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Starosta RT, Jensen N, Couteranis S, Slaugh R, Easterlin D, Tate V, Sams EI, Valle K, Akinwe T, Hou YCC, Turner TN, Cole FS, Milbrandt J, Dickson P. Using a new analytic approach for genotyping and phenotyping chromosome 9p deletion syndrome. Eur J Hum Genet 2024:10.1038/s41431-024-01667-y. [PMID: 38972963 DOI: 10.1038/s41431-024-01667-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/16/2024] [Accepted: 06/26/2024] [Indexed: 07/09/2024] Open
Abstract
Using a new analytic method ("unique non-overlapping region" (UNOR) analysis), we characterized the genotypes and phenotypes of a large cohort of individuals diagnosed with chromosome 9p deletion syndrome (9PMS) and defined critical genomic regions. We extracted phenotypic information from 48 individuals with 9PMS from medical records and used a guided interview with caregivers to clarify ambiguities. Using high-resolution whole-genome sequencing for breakpoint definition, we aligned deletions and drew virtual breakpoints to obtain UNORs associated with phenotypic characteristics. We next extracted genotype and phenotype data for 57 individuals identified from a systematic review of the 9PMS literature and analyzed these as above. Common phenotypic features included developmental delay/intellectual disability, dysmorphic features, hypotonia, genital defects in XY individuals, psychiatric diagnoses, chronic constipation, atopic disease, vision problems, autism spectrum disorder, gastroesophageal reflux disease, trigonocephaly, congenital heart disease, and neonatal hypoglycemia. Our approach confirmed previous literature reports of an association of FREM1 with trigonocephaly and suggested a possible modifier element for this phenotype. In conclusion, the UNOR approach delineated phenotypic characteristics for 9PMS and confirmed the critical role of FREM1 and a possible long-distance regulatory element in pathogenesis of trigonocephaly that will need to be replicated in future studies.
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Affiliation(s)
- Rodrigo Tzovenos Starosta
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA.
| | - Nathaniel Jensen
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
| | - Sophia Couteranis
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
| | - Dawn Easterlin
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
| | - Victoria Tate
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
| | - Eleanor I Sams
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kostandin Valle
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Titilope Akinwe
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ying-Chen Claire Hou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - F Sessions Cole
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Patricia Dickson
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
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Ozyavuz Cubuk P. New candidate region for mirror hand movements: two patients with terminal 9p deletion and 20p duplication. Mol Biol Rep 2024; 51:243. [PMID: 38300327 DOI: 10.1007/s11033-023-09192-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024]
Abstract
The 9p deletion syndrome, which was defined in a detailed way in the previous studies, was characterized by various clinical features such as psychomotor retardation, dysmorphic features and genital anomalies. In contrast to 9p deletion syndrome, 20p duplication was rarely reported in the literature with only a few case reports. Regarding the combination of 9p deletion syndrome and 20p duplication, we found that it was reported in only four patients. In the current study, we aimed to investigate a rare chromosomal rearrangement, partial monosomy 9p and trisomy 20p which was observed in two patients with mirror hand movements. The mirror hand movements was influenced by the combination of genetic and environmental factors. While some cases have been associated with mutations in the DCC, NTN1, RAD51, and DNAL4, there were many cases where the genetic basis of mirror hand movements remained unexplained. There was no alteration detected in genes that were previously known as a cause of mirror hand movement in our patients. This new finding could potentially be attributed to the dosage effect of genes within the 9p deletion or 20p duplication regions or to the genes disrupted within the breakpoint region. Future research focusing on the genes within this genomic locus may hold the potential to uncover novel etiologic reasons for mirror hand movements.
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Affiliation(s)
- Pelin Ozyavuz Cubuk
- Department of Medical Genetics, Haseki Education and Research Hospital, Health Sciences University, Istanbul, Turkey.
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3
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Insights into the Cardiac Phenotype in 9p Deletion Syndrome: A Multicenter Italian Experience and Literature Review. Genes (Basel) 2023; 14:genes14010146. [PMID: 36672887 PMCID: PMC9859094 DOI: 10.3390/genes14010146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/06/2023] Open
Abstract
Chromosome 9p deletion syndrome is a rare autosomal dominant disorder presenting with a broad spectrum of clinical features, including congenital heart defects (CHDs). To date, studies focused on a deep characterization of cardiac phenotype and function associated with this condition are lacking. We conducted a multicentric prospective observational study on a cohort of 10 patients with a molecular diagnosis of 9p deletion syndrome, providing a complete cardiological assessment through conventional echocardiography and tissue Doppler imaging echo modality. As a result, we were able to demonstrate that patients with 9p deletion syndrome without major CHDs may display subclinical cardiac structural changes and left-ventricle systolic and diastolic dysfunction. Albeit needing validation in a larger cohort, our findings support the idea that a complete cardiac assessment should be performed in patients with 9p deletion syndrome and should be integrated in the context of a long-term follow-up.
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Sams EI, Ng JK, Tate V, Claire Hou YC, Cao Y, Antonacci-Fulton L, Belhassan K, Neidich J, Mitra RD, Cole FS, Dickson P, Milbrandt J, Turner TN. From karyotypes to precision genomics in 9p deletion and duplication syndromes. HGG ADVANCES 2022; 3:100081. [PMID: 35047865 PMCID: PMC8756500 DOI: 10.1016/j.xhgg.2021.100081] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 12/21/2021] [Indexed: 11/27/2022] Open
Abstract
While 9p deletion and duplication syndromes have been studied for several years, small sample sizes and minimal high-resolution data have limited a comprehensive delineation of genotypic and phenotypic characteristics. In this study, we examined genetic data from 719 individuals in the worldwide 9p Network Cohort: a cohort seven to nine times larger than any previous study of 9p. Most breakpoints occur in bands 9p22 and 9p24, accounting for 35% and 38% of all breakpoints, respectively. Bands 9p11 and 9p12 have the fewest breakpoints, with each accounting for 0.6% of all breakpoints. The most common phenotype in 9p deletion and duplication syndromes is developmental delay, and we identified eight known neurodevelopmental disorder genes in 9p22 and 9p24. Since it has been previously reported that some individuals have a secondary structural variant related to the 9p variant, we examined our cohort for these variants and found 97 events. The top secondary variant involved 9q in 14 individuals (1.9%), including ring chromosomes and inversions. We identified a gender bias with significant enrichment for females (p = 0.0006) that may arise from a sex reversal in some individuals with 9p deletions. Genes on 9p were characterized regarding function, constraint metrics, and protein-protein interactions, resulting in a prioritized set of genes for further study. Finally, we achieved precision genomics in one child with a complex 9p structural variation using modern genomic technologies, demonstrating that long-read sequencing will be integral for some cases. Our study is the largest ever on 9p-related syndromes and provides key insights into genetic factors involved in these syndromes.
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Affiliation(s)
- Eleanor I. Sams
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey K. Ng
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Victoria Tate
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ying-Chen Claire Hou
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yang Cao
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Khadija Belhassan
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Julie Neidich
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robi D. Mitra
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - F. Sessions Cole
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Patricia Dickson
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
- Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, MO, USA
| | - Tychele N. Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
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Mohamed AM, Kamel AK, Eid MM, Eid OM, Mekkawy M, Hussein SH, Zaki MS, Esmail S, Afifi HH, El-Kamah GY, Otaify GA, El-Awady HA, Elaidy A, Essa MY, El-Ruby M, Ashaat EA, Hammad SA, Mazen I, Abdel-Salam GMH, Aglan M, Temtamy S. Chromosome 9p terminal deletion in nine Egyptian patients and narrowing of the critical region for trigonocephaly. Mol Genet Genomic Med 2021; 9:e1829. [PMID: 34609792 PMCID: PMC8606205 DOI: 10.1002/mgg3.1829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 05/22/2021] [Accepted: 09/07/2021] [Indexed: 11/30/2022] Open
Abstract
Background This study aimed to delineate the clinical phenotype of patients with 9p deletions, pinpoint the chromosomal breakpoints, and identify the critical region for trigonocephaly, which is a frequent finding in 9p terminal deletion. Methods We investigated a cohort of nine patients with chromosome 9p terminal deletions who all displayed developmental delay, intellectual disability, hypotonia, and dysmorphic features. Of them, eight had trigonocephaly, seven had brain anomalies, seven had autistic manifestations, seven had fair hair, and six had a congenital heart defect (CHD). Results Karyotyping revealed 9p terminal deletion in all patients, and patients 8 and 9 had additional duplication of other chromosomal segments. We used six bacterial artificial chromosome (BAC) clones that could identify the breakpoints at 17–20 Mb from the 9p terminus. Array CGH identified the precise extent of the deletion in six patients; the deleted regions ranged from 16 to 18.8 Mb in four patients, patient 8 had an 11.58 Mb deletion and patient 9 had a 2.3 Mb deletion. Conclusion The gene deletion in the 9p24 region was insufficient to cause ambiguous genitalia because six of the nine patients had normal genitalia. We suggest that the critical region for trigonocephaly lies between 11,575 and 11,587 Mb from the chromosome 9p terminus. To the best of our knowledge, this is the minimal critical region reported for trigonocephaly in 9p deletion syndrome, and it warrants further delineation.
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Affiliation(s)
- Amal M Mohamed
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Alaa K Kamel
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Maha M Eid
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Ola M Eid
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Mona Mekkawy
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Shymaa H Hussein
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Maha S Zaki
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Samira Esmail
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Hanan H Afifi
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Ghada Y El-Kamah
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Ghada A Otaify
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Heba Ahmed El-Awady
- Department of Pediatrics, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Aya Elaidy
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Mahmoud Y Essa
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Mona El-Ruby
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Engy A Ashaat
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Saida A Hammad
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Inas Mazen
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Ghada M H Abdel-Salam
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Mona Aglan
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Samia Temtamy
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
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6
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The Clinical Dilemma of Autism Spectrum Disorder Diagnosis in a Child with 9p Deletion. J Pediatr Genet 2021; 10:250-252. [PMID: 34504731 DOI: 10.1055/s-0040-1713431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/14/2020] [Indexed: 10/24/2022]
Abstract
We reported on a 3-year-old girl child patient with the presence of trigonocephaly, broad nasal bridge, flattened occiput, and midface hypoplasia. Formal assessment of her development profile demonstrated expressive and receptive language delays, fine and gross motor delays, and no imaginative or symbolic representative play. Investigation of the etiology of her developmental delays revealed a genetic diagnosis of a 9p24 deletion by chromosomal microarray analysis. The possibility of an additional co-occurring disorder of autism spectrum disorder (ASD) was also raised by a referring clinician. This case report highlighted the clinical dilemma of diagnosing ASD in those with existing genetic syndromes.
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Markova ZG, Minzhenkova ME, Bessonova LA, Shilova NV. A new case of 17p13.3p13.1 microduplication resulted from unbalanced translocation: clinical and molecular cytogenetic characterization. Mol Cytogenet 2021; 14:41. [PMID: 34465353 PMCID: PMC8408977 DOI: 10.1186/s13039-021-00562-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/29/2021] [Indexed: 11/30/2022] Open
Abstract
Copy number gain 17 p13.3p13.1 was detected by chromosomal microarray (CMA) in a girl with developmental/speech delay and facial dysmorphism. FISH studies made it possible to establish that the identified genomic imbalance is the unbalanced t(9;17) translocation of maternal origin. Clinical features of the patient are also discussed. The advisability of using the combination of CMA and FISH analysis is shown. Copy number gains detected by clinical CMA should be confirmed using FISH analysis in order to determine the physical location of the duplicated segment. Parental follow-up studies is an important step to determine the origin of genomic imbalance. This approach not only allows a most comprehensive characterization of an identified chromosomal/genomic imbalance but also provision of an adequate medical and genetic counseling for a family taking into account a balanced chromosomal rearrangement.
