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Oza VH, Fisher JL, Darji R, Lasseigne BN. CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability. PeerJ 2023; 11:e15244. [PMID: 37123011 PMCID: PMC10143595 DOI: 10.7717/peerj.15244] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Genomic instability is an important hallmark of cancer and more recently has been identified in others like neurodegenrative diseases. Chromosomal instability, as a measure of genomic instability, has been used to characterize clinical and biological phenotypes associated with these diseases by measuring structural and numerical chromosomal alterations. There have been multiple chromosomal instability scores developed across many studies in the literature; however, these scores have not been compared because of the lack of a single tool available to calculate and facilitate these various metrics. Here, we provide an R package CINmetrics, that calculates six different chromosomal instability scores and allows direct comparison between them. We also demonstrate how these scores differ by applying CINmetrics to breast cancer data from The Cancer Genome Atlas (TCGA). The package is available on CRAN at https://cran.rproject.org/package=CINmetrics and on GitHub at https://github.com/lasseignelab/CINmetrics.
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Affiliation(s)
- Vishal H. Oza
- Department of Cell, Developmental and Integrative Biology, University of Alabama - Birmingham, Birmingham, AL, United States of America
| | - Jennifer L. Fisher
- Department of Cell, Developmental and Integrative Biology, University of Alabama - Birmingham, Birmingham, AL, United States of America
| | - Roshan Darji
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, University of Alabama - Birmingham, Birmingham, AL, United States of America
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2
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Juang JMJ, Binda A, Lee SJ, Hwang JJ, Chen WJ, Liu YB, Lin LY, Yu CC, Ho LT, Huang HC, Chen CYJ, Lu TP, Lai LC, Yeh SFS, Lai LP, Chuang EY, Rivolta I, Antzelevitch C. GSTM3 variant is a novel genetic modifier in Brugada syndrome, a disease with risk of sudden cardiac death. EBioMedicine 2020; 57:102843. [PMID: 32645615 PMCID: PMC7341360 DOI: 10.1016/j.ebiom.2020.102843] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/28/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Brugada syndrome (BrS) is a rare inherited disease causing sudden cardiac death (SCD). Copy number variants (CNVs) can contribute to disease susceptibility, but their role in Brugada syndrome (BrS) is unknown. We aimed to identify a CNV associated with BrS and elucidated its clinical implications. METHODS We enrolled 335 unrelated BrS patients from 2000 to 2018 in the Taiwanese population. Microarray and exome sequencing were used for discovery phase whereas Sanger sequencing was used for the validation phase. HEK cells and zebrafish were used to characterize the function of the CNV variant. FINDINGS A copy number deletion of GSTM3 (chr1:109737011-109737301, hg38) containing the eighth exon and the transcription stop codon was observed in 23.9% of BrS patients versus 0.8% of 15,829 controls in Taiwan Biobank (P < 0.001), and 0% in gnomAD. Co-segregation analysis showed that the co-segregation rate was 20%. Patch clamp experiments showed that in an oxidative stress environment, GSTM3 down-regulation leads to a significant decrease of cardiac sodium channel current amplitude. Ventricular arrhythmia incidence was significantly greater in gstm3 knockout zebrafish at baseline and after flecainide, but was reduced after quinidine, consistent with clinical observations. BrS patients carrying the GSTM3 deletion had higher rates of sudden cardiac arrest and syncope compared to those without (OR: 3.18 (1.77-5.74), P<0.001; OR: 1.76 (1.02-3.05), P = 0.04, respectively). INTERPRETATION This GSTM3 deletion is frequently observed in BrS patients and is associated with reduced INa, pointing to this as a novel potential genetic modifier/risk predictor for the development of the electrocardiographic and arrhythmic manifestations of BrS. FUNDING This work was supported by the Ministry of Science and Technology (107-2314-B-002-261-MY3 to J.M.J. Juang), and by grants HL47678, HL138103 and HL152201 from the National Institutes of Health to CA.
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Affiliation(s)
- Jyh-Ming Jimmy Juang
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Anna Binda
- University of Milano Bicocca School of Medicine and Surgery, Via Cadore, 48, 20900 Monza (MB), Italy
| | - Shyh-Jye Lee
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Juey-Jen Hwang
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wen-Jone Chen
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yen-Bin Liu
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Lian-Yu Lin
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chih-Chieh Yu
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Li-Ting Ho
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hui-Chun Huang
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ching-Yu Julius Chen
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan; Department of Public Health, National Taiwan University, Taipei, Taiwan.
| | - Liang-Chuan Lai
- Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan
| | - Shih-Fan Sherri Yeh
- Department of Environmental and Occupational Medicine, National Taiwan University Hospital, Hsin-Chu branch and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ling-Ping Lai
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Eric Y Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Ilaria Rivolta
- University of Milano Bicocca School of Medicine and Surgery, Via Cadore, 48, 20900 Monza (MB), Italy
| | - Charles Antzelevitch
- Lankenau Institute for Medical Research and Lankenau Heart Institute, Wynnewood, PA and Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, USA.
