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Goyal M, Faruq M, Gupta A, Shrivastava D, Shamim U. The Clinical Diagnostic Utility of Array CGH in Children with Syndromic Microcephaly. Ann Indian Acad Neurol 2022; 25:1067-1074. [PMID: 36911451 PMCID: PMC9996492 DOI: 10.4103/aian.aian_202_22] [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: 02/25/2022] [Revised: 05/06/2022] [Accepted: 06/20/2022] [Indexed: 11/18/2022] Open
Abstract
Background A prospective study using array CGH in children with Syndromic microcephaly from a tertiary pediatric healthcare centre in India. Aim To identify the copy number variations causative of microcephaly detected through chromosomal array CGH. Patients and Methods Of the 60 patients, 33 (55%) males and 27 (45%) females who consulted the Rare Disease Clinic at Department of Pediatrics, SMS Medical College, Jaipur, with developmental delay/facial dysmorphism/congenital anomalies in combination with microcephaly were included. Exclusion Criteria Children with acquired or non-genetic causes of microcephaly, craniosynostosis, metabolic diseases, known chromosomal aneuploidy such as trisomy 21, 13, and 18 and abnormal karyotype were excluded. The cohort was analyzed by array CGH in order to identify potentially pathogenic copy number variants (CNVs). Results Clinically relevant pathogenic or likely pathogenic copy number variations (CNVs) were identified in 20/60 (33.3%) patients, variant of uncertain significance (VOUS) in 4/60 (6.6%) cases and benign CNVs in 3/60 (5%) of total cases. Out of 20 cases with pathogenic CNVs, 12 (60%) patients detected with a deletion, five (25%) patients with duplication and three (15%) patients resulted with a complex chromosomal rearrangement. Twelve cases present CNVs containing genes known to be implicated in microcephaly etiology. Conclusion This research highlights the contribution of submicroscopic chromosomal changes in the etiology of microcephaly in combination with developmental delay/facial dysmorphism/congenital anomalies (syndromic microcephaly). Our studies provide more insights into the benefits derived by using array CGH analysis in patients with syndromic microcephaly.
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Affiliation(s)
- Manisha Goyal
- Department of Pediatrics, Centre of Rare Diseases, SMS Medical College, Jaipur, Rajasthan, India
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Ashok Gupta
- Department of Pediatrics, Centre of Rare Diseases, SMS Medical College, Jaipur, Rajasthan, India
| | - Divya Shrivastava
- School of Life Sciences, Jaipur National University, Jaipur, Rajasthan, India
| | - Uzma Shamim
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
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Al-Hamed MH, Kurdi W, Khan R, Tulbah M, AlNemer M, AlSahan N, AlMugbel M, Rafiullah R, Assoum M, Monies D, Shah Z, Rahbeeni Z, Derar N, Hakami F, Almutairi G, AlOtaibi A, Ali W, AlShammasi A, AlMubarak W, AlDawoud S, AlAmri S, Saeed B, Bukhari H, Ali M, Akili R, Alquayt L, Hagos S, Elbardisy H, Akilan A, Almuhana N, AlKhalifah A, Abouelhoda M, Ramzan K, Sayer JA, Imtiaz F. Prenatal exome sequencing and chromosomal microarray analysis in fetal structural anomalies in a highly consanguineous population reveals a propensity of ciliopathy genes causing multisystem phenotypes. Hum Genet 2021; 141:101-126. [PMID: 34853893 DOI: 10.1007/s00439-021-02406-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/26/2021] [Indexed: 12/25/2022]
Abstract
Fetal abnormalities are detected in 3% of all pregnancies and are responsible for approximately 20% of all perinatal deaths. Chromosomal microarray analysis (CMA) and exome sequencing (ES) are widely used in prenatal settings for molecular genetic diagnostics with variable diagnostic yields. In this study, we aimed to determine the diagnostic yield of trio-ES in detecting the cause of fetal abnormalities within a highly consanguineous population. In families with a history of congenital anomalies, a total of 119 fetuses with structural anomalies were recruited and DNA from invasive samples were used together with parental DNA samples for trio-ES and CMA. Data were analysed to determine possible underlying genetic disorders associated with observed fetal phenotypes. The cohort had a known consanguinity of 81%. Trio-ES led to diagnostic molecular genetic findings in 59 fetuses (with pathogenic/likely pathogenic variants) most with multisystem or renal abnormalities. CMA detected chromosomal abnormalities compatible with the fetal phenotype in another 7 cases. Monogenic ciliopathy disorders with an autosomal recessive inheritance were the predominant cause of multisystem fetal anomalies (24/59 cases, 40.7%) with loss of function variants representing the vast majority of molecular genetic abnormalities. Heterozygous de novo pathogenic variants were found in four fetuses. A total of 23 novel variants predicted to be associated with the phenotype were detected. Prenatal trio-ES and CMA detected likely causative molecular genetic defects in a total of 55% of families with fetal anomalies confirming the diagnostic utility of trio-ES and CMA as first-line genetic test in the prenatal diagnosis of multisystem fetal anomalies including ciliopathy syndromes.