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Affiliation(s)
- Zhanna G Markova
- Research Centre for Medical Genetics, Moskvorechye St., 1, Moscow, Russia, 115522.
| | - Marina E Minzhenkova
- Research Centre for Medical Genetics, Moskvorechye St., 1, Moscow, Russia, 115522
| | - Lyudmila A Bessonova
- Research Centre for Medical Genetics, Moskvorechye St., 1, Moscow, Russia, 115522
| | - Nadezda V Shilova
- Research Centre for Medical Genetics, Moskvorechye St., 1, Moscow, Russia, 115522
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Wang HLV, Forestier S, Corces VG. Exposure to sevoflurane results in changes of transcription factor occupancy in sperm and inheritance of autism. Biol Reprod 2021; 105:705-719. [PMID: 33982067 DOI: 10.1093/biolre/ioab097] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
One in 54 children in the U.S. is diagnosed with Autism Spectrum Disorder (ASD). De novo germline and somatic mutations cannot account for all cases of ASD, suggesting that epigenetic alterations triggered by environmental exposures may be responsible for a subset of ASD cases. Human and animal studies have shown that exposure of the developing brain to general anesthetic (GA) agents can trigger neurodegeneration and neurobehavioral abnormalities but the effects of general anesthetics on the germ line have not been explored in detail. We exposed pregnant mice to sevoflurane during the time of embryonic development when the germ cells undergo epigenetic reprogramming and found that more than 38% of the directly exposed F1 animals exhibit impairments in anxiety and social interactions. Strikingly, 44-47% of the F2 and F3 animals, which were not directly exposed to sevoflurane, show the same behavioral problems. We performed ATAC-seq and identified more than 1200 differentially accessible sites in the sperm of F1 animals, 69 of which are also present in the sperm of F2 animals. These sites are located in regulatory regions of genes strongly associated with ASD, including Arid1b, Ntrk2, and Stmn2. These findings suggest that epimutations caused by exposing germ cells to sevoflurane can lead to ASD in the offspring, and this effect can be transmitted through the male germline inter and trans-generationally.
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Affiliation(s)
- Hsiao-Lin V Wang
- Department of Human Genetics, Emory University School of Medicine, 615 Michael St, Atlanta, GA 30322, USA
| | - Samantha Forestier
- Department of Human Genetics, Emory University School of Medicine, 615 Michael St, Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, 615 Michael St, Atlanta, GA 30322, USA
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Cordes Selby S, Iwata‐Otsubo A, Delk P, Nebesio TD, Gohil A, Matlock P, Torres‐Martinez W, Vance GH. A brother and sister with the same karyotype: Case report of two siblings with partial 3p duplication and partial 9p deletion and sex reversal. Clin Case Rep 2021; 9:e04141. [PMID: 34026173 PMCID: PMC8136447 DOI: 10.1002/ccr3.4141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 11/09/2022] Open
Abstract
Two siblings with the same male unbalanced karyotype demonstrate sex reversal. The older sib appeared phenotypically female and the younger sib demonstrated a male gender. The female had gonadal dysgenesis with bilateral ovatestes. The male had bilateral testes. The report discusses the phenotypical differences and genes associated with sex reversal.
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Affiliation(s)
| | - Aiko Iwata‐Otsubo
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisINUSA
| | - Paula Delk
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisINUSA
| | - Todd D. Nebesio
- Division of Pediatric Endocrinology/DiabetologyDepartment of PediatricsIndiana University School of MedicineIndianapolisINUSA
| | - Anisha Gohil
- Division of Pediatric Endocrinology/DiabetologyDepartment of PediatricsIndiana University School of MedicineIndianapolisINUSA
| | - Peggy Matlock
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisINUSA
| | - Wilfredo Torres‐Martinez
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisINUSA
| | - Gail H. Vance
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisINUSA
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Santi M, Graf S, Zeino M, Cools M, Van De Vijver K, Trippel M, Aliu N, Flück CE. Approach to the Virilizing Girl at Puberty. J Clin Endocrinol Metab 2021; 106:1530-1539. [PMID: 33367768 PMCID: PMC8063244 DOI: 10.1210/clinem/dgaa948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Indexed: 11/19/2022]
Abstract
UNLABELLED Virilization is the medical term for describing a female who develops characteristics associated with male hormones (androgens) at any age, or when a newborn girl shows signs of prenatal male hormone exposure at birth. In girls, androgen levels are low during pregnancy and childhood. A first physiologic rise of adrenal androgens is observed at the age of 6 to 8 years and reflects functional activation of the zona reticularis of the adrenal cortex at adrenarche, manifesting clinically with first pubic and axillary hairs. Early adrenarche is known as "premature adrenarche." It is mostly idiopathic and of uncertain pathologic relevance but requires the exclusion of other causes of androgen excess (eg, nonclassic congenital adrenal hyperplasia) that might exacerbate clinically into virilization. The second modest physiologic increase of circulating androgens occurs then during pubertal development, which reflects the activation of ovarian steroidogenesis contributing to the peripheral androgen pool. However, at puberty initiation (and beyond), ovarian steroidogenesis is normally devoted to estrogen production for the development of secondary female bodily characteristics (eg, breast development). Serum total testosterone in a young adult woman is therefore about 10- to 20-fold lower than in a young man, whereas midcycle estradiol is about 10- to 20-fold higher. But if androgen production starts too early, progresses rapidly, and in marked excess (usually more than 3 to 5 times above normal), females will manifest with signs of virilization such as masculine habitus, deepening of the voice, severe acne, excessive facial and (male typical) body hair, clitoromegaly, and increased muscle development. Several medical conditions may cause virilization in girls and women, including androgen-producing tumors of the ovaries or adrenal cortex, (non)classical congenital adrenal hyperplasia and, more rarely, other disorders (also referred to as differences) of sex development (DSD). The purpose of this article is to describe the clinical approach to the girl with virilization at puberty, focusing on diagnostic challenges. The review is written from the perspective of the case of an 11.5-year-old girl who was referred to our clinic for progressive, rapid onset clitoromegaly, and was then diagnosed with a complex genetic form of DSD that led to abnormal testosterone production from a dysgenetic gonad at onset of puberty. Her genetic workup revealed a unique translocation of an abnormal duplicated Y-chromosome to a deleted chromosome 9, including the Doublesex and Mab-3 Related Transcription factor 1 (DMRT1) gene. LEARNING OBJECTIVES Identify the precise pathophysiologic mechanisms leading to virilization in girls at puberty considering that virilization at puberty may be the first manifestation of an endocrine active tumor or a disorder/difference of sex development (DSD) that remained undiagnosed before and may be life-threatening. Of the DSDs, nonclassical congenital adrenal hyperplasia occurs most often.Provide a step-by-step diagnostic workup plan including repeated and expanded biochemical and genetic tests to solve complex cases.Manage clinical care of a girl virilizing at puberty using an interdisciplinary team approach.Care for complex cases of DSD manifesting at puberty, such as the presented girl with a Turner syndrome-like phenotype and virilization resulting from a complex genetic variation.
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Affiliation(s)
- Maristella Santi
- Pediatric Endocrinology, Diabetology, and Metabolism, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Stefanie Graf
- Pediatric Endocrinology, Diabetology, and Metabolism, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Mazen Zeino
- Department of Pediatric Surgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Martine Cools
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | | | - Mafalda Trippel
- Institute of Pathology, Inselspital, University of Bern, Bern, Switzerland
| | - Nijas Aliu
- University Clinic for Pediatrics, Human Genetics, Inselspital, University of Bern, Bern, Switzerland
| | - Christa E Flück
- Pediatric Endocrinology, Diabetology, and Metabolism, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Correspondence: Christa E. Flück, Pediatric Endocrinology and Diabetology, University Children’s Hospital, Freiburgstrasse 15 / C845, 3010 Bern, Switzerland. E-mail:
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11
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Chai H, Ji W, Wen J, DiAdamo A, Grommisch B, Hu Q, Szekely AM, Li P. Ring chromosome formation by intra-strand repairing of subtelomeric double stand breaks and clinico-cytogenomic correlations for ring chromosome 9. Am J Med Genet A 2020; 182:3023-3028. [PMID: 32978894 DOI: 10.1002/ajmg.a.61890] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/20/2020] [Accepted: 09/05/2020] [Indexed: 11/09/2022]
Abstract
Constitutional ring chromosome 9, r(9), is a rare chromosomal disorder. Cytogenomic analyses by karyotyping, array comparative genomic hybridization (aCGH) and whole genome sequencing (WGS) were performed in a patient of r(9). Karyotyping detected a mosaic pattern of r(9) and monosomy 9 in 83% and 17% of cells, respectively. aCGH detected subtelomeric deletions of 407 kb at 9p24.3 and 884 kb at 9q34.3 and an interstitial duplication of 5.879 Mb at 9q33.2q34.11. WGS revealed double strand breaks (DSBs) at ends of 9p24.3 and 9q34.3, inverted repeats at ends of subtelomeric and 9q33.2q34.11 regions, and microhomology sequences at the junctions of this r(9). This is the first report of r(9) analyzed by WGS to delineate the mechanism of ring chromosome formation from repairing of subtelomeric DSBs. The loss of telomeres by subtelomeric DSBs triggered inverted repeats induced intra-strand foldback and then microhomology mediated synthesis and ligation, which resulted in the formation of this r(9) with distal deletions and an interstitial duplication. Review of literature found seven patients of r(9) with clinical and cytogenomic findings. These patients and the present patient were registered into the Human Ring Chromosome Registry and a map correlating critical regions and candidate genes with relevant phenotypes was constructed. Variable phenotypes of r(9) patients could be explained by critical regions and genes of DOCK8, DMRT, SMARCA2, CD274, IL33, PTPRD, CER1, FREM1 for 9p deletions, and the EHMT1 gene for 9q34 deletion syndrome. This interactive registry of r(9) could provide information for cytogenomic diagnosis, genetics counseling and clinical management.
