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Belohlavkova A, Sterbova K, Betzler C, Burkhard S, Panzer A, Wolff M, Lassuthova P, Vlckova M, Kyncl M, Benova B, Jahodova A, Kudr M, Goerg M, Dusek P, Seeman P, Kluger G, Krsek P. Clinical features and blood iron metabolism markers in children with beta-propeller protein associated neurodegeneration. Eur J Paediatr Neurol 2020; 28:81-88. [PMID: 32811771 DOI: 10.1016/j.ejpn.2020.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/16/2020] [Accepted: 07/28/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Neurodegeneration with brain iron accumulation constitutes a group of rare progressive movement disorders sharing intellectual disability and neuroimaging findings as common denominators. Beta-propeller protein-associated neurodegeneration (BPAN) represents approximately 7% of the cases, and its first signs are typically epilepsy and developmental delay. We aimed to describe in detail the phenotype of BPAN with a special focus on iron metabolism. MATERIAL AND METHODS We present a cohort of paediatric patients with pathogenic variants of WD-Repeat Domain 45 gene (WDR45). The diagnosis was established by targeted panel sequencing of genes associated with epileptic encephalopathies (n = 9) or by Sanger sequencing of WDR45 (n = 1). Data on clinical characteristics, molecular-genetic findings and other performed investigations were gathered from all participating centres. Markers of iron metabolism were analysed in 6 patients. RESULTS Ten children (3 males, 7 females, median age 8.4 years) from five centres (Prague, Berlin, Vogtareuth, Tubingen and Cologne) were enrolled in the study. All patients manifested first symptoms (e.g. epilepsy, developmental delay) between 2 and 31 months (median 16 months). Seven patients were seizure-free (6 on antiepileptic medication, one drug-free) at the time of data collection. Neurological findings were non-specific with deep tendon hyperreflexia (n = 4) and orofacial dystonia (n = 3) being the most common. Soluble transferrin receptor/log ferritin ratio was elevated in 5/6 examined subjects; other parameters of iron metabolism were normal. CONCLUSION Severity of epilepsy often gradually decreases in BPAN patients. Elevation of soluble transferrin receptor/log ferritin ratio could be another biochemical marker of the disease and should be explored by further studies.
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Affiliation(s)
- Anezka Belohlavkova
- Department of Paediatric Neurology, Charles University, Second Faculty of Medicine and Motol University Hospital, Member of the ERN EpiCARE Motol Epilepsy Center, V Uvalu 84, 15006, Prague, Czech Republic
| | - Katalin Sterbova
- Department of Paediatric Neurology, Charles University, Second Faculty of Medicine and Motol University Hospital, Member of the ERN EpiCARE Motol Epilepsy Center, V Uvalu 84, 15006, Prague, Czech Republic
| | - Cornelia Betzler
- Clinic for Neuropediatrics and Neurorehabilitation, Epilepsy Center for Children and Adolescents, Schön Klinik, Vogtareuth, Germany; Research Institute for Rehabilitation, Transition and Palliation, Paracelsus Medical University Salzburg, Austria
| | - Stuve Burkhard
- Children's Hospital Amsterdamer Straße, Kliniken der Stadt Köln, Cologne, Germany
| | - Axel Panzer
- Epilepsy Center, Paediatric Neurology, DRK Kliniken Berlin-Westend, Berlin, Germany
| | - Markus Wolff
- Department of Neuropediatrics, University Children's Hospital, Tübingen, Germany
| | - Petra Lassuthova
- Department of Paediatric Neurology, Charles University, Second Faculty of Medicine and Motol University Hospital, Member of the ERN EpiCARE Motol Epilepsy Center, V Uvalu 84, 15006, Prague, Czech Republic
| | - Marketa Vlckova
- Department of Biology and Medical Genetics, Charles University, Second Faculty of Medicine and Motol University Hospital, V Uvalu 84, 15006, Prague, Czech Republic
| | - Martin Kyncl
- Department of Radiology, Charles University, Second Faculty of Medicine and Motol University Hospital, V Uvalu 84, 15006, Prague, Czech Republic
| | - Barbora Benova
- Department of Paediatric Neurology, Charles University, Second Faculty of Medicine and Motol University Hospital, Member of the ERN EpiCARE Motol Epilepsy Center, V Uvalu 84, 15006, Prague, Czech Republic
| | - Alena Jahodova
- Department of Paediatric Neurology, Charles University, Second Faculty of Medicine and Motol University Hospital, Member of the ERN EpiCARE Motol Epilepsy Center, V Uvalu 84, 15006, Prague, Czech Republic
| | - Martin Kudr
- Department of Paediatric Neurology, Charles University, Second Faculty of Medicine and Motol University Hospital, Member of the ERN EpiCARE Motol Epilepsy Center, V Uvalu 84, 15006, Prague, Czech Republic
| | - Maria Goerg
- Department of Neuropaediatrics, Centrum for Social Paediatry, St. Mary´s Children Hospital, Landshut, Germany
| | - Petr Dusek
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic
| | - Pavel Seeman
- Department of Paediatric Neurology, Charles University, Second Faculty of Medicine and Motol University Hospital, Member of the ERN EpiCARE Motol Epilepsy Center, V Uvalu 84, 15006, Prague, Czech Republic
| | - Gerhard Kluger
- Clinic for Neuropediatrics and Neurorehabilitation, Epilepsy Center for Children and Adolescents, Schön Klinik, Vogtareuth, Germany; Research Institute for Rehabilitation, Transition and Palliation, Paracelsus Medical University Salzburg, Austria
| | - Pavel Krsek
- Department of Paediatric Neurology, Charles University, Second Faculty of Medicine and Motol University Hospital, Member of the ERN EpiCARE Motol Epilepsy Center, V Uvalu 84, 15006, Prague, Czech Republic.
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Development of two different pharmacogenomics detection methods for second-generation antipsychotic drugs quetiapine and aripiprazole. JOURNAL OF BIO-X RESEARCH 2020. [DOI: 10.1097/jbr.0000000000000058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Spieler D, Velayos-Baeza A, Mühlbäck A, Castrop F, Maegerlein C, Slotta-Huspenina J, Bader B, Haslinger B, Danek A. Identification of two compound heterozygous VPS13A large deletions in chorea-acanthocytosis only by protein and quantitative DNA analysis. Mol Genet Genomic Med 2020; 8:e1179. [PMID: 32056394 PMCID: PMC7507471 DOI: 10.1002/mgg3.1179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 01/09/2020] [Accepted: 01/30/2020] [Indexed: 01/04/2023] Open
Abstract
Background Chorea‐acanthocytosis (ChAc; OMIM #200150) is a rare autosomal recessive condition with onset in early adulthood that is caused by mutations in the vacuolar protein sorting 13A (VPS13A) gene encoding chorein. Several diagnostic genomic DNA (gDNA) sequencing approaches are widely used. However, their limitations appear not to be acknowledged thoroughly enough. Methods Clinically, we deployed magnetic resonance imaging, blood smear analysis, and clinical chemistry for the index patient's characterization. The molecular analysis of the index patient next to his parents covered genomic DNA (gDNA) sequencing approaches, RNA/cDNA sequencing, and chorein specific Western blot. Results We report a 33‐year‐old male patient without functional protein due to compound heterozygosity for two VPS13A large deletions of 1168 and 1823 base pairs (bp) affecting, respectively, exons 8 and 9, and exon 13. To our knowledge, this represents the first ChAc case with two compound heterozygous large deletions identified so far. Of note, standard genomic DNA (gDNA) Sanger sequencing approaches alone yielded false negative findings. Conclusion Our case demonstrates the need to carry out detection of chorein in patients suspected of having ChAc as a helpful and potentially decisive tool to establish diagnosis. Furthermore, the course of the molecular analysis in this case discloses diagnostic pitfalls in detecting some variations, such as deletions, using only standard genomic DNA (gDNA) Sanger sequencing approaches and exemplifies alternative methods, such as RNA/cDNA sequencing or qRT‐PCR analysis, necessary to avoid false negative results.
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Affiliation(s)
- Derek Spieler
- Department of Psychosomatic Medicine and Psychotherapy, Center for Mental Health, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.,Institute of Epidemiology, Mental Health Research Unit, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Department of Neurology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | | | - Alžbeta Mühlbäck
- kbo-Isar-Amper-Klinikum Taufkirchen (Vils), Taufkirchen (Vils), Germany.,Department of Neurology and Centre of Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital Prague, Prague, Czech Republic
| | - Florian Castrop
- Department of Neurology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Christian Maegerlein
- Department of Neuroradiology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Julia Slotta-Huspenina
- Institut für Allgemeine Pathologie und Pathologische Anatomie der Technischen Universität München, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Benedikt Bader
- Neurologische Klinik und Poliklinik, Ludwigs-Maximilians Universität München, Munich, Germany
| | - Bernhard Haslinger
- Department of Neurology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Adrian Danek
- Neurologische Klinik und Poliklinik, Ludwigs-Maximilians Universität München, Munich, Germany
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Zhou W, Shi Y, Li F, Wu X, Huai C, Shen L, Yi Z, He L, Liu C, Qin S. Study of the association between Schizophrenia and microduplication at the 16p11.2 locus in the Han Chinese population. Psychiatry Res 2018; 265:198-199. [PMID: 29730539 DOI: 10.1016/j.psychres.2018.04.049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 11/30/2022]
Abstract
Copy number variants are essential in the etiology of Schizophrenia. We assessed the role of the 16p11.2 locus in the pathogenesis of Schizophrenia in the Han Chinese population. In total, 659 patients with Schizophrenia and 650 healthy controls were genotyped and followed by a meta-analysis, involving 9384 patients and 15,457 controls. We found the microduplications at the 16p11.2 locus to be strongly associated with the SZ. The frequency of this microduplication is significantly higher in Schizophrenia patients than in healthy controls. These results highlight the role of the 16p11.2 locus in the development of SZ in the Han Chinese population.
