pediatrics, Beijing, Chaoyang District, Beijing , China
| | - Li He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Shanghai Fudan University, the Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
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39
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Kunishima S, Imai T, Kobayashi R, Kato M, Ogawa S, Saito H. Bernard-Soulier syndrome caused by a hemizygous GPIbβ mutation and 22q11.2 deletion. Pediatr Int 2013; 55:434-7. [PMID: 23566026 DOI: 10.1111/ped.12105] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 12/17/2012] [Accepted: 03/25/2013] [Indexed: 11/30/2022]
Abstract
BACKGROUND Bernard-Soulier syndrome (BSS) is a rare autosomal recessive bleeding disorder characterized by giant platelets, thrombocytopenia, and a prolonged bleeding time, which is caused by homozygous mutations in the GPIbα, GPIbβ, or GPIX genes. The 22q11.2 deletion syndrome (22q11.2DS) is caused by a microdeletion on chromosome 22, which includes the GPIbβ gene, and is characterized by abnormal development of the pharyngeal apparatus and heart. Thus, patients with 22q11.2DS are obligate carriers for BSS. METHODS We evaluated two infants with BSS and performed the genetic analysis of the GPIbα, GPIbβ, or GPIX genes, and investigated the segregation of the mutation within the families. The status of the 22q11.2 deletion was examined by fluorescence in situ hybridization and single-nucleotide polymorphism array copy number analysis. RESULTS DNA sequencing analysis revealed that the infants were compound heterozygous for a hemizygous mutation in the GPIbβ gene (p.Trp148X and p.Leu97Phe, respectively) and 22q11.2 deletion in the other chromosome. Both infants had the common 3Mb 22q11.2 deletion but did not show major phenotypic features of 22q11.2DS, such as developmental delay, cardiac defects, dysmorphic facial features, palatal anomalies, hypocalcemia, and immune deficiency. The 22q11.2DS would not have become clear if detailed molecular genetic analyses of BSS had not been performed. CONCLUSIONS Our cases illustrate that a suspicion of 22q11.2 deletion is warranted in pediatric BSS patients with a mutation in the GPIbβ gene, even without remarkable symptoms.
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Affiliation(s)
- Shinji Kunishima
- Department of Advanced Diagnosis, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan.
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40
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Villalon-Reina J, Jahanshad N, Beaton E, Toga AW, Thompson PM, Simon TJ. White matter microstructural abnormalities in girls with chromosome 22q11.2 deletion syndrome, Fragile X or Turner syndrome as evidenced by diffusion tensor imaging. Neuroimage 2013; 81:441-454. [PMID: 23602925 DOI: 10.1016/j.neuroimage.2013.04.028] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 04/03/2013] [Accepted: 04/10/2013] [Indexed: 12/19/2022] Open
Abstract
Children with chromosome 22q11.2 deletion syndrome (22q11.2DS), Fragile X syndrome (FXS), or Turner syndrome (TS) are considered to belong to distinct genetic groups, as each disorder is caused by separate genetic alterations. Even so, they have similar cognitive and behavioral dysfunctions, particularly in visuospatial and numerical abilities. To assess evidence for common underlying neural microstructural alterations, we set out to determine whether these groups have partially overlapping white matter abnormalities, relative to typically developing controls. We scanned 101 female children between 7 and 14years old: 25 with 22q11.2DS, 18 with FXS, 17 with TS, and 41 aged-matched controls using diffusion tensor imaging (DTI). Anisotropy and diffusivity measures were calculated and all brain scans were nonlinearly aligned to population and site-specific templates. We performed voxel-based statistical comparisons of the DTI-derived metrics between each disease group and the controls, while adjusting for age. Girls with 22q11.2DS showed lower fractional anisotropy (FA) than controls in the association fibers of the superior and inferior longitudinal fasciculi, the splenium of the corpus callosum, and the corticospinal tract. FA was abnormally lower in girls with FXS in the posterior limbs of the internal capsule, posterior thalami, and precentral gyrus. Girls with TS had lower FA in the inferior longitudinal fasciculus, right internal capsule and left cerebellar peduncle. Partially overlapping neurodevelopmental anomalies were detected in all three neurogenetic disorders. Altered white matter integrity in the superior and inferior longitudinal fasciculi and thalamic to frontal tracts may contribute to the behavioral characteristics of all of these disorders.
