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Chen Y, Karaca E, Robin NH, Goodloe D, Al-Beshri A, Dean SJ, Hurst ACE, Carroll AJ, Mikhail FM. DLG2 intragenic exonic deletions reinforce the link to neurodevelopmental disorders and suggest a potential association with congenital anomalies and dysmorphism. Genet Med 2024; 26:101010. [PMID: 37860969 DOI: 10.1016/j.gim.2023.101010] [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: 05/10/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023] Open
Abstract
PURPOSE Multiple studies suggest an association between DLG2 and neurodevelopmental disorders and indicate the haploinsufficiency of this gene; however, few cases have been thoroughly described. We performed additional studies to confirm this clinical association and DLG2 haploinsufficiency. METHODS Chromosomal microarray analysis was performed on 11,107 patients at the Cytogenetics Laboratory at the University of Alabama at Birmingham. The Database of Genomic Variants-Gold Standard Variants and the Genome Aggregation Database were selected for the association analysis. Fifty-nine patients from the literature and DECIPHER, all having DLG2 intragenic deletions, were included for comprehensive analysis of the distribution of these deletions. RESULTS A total of 13 patients with DLG2 intragenic deletions, from 10 families in our cohort, were identified. Nine of 10 probands presented with clinical features of neurodevelopmental disorders. Congenital anomalies and dysmorphism were common in our cohort of patients. Association analysis showed that the frequency of DLG2 deletions in our cohort is significantly higher than those in the Database of Genomic Variants-Gold Standard Variants and the Genome Aggregation Database. Most of DLG2 intragenic deletions identified in 69 unrelated patients from our cohort, the literature, and DECIPHER map to the 5' region of the gene, with a hotspot centered around HPin7, exon 8, and HPin8. CONCLUSION Our findings reinforce the link between DLG2 intragenic deletions and neurodevelopmental disorders, strongly support the haploinsufficiency of this gene, and indicate that these deletions might also have an association with congenital anomalies and dysmorphism.
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Affiliation(s)
- Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Ender Karaca
- Department of Pathology, Baylor University Medical Center, Dallas, TX; Texas A&M School of Medicine, Dallas, TX
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Dana Goodloe
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Ali Al-Beshri
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - S Joy Dean
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL.
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2
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Zhou R, Jiao J, Wang Y, Meng L, Li Y, Xu Y, Hu P, Xu Z. Systematic analysis of copy number variants of uncertain significance partially overlapping with the haploinsufficient or triplosensitive genes in clinical testing. Ann Med 2023; 55:2276824. [PMID: 37917952 PMCID: PMC10623895 DOI: 10.1080/07853890.2023.2276824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023] Open
Abstract
Background: Copy number variants of uncertain significance (VUS) has brought much distress for patients and great counselling challenges for clinicians. Of these, a special type of VUS (HT-VUS), harbouring one or both breakpoints within the established haploinsufficient or triplosensitive genes, were considered to be more likely to cause clinical effects compared with other types of VUS.Methods: We retrospectively evaluated the properties and clinical significance of those HT-VUS samples in clinical testing for chromosome microarray analysis (CMA).Results: A total of 7150 samples were selected for HT-VUS screening, and 75 (1.05%) subjects with 75 HT-VUS were found. The majority of these HT-VUS were heterozygous duplications and chromosome X had the most HT-VUS. The prevalence of HT-VUS was 0.90% (28/3116) for prenatal low-risk samples, 1.18% (26/2196) for prenatal high-risk samples, 1.37% (10/728) for postnatal samples and 0.99% (11/1110) for early pregnancy loss samples. However, the incidence of HT-VUS was not statistically different between different groups.Conclusions: HT-VUS (deletions or duplications) involving introns and HT-VUS (duplications) including terminal coding exons (either the first or last exons) might be clinically neutral. Our study will be helpful for both interpretation and genetic counselling in the future.
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Affiliation(s)
- Ran Zhou
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Jiao Jiao
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yan Wang
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Lulu Meng
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yiming Li
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yiyun Xu
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ping Hu
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
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Kubota N, Takeda R, Kobayashi J, Hidaka E, Nishi E, Takano K, Wakui K. Reanalysis of Chromosomal Microarray Data Using a Smaller Copy Number Variant Call Threshold Identifies Four Cases with Heterozygous Multiexon Deletions of ARID1B, EHMT1, and FOXP1 Genes. Mol Syndromol 2023; 14:394-404. [PMID: 37901861 PMCID: PMC10601822 DOI: 10.1159/000530252] [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: 10/22/2022] [Accepted: 03/16/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction Chromosomal microarray (CMA) is a highly accurate and established method for detecting copy number variations (CNVs) in clinical genetic testing. CNVs are important etiological factors for disorders such as intellectual disability, developmental delay, and multiple congenital anomalies. Recently developed analytical methods have facilitated the identification of smaller CNVs. Therefore, reanalyzing CMA data using a smaller CNV calling threshold may yield useful information. However, this method was left to the discretion of each institution. Methods We reanalyzed the CMA data of 131 patients using a smaller CNV call threshold: 50 kb 50 probes for gain and 25 kb 25 probes for loss. We interpreted the reanalyzed CNVs based on the most recently available information. In the reanalysis, we filtered the data using the Clinical Genome Resource dosage sensitivity gene list as an index to quickly and efficiently check morbid genes. Results The number of copy number loss was approximately 20 times greater, and copy number gain was approximately three times greater compared to those in the previous analysis. We detected new likely pathogenic CNVs in four participants: a 236.5 kb loss within ARID1B, a 50.6 kb loss including EHMT1, a 46.5 kb loss including EHMT1, and an 89.1 kb loss within the FOXP1 gene. Conclusion The method employed in this study is simple and effective for CMA data reanalysis using a smaller CNV call threshold. Thus, this method is efficient for both ongoing and repeated analyses. This study may stimulate further discussion of reanalysis methodology in clinical laboratories.
