1
|
Mudassir BU, Alotaibi MA, Kizilbash N, Alruwaili D, Alruwaili A, Alenezi M, Agha Z. Genome-wide CNV analysis uncovers novel pathogenic regions in cohort of five multiplex families with neurodevelopmental disorders. Heliyon 2023; 9:e19718. [PMID: 37810058 PMCID: PMC10558996 DOI: 10.1016/j.heliyon.2023.e19718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 10/10/2023] Open
Abstract
Structural reorganization of chromosomes by genomic duplications and/or deletions are known as copy number variations (CNVs). Pathogenic and disease susceptible CNVs alter gene dosage and its phenotypic expression that often leads to human genetic diseases including Neurological disorders. CNVs affecting same common genes in multiple neurodevelopmental disorders can better explain the shared clinical and genetic aetiology across brain diseases. Our study presents the novel copy number variations in a cohort of five multiplex consanguineous families with intellectual disability, microcephaly, ASD, epilepsy, and neurological syndromic features. Cytoscan HD microarray suite has revealed genome wide deletions, duplications and LOH regions which are co-segregating in the family members for the rare neurodevelopmental syndromic phenotypes. This study identifies 1q21.1 microduplication, 16p11.2 microduplication, Xp11.22 microduplication, 4p12 microdeletion and Xq21.1 microdeletion that significantly contribute to primary disease onset and its progression for the first time in Pakistani families. Our study has potential impact on the understanding of pathogenic genetic predisposition for appearance of complex and heterogeneous neurodevelopmental disorders with otherwise unexplained syndromic features. Identification of altered gene dosage across the genome is helpful in improved diagnosis, better disease management in day-to-day life activities of patients with cognitive impairment and genetic counselling of families where consanguinity is a tradition. Our study will contribute to expand the knowledge of genotype-phenotype expression and future gateways in therapeutics and precision medicine research will be open in Pakistan.
Collapse
Affiliation(s)
- Behjat Ul Mudassir
- Translational Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Nadeem Kizilbash
- Department of Medical Laboratory Technology, Northern Border University, Arar, Saudi Arabia
| | - Daliyah Alruwaili
- Department of Medical Laboratory Technology, Northern Border University, Arar, Saudi Arabia
| | - Anwar Alruwaili
- Department of Medical Laboratory Technology, Northern Border University, Arar, Saudi Arabia
| | - Modhi Alenezi
- Department of Medical Laboratory Technology, Northern Border University, Arar, Saudi Arabia
| | - Zehra Agha
- Translational Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| |
Collapse
|
2
|
Zhang L, Tie X, Che F, Wang G, Ge Y, Li B, Yang Y. Novel maternal duplication of 6p22.3-p25.3 with subtelomeric 6p25.3 deletion: new clinical findings and genotype-phenotype correlations. Mol Cytogenet 2023; 16:11. [PMID: 37303060 DOI: 10.1186/s13039-023-00640-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/24/2023] [Indexed: 06/13/2023] Open
Abstract
BACKGROUND Copy-number variants (CNVs) drive many neurodevelopmental-related disorders. Although many neurodevelopmental-related CNVs can give rise to widespread phenotypes, it is necessary to identify the major genes contributing to phenotypic presentation. Copy-number variations in chromosome 6, such as independent 6p deletion and 6p duplication, have been reported in several live-born infants and present widespread abnormalities such as intellectual disability, growth deficiency, developmental delay, and multiple dysmorphic facial features. However, a contiguous deletion and duplication in chromosome 6p regions have been reported in only a few cases. CASE PRESENTATION In this study, we reported the first duplication of chromosome band 6p25.3-p22.3 with deletion of 6p25.3 in a pedigree. This is the first case reported involving CNVs in these chromosomal regions. In this pedigree, we reported a 1-year-old boy with maternal 6p25-pter duplication characterized by chromosome karyotype. Further analysis using CNV-seq revealed a 20.88-Mb duplication at 6p25.3-p22.3 associated with a contiguous 0.66-Mb 6p25.3 deletion. Whole exome sequencing confirmed the deletion/duplication and identified no pathogenic or likely pathogenic variants related with the patient´s phenotype. The proband presented abnormal growth, developmental delay, skeletal dysplasia, hearing loss, and dysmorphic facial features. Additionally, he presented recurrent infection after birth. CNV-seq using the proband´s parental samples showed that the deletion/duplication was inherited from the proband´s mother, who exhibited a similar phenotype to the proband. When compared with other cases, this proband and his mother presented a new clinical finding: forearm bone dysplasia. The major candidate genes contributing to recurrent infection, eye development, hearing loss features, neurodevelopmental development, and congenital bone dysplasia were further discussed. CONCLUSIONS Our results showed a new clinical finding of a contiguous deletion and duplication in chromosome 6p regions and suggested candidate genes associated with phenotypic features, such as FOXC1, SERPINB6, NRN1, TUBB2A, IRF4, and RIPK1.
