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Yu X, Luo X, Cai G, Xiao F. OSCAA: A two-dimensional Gaussian mixture model for copy number variation association analysis. Genet Epidemiol 2024. [PMID: 38533840 DOI: 10.1002/gepi.22558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/30/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
Copy number variants (CNVs) are prevalent in the human genome and are found to have a profound effect on genomic organization and human diseases. Discovering disease-associated CNVs is critical for understanding the pathogenesis of diseases and aiding their diagnosis and treatment. However, traditional methods for assessing the association between CNVs and disease risks adopt a two-stage strategy conducting quantitative CNV measurements first and then testing for association, which may lead to biased association estimation and low statistical power, serving as a major barrier in routine genome-wide assessment of such variation. In this article, we developed One-Stage CNV-disease Association Analysis (OSCAA), a flexible algorithm to discover disease-associated CNVs for both quantitative and qualitative traits. OSCAA employs a two-dimensional Gaussian mixture model that is built upon the PCs from copy number intensities, accounting for technical biases in CNV detection while simultaneously testing for their effect on outcome traits. In OSCAA, CNVs are identified and their associations with disease risk are evaluated simultaneously in a single step, taking into account the uncertainty of CNV identification in the statistical model. Our simulations demonstrated that OSCAA outperformed the existing one-stage method and traditional two-stage methods by yielding a more accurate estimate of the CNV-disease association, especially for short CNVs or CNVs with weak signals. In conclusion, OSCAA is a powerful and flexible approach for CNV association testing with high sensitivity and specificity, which can be easily applied to different traits and clinical risk predictions.
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Affiliation(s)
- Xuanxuan Yu
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, South Carolina, USA
| | - Xizhi Luo
- Data and Statistical Sciences, AbbVie Inc., North Chicago, Illinois, USA
| | - Guoshuai Cai
- Department of Surgery, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Feifei Xiao
- Department of Biostatistics, College of Public Health and Health Promotion & College of Medicine, University of Florida, Gainesville, Florida, USA
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Al-Shuhaib MBS, Hashim HO. Mastering DNA chromatogram analysis in Sanger sequencing for reliable clinical analysis. J Genet Eng Biotechnol 2023; 21:115. [PMID: 37955813 PMCID: PMC10643650 DOI: 10.1186/s43141-023-00587-6] [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: 10/04/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND Sanger dideoxy sequencing is vital in clinical analysis due to its accuracy, ability to analyze genetic markers like SNPs and STRs, capability to generate reliable DNA profiles, and its role in resolving complex clinical cases. The precision and robustness of Sanger sequencing contribute significantly to the scientific basis of clinical investigations. Though the reading of chromatograms seems to be a routine step, many errors conducted in PCR may lead to consequent limitations in the readings of AGCT peaks. These errors are possibly associated with improper DNA amplification and its subsequent interpretation of DNA sequencing files, such as noisy peaks, artifacts, and confusion between double-peak technical errors, heterozygosity, and double infection potentials. Thus, it is not feasible to read nucleic acid sequences without giving serious attention to these technical problems. To ensure the accuracy of DNA sequencing outcomes, it is also imperative to detect and rectify technical challenges that may lead to misinterpretation of the DNA sequence, resulting in errors and incongruities in subsequent analyses. SHORT CONCLUSION This overview sheds light on prominent technical concerns that can emerge prior to and during the interpretation of DNA chromatograms in Sanger sequencing, along with offering strategies to address them effectively. The significance of identifying and tackling these technical limitations during the chromatogram analysis is underscored in this review. Recognizing these concerns can aid in enhancing the quality of downstream analyses for Sanger sequencing results, which holds notable improvement in accuracy, reliability, and ability to provide crucial genetic information in clinical analysis.
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Affiliation(s)
- Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim 8, Babil, 51001, Iraq.
| | - Hayder O Hashim
- Department of Clinical Laboratory Sciences, College of Pharmacy, University of Babylon, Babil, 51001, Iraq
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3
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Lavoie PM, Rayment JH. Genetics of bronchopulmonary dysplasia: An update. Semin Perinatol 2023; 47:151811. [PMID: 37775368 DOI: 10.1016/j.semperi.2023.151811] [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] [Indexed: 10/01/2023]
Abstract
Bronchopulmonary dysplasia (BPD) is a multi-factorial disease that results from multiple clinical factors, including lung immaturity, mechanical ventilation, oxidative stress, pulmonary congestion due to increasing cardiac blood shunting, nutritional and immunological factors. Twin studies have indicated that susceptibility to BPD can be strongly inherited in some settings. Studies have reported associations between common genetic variants and BPD in preterm infants. Recent genomic studies have highlighted a potential role for molecular pathways involved in inflammation and lung development in affected infants. Rare mutations in genes encoding the lipid transporter ATP-binding cassette, sub-family A, member 3 (ABCA3 gene) which is involved in surfactant synthesis in alveolar type II cells, as well as surfactant protein B (SFTPB) and C (SFTPC) can also result in severe form of neonatal-onset interstitial lung diseases and may also potentially affect the course of BPD. This chapter summarizes the current state of knowledge on the genetics of BPD.