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Affiliation(s)
- Noriko Kubota
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Ryojun Takeda
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
- Division of Medical Genetics, Nagano Children’s Hospital, Azumino, Japan
| | - Jun Kobayashi
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Eiko Hidaka
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Eriko Nishi
- Division of Medical Genetics, Nagano Children’s Hospital, Azumino, Japan
| | - Kyoko Takano
- Division of Medical Genetics, Nagano Children’s Hospital, Azumino, Japan
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
| | - Keiko Wakui
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
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4
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Salah S, Jaber H, Frumkin A, Harel T. Homozygous 22q11.2 distal type II microdeletion is associated with syndromic neurodevelopmental delay. Am J Med Genet A 2023; 191:2623-2630. [PMID: 37365930 DOI: 10.1002/ajmg.a.63326] [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: 12/04/2022] [Revised: 05/19/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023]
Abstract
Genomic disorders result from heterozygous copy number variants (CNVs). Homozygous deletions spanning numerous genes are rare, despite the potential contribution of consanguinity to such instances. CNVs in the 22q11.2 region are mediated by nonallelic homologous recombination between pairs of low copy repeats (LCRs), from amongst eight LCRs designated A-H. Heterozygous distal type II deletions (LCR-E to LCR-F) have incomplete penetrance and variable expressivity, and can lead to neurodevelopmental issues, minor craniofacial anomalies, and congenital abnormalities. We report siblings with global developmental delay, hypotonia, minor craniofacial anomalies, ocular abnormalities, and minor skeletal issues, in whom chromosomal microarray identified a homozygous distal type II deletion. The deletion was brought to homozygosity as a result of a consanguineous marriage between two heterozygous carriers of the deletion. The phenotype of the children was strikingly more severe and complex than that of the parents. This report suggests that the distal type II deletion harbors a dosage-sensitive gene or regulatory element, which leads to a more severe phenotype when deleted on both chromosomes.
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Affiliation(s)
- Somaya Salah
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Hiba Jaber
- Pediatric Neurology Unit, Hadassah Medical Center, Jerusalem, Israel
| | - Ayala Frumkin
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Israel
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5
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Wen S, Wang M, Qian X, Li Y, Wang K, Choi J, Pennesi ME, Yang P, Marra M, Koenekoop RK, Lopez I, Matynia A, Gorin M, Sui R, Yao F, Goetz K, Porto FBO, Chen R. Systematic assessment of the contribution of structural variants to inherited retinal diseases. Hum Mol Genet 2023; 32:2005-2015. [PMID: 36811936 PMCID: PMC10244226 DOI: 10.1093/hmg/ddad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/03/2023] [Accepted: 02/11/2023] [Indexed: 02/24/2023] Open
Abstract
Despite increasing success in determining genetic diagnosis for patients with inherited retinal diseases (IRDs), mutations in about 30% of the IRD cases remain unclear or unsettled after targeted gene panel or whole exome sequencing. In this study, we aimed to investigate the contributions of structural variants (SVs) to settling the molecular diagnosis of IRD with whole-genome sequencing (WGS). A cohort of 755 IRD patients whose pathogenic mutations remain undefined were subjected to WGS. Four SV calling algorithms including include MANTA, DELLY, LUMPY and CNVnator were used to detect SVs throughout the genome. All SVs identified by any one of these four algorithms were included for further analysis. AnnotSV was used to annotate these SVs. SVs that overlap with known IRD-associated genes were examined with sequencing coverage, junction reads and discordant read pairs. Polymerase Chain Reaction (PCR) followed by Sanger sequencing was used to further confirm the SVs and identify the breakpoints. Segregation of the candidate pathogenic alleles with the disease was performed when possible. A total of 16 candidate pathogenic SVs were identified in 16 families, including deletions and inversions, representing 2.1% of patients with previously unsolved IRDs. Autosomal dominant, autosomal recessive and X-linked inheritance of disease-causing SVs were observed in 12 different genes. Among these, SVs in CLN3, EYS and PRPF31 were found in multiple families. Our study suggests that the contribution of SVs detected by short-read WGS is about 0.25% of our IRD patient cohort and is significantly lower than that of single nucleotide changes and small insertions and deletions.