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Affiliation(s)
- Mohamed H Al-Hamed
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia.
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia.
| | - Wesam Kurdi
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Rubina Khan
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Maha Tulbah
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Maha AlNemer
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Nada AlSahan
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Maisoon AlMugbel
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Rafiullah Rafiullah
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Mirna Assoum
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Dorota Monies
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Zeeshan Shah
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Zuhair Rahbeeni
- Medical Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Nada Derar
- Medical Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Fahad Hakami
- King Abdulaziz Medical City/King Saud bin Abdulaziz University for Health Science, Jeddah, Saudi Arabia
| | - Gawaher Almutairi
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Afaf AlOtaibi
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Wafaa Ali
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Amal AlShammasi
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Wardah AlMubarak
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Samia AlDawoud
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Saja AlAmri
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Bashayer Saeed
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Hanifa Bukhari
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Mohannad Ali
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Rana Akili
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Laila Alquayt
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Samia Hagos
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Hadeel Elbardisy
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Asma Akilan
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Nora Almuhana
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Abrar AlKhalifah
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Mohamed Abouelhoda
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Khushnooda Ramzan
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - John A Sayer
- Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
- Renal Services, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle University, Tyne and Wear, Newcastle upon Tyne, NE4 5PL, UK
| | - Faiqa Imtiaz
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia.
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia.
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Tritto G, Ricca I, Turi M, Gemma A, Muratori F, Scarano G, Lonardo F. Clinical Characterization of a 6-Year-Old Patient with Autism and Two Adjacent Duplications on 10q11.22q11.23. A Case Report. CHILDREN-BASEL 2021; 8:children8060518. [PMID: 34207052 PMCID: PMC8235778 DOI: 10.3390/children8060518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 11/21/2022]
Abstract
Autism is a neurodevelopmental disorder presenting in the first 3 years of life. Deficits occur in the core areas of social communication and interaction and restricted, repetitive patterns of behavior, interests or activities. The causes of autism are unknown, but clinical genetic studies show strong evidence in favor of the involvement of genetic factors in etiology. Molecular genetic studies report some associations with candidate genes, and candidate regions have emerged from several genome-wide linkage studies. Here, we report a clinical case of autism in a 6-year-old boy with double duplication on 10q11.22q11.23 with ASD (Autism Spectrum Disorder), intellectual disability, developmental delay, hypotonia, gross-motor skills deficit, overgrowth and mild dysmorphic features. In the literature, only five cases of ASD with 10q11.21q11.23 duplication are reported. This is the first extensive clinical description of an ASD subject with 10q11.22q11.23 duplication. Our findings suggest that 10q11.21q11.23 microduplication could represent a copy number variant that predisposes to autism.
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Affiliation(s)
- Giovanna Tritto
- Fondazione Stella Maris Mediterraneo, 85100 Potenza, Italy; (G.T.); (A.G.)
| | - Ivana Ricca
- Department of Developmental Neurocience, IRCCS Fondazione Stella Maris, 56128 Pisa, Italy; (I.R.); (F.M.)
| | - Marco Turi
- Fondazione Stella Maris Mediterraneo, 85100 Potenza, Italy; (G.T.); (A.G.)