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Affiliation(s)
- Pascal M Lavoie
- Division of Neonatology, Department of Pediatrics, University of British Columbia, Vancouver, Canada; BC Children's Hospital Research Institute, Vancouver, Canada.
| | - Jonathan H Rayment
- BC Children's Hospital Research Institute, Vancouver, Canada; Division of Respiratory Medicine, Department of Pediatrics, University of British Columbia, Vancouver, Canada; Division of Respiratory Medicine, BC Children's Hospital, Vancouver, Canada
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Yu X, Luo X, Cai G, Xiao F. OSCAA: A Two-Dimensional Gaussian Mixture Model for Copy Number Variation Association Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559392. [PMID: 37808739 PMCID: PMC10557568 DOI: 10.1101/2023.09.25.559392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Copy number variants (CNVs) are prevalent in the human genome which provide profound effect on genomic organization and human diseases. Discovering disease associated CNVs is critical for understanding the pathogenesis of diseases and aiding their diagnosis and treatment. However, traditional methods for assessing the association between CNVs and disease risks adopt a two-stage strategy conducting quantitative CNV measurements first and then testing for association, which may lead to biased association estimation and low statistical power, serving as a major barrier in routine genome wide assessment of such variation. In this article, we developed OSCAA, a flexible algorithm to discover disease associated CNVs for both quantitative and qualitative traits. OSCAA employs a two-dimensional Gaussian mixture model that is built upon the principal components from copy number intensities, accounting for technical biases in CNV detection while simultaneously testing for their effect on outcome traits. In OSCAA, CNVs are identified and their associations with disease risk are evaluated simultaneously in a single step, taking into account the uncertainty of CNV identification in the statistical model. Our simulations demonstrated that OSCAA outperformed the existing one-stage method and traditional two-stage methods by yielding a more accurate estimate of the CNV-disease association, especially for short CNVs or CNVs with weak signal. In conclusion, OSCAA is a powerful and flexible approach for CNV association testing with high sensitivity and specificity, which can be easily applied to different traits and clinical risk predictions.
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5
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Xu Y, Wu Q, Tang Z, Tan Z, Pu D, Tan W, Zhang W, Liu S. Comprehensive Analysis of Necroptosis-Related Genes as Prognostic Factors and Immunological Biomarkers in Breast Cancer. J Pers Med 2022; 13:jpm13010044. [PMID: 36675706 PMCID: PMC9863352 DOI: 10.3390/jpm13010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Breast cancer (BC) is a lethal malignancy with a poor prognosis. Necroptosis is critical in the progression of cancer. However, the expression of genes involved in necroptosis in BC and their association with prognosis remain unclear. We investigated the predictive potential of necroptosis-related genes in BC samples from the TCGA dataset. We used LASSO regression to build a risk model consisting of twelve necroptosis-related genes in BC. Using the necroptosis-related risk model, we were able to successfully classify BC patients into high- and low-risk groups with significant prognostic differences (p = 4.872 × 10 -7). Additionally, we developed a matched nomogram predicting 5, 7, and 10-year overall survival in BC patients based on this necroptosis-related risk model. Our next step was to perform multiple GSEA analyses to explore the biological pathways through which these necroptosis-related risk genes influence cancer progression. For these twelve risk model genes, we analyzed CNV, SNV, OS, methylation, immune cell infiltration, and drug sensitivity in pan-cancer. In addition, immunohistochemical data from the THPA database were used to validate the protein expression of these risk model genes in BC. Taken together, we believe that necroptosis-related genes are considered potential therapeutic targets in BC and should be further investigated.
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Identification of Copy Number Alterations from Next-Generation Sequencing Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:55-74. [DOI: 10.1007/978-3-030-91836-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Çalışkan E, Şahin MN, Güldağ MA. Oxytocin and Oxytocin Receptor Gene Regulation in Williams Syndrome: A Systematic Review. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2021; 94:623-635. [PMID: 34970101 PMCID: PMC8686774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Williams Syndrome (WS) is a rare genetic multisystem disorder that occurs because of a deletion of approximately 25 genes in the 7q11.23 chromosome region. This causes dysmorphic facial appearances, multiple congenital cardiovascular defects, delayed motor skills, and abnormalities in connective tissues and the endocrine system. The patients are mostly diagnosed with mild to moderate mental retardation, however, they have a hyper sociable, socially dis-inhibited, and outgoing personality, empathetic behavior, and are highly talkative. Oxytocin (OT), a neuropeptide synthesized at the hypothalamus, plays an important role in cognition and behavior, and is thought to be affecting WS patients' attitudes at its different amounts. Oxytocin receptor gene (OXTR), on chromosome 3p25.3, is considered regulating oxytocin receptors, via which OT exerts its effect. WS is a crucial disorder to understand gene, hormone, brain, and behavior associations in terms of sociality and neuropsychiatric conditions. Alterations to the WS gene region offer an opportunity to deepen our understandings of autism spectrum disorder, schizophrenia, anxiety, or depression. We aim to systematically present the data available of OT/OXTR regulation and expression, and the evidence for whether these mechanisms are dysregulated in WS. These results are important, as they predict strong epigenetic control over social behavior by methylation, single nucleotide polymorphisms, and other alterations. The comparison and collaboration of these studies may help to establish a better treatment or management approach for patients with WS if backed up with future research.