Collapse
Affiliation(s)
- Liyu Zhang
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Xiaoling Tie
- Department of Rehabilitation, Xi'an Children's Hospital, Xi'an, China
| | - Fengyu Che
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Guoxia Wang
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Ying Ge
- The Center Laboratory Medicine, Xi'an Children's Hospital, Xi'an, China
| | - Benchang Li
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Ying Yang
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China.
| |
Collapse
|
3
|
Pennings M, Meijer RPP, Gerrits M, Janssen J, Pfundt R, de Leeuw N, Gilissen C, Gardeitchik T, Schouten M, Voermans N, van de Warrenburg B, Kamsteeg EJ. Copy number variants from 4800 exomes contribute to ~7% of genetic diagnoses in movement disorders, muscle disorders and neuropathies. Eur J Hum Genet 2023; 31:654-662. [PMID: 36781956 PMCID: PMC10250492 DOI: 10.1038/s41431-023-01312-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/11/2023] [Accepted: 02/01/2023] [Indexed: 02/15/2023] Open
Abstract
Various groups of neurological disorders, including movement disorders and neuromuscular diseases, are clinically and genetically heterogeneous. Diagnostic panel-based exome sequencing is a routine test for these disorders. Despite the success rates of exome sequencing, it results in the detection of causative sequence variants in 'only' 25-30% of cases. Copy number variants (CNVs), i.e. deletion or duplications, explain 10-20% of individuals with multisystemic phenotypes, such as co-existing intellectual disability, but may also have a role in disorders affecting a single system (organ), like neurological disorders with normal intelligence. In this study, CNVs were extracted from clinical exome sequencing reports of 4800 probands primarily with a movement disorder, myopathy or neuropathy. In 88 (~2%) probands, phenotype-matching CNVs were detected, representing ~7% of genetically confirmed cases. CNVs varied from involvement of over 100 genes to single exons and explained X-linked, autosomal dominant, or - recessive disorders, the latter due to either a homozygous CNV or a compound heterozygous CNV with a sequence variant on the other allele. CNVs were detected affecting genes where deletions or duplications are established as a common mechanism, like PRKN (in Parkinson's disease), DMD (in Duchenne muscular dystrophy) and PMP22 (in neuropathies), but also genes in which no intragenic CNVs have been reported to date. Analysis of CNVs as part of panel-based exome sequencing for genetically heterogeneous neurological diseases provides an additional diagnostic yield of ~2% without extra laboratory costs. Therefore it is recommended to perform CNV analysis for movement disorders, muscle disease, neuropathies, or any other single-system disorder.