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Affiliation(s)
- Wei Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ye Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Fengzhen Li
- Laigang Hospital, Laiwu, Shandong Province, People's Republic of China
| | - Xi Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Cong Huai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Lu Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zenhui Yi
- State Key Laboratory of Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Chuanxin Liu
- College of Mental Health in Jining Medical University, Jining, Shandong Province, People's Republic of China.
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
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Gaspar H, Lutz B, Reicherter K, Lühl S, Taurman R, Gabriel H, Brenner RE, Borck G. 4.7 Mb deletion encompassing TGFB2 associated with features of Loeys-Dietz syndrome and osteoporosis in adulthood. Am J Med Genet A 2017; 173:2289-2292. [PMID: 28544325 DOI: 10.1002/ajmg.a.38286] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Harald Gaspar
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Bernd Lutz
- Department of Orthopedics, University of Ulm, Ulm, Germany
| | - Kerstin Reicherter
- Center for Genomics and Transcriptomics and Praxis fuer Humangenetik Tuebingen, Tuebingen, Germany
| | - Simon Lühl
- Division of Pediatric Neurology, Children's Hospital, University of Ulm, Ulm, Germany
| | - Rita Taurman
- Department of Orthopedics, University of Ulm, Ulm, Germany
| | - Heinz Gabriel
- Center for Genomics and Transcriptomics and Praxis fuer Humangenetik Tuebingen, Tuebingen, Germany
| | - Rolf E Brenner
- Division for Biochemistry of Joint and Connective Tissue Diseases, Department of Orthopedics, University of Ulm, Ulm, Germany
| | - Guntram Borck
- Institute of Human Genetics, University of Ulm, Ulm, Germany
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Hoekstra AS, van den Ende B, Julià XP, van Breemen L, Scheurwater K, Tops CM, Malinoc A, Devilee P, Neumann HPH, Bayley JP. Simple and rapid characterization of novel large germline deletions in SDHB, SDHC and SDHD-related paraganglioma. Clin Genet 2016; 91:536-544. [PMID: 27485256 DOI: 10.1111/cge.12843] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/21/2016] [Accepted: 07/27/2016] [Indexed: 12/17/2022]
Abstract
Germline mutations in genes encoding subunits of succinate dehydrogenase (SDH) are associated with hereditary paraganglioma and pheochromocytoma. Although most mutations in SDHB, SDHC and SDHD are intraexonic variants, large germline deletions may represent up to 10% of all variants but are rarely characterized at the DNA sequence level. Additional phenotypic effects resulting from deletions that affect neighboring genes are also not understood. We performed multiplex ligation-dependent probe amplification, followed by a simple long-range PCR 'chromosome walking' protocol to characterize breakpoints in 20 SDHx-linked paraganglioma-pheochromocytoma patients. Breakpoints were confirmed by conventional PCR and Sanger sequencing. Heterozygous germline deletions of up to 104 kb in size were identified in SDHB, SDHC, SDHD and flanking genes in 20 paraganglioma-pheochromocytoma patients. The exact breakpoint could be determined in 16 paraganglioma-pheochromocytoma patients of which 15 were novel deletions. In six patients proximal genes were also deleted, including PADI2, MFAP2, ATP13A2 (PARK9), CFAP126, TIMM8B and C11orf57. These genes were either partially or completely deleted, but did not modify the phenotype. This study increases the number of known SDHx deletions by over 50% and demonstrates that a significant proportion of large gene deletions can be resolved at the nucleotide level using a simple and rapid method.
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Affiliation(s)
- A S Hoekstra
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - B van den Ende
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - X P Julià
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - L van Breemen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - K Scheurwater
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - C M Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - A Malinoc
- Department of Nephrology, University Medical Center Freiburg, Freiburg, Germany
| | - P Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - H P H Neumann
- Department of Nephrology, University Medical Center Freiburg, Freiburg, Germany
| | - J-P Bayley
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Chen Z, Zheng W, Huang P, Tu D, Zhou S, Huang M, Chen X. Lanthanide-doped luminescent nano-bioprobes for the detection of tumor markers. NANOSCALE 2015; 7:4274-4290. [PMID: 25532615 DOI: 10.1039/c4nr05697c] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Sensitive and specific biodetection of tumor markers is essential for early-stage cancer diagnosis and therapy, and will ultimately increase the patient survival rate. As a new generation of luminescent bioprobes, lanthanide (Ln(3+))-doped inorganic luminescent nanoparticles have attracted considerable interest for a variety of biomedical applications due to their superior physicochemical properties. In this feature article, we provide a brief overview of the most recent advances in the development of Ln(3+)-doped luminescent nano-bioprobes and their promising applications for in vitro detection of tumor markers with an emphasis on the establishment of state-of-the-art assay techniques, such as heterogeneous time-resolved (TR) luminescent bioassay, dissolution-enhanced luminescent bioassay, upconversion (UC) luminescent bioassay, homogeneous TR Förster resonance energy transfer (TR-FRET) and UC-FRET bioassays. Some future prospects and efforts towards this emerging field are also envisioned.
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Affiliation(s)
- Zhuo Chen
- Key Laboratory of Optoelectronic Materials Chemistry and Physics, and Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China.
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Abstract
PURPOSE This study was performed on miscarriage samples for chromosome analysis to detect copy number variations (CNVs) related to subtelomeric regions, and with these results we aimed to adapt multiplex ligation-dependent probe amplification (MLPA) method for prenatal diagnosis. MATERIALS AND METHODS The cell cultures and DNA isolations were performed on 60 miscarriage samples. For maternal contamination analysis, DNA isolations and quantitative fluorescent polymerase chain reactions were done using peripheric blood of mothers who had miscarriages. We compared short tandem repeat peak profiles of miscarriage samples and mothers. The subtelomeric regions of the chromosomes were assessed using the MLPA method. RESULTS Of 43 miscarriage samples, 19 had normal karyotype (44.2%), 10 had numerical abnormalities (23.3%), and 2 had structural abnormalities (4.7%). Subtelomeric 16q duplication was determined in 2 of the 30 miscarriage samples investigated with MLPA method (6.6%). CONCLUSION There is no statistically significant difference between two groups (p > 0.05). However, the fact that the 6.6% subtelomeric CNV found in miscarriage samples was not found in controls, showed that further studies are required. We recommend that the miscarriage samples of the couples with recurrent miscarriage should be analyzed in terms of subtelomeric CNV after the exclusion of other clinical reasons.
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Affiliation(s)
- Akin Tekcan
- a School of Health, Ahi Evran University , Kirsehir , Turkey
| | - Mehmet Elbistan
- b Section of Medical Genetic, Department of Medical Biology , and
| | - Sengul Tural
- b Section of Medical Genetic, Department of Medical Biology , and
| | - Mehmet Bilge Çetinkaya
- c Department of Gynecology and Obstetrics, Faculty of Medicine , Ondokuz Mayis University , Samsun , Turkey
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Dong WW, Huang HL, Yang W, Liu J, Yu Y, Zhou SL, Wang W, Lv XC, Li ZY, Zhang MY, Zheng ZH, Yan W. Testis-specific Fank1 gene in knockdown mice produces oligospermia via apoptosis. Asian J Androl 2014; 16:124-30. [PMID: 24369145 PMCID: PMC3901870 DOI: 10.4103/1008-682x.122592] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Fank1 is exclusively expressed in the testis from the meiosis phase to the haploid phase of spermatogenesis. In this study, we examined the function of Fank1 by establishing a Fank1-knockdown transgenic mouse model. The apoptotic statuses of the testes of the transgenic mice were tested using the terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) method. The FANK1 consensus DNA-binding sequence was identified using cyclic amplification of sequence target (CAST) analysis. Differentially expressed genes were examined using microarray analysis. A reduction in sperm number and an increase in apoptotic spermatocytes were observed in Fank1-knockdown mice, and the apoptotic cells were found to be primarily spermatogonia and spermatocytes. The CAST results demonstrated that the consensus DNA-binding sequence was AAAAAG, in which the percentage occurrence of each base at each position ranged from 55 to 86%. This sequence was present in the promoter regions of 10 differentially expressed genes that were examined using microarray analysis. In total, 17 genes were differentially expressed with changes in their expression levels greater than twofold. The abnormal expression of Fank1 target genes that were regulated directly or indirectly by Fank1 reduced the number of sperm in the knockdown mice. Thus, FANK1 may play a pivotal role in spermatogenesis as a transcription factor.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zhi-Hong Zheng
- Laboratory Animal Centre; Department of Pathology and Pathophysiology Research, China Medical University, Shenyang, China
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Liu J, Fu S, Xu Y, Zheng Z. RNA interference targeting inhibition of S100A4 suppresses cell growth and promotes apoptosis in human laryngeal carcinoma Hep‑2 cells. Mol Med Rep 2014; 10:1389-94. [PMID: 24969174 DOI: 10.3892/mmr.2014.2345] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 05/09/2014] [Indexed: 11/06/2022] Open
Abstract
S100A4 is a small Ca2+ binding protein that belongs to the S100 family and is involved in a number of cellular functions, including cell cycle control, proliferation, apoptosis, and has a significant role in angiogenesis and neurite extension. However, the exact function and mechanism of S100A4 in laryngeal carcinogenesis remains to be elucidated. The present study was designed to investigate the potential use of RNA interference to inhibit S100A4 expression and activation, as well as the subsequent effect on human laryngeal cancer cell growth and apoptosis. The present study demonstrated that knockdown of S100A4 decreased the proliferation and growth of the human laryngeal cancer Hep‑2 cell line. The percentages of the apoptotic cells were 4.23±1.22, 4.92±1.85 and 11.70±4.02% in the control, negative control and S100A4 short hairpin RNA (shRNA) groups, respectively, indicating significant differences among the different groups. The S100A4‑mediated induction of apoptosis was demonstrated to be associated with the activation of caspase‑3, caspase‑8 and caspase‑9. Intratumoral injection of S100A4‑shRNA inhibited tumor growth in nude mice. Thus, knockdown of S100A4 inhibited the progression of laryngeal squamous carcinoma, decreased proliferation and promoted apoptosis. S100A4 is a potential candidate for therapeutic targeting of laryngeal carcinoma cells.