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Affiliation(s)
- Elif Çalışkan
- Trakya University School of Medicine, Edirne,
Turkey,To whom all correspondence should be addressed:
Elif Çalışkan, Trakya University School of Medicine, Edirne, Turkey;
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Abdelwahed M, Maaloul I, Benoit V, Hilbert P, Hachicha M, Kamoun H, Keskes-Ammar L, Belguith N. Copy-number variation of the NPHP1 gene in patients with juvenile Nephronophthisis. Acta Clin Belg 2021; 76:16-24. [PMID: 31402777 DOI: 10.1080/17843286.2019.1655231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Objective: Juvenile nephronophthisis (NPHP) is an autosomal recessive cystic disease of the kidney. It represents the most frequent genetic cause of chronic renal failure in children. Methods: we investigated clinical and molecular features in two children with Juvenile nephronophthisis using firstly Multiplex ligation-dependent probe amplification (MLPA) and secondly multiplex PCR. Results: we report a homozygous NPHP1 deletion in two children. Conclusion: NPHP1 deletion analysis using diagnostic methods (e.g. MLPA, Multiplex PCR) should always be considered in patients with nephronophthisis, especially from consanguineous families. Our results provide insights into genotype-phenotype correlations in juvenile nephronophthisis that can be utilized in genetic counseling.
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Affiliation(s)
- Mayssa Abdelwahed
- Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Sfax, Tunisia
| | - Ines Maaloul
- Pediatric Department of Hedi Chaker Hospital, Sfax, Tunisia
| | - Valerie Benoit
- Center of Human Genetics, Institute of Pathology and Genetics, Biopark Charleroi Brussels, Gosselies, Belgium
| | - Pascale Hilbert
- Center of Human Genetics, Institute of Pathology and Genetics, Biopark Charleroi Brussels, Gosselies, Belgium
| | | | - Hassen Kamoun
- Medical Genetics Department of Hedi Chaker Hospital, Sfax, Tunisia
| | - Leila Keskes-Ammar
- Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Sfax, Tunisia
| | - Neila Belguith
- Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Sfax, Tunisia
- Medical Genetics Department of Hedi Chaker Hospital, Sfax, Tunisia
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Alves MMC, Almeida M, Oliani AH, Breitenfeld L, Ramalhinho AC. Women with polycystic ovary syndrome and other causes of infertility have a higher prevalence of GSTT1 deletion. Reprod Biomed Online 2020; 41:892-901. [PMID: 32855063 DOI: 10.1016/j.rbmo.2020.06.010] [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: 01/08/2020] [Revised: 06/05/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
RESEARCH QUESTION Is GSTM1 and GSTT1 deletion associated with the development of polycystic ovary syndrome (PCOS)? DESIGN A case-control study was designed to investigate the association between GSTM1 and GSTT1 gene polymorphisms with PCOS. Blood samples from 201 women diagnosed with infertility were taken, of which 69 women were diagnosed with PCOS. Genomic DNA was extracted, and genotyping analyses were conducted by polymerase chain reaction-based methods. Odds ratios and 95% confidence intervals were calculated by unconditional logistic regression. RESULTS An increased risk of PCOS was found to be associated with GSTT1 null genotype (OR 4.890, 95% CI 2.261 to 9.122; P < 0.001). A strong association between GSTT1 null genotype was found with female infertility, regardless of the associated cause (OR 5.300, 95% CI 3.238 to 8.675; P < 0.001) as well as with the GSTM1 null genotype (OR 1.620, 95% CI 1.067 to 2.459; P = 0.026). A statistically significant association with the development of infertility was also found when carriers of the combined genotype GSTT1+/GSTM1+ was compared with carriers of the combined genotype GSTT1-/ GSTM1+ (OR 3.600 95% CI 1.864 to 6.956; P < 0.001). The two-way combination of GSTT1 and GSTM1 null genotypes resulted in an increased susceptibility to infertility development (OR 11.136; 95% CI 5.035 to 24.629; P < 0.001). CONCLUSIONS Carriers of GSTT1 null genotype seem to have higher susceptibility to developing PCOS and infertility from other causes. Also, GSTT1 null genotype, alone or in association, are related with increased susceptibility to infertility development, independently of its cause. GSTM1 null genotype is only associated with all cause of infertility when the GSTT1 is null.