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Affiliation(s)
- Julio Villalon-Reina
- Imaging Genetics Center, Laboratory of Neuro Imaging, Dept. of Neurology, University of California Los Angeles, School of Medicine, Los Angeles, CA 90095, USA
| | - Neda Jahanshad
- Imaging Genetics Center, Laboratory of Neuro Imaging, Dept. of Neurology, University of California Los Angeles, School of Medicine, Los Angeles, CA 90095, USA
| | - Elliott Beaton
- Stress, Cognition, and Affective Neuroscience Laboratory, Department of Psychology, University of New Orleans, New Orleans, LA, 70148
| | - Arthur W Toga
- Laboratory of Neuro Imaging, Dept. of Neurology, University of California Los Angeles, School of Medicine, Los Angeles, CA 90095, USA
| | - Paul M Thompson
- Imaging Genetics Center, Laboratory of Neuro Imaging, Dept. of Neurology, University of California Los Angeles, School of Medicine, Los Angeles, CA 90095, USA.
| | - Tony J Simon
- Dept. of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento, CA, 95618, USA; MIND Institute, Dept. of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento, CA, 95618, USA
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Tremolada G, Longeri M, Polli M, Parma P, Acocella F. Persistent right aortic arch and associated axial skeletal malformations in cats. J Feline Med Surg 2013; 15:68-73. [PMID: 22989559 PMCID: PMC10816655 DOI: 10.1177/1098612x12459736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Persistent right aortic arch (PRAA) in cats is an uncommon vascular anomaly with clinical signs referable to oesophageal obstruction. To our knowledge no reports of axial skeletal malformations concomitant to PRAA have been reported in cats. The aim of this study is to depict a new clinical feature in cats affected by PRAA. In the study six cats with a diagnosis of vascular ring anomaly were enrolled. A complete physical examination, a neurological examination and a total body radiograph were performed on each animal. Four of the six cats showed contemporary PRAA and skeletal malformations. Additionally, for the first time, a genetic test was performed on one subject to detect DNA alterations in the homologous DiGeorge region of cat. The percentage of skeletal malformations reported in the normal population was compared with animals with PRAA and showed a higher frequency. Genetic testing failed to demonstrate a correlation between PRAA and DiGeorge genomic deletion. A review of veterinary and human diseases that presented both conditions was assessed. The few animals enrolled do not allow definitive conclusions. Further studies are required to corroborate the correlation between PRAA and axial skeletal malformations in cats.
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Affiliation(s)
- Giovanni Tremolada
- Department of Veterinary Medical Science, University of Milan, Milan, Italy
| | - Maria Longeri
- Department of Veterinary Science and Public Health, University of Milan, Milan, Italy
| | - Michele Polli
- Department of Veterinary Science and Public Health, University of Milan, Milan, Italy
| | - Pietro Parma
- Department of Animal Science, Agronomy Faculty, University of Milan, Milan, Italy
| | - Fabio Acocella
- Department of Veterinary Medical Science, University of Milan, Milan, Italy
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Squarcione C, Torti MC, Di Fabio F, Biondi M. 22q11 deletion syndrome: a review of the neuropsychiatric features and their neurobiological basis. Neuropsychiatr Dis Treat 2013; 9:1873-84. [PMID: 24353423 PMCID: PMC3862513 DOI: 10.2147/ndt.s52188] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The 22q11.2 deletion syndrome (22q11DS) is caused by an autosomal dominant microdeletion of chromosome 22 at the long arm (q) 11.2 band. The 22q11DS is among the most clinically variable syndromes, with more than 180 features related with the deletion, and is associated with an increased risk of psychiatric disorders, accounting for up to 1%-2% of schizophrenia cases. In recent years, several genes located on chromosome 22q11 have been linked to schizophrenia, including those encoding catechol-O-methyltransferase and proline dehydrogenase, and the interaction between these and other candidate genes in the deleted region is an important area of research. It has been suggested that haploinsufficiency of some genes within the 22q11.2 region may contribute to the characteristic psychiatric phenotype and cognitive functioning of schizophrenia. Moreover, an extensive literature on neuroimaging shows reductions of the volumes of both gray and white matter, and these findings suggest that this reduction may be predictive of increased risk of prodromal psychotic symptoms in 22q11DS patients. Experimental and standardized cognitive assessments alongside neuroimaging may be important to identify one or more endophenotypes of schizophrenia, as well as a predictive prodrome that can be preventively treated during childhood and adolescence. In this review, we summarize recent data about the 22q11DS, in particular those addressing the neuropsychiatric and cognitive phenotypes associated with the deletion, underlining the recent advances in the studies about the genetic architecture of the syndrome.