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Affiliation(s)
- Jia Liu
- Laboratory Animal Center, China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Shuang Fu
- Department of Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110022, P.R. China
| | - Yingqi Xu
- Laboratory Animal Center, China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Zhihong Zheng
- Laboratory Animal Center, China Medical University, Shenyang, Liaoning 110001, P.R. China
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Abstract
Fluorescent dyes that bind DNA have been demonstrated as a useful alternative to radionucleotides for the quantification of DNA and the in vitro measurement of the activity of DNA polymerases and nucleases. However, this approach is generally used in a semi‐quantitative way to determine relative rates of reaction. In this report, we demonstrate a method for the simultaneous quantification of DNA in both its single‐strand and double‐strand forms using the dye PicoGreen. This approach is used in a steady‐state assay of DNA polymerase Klenow fragment exo−, where we determine kcat and Km values for the DNA polymerase that are in excellent agreement with literature values.
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Affiliation(s)
- Max D. Driscoll
- Manchester Institute of Biotechnology and Faculty of Life SciencesUniversity of ManchesterUK
| | - Julius Rentergent
- Manchester Institute of Biotechnology and Faculty of Life SciencesUniversity of ManchesterUK
| | - Sam Hay
- Manchester Institute of Biotechnology and Faculty of Life SciencesUniversity of ManchesterUK
- Correspondence
S. Hay, Manchester Institute of Biotechnology and Faculty of Life Sciences, University of Manchester, 131 Princess Street, Greater Manchester M1 7DN, UK
Fax: +44 0 161 306 5201
Tel: +44 0 161 306 5141
E‐mail:
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Wang R, Carter J, Lench N. Evaluation of real-time quantitative PCR as a standard cytogenetic diagnostic tool for confirmation of microarray (aCGH) results and determination of inheritance. Genet Test Mol Biomarkers 2013; 17:821-5. [PMID: 24024523 DOI: 10.1089/gtmb.2013.0284] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIM To evaluate the use of real-time quantitative PCR (qPCR) as a diagnostic tool for follow up of abnormal microarray (aCGH) results. METHOD qPCR was performed on 207 samples with known aCGH results to detect chromosomal abnormality and determine the capability of qPCR. Eighty-four samples were processed and the results compared with the original aCGH result and with one or more of the alternative follow-up methods: aCGH, fluorescence in situ hybridization (FISH), or karyotyping. A separate cohort of 107 samples was used to determine critical threshold values for qPCR. A further 16 samples were assessed in reproducibility and sensitivity studies. RESULTS All qPCR findings were consistent with the original aCGH results, and qPCR was found to be a superior follow-up method compared to FISH and karyotyping. Critical threshold values were also determined from this study. CONCLUSION In this study, qPCR analysis identified all copy number changes. qPCR is an accurate, rapid, reliable, and inexpensive technique for confirming copy number changes, and for determining the inheritance of such abnormalities to aid interpretation of results. We also present the critical threshold values required for qPCR as a practical tool. This technique has now been successfully implemented as part of the clinical diagnostic service within our laboratory.
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Affiliation(s)
- Rubin Wang
- NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children , London, United Kingdom
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Quelin C, Saillour Y, Poirier K, Roubertie A, Boddaert N, Desguerre I, Letourneur F, Beldjord C, Chelly J, Bahi-Buisson N. Focal polymicrogyria are associated with submicroscopic chromosomal rearrangements detected by CGH microarray analysis. Eur J Med Genet 2012; 55:527-30. [DOI: 10.1016/j.ejmg.2012.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 06/09/2012] [Indexed: 11/30/2022]
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14
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Mosaic DCX deletion causes subcortical band heterotopia in males. Neurogenetics 2012; 13:367-73. [DOI: 10.1007/s10048-012-0339-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 07/09/2012] [Indexed: 10/28/2022]
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Pauli S, Steinemann D, Dittmann K, Wienands J, Shoukier M, Möschner M, Burfeind P, Manukjan G, Göhring G, Escherich G. Occurrence of acute lymphoblastic leukemia and juvenile myelomonocytic leukemia in a patient with Noonan syndrome carrying the germline PTPN11 mutation p.E139D. Am J Med Genet A 2012; 158A:652-8. [DOI: 10.1002/ajmg.a.34439] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 11/02/2011] [Indexed: 11/07/2022]
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Wat MJ, Veenma D, Hogue J, Holder AM, Yu Z, Wat JJ, Hanchard N, Shchelochkov OA, Fernandes CJ, Johnson A, Lally KP, Slavotinek A, Danhaive O, Schaible T, Cheung SW, Rauen KA, Tonk VS, Tibboel D, de Klein A, Scott DA. Genomic alterations that contribute to the development of isolated and non-isolated congenital diaphragmatic hernia. J Med Genet 2011; 48:299-307. [PMID: 21525063 DOI: 10.1136/jmg.2011.089680] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND Congenital diaphragmatic hernia (CDH) is a life threatening birth defect. Most of the genetic factors that contribute to the development of CDH remain unidentified. OBJECTIVE To identify genomic alterations that contribute to the development of diaphragmatic defects. METHODS A cohort of 45 unrelated patients with CDH or diaphragmatic eventrations was screened for genomic alterations by array comparative genomic hybridisation or single nucleotide polymorphism based copy number analysis. RESULTS Genomic alterations that were likely to have contributed to the development of CDH were identified in 8 patients. Inherited deletions of ZFPM2 were identified in 2 patients with isolated diaphragmatic defects and a large de novo 8q deletion overlapping the same gene was found in a patient with non-isolated CDH. A de novo microdeletion of chromosome 1q41q42 and two de novo microdeletions on chromosome 16p11.2 were identified in patients with non-isolated CDH. Duplications of distal 11q and proximal 13q were found in a patient with non-isolated CDH and a de novo single gene deletion of FZD2 was identified in a patient with a partial pentalogy of Cantrell phenotype. CONCLUSIONS Haploinsufficiency of ZFPM2 can cause dominantly inherited isolated diaphragmatic defects with incomplete penetrance. These data define a new minimal deleted region for CDH on 1q41q42, provide evidence for the existence of CDH related genes on chromosomes 16p11.2, 11q23-24 and 13q12, and suggest a possible role for FZD2 and Wnt signalling in pentalogy of Cantrell phenotypes. These results demonstrate the clinical utility of screening for genomic alterations in individuals with both isolated and non-isolated diaphragmatic defects.
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Affiliation(s)
- Margaret J Wat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Suh JH, Yoon JS, Kwon JB, Kim HW, Wang YP. Identification of genomic aberrations by array comparative genomic hybridization in patients with aortic dissections. THE KOREAN JOURNAL OF THORACIC AND CARDIOVASCULAR SURGERY 2011; 44:123-30. [PMID: 22263138 PMCID: PMC3249287 DOI: 10.5090/kjtcs.2011.44.2.123] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2009] [Revised: 01/09/2011] [Accepted: 02/08/2011] [Indexed: 11/16/2022]
Abstract
Background The aim of the present study was to identify chromosomal loci that contribute to the pathogenesis of aortic dissection (AD) in a Korean population using array comparative genomic hybridization (CGH) and to confirm the results using real-time polymerase chain reaction (PCR). Materials and Methods Eighteen patients with ADs were enrolled in this study. Genomic DNA was extracted from individual blood samples, and array CGH analyses were performed. Four corresponding genes with obvious genomic changes were analyzed using real-time PCR in order to assess the level of genomic imbalance identified by array CGH. Results Genomic gains were most frequently detected at 8q24.3 (56%), followed by regions 7q35, 11q12.2, and 15q25.2 (50%). Genomic losses were most frequently observed at 4q35.2 (56%). Real-time PCR confirmed the results of the array CGH studies of the COL6A2, DGCR14, PCSK6, and SDHA genes. Conclusion This is the first study to identify candidate regions by array CGH in patients with ADs. The identification of genes that may predispose an individual to AD may lead to a better understanding of the mechanism of AD formation. Further multicenter studies comparing cohorts of patients of different ethnicities are warranted.