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Affiliation(s)
- Shu Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xinye Qian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Keqing Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jongsu Choi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Molly Marra
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, Montreal, Quebec, H4A 3S5, Canada
| | - Irma Lopez
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, Montreal, Quebec, H4A 3S5, Canada
| | - Anna Matynia
- Jules Stein Eye Institute, Los Angeles, CA 90095, USA
- Ophthalmology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Michael Gorin
- Jules Stein Eye Institute, Los Angeles, CA 90095, USA
- Ophthalmology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Fengxia Yao
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Kerry Goetz
- Office of the Director, National Eye Institute/National Institutes of Health, Bethesda, MD 20892, USA
| | - Fernanda Belga Ottoni Porto
- INRET Clínica e Centro de Pesquisa, Belo Horizonte, Minas Gerais, 30150270, Brazil
- Department of Ophthalmology, Santa Casa de Misericórdia de Belo Horizonte, Belo Horizonte, Minas Gerais, 30150221, Brazil
- Centro Oftalmológico de Minas Gerais, Belo Horizonte, Minas Gerais, 30180070, Brazil
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
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6
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Wen S, Wang M, Qian X, Li Y, Wang K, Choi J, Pennesi ME, Yang P, Marra M, Koenekoop RK, Lopez I, Matynia A, Gorin M, Sui R, Yao F, Goetz K, Porto FBO, Chen R. Systematic assessment of the contribution of structural variants to inherited retinal diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.02.522522. [PMID: 36789417 PMCID: PMC9928032 DOI: 10.1101/2023.01.02.522522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Despite increasing success in determining genetic diagnosis for patients with inherited retinal diseases (IRDs), mutations in about 30% of the IRD cases remain unclear or unsettled after targeted gene panel or whole exome sequencing. In this study, we aimed to investigate the contributions of structural variants (SVs) to settling the molecular diagnosis of IRD with whole-genome sequencing (WGS). A cohort of 755 IRD patients whose pathogenic mutations remain undefined was subjected to WGS. Four SV calling algorithms including include MANTA, DELLY, LUMPY, and CNVnator were used to detect SVs throughout the genome. All SVs identified by any one of these four algorithms were included for further analysis. AnnotSV was used to annotate these SVs. SVs that overlap with known IRD-associated genes were examined with sequencing coverage, junction reads, and discordant read pairs. PCR followed by Sanger sequencing was used to further confirm the SVs and identify the breakpoints. Segregation of the candidate pathogenic alleles with the disease was performed when possible. In total, sixteen candidate pathogenic SVs were identified in sixteen families, including deletions and inversions, representing 2.1% of patients with previously unsolved IRDs. Autosomal dominant, autosomal recessive, and X-linked inheritance of disease-causing SVs were observed in 12 different genes. Among these, SVs in CLN3, EYS, PRPF31 were found in multiple families. Our study suggests that the contribution of SVs detected by short-read WGS is about 0.25% of our IRD patient cohort and is significantly lower than that of single nucleotide changes and small insertions and deletions.
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7
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Phenotypic Spectrum of NFIA Haploinsufficiency: Two Additional Cases and Review of the Literature. Genes (Basel) 2022; 13:genes13122249. [PMID: 36553517 PMCID: PMC9777632 DOI: 10.3390/genes13122249] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/21/2022] [Accepted: 11/26/2022] [Indexed: 12/02/2022] Open
Abstract
The NFIA (nuclear factor I/A) gene encodes for a transcription factor belonging to the nuclear factor I family and has key roles in various embryonic differentiation pathways. In humans, NFIA is the major contributor to the phenotypic traits of "Chromosome 1p32p31 deletion syndrome". We report on two new cases with deletions involving NFIA without any other pathogenic protein-coding gene alterations. A cohort of 24 patients with NFIA haploinsufficiency as the sole anomaly was selected by reviewing the literature and public databases in order to analyze all clinical features reported and their relative frequencies. This process was useful because it provided an overall picture of the phenotypic outcome of NFIA haploinsufficiency and helped to define a cluster of phenotypic traits that can facilitate clinicians in identifying affected patients. NFIA haploinsufficiency can be suspected by a careful observation of the dysmorphisms (macrocephaly, craniofacial, and first-finger anomalies), and this potential diagnosis is strengthened by the presence of intellectual and developmental disabilities or other neurodevelopmental disorders. Further clues of NFIA haploinsufficiency can be provided by instrumental tests such as MRI and kidney urinary tract ultrasound and confirmed by genetic testing.
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8
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Colijn MA, Hrynchak M, Hrazdil CT, Willaeys V, White RF, Stowe RM. A 1p31.3 deletion encompassing the nuclear factor 1A gene presenting as possible temporal lobe epilepsy in association with schizoaffective disorder. Neurocase 2022; 28:382-387. [PMID: 36209511 DOI: 10.1080/13554794.2022.2132869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Abstract
Chromosome 1p32-p31 deletion syndrome, which is characterized by a variety of neurodevelopmental abnormalities, is thought to occur as a result of nuclear factor 1A (NFIA) haploinsufficiency. We present a case of a right-handed 40-year-old female with a 1p31.3 deletion, who exhibited numerous common features of this syndrome, in addition to treatment resistant schizoaffective disorder and possible temporal lobe epilepsy, making her presentation unique. While neither psychosis nor temporal lobe epilepsy has been described in this syndrome previously, these conditions likely occurred in our patient as a result of NFIA haploinsufficiency.