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Affiliation(s)
- Hongyan Chai
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Weizhen Ji
- Pediatric Genomic Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jiadi Wen
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Autumn DiAdamo
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Brittany Grommisch
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Qiping Hu
- Departments of Cell Biology and Genetics, Guangxi Medical University, Nanning, China
| | - Anna M Szekely
- Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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12
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Ng J, Sams E, Baldridge D, Kremitzki M, Wegner DJ, Lindsay T, Fulton R, Cole FS, Turner TN. Precise breakpoint detection in a patient with 9p- syndrome. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005348. [PMID: 32532883 PMCID: PMC7304358 DOI: 10.1101/mcs.a005348] [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: 02/21/2020] [Accepted: 04/27/2020] [Indexed: 11/24/2022] Open
Abstract
We present a case of 9p- syndrome with a complex chromosomal event originally characterized by the classical karyotype approach as 46,XX,der(9)t(9;13)(p23;q13). We used advanced technologies (Bionano Genomics genome imaging and 10× Genomics sequencing) to characterize the location of the translocation and accompanying deletion on Chromosome 9 and duplication on Chromosome 13 with single-nucleotide breakpoint resolution. The translocation breakpoint was at Chr 9:190938 and Chr 13:50850492, the deletion at Chr 9:1-190938, and the duplication at Chr 13:50850492-114364328. We identified genes in the deletion and duplication regions that are known to be associated with this patient's phenotype (e.g., ZIC2 in dysmorphic facial features, FOXD4 in developmental delay, RNASEH2B in developmental delay, and PCDH9 in autism). Our results indicate that clinical genomic assessment of individuals with complex karyotypes can be refined to a single-base-pair resolution when utilizing Bionano and 10× Genomics sequencing. With the 10× Genomics data, we were also able to characterize other variation (e.g., loss of function) throughout the remainder of the patient's genome. Overall, the Bionano and 10× technologies complemented each other and provided important insight into our patient with 9p- syndrome. Altogether, these results indicate that newer technologies can identify precise genomic variants associated with unique patient phenotypes that permit discovery of novel genotype-phenotype correlations and therapeutic strategies.
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Affiliation(s)
- Jeffrey Ng
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Eleanor Sams
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Dustin Baldridge
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, and St. Louis Children's Hospital, St. Louis, Missouri 63110, USA
| | - Milinn Kremitzki
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Daniel J Wegner
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, and St. Louis Children's Hospital, St. Louis, Missouri 63110, USA
| | - Tina Lindsay
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Robert Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - F Sessions Cole
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, and St. Louis Children's Hospital, St. Louis, Missouri 63110, USA
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Leung KCP, Ko TCS. Identification of a possible association of JAK2 in development of microphthalmia, anophthalmia, and coloboma (MAC) complex in a child with 9p deletion and duplication. Ophthalmic Genet 2020; 41:373-376. [PMID: 32506980 DOI: 10.1080/13816810.2020.1776338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND Microphthalmia, anophthalmia, coloboma (MAC) complex is a spectrum of ocular abnormalities that occur in isolation or as part of a syndrome. Genetic abnormalities have been shown to account for 80% of cases in bilateral anophthalmia or severe microphthalmia, where 25-30% were attributed to chromosomal defects in this subset of MAC patients. To date, chromosome 9 short arm (9p) abnormalities have not been shown to associate with development of MAC. PURPOSE To report a case of MAC spectrum disorder that is related to 9p deletion and duplication. MATERIALS AND METHODS A child who exhibited signs of MAC was evaluated retrospectively. Genetic analysis with comparative genomic hybridization (CGH) and a family pedigree was obtained from the proband. RESULTS A 3-year-old girl with a history of an atrial septal defect, a horseshoe kidney and global developmental delay was presented. Ophthalmic examination revealed bilateral iris coloboma, bilateral choroidal-retinal coloboma, and left-sided microphthalmia. Subsequent oligonucleotide-based array CGH revealed two different sites of duplication and deletion on 9p (9p24.3 (209020_1143516)x1, 9p24.3p24.1 (1158662_6395264)x3). CONCLUSION We present the first case of MAC spectrum disorder that is related to 9p deletion and duplication. The link between the associated genetic abnormality and the phenotypic features is yet to be established. Duplication of JAK2 gene, which is within the same region of abnormalities, may have potentiated the development of MAC spectrum disease.
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Affiliation(s)
| | - Tak Chuen Simon Ko
- Department of Ophthalmology, Tung Wah Eastern Hosptial , Causewaybay, Hong Kong
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Kanda S, Ohmuraya M, Akagawa H, Horita S, Yoshida Y, Kaneko N, Sugawara N, Ishizuka K, Miura K, Harita Y, Yamamoto T, Oka A, Araki K, Furukawa T, Hattori M. Deletion in the Cobalamin Synthetase W Domain-Containing Protein 1 Gene Is associated with Congenital Anomalies of the Kidney and Urinary Tract. J Am Soc Nephrol 2020; 31:139-147. [PMID: 31862704 PMCID: PMC6934996 DOI: 10.1681/asn.2019040398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 10/02/2019] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Researchers have identified about 40 genes with mutations that result in the most common cause of CKD in children, congenital anomalies of the kidney and urinary tract (CAKUT), but approximately 85% of patients with CAKUT lack mutations in these genes. The anomalies that comprise CAKUT are clinically heterogenous, and thought to be caused by disturbances at different points in kidney development. However, identification of novel CAKUT-causing genes remains difficult because of their variable expressivity, incomplete penetrance, and heterogeneity. METHODS We investigated two generations of a family that included two siblings with CAKUT. Although the parents and another child were healthy, the two affected siblings presented the same manifestations, unilateral renal agenesis and contralateral renal hypoplasia. To search for a novel causative gene of CAKUT, we performed whole-exome and whole-genome sequencing of DNA from the family members. We also generated two lines of genetically modified mice with a gene deletion present only in the affected siblings, and performed immunohistochemical and phenotypic analyses of these mice. RESULTS We found that the affected siblings, but not healthy family members, had a homozygous deletion in the Cobalamin Synthetase W Domain-Containing Protein 1 (CBWD1) gene. Whole-genome sequencing uncovered genomic breakpoints, which involved exon 1 of CBWD1, harboring the initiating codon. Immunohistochemical analysis revealed high expression of Cbwd1 in the nuclei of the ureteric bud cells in the developing kidneys. Cbwd1-deficient mice showed CAKUT phenotypes, including hydronephrosis, hydroureters, and duplicated ureters. CONCLUSIONS The identification of a deletion in CBWD1 gene in two siblings with CAKUT implies a role for CBWD1 in the etiology of some cases of CAKUT.
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Affiliation(s)
- Shoichiro Kanda
- Department of Pediatrics, The University of Tokyo, Tokyo, Japan;
- Department of Pediatric Nephrology
| | - Masaki Ohmuraya
- Department of Genetics, Hyogo College of Medicine, Hyogo, Japan
| | - Hiroyuki Akagawa
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
| | - Shigeru Horita
- Department of Pathology, Kidney Center, School of Medicine, and
| | | | | | | | | | | | - Yutaka Harita
- Department of Pediatrics, The University of Tokyo, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Akira Oka
- Department of Pediatrics, The University of Tokyo, Tokyo, Japan
| | - Kimi Araki
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan; and
| | - Toru Furukawa
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
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Marsudi BA, Kartapradja H, Paramayuda C, Batubara JRL, Harahap AR, Marzuki NS. Loss of DMRT1 gene in a Mos 45,XY,-9[8]/46,XY,r(9)[29]/47,XY,+idic r(9)× 2[1]/46,XY,idic r(9)[1]/46,XY[1] female presenting with short stature. Mol Cytogenet 2018; 11:28. [PMID: 29760778 PMCID: PMC5941566 DOI: 10.1186/s13039-018-0379-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 04/23/2018] [Indexed: 02/04/2023] Open
Abstract
Background A 46,XY sex reversal syndrome is characterized by discordant genetic and phenotypic sex, leading to normal external female genitalia, undeveloped gonads and presence of Müllerian structures in an otherwise 46,XY individual. Chromosome 9pter aberrations, such as ring chromosome have been reported to cause 46,XY disorders of sex development (DSD), due to involvement of DMRT1 gene located at the 9p24.3 region. Case presentation This study presents a unique case of a 12-year-old female with mos 46,XY, (r)9[31]/45,XY,-9[9] karyotype, presenting with intellectual disability and short stature, mimicking Turner syndrome. Re-karyotyping was performed using standard GTL-banding technique. Further cytogenetic study using standard metaphase fluorescent in situ hybridization (FISH) technique was applied to cultured lymphocytes from peripheral blood, hybridized using green control probe specific to 9q21 loci, and red DMRT1 probe specific to 9p24.3 loci. Cytogenetics and FISH analysis revealed mos 45,XY,-9[8]/46,XY,r(9)[29]/47,XY,+idic r(9)× 2[1]/46,XY,idic r(9)[1]/46,XY[1] and haploinsufficiency of DMRT1 gene in most cells. CGH array revealed a deletion around 1.25 Mb at 9p24.3 loci [arr 9p24.3(204,193-1,457,665)× 1] and three duplications around 13 Mb [9p24.3p22.3(1,477,660-14,506,754)× 3] near the breakage point that formed the ring chromosome 9. Conclusions The clinical presentation of the subject that mimics Turner syndrome highlights the importance of cytogenetic analysis to detect the possibility of ring chromosome 9. Sex reversal due to haploinsufficiency of DMRT1 gene in ring chromosome 9 structures is exceedingly rare with only a handful of cases ever reported. This finding further highlights the importance of DMRT1 gene in sex determination and differentiation in males. More research is required to pinpoint the exact mechanism that underlies sex reversal caused by DMRT1 haploinsufficiency.
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Affiliation(s)
- Bagas A Marsudi
- 1Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | | | - Jose R L Batubara
- 2Department of Child Health, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Alida R Harahap
- 1Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Nanis S Marzuki
- 1Eijkman Institute for Molecular Biology, Jakarta, Indonesia
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16
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Bayat A, Kirchhoff M, Madsen CG, Kreiborg S. Neonatal hyperinsulinemic hypoglycemia in a patient with 9p deletion syndrome. Eur J Med Genet 2018; 61:473-477. [PMID: 29601900 DOI: 10.1016/j.ejmg.2018.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/25/2018] [Accepted: 03/21/2018] [Indexed: 11/15/2022]
Abstract
We report the clinical and neuroradiological findings in a young boy harboring the 9p deletion syndrome including the novel findings of thalamic infarction and germinal matrix haemorrhage and neonatal hyperinsulinemic hypoglycemia. Both the hypoglycemic events and the ventriculomegaly found in this patient have previously only been reported in two patients, while the thalamic infarction and germinal matrix haemorrhage are novel features.