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Affiliation(s)
- Jong Hui Suh
- Department of Thoracic and Cardiovascular Surgery, Incheon St. Mary's Hospital, The Catholic University of Korea, College of Medicine, Korea
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18
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Basel-Vanagaite L, Goldberg-Stern H, Mimouni-Bloch A, Shkalim V, Böhm D, Kohlhase J. An emerging 1q21.1 deletion-associated neurodevelopmental phenotype. J Child Neurol 2011; 26:113-6. [PMID: 21212457 DOI: 10.1177/0883073810377658] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this study, we describe the neurodevelopmental and epileptic phenotypes in a family with an inherited 1q21.1 deletion. During the pregnancy with the proband, increased nuchal translucency and oligohydramnion were detected. The proband showed mild global developmental delay and ataxic gait. Seizures started in the proband at the age of 2 years and manifested as generalized tonic-clonic seizures, atypical absence seizures, head drops, and drop attacks with no abnormal findings on interictal electroencephalogram. We performed an Agilent Human Genome CGH (comparative genomic hybridization) Microarray 105A, and a microdeletion on chromosome 1q21.1 was identified in both the patient and his asymptomatic father. This deletion encompasses 1.65 Mb and is larger than the reported recurrent class I deletions in this region. Cryptic cytogenetic abnormalities should be considered in patients with neurodevelopmental problems and atypical presentation of epilepsy with a normal electroencephalography (EEG).
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19
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Yis U, Uyanik G, Heck PB, Smitka M, Nobel H, Ebinger F, Dirik E, Feng L, Kurul SH, Brocke K, Unalp A, Özer E, Cakmakci H, Sewry C, Cirak S, Muntoni F, Hehr U, Morris-Rosendahl DJ. Fukutin mutations in non-Japanese patients with congenital muscular dystrophy: less severe mutations predominate in patients with a non-Walker-Warburg phenotype. Neuromuscul Disord 2010; 21:20-30. [PMID: 20961758 DOI: 10.1016/j.nmd.2010.08.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 08/27/2010] [Indexed: 11/16/2022]
Abstract
Six genes including POMT1, POMT2, POMGNT1, FKRP, Fukutin (FKTN) and LARGE encode proteins involved in the glycosylation of α-dystroglycan (α-DG). Abnormal glycosylation of α-DG is a common finding in Walker-Warburg syndrome (WWS), muscle-eye-brain disease (MEB), Fukuyama congenital muscular dystrophy (FCMD), congenital muscular dystrophy types 1C and 1D and some forms of autosomal recessive limb-girdle muscular dystrophy (LGMD2I, LGMD2K, LGMD2M), and is associated with mutations in the above genes. FCMD, caused by mutations in Fukutin (FKTN), is most frequent in Japan, but an increasing number of FKTN mutations are being reported outside of Japan. We describe four new patients with FKTN mutations and phenotypes ranging from: severe WWS in a Greek-Croatian patient, to congenital muscular dystrophy and cobblestone lissencephaly resembling MEB-FCMD in two Turkish patients, and limb-girdle muscular dystrophy and no mental retardation in a German patient. Four of the five different FKTN mutations have not been previously described.
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Affiliation(s)
- Uluc Yis
- Gaziantep Children's Hospital, Department of Pediatric Neurology, Gaziantep, Turkey
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20
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Ellison G, Donald E, McWalter G, Knight L, Fletcher L, Sherwood J, Cantarini M, Orr M, Speake G. A comparison of ARMS and DNA sequencing for mutation analysis in clinical biopsy samples. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2010; 29:132. [PMID: 20925915 PMCID: PMC2988723 DOI: 10.1186/1756-9966-29-132] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 10/06/2010] [Indexed: 12/21/2022]
Abstract
BACKGROUND We have compared mutation analysis by DNA sequencing and Amplification Refractory Mutation System™ (ARMS™) for their ability to detect mutations in clinical biopsy specimens. METHODS We have evaluated five real-time ARMS assays: BRAF 1799T>A, [this includes V600E and V600K] and NRAS 182A>G [Q61R] and 181C>A [Q61K] in melanoma, EGFR 2573T>G [L858R], 2235-2249del15 [E746-A750del] in non-small-cell lung cancer, and compared the results to DNA sequencing of the mutation 'hot-spots' in these genes in formalin-fixed paraffin-embedded tumour (FF-PET) DNA. RESULTS The ARMS assays maximised the number of samples that could be analysed when both the quality and quantity of DNA was low, and improved both the sensitivity and speed of analysis compared with sequencing. ARMS was more robust with fewer reaction failures compared with sequencing and was more sensitive as it was able to detect functional mutations that were not detected by DNA sequencing. DNA sequencing was able to detect a small number of lower frequency recurrent mutations across the exons screened that were not interrogated using the specific ARMS assays in these studies. CONCLUSIONS ARMS was more sensitive and robust at detecting defined somatic mutations than DNA sequencing on clinical samples where the predominant sample type was FF-PET.
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Affiliation(s)
- Gillian Ellison
- AstraZeneca, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK.
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21
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Christofolini DM, de Paula Ramos MA, Kulikowski LD, da Silva Bellucco FT, Belangero SIN, Brunoni D, Melaragno MI. Subtelomeric rearrangements and copy number variations in people with intellectual disabilities. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2010; 54:938-942. [PMID: 20807304 DOI: 10.1111/j.1365-2788.2010.01325.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
BACKGROUND The most prevalent type of structural variation in the human genome is represented by copy number variations that can affect transcription levels, sequence, structure and function of genes. METHOD In the present study, we used the multiplex ligation-dependent probe amplification (MLPA) technique and quantitative PCR for the detection of copy number variation in 132 intellectually disabled male patients with normal karyotypes and negative fragile-X-testing. RESULTS Ten of these patients (7.6%) showed copy number variation in the subtelomeric regions, including deletions and duplications. DISCUSSION Duplications of the SECTM1 gene, located at 17q25.3, and of the FLJ22115 gene, located at 20p13, could be associated with phenotype alterations. This study highlights the relevance in the aetiology of intellectual disability of subtelomeric rearrangements that can be screened by MLPA and other molecular techniques.
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Affiliation(s)
- D M Christofolini
- Morphology and Genetics Department, Universidade Federal de São Paulo, São Paulo, SP, Brazil
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22
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Mitter D, Chiaie BD, Lüdecke HJ, Gillessen-Kaesbach G, Bohring A, Kohlhase J, Caliebe A, Siebert R, Roepke A, Ramos-Arroyo MA, Nieva B, Menten B, Loeys B, Mortier G, Wieczorek D. Genotype-phenotype correlation in eight new patients with a deletion encompassing 2q31.1. Am J Med Genet A 2010; 152A:1213-24. [PMID: 20425826 DOI: 10.1002/ajmg.a.33344] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Microdeletions of the 2q31.1 region are rare. We present the clinical and molecular findings of eight previously unreported patients with overlapping deletions in 2q31.1. The patients have a variable clinical phenotype and present with developmental delay (7/8), growth retardation (5/8), seizures (2/8) and a craniofacial dysmorphism consisting of microcephaly (4/8), short palpebral fissures (7/8), broad eyebrows with lateral flare (7/8), low-set ears with thickened helices and lobules (5/8), and micrognathia (6/8). Additional congenital anomalies were noted, including limb abnormalities (8/8), heart defects (3/8), genital anomalies (3/8), and craniosynostosis (1/8). Six of these microdeletions, ranging in size from 1.24 to 8.35 Mb, were identified by array CGH, one larger deletion (19.7 Mb) was detected by conventional karyotyping and further characterized by array CGH analysis. The smallest region of overlap in all eight patients spans at most 88 kb and includes only the WIPF1 gene. This gene codes for the WAS/WASL interacting protein family member 1. The patients described here do not present with clinical signs of the Wiskott-Aldrich syndrome and the deletion of this single gene does not allow explaining the phenotype in our patients. It is likely that the deletion of different but overlapping sets of genes from 2q31 is responsible for the clinical variability in these patients. To further dissect the complex phenotype associated with deletions in 2q31, additional patients with overlapping phenotypes should be examined with array CGH. This should help to link particular phenotypes to specific genes, and add to our understanding of the underlying developmental processes.
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MESH Headings
- Adult
- Child
- Child, Preschool
- Chromosome Breakage
- Chromosome Deletion
- Chromosomes, Human, Pair 2/genetics
- Comparative Genomic Hybridization
- Female
- Foot Deformities, Congenital/complications
- Foot Deformities, Congenital/diagnostic imaging
- Foot Deformities, Congenital/genetics
- Genetic Association Studies
- Hand Deformities, Congenital/complications
- Hand Deformities, Congenital/diagnostic imaging
- Hand Deformities, Congenital/genetics
- Humans
- Infant
- Infant, Newborn
- Karyotyping
- Male
- Pregnancy
- Radiography
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Affiliation(s)
- Diana Mitter
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany.