Collapse
Affiliation(s)
- Maartje Pennings
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Rowdy P P Meijer
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Monique Gerrits
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Jannie Janssen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Thatjana Gardeitchik
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Meyke Schouten
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Nicol Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical Center, Nijmegen, the Netherlands
| | - Bart van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical Center, Nijmegen, the Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.
| |
Collapse
|
4
|
Kerry RG, Montalbo FJP, Das R, Patra S, Mahapatra GP, Maurya GK, Nayak V, Jena AB, Ukhurebor KE, Jena RC, Gouda S, Majhi S, Rout JR. An overview of remote monitoring methods in biodiversity conservation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:80179-80221. [PMID: 36197618 PMCID: PMC9534007 DOI: 10.1007/s11356-022-23242-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Conservation of biodiversity is critical for the coexistence of humans and the sustenance of other living organisms within the ecosystem. Identification and prioritization of specific regions to be conserved are impossible without proper information about the sites. Advanced monitoring agencies like the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) had accredited that the sum total of species that are now threatened with extinction is higher than ever before in the past and are progressing toward extinct at an alarming rate. Besides this, the conceptualized global responses to these crises are still inadequate and entail drastic changes. Therefore, more sophisticated monitoring and conservation techniques are required which can simultaneously cover a larger surface area within a stipulated time frame and gather a large pool of data. Hence, this study is an overview of remote monitoring methods in biodiversity conservation via a survey of evidence-based reviews and related studies, wherein the description of the application of some technology for biodiversity conservation and monitoring is highlighted. Finally, the paper also describes various transformative smart technologies like artificial intelligence (AI) and/or machine learning algorithms for enhanced working efficiency of currently available techniques that will aid remote monitoring methods in biodiversity conservation.
Collapse
Affiliation(s)
- Rout George Kerry
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | | | - Rajeswari Das
- Department of Soil Science and Agricultural Chemistry, School of Agriculture, GIET University, Gunupur, Rayagada, Odisha 765022 India
| | - Sushmita Patra
- Indian Council of Agricultural Research-Directorate of Foot and Mouth Disease-International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar, Odisha 752050 India
| | | | - Ganesh Kumar Maurya
- Zoology Section, Mahila MahaVidyalya, Banaras Hindu University, Varanasi, 221005 India
| | - Vinayak Nayak
- Indian Council of Agricultural Research-Directorate of Foot and Mouth Disease-International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar, Odisha 752050 India
| | - Atala Bihari Jena
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | | | - Ram Chandra Jena
- Department of Pharmaceutical Sciences, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | - Sushanto Gouda
- Department of Zoology, Mizoram University, Aizawl, 796009 India
| | - Sanatan Majhi
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | - Jyoti Ranjan Rout
- School of Biological Sciences, AIPH University, Bhubaneswar, Odisha 752101 India
| |
Collapse
|
5
|
Bedri SK, Evertsson B, Khademi M, Al Nimer F, Olsson T, Hillert J, Glaser A. Copy number variations across the blood-brain barrier in multiple sclerosis. Ann Clin Transl Neurol 2022; 9:962-976. [PMID: 35560551 PMCID: PMC9268884 DOI: 10.1002/acn3.51573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/30/2022] [Accepted: 04/12/2022] [Indexed: 12/29/2022] Open
Abstract
Objective Multiple sclerosis (MS) is a neuroinflammatory disease where immune cells cross the blood–brain barrier (BBB) into the central nervous system (CNS). What predisposes these immune cells to cross the BBB is still unknown. Here, we examine the possibility that genomic rearrangements could predisposespecific immune cells in the peripheral blood to cross the BBB and form sub‐populations of cells involved in the inflammatory process in the CNS. Methods We compared copy number variations in paired peripheral blood mononuclear cells (PBMCs) and cerebrospinal fluid (CSF) cells from MS patients. Thereafter, using next generation sequencing, we studied the T‐cell receptor beta (TRB) locus rearrangements and profiled the αβ T cell repertoire in peripheral CD4+ and CD8+ T cells and in the CSF. Results We identified deletions in the T‐cell receptor alpha/delta (TRA/D), gamma (TRG), and TRB loci in CSF cells compared to PBMCs. Further characterization revealed diversity of the TRB locus which was used to describe the character and clonal expansion of T cells in the CNS. T‐cell repertoire profiling from either side of the BBB concluded that the most frequent clones in the CSF samples are unique to an individual. Furthermore, we observed a difference in the proportion of expanded T‐cell clones when comparing samples from MS patients in relapse and remission with opposite trends in CSF and peripheral blood. Interpretation This study provides a characterization of the T cells in the CSF and might indicate a role of expanded clones in MS pathogenicity.