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Affiliation(s)
- Allan Bayat
- Department of Pediatrics, University Hospital of Hvidovre, Hvidovre, Denmark.
| | - Maria Kirchhoff
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Denmark
| | - Camilla Gøbel Madsen
- Department for Radiology, Centre for Functional and Diagnostic Imaging and Research, Hvidovre Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sven Kreiborg
- Department of Pediatric Dentistry and Clinical Genetics, School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; 3D Craniofacial Image Research Laboratory, School of Dentistry, Copenhagen University Hospital Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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17
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D’Angelo CS, Varela MC, de Castro CIE, Otto PA, Perez ABA, Lourenço CM, Kim CA, Bertola DR, Kok F, Garcia-Alonso L, Koiffmann CP. Chromosomal microarray analysis in the genetic evaluation of 279 patients with syndromic obesity. Mol Cytogenet 2018; 11:14. [PMID: 29441128 PMCID: PMC5800070 DOI: 10.1186/s13039-018-0363-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/22/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Syndromic obesity is an umbrella term used to describe cases where obesity occurs with additional phenotypes. It often arises as part of a distinct genetic syndrome with Prader-Willi syndrome being a classical example. These rare forms of obesity provide a unique source for identifying obesity-related genetic changes. Chromosomal microarray analysis (CMA) has allowed the characterization of new genetic forms of syndromic obesity, which are due to copy number variants (CNVs); however, CMA in large cohorts requires more study. The aim of this study was to characterize the CNVs detected by CMA in 279 patients with a syndromic obesity phenotype. RESULTS Pathogenic CNVs were detected in 61 patients (22%) and, among them, 35 had overlapping/recurrent CNVs. Genomic imbalance disorders known to cause syndromic obesity were found in 8.2% of cases, most commonly deletions of 1p36, 2q37 and 17p11.2 (5.4%), and we also detected deletions at 1p21.3, 2p25.3, 6q16, 9q34, 16p11.2 distal and proximal, as well as an unbalanced translocation resulting in duplication of the GNB3 gene responsible for a syndromic for of childhood obesity. Deletions of 9p terminal and 22q11.2 proximal/distal were found in 1% and 3% of cases, respectively. They thus emerge as being new putative obesity-susceptibility loci. We found additional CNVs in our study that overlapped with CNVs previously reported in cases of syndromic obesity, including a new case of 13q34 deletion (CHAMP1), bringing to 7 the number of patients in whom such defects have been described in association with obesity. Our findings implicate many genes previously associated with obesity (e.g. PTBP2, TMEM18, MYT1L, POU3F2, SIM1, SH2B1), and also identified other potentially relevant candidates including TAS1R3, ALOX5AP, and GAS6. CONCLUSION Understanding the genetics of obesity has proven difficult, and considerable insight has been obtained from the study of genomic disorders with obesity associated as part of the phenotype. In our study, CNVs known to be causal for syndromic obesity were detected in 8.2% of patients, but we provide evidence for a genetic basis of obesity in as many as 14% of cases. Overall, our results underscore the genetic heterogeneity in syndromic forms of obesity, which imposes a substantial challenge for diagnosis.
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Affiliation(s)
- Carla Sustek D’Angelo
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
| | - Monica Castro Varela
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
| | - Claudia Irene Emílio de Castro
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
| | - Paulo Alberto Otto
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
| | - Ana Beatriz Alvarez Perez
- Department of Morphology and Genetics, Paulista School of Medicine, Federal University of Sao Paulo (UNIFESP), Sao Paulo, SP Brazil
| | - Charles Marques Lourenço
- Neurogenetics Unit, Clinics Hospital of Ribeirao Preto, Faculty of Medicine, University of Sao Paulo, FMRP-USP, Ribeirao Preto, SP Brazil
| | - Chong Ae Kim
- Genetic Unit, Children’s Institute, Faculty of Medicine, University of Sao Paulo, FMUSP, Sao Paulo, SP Brazil
| | - Debora Romeo Bertola
- Genetic Unit, Children’s Institute, Faculty of Medicine, University of Sao Paulo, FMUSP, Sao Paulo, SP Brazil
| | - Fernando Kok
- Department of Neurology, Faculty of Medicine, University of Sao Paulo, FMUSP, Sao Paulo, SP Brazil
| | - Luis Garcia-Alonso
- Department of Morphology and Genetics, Paulista School of Medicine, Federal University of Sao Paulo (UNIFESP), Sao Paulo, SP Brazil
| | - Celia Priszkulnik Koiffmann
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
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18
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Borlot F, Regan BM, Bassett AS, Stavropoulos DJ, Andrade DM. Prevalence of Pathogenic Copy Number Variation in Adults With Pediatric-Onset Epilepsy and Intellectual Disability. JAMA Neurol 2017; 74:1301-1311. [PMID: 28846756 DOI: 10.1001/jamaneurol.2017.1775] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Importance Copy number variation (CNV) is an important cause of neuropsychiatric disorders. Little is known about the role of CNV in adults with epilepsy and intellectual disability. Objectives To evaluate the prevalence of pathogenic CNVs and identify possible candidate CNVs and genes in patients with epilepsy and intellectual disability. Design, Setting, and Participants In this cross-sectional study, genome-wide microarray was used to evaluate a cohort of 143 adults with unexplained childhood-onset epilepsy and intellectual disability who were recruited from the Toronto Western Hospital epilepsy outpatient clinic from January 1, 2012, through December 31, 2014. The inclusion criteria were (1) pediatric seizure onset with ongoing seizure activity in adulthood, (2) intellectual disability of any degree, and (3) no structural brain abnormalities or metabolic conditions that could explain the seizures. Main Outcomes and Measures DNA screening was performed using genome-wide microarray platforms. Pathogenicity of CNVs was assessed based on the American College of Medical Genetics guidelines. The Residual Variation Intolerance Score was used to evaluate genes within the identified CNVs that could play a role in each patient's phenotype. Results Of the 2335 patients, 143 probands were investigated (mean [SD] age, 24.6 [10.8] years; 69 male and 74 female). Twenty-three probands (16.1%) and 4 affected relatives (2.8%) (mean [SD] age, 24.1 [6.1] years; 11 male and 16 female) presented with pathogenic or likely pathogenic CNVs (0.08-18.9 Mb). Five of the 23 probands with positive results (21.7%) had more than 1 CNV reported. Parental testing revealed de novo CNVs in 11 (47.8%), with CNVs inherited from a parent in 4 probands (17.4%). Sixteen of 23 probands (69.6%) presented with previously cataloged human genetic disorders and/or defined CNV hot spots in epilepsy. Eight nonrecurrent rare CNVs that overlapped 1 or more genes associated with intellectual disability, autism, and/or epilepsy were identified: 2p16.1-p15 duplication, 6p25.3-p25.1 duplication, 8p23.3p23.1 deletion, 9p24.3-p23 deletion, 10q11.22-q11.23 duplication, 12p13.33-13.2 duplication, 13q34 deletion, and 16p13.2 duplication. Five genes are of particular interest given their potential pathogenicity in the corresponding phenotypes and least tolerability to variation: ABAT, KIAA2022, COL4A1, CACNA1C, and SMARCA2. ABAT duplication was associated with Lennox-Gastaut syndrome and KIAA2022 deletion with Jeavons syndrome. Conclusions and Relevance The high prevalence of pathogenic CNVs in this study highlights the importance of microarray analysis in adults with unexplained childhood-onset epilepsy and intellectual disability. Additional studies and comparison with similar cases are required to evaluate the effects of deletions and duplications that overlap specific genes.
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Affiliation(s)
- Felippe Borlot
- Epilepsy Genetics Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, Ontario, Canada.,Clinical Neurosciences Center, Department of Neurology, University of Utah, Salt Lake City
| | - Brigid M Regan
- Epilepsy Genetics Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, Ontario, Canada
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - D James Stavropoulos
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Danielle M Andrade
- Epilepsy Genetics Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, Ontario, Canada.,Division of Neurology, Krembil Neuroscience Centre, Toronto Western Hospital, University of Toronto, Toronto, Ontario, Canada
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Ittleman BR, Mckissick J, Bosanko KA, Ocal E, Golinko M, Zarate YA. Less common underlying genetic diagnoses found in a cohort of 139 individuals surgically corrected for craniosynostosis. Am J Med Genet A 2017; 176:487-491. [PMID: 29160013 DOI: 10.1002/ajmg.a.38532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/09/2017] [Accepted: 10/15/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Benjamin R Ittleman
- Department of Pediatrics, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jasmine Mckissick
- University of Arkansas for Medical Sciences College of Medicine, Little Rock, Arkansas
| | - Katherine A Bosanko
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Eylem Ocal
- Department of Neurosurgery, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Michael Golinko
- Division of Plastic Surgery, Department of Surgery, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Yuri A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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20
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Clinical findings and molecular cytogenetic study of de novo pure chromosome 9p deletion: Pre- and postnatal diagnosis. Taiwan J Obstet Gynecol 2017; 55:867-870. [PMID: 28040136 DOI: 10.1016/j.tjog.2016.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2016] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE The aim of this report is to describe the phenotype-genotype correlation of chromosome 9p deletion syndrome cases, particularly the prenatal cases. MATERIALS AND METHODS A 30-year-old woman was referred to a hospital at 19+1 weeks of gestation because of omphalocele detected in the fetus. The conventional karyotyping analysis and array comparative genomic hybridization (aCGH) were utilized for the prenatal diagnosis and genetic counseling in the fetus. The prenatal abnormality and cytogenetic findings in the fetus were compared with other patients with 9p deletion. RESULTS Karyotype analysis of the fetus cell showed a karyotype of 46,XX,del(9)(p22). aCGH analysis detected a deletion as arr[hg19] 9p24.2p22.2(226,7812-1,7466,907)×1. Individuals with 9p deletions tend to have features with widely variable expressivity. The common clinical manifestations of the 9p deletion include development delay, learning difficulties, hypotonia and trigonocephaly. CONCLUSION Phenotypes of 9p deletion cases are broadly in line. The prenatal diagnosis of the omphalocele provides evidence for a correlation with distal 9q deletion.
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21
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Sivasankaran A, Kanakavalli MK, Anuradha D, Samuel CR, Kandukuri LR. Ring Chromosome 9 and Chromosome 9p Deletion Syndrome in a Patient Associated with Developmental Delay: A Case Report and Review of the Literature. Cytogenet Genome Res 2016; 148:165-73. [DOI: 10.1159/000445862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2016] [Indexed: 11/19/2022] Open
Abstract
Ring chromosomes have been described for all human chromosomes and are typically associated with physical and/or mental abnormalities resulting from a deletion of the terminal ends of both chromosome arms. This report describes the presence of a ring chromosome 9 in a 2-year-old male child associated with developmental delay. The proband manifested a severe phenotype comprising facial dysmorphism, congenital heart defects, and seizures. The child also exhibited multiple cell lines with mosaic patterns of double rings, a dicentric ring and loss of the ring associated with mitotic instability and dynamic tissue-specific mosaicism. His karyotype was 46,XY,r(9)(p22q34)[89]/46,XY,dic r(9; 9)(p22q34;p22q34)[6]/45, XY,-9[4]/47,XY,r(9),+r(9)[1]. However, the karyotypes of his parents and elder brother were normal. FISH using mBAND probe and subtelomeric probes specific for p and q arms for chromosome 9 showed no deletion in any of the regions. Chromosomal microarray analysis led to the identification of a heterozygous deletion of 15.7 Mb from 9p22.3 to 9p24.3. The probable role of the deleted genes in the manifestation of the phenotype of the proband is discussed.
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Clinical and neuroradiological features of the 9p deletion syndrome. Childs Nerv Syst 2016; 32:327-35. [PMID: 26597681 DOI: 10.1007/s00381-015-2957-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/05/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND The 9p deletion syndrome is a rare condition, which associates trigonocephaly, facial dysmorphism and developmental delay. The neuroradiological aspects of this syndrome have not yet been described. The purpose of this article is to identify the clinical and neuroradiological features, that should be recognized by all specialists treating these children, for a proper and early diagnosis. METHODS Among patients with trigonocephaly treated at our institution, we retrospectively analyzed the clinical and neuroradiological aspects of children with genetically confirmed 9p deletion syndrome. RESULTS 6 patients were identified. Beside trigonocephaly, the most frequent clinical findings were small ears, long philtrum, upslanting palpebral fissures, flat nasal bridge and variable psycho-motor delay. Hypertelorism was present in 4 of 6 patient, which is opposite to the hypotelorism typical of non-syndromic trigonocephaly. Among neuroradiological findings, large, anteriorly rotated sylvian cisterns and altered shape of the septum pellucidum were found in all patients, as well as the compression of the frontal cortex due to the metopic synostosis (MS). A thin or dysmorphic corpus callosum and a diffuse white matter hypoplasia were present in more than half of the cases. Futhermore we compared these MRI findings with those of a control group of 30 non-syndromic trigonocephalies. CONCLUSIONS Some recurrent neuroradiological alterations can be found in 9p deletion syndrome. The presence of these signs on MRI of a trigonocephalic patient should raise the suspicion of an underlying chromosomal alteration, such as the 9p deletion syndrome and prompt genetic investigations.