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23
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Lai LA, Kostadinov R, Barrett MT, Peiffer DA, Pokholok D, Odze R, Sanchez CA, Maley CC, Reid BJ, Gunderson KL, Rabinovitch PS. Deletion at fragile sites is a common and early event in Barrett's esophagus. Mol Cancer Res 2010; 8:1084-94. [PMID: 20647332 DOI: 10.1158/1541-7786.mcr-09-0529] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Barrett's esophagus (BE) is a premalignant intermediate to esophageal adenocarcinoma, which develops in the context of chronic inflammation and exposure to bile and acid. We asked whether there might be common genomic alterations that could be identified as potential clinical biomarker(s) for BE by whole genome profiling. We detected copy number alterations and/or loss of heterozygosity at 56 fragile sites in 20 patients with premalignant BE. Chromosomal fragile sites are particularly sensitive to DNA breaks and are frequent sites of rearrangement or loss in many human cancers. Seventy-eight percent of all genomic alterations detected by array-CGH were associated with fragile sites. Copy number losses in early BE were observed at particularly high frequency at FRA3B (81%), FRA9A/C (71.4%), FRA5E (52.4%), and FRA 4D (52.4%), and at lower frequencies in other fragile sites, including FRA1K (42.9%), FRAXC (42.9%), FRA 12B (33.3%), and FRA16D (33.3%). Due to the consistency of the region of copy number loss, we were able to verify these results by quantitative PCR, which detected the loss of FRA3B and FRA16D, in 83% and 40% of early molecular stage BE patients, respectively. Loss of heterozygosity in these cases was confirmed through pyrosequencing at FRA3B and FRA16D (75% and 70%, respectively). Deletion and genomic instability at FRA3B and other fragile sites could thus be a biomarker of genetic damage in BE patients and a potential biomarker of cancer risk.
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Affiliation(s)
- Lisa A Lai
- Department of Pathology,University of Washington, Seattle, WA, USA
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Liu BL, Cheng JX, Zhang W, Zhang X, Wang R, Lin H, Huo JL, Cheng H. Quantitative detection of multiple gene promoter hypermethylation in tumor tissue, serum, and cerebrospinal fluid predicts prognosis of malignant gliomas. Neuro Oncol 2010; 12:540-8. [PMID: 20154338 PMCID: PMC2940650 DOI: 10.1093/neuonc/nop064] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 10/07/2009] [Indexed: 11/13/2022] Open
Abstract
Aberrant promoter hypermethylation of several known or putative tumor suppressor genes occurs frequently during the malignant transformation in gliomas. We hypothesized that quantitative analysis of methylated genes will provide prognostic values in malignant glioma patients. We used an immunocapturing approach followed by real-time polymerase chain reaction analysis to detect altered patterns of promoter methylation in O-6-methylguanine-DNA methyltransferase (MGMT), p16INK4a, tissue inhibitor of metalloproteinase-3 (TIMP-3), and thrombospondin 1 (THBS1). The tumor tissue and paired serum as well as cerebrospinal fluid (CSF) from 66 patients with malignant gliomas were studied. Serum and CSF from 20 age-matched noncancer individuals were used as control. Promoter hypermethylation in MGMT, p16INK4a, TIMP-3, and THBS1 was detected at high frequencies in tumor tissue, serum, and CSF. None of the control serum or CSF showed aberrant methylation. Hypermethylation in serum and CSF DNA was all accompanied with methylation in the corresponding tumor tissues with 100% specificity. Highly elevated MGMT, p16INK4a, and THBS1 methylation levels in gliomas serum were the sole independent factors predicting inferior overall survival in this cohort. For progression-free survival, hypermethylation of MGMT and THBS1 in CSF were the independent prognostic factors. Multiple gene promoter hypermethylation analysis appears to be promising as a prognostic factor in glioma and as a mini-invasive tumor marker in serum and/or CSF DNA. Evaluation of these changes may help in selecting glioma patients for optimal adjuvant treatments and modifying chemotherapy.
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Affiliation(s)
- Bo-Lin Liu
- Department of Neurosurgery, Xijing Institute of Clinical Neuroscience, Xijing Hospital, Fourth Military Medical University, West Changle Road, No. 127, Xi'an, Shaanxi Province 710032, People's Republic of China.
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25
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Frequency of progranulin mutations in a German cohort of 79 frontotemporal dementia patients. J Neurol 2009; 256:2043-51. [PMID: 19618231 DOI: 10.1007/s00415-009-5248-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 06/16/2009] [Accepted: 07/03/2009] [Indexed: 12/12/2022]
Abstract
Mutations of the progranulin gene lead to progranulin haploinsufficiency and to frontotemporal lobar degeneration (FTD) with TDP-43 positive inclusions. It is assumed that unknown genetic, epigenetic and environmental factors are responsible for the observed marked degree of phenotypic variability among mutation carriers. This is the first published series of German FTD cases screened for progranulin mutations. Mean age at onset was 62 years, 19 patients (24%) had a positive family history of dementia, and 11 patients (14%) had a positive family history for probable FTD. Data on FTD subtypes are presented. Two mutations were identified (3%), one of which has been described previously. Clinically, both patients showed the frontal-behavioural variant type of FTD. Remarkably, a sibling of one case presented with progressive nonfluent aphasia, clinically distinct from the brother. We also performed quantitative PCR analyses to detect potential whole progranulin gene and exon deletions. Here, results were negative.
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Abstract
An overall burden of rare structural genomic variants has not been reported in bipolar disorder (BD), although there have been reports of cases with microduplication and microdeletion. Here, we present a genome-wide copy number variant (CNV) survey of 1001 cases and 1034 controls using the Affymetrix single nucleotide polymorphism (SNP) 6.0 SNP and CNV platform. Singleton deletions (deletions that appear only once in the dataset) more than 100 kb in length are present in 16.2% of BD cases in contrast to 12.3% of controls (permutation P=0.007). This effect was more pronounced for age at onset of mania <or=18 years old. Our results strongly suggest that BD can result from the effects of multiple rare structural variants.
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27
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Auber B, Bruemmer V, Zoll B, Burfeind P, Boehm D, Liehr T, Brockmann K, Wilichowski E, Argyriou L, Bartels I. Identification of subtelomeric genomic imbalances and breakpoint mapping with quantitative PCR in 296 individuals with congenital defects and/or mental retardation. Mol Cytogenet 2009; 2:10. [PMID: 19284615 PMCID: PMC2660352 DOI: 10.1186/1755-8166-2-10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Accepted: 03/12/2009] [Indexed: 01/04/2023] Open
Abstract
Background Submicroscopic imbalances in the subtelomeric regions of the chromosomes are considered to play an important role in the aetiology of mental retardation (MR). The aim of the study was to evaluate a quantitative PCR (qPCR) protocol established by Boehm et al. (2004) in the clinical routine of subtelomeric testing. Results 296 patients with MR and a normal karyotype (500–550 bands) were screened for subtelomeric imbalances by using qPCR combined with SYBR green detection. In total, 17 patients (5.8%) with 20 subtelomeric imbalances were identified. Six of the aberrations (2%) were classified as causative for the symptoms, because they occurred either de novo in the patients (5 cases) or the aberration were be detected in the patient and an equally affected parent (1 case). The extent of the deletions ranged from 1.8 to approximately 10 Mb, duplications were 1.8 to approximately 5 Mb in size. In 6 patients, the copy number variations (CNVs) were rated as benign polymorphisms, and the clinical relevance of these CNVs remains unclear in 5 patients (1.7%). Therefore, the overall frequency of clinically relevant imbalances ranges between 2% and 3.7% in our cohort. Conclusion This study illustrates that the qPCR/SYBR green technique represents a rapid and versatile method for the detection of subtelomeric imbalances and the option to map the breakpoint. Thus, this technique is highly suitable for genotype/phenotype studies in patients with MR/developmental delay and/or congenital defects.
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Affiliation(s)
- Bernd Auber
- Institute of Human Genetics, Georg August University, Göttingen, Germany.
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28
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Franke G, Bausch B, Hoffmann MM, Cybulla M, Wilhelm C, Kohlhase J, Scherer G, Neumann HPH. Alu-Alurecombination underlies the vast majority of largeVHLgermline deletions: Molecular characterization and genotype-phenotype correlations in VHL patients. Hum Mutat 2009; 30:776-86. [PMID: 19280651 DOI: 10.1002/humu.20948] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Gerlind Franke
- Department of Nephrology, University Medical Center Freiburg, Freiburg, Germany
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29
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Shirneshan K, Binder S, Böhm D, Wolf S, Sancken U, Meinhardt A, Schmid M, Engel W, Adham IM. Directed overexpression of insulin in Leydig cells causes a progressive loss of germ cells. Mol Cell Endocrinol 2008; 295:79-86. [PMID: 18692115 DOI: 10.1016/j.mce.2008.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 07/03/2008] [Accepted: 07/05/2008] [Indexed: 11/30/2022]
Abstract
The primary goal of this study was to determine the 5'region of the Insl3 gene that specifically targets the expression of human insulin to Leydig cells, and to explore whether the testicular proinsulin is efficiently processed to insulin that is able to rescue the diabetes in different mouse models of diabetes. We show here that the sequence between nucleotides -690 and +4 of mouse Insl3 promoter is sufficient to direct the Leydig cell-specific expression of the human insulin transgene (Insl3-hIns). We also found that the 3'untranslated region (3'UTR) of Insl3 was effective in enhancing transgene expression of the insulin in vivo. Expression analysis revealed that the temporal expression pattern of the hIns transgene in Leydig cells of transgenic testes is roughly the same as that of the endogenous Insl3. Despite the Leydig cells translate human proinsulin and secrete a significant level of free C-peptide into the serum, the Leydig cell-derived insulin is not able to overcome the diabetes in different mouse models of diabetes, suggesting a lack of glucose sensing mechanisms in the Leydig cells. A consequence of overexpression of the human proinsulin in Leydig cells was the decrease of fertility of transgenic males at older ages. Germ cells in transgenic males were able to initiate and complete spermatogenesis. However, there was a progressive and age-dependent degeneration of the germ cells that lead to male infertility with increasing age.