Collapse
Affiliation(s)
- Sahl Khalid Bedri
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Björn Evertsson
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Hospital, Tema Neuro, Stockholm, Sweden
| | - Mohsen Khademi
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Faiez Al Nimer
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Hospital, Tema Neuro, Stockholm, Sweden
| | - Tomas Olsson
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Hospital, Tema Neuro, Stockholm, Sweden
| | - Jan Hillert
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Hospital, Tema Neuro, Stockholm, Sweden
| | - Anna Glaser
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
6
|
Aqil B, Gao J, Stalling M, Sukhanova M, Duncavage EJ, Lu X, Wolniak KL, Kreisel F, Yaseen NR. Distinctive Flow Cytometric and Mutational Profile of Acute Myeloid Leukemia With t(8;16)(p11;p13) Translocation. Am J Clin Pathol 2022; 157:701-708. [PMID: 34698340 DOI: 10.1093/ajcp/aqab178] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 09/19/2021] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Acute myeloid leukemia (AML) with t(8;16)(p11;p13) abnormalities is a rare, aggressive, and diagnostically challenging subtype that results in KAT6A-CREBBP gene fusion. METHODS To investigate their immunophenotype and genomic features, we identified 5 cases of AML with t(8;16) through a retrospective review of the databases at Northwestern Memorial Hospital in Chicago, IL, and Washington University Medical Center, in St Louis, MO. RESULTS In all, 4 of 5 cases were therapy related and 1 was possibly therapy related. The leukemic blasts showed distinctive features, including bright CD45 expression and remarkably high side scatter that overlapped with maturing myeloid elements, making the blasts difficult to identify on initial examination. They were positive for CD13, CD33, and CD64 and negative for CD34 and CD117. Next-generation sequencing profiling of 4 cases revealed pathogenic ASXL1 (2 cases), FLT3-tyrosine kinase domain (TKD) mutations (2 cases), and other pathogenic mutations. In 3 patients, t(8;16) was the sole cytogenetic abnormality; additional aberrations were found in 2 patients. Single nucleotide polymorphism microarray revealed 1 case with 7q deletion as a secondary clone. CONCLUSIONS Our data highlight the distinctive immunophenotypic profile of AML with t(8;16), which, along with its unique morphology, often presents a diagnostic challenge. We showed that mutations of either ASXL1 or FLT3-TKD are seen in most cases of this leukemia.
Collapse
Affiliation(s)
- Barina Aqil
- Division of Hematopathology, Department of Pathology, Northwestern University Feinberg School of Medicine , Chicago, IL , USA
| | - Juehua Gao
- Division of Hematopathology, Department of Pathology, Northwestern University Feinberg School of Medicine , Chicago, IL , USA
| | - Melissa Stalling
- Division of Hematopathology, Department of Pathology, Northwestern University Feinberg School of Medicine , Chicago, IL , USA
| | - Madina Sukhanova
- Division of Hematopathology, Department of Pathology, Northwestern University Feinberg School of Medicine , Chicago, IL , USA
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine , St Louis, MO , USA
| | - Xinyan Lu
- Division of Hematopathology, Department of Pathology, Northwestern University Feinberg School of Medicine , Chicago, IL , USA
| | - Kristy L Wolniak
- Division of Hematopathology, Department of Pathology, Northwestern University Feinberg School of Medicine , Chicago, IL , USA
| | | | - Nabeel R Yaseen
- Division of Hematopathology, Department of Pathology, Northwestern University Feinberg School of Medicine , Chicago, IL , USA
| |
Collapse
|
7
|
Scionti F, Arbitrio M, Caracciolo D, Pensabene L, Tassone P, Tagliaferri P, Di Martino MT. Integration of DNA Microarray with Clinical and Genomic Data. Methods Mol Biol 2022; 2401:239-248. [PMID: 34902132 DOI: 10.1007/978-1-0716-1839-4_15] [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] [Indexed: 06/14/2023]
Abstract
DNA microarrays have been widely employed to understand cancer development. This technology is able to measure expression levels of a large numbers of genes or to genotype multiple regions of a genome in a massively parallel experiment. In addition, the detection of methylation patterns and gene copy number variations are also performed. Clinicians began to apply these findings in personalized medicine for the selection of cancer therapy according to the individual's cancer genomic profile. Because cancer is a complex disease it is of great value to integrate microarray data with genomic and clinical data. Here, we presented an overview of DNA microarray technology and discuss about benefits and challenging of microarray data integration.