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Interstitial 9p24.3 deletion involving only DOCK8 and KANK1 genes in two patients with non-overlapping phenotypic traits. Eur J Med Genet 2015; 59:20-5. [PMID: 26656975 DOI: 10.1016/j.ejmg.2015.11.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 10/15/2015] [Accepted: 11/24/2015] [Indexed: 11/21/2022]
Abstract
Chromosome 9p deletion represents a clinically and genetically heterogeneous condition characterized by a wide spectrum of phenotypic manifestations and a variable size of the deleted region. The deletion breakpoint occurs from 9p22 to 9p24 bands, and the large majority of cases have either terminal deletions or translocations involving another chromosome. Here we report on two patients with similar inherited interstitial 9p24.3 deletion involving only DOCK8 and KANK1 genes. Interestingly, the two patients showed non-overlapping phenotypic traits ranging from a complex phenotype in one to only trigonocephaly with minor dysmorphic features and hand anomalies in the other one. The factors underlying the phenotypic variation associated with seemingly identical genomic alterations are not entirely clear, even if smaller variants, single-nucleotide changes, and epigenetic or stochastic factors altering the expression of genes within functionally relevant pathways have been recently shown to contribute to phenotypic variation. We discuss the role of the two genes and propose possible explanations for the clinical heterogeneity of the phenotype of the two patients.
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Lara-Navarro IJ, Córdova-Fletes C, García-Ruiz A, Rivera H. A further inv dup/del 9p de novo rearrangement. Reappraisal of 25 instances. GENE REPORTS 2015. [DOI: 10.1016/j.genrep.2015.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Erol I, Saygı S, Demir Ş, Alehan F, Sahin FI. West syndrome associated with a novel chromosomal anomaly; partial trisomy 8P together with partial monosomy 9P, resulting from a familial unbalanced reciprocal translocation. J Pediatr Neurosci 2015; 10:25-7. [PMID: 25878738 PMCID: PMC4395939 DOI: 10.4103/1817-1745.154324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
West syndrome is classified according to the underlying etiology into an acquired West syndrome, a congenital/developmental West syndrome, and West syndrome of unknown etiology. Causes of a congenital/developmental West syndrome are extensive and include chromosomal anomalies. We report on a patient carrying a derivative chromosome originating from the reciprocal unbalanced translocation t (8;9) (p11.2;p22) and presenting with macrocephaly, West syndrome, severe mental motor retardation and hypotonia. As far as we know, this is a new chromosomal anomaly associated with West syndrome.
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Affiliation(s)
- Ilknur Erol
- Department of Pediatrics, Pediatric Neurology Unit, Adana, Turkey
| | - Semra Saygı
- Department of Pediatrics, Pediatric Neurology Unit, Adana, Turkey
| | - Şenay Demir
- Department of Radiology, Adana Teaching and Medical Research Center, Adana, Turkey
| | - Fusun Alehan
- Department of Pediatrics, Pediatric Neurology Unit, Baskent University Faculty of Medicine, Ankara, Turkey
| | - Feride Iffet Sahin
- Department of Medical Genetics, Baskent University, Faculty of Medicine, Adana, Turkey
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26
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Tabet AC, Verloes A, Pilorge M, Delaby E, Delorme R, Nygren G, Devillard F, Gérard M, Passemard S, Héron D, Siffroi JP, Jacquette A, Delahaye A, Perrin L, Dupont C, Aboura A, Bitoun P, Coleman M, Leboyer M, Gillberg C, Benzacken B, Betancur C. Complex nature of apparently balanced chromosomal rearrangements in patients with autism spectrum disorder. Mol Autism 2015; 6:19. [PMID: 25844147 PMCID: PMC4384291 DOI: 10.1186/s13229-015-0015-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/06/2015] [Indexed: 12/21/2022] Open
Abstract
Background Apparently balanced chromosomal rearrangements can be associated with an abnormal phenotype, including intellectual disability and autism spectrum disorder (ASD). Genome-wide microarrays reveal cryptic genomic imbalances, related or not to the breakpoints, in 25% to 50% of patients with an abnormal phenotype carrying a microscopically balanced chromosomal rearrangement. Here we performed microarray analysis of 18 patients with ASD carrying balanced chromosomal abnormalities to identify submicroscopic imbalances implicated in abnormal neurodevelopment. Methods Eighteen patients with ASD carrying apparently balanced chromosomal abnormalities were screened using single nucleotide polymorphism (SNP) arrays. Nine rearrangements were de novo, seven inherited, and two of unknown inheritance. Genomic imbalances were confirmed by fluorescence in situ hybridization and quantitative PCR. Results We detected clinically significant de novo copy number variants in four patients (22%), including three with de novo rearrangements and one with an inherited abnormality. The sizes ranged from 3.3 to 4.9 Mb; three were related to the breakpoint regions and one occurred elsewhere. We report a patient with a duplication of the Wolf-Hirschhorn syndrome critical region, contributing to the delineation of this rare genomic disorder. The patient has a chromosome 4p inverted duplication deletion, with a 0.5 Mb deletion of terminal 4p and a 4.2 Mb duplication of 4p16.2p16.3. The other cases included an apparently balanced de novo translocation t(5;18)(q12;p11.2) with a 4.2 Mb deletion at the 18p breakpoint, a subject with de novo pericentric inversion inv(11)(p14q23.2) in whom the array revealed a de novo 4.9 Mb deletion in 7q21.3q22.1, and a patient with a maternal inv(2)(q14.2q37.3) with a de novo 3.3 Mb terminal 2q deletion and a 4.2 Mb duplication at the proximal breakpoint. In addition, we identified a rare de novo deletion of unknown significance on a chromosome unrelated to the initial rearrangement, disrupting a single gene, RFX3. Conclusions These findings underscore the utility of SNP arrays for investigating apparently balanced chromosomal abnormalities in subjects with ASD or related neurodevelopmental disorders in both clinical and research settings.
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Affiliation(s)
- Anne-Claude Tabet
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
| | - Alain Verloes
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Marion Pilorge
- INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
| | - Elsa Delaby
- INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
| | - Richard Delorme
- Department of Child and Adolescent Psychiatry, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Fondation Fondamental, 40 rue de Mesly, 94000 Créteil, France
| | - Gudrun Nygren
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Kungsgatan 12, 41119 Göteborg, Sweden
| | - Françoise Devillard
- Département de Génétique et Procréation, CHU de Grenoble, Hôpital Couple-Enfant, avenue du Maquis du Grésivaudan, 38043 Grenoble, France
| | - Marion Gérard
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Sandrine Passemard
- INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Neurology Unit, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Delphine Héron
- Medical Genetics Unit, AP-HP, Pitié-Salpêtrière University Hospital, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Jean-Pierre Siffroi
- Service de Génétique et d'Embryologie Médicales, AP-HP, Trousseau Hospital, 26 avenue du Docteur Arnold Netter, 75012 Paris, France
| | - Aurelia Jacquette
- Medical Genetics Unit, AP-HP, Pitié-Salpêtrière University Hospital, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Andrée Delahaye
- INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Cytogenetics Unit, AP-HP, Jean Verdier Hospital, allée du 14 Juillet, 93140 Bondy, France ; Paris 13 University, Sorbonne Paris Cité, UFR SMBH, 74 rue Marcel Cachin, 93000 Bobigny, France
| | - Laurence Perrin
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Céline Dupont
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Azzedine Aboura
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Pierre Bitoun
- Medical Genetics Unit, AP-HP, Jean Verdier Hospital, allée du 14 Juillet, 93140 Bondy, France
| | - Mary Coleman
- Foundation for Autism Research, 3081 Quail Hollow, Sarasota, FL 34235 USA
| | - Marion Leboyer
- Fondation Fondamental, 40 rue de Mesly, 94000 Créteil, France ; Department of Psychiatry, AP-HP, Henri Mondor-Albert Chenevier Hospital, 40 rue de Mesly, 94000 Créteil, France ; INSERM U955, Institut Mondor de Recherche Biomédicale, Psychiatric Genetics, 8 rue du Général Sarrail, 94000 Créteil, France ; Faculty of Medicine, University Paris-Est Créteil, 8 rue du Général Sarrail, 94000 Créteil, France
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Kungsgatan 12, 41119 Göteborg, Sweden
| | - Brigitte Benzacken
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Cytogenetics Unit, AP-HP, Jean Verdier Hospital, allée du 14 Juillet, 93140 Bondy, France ; Paris 13 University, Sorbonne Paris Cité, UFR SMBH, 74 rue Marcel Cachin, 93000 Bobigny, France
| | - Catalina Betancur
- INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
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Guilherme RS, Meloni VA, Perez ABA, Pilla AL, de Ramos MAP, Dantas AG, Takeno SS, Kulikowski LD, Melaragno MI. Duplication 9p and their implication to phenotype. BMC MEDICAL GENETICS 2014; 15:142. [PMID: 25526829 PMCID: PMC4411943 DOI: 10.1186/s12881-014-0142-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022]
Abstract
Background Trisomy 9p is one of the most common partial trisomies found in newborns. We report the clinical features and cytogenomic findings in five patients with different chromosome rearrangements resulting in complete 9p duplication, three of them involving 9p centromere alterations. Methods The rearrangements in the patients were characterized by G-banding, SNP-array and fluorescent in situ hybridization (FISH) with different probes. Results Two patients presented de novo dicentric chromosomes: der(9;15)t(9;15)(p11.2;p13) and der(9;21)t(9;21)(p13.1;p13.1). One patient presented two concomitant rearranged chromosomes: a der(12)t(9;12)(q21.13;p13.33) and an psu i(9)(p10) which showed FISH centromeric signal smaller than in the normal chromosome 9. Besides the duplication 9p24.3p13.1, array revealed a 7.3 Mb deletion in 9q13q21.13 in this patient. The break in the psu i(9)(p10) probably occurred in the centromere resulting in a smaller centromere and with part of the 9q translocated to the distal 12p with the deletion 9q occurring during this rearrangement. Two patients, brother and sister, present 9p duplication concomitant to 18p deletion due to an inherited der(18)t(9;18)(p11.2;p11.31)mat. Conclusions The patients with trisomy 9p present a well-recognizable phenotype due to facial appearance, although the genotype-phenotype correlation can be difficult due to concomitant partial monosomy of other chromosomes. The chromosome 9 is rich in segmental duplication, especially in pericentromeric region, with high degree of sequence identity to sequences in 15p, 18p and 21p, chromosomes involved in our rearrangements. Thus, we suggest that chromosome 9 is prone to illegitimate recombination, either intrachromosomal or interchromosomal, which predisposes it to rearrangements, frequently involving pericentromeric regions.