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Affiliation(s)
- Maria Manuel Casteleiro Alves
- Health Sciences Research Centre (CICS), Faculty of Health Sciences, University of Beira Interior (UBI); Avenida Infante D. Henrique 6200-506 Covilhã, Portugal; Assisted Reproduction Laboratory of Academic Hospital of Cova da Beira (CHUCB); Quinta do Alvito 6200-251 Covilhã, Portugal
| | - Micaela Almeida
- Health Sciences Research Centre (CICS), Faculty of Health Sciences, University of Beira Interior (UBI); Avenida Infante D. Henrique 6200-506 Covilhã, Portugal
| | - António Hélio Oliani
- Assisted Reproduction Laboratory of Academic Hospital of Cova da Beira (CHUCB); Quinta do Alvito 6200-251 Covilhã, Portugal; São José do Rio Preto School of Medicine (FAMERP), Gynaecology and Obstetrics São José do Rio Preto; Avenida Brg. Faria Lima 5416 Vila São Pedro, São José do Rio Preto, São Paulo, 15090-000 Brazil
| | - Luiza Breitenfeld
- Health Sciences Research Centre (CICS), Faculty of Health Sciences, University of Beira Interior (UBI); Avenida Infante D. Henrique 6200-506 Covilhã, Portugal
| | - Ana Cristina Ramalhinho
- Health Sciences Research Centre (CICS), Faculty of Health Sciences, University of Beira Interior (UBI); Avenida Infante D. Henrique 6200-506 Covilhã, Portugal; Assisted Reproduction Laboratory of Academic Hospital of Cova da Beira (CHUCB); Quinta do Alvito 6200-251 Covilhã, Portugal.
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Bruders R, Van Hollebeke H, Osborne EJ, Kronenberg Z, Maclary E, Yandell M, Shapiro MD. A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia). PLoS Genet 2020; 16:e1008274. [PMID: 32433666 PMCID: PMC7239393 DOI: 10.1371/journal.pgen.1008274] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 04/09/2020] [Indexed: 12/15/2022] Open
Abstract
Rock pigeons (Columba livia) display an extraordinary array of pigment pattern variation. One such pattern, Almond, is characterized by a variegated patchwork of plumage colors that are distributed in an apparently random manner. Almond is a sex-linked, semi-dominant trait controlled by the classical Stipper (St) locus. Heterozygous males (ZStZ+ sex chromosomes) and hemizygous Almond females (ZStW) are favored by breeders for their attractive plumage. In contrast, homozygous Almond males (ZStZSt) develop severe eye defects and often lack plumage pigmentation, suggesting that higher dosage of the mutant allele is deleterious. To determine the molecular basis of Almond, we compared the genomes of Almond pigeons to non-Almond pigeons and identified a candidate St locus on the Z chromosome. We found a copy number variant (CNV) within the differentiated region that captures complete or partial coding sequences of four genes, including the melanosome maturation gene Mlana. We did not find fixed coding changes in genes within the CNV, but all genes are misexpressed in regenerating feather bud collar cells of Almond birds. Notably, six other alleles at the St locus are associated with depigmentation phenotypes, and all exhibit expansion of the same CNV. Structural variation at St is linked to diversity in plumage pigmentation and gene expression, and thus provides a potential mode of rapid phenotypic evolution in pigeons. The genetic changes responsible for different animal color patterns are poorly understood, due in part to a paucity of research organisms that are both genetically tractable and phenotypically diverse. Domestic pigeons (Columba livia) have been artificially selected for many traits, including an enormous variety of color patterns that are variable both within and among different breeds of this single species. We investigated the genetic basis of a sex-linked color pattern in pigeons called Almond that is characterized by a sprinkled pattern of plumage pigmentation. Pigeons with one copy of the Almond allele have desirable color pattern; however, male pigeons with two copies of the Almond mutation have severely depleted pigmentation and congenital eye defects. By comparing the genomes of Almond and non-Almond pigeons, we discovered that Almond pigeons have extra copies of a chromosome region that contains a gene that is critical for the formation of pigment granules. We also found that different numbers of copies of this region are associated with varying degrees of pigment reduction. The Almond phenotype in pigeons bears a remarkable resemblance to Merle coat color mutants in dogs, and our new results from pigeons suggest that similar genetic mechanisms underlie these traits in both species. Our work highlights the role of gene copy number variation as a potential driver of rapid phenotypic evolution.
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Affiliation(s)
- Rebecca Bruders
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Hannah Van Hollebeke
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Edward J. Osborne
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Zev Kronenberg
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Emily Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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Qureshi AH, Liang D, Canas J, Hooks J, Arrregui SW, Saxena V, Rooney R, Nolan V, Schwaderer AL, Hains DS. DCHS1 DNA copy number loss associated with pediatric urinary tract infection risk. Innate Immun 2020; 26:473-481. [PMID: 32295462 PMCID: PMC7491237 DOI: 10.1177/1753425920917193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Urinary tract infections (UTI), associated with vesicoureteral reflux (VUR), can lead to chronic kidney disease. Genetic alterations in the innate immune defenses contribute to UTI risk. We investigated a novel gene, Dachsous Cadherin-Related 1 (DCHS1), in children with UTI. We determined absolute DNA copy number (CN) of DCHS1 in children with UTI. In this case-control study, we utilized multiple complementary methods to determine the genomic CN of DCHS1. Children with (n = 370) and without (n = 71) VUR from two well-phenotyped clinical trials of UTI were copy-typed and compared to 491 healthy controls with no known history of VUR or UTI. Less than 1% of controls had a single copy of DCHS1, while 31% of children with UTI and no VUR and 7% of children with UTI and VUR had a single copy of the DCHS1 gene. Using immunostaining, we localized expression postnatally to the bladder and renal epithelia. Mice were also challenged with two uropathogenic Escherichia coli strains, and Dchs1 mRNA was quantified. This study represents the first report of DCHS1 in association with pediatric UTI. We hypothesize that its role in innate immunity is critical to lower urinary tract defense. Further investigation is required to determine the role of DCHS1 in innate immunity.