Collapse
Affiliation(s)
- Francesca Scionti
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Messina, Italy
| | - Mariamena Arbitrio
- Institute for Biomedical Research and Innovation (IRIB-CNR), Section of Catanzaro, Catanzaro, Italy
| | - Daniele Caracciolo
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | - Licia Pensabene
- Department of Medical and Surgical Sciences, Pediatric Unit, Magna Græcia University, Catanzaro, Italy
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | | | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy.
| |
Collapse
|
8
|
Cheng MC, Chien WH, Huang YS, Fang TH, Chen CH. Translational Study of Copy Number Variations in Schizophrenia. Int J Mol Sci 2021; 23:ijms23010457. [PMID: 35008879 PMCID: PMC8745588 DOI: 10.3390/ijms23010457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/11/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Rare copy number variations (CNVs) are part of the genetics of schizophrenia; they are highly heterogeneous and personalized. The CNV Analysis Group of the Psychiatric Genomic Consortium (PGC) conducted a large-scale analysis and discovered that recurrent CNVs at eight genetic loci were pathogenic to schizophrenia, including 1q21.1, 2p16.3 (NRXN1), 3q29, 7q11.23, 15q13.3, distal 16p11.2, proximal 16p11.2, and 22q11.2. We adopted a two-stage strategy to translate this knowledge into clinical psychiatric practice. As a screening test, we first developed a real-time quantitative PCR (RT-qPCR) panel that simultaneously detected these pathogenic CNVs. Then, we tested the utility of this screening panel by investigating a sample of 557 patients with schizophrenia. Chromosomal microarray analysis (CMA) was used to confirm positive cases from the screening test. We detected and confirmed thirteen patients who carried CNVs at these hot loci, including two patients at 1q21.1, one patient at 7q11.2, three patients at 15q13.3, two patients at 16p11.2, and five patients at 22q11.2. The detection rate in this sample was 2.3%, and the concordance rate between the RT-qPCR test panel and CMA was 100%. Our results suggest that a two-stage approach is cost-effective and reliable in achieving etiological diagnosis for some patients with schizophrenia and improving the understanding of schizophrenia genetics.