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Woodbury-Smith M, Zarrei M, Wei J, Thiruvahindrapuram B, O'Connor I, Paterson AD, Yuen RKC, Dastan J, Stavropoulos DJ, Howe JL, Thompson A, Parlier M, Fernandez B, Piven J, Anagnostou E, Scherer SW, Vieland VJ, Szatmari P. Segregating patterns of copy number variations in extended autism spectrum disorder (ASD) pedigrees. Am J Med Genet B Neuropsychiatr Genet 2020; 183:268-276. [PMID: 32372567 DOI: 10.1002/ajmg.b.32785] [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: 05/10/2019] [Revised: 11/05/2019] [Accepted: 03/03/2020] [Indexed: 01/10/2023]
Abstract
Autism spectrum disorder (ASD) is a relatively common childhood onset neurodevelopmental disorder with a complex genetic etiology. While progress has been made in identifying the de novo mutational landscape of ASD, the genetic factors that underpin the ASD's tendency to run in families are not well understood. In this study, nine extended pedigrees each with three or more individuals with ASD, and others with a lesser autism phenotype, were phenotyped and genotyped in an attempt to identify heritable copy number variants (CNVs). Although these families have previously generated linkage signals, no rare CNV segregated with these signals in any family. A small number of clinically relevant CNVs were identified. Only one CNV was identified that segregated with ASD phenotype; namely, a duplication overlapping DLGAP2 in three male offspring each with an ASD diagnosis. This gene encodes a synaptic scaffolding protein, part of a group of proteins known to be pathologically implicated in ASD. On the whole, however, the heritable nature of ASD in the families studied remains poorly understood.
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Affiliation(s)
- Marc Woodbury-Smith
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Irene O'Connor
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
| | - Andrew D Paterson
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Epidemiology and Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Ryan K C Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jila Dastan
- Department of Paediatric Laboratory Medicine, Molecular Genetics Laboratory, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatric Laboratory Medicine, Molecular Genetics Laboratory, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jennifer L Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ann Thompson
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
| | - Morgan Parlier
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | - Bridget Fernandez
- Provincial Medical Genetics Program, Health Sciences Center, St. John's, Newfoundland, Canada
| | - Joseph Piven
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | | | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Veronica J Vieland
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Peter Szatmari
- Centre for Addiction and Mental Health, The Hospital for Sick Children & University of Toronto, Toronto, Ontario, Canada
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Sapkota Y, Narasimhan A, Kumaran M, Sehrawat BS, Damaraju S. A Genome-Wide Association Study to Identify Potential Germline Copy Number Variants for Sporadic Breast Cancer Susceptibility. Cytogenet Genome Res 2016; 149:156-164. [PMID: 27668787 DOI: 10.1159/000448558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 11/19/2022] Open
Abstract
Breast cancer (BC) predisposition in populations arises from both genetic and nongenetic risk factors. Structural variations such as copy number variations (CNVs) are heritable determinants for disease susceptibility. The primary objectives of this study are (1) to identify CNVs associated with sporadic BC using a genome-wide association study (GWAS) design; (2) to utilize 2 distinct CNV calling algorithms to identify concordant CNVs as a strategy to reduce false positive associations in the hypothesis-generating GWAS discovery phase, and (3) to identify potential candidate CNVs for follow-up replication studies. We used Affymetrix SNP Array 6.0 data profiled on Caucasian subjects (422 cases/348 controls) to call CNVs using algorithms implemented in Nexus Copy Number and Partek Genomics Suite software. Nexus algorithm identified CNVs associated with BC (731 autosomal CNVs with >5% frequency in the total sample and Q < 0.05). Thirteen CNVs were identified when Partek algorithm-called CNVs were overlapped with Nexus-identified CNVs; these CNVs showed concordances for frequency, effect size, and direction. Coding genes present within BC-associated CNVs were known to play a role in disease etiology and prognosis. Long noncoding RNAs identified within CNVs showed tissue-specific expression, indicating potential functional relevance of the findings. The identified candidate CNVs warrant independent replication.
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Affiliation(s)
- Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tenn., USA
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Spurlock CF, Tossberg JT, Olsen NJ, Aune TM. Cutting Edge: Chronic NF-κB Activation in CD4+ T Cells in Rheumatoid Arthritis Is Genetically Determined by HLA Risk Alleles. THE JOURNAL OF IMMUNOLOGY 2015; 195:791-5. [PMID: 26091715 DOI: 10.4049/jimmunol.1500267] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/24/2015] [Indexed: 11/19/2022]
Abstract
Of identified genetic variants, HLA polymorphisms confer the greatest risk for developing autoimmune diseases, including rheumatoid arthritis (HLA-DRB1*04). There are strong influences of HLA polymorphisms on cell type-specific gene expression in B cells and monocytes. Their influence on gene expression in CD4(+) T cells is not known. We determined transcript and proteins levels of target genes in lymphocyte/monocyte subsets in healthy controls and rheumatoid arthritis subjects as a function of HLA-DRB1*04 haplotype. We identified gene expression dependent on HLA-DRB1*04 genotype in CD4(+) T cells. NF-κB activity in CD4(+) T cells was also dependent on HLA-DRB1*04 genotype, and blocking HLA-DR inhibited NF-κB activity in CD4(+) T cells and normalized gene expression, as did pharmacologic inhibition of NF-κB. We conclude that interactions between TCR and MHC class II encoded by HLA-DRB1*04 create a proinflammatory "hum" altering CD4(+) T cell phenotype.