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Affiliation(s)
- Aslam H Qureshi
- Division of Pediatric Nephrology, Department of Pediatrics, University of Tennessee Health Science Center, USA.,Department of Pediatrics, Children's Hospital at Erlanger, University of Tennessee College of Medicine, USA
| | - Dong Liang
- Department of Pediatrics, Indiana University School of Medicine, USA
| | - Jorge Canas
- Department of Pediatrics, Indiana University School of Medicine, USA
| | - Jenaya Hooks
- Department of Pediatrics, Indiana University School of Medicine, USA
| | - Samuel W Arrregui
- Department of Pediatrics, Indiana University School of Medicine, USA
| | - Vijay Saxena
- Department of Pediatrics, Indiana University School of Medicine, USA
| | - Robert Rooney
- Integrative Genomics Biorepository, Department of Pediatrics, University of Tennessee Health Science Center, USA
| | - Vikki Nolan
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, USA
| | - Andrew L Schwaderer
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, USA
| | - David S Hains
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, USA
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MR imaging phenotype correlates with extent of genome-wide copy number abundance in IDH mutant gliomas. Neuroradiology 2019; 61:1023-1031. [PMID: 31134296 DOI: 10.1007/s00234-019-02219-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 04/29/2019] [Indexed: 12/15/2022]
Abstract
PURPOSE There is variability in survival within IDH mutant gliomas determined by chromosomal events. Copy number variation (CNV) abundance associated with survival in low-grade and IDH mutant astrocytoma has been reported. Our purpose was to correlate the extent of genome-wide CNV abundance in IDH mutant astrocytomas with MRI features. METHODS Presurgical MRI and CNV plots derived from Illumina 850k EPIC DNA methylation arrays of 18 cases of WHO grade II-IV IDH mutant astrocytomas were reviewed. IDH mutant astrocytomas were divided into CNV stable group (CNV-S) with ≤ 3 chromosomal gains or losses and lack of focal gene amplifications and CNV unstable group (CNV-U) with > 3 large chromosomal gains/losses and/or focal amplifications. The associations between MR features, relative cerebral blood volume (rCBV), CNV abundance, and time to progression were assessed. Tumor rCBV estimates were obtained using DSC T2* perfusion analysis. RESULTS There were nine (50%) CNV-S and nine (50%) CNV-U IDH mutant astrocytomas. CNV-U tumors showed larger mean tumor size (P = 0.004) and maximum diameter on FLAIR (P = 0.004) and also demonstrated significantly higher median rCBV than CNV-S tumors (2.62 vs 0.78, P = 0.019). CNV-U tumors tended to have shorter time to progression although without statistical significance (P = 0.393). CONCLUSIONS Larger size/diameter and higher rCBVs were seen associated CNV-U astrocytomas, suggesting a correlation of aggressive imaging phenotype with unstable and aggressive genotype in IDH mutant astrocytomas.
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Shahba S, Jafari Shakib R, Jamshidi A, Vojdanian M, Akhtari M, Aslani S, Poursani S, Nikokar I, Mahmoudi M. Association study of copy number variation in BMP8A gene with the risk of ankylosing spondylitis in Iranian population. J Cell Biochem 2019; 120:8359-8365. [PMID: 30485530 DOI: 10.1002/jcb.28120] [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: 08/26/2018] [Accepted: 10/31/2018] [Indexed: 01/24/2023]
Abstract
BACKGROUND Copy number variation (CNV) of DNA segments has been considered as an important component of genetic variation, affecting the quality and quantity of gene expression. Bone morphogenic protein 8A (BMP8A) has been reported to function in bone formation. With respect to the bone and joint complications in ankylosing spondylitis (AS), this investigation aimed to study the role of BMP8A gene CNV in impressing the gene expression as well as the disease risk. METHODS A total of 900 individuals, including 450 patients with AS and 450 healthy controls were enrolled. The copy numbers of BMP8A gene were detected by TaqMan real-time polymerase chain reaction (PCR) method. BMP8A messenger RNA (mRNA) transcript level in peripheral blood mononuclear cells (PBMCs) was also measured by SYBR Green real-time gene expression PCR method. RESULTS No significant association of BMP8A copy number was detected with the risk of AS. BMP8A mRNA expression level was significantly downregulated in patients compared with controls. mRNA expression level of BMP8A in both AS patients with and without syndesmophyte was significantly lower than the healthy control group. There was no correlation between the mRNA expression level of BMP8A and both demographic and clinical data of the patients. CONCLUSIONS Although BMP8A gene expression was downregulated in patients with AS, its copy number could not affect the transcript level of BMP8A gene in PBMCs and was not associated with susceptibility to AS in Iranian population. BMP8a may take into account as an indicator of bone formation process in AS, but it seems that mechanisms other than CNV may regulate this protein.