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Affiliation(s)
- Katayoon Shirneshan
- Institute of Human Genetics, University of Göttingen, Heinrich-Düker-Weg 12, D-37073 Göttingen, Germany
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Gouas L, Goumy C, Véronèse L, Tchirkov A, Vago P. Gene dosage methods as diagnostic tools for the identification of chromosome abnormalities. ACTA ACUST UNITED AC 2008; 56:345-53. [DOI: 10.1016/j.patbio.2008.03.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 03/14/2008] [Indexed: 10/22/2022]
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Park HK, Kim HJ, Kim HJ, Han SH, Kim YJ, Kim SH. Screening of subtelomeric rearrangements in 100 Korean Pediatric patients with unexplained mental retardation and anomalies using subtelomeric FISH (fluorescence in situ hybridization). J Korean Med Sci 2008; 23:573-8. [PMID: 18756040 PMCID: PMC2526410 DOI: 10.3346/jkms.2008.23.4.573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Abstract
Rearrangements of the subtelomeric regions of chromosomes account for a significant proportion of the underlying genetic defects in both idiopathic mental retardation (MR) and multiple congenital anomalies. To detect the rearrangements, a set of subtelomeric fluorescence in situ hybridization (FISH) probes has been developed. The aim of this study was to reveal the frequency of subtelomeric rearrangements in Korean patients with MR or multiple anomalies. We performed a FISH study using a commercially available subtelomeric FISH probes on a series of unrelated Korean pediatric patients with MR or multiple anomalies without identifiable causes. We used a checklist to evaluate the developmental delay and/or MR. Patients who were shown to have chromosome abnormalities, metabolic disorders, or recognizable dysmorphic syndromes by clinical and laboratory findings were excluded. As a result, 100 patients were eligible for the Subtelomeric FISH study, and a total of 29 patients (29%) were suspected to have subtelomeric rearrangements on initial screening by the multiprobe FISH kit. Among theses, confirmatory FISH studies by using single locus-specific FISH probes were performed in 24 patients. One patient (a 10- yr-old girl) was confirmed to have rearrangement, deletion of the telomeric portion of the short arm of chromosome 4 (4p). Her clinical manifestation was compatible with Wolf-Hirschhorn syndrome, which is known to be caused by 4p deletion. The frequency of subtelomeric rearrangements in this study was 1.1% (1/95), lower than those previously reported (0.5-16.3%). We suggest that subtelomeric FISH test is a useful screening tool for patients with idiopathic MR and/or dysmorphism regardless of its false positive value.
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Affiliation(s)
- Hyun-Kyung Park
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee-Jin Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyun-Jun Kim
- Department of Obstetrics and Gynecology, School of Medicine, Konkuk University, Chungju, Korea
| | - Sung-Hee Han
- Department of Cytogenetics and Molecular Genetics, Seoul Medical Science Institute, Seoul Clinical Laboratories, Seoul, Korea
| | - Young-Jae Kim
- Department of Laboratory Mecidine, Masan Samsung Hospital, Sungkyunkwan University School of Medicine, Masan, Korea
| | - Sun-Hee Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Schubert S, Kamino K, Böhm D, Adham I, Engel W, Wasielewski RV, Moharregh-Khiabani D, Mauceri G, Vaske B, Meinhardt A, Schöner A, Gonzalez-Fassrainer D, Schmidtke J. TSPY Expression Is Variably Altered in Transgenic Mice with Testicular Feminization1. Biol Reprod 2008; 79:125-33. [DOI: 10.1095/biolreprod.107.067025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Zhang F, Li Z, Wen B, Jiang J, Shao M, Zhao Y, He Y, Song X, Qian J, Lu D, Jin L. A Frequent Partial AZFc Deletion does not Render an Increased Risk of Spermatogenic Impairment in East Asians. Ann Hum Genet 2008; 70:304-13. [PMID: 16674553 DOI: 10.1111/j.1529-8817.2005.00231.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gene families in the AZFc region of the Y chromosome have been shown to be functionally important in human spermatogenesis. The gr/gr deletion, a partial AZFc deletion that reduces the copy numbers of all the AZFc gene families, was identified as a significant risk factor for spermatogenic impairment in Dutch, Spanish and Italians. However, the presence of this deletion in healthy French and Germans questioned its importance in male infertility. In this study, we have shown that the gr/gr deletion does not render an increased risk in Han Chinese. In fact, the gr/gr deletion is frequent (about 8%) in our survey of 886 East Asians from 8 ethnic groups. Furthermore, the DAZ1/DAZ2 deletion has been detected as the primary subtype of the gr/gr deletion in East Asians, though this doublet has been considered as crucial for normal spermatogenesis in Europeans. The different spermatogenic effects of various types of the partial AZFc deletion suggest that the functional difference between AZFc gene copies is a likely cause of inconsistent associations of the gr/gr deletion with spermatogenic impairment across populations.
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Affiliation(s)
- F Zhang
- State Key Laboratory of Genetic Engineering and Center for Anthropological Studies, School of Life Sciences, Fudan University, Shanghai, China
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34
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Mochizuki J, Saitsu H, Mizuguchi T, Nishimura A, Visser R, Kurotaki N, Miyake N, Unno N, Matsumoto N. Alu-related 5q35 microdeletions in Sotos syndrome. Clin Genet 2008; 74:384-91. [DOI: 10.1111/j.1399-0004.2008.01032.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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35
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Joshi VA, Mancini-DiNardo D, Funke BH. Selection of a platform for mutation detection. ACTA ACUST UNITED AC 2008; Chapter 7:Unit 7.15. [PMID: 18428425 DOI: 10.1002/0471142905.hg0715s56] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
New mutation detection technologies must keep pace by becoming more cost-effective while offering improved technical sensitivity and higher throughput capacity. In recent years, the number of mutation detection platforms available to the clinical researcher has grown to a point where it is difficult to keep track of all available options as well as their benefits and pitfalls. This unit provides an entry point for a variety of researchers who wish to analyze samples for known or novel mutations and need to determine which platform is most suited for their particular needs. A practical guide is provided in this unit, including a brief overview, information on assay parameters, design and cost considerations, as well as platform flexibility and scalability of the assay. Although the focus here is on applications involving human disease, many of these platforms can be easily adapted to the study of other organisms.
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Affiliation(s)
- Victoria A Joshi
- Harvard Medical School-Partners Healthcare Center for Genetics and Genomics, Cambridge, Massachusetts, USA
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36
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Wang X, Li S, Liu H, Wood M, Chen WR, Zheng B. Automated identification of analyzable metaphase chromosomes depicted on microscopic digital images. J Biomed Inform 2008; 41:264-71. [PMID: 17681496 PMCID: PMC2440955 DOI: 10.1016/j.jbi.2007.06.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Revised: 05/22/2007] [Accepted: 06/29/2007] [Indexed: 11/26/2022]
Abstract
Visual search and identification of analyzable metaphase chromosomes using optical microscopes is a very tedious and time-consuming task that is routinely performed in genetic laboratories to detect and diagnose cancers and genetic diseases. The purpose of this study is to develop and test a computerized scheme that can automatically identify chromosomes in metaphase stage and classify them into analyzable and un-analyzable groups. Two independent datasets involving 170 images are used to train and test the scheme. The scheme uses image filtering, threshold, and labeling algorithms to detect chromosomes, followed by computing a set of features for each individual chromosome as well as for each identified metaphase cell. Two machine learning classifiers including a decision tree (DT) based on the features of individual chromosomes and an artificial neural network (ANN) using the features of the metaphase cells are optimized and tested to classify between analyzable and un-analyzable cells. Using the DT based classifier the Kappa coefficients for agreement between the cytogeneticist and the scheme are 0.83 and 0.89 for the training and testing datasets, respectively. We apply an independent testing and a 2-fold cross-validation method to assess the performance of the ANN-based classifier. The area under and receiver operating characteristic (ROC) curve is 0.93 for the complete dataset. This preliminary study demonstrates the feasibility of developing a computerized scheme to automatically identify and classify metaphase chromosomes.
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Affiliation(s)
- Xingwei Wang
- Center for Bioengineering and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK 73019, USA
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37
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Shoukier M, Teske U, Weise A, Engel W, Argyriou L. Characterization of five novel large deletions causing hereditary haemorrhagic telangiectasia. Clin Genet 2008; 73:320-30. [DOI: 10.1111/j.1399-0004.2008.00968.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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38
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Udaka T, Imoto I, Aizu Y, Torii C, Izumi K, Kosaki R, Takahashi T, Hayashi S, Inazawa J, Kosaki K. Multiplex PCR/liquid chromatography assay for screening of subtelomeric rearrangements. ACTA ACUST UNITED AC 2008; 11:241-8. [PMID: 17949285 DOI: 10.1089/gte.2007.9993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In idiopathic or nonspecific mental retardation, the overall rate of cryptic subtelomeric rearrangements is estimated to be about 5%. Development of cost-effective screening for subtelomeric deletions would help clinical geneticists to make specific diagnoses in children with idiopathic mental retardation. Current screening modalities include fluorescence in situ hybridization (FISH) using subtelomeric probes and PCR-based quantitative analyses. Reductions in the cost and turnaround time will make the complete screening of subtelomeric rearrangements more widely used in clinical settings. Recently, a versatile method, called the multiplex PCR/liquid chromatography assay (MP/LC), was developed to assess copy numbers in this assay. Multiple genomic regions are amplified using unlabeled primers, then separated by ion-pair reversed-phase high-performance liquid chromatography. In the present study, we developed an MP/LC-based subtelomeric screening system that involves 21 multiple reactions and validated the protocol by analyzing 16 publicly available cell lines with known cytogenetic abnormalities involving at least one subtelomere per patient. To confirm the validity of the MP/LC method, we analyzed these cell lines concurrently with array-based comparative genomic hybridization (array-CGH), which gives higher resolution than the conventional G-banding technique. Among those 16 samples, the results from MP/LC and array-CGH agreed with each other perfectly. In 2 of the 16 samples, MP/LC correctly revealed subtelomeric duplications that were detected by array-CGH but were undetected by conventional cytogenetics, demonstrating the sensitivity of the MP/LC assay. This system is expected to be useful for making specific diagnoses and in genetic counseling for children with idiopathic mental retardation, a sizable fraction of whom have subtelomeric rearrangements.