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Affiliation(s)
- Roberta Santos Guilherme
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, CEP, 04023-900, São Paulo, Brazil.
| | - Vera Ayres Meloni
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, CEP, 04023-900, São Paulo, Brazil.
| | - Ana Beatriz Alvarez Perez
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, CEP, 04023-900, São Paulo, Brazil.
| | - Ana Luiza Pilla
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, CEP, 04023-900, São Paulo, Brazil.
| | - Marco Antonio Paula de Ramos
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, CEP, 04023-900, São Paulo, Brazil.
| | - Anelisa Gollo Dantas
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, CEP, 04023-900, São Paulo, Brazil.
| | - Sylvia Satomi Takeno
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, CEP, 04023-900, São Paulo, Brazil.
| | - Leslie Domenici Kulikowski
- Department of Pathology, Laboratório de Citogenômica, Universidade de São Paulo, Avenida Dr. Eneas Carvalho de Aguiar 647, CEP, 05403-000, São Paulo, Brazil.
| | - Maria Isabel Melaragno
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, CEP, 04023-900, São Paulo, Brazil.
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Post-zygotic breakage of a dicentric chromosome results in mosaicism for a telocentric 9p marker chromosome in a boy with developmental delay. Gene 2014; 533:403-10. [DOI: 10.1016/j.gene.2013.09.090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/20/2013] [Accepted: 09/25/2013] [Indexed: 02/07/2023]
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Mundhofir FEP, Nillesen WM, Van Bon BWM, Smeets D, Pfundt R, van de Ven-Schobers G, Ruiterkamp-Versteeg M, Winarni TI, Hamel BCJ, Yntema HG, Faradz SMH. Subtelomeric chromosomal rearrangements in a large cohort of unexplained intellectually disabled individuals in Indonesia: A clinical and molecular study. INDIAN JOURNAL OF HUMAN GENETICS 2013; 19:171-8. [PMID: 24019618 PMCID: PMC3758723 DOI: 10.4103/0971-6866.116118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
CONTEXT Unbalanced subtelomeric chromosomal rearrangements are often associated with intellectual disability (ID) and malformation syndromes. The prevalence of such rearrangements has been reported to be 5-9% in ID populations. AIMS To study the prevalence of subtelomeric rearrangements in the Indonesian ID population. MATERIALS AND METHODS We tested 436 subjects with unexplained ID using multiplex ligation dependent probe amplification (MLPA) using the specific designed sets of probes to detect human subtelomeric chromosomal imbalances (SALSA P070 and P036D). If necessary, abnormal findings were confirmed by other MLPA probe kits, fluorescent in situ hybridization or Single Nucleotide Polymorphism array. RESULTS A subtelomeric aberration was identified in 3.7% of patients (16/436). Details on subtelomeric aberrations and confirmation analyses are discussed. CONCLUSION This is the first study describing the presence of subtelomeric rearrangements in individuals with ID in Indonesia. Furthermore, it shows that also in Indonesia such abnormalities are a prime cause of ID and that in developing countries with limited diagnostic services such as Indonesia, it is important and feasible to uncover the genetic etiology in a significant number of cases with ID.
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Affiliation(s)
- Farmaditya E P Mundhofir
- Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine Diponegoro University, Semarang, Indonesia ; Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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30
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Child with deletion 9p syndrome presenting with craniofacial dysmorphism, developmental delay, and multiple congenital malformations. Case Rep Genet 2013; 2013:785830. [PMID: 23984121 PMCID: PMC3741698 DOI: 10.1155/2013/785830] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 07/09/2013] [Indexed: 02/03/2023] Open
Abstract
A 4-month-old Sri Lankan male child case with a de novo terminal deletion in the p22→pter region of chromosome 9 is described. The child presented with craniofacial dysmorphism, developmental delay, and congenital malformations in agreement with the consensus phenotype. A distinctive feature observed in this child was complete collapse of the left lung due to malformation of lung tissue. Cytogenetic studies confirmed terminal deletion of the short arm of chromosome 9 distal to band p22 [46,XY,del(9)(p22→pter)]. This is the first reported case of a de novo deletion 9p syndrome associated with pulmonary hypoplasia. This finding contributes to the widening of the spectrum of phenotypic features associated with deletion 9p syndrome.
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31
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Prenatal diagnosis and molecular cytogenetic characterization of a de novo pure distal 9p deletion and literature review. Genomics 2013; 102:265-9. [PMID: 23981964 DOI: 10.1016/j.ygeno.2013.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 06/22/2013] [Accepted: 08/16/2013] [Indexed: 11/21/2022]
Abstract
We present rapid aneuploidy diagnosis of distal 9p deletion by array comparative genomic hybridization using uncultured amniocytes in a pregnancy associated with an abnormal maternal serum screening result and intrauterine growth restriction (IUGR) in the fetus. We review the literature of prenatal diagnosis of distal 9p deletion, and add abnormal maternal serum biochemistry and fetal IUGR in the distinctive prenatal findings in pregnancy with fetal distal 9p deletion. We discuss the consequence of haploinsufficiency of DOCK8, KANK1, VLDLR and DMRT1 in this case.
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Bartels I, Pütz I, Reintjes N, Netzer C, Shoukier M. Normal intelligence and premature ovarian failure in an adult female with a 7.6 Mb de novo terminal deletion of chromosome 9p. Eur J Med Genet 2013; 56:458-62. [PMID: 23811035 DOI: 10.1016/j.ejmg.2013.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/13/2013] [Indexed: 11/27/2022]
Abstract
Distal deletion 9p is associated with gonadal dysfunction in XY individuals. Little is known about the gonadal function and fertility of XX females with this condition. We report on an affected 31-year-old infertile woman presenting with premature ovarian failure, mild dysmorphic features, a history of mild developmental delay and an otherwise normal female phenotype. Cytogenetic analysis showed a deletion 9p with the karyotype 46,XX,del(9)(p23-24) in lymphocytes. The subsequent oligonucleotide array-based CGH analysis with genomic DNA from peripheral blood revealed a terminal deletion of approximately 7.6 Mb. SNP microarray analyses of the patient and her unaffected parents confirmed the deletion breakpoint and revealed a de novo mutation of paternal origin. This is apparently the first description of an adult woman with a cytogenetically visible terminal deletion of chromosome 9p. The fertility problems observed in this patient complement earlier findings in prepubertal and pubertal 46,XX-girls with 9p deletions, who displayed a phenotype ranging from primary ovarian dysfunction and mild gonadotropin hyperresponses to positive menses. DMRT1 is hemizygous in our patient. We discuss the role of DMRT1 in female gonadal development.
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Affiliation(s)
- Iris Bartels
- Institute of Human Genetics, University Medical Center Goettingen, Germany.
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Quinonez SC, Park JM, Rabah R, Owens KM, Yashar BM, Glover TW, Keegan CE. 9p partial monosomy and disorders of sex development: Review and postulation of a pathogenetic mechanism. Am J Med Genet A 2013; 161A:1882-96. [DOI: 10.1002/ajmg.a.36018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/27/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Shane C. Quinonez
- Department of Pediatrics, Division of Genetics; University of Michigan; Ann Arbor; Michigan
| | - John M. Park
- Department of Urology; University of Michigan; Ann Arbor; Michigan
| | - Raja Rabah
- Department of Pathology; University of Michigan; Ann Arbor; Michigan
| | - Kailey M. Owens
- Department of Pediatrics, Division of Genetics; University of Michigan; Ann Arbor; Michigan
| | - Beverly M. Yashar
- Department of Human Genetics; University of Michigan; Ann Arbor; Michigan
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Sibbesen ELC, Jespersgaard C, Alosi D, Bisgaard AM, Tümer Z. Ring chromosome 9 in a girl with developmental delay and dysmorphic features: Case report and review of the literature. Am J Med Genet A 2013; 161A:1447-52. [DOI: 10.1002/ajmg.a.35901] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 01/20/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Else la Cour Sibbesen
- Applied Human Molecular Genetics, Kennedy Center; Copenhagen University Hospital; Rigshospitalet, Glostrup; Denmark
| | - Cathrine Jespersgaard
- Applied Human Molecular Genetics, Kennedy Center; Copenhagen University Hospital; Rigshospitalet, Glostrup; Denmark
| | - Daniela Alosi
- Applied Human Molecular Genetics, Kennedy Center; Copenhagen University Hospital; Rigshospitalet, Glostrup; Denmark
| | | | - Zeynep Tümer
- Applied Human Molecular Genetics, Kennedy Center; Copenhagen University Hospital; Rigshospitalet, Glostrup; Denmark
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35
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Mitsui N, Shimizu K, Nishimoto H, Mochizuki H, Iida M, Ohashi H. Patient with terminal 9 Mb deletion of chromosome 9p: refining the critical region for 9p monosomy syndrome with trigonocephaly. Congenit Anom (Kyoto) 2013; 53:49-53. [PMID: 23480358 DOI: 10.1111/j.1741-4520.2012.00362.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a patient with typical manifestations of 9p monosomy syndrome, including trigonocephaly and sex reversal. Array comparative genomic hybridization (CGH) revealed a 9p terminal deletion of approximately 9 Mb with the breakpoint at 9p23. We compared the deleted segments of 9p associated with reported cases of 9p monosomy syndrome with trigonocephaly. We did not identify a region that was shared by all patients; however, when only pure terminal or interstitial deletions that did not involve material from any other chromosome were compared, we identified a segment from D9S912 to RP11-439I6 of approximately 1 Mb that was deleted in every patient. We propose that this 1-Mb segment might be the critical region for 9p monosomy syndrome with trigonocephaly.
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Affiliation(s)
- Norimasa Mitsui
- Department of Clinical Laboratory, Divisions of Medical Genetics Neurosurgery Metabolism and Endocrinology, Saitama Children's Medical Center, Saitama, Japan
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Independent post-zygotic breaks of a dicentric chromosome result in mosaicism for an inverted duplication deletion 9p and terminal deletion 9p. Eur J Med Genet 2013; 56:229-35. [PMID: 23416622 DOI: 10.1016/j.ejmg.2013.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 01/22/2013] [Indexed: 01/30/2023]
Abstract
Mosaicism with two cell lines having different rearrangements of the same chromosome is rare. Only a few cases of mosaicism have been described in association with chromosomal inverted duplication deletion (inv dup del) rearrangements. A well-established mechanism of formation of inv dup del rearrangements involves a dicentric intermediate, which undergoes breakage during cell division, generating cells with either an inv dup del or a simple deletion. A patient with developmental delay and dysmorphic features was found to carry two cell lines with rearrangements of 9p: an inv dup del 9p and a terminal deletion 9p. Microarray and FISH analysis showed that these cell lines do not constitute the reciprocal products of a single dicentric breakage event. We propose that independent post-zygotic breaks of a dicentric chromosome as a likely mechanism leading to the generation of the observed cell lines. The post-zygotic origin of the inv dup del rearrangements and the associated mosaicism can be a more frequent phenomenon than currently appreciated. Therefore, genotype-phenotype correlations in the inv dup del rearrangements need to take into account the possible presence of other abnormal cell lines during early development.