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Affiliation(s)
- Sara Shahba
- Medical Biotechnology Research Center, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran.,Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Jafari Shakib
- Department of Immunology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Ahmadreza Jamshidi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Vojdanian
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Akhtari
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeed Aslani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shiva Poursani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Iraj Nikokar
- Laboratory of Microbiology and Immunology of Infectious Diseases, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
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14
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Zhang Y, Zhang J, Sheng H, Li H, Wang R. Acute phase reactant serum amyloid A in inflammation and other diseases. Adv Clin Chem 2019; 90:25-80. [PMID: 31122611 DOI: 10.1016/bs.acc.2019.01.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Acute-phase reactant serum amyloid A (A-SAA) plays an important role in acute and chronic inflammation and is used in clinical laboratories as an indicator of inflammation. Although both A-SAA and C-reactive protein (CRP) are acute-phase proteins, the detection of A-SAA is more conclusive than the detection of CRP in patients with viral infections, severe acute pancreatitis, and rejection reactions to kidney transplants. A-SAA has greater clinical diagnostic value in patients who are immunosuppressed, patients with cystic fibrosis who are treated with corticoids, and preterm infants with late-onset sepsis. Nevertheless, for the assessment of the inflammation status and identification of viral infection in other pathologies, such as bacterial infections, the combinatorial use of A-SAA and other acute-phase proteins (APPs), such as CRP and procalcitonin (PCT), can provide more information and sensitivity than the use of any of these proteins alone, and the information generated is important in guiding antibiotic therapy. In addition, A-SAA-associated diseases and the diagnostic value of A-SAA are discussed. However, the relationship between different A-SAA isotypes and their human diseases are mostly derived from research laboratories with limited clinical samples. Thus, further clinical evaluations are necessary to confirm the clinical significance of each A-SAA isotype. Furthermore, the currently available A-SAA assays are based on polyclonal antibodies, which lack isotype specificity and are associated with many inflammatory diseases. Therefore, these assays are usually used in combination with other biomarkers in the clinic.
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Affiliation(s)
- Yan Zhang
- Shanghai R&D Center, DiaSys Diagnostic Systems (Shanghai) Co., Ltd., Shanghai, China
| | - Jie Zhang
- Shanghai R&D Center, DiaSys Diagnostic Systems (Shanghai) Co., Ltd., Shanghai, China
| | - Huiming Sheng
- Department of Laboratory Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haichuan Li
- C.N. Maternity & Infant Health Hospital, Shanghai, China
| | - Rongfang Wang
- Shanghai R&D Center, DiaSys Diagnostic Systems (Shanghai) Co., Ltd., Shanghai, China.
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15
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Di Gerlando R, Mastrangelo S, Sardina MT, Ragatzu M, Spaterna A, Portolano B, Biscarini F, Ciampolini R. A Genome-Wide Detection of Copy Number Variations Using SNP Genotyping Arrays in Braque Français Type Pyrénées Dogs. Animals (Basel) 2019; 9:E77. [PMID: 30832273 PMCID: PMC6466271 DOI: 10.3390/ani9030077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/21/2019] [Accepted: 02/28/2019] [Indexed: 01/07/2023] Open
Abstract
Copy number variants (CNVs) are an important source of genetic variation complementary to single nucleotide polymorphisms (SNPs). Only few studies have been conducted in dogs on CNVs derived from high-density SNP array data, and many canine breeds still remain uncharacterized, e.g., the Braque Français, type Pyrénées breed (BRA). Therefore, in an effort to more comprehensively investigate the canine genome for CNVs, we used a high-density SNP array (170 K) to discover CNVs in BRA. The CNV regions (CNVRs) were identified through the merging of two different CNVRs datasets, obtained separately from SNP data using the PennCNV and SVS software. A total of 45 stringent CNVRs, ranging from 3.5 kb to 458,716 kb in length were detected in 26 dog samples. Results overlapped moderately in comparison with previous studies on CNVs in dogs, leading to the identification of 16 novel CNVRs. A total of 159 genes were annotated in the CNVRs detected with stringent quality criteria in particular high classification stringency and false discovery rate correction. The gene ontology enrichment analysis provided information on biological processes and cellular components related to muscle structure development and muscle cell differentiation. Considering that BRA is a breed used for speed in hunting and retrieval, for the ability to find feathered game, and for pointing, we can hypothesize that selection for such hunting behavior could have driven, at least in part, the presence of these genes into the CNVRs.
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Affiliation(s)
- Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy.
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy.
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy.
| | - Marco Ragatzu
- Club Italiano Braque Français Type Pyrénées, 58011 Capalbio, Italy.
| | - Andrea Spaterna
- Scuola di Scienze Mediche Veterinarie, University of Camerino, 62024 Matelica, Italy.
- Centro interuniversitario di ricerca e di consulenza sulla genetica e la clinica del cane, 62024, Matelica, MC, Italy.
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy.
| | - Filippo Biscarini
- Consiglio Nazionale delle Ricerche-Istituto di Biologia e Biotecnologia Agraria, 20133 Milano, Italy.
| | - Roberta Ciampolini
- Centro interuniversitario di ricerca e di consulenza sulla genetica e la clinica del cane, 62024, Matelica, MC, Italy.
- Dipartimento di Scienze Veterinarie, University of Pisa, 56100 Pisa, Italy.