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Affiliation(s)
- Chiara Squarcione
- Department of Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy
| | - Maria Chiara Torti
- Department of Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy
| | - Fabio Di Fabio
- Department of Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy
| | - Massimo Biondi
- Department of Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy
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Michaelovsky E, Frisch A, Carmel M, Patya M, Zarchi O, Green T, Basel-Vanagaite L, Weizman A, Gothelf D. Genotype-phenotype correlation in 22q11.2 deletion syndrome. BMC MEDICAL GENETICS 2012; 13:122. [PMID: 23245648 PMCID: PMC3548696 DOI: 10.1186/1471-2350-13-122] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 12/10/2012] [Indexed: 12/31/2022]
Abstract
BACKGROUND The 22q11.2 deletion syndrome (22q11.2DS) is caused by hemizygous microdeletions on chromosome 22q11.2 with highly variable physical and neuropsychiatric manifestations. We explored the genotype-phenotype relationship in a relatively large 22q11.2DS cohort treated and monitored in our clinic using comprehensive clinical evaluation and detailed molecular characterization of the deletion. METHODS Molecular analyses in 142 subjects with 22q11.2DS features were performed by FISH and MLPA methods. Participants underwent clinical assessment of physical symptoms and structured psychiatric and cognitive evaluation. RESULTS Deletions were found in 110 individuals including one with an atypical nested distal deletion which was missed by the FISH test. Most subjects (88.2%) carried the 3Mb typically deleted region and 11.8% carried 4 types of deletions differing in size and location. No statistically significant genotype-phenotype correlations were found between deletion type and clinical data although some differences in hypocalcemia and cardiovascular anomalies were noted.Analysis of the patient with the distal nested deletion suggested a redundancy of genes causing the physical and neuropsychiatric phenotype in 22q11.2DS and indicating that the psychiatric and cognitive trajectories may be governed by different genes. CONCLUSIONS MLPA is a useful and affordable molecular method combining accurate diagnosis and detailed deletion characterization. Variations in deletion type and clinical manifestations impede the detection of significant differences in samples of moderate size, but analysis of individuals with unique deletions may provide insight into the underlying biological mechanisms.Future genotype-phenotype studies should involve large multicenter collaborations employing uniform clinical standards and high-resolution molecular methods.
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Scharpf RB, Beaty TH, Schwender H, Younkin SG, Scott AF, Ruczinski I. Fast detection of de novo copy number variants from SNP arrays for case-parent trios. BMC Bioinformatics 2012; 13:330. [PMID: 23234608 PMCID: PMC3576329 DOI: 10.1186/1471-2105-13-330] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 12/07/2012] [Indexed: 11/10/2022] Open
Abstract
Background In studies of case-parent trios, we define copy number variants (CNVs) in the offspring that differ from the parental copy numbers as de novo and of interest for their potential functional role in disease. Among the leading array-based methods for discovery of de novo CNVs in case-parent trios is the joint hidden Markov model (HMM) implemented in the PennCNV software. However, the computational demands of the joint HMM are substantial and the extent to which false positive identifications occur in case-parent trios has not been well described. We evaluate these issues in a study of oral cleft case-parent trios. Results Our analysis of the oral cleft trios reveals that genomic waves represent a substantial source of false positive identifications in the joint HMM, despite a wave-correction implementation in PennCNV. In addition, the noise of low-level summaries of relative copy number (log R ratios) is strongly associated with batch and correlated with the frequency of de novo CNV calls. Exploiting the trio design, we propose a univariate statistic for relative copy number referred to as the minimum distance that can reduce technical variation from probe effects and genomic waves. We use circular binary segmentation to segment the minimum distance and maximum a posteriori estimation to infer de novo CNVs from the segmented genome. Compared to PennCNV on simulated data, MinimumDistance identifies fewer false positives on average and is comparable to PennCNV with respect to false negatives. Genomic waves contribute to discordance of PennCNV and MinimumDistance for high coverage de novo calls, while highly concordant calls on chromosome 22 were validated by quantitative PCR. Computationally, MinimumDistance provides a nearly 8-fold increase in speed relative to the joint HMM in a study of oral cleft trios. Conclusions Our results indicate that batch effects and genomic waves are important considerations for case-parent studies of de novo CNV, and that the minimum distance is an effective statistic for reducing technical variation contributing to false de novo discoveries. Coupled with segmentation and maximum a posteriori estimation, our algorithm compares favorably to the joint HMM with MinimumDistance being much faster.