Collapse
Affiliation(s)
- Min-Chih Cheng
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien 981, Taiwan;
| | - Wei-Hsien Chien
- Department of Occupational Therapy, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan;
| | - Yu-Shu Huang
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan;
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Ting-Hsuan Fang
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan;
- Department and Institute of Biomedical Sciences, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence:
| |
Collapse
|
9
|
Gabrielaite M, Torp MH, Rasmussen MS, Andreu-Sánchez S, Vieira FG, Pedersen CB, Kinalis S, Madsen MB, Kodama M, Demircan GS, Simonyan A, Yde CW, Olsen LR, Marvig RL, Østrup O, Rossing M, Nielsen FC, Winther O, Bagger FO. A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data. Cancers (Basel) 2021; 13:cancers13246283. [PMID: 34944901 PMCID: PMC8699073 DOI: 10.3390/cancers13246283] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 12/28/2022] Open
Abstract
Copy-number variations (CNVs) have important clinical implications for several diseases and cancers. Relevant CNVs are hard to detect because common structural variations define large parts of the human genome. CNV calling from short-read sequencing would allow single protocol full genomic profiling. We reviewed 50 popular CNV calling tools and included 11 tools for benchmarking in a reference cohort encompassing 39 whole genome sequencing (WGS) samples paired current clinical standard-SNP-array based CNV calling. Additionally, for nine samples we also performed whole exome sequencing (WES), to address the effect of sequencing protocol on CNV calling. Furthermore, we included Gold Standard reference sample NA12878, and tested 12 samples with CNVs confirmed by multiplex ligation-dependent probe amplification (MLPA). Tool performance varied greatly in the number of called CNVs and bias for CNV lengths. Some tools had near-perfect recall of CNVs from arrays for some samples, but poor precision. Several tools had better performance for NA12878, which could be a result of overfitting. We suggest combining the best tools also based on different methodologies: GATK gCNV, Lumpy, DELLY, and cn.MOPS. Reducing the total number of called variants could potentially be assisted by the use of background panels for filtering of frequently called variants.
Collapse
Affiliation(s)
- Migle Gabrielaite
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Mathias Husted Torp
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Malthe Sebro Rasmussen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Sergio Andreu-Sánchez
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Filipe Garrett Vieira
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Christina Bligaard Pedersen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Ørsteds Pl. 345C, 2800 Kgs. Lyngby, Denmark
| | - Savvas Kinalis
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Majbritt Busk Madsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Miyako Kodama
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Gül Sude Demircan
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Arman Simonyan
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Christina Westmose Yde
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Lars Rønn Olsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Ørsteds Pl. 345C, 2800 Kgs. Lyngby, Denmark
| | - Rasmus L. Marvig
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Olga Østrup
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Maria Rossing
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
| | - Ole Winther
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Matematiktorvet 303B, 2800 Kgs. Lyngby, Denmark
| | - Frederik Otzen Bagger
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark; (M.G.); (M.H.T.); (M.S.R.); (S.A.-S.); (F.G.V.); (C.B.P.); (S.K.); (M.B.M.); (M.K.); (G.S.D.); (A.S.); (C.W.Y.); (L.R.O.); (R.L.M.); (O.Ø.); (M.R.); (F.C.N.); (O.W.)
- Department of Biomedicine, UKBB Universitats-Kinderspital Basel, 4031 Basel, Switzerland
- Swiss Institute of Bioinformatics, Hebelstrasse 20, 4031 Basel, Switzerland
- Correspondence:
| |
Collapse
|
10
|
Involvement of Rare Mutations of SCN9A, DPP4, ABCA13, and SYT14 in Schizophrenia and Bipolar Disorder. Int J Mol Sci 2021; 22:ijms222413189. [PMID: 34947986 PMCID: PMC8709054 DOI: 10.3390/ijms222413189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/05/2021] [Accepted: 12/05/2021] [Indexed: 02/07/2023] Open
Abstract
Rare mutations associated with schizophrenia (SZ) and bipolar disorder (BD) usually have high clinical penetrance; however, they are highly heterogeneous and personalized. Identifying rare mutations is instrumental in making the molecular diagnosis, understanding the pathogenesis, and providing genetic counseling for the affected individuals and families. We conducted whole-genome sequencing analysis in two multiplex families with the dominant inheritance of SZ and BD. We detected a G327E mutation of SCN9A and an A654V mutation of DPP4 cosegregating with SZ and BD in one three-generation multiplex family. We also identified three mutations cosegregating with SZ and BD in another two-generation multiplex family, including L711S of SCN9A, M4554I of ABCA13, and P159L of SYT14. These five missense mutations were rare and deleterious. Mutations of SCN9A have initially been reported to cause congenital insensitivity to pain and neuropathic pain syndromes. Further studies showed that rare mutations of SCN9A were associated with seizure and autism spectrum disorders. Our findings suggest that SZ and BD might also be part of the clinical phenotype spectra of SCN9A mutations. Our study also indicates the oligogenic involvement in SZ and BD and supports the multiple-hit model of SZ and BD.