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Affiliation(s)
- Toru Udaka
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
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39
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Guan Y, Hata N, Kuga D, Yoshimoto K, Mizoguchi M, Shono T, Suzuki SO, Tahira T, Kukita Y, Higasa K, Yokoyama N, Nagata S, Iwaki T, Sasaki T, Hayashi K. Narrowing of the regions of allelic losses of chromosome 1p36 in meningioma tissues by an improved SSCP analysis. Int J Cancer 2007; 122:1820-6. [DOI: 10.1002/ijc.23297] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Auber B, Burfeind P, Herold S, Schoner K, Simson G, Rauskolb R, Rehder H. A disease causing deletion of 29 base pairs in intron 15 in the MKS1 gene is highly associated with the campomelic variant of the Meckel-Gruber syndrome. Clin Genet 2007; 72:454-9. [DOI: 10.1111/j.1399-0004.2007.00880.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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Bausch B, Borozdin W, Mautner VF, Hoffmann MM, Boehm D, Robledo M, Cascon A, Harenberg T, Schiavi F, Pawlu C, Peczkowska M, Letizia C, Calvieri S, Arnaldi G, Klingenberg-Noftz RD, Reisch N, Fassina A, Brunaud L, Walter MA, Mannelli M, MacGregor G, Palazzo FF, Barontini M, Walz MK, Kremens B, Brabant G, Pfäffle R, Koschker AC, Lohoefner F, Mohaupt M, Gimm O, Jarzab B, McWhinney SR, Opocher G, Januszewicz A, Kohlhase J, Eng C, Neumann HPH. Germline NF1 mutational spectra and loss-of-heterozygosity analyses in patients with pheochromocytoma and neurofibromatosis type 1. J Clin Endocrinol Metab 2007; 92:2784-92. [PMID: 17426081 DOI: 10.1210/jc.2006-2833] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Neurofibromatosis type 1 (NF1) is a pheochromocytoma-associated syndrome. Because of the low prevalence of pheochromocytoma in NF1, we ascertained subjects by pheochromocytoma that also had NF1 in the hope of describing the germline NF1 mutational spectra of NF1-related pheochromocytoma. MATERIALS AND METHODS An international registry for NF1-pheochromocytomas was established. Mutation scanning was performed using denaturing HPLC for intragenic variation and quantitative PCR for large deletions. Loss-of-heterozygosity analysis using markers in and around NF1 was performed. RESULTS There were 37 eligible subjects (ages 14-70 yr). Of 21 patients with corresponding tumor available, 67% showed somatic loss of the nonmutated allele at the NF1 locus vs. 0 of 12 sporadic tumors (P = 0.0002). Overall, 86% of the 37 patients had exonic or splice site mutations, 14% large deletions or duplications; 79% of the mutations are novel. The cysteine-serine rich domain (CSR) was affected in 35% but the RAS GTPase activating protein domain (RGD) in only 13%. There did not appear to be an association between any clinical features, particularly pheochromocytoma presentation and severity, and NF1 mutation genotype. CONCLUSIONS The germline NF1 mutational spectra comprise intragenic mutations and deletions in individuals with pheochromocytoma and NF1. NF1 mutations tended to cluster in the CSR over the RAS-GAP domain, suggesting that CSR plays a more prominent role in individuals with NF1-pheochromocytoma than in NF1 individuals without this tumor. Loss-of-heterozygosity of NF1 markers in NF1-related pheochromocytoma was significantly more frequent than in sporadic pheochromocytoma, providing further molecular evidence that pheochromocytoma is a true component of NF1.
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Affiliation(s)
- Birke Bausch
- Department of Neurology, University Medical Center Freiburg, Germany
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42
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Sauter SM, Böhm D, Bartels I, Burfeind P, Laccone FA, Neesen J, Wilken B, Liehr T, Zoll B. Partial trisomy of distal 19q detected by quantitative real-time PCR and FISH in a girl with mild facial dysmorphism, hypotonia and developmental delay. Am J Med Genet A 2007; 143A:1091-9. [PMID: 17431920 DOI: 10.1002/ajmg.a.31686] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We report on a 2 7/12-year-old girl who was referred to us because of psychomotor developmental delay. She is the second child of healthy, non-consanguineous parents. Pregnancy and birth were uneventful. Milestones of motor development were delayed: grasping at 6 months, sitting without support at 16 months, crawling at 16 months and walking at 2 4/12 years of age. She spoke about five words and followed simple instructions. Banding cytogenetics revealed a numerically and structurally normal female karyotype of 46,XX. By quantitative real-time PCR analysis of all subtelomeric regions, a partial trisomy of the subtelomeric region of 19q could be detected. This result was confirmed by FISH-analysis with a subtelomeric probe for 19q. The additional material of chromosome 19q was localized on chromosome 6q. However, a deletion of the subtelomeric region of 6q could not be detected with a subtelomeric FISH probe for 6q. Conventional cytogenetic analysis as well as FISH with subtelomeric probes for 19q and 6q showed normal results in the parents. The detected chromosomal aberration probably occurred de novo. The clinical features are very likely to be caused solely by the partial trisomy 19q.
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Affiliation(s)
- S M Sauter
- Institut für Humangenetik, Georg-August-Universität Göttingen, Heinrich-Düker-Weg 12, Göttingen, Germany.
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43
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Boehm D, Bacher J, Neumann HPH. Gross genomic rearrangement involving the TSC2-PKD1 contiguous deletion syndrome: characterization of the deletion event by quantitative polymerase chain reaction deletion assay. Am J Kidney Dis 2007; 49:e11-21. [PMID: 17185137 DOI: 10.1053/j.ajkd.2006.10.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 10/12/2006] [Indexed: 02/01/2023]
Abstract
Tuberous sclerosis complex (TSC) was instrumented for identification of the gene causing autosomal dominant polycystic kidney disease type 1 (PKD1) because a patient showing both diseases gave rise to the suggestion that the TSC2 gene is located in close vicinity on chromosome 16p13. However, distinct molecular genetic characterization of such patients is sparse in the literature. A 41-year-old woman was admitted because of chylous ascites and pleural effusions. She was on hemodialysis therapy for 6 years because of end-stage renal failure from PKD. Both kidneys had been removed at ages 35 and 36 years. Histologically, both specimens also showed multiple angioleiomyolipoma. Mild, but classic, lesions of the TSC complex were present on her face and hands and in the central nervous system. The genetic defect was identified by using quantitative real-time polymerase chain reaction (qPCR), long-range PCR (LR-PCR), and sequencing. qPCR confirmed the existence of a TSC2-PKD1 contiguous gene deletion spanning the entire TSC2 and PKD1 genes. Additional analysis showed expansion of the deletion affecting the adjacent downstream-located genes RAB26 and TRAF7, as well as the great majority of CASKIN1. LR-PCR and sequencing identified flanking simple tandem repeats. A nonhomologous misalignment mechanism has driven the recombination, most likely by replication slippage between a 3-bp homology (ATG) at the breakpoint regions. Our results confirm that patients with both TSC and PKD have a genetically contiguous gene syndrome with hemizygous deletion of the TSC2 and PKD1 genes. Despite this maximal genetic defect, the typical signs of TSC, mental retardation and seizures, can be absent.
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Affiliation(s)
- Detlef Boehm
- Department of Nephrology and Hypertension Medicine, Medical Clinic, Albert-Ludwig-University, Freiburg, Germany
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44
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Yan PS, Venkataramu C, Ibrahim A, Liu JC, Shen RZ, Diaz NM, Centeno B, Weber F, Leu YW, Shapiro CL, Eng C, Yeatman TJ, Huang THM. Mapping geographic zones of cancer risk with epigenetic biomarkers in normal breast tissue. Clin Cancer Res 2007; 12:6626-36. [PMID: 17121881 DOI: 10.1158/1078-0432.ccr-06-0467] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Genetic alterations were previously identified in normal epithelia adjacent to invasive cancers. The aim of this study was to determine DNA methylation in histologically normal tissues from multiple geographic zones adjacent to primary breast tumors. EXPERIMENTAL DESIGN First, methylation status of a 4-kb region of RASSF1A promoter was interrogated using oligonucleotide-based microarray in 144 samples (primary tumors, 47; adjacent normals, 69; reduction mammoplasty tissues, 28). Second, allelic imbalance (AI)/loss of heterozygosity (LOH) surrounding RASSF1A promoter were analyzed in 30 samples (tumors, 8; adjacent normals, 22). Third, global methylation screening of 49 samples (tumors, 12; adjacent normals, 25; reduction mammoplasty, 12) was done by differential methylation hybridization. Real-time quantitative methylation-specific PCR was used to validate the microarray findings. RESULTS DNA methylation in the core RASSF1A promoter was low in reduction mammoplasty tissues (P=0.0001) when compared with primary tumors. The adjacent normals had an intermediate level of methylation. The regions surrounding the core were highly methylated in all sample types. Microsatellite markers showed AI/LOH in tumors and some of the adjacent normals. Concurrent AI/LOH and DNA methylation in RASSF1A promoter occurred in two of six tumors. Global methylation screening uncovered genes more methylated in adjacent normals than in reduction mammoplasty tissues. The methylation status of four genes was confirmed by quantitative methylation-specific PCR. CONCLUSIONS Our findings suggest a field of methylation changes extending as far as 4 cm from primary tumors. These frequent alterations may explain why normal tissues are at risk for local recurrence and are useful in disease prognostication.