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Affiliation(s)
- Mark A Colijn
- Department of Psychiatry, The University of Calgary, Calgary, AB, Canada
| | - Monica Hrynchak
- Molecular Cytogenetic Laboratory, Royal Columbian Hospital, The University of British Columbia, New Westminster, BC, Canada
| | - Chantelle T Hrazdil
- Division of Neurology, Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Veerle Willaeys
- BC Psychosis Program, British Columbia Mental Health & Substance Use Services, Vancouver, BC, Canada
| | - Randall F White
- BC Psychosis Program, British Columbia Mental Health & Substance Use Services, Vancouver, BC, Canada.,Department of Psychiatry, The University of British Columbia, Vancouver, BC, Canada
| | - Robert M Stowe
- BC Neuropsychiatry Program, Departments of Psychiatry and Neurology (Medicine), and Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, BC, Canada
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9
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Ogura Y, Uehara T, Ujibe K, Yoshihashi H, Yamada M, Suzuki H, Takenouchi T, Kosaki K, Hirata H. The p.Thr395Met missense variant of NFIA found in a patient with intellectual disability is a defective variant. Am J Med Genet A 2022; 188:1184-1192. [PMID: 35018717 DOI: 10.1002/ajmg.a.62638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/05/2021] [Accepted: 12/11/2021] [Indexed: 12/17/2022]
Abstract
Nuclear factor one A (NFIA) is a transcription factor that regulates the development of the central nervous system. Haploinsufficiency of the NFIA gene causes NFIA-related disorder, which includes brain abnormalities and intellectual disability, with or without urinary tract defects. Intragenic deletions, nonsense variants, frameshift variants, and missense variants in one allele of the NFIA gene have been reported to cause various neurological and urogenital symptoms. Here we report a 10-year-old male patient with developmental delay, coarctation of the aorta, and distinctive facial features. Exome analysis identified a rare de novo heterozygous missense variant p.Thr395Met in NFIA. We employed zebrafish as a model organism in our NFIA analysis and found that nfia-/- zebrafish initially showed a loss of commissural axons in the brain, and eventually underwent growth retardation resulting in premature death. Impairment of the commissural neurons in nfia-/- zebrafish embryos could be restored by the expression of wild-type human NFIA protein, but not of mutant human protein harboring the p.Thr395Met substitution, indicating that this variant affects the function of NFIA protein. Taken together, we suggest that the p.Thr395Met allele in the NFIA gene is relevant to the pathogenesis of NFIA-related disorder.
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Affiliation(s)
- Yurie Ogura
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.,Department of Clinical Genetics, Aichi Developmental Disability Center Central Hospital, Aichi, Japan
| | - Kota Ujibe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
| | - Hiroshi Yoshihashi
- Department of Clinical Genetics, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hiromi Hirata
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
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10
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Increased Diagnostic Yield of Array Comparative Genomic Hybridization for Autism Spectrum Disorder in One Institution in Taiwan. Medicina (B Aires) 2021; 58:medicina58010015. [PMID: 35056323 PMCID: PMC8779646 DOI: 10.3390/medicina58010015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/31/2022] Open
Abstract
Background and Objectives: Chromosomal microarray offers superior sensitivity for identification of submicroscopic copy number variants (CNVs) and is recommended for the initial genetic testing of patients with autism spectrum disorder (ASD). This study aims to determine the diagnostic yield of array comparative genomic hybridization (array-CGH) in ASD patients from a cohort of Chinese patients in Taiwan. Materials and Methods: Enrolled in this study were 80 ASD children (49 males and 31 females; 2–16 years old) followed up at Taipei MacKay Memorial Hospital between January 2010 and December 2020. The genomic DNA extracted from blood samples was analyzed by array-CGH via the Affymetrix GeneChip Genome-Wide Human single nucleotide polymorphism (SNP) and NimbleGen International Standards for Cytogenomic Arrays (ISCA) Plus Cytogenetic Arrays. The CNVs were classified into five groups: pathogenic (pathologic variant), likely pathogenic (potential pathologic variant), likely benign (potential normal genomic variant), benign (normal genomic variant), and uncertain clinical significance (variance of uncertain significance), according to the American College of Medical Genetics (ACMG) guidelines. Results: We identified 47 CNVs, 31 of which in 27 patients were clinically significant. The overall diagnostic yield was 33.8%. The most frequently clinically significant CNV was 15q11.2 deletion, which was present in 4 (5.0%) patients. Conclusions: In this study, a satisfactory diagnostic yield of array-CGH was demonstrated in a Taiwanese ASD patient cohort, supporting the clinical usefulness of array-CGH as the first-line testing of ASD in Taiwan.
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11
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Uehara T, Sanuki R, Ogura Y, Yokoyama A, Yoshida T, Futagawa H, Yoshihashi H, Yamada M, Suzuki H, Takenouchi T, Matsubara K, Hirata H, Kosaki K, Takano‐Shimizu T. Recurrent NFIA K125E substitution represents a loss-of-function allele: Sensitive in vitro and in vivo assays for nontruncating alleles. Am J Med Genet A 2021; 185:2084-2093. [PMID: 33973697 PMCID: PMC8251549 DOI: 10.1002/ajmg.a.62226] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 01/09/2023]
Abstract
Nuclear factor I A (NFIA) is a transcription factor that belongs to the NFI family. Truncating variants or intragenic deletion of the NFIA gene are known to cause the human neurodevelopmental disorder known as NFIA‐related disorder, but no patient heterozygous for a missense mutation has been reported. Here, we document two unrelated patients with typical phenotypic features of the NFIA‐related disorder who shared a missense variant p.Lys125Glu (K125E) in the NFIA gene. Patient 1 was a 6‐year‐old female with global developmental delay, corpus callosum anomaly, macrocephaly, and dysmorphic facial features. Patient 2 was a 14‐month‐old male with corpus callosum anomaly and macrocephaly. By using Drosophila and zebrafish models, we functionally evaluated the effect of the K125E substitution. Ectopic expression of wild‐type human NFIA in Drosophila caused developmental defects such as eye malformation and premature death, while that of human NFIA K125E variant allele did not. nfia‐deficient zebrafish embryos showed defects of midline‐crossing axons in the midbrain/hindbrain boundary. This impairment of commissural neurons was rescued by expression of wild‐type human NFIA, but not by that of mutant variant harboring K125E substitution. In accordance with these in vivo functional analyses, we showed that the K125E mutation impaired the transcriptional regulation of HES1 promoter in cultured cells. Taken together, we concluded that the K125E variant in the NFIA gene is a loss‐of‐function mutation.