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16
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Di Gerlando R, Sardina MT, Tolone M, Sutera AM, Mastrangelo S, Portolano B. Genome-wide detection of copy-number variations in local cattle breeds. ANIMAL PRODUCTION SCIENCE 2019. [DOI: 10.1071/an17603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The aim of the present study was to identify copy-number variations (CNVs) in Cinisara (CIN) and Modicana (MOD) cattle breeds on the basis of signal intensity (logR ratio) and B allele frequency of each marker, using Illumina’s BovineSNP50K Genotyping BeadChip. The CNVs were detected with the PennCNV and SVS 8.7.0 software and were aggregated into CNV regions (CNVRs). PennCNV identified 487 CNVs in CIN that aggregated into 86 CNVRs, and 424 CNVs in MOD that aggregated into 81 CNVRs. SVS identified a total of 207 CNVs in CIN that aggregated into 39 CNVRs, and 181 CNVs in MOD that aggregated into 41 CNVRs. The CNVRs identified with the two softwares contained 29 common CNVRs in CIN and 17 common CNVRs in MOD. Only a small number of CNVRs identified in the present study have been identified elsewhere, probably because of the limitations of the array used. In total, 178 and 208 genes were found within the CNVRs of CIN and MOD respectively. Gene Ontology and KEGG pathway analyses showed that several of these genes are involved in milk production, reproduction and behaviour, the immune response, and resistance/susceptibility to infectious diseases. Our results have provided significant information for the construction of more-complete CNV maps of the bovine genome and offer an important resource for the investigation of genomic changes and traits of interest in the CIN and MOD cattle breeds. Our results will also be valuable for future studies and constitute a preliminary report of the CNV distribution resources in local cattle genomes.
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17
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Holden LA, Wilson C, Heineman Z, Dobrinski KP, Brown KH. An Interrogation of Shared and Unique Copy Number Variants Across Genetically Distinct Zebrafish Strains. Zebrafish 2018; 16:29-36. [PMID: 30418105 DOI: 10.1089/zeb.2018.1644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Zebrafish (Danio rerio) are a widely utilized model system for human disorders, but common laboratory strains have distinct behavioral and physiological differences. Accompanying these known strain differences, commonly used "wildtype" zebrafish strains have both shared and unique suites of single nucleotide polymorphisms and copy number variants (CNVs). Despite this, genomic variation is often ignored in study design, and the actual strain used is often not adequately reported. The goal of this study was to assess CNVs across three common laboratory strains of zebrafish-AB, Tubingen (TU), and WIK-and provide these data as a tool for the zebrafish community. Herein we identified 1351 CNV regions within the most recent genome assembly (GRCz11) covering 1.9% of the zebrafish genome (31.7 Mb). CNVs were found across all chromosomes, and 2200 genes (5121 transcripts) lie within ±5 kb of identified CNVs, pointing to likely cis regulatory actions of CNVs on nearby gene neighbors. We have created a Public Session accessible on the UCSC Genome Browser to view CNVs from this study titled "danRer11 zebrafish CNV across strains" as a tool for the zebrafish community.
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Affiliation(s)
- Lindsay A Holden
- 1 Department of Biology, Portland State University, Portland, Oregon
| | - Charles Wilson
- 1 Department of Biology, Portland State University, Portland, Oregon
| | - Zachary Heineman
- 1 Department of Biology, Portland State University, Portland, Oregon
| | | | - Kim H Brown
- 1 Department of Biology, Portland State University, Portland, Oregon
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18
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Zhang J, Guo W, Shi C, Zhang Y, Zhang C, Zhang L, Wang R, Pan B. Copy Number Variations in Serum Amyloid A Play a Role in the Determination of its Individual Baseline Concentrations. Clin Chem 2018; 64:402-404. [PMID: 29046329 DOI: 10.1373/clinchem.2017.279372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jie Zhang
- Shanghai R&D Center DiaSys Diagnostic Systems (Shanghai) Co., Ltd. Shanghai, China
- Department of Biochemical Engineering School of Chemical Engineering and Technology Tianjin University, Tianjin, China
- Tianjin International Joint Academy of Biomedicine (TJAB) TEDA, Tianjin, China
| | - Wei Guo
- Department of Laboratory Medicine Zhongshan Hospital Fudan University Shanghai, China
| | - Changgen Shi
- Shanghai R&D Center DiaSys Diagnostic Systems (Shanghai) Co., Ltd. Shanghai, China
- School of Life Sciences Fudan University, Shanghai, China
| | - Yan Zhang
- Shanghai R&D Center DiaSys Diagnostic Systems (Shanghai) Co., Ltd. Shanghai, China
| | - Chunyan Zhang
- Department of Laboratory Medicine Zhongshan Hospital Fudan University Shanghai, China
| | - Lei Zhang
- Department of Biochemical Engineering School of Chemical Engineering and Technology Tianjin University, Tianjin, China
| | - Rongfang Wang
- Shanghai R&D Center DiaSys Diagnostic Systems (Shanghai) Co., Ltd. Shanghai, China
- Tianjin International Joint Academy of Biomedicine (TJAB) TEDA, Tianjin, China
| | - Baishen Pan
- Department of Laboratory Medicine Zhongshan Hospital Fudan University Shanghai, China
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19
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The research on association of copy number variation in chromosome 9p21 region with atherothrombotic stroke in the Han Chinese population. J Neurol Sci 2017; 377:88-94. [PMID: 28477716 DOI: 10.1016/j.jns.2017.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 03/01/2017] [Accepted: 04/03/2017] [Indexed: 11/23/2022]
Abstract
BACKGROUND/PURPOSE The copy number variants (CNVs) contain more genetic information compared with SNPs. The aim of this study was to elucidate whether the CNVs in Chromosome 9p21 region are associated with increased risk of Atherothrombotic stroke (ATS) in a Han Chinese population. METHODS A case-controlled association study was conducted in which only patients with ATS were enrolled. The CNVs were detected by the method of multiplex competitive amplification. The differences in distribution of CNVs between cases and controls were analyzed using univariate and multivariate logistic regression analysis. Subgroup analyses were also carried out to determine whether the effect of the CNVs was specific to age and gender among the subjects. RESULTS A total of 274 ATS patients and 282 health controls were included in the present study. 4 genes (ANRIL, CDKN2A, CDKN2B, and MTAP) including eight gene fragments in all were analyzed for CNV. The results showed that the copied number of most CNV in the 4 genes is two. There was no significant difference of CNV frequency between groups. CONCLUSIONS The obtained data suggested a negative association between CNV of the four genes and ATS. It is necessary to perform sequencing analyses across the entire 9p21 region for detecting rare or uncommon CNV.