- Correspondence:
| | - Andrea Gemma
- Fondazione Stella Maris Mediterraneo, 85100 Potenza, Italy; (G.T.); (A.G.)
| | - Filippo Muratori
- Department of Developmental Neurocience, IRCCS Fondazione Stella Maris, 56128 Pisa, Italy; (I.R.); (F.M.)
| | - Gioacchino Scarano
- Medical Genetics Unit, A.O.R.N. San Pio, 82100 Benevento, Italy; (G.S.); (F.L.)
| | - Fortunato Lonardo
- Medical Genetics Unit, A.O.R.N. San Pio, 82100 Benevento, Italy; (G.S.); (F.L.)
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4
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Whitman MC, Di Gioia SA, Chan WM, Gelber A, Pratt BM, Bell JL, Collins TE, Knowles JA, Armoskus C, Pato M, Pato C, Shaaban S, Staffieri S, MacKinnon S, Maconachie GDE, Elder JE, Traboulsi EI, Gottlob I, Mackey DA, Hunter DG, Engle EC. Recurrent Rare Copy Number Variants Increase Risk for Esotropia. Invest Ophthalmol Vis Sci 2021; 61:22. [PMID: 32780866 PMCID: PMC7443120 DOI: 10.1167/iovs.61.10.22] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To determine whether rare copy number variants (CNVs) increase risk for comitant esotropia. Methods CNVs were identified in 1614 Caucasian individuals with comitant esotropia and 3922 Caucasian controls from Illumina SNP genotyping using two Hidden Markov model (HMM) algorithms, PennCNV and QuantiSNP, which call CNVs based on logR ratio and B allele frequency. Deletions and duplications greater than 10 kb were included. Common CNVs were excluded. Association testing was performed with 1 million permutations in PLINK. Significant CNVs were confirmed with digital droplet polymerase chain reaction (ddPCR). Whole genome sequencing was performed to determine insertion location and breakpoints. Results Esotropia patients have similar rates and proportions of CNVs compared with controls but greater total length and average size of both deletions and duplications. Three recurrent rare duplications significantly (P = 1 × 10−6) increase the risk of esotropia: chromosome 2p11.2 (hg19, 2:87428677-87965359), spanning one long noncoding RNA (lncRNA) and two microRNAs (OR 14.16; 95% confidence interval [CI] 5.4–38.1); chromosome 4p15.2 (hg19, 4:25554332-25577184), spanning one lncRNA (OR 11.1; 95% CI 4.6–25.2); chromosome 10q11.22 (hg19, 10:47049547-47703870) spanning seven protein-coding genes, one lncRNA, and four pseudogenes (OR 8.96; 95% CI 5.4–14.9). Overall, 114 cases (7%) and only 28 controls (0.7%) had one of the three rare duplications. No case nor control had more than one of these three duplications. Conclusions Rare CNVs are a source of genetic variation that contribute to the genetic risk for comitant esotropia, which is likely polygenic. Future research into the functional consequences of these recurrent duplications may shed light on the pathophysiology of esotropia.
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Affiliation(s)
- Mary C Whitman
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Silvio Alessandro Di Gioia
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Wai-Man Chan
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Alon Gelber
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Brandon M Pratt
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Jessica L Bell
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Thomas E Collins
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - James A Knowles
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York, United States
| | - Christopher Armoskus
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York, United States
| | - Michele Pato
- Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, New York, United States
| | - Carlos Pato
- Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, New York, United States
| | - Sherin Shaaban
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States.,Present address: Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Sandra Staffieri
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Sarah MacKinnon
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - Gail D E Maconachie
- Department of Neuroscience, Psychology and Behavior, The University of Leicester Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - James E Elder
- Department of Ophthalmology, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia.,Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Elias I Traboulsi
- Department of Pediatric Ophthalmology and Strabismus, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, United States
| | - Irene Gottlob
- Department of Neuroscience, Psychology and Behavior, The University of Leicester Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia.,Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia.,Centre for Eye Research Australia, University of Melbourne, Melbourne, Australia
| | - David G Hunter
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - Elizabeth C Engle
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, United States.,Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
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