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Affiliation(s)
- Tomoko Uehara
- Center for Medical GeneticsKeio University School of MedicineTokyoJapan
| | - Rikako Sanuki
- Advanced Insect Research Promotion CenterKyoto Institute of TechnologyKyotoJapan
| | - Yurie Ogura
- Department of Chemistry and Biological ScienceCollege of Science and Engineering, Aoyama Gakuin UniversitySagamiharaKanagawaJapan
| | - Atsushi Yokoyama
- Department of PediatricsKyoto University Graduate School of MedicineTokyoJapan
| | - Takeshi Yoshida
- Department of PediatricsKyoto University Graduate School of MedicineTokyoJapan
| | - Hiroshi Futagawa
- Department of GeneticsTokyo Metropolitan Children's Medical CenterTokyoJapan
| | - Hiroshi Yoshihashi
- Department of GeneticsTokyo Metropolitan Children's Medical CenterTokyoJapan
| | - Mamiko Yamada
- Center for Medical GeneticsKeio University School of MedicineTokyoJapan
| | - Hisato Suzuki
- Center for Medical GeneticsKeio University School of MedicineTokyoJapan
| | | | - Kohei Matsubara
- Advanced Insect Research Promotion CenterKyoto Institute of TechnologyKyotoJapan
| | - Hiromi Hirata
- Department of Chemistry and Biological ScienceCollege of Science and Engineering, Aoyama Gakuin UniversitySagamiharaKanagawaJapan
| | - Kenjiro Kosaki
- Center for Medical GeneticsKeio University School of MedicineTokyoJapan
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12
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How geneticists think about Differences/Disorders of Sexual Development (DSD): A conversation. J Pediatr Urol 2020; 16:760-767. [PMID: 32893165 DOI: 10.1016/j.jpurol.2020.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/27/2022]
Abstract
A multidisciplinary DSD clinic offers the opportunity for different specialties to learn from each other, as each provides their own perspective and expertise to the management of these complex patients, leading to collaborative care. For the patient, a multi-disciplinary clinic can improve access to care and decrease stress, as patients see all of the specialists on one day. For urologists seeing patients with DSD within a multi-disciplinary DSD clinic as well as independently, understanding what other specialists provide can help facilitate care and referral. Medical genetics is part of a multi-disciplinary DSD clinic. Given the recent advances in genetic diagnostics, many of the offered tests may be less familiar to the pediatric urologist. Therefore, this conversation reviews the clinical presentations and genetic testing options including chromosomal microarray, genetic testing panel, whole exome sequencing, and whole genome sequencing and how these can be helpful in the diagnosis and management of patients with DSD conditions.
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13
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Zenker M, Bunt J, Schanze I, Schanze D, Piper M, Priolo M, Gerkes EH, Gronostajski RM, Richards LJ, Vogt J, Wessels MW, Hennekam RC. Variants in nuclear factor I genes influence growth and development. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:611-626. [DOI: 10.1002/ajmg.c.31747] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/26/2019] [Accepted: 10/09/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Martin Zenker
- Institute of Human GeneticsUniversity Hospital, Otto‐von‐Guericke‐University Magdeburg Germany
| | - Jens Bunt
- Queensland Brain InstituteThe University of Queensland Brisbane Queensland Australia
| | - Ina Schanze
- Institute of Human GeneticsUniversity Hospital, Otto‐von‐Guericke‐University Magdeburg Germany
| | - Denny Schanze
- Institute of Human GeneticsUniversity Hospital, Otto‐von‐Guericke‐University Magdeburg Germany
| | - Michael Piper
- Queensland Brain InstituteThe University of Queensland Brisbane Queensland Australia
- School of Biomedical SciencesThe University of Queensland Brisbane Queensland Australia
| | - Manuela Priolo
- Operative Unit of Medical GeneticsGreat Metropolitan Hospital Bianchi‐Melacrino‐Morelli Reggio Calabria Italy
| | - Erica H. Gerkes
- Department of Genetics, University of GroningenUniversity Medical Center Groningen Groningen the Netherlands
| | - Richard M. Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life SciencesState University of New York Buffalo NY
| | - Linda J. Richards
- Queensland Brain InstituteThe University of Queensland Brisbane Queensland Australia
- School of Biomedical SciencesThe University of Queensland Brisbane Queensland Australia
| | - Julie Vogt
- West Midlands Regional Clinical Genetics Service and Birmingham Health PartnersWomen's and Children's Hospitals NHS Foundation Trust Birmingham UK
| | - Marja W. Wessels
- Department of Clinical Genetics, Erasmus MCUniversity Medical Center Rotterdam Rotterdam The Netherlands
| | - Raoul C. Hennekam
- Department of PediatricsUniversity of Amsterdam Amsterdam The Netherlands
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14
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Challenges in the clinical interpretation of small de novo copy number variants in neurodevelopmental disorders. Gene 2019; 706:162-171. [PMID: 31085274 DOI: 10.1016/j.gene.2019.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/27/2019] [Accepted: 05/03/2019] [Indexed: 12/17/2022]
Abstract
In clinical genetics, the need to discriminate between benign and pathogenic variants identified in patients with neurodevelopmental disorders is an absolute necessity. Copy number variants (CNVs) of small size can enable the identification of genes that are critical for neurologic development. However, assigning a definite association with a specific disorder is a difficult task. Among 328 trios analyzed over seven years of activity in a single laboratory, we identified 19 unrelated patients (5.8%) who carried a small (<500 kb) de novo CNV. Four patients had an additional independent de novo CNV. Nine had a variant that could be assigned as definitely pathogenic, whereas the remaining CNVs were considered as variants of unknown significance (VUS). We report clinical and molecular findings of patients harboring VUS. We reviewed the medical literature available for genes impacted by CNVs, obtained the probability of truncating loss-of-function intolerance, and compared overlapping CNVs reported in databases. The classification of small non-recurrent CNVs remains difficult but, among our findings, we provide support for a role of SND1 in the susceptibility of autism, describe a new case of the rare 17p13.1 microduplication syndrome, and report an X-linked duplication involving KIF4A and DLG3 as a likely cause of epilepsy.