Collapse
|
11
|
Chen CH, Huang A, Huang YS, Fang TH. Identification of a Rare Novel KMT2C Mutation That Presents with Schizophrenia in a Multiplex Family. J Pers Med 2021; 11:jpm11121254. [PMID: 34945726 PMCID: PMC8707139 DOI: 10.3390/jpm11121254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 01/18/2023] Open
Abstract
Schizophrenia is a complex genetic disorder involving many common variants with modest effects and rare mutations with high penetrance. Rare mutations associated with schizophrenia are highly heterogeneous and private for affected individuals and families. Identifying such mutations can help establish the molecular diagnosis, elucidate the pathogenesis, and provide helpful genetic counseling for affected patients and families. We performed a whole-exome sequencing analysis to search for rare pathogenic mutations co-segregating with schizophrenia transmitted in a dominant inheritance in a two-generation multiplex family. We identified a rare missense mutation H1574R (Histidine1574Arginine, rs199796552) of KMT2C (lysine methyltransferase 2C) co-segregating with affected members in this family. The mutation is a novel deleterious mutation of KMT2C, not reported before in the literature. The KMT2C encodes a histone 3 lysine 4 (H3K4)-specific methyltransferase and involves epigenetic regulation of brain gene expression. Mutations of KMT2C have been found in neurodevelopmental disorders, such as Kleefstra syndrome, intellectual disability, and autism spectrum disorders. Our finding suggests that schizophrenia might be one of the clinical phenotype spectra of KMT2C mutations, and KMT2C might be a novel risk gene for schizophrenia. Nevertheless, the co-segregation of this mutation with schizophrenia in this family might also be due to chance; functional assays of this mutation are needed to address this issue.
Collapse
Affiliation(s)
- Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan;
- Department and Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
- Correspondence:
| | - Ailing Huang
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien 981, Taiwan;
| | - Yu-Shu Huang
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan;
| | - Ting-Hsuan Fang
- Department and Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| |
Collapse
|
12
|
Jobanputra V, Andrews P, Felice V, Abhyankar A, Kozon L, Robinson D, London F, Hakker I, Wrzeszczynski K, Ronemus M. Detection of Copy Number Variants by Short Multiply Aggregated Sequence Homologies. J Mol Diagn 2020; 22:1476-1481. [PMID: 33132082 DOI: 10.1016/j.jmoldx.2020.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/17/2020] [Accepted: 09/24/2020] [Indexed: 11/25/2022] Open
Abstract
Chromosomal microarray testing is indicated for patients with diagnoses including unexplained developmental delay or intellectual disability, autism spectrum disorders, and multiple congenital anomalies. The short multiply aggregated sequence homologies (SMASH) genomic assay is a novel next-generation sequencing technology that performs copy number analysis at resolution similar to high-coverage whole genome sequencing but requires far less capacity. We benchmarked the performance of SMASH on a panel of genomic DNAs containing known copy number variants (CNVs). SMASH was able to detect pathogenic copy number variants of ≥10 kb in 77 of 77 samples. No pathogenic events were seen in 32 of 32 controls, indicating 100% sensitivity and specificity for detecting pathogenic CNVs >10 kb. Repeatability (interassay precision) and reproducibility (intra-assay precision) were assessed with 13 samples and showed perfect concordance. We also established that SMASH had a limit of detection of 20% for detection of large mosaic CNVs. Finally, we analyzed seven blinded specimens by SMASH analysis and successfully identified all pathogenic events. These results establish the efficacy of the SMASH genomic assay as a clinical test for the detection of pathogenic copy number variants at a resolution comparable to chromosomal microarray analysis.
Collapse
Affiliation(s)
- Vaidehi Jobanputra
- New York Genome Center, New York, New York; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York.
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | | | | | | | | | | | - Inessa Hakker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | | | - Michael Ronemus
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
| |
Collapse
|