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Affiliation(s)
- Robert B Scharpf
- Department of Oncology, Johns Hopkins University, Baltimore, MD, USA.
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Yu S, Graf W, Ramalingam A, Brawner S, Joyce J, Fiedler S, Zhou XG, Liu HY. Identification of Copy Number Variants on Human Chromosome 22 in Patients with a Variety of Clinical Findings. Cytogenet Genome Res 2011; 134:260-8. [DOI: 10.1159/000330123] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2011] [Indexed: 12/26/2022] Open
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Mosca-Boidron AL, Bouquillon S, Faivre L, Callier P, Andrieux J, Marle N, Bonnet C, Vincent-Delorme C, Berri M, Plessis G, Manouvrier-Hanu S, Dieux-Coeslier A, Thauvin-Robinet C, Pipiras E, Delahaye A, Payet M, Ragon C, Masurel-Paulet A, Questiaux E, Benzacken B, Jonveaux P, Mugneret F, Holder-Espinasse M. What can we learn from old microdeletion syndromes using array-CGH screening? Clin Genet 2011; 82:41-7. [DOI: 10.1111/j.1399-0004.2011.01747.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Drew LJ, Crabtree GW, Markx S, Stark KL, Chaverneff F, Xu B, Mukai J, Fenelon K, Hsu PK, Gogos JA, Karayiorgou M. The 22q11.2 microdeletion: fifteen years of insights into the genetic and neural complexity of psychiatric disorders. Int J Dev Neurosci 2011; 29:259-81. [PMID: 20920576 PMCID: PMC3074020 DOI: 10.1016/j.ijdevneu.2010.09.007] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 09/17/2010] [Accepted: 09/20/2010] [Indexed: 12/22/2022] Open
Abstract
Over the last fifteen years it has become established that 22q11.2 deletion syndrome (22q11DS) is a true genetic risk factor for schizophrenia. Carriers of deletions in chromosome 22q11.2 develop schizophrenia at rate of 25-30% and such deletions account for as many as 1-2% of cases of sporadic schizophrenia in the general population. Access to a relatively homogeneous population of individuals that suffer from schizophrenia as the result of a shared etiological factor and the potential to generate etiologically valid mouse models provides an immense opportunity to better understand the pathobiology of this disease. In this review we survey the clinical literature associated with the 22q11.2 microdeletions with a focus on neuroanatomical changes. Then, we highlight results from work modeling this structural mutation in animals. The key biological pathways disrupted by the mutation are discussed and how these changes impact the structure and function of neural circuits is described.