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15
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Wang JC, Radcliff J, Coe SJ, Mahon LW. Effects of platforms, size filter cutoffs, and targeted regions of cytogenomic microarray on detection of copy number variants and uniparental disomy in prenatal diagnosis: Results from 5026 pregnancies. Prenat Diagn 2019; 39:137-156. [PMID: 30734327 DOI: 10.1002/pd.5375] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 10/02/2018] [Accepted: 10/10/2018] [Indexed: 12/24/2022]
Abstract
OBJECTIVE We evaluated the effects of platforms, size filter cutoffs, and targeted regions of cytogenomic microarray (CMA) on the detection of copy number variants (CNVs) and uniparental disomy (UPD) in prenatal diagnosis. METHODS Five thousand twenty-six consecutive prenatal specimens (>98% high-risk pregnancy) were studied by high-resolution CMA, with cutoffs of 50 kb for losses and 200 kb for gains in nontargeted regions and 20 kb for losses and 100 kb for gains in targeted regions. We assessed actual detection rates using the current assay as well as hypothetical detection rates using platforms with the same or lower resolution and smaller or larger cutoffs. RESULTS The detection rate of our current assay was 11.2% (562 of 5026), including abnormal findings in 543 cases and likely pathogenic variants in 19. The hypothetical decrease in the overall detection of variants (excluding likely benign) and UPD ranged from 3.8% to 23.0%. For the subgroup of pathogenic and likely pathogenic CNVs < 1 Mb, the decrease of detection ranged from 2.7% to 24.3%. CONCLUSIONS These findings underscore the significant effects of chosen CMA platform, as well as size filter cutoffs and targeted regions used in data analysis, on detection of CNVs and UPDs in a cohort of prenatal cases.
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Affiliation(s)
- Jia-Chi Wang
- Cytogenetics and Genomics, Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Jeff Radcliff
- Cytogenetics and Genomics, Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Sandra J Coe
- Cytogenetics and Genomics, Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Loretta W Mahon
- Cytogenetics and Genomics, Quest Diagnostics Nichols Institute, San Juan Capistrano, California
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16
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The Cytoscan HD Array in the Diagnosis of Neurodevelopmental Disorders. High Throughput 2018; 7:ht7030028. [PMID: 30223503 PMCID: PMC6164295 DOI: 10.3390/ht7030028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022] Open
Abstract
Submicroscopic chromosomal copy number variations (CNVs), such as deletions and duplications, account for about 15–20% of patients affected with developmental delay, intellectual disability, multiple congenital anomalies, and autism spectrum disorder. Most of CNVs are de novo or inherited rearrangements with clinical relevance, but there are also rare inherited imbalances with unknown significance that make difficult the clinical management and genetic counselling. Chromosomal microarrays analysis (CMA) are recognized as the first-line test for CNV detection and are now routinely used in the clinical diagnostic laboratory. The recent use of CMA platforms that combine classic copy number analysis with single-nucleotide polymorphism (SNP) genotyping has increased the diagnostic yields. Here we discuss the application of the Cytoscan high-density (HD) SNP-array for the detection of CNVs. We provide an overview of molecular analyses involved in identifying pathogenic CNVs and highlight important guidelines to establish pathogenicity of CNV.
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17
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Xia Y, Yang Y, Huang S, Wu Y, Li P, Zhuang J. Clinical application of chromosomal microarray analysis for the prenatal diagnosis of chromosomal abnormalities and copy number variations in fetuses with congenital heart disease. Prenat Diagn 2018; 38:406-413. [PMID: 29573438 DOI: 10.1002/pd.5249] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 02/17/2018] [Accepted: 03/07/2018] [Indexed: 12/23/2022]
Abstract
OBJECTIVES This study aimed to determine chromosomal abnormalities and copy number variations (CNVs) in fetuses with congenital heart disease (CHD) by chromosomal microarray analysis (CMA). METHODS One hundred and ten cases with CHD detected by prenatal echocardiography were enrolled in the study; 27 cases were simple CHDs, and 83 were complex CHDs. Chromosomal microarray analysis was performed on the Affymetrix CytoScan HD platform. All annotated CNVs were validated by quantitative PCR. RESULTS Chromosomal microarray analysis identified 6 cases with chromosomal abnormalities, including 2 cases with trisomy 21, 2 cases with trisomy 18, 1 case with trisomy 13, and 1 unusual case of mosaic trisomy 21. Pathogenic CNVs were detected in 15.5% (17/110) of the fetuses with CHDs, including 13 cases with CHD-associated CNVs. We further identified 10 genes as likely novel CHD candidate genes through gene functional enrichment analysis. We also found that pathogenic CMA results impacted the rate of pregnancy termination. CONCLUSIONS This study shows that CMA is particularly effective for identifying chromosomal abnormalities and CNVs in fetuses with CHDs as well as having an effect on obstetrical outcomes. The elucidation of the genetic basis of CHDs will continue to expand our understanding of the etiology of CHDs.