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Affiliation(s)
- Pearlly S Yan
- Department of Hematology and Oncology, Comprehensive Cancer Center, College of Medicine and Public Health, The Ohio State University, Columbus, Ohio 43210, USA, and Department of Pathology, Addenbrooks' Hospital, Cambridge, UK
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45
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Scott DA, Klaassens M, Holder AM, Lally KP, Fernandes CJ, Galjaard RJ, Tibboel D, de Klein A, Lee B. Genome-wide oligonucleotide-based array comparative genome hybridization analysis of non-isolated congenital diaphragmatic hernia. Hum Mol Genet 2007; 16:424-30. [PMID: 17210672 DOI: 10.1093/hmg/ddl475] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Non-isolated congenital diaphragmatic hernia (CDH+) is a severe birth defect that is often caused by de novo chromosomal anomalies. In this report, we use genome-wide oligonucleotide-based array comparative genome hybridization (aCGH) followed by rapid real-time quantitative PCR analysis to identify, confirm and map chromosomal anomalies in a cohort of 26 CDH+ patients. One hundred and five putative copy number changes were identified by aCGH in our cohort of CDH+ patients. Sixty-one of these changes (58%) had been previously described in normal controls. Twenty of the remaining 44 changes (45%) were confirmed by quantitative real-time PCR or standard cytogenetic techniques. These changes included de novo chromosomal abnormalities in five of the 26 patients (19%), two of whom had previously normal G-banded chromosome analyses. Data from these patients provide evidence for the existence of CDH-related genes on chromosomes 2q37, 6p22-25 and 14q, and refine the CDH minimal deleted region on 15q26 to an interval that contains COUP-TFII and only eight other known genes. Although COUP-TFII is likely to play a role in the development of CDH in patients with 15q26 deletions, we did not find COUP-TFII mutations in 73 CDH samples. We conclude that the combination of oligonucleotide-based aCGH and quantitative real-time PCR is an effective method of identifying, confirming and mapping clinically relevant copy number changes in patients with CDH+. This method is more sensitive than G-banded chromosome analysis and may find wide application in screening patients with congenital anomalies.
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MESH Headings
- Chromosome Aberrations
- Chromosome Banding
- Chromosomes, Human, Pair 14
- Chromosomes, Human, Pair 2
- Chromosomes, Human, Pair 6
- Female
- Gene Dosage
- Gene Expression Profiling
- Genetic Testing
- Genome, Human
- Hernia, Diaphragmatic/genetics
- Hernias, Diaphragmatic, Congenital
- Humans
- Male
- Nucleic Acid Hybridization/methods
- Oligonucleotide Array Sequence Analysis
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Affiliation(s)
- Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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46
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Sato K, Iwakoshi M, Shimokawa O, Sakai H, Ohta T, Saitoh S, Miyake N, Niikawa N, Harada N, Saitsu H, Mizuguchi T, Matsumoto N. Angelman syndrome caused by an identical familial 1,487-kb deletion. Am J Med Genet A 2007; 143A:98-101. [PMID: 17152063 DOI: 10.1002/ajmg.a.31550] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kanako Sato
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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47
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Borozdin W, Bravo-Ferrer Acosta AM, Seemanova E, Leipoldt M, Bamshad MJ, Unger S, Kohlhase J. Contiguous hemizygous deletion ofTBX5,TBX3, andRBM19 resulting in a combined phenotype of Holt-Oram and ulnar-mammary syndromes. Am J Med Genet A 2006; 140A:1880-6. [PMID: 16892408 DOI: 10.1002/ajmg.a.31340] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Wiktor Borozdin
- Institut für Humangenetik und Anthropologie, Universität Freiburg, Freiburg, Germany
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48
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Mattarucchi E, Marsoni M, Passi A, Lo Curto F, Pasquali F, Porta G. Establishment and study of different real-time polymerase chain reaction assays for the quantification of cells with deletions of chromosome 7. J Mol Diagn 2006; 8:218-24. [PMID: 16645208 PMCID: PMC1867589 DOI: 10.2353/jmoldx.2006.050111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The evaluation of residual disease, which has prognostic value in the treatment of hematological malignancies, is currently assessed by scoring a limited number of cells by karyotyping and molecular cytogenetics. Real-time polymerase chain reaction (PCR) is an easier and more sensitive technique, enables analysis of a larger number of cells, and decreases sampling error. However, real-time PCR has been applied only to target transcripts of fusion genes. Here, we considered two real-time PCR strategies to quantify a number of cells carrying a partial deletion of chromosome 7 mixed with normal disomic cells. The first strategy was based on the amplification of two sequences, one on chromosome 7 and the other on chromosome 14. In the second strategy residual disease was assessed by the ratio between the two alleles of a bi-allelic marker, mapped on chromosome 7, measured with allele-specific assays. Precision and accuracy of the two approaches were tested by reference samples with nominal values of residual disease ranging from 2 to 95%. As expected the second strategy resulted in more precise and accurate monitoring within the range from 5 to 95%. Furthermore, this method may be applied to assess the number of dysplastic or neoplastic clones carrying any unbalanced chromosome changes.
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Affiliation(s)
- Elia Mattarucchi
- Department of Experimental and Clinical Biomedical Sciences, University of Insubria, Via Dunant 5, 21100 Varese, Italy
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49
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Boehm D, Laccone F, Burfeind P, Herold S, Schubert C, Zoll B, Männer J, Pauer HU, Bartels I. Prenatal diagnosis of a large de novo terminal deletion of chromosome 11q. Prenat Diagn 2006; 26:286-90. [PMID: 16506277 DOI: 10.1002/pd.1408] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To describe the prenatal phenotype of the 11q deletion syndrome (Jacobsen syndrome) and present the molecular characterization of the deletion in the case presented. CASE Ultrasound at 18 and 20 weeks of gestation, on a 34-year-old woman who presented for amniocentesis, revealed slow movements, oligohydramnios and dilatation of the cerebral ventricles in the fetus. Maternal and paternal ages were 34 and 38 years, respectively. RESULTS Prenatal karyotyping of cultured amniotic fluid cells revealed an 11q terminal deletion, 46,XX,del(11)(q23) (Jacobsen syndrome). Real-time quantitative PCR analysis was used to identify and map the breakpoint physically to a 45-kb region located 14.5 Mb from the 11q telomere. Polymorphic DNA marker analysis showed that DNA sequences on the paternally derived chromosome are deleted. At autopsy, facial dysmorphism without major malformations was recorded. Examination of the internal organs disclosed the following abnormalities: a Meckels' diverticulum of 4-mm length, adhesion between the gall bladder and the transverse colon, and bilaterally bilobed lungs without further situs anomalies. CONCLUSION Our case demonstrates significant phenotypic variability of Jacobsen syndrome at midtrimester pregnancy; the syndrome may be manifested at this stage only by mild to moderate ventriculomegaly of the brain.
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Affiliation(s)
- D Boehm
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
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50
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Has C, Wessagowit V, Pascucci M, Baer C, Didona B, Wilhelm C, Pedicelli C, Locatelli A, Kohlhase J, Ashton GHS, Tadini G, Zambruno G, Bruckner-Tuderman L, McGrath JA, Castiglia D. Molecular Basis of Kindler Syndrome in Italy: Novel and Recurrent Alu/Alu Recombination, Splice Site, Nonsense, and Frameshift Mutations in the KIND1 Gene. J Invest Dermatol 2006; 126:1776-83. [PMID: 16675959 DOI: 10.1038/sj.jid.5700339] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Kindler syndrome (KS) is a rare autosomal recessive disorder characterized by skin blistering in childhood followed by photosensitivity and progressive poikiloderma. Most cases of KS result from mutations in the KIND1 gene encoding kindlin-1, a component of focal adhesions in keratinocytes. Here, we report novel and recurrent KIND1 gene mutations in nine unrelated Italian KS individuals. A novel genomic deletion of approximately 3.9 kb was identified in four patients originating from the same Italian region. This mutation deletes exons 10 and 11 from the KIND1 mRNA leading to a truncated kindlin-1. The deletion breakpoint was embedded in AluSx repeats, specifically in identical 30-bp sequences, suggesting Alu-mediated homologous recombination as the pathogenic mechanism. KIND1 haplotype analysis demonstrated that patients with this large deletion were ancestrally related. Five additional mutations were disclosed, two of which were novel. To date, four recurrent mutations have been identified in Italian patients accounting for approximately approximately 75% of KS alleles in this population. The abundance of repetitive elements in intronic regions of KIND1, together with the identification of a large deletion, suggests that genomic rearrangements could be responsible for a significant proportion of KS cases. This finding has implications for optimal KIND1 mutational screening in KS individuals.
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Affiliation(s)
- Cristina Has
- Department of Dermatology, University of Freiburg, Freiburg, Germany
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