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Affiliation(s)
- Liam J. Drew
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Gregg W. Crabtree
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Sander Markx
- Department of Psychiatry, Columbia University, New York, New York 10032, USA
| | - Kimberly L. Stark
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
- Department of Psychiatry, Columbia University, New York, New York 10032, USA
| | - Florence Chaverneff
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Bin Xu
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
- Department of Psychiatry, Columbia University, New York, New York 10032, USA
| | - Jun Mukai
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Karine Fenelon
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Pei-Ken Hsu
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
- Integrated Program in Cellular, Molecular, and Biophysical Studies, Columbia University, New York, New York 10032, USA
| | - Joseph A. Gogos
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
- Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Maria Karayiorgou
- Department of Psychiatry, Columbia University, New York, New York 10032, USA
- New York State Psychiatric Institute, New York, New York 10032, USA
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Schramm C, Draaken M, Bartels E, Boemers TM, Aretz S, Brockschmidt FF, Nöthen MM, Ludwig M, Reutter H. De novo microduplication at 22q11.21 in a patient with VACTERL association. Eur J Med Genet 2011; 54:9-13. [DOI: 10.1016/j.ejmg.2010.09.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 09/06/2010] [Indexed: 01/27/2023]
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Verhoeven W, Egger J, Brunner H, de Leeuw N. A patient with a de novo distal 22q11.2 microdeletion and anxiety disorder. Am J Med Genet A 2010; 155A:392-7. [PMID: 21271660 DOI: 10.1002/ajmg.a.33802] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 09/26/2010] [Indexed: 11/08/2022]
Abstract
We report on a young female with normal intelligence evaluated for long-term anxiety. Her history includes prematurity, neonatal feeding problems, surgical correction of congenital heart defects, recurrent upper airway and urinary tract infections, and delayed motor and developmental milestones. Physical examination disclosed small stature and minor dysmorphisms. Chromosome analysis, 22q11.2 FISH analysis, and subtelomeric MLPA testing did not detect any abnormalities. Genome wide SNP Array analysis showed a de novo deletion in 22q11.21q11.22, the so-called distal 22q11 microdeletion that involves the MAPK1 gene. A diagnosis of panic disorder was made and the patient was successfully treated with a daily dose of 20 mg citalopram. To our knowledge, this is the first adolescent patient with a long history of complaints about anxiety and a distal 22q11 microdeletion. We speculate that genes from the deleted region, especially MAPK1, increase the neurobiological susceptibility to anxiety disorders that may be a part of the psychopathological phenotype of the distal 22q11.2 microdeletion syndrome.
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Affiliation(s)
- Willem Verhoeven
- Vincent van Gogh Institute for Psychiatry, Centre of Excellence for Neuropsychiatry, Venray, The Netherlands.
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Bedoyan JK, Lesperance MM, Ackley T, Iyer RK, Innis JW, Misra VK. A complex 6p25 rearrangement in a child with multiple epiphyseal dysplasia. Am J Med Genet A 2010; 155A:154-63. [PMID: 21204225 DOI: 10.1002/ajmg.a.33751] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 09/12/2010] [Indexed: 11/08/2022]
Abstract
Genomic rearrangements are increasingly recognized as important contributors to human disease. Here we report on an 11½-year-old child with myopia, Duane retraction syndrome, bilateral mixed hearing loss, skeletal anomalies including multiple epiphyseal dysplasia, and global developmental delay, and a complex 6p25 genomic rearrangement. We have employed oligonucleotide-based comparative genomic hybridization arrays (aCGH) of different resolutions (44 and 244K) as well as a 1 M single nucleotide polymorphism (SNP) array to analyze this complex rearrangement. Our analyses reveal a complex rearrangement involving a ∼2.21 Mb interstitial deletion, a ∼240 kb terminal deletion, and a 70-80 kb region in between these two deletions that shows maintenance of genomic copy number. The interstitial deletion contains eight known genes, including three Forkhead box containing (FOX) transcription factors (FOXQ1, FOXF2, and FOXC1). The region maintaining genomic copy number partly overlaps the dual specificity protein phosphatase 22 (DUSP22) gene. Array analyses suggest a homozygous loss of genomic material at the 5' end of DUSP22, which was corroborated using TaqMan® copy number analysis. It is possible that this homozygous genomic loss may render both copies of DUSP22 or its products non-functional. Our analysis suggests a rearrangement mechanism distinct from a previously reported replication-based error-prone mechanism without template switching for a specific 6p25 rearrangement with a 1.22 Mb interstitial deletion. Our study demonstrates the utility and limitations of using oligonucleotide-based aCGH and SNP array technologies of increasing resolutions in order to identify complex DNA rearrangements and gene disruptions.
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Affiliation(s)
- Jirair K Bedoyan
- Department of Pediatrics, The University of Michigan Medical School, Ann Arbor, USA.
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