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Affiliation(s)
- Yu Xia
- Prenatal Diagnosis Center, Guangdong General Hospital, Guangdong Academy of Medical Science, Guangdong, China.,Department of Cardiovascular Surgery of Guangdong Provincial Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangdong, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong General Hospital, Guangdong Academy of Medical Science, Guangdong, China
| | - Yongchao Yang
- Prenatal Diagnosis Center, Guangdong General Hospital, Guangdong Academy of Medical Science, Guangdong, China.,Department of Cardiovascular Surgery of Guangdong Provincial Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Shufang Huang
- Prenatal Diagnosis Center, Guangdong General Hospital, Guangdong Academy of Medical Science, Guangdong, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong General Hospital, Guangdong Academy of Medical Science, Guangdong, China
| | - Yueheng Wu
- Prenatal Diagnosis Center, Guangdong General Hospital, Guangdong Academy of Medical Science, Guangdong, China.,Department of Cardiovascular Surgery of Guangdong Provincial Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangdong, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong General Hospital, Guangdong Academy of Medical Science, Guangdong, China
| | - Ping Li
- Prenatal Diagnosis Center, Guangdong General Hospital, Guangdong Academy of Medical Science, Guangdong, China.,Department of Obstetrics and Gynecology, Guangdong General Hospital, Guangdong Academy of Medical Science, Guangdong, China
| | - Jian Zhuang
- Department of Cardiovascular Surgery of Guangdong Provincial Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangdong, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong General Hospital, Guangdong Academy of Medical Science, Guangdong, China
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18
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Pogue RE, Cavalcanti DP, Shanker S, Andrade RV, Aguiar LR, de Carvalho JL, Costa FF. Rare genetic diseases: update on diagnosis, treatment and online resources. Drug Discov Today 2017; 23:187-195. [PMID: 29129805 DOI: 10.1016/j.drudis.2017.11.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/28/2017] [Accepted: 11/02/2017] [Indexed: 12/23/2022]
Abstract
Rare genetic diseases collectively impact a significant portion of the world's population. For many diseases there is limited information available, and clinicians can find difficulty in differentiating between clinically similar conditions. This leads to problems in genetic counseling and patient treatment. The biomedical market is affected because pharmaceutical and biotechnology industries do not see advantages in addressing rare disease treatments, or because the cost of the treatments is too high. By contrast, technological advances including DNA sequencing and analysis, together with computer-aided tools and online resources, are allowing a more thorough understanding of rare disorders. Here, we discuss how the collection of various types of information together with the use of new technologies is facilitating diagnosis and, consequently, treatment of rare diseases.
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Affiliation(s)
- Robert E Pogue
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Distrito Federal, Brazil.
| | | | - Shreya Shanker
- Illinois Mathematics and Science Academy (IMSA), IL, USA
| | - Rosangela V Andrade
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Distrito Federal, Brazil
| | - Lana R Aguiar
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Distrito Federal, Brazil
| | - Juliana L de Carvalho
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Distrito Federal, Brazil; OneSkin Technologies, San Francisco, CA, USA
| | - Fabrício F Costa
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Distrito Federal, Brazil; MATTER, Chicago, IL, USA; The Founder Institute, San Francisco, CA, USA.
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19
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Abstract
There have been major advances in genetic testing especially over the last 10 years. We have advanced from looking at simple chromosomes under a microscope to more sophisticated analysis of the DNA makeup of chromosomes and from testing a single gene to sequencing almost all of our genetic material. Similarly, in the field of prenatal testing we have made great strides in screening and diagnostic testing in the hope of detecting significant abnormalities in the fetus while decreasing the risk to the pregnancy. In this article the major types of genetic screening and diagnostic testing, both prenatal and postnatal, will be reviewed. [Pediatr Ann. 2017;46(11):e423-e427.].
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20
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Chromosome copy number variation in telomerized human bone marrow stromal cells; insights for monitoring safe ex-vivo expansion of adult stem cells. Stem Cell Res 2017; 25:6-17. [PMID: 28988007 DOI: 10.1016/j.scr.2017.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/14/2017] [Accepted: 09/20/2017] [Indexed: 12/24/2022] Open
Abstract
Adult human bone marrow stromal cells (hBMSC) cultured for cell therapy require evaluation of potency and stability for safe use. Chromosomal aberrations upsetting genomic integrity in such cells have been contrastingly described as "Limited" or "Significant". Previously reported stepwise acquisition of a spontaneous neoplastic phenotype during three-year continuous culture of telomerized cells (hBMSC-TERT20) didn't alter a diploid karyotype measured by spectral karyotype analysis (SKY). Such screening may not adequately monitor abnormal and potentially tumorigenic hBMSC in clinical scenarios. We here used array comparative genomic hybridization (aCGH) to more stringently compare non-tumorigenic parental hBMSC-TERT strains with their tumorigenic subcloned populations. Confirmation of a known chromosome 9p21 microdeletion at locus CDKN2A/B, showed it also impinged upon the adjacent MTAP gene. Compared to reference diploid human fibroblast genomic DNA, the non-tumorigenic hBMSC-TERT4 cells had a copy number variation (CNV) in at least 14 independent loci. The pre-tumorigenic hBMSC-TERT20 cell strain had further CNV including 1q44 gain enhancing SMYD3 expression and 11q13.1 loss downregulating MUS81 expression. Bioinformatic analysis of gene products reflecting 11p15.5 CNV gain in tumorigenic hBMSC-TERT20 cells highlighted networks implicated in tumorigenic progression involving cell cycle control and mis-match repair. We provide novel biomarkers for prospective risk assessment of expanded stem cell cultures.