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Resta N, De Cosmo L, Susca FC, Capodiferro D, Nardone AM, Pastorivo D, Bertoli M, Serlenga C, Burattini M, Schettini F, Laforgia N. De novo unbalanced translocation leading to monosomy 9p24.3p24.1 and trisomy 19q13.42q13.43 characterized by microarray-based comparative genomic hybridization in a child with partial cortical dysplasia and craniofacial dysmorphisms without trigonocephaly. Am J Med Genet A 2013; 161A:632-6. [PMID: 23401394 DOI: 10.1002/ajmg.a.35777] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 10/18/2012] [Indexed: 11/08/2022]
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Filges I, Kang A, Klug V, Wenzel F, Heinimann K, Tercanli S, Miny P. Array comparative genomic hybridization in prenatal diagnosis of first trimester pregnancies at high risk for chromosomal anomalies. Mol Cytogenet 2012; 5:38. [PMID: 22979998 PMCID: PMC3462716 DOI: 10.1186/1755-8166-5-38] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 07/30/2012] [Indexed: 01/14/2023] Open
Abstract
Objective To describe the diagnostic performance of array comparative genomic hybridization (aCGH) as a potential first line diagnostic method in first trimester high risk pregnancies. Method In a retrospective study we performed aCGH using a targeted array BAC platform (Constitutional Chip® 4.0, PerkinElmer, Turku Finland, median resolution 600 kB) and the Affymetrix Cytogenetics® Whole Genome 2.7 M array (at a resolution of 400kB) on 100 anonymized prenatal samples from first trimester high risk pregnancies with normal conventional karyotype. We studied the technical feasibility and turn-around-time as well as the detection rate of pathogenic submicroscopic chromosome anomalies and CNVs of unknown significance. Results We obtained results in 98 of 100 samples in 3 to a maximum of 5 days after DNA extraction. At the given resolution we did not identify any additional pathogenic CNVs but two CNVs of unknown significance in the chromosomal regions 1q21.1q21.2 (deletion) and 5p15.33 (duplication) (2%). Conclusion In accordance with a growing number of reports this study supports the concept that aCGH at a resolution of 400-600kB may be used as a first line prenatal diagnostic test with high diagnostic safety and rapid turn-around time in high-risk first trimester pregnancies. Detection rate of CNVs of unknown significance, considered as a major hindrance for replacing conventional karyotyping by aCGH, is 2%, but the diagnosis of additional submicroscopic anomalies in this heterogeneous group of patients seems to be rare.
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Affiliation(s)
- Isabel Filges
- Dr, med, Isabel Filges, Division of Medical Genetics, University Children's Hospital and Department of Biomedicine, University of Basel, Burgfelderstrasse 101, Building J, CH-4055, Basel, Switzerland.
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Kowalczyk M, Tomaszewska A, Podbioł-Palenta A, Constantinou M, Wawrzkiewicz-Witkowska A, Kowalski J, Kałużewski B, Zajączek S, Srebniak MI. Another rare case of a child with de novo terminal 9p deletion and co-existing interstitial 9p duplication: clinical findings and molecular cytogenetic study by array-CGH. Cytogenet Genome Res 2012; 139:9-16. [PMID: 22965227 DOI: 10.1159/000342165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2012] [Indexed: 11/19/2022] Open
Abstract
Trisomy 9p is the fourth most common chromosome abnormality found in liveborns. We report on a rare case of partial trisomy 9p complicated by partial monosomy 9p. Clinical manifestation included craniofacial abnormalities typical for trisomy 9p syndrome, developmental delay, mental retardation and brain anomaly in the form of Dandy-Walker malformation. The cytogenetic abnormality was investigated with FISH and array-CGH to characterize the breakpoints of the complex rearrangement. The patient's karyotype was 46,XX,der(9)del(9)(p24)dup(9)(p21p24)dn.arr 9p24.3p24.2 (1-2,414,485)×1,9p24.2p21.3(2,414,485-24,101,280)×3. The cytogenetic rearrangement led to a 2.4-Mb deletion of 9p24.2pter and a 21.6-Mb duplication of 9p24.2p21.3. The clinical and cytogenetic findings in our and other similar patients are compared.
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Affiliation(s)
- M Kowalczyk
- Department of Medical Genetics, Medical University of Silesia, Sosnowiec, Poland.
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40
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Onesimo R, Orteschi D, Scalzone M, Rossodivita A, Nanni L, Zannoni GF, Marrocco G, Battaglia D, Fundarò C, Neri G. Chromosome 9p deletion syndrome and sex reversal: novel findings and redefinition of the critically deleted regions. Am J Med Genet A 2012; 158A:2266-71. [PMID: 22821627 DOI: 10.1002/ajmg.a.35489] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 04/21/2012] [Indexed: 01/29/2023]
Abstract
Deletions of the short arm of chromosome 9 are associated with two distinct clinical entities. Small telomeric 9p24.3 deletions cause genital anomalies in male subjects, ranging from disorder of gonadal sex to genital differentiation anomalies, while large terminal or interstitial deletions result in 9p-malformation syndrome phenotype. The critical region for non-syndromic 46,XY sex reversal was assigned to a 1 Mb interval of chromosome 9p, extending from the telomere to the DMRT genes cluster. The 9p-syndrome was assigned to bands 9p22.3p24.1, but a phenotypic map has not been established for this condition, probably because of the lack of detailed molecular and/or phenotypic characterization, as well as frequent involvement of additional chromosome rearrangements. Here, we describe a unique patient with a small isolated 9p terminal deletion, characterized by array-CGH and FISH, who shows a complex phenotype with multiple physical anomalies, resembling the 9p-syndrome, disorder of sex development with gonadoblastoma, congenital heart defect and epilepsy. The observed deletion includes the 46,XY sex-reversal critical region, excluding the region so far associated with the 9p-syndrome. Genotype-phenotype correlations are tentatively established comparing our patient to seven other previously reported males with isolated terminal 9p deletions, finely defined at a molecular level. Our observations expand the 9p deletion clinical spectrum, and add significantly to the definition of a 9p-syndrome critical region.
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Affiliation(s)
- Roberta Onesimo
- Department of Pediatrics, Catholic University School of Medicine, and Department Pediatric Surgery, San Camillo De Lellis Hospital, Rome, Italy
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Di Bartolo DL, El Naggar M, Owen R, Sahoo T, Gilbert F, Pulijaal VR, Mathew S. Characterization of a complex rearrangement involving duplication and deletion of 9p in an infant with craniofacial dysmorphism and cardiac anomalies. Mol Cytogenet 2012; 5:31. [PMID: 22768875 PMCID: PMC3419606 DOI: 10.1186/1755-8166-5-31] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 07/09/2012] [Indexed: 11/10/2022] Open
Abstract
Partial duplication and partial deletion of the short arm of chromosome 9 have each been reported in the literature as clinically recognizable syndromes. We present clinical, cytogenetic, and molecular findings on a five-week-old female infant with concomitant duplication and terminal deletion of the short arm of chromosome 9. To our knowledge ten such cases have previously been reported. Conventional cytogenetic analysis identified additional material on chromosome 9 at band p23. FISH analysis aided in determining the additional material consisted of an inverted duplication with a terminal deletion of the short arm. Microarray analysis confirmed this interpretation and further characterized the abnormality as a duplication of about 32.7 Mb, from 9p23 to 9p11.2, and a terminal deletion of about 11.5 Mb, from 9p24.3 to 9p23. The infant displayed characteristic features of Duplication 9p Syndrome (hypotonia, bulbous nose, single transverse palmar crease, cranial anomalies), as well as features associated with Deletion 9p Syndrome (flat nasal bridge, long philtrum, cardiac anomalies) despite the deletion being distal to the reported critical region for this syndrome. This case suggests that there are genes or regulatory elements that lie outside of the reported critical region responsible for certain phenotypic features associated with Deletion 9p Syndrome. It also underscores the importance of utilizing array technology to precisely define abnormalities involving the short arm of 9p in order to further refine genotype/phenotype associations and to identify additional cases of duplication/deletion.
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Affiliation(s)
- Daniel L Di Bartolo
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College/NewYork-Presbyterian Hospital, New York, NY, USA.
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Neira VA, Córdova-Fletes C, Grondin Y, Ramirez-Velazco A, Figuera LE, Ortíz-López R, Barbaro M. Complex 9p rearrangement in an XY patient with ambiguous genitalia and features of both 9p duplication and deletion. Am J Med Genet A 2012; 158A:1498-502. [DOI: 10.1002/ajmg.a.35344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 02/02/2012] [Indexed: 11/12/2022]
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Meloni VDFA, Piazzon FB, Soares MDFDF, Takeno SS, Christofolini DM, Kulikowski LD, Brunoni D, Melaragno MI. Cytogenomic characterization of an unexpected 17.6 Mb 9p deletion associated to a 14.8 Mb 20p duplication in a dysmorphic patient with multiple congenital anomalies presenting a normal G-banding karyotype. Gene 2012; 496:59-62. [PMID: 22285927 DOI: 10.1016/j.gene.2012.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 01/02/2012] [Accepted: 01/05/2012] [Indexed: 11/28/2022]
Abstract
We describe a female patient with developmental delay, dysmorphic features and multiple congenital anomalies who presented a normal G-banded karyotype at the 550-band resolution. Array and multiplex-ligation probe amplification (MLPA) techniques identified an unexpected large unbalanced genomic aberration: a 17.6Mb deletion of 9p associated to a 14.8 Mb duplication of 20p. The deleted 9p genes, especially CER1 and FREM1, seem to be more relevant to the phenotype than the duplicated 20p genes. This study also shows the relevance of using molecular techniques to make an accurate diagnosis in patients with dysmorphic features and multiple anomalies suggestive of chromosome aberration, even if on G-banding their karyotype appears to be normal. Fluorescence in situ hybridization (FISH) was necessary to identify a masked balanced translocation in the patient's mother, indicating the importance of associating cytogenetic and molecular techniques in clinical genetics, given the implications for patient management and genetic counseling.
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Freitas ÉL, Gribble SM, Simioni M, Vieira TP, Silva-Grecco RL, Balarin MAS, Prigmore E, Krepischi-Santos AC, Rosenberg C, Szuhai K, van Haeringen A, Carter NP, Gil-da-Silva-Lopes VL. Maternally inherited partial monosomy 9p (pter → p24.1) and partial trisomy 20p (pter → p12.1) characterized by microarray comparative genomic hybridization. Am J Med Genet A 2011; 155A:2754-61. [PMID: 21948691 PMCID: PMC3428835 DOI: 10.1002/ajmg.a.34168] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 05/22/2011] [Indexed: 11/09/2022]
Abstract
We report on a 17-year-old patient with midline defects, ocular hypertelorism, neuropsychomotor development delay, neonatal macrosomy, and dental anomalies. DNA copy number investigations using a Whole Genome TilePath array consisting, of 30K BAC/PAC clones showed a 6.36 Mb deletion in the 9p24.1-p24.3 region and a 14.83 Mb duplication in the 20p12.1-p13 region, which derived from a maternal balanced t(9;20)(p24.1;p12.1) as shown by FISH studies. Monosomy 9p is a well-delineated chromosomal syndrome with characteristic clinical features, while chromosome 20p duplication is a rare genetic condition. Only a handful of cases of monosomy 9/trisomy 20 have been previously described. In this report, we compare the phenotype of our patient with those already reported in the literature, and discuss the role of DMRT, DOCK8, FOXD4, VLDLR, RSPO4, AVP, RASSF2, PROKR2, BMP2, MKKS, and JAG1, all genes mapping to the deleted and duplicated regions.