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Affiliation(s)
- Charles F Spurlock
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - John T Tossberg
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Nancy J Olsen
- Department of Medicine, Penn State Hershey Milton S. Hershey Medical Center, Hershey, PA 17033; and
| | - Thomas M Aune
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232; Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232
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Copy number variation distribution in six monozygotic twin pairs discordant for schizophrenia. Twin Res Hum Genet 2014; 17:108-20. [PMID: 24556202 DOI: 10.1017/thg.2014.6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have evaluated copy number variants (CNVs) in six monozygotic twin pairs discordant for schizophrenia. The data from Affymetrix® Human SNP 6.0 arrays™ were analyzed using Affymetrix® Genotyping Console™, Partek® Genomics Suite™, PennCNV, and Golden Helix SVS™. This yielded both program-specific and overlapping results. Only CNVs called by Affymetrix Genotyping Console, Partek Genomics Suite, and PennCNV were used in further analysis. This analysis included an assessment of calls in each of the six twin pairs towards identification of unique CNVs in affected and unaffected co-twins. Real time polymerase chain reaction (PCR) experiments confirmed one CNV loss at 7q11.21 that was found in the affected patient but not in the unaffected twin. The results identified CNVs and genes that were previously implicated in mental abnormalities in four of the six twin pairs. It included PYY (twin pairs 1 and 5), EPHA3 (twin pair 3), KIAA1211L (twin pair 4), and GPR139 (twin pair 5). They represent likely candidate genes and CNVs for the discordance of four of the six monozygotic twin pairs for this heterogeneous neurodevelopmental disorder. An explanation for these differences is ontogenetic de novo events that differentiate in the monozygotic twins during development.
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7
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Abstract
MOTIVATION Data quality is a critical issue in the analyses of DNA copy number alterations obtained from microarrays. It is commonly assumed that copy number alteration data can be modeled as piecewise constant and the measurement errors of different probes are independent. However, these assumptions do not always hold in practice. In some published datasets, we find that measurement errors are highly correlated between probes that interrogate nearby genomic loci, and the piecewise-constant model does not fit the data well. The correlated errors cause problems in downstream analysis, leading to a large number of DNA segments falsely identified as having copy number gains and losses. METHOD We developed a simple tool, called autocorrelation scanning profile, to assess the dependence of measurement error between neighboring probes. RESULTS Autocorrelation scanning profile can be used to check data quality and refine the analysis of DNA copy number data, which we demonstrate in some typical datasets. CONTACT lzhangli@mdanderson.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Liangcai Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA and Department of Biophysics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
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Malek JA, Mery E, Mahmoud YA, Al-Azwani EK, Roger L, Huang R, Jouve E, Lis R, Thiery JP, Querleu D, Rafii A. Copy number variation analysis of matched ovarian primary tumors and peritoneal metastasis. PLoS One 2011; 6:e28561. [PMID: 22194851 PMCID: PMC3237432 DOI: 10.1371/journal.pone.0028561] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 11/10/2011] [Indexed: 11/18/2022] Open
Abstract
Ovarian cancer is the most deadly gynecological cancer. The high rate of mortality is due to the large tumor burden with extensive metastatic lesion of the abdominal cavity. Despite initial chemosensitivity and improved surgical procedures, abdominal recurrence remains an issue and results in patients' poor prognosis. Transcriptomic and genetic studies have revealed significant genome pathologies in the primary tumors and yielded important information regarding carcinogenesis. There are, however, few studies on genetic alterations and their consequences in peritoneal metastatic tumors when compared to their matched ovarian primary tumors. We used high-density SNP arrays to investigate copy number variations in matched primary and metastatic ovarian cancer from 9 patients. Here we show that copy number variations acquired by ovarian tumors are significantly different between matched primary and metastatic tumors and these are likely due to different functional requirements. We show that these copy number variations clearly differentially affect specific pathways including the JAK/STAT and cytokine signaling pathways. While many have shown complex involvement of cytokines in the ovarian cancer environment we provide evidence that ovarian tumors have specific copy number variation differences in many of these genes.
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Affiliation(s)
- Joel A. Malek
- Genomics Core, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | | | - Yasmin A. Mahmoud
- Genomics Core, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Eman K. Al-Azwani
- Genomics Core, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | | | - Ruby Huang
- Department of Obstetrics and Gynecology and Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Eva Jouve
- Institut Claudius Regaud, Toulouse, France
| | - Raphael Lis
- Stem Cell and Microenvironment Laboratory, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Jean-Paul Thiery
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Denis Querleu
- Institut Claudius Regaud, Toulouse, France
- McGill University, Montreal, Canada
| | - Arash Rafii
- Stem Cell and Microenvironment Laboratory, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
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