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21
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Revah-Politi A, Ganapathi M, Bier L, Cho MT, Goldstein DB, Hemati P, Iglesias A, Juusola J, Pappas J, Petrovski S, Wilson AL, Aggarwal VS, Anyane-Yeboa K. Loss-of-function variants in NFIA provide further support that NFIA is a critical gene in 1p32-p31 deletion syndrome: A four patient series. Am J Med Genet A 2017; 173:3158-3164. [PMID: 28941020 DOI: 10.1002/ajmg.a.38460] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/27/2017] [Accepted: 08/04/2017] [Indexed: 11/07/2022]
Abstract
The association between 1p32-p31 contiguous gene deletions and a distinct phenotype that includes anomalies of the corpus callosum, ventriculomegaly, developmental delay, seizures, and dysmorphic features has been long recognized and described. Recently, the observation of overlapping phenotypes in patients with chromosome translocations that disrupt NFIA (Nuclear factor I/A), a gene within this deleted region, and NFIA intragenic deletions has led to the hypothesis that NFIA is a critical gene within this region. The wide application and increasing accessibility of whole exome sequencing (WES) has helped identify new cases to support this hypothesis. Here, we describe four patients with loss-of-function variants in the NFIA gene identified through WES. The clinical presentation of these patients significantly overlaps with the phenotype described in previously reported cases of 1p32-p31 deletion syndrome, NFIA gene disruptions and intragenic NFIA deletions. Our cohort includes a mother and daughter as well as an unrelated individual who share the same nonsense variant (c.205C>T, p.Arg69Ter; NM_001145512.1). We also report a patient with a frameshift NFIA variant (c.159_160dupCC, p.Gln54ProfsTer49). We have compared published cases of 1p32-p31 microdeletion syndrome, translocations resulting in NFIA gene disruption, intragenic deletions, and loss-of-function mutations (including our four patients) to reveal that abnormalities of the corpus callosum, ventriculomegaly/hydrocephalus, macrocephaly, Chiari I malformation, dysmorphic features, developmental delay, hypotonia, and urinary tract defects are common findings. The consistent overlap in clinical presentation provides further evidence of the critical role of NFIA haploinsufficiency in the development of the 1p32-p31 microdeletion syndrome phenotype.
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Affiliation(s)
- Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Louise Bier
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | | | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Parisa Hemati
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Alejandro Iglesias
- Department of Pediatrics, Division of Clinical Genetics, Columbia University Medical Center (CUMC), New York, New York
| | | | - John Pappas
- Department of Pediatrics, New York University School of Medicine, New York, New York
| | - Slavé Petrovski
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York.,Department of Medicine, Austin Health and Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Ashley L Wilson
- Department of Pediatrics, Children's Hospital of New York-Presbyterian, New York, New York
| | - Vimla S Aggarwal
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Kwame Anyane-Yeboa
- Department of Pediatrics, Division of Clinical Genetics, Columbia University Medical Center (CUMC), New York, New York
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22
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Yao R, Zhang C, Yu T, Li N, Hu X, Wang X, Wang J, Shen Y. Evaluation of three read-depth based CNV detection tools using whole-exome sequencing data. Mol Cytogenet 2017; 10:30. [PMID: 28852425 PMCID: PMC5569469 DOI: 10.1186/s13039-017-0333-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/15/2017] [Indexed: 12/16/2022] Open
Abstract
Background Whole exome sequencing (WES) has been widely accepted as a robust and cost-effective approach for clinical genetic testing of small sequence variants. Detection of copy number variants (CNV) within WES data have become possible through the development of various algorithms and software programs that utilize read-depth as the main information. The aim of this study was to evaluate three commonly used, WES read-depth based CNV detection programs using high-resolution chromosomal microarray analysis (CMA) as a standard. Methods Paired CMA and WES data were acquired for 45 samples. A total of 219 CNVs (size ranged from 2.3 kb – 35 mb) identified on three CMA platforms (Affymetrix, Agilent and Illumina) were used as standards. CNVs were called from WES data using XHMM, CoNIFER, and CNVnator with modified settings. Results All three software packages detected an elevated proportion of small variants (< 20 kb) compared to CMA. XHMM and CoNIFER had poor detection sensitivity (22.2 and 14.6%), which correlated with the number of capturing probes involved. CNVnator detected most variants and had better sensitivity (87.7%); however, suffered from an overwhelming detection of small CNVs below 20 kb, which required further confirmation. Size estimation of variants was exaggerated by CNVnator and understated by XHMM and CoNIFER. Conclusion Low concordances of CNV, detected by three different read-depth based programs, indicate the immature status of WES-based CNV detection. Low sensitivity and uncertain specificity of WES-based CNV detection in comparison with CMA based CNV detection suggests that CMA will continue to play an important role in detecting clinical grade CNV in the NGS era, which is largely based on WES. Electronic supplementary material The online version of this article (doi:10.1186/s13039-017-0333-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China
| | - Cheng Zhang
- Boston Children's Hospital, Boston, MA 02115 USA
| | - Tingting Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China
| | - Xuyun Hu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China.,Boston Children's Hospital, Boston, MA 02115 USA
| | - Xiumin Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China
| | - Yiping Shen
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China.,Boston Children's Hospital, Boston, MA 02115 USA
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