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Affiliation(s)
- Érika L. Freitas
- Faculty of Medical Sciences, Department of Medical Genetics, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Bioscience Institute, University of São Paulo, São Paulo, Brazil
| | - Susan M. Gribble
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Milena Simioni
- Faculty of Medical Sciences, Department of Medical Genetics, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Társis P. Vieira
- Faculty of Medical Sciences, Department of Medical Genetics, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Roseane L. Silva-Grecco
- Department of Biological Science, Federal University of Triangulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Marly A. S. Balarin
- Department of Biological Science, Federal University of Triangulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Elena Prigmore
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ana C. Krepischi-Santos
- Department of Genetics and Evolutionary Biology, Bioscience Institute, University of São Paulo, São Paulo, Brazil
- A.C. Camargo Hospital, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Bioscience Institute, University of São Paulo, São Paulo, Brazil
| | - Karoly Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Nigel P. Carter
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Vera Lúcia Gil-da-Silva-Lopes
- Faculty of Medical Sciences, Department of Medical Genetics, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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Chen CP, Su YN, Chern SR, Hsu CY, Tsai FJ, Wu PC, Lee CC, Chen YT, Lee MS, Wang W. Inv dup del(9p): prenatal diagnosis and molecular cytogenetic characterization by fluorescence in situ hybridization and array comparative genomic hybridization. Taiwan J Obstet Gynecol 2011; 50:67-73. [PMID: 21482378 DOI: 10.1016/j.tjog.2011.01.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2010] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVE To present molecular cytogenetic characterization of prenatally detected inverted duplication and deletion of 9p, or inv dup del(9p). MATERIALS, METHODS, AND RESULTS A 35-year-old primigravid woman underwent amniocentesis at 16 weeks of gestation because of advanced maternal age. Amniocentesis revealed a derivative chromosome 9, or der(9) with additional material at the end of the short arm of one chromosome 9. Parental karyotypes were normal. Level II ultrasound showed ventriculomegaly and normal male external genitalia. Repeated amniocentesis was performed at 20 weeks of gestation. Array comparative genomic hybridization revealed a 0.70-Mb deletion at 9p24.3 and an 18.36-Mb duplication from 9p24.3 to 9p22.1. The distal 9p deletion encompassed the genes of DOCK8, ANKRD15, FOXD4, DMRT1, and DMRT3. Fluorescence in situ hybridization analysis using bacterial artificial chromosome clone probes specific for 9p confirmed that the der(9) was derived from the inv dup del(9p). The karyotype of the fetus was 46,XY,inv dup del(9)(:p22.1-->p24.3::p24.3-->qter)dn or 46,XY,der(9) del(9)(p24.3) inv dup(9)(p22.1p24.3)dn. Polymorphic DNA marker analysis determined a maternal origin of the inv dup del(9p). A 512-g male fetus was subsequently terminated at 22 weeks of gestation with facial dysmorphism. The fetus had normal male external genitalia without sex reversal. CONCLUSION Fluorescence in situ hybridization and array comparative genomic hybridization are useful to determine the nature of a prenatally detected aberrant chromosome derived from the inv dup del. Male fetuses with inv dup del(9p) and haploinsufficiency of DMRT1 and DMRT3 may present normal male external genitalia without sex reversal.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan.
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Luo Y, Hermetz KE, Jackson JM, Mulle JG, Dodd A, Tsuchiya KD, Ballif BC, Shaffer LG, Cody JD, Ledbetter DH, Martin CL, Rudd MK. Diverse mutational mechanisms cause pathogenic subtelomeric rearrangements. Hum Mol Genet 2011; 20:3769-78. [PMID: 21729882 DOI: 10.1093/hmg/ddr293] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chromosome rearrangements are a significant cause of intellectual disability and birth defects. Subtelomeric rearrangements, including deletions, duplications and translocations of chromosome ends, were first discovered over 40 years ago and are now recognized as being responsible for several genetic syndromes. Unlike the deletions and duplications that cause some genomic disorders, subtelomeric rearrangements do not typically have recurrent breakpoints and involve many different chromosome ends. To capture the molecular mechanisms responsible for this heterogeneous class of chromosome abnormality, we coupled high-resolution array CGH with breakpoint junction sequencing of a diverse collection of subtelomeric rearrangements. We analyzed 102 breakpoints corresponding to 78 rearrangements involving 28 chromosome ends. Sequencing 21 breakpoint junctions revealed signatures of non-homologous end-joining, non-allelic homologous recombination between interspersed repeats and DNA replication processes. Thus, subtelomeric rearrangements arise from diverse mutational mechanisms. In addition, we find hotspots of subtelomeric breakage at the end of chromosomes 9q and 22q; these sites may correspond to genomic regions that are particularly susceptible to double-strand breaks. Finally, fine-mapping the smallest subtelomeric rearrangements has narrowed the critical regions for some chromosomal disorders.
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Affiliation(s)
- Yue Luo
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
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Vásquez-Velásquez AI, García-Castillo HA, González-Mercado MG, Dávalos IP, Raca G, Xu X, Dwyer E, Rivera H. Duplication 5q and deletion 9p due to a t(5;9)(q34;p23) in 2 cousins with features of Hunter-McAlpine syndrome and hypothyroidism. Cytogenet Genome Res 2010; 132:233-8. [PMID: 21063078 DOI: 10.1159/000321647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2010] [Indexed: 11/19/2022] Open
Abstract
We report on 2 similarly affected cousins with a compound imbalance resulting from a familial t(5;9)(q34;p23) and entailing both an ∼17-Mb 5q terminal duplication and an ∼12-Mb 9p terminal deletion as determined by G-banding, subtelomere FISH, and aCGH. The proband's karyotype was 46,XX,der(9)t(5;9)(q34;p23)mat.ish der(9)t(5;9)(q34;p23)(9pter-,5qter+).arr 5q34q35(163,328,000-180,629,000)×3, 9p24p23(194,000-12,664,000)×1. Her cousin had the same unbalanced karyotype inherited from his father. The clinical phenotype mainly consists of a distinct craniofacial dysmorphism featuring microcephaly, flat facies, down slanting palpebral fissures, small flat nose, long philtrum, and small mouth with thin upper lip. Additional remarkable findings were craniosynostosis of several sutures, craniolacunia and preaxial polydactyly in the proband and hypothyroidism in both subjects. The observed clinical constellation generally fits the phenotypic spectrum of the 5q distal duplication syndrome (known also as Hunter-McAlpine syndrome), except for the thyroid insufficiency which can likely be ascribed to the concurrent 9p deletion, as at least 4 other 9pter monosomic patients without chromosome 5 involvement had this hormonal disorder. The present observation further confirms the etiology of the HMS phenotype from gain of the 5q35→qter region, expands the clinical pictures of partial trisomy 5q and monosomy 9p, and provides a comprehensive list of 160 patients with 5q distal duplication.
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Affiliation(s)
- A I Vásquez-Velásquez
- División de Genética, CIBO, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
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Kini U, Hurst JA, Byren JC, Wall SA, Johnson D, Wilkie AOM. Etiological heterogeneity and clinical characteristics of metopic synostosis: Evidence from a tertiary craniofacial unit. Am J Med Genet A 2010; 152A:1383-9. [PMID: 20503312 DOI: 10.1002/ajmg.a.33435] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Metopic synostosis (MS) accounts for approximately 10-15% of all craniosynostosis and is etiologically heterogeneous. This study aimed to examine the causes of MS, as observed in a tertiary craniofacial unit. We reviewed the case notes of 110 children with a diagnosis of MS, attending the craniofacial unit in Oxford between 1991 and 2008. Our results showed 38 children (38/110 or 34.6%) who had at least one additional structural abnormality or had a known syndromic diagnosis were classed as having syndromic MS. Chromosomal abnormalities were noted in 8/38 (21.4%) children: mosaic marker chromosome 2, 9p deletion (2/8), 11q deletion, 12pter deletion and duplication of 15q25 with other additional chromosomal abnormalities (3/8). Other syndromic diagnoses included Silver-Russell syndrome and Greig cephalopolysyndactyly. Prenatal exposure to sodium valproate (VPA) was noted in 8/110 children (7.8%), with the dose of the VPA being >or=1,000 mg/day in all cases. Other prenatal exposures reported in this study were: maternal diabetes (6/110), enoxaparin for hypercoagulable state (1/110), and thyroxine (1/110). The majority of patients (72/110 or 65.4%) had nonsyndromic MS. Speech delay was present in 11 children with nonsyndromic MS (11/72 or 15.3%) and 10 children with syndromic MS (10/38 or 26.3%). We conclude that approximately two-thirds of all MS is nonsyndromic. Prenatal exposure to VPA is a common cause of MS. Maternal diabetes, not previously linked to MS, was noted in 5.5% of cases. Chromosomal abnormalities account for about 6% of MS. An increased risk of speech delay is seen with both the syndromic and nonsyndromic forms.
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Affiliation(s)
- Usha Kini
- Department of Clinical Genetics, The Churchill Hospital, Oxford, UK.
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Heard PL, Carter EM, Crandall AC, Sebold C, Hale DE, Cody JD. High resolution genomic analysis of 18q- using oligo-microarray comparative genomic hybridization (aCGH). Am J Med Genet A 2009; 149A:1431-7. [PMID: 19533772 DOI: 10.1002/ajmg.a.32900] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The advent of oligonucleotide array comparative genomic hybridization (aCGH) has revolutionized diagnosis of chromosome abnormalities in the genetics clinic. This new technology also has valuable potential as a research tool to investigate larger genomic rearrangements that are typically diagnosed via routine karyotype. aCGH was used as a tool for the high-resolution analysis of chromosome content in individuals with known deletions of chromosome 18. The aim of this study was to clarify the precise location of the breakpoints as well as to determine the presence of occult translocations creating additional deletions and duplications. One hundred eighty-nine DNA samples from individuals with 18q deletions were analyzed. No breakpoint clusters were identified, as no more than two individuals had breakpoints within 2 kb of each other. Only two regions of 18q were never found to be haploid, suggesting the existence of haplolethal genes in those regions. Of the individuals with only a chromosome 18 abnormality, 17% (n = 29) had interstitial deletions. Six percent (n = 11) had a region of duplication immediately proximal to the deletion. Eight percent (n = 15) had more complex rearrangements with captured (non-18q) telomeres thus creating a trisomic region. The 15 captured telomeres originated from a limited number of other telomeres (4q, 10q, 17p, 18p, 20q, and Xq). These data were converted into a format for ease of viewing and analysis by creating custom tracks for the UCSC Genome Browser. Taken together, these findings confirm a higher level of variability and genomic complexity surrounding deletions of 18q than has previously been appreciated.
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Affiliation(s)
- Patricia L Heard
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
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Shimojima K, Yamamoto T. Investigation of the candidate region for trigonocephaly in a patient with monosomy 9p syndrome using array-CGH. Am J Med Genet A 2009; 149A:1076-80. [PMID: 19396833 DOI: 10.1002/ajmg.a.32783] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Keiko Shimojima
- International Research and Educational Institute for Integrated Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
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