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20
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Zare F, Dow M, Monteleone N, Hosny A, Nabavi S. An evaluation of copy number variation detection tools for cancer using whole exome sequencing data. BMC Bioinformatics 2017; 18:286. [PMID: 28569140 PMCID: PMC5452530 DOI: 10.1186/s12859-017-1705-x] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/22/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have created an opportunity for detecting CNVs more accurately. Recently whole exome sequencing (WES) has become primary strategy for sequencing patient samples and study their genomics aberrations. However, compared to whole genome sequencing, WES introduces more biases and noise that make CNV detection very challenging. Additionally, tumors' complexity makes the detection of cancer specific CNVs even more difficult. Although many CNV detection tools have been developed since introducing NGS data, there are few tools for somatic CNV detection for WES data in cancer. RESULTS In this study, we evaluated the performance of the most recent and commonly used CNV detection tools for WES data in cancer to address their limitations and provide guidelines for developing new ones. We focused on the tools that have been designed or have the ability to detect cancer somatic aberrations. We compared the performance of the tools in terms of sensitivity and false discovery rate (FDR) using real data and simulated data. Comparative analysis of the results of the tools showed that there is a low consensus among the tools in calling CNVs. Using real data, tools show moderate sensitivity (~50% - ~80%), fair specificity (~70% - ~94%) and poor FDRs (~27% - ~60%). Also, using simulated data we observed that increasing the coverage more than 10× in exonic regions does not improve the detection power of the tools significantly. CONCLUSIONS The limited performance of the current CNV detection tools for WES data in cancer indicates the need for developing more efficient and precise CNV detection methods. Due to the complexity of tumors and high level of noise and biases in WES data, employing advanced novel segmentation, normalization and de-noising techniques that are designed specifically for cancer data is necessary. Also, CNV detection development suffers from the lack of a gold standard for performance evaluation. Finally, developing tools with user-friendly user interfaces and visualization features can enhance CNV studies for a broader range of users.
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Affiliation(s)
- Fatima Zare
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Michelle Dow
- Biomedical Informatics Department, University of California San Diego, San Diego, CA, USA
| | - Nicholas Monteleone
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Abdelrahman Hosny
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Sheida Nabavi
- Computer Science and Engineering Department and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
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21
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Yamamoto Y, Suehiro Y, Suzuki A, Nawata R, Kawai Y, Inoue R, Hirata H, Matsumoto H, Yamasaki T, Sasaki K, Matsuyama H. Germline DNA copy number variations as potential prognostic markers for non-muscle invasive bladder cancer progression. Oncol Lett 2017; 14:1193-1199. [PMID: 28693295 DOI: 10.3892/ol.2017.6233] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/28/2017] [Indexed: 01/21/2023] Open
Abstract
Accumulating evidence has suggested that germline DNA copy number variations (CNVs) affect various disorders, including human malignancies. However, the significance of CNVs in non-muscle invasive bladder cancer (NMIBC) remains unclear. The purpose of the present study was to identify the role of CNVs in NMIBC. Array comparative genomic hybridization (CGH) analysis was performed to search for candidate CNVs associated with NMIBC susceptibility. Quantitative polymerase chain reaction was carried out to evaluate CNVs associated with patient outcome in 189 NMIBC cases. In total, 11 CNVs were associated with NMIBC risk in array CGH analysis. Out of the 189 CNVs examined, family with sequence similarity 81 member A (FAM81A) and proprotein convertase subtilisin/kexin type 6 (PCSK6) CNVs exhibited a significant association with recurrence and disease progression in NMIBC. PCSK6 has been reported to regulate proliferation and tumor progression in breast and prostate malignancies. Notably, patients with pT1 stage had significantly lower PCSK6 relative copy number than those with pTa (P=0.0196). In multivariate analyses, PCSK6 copy number was an independent prognostic factor for progression-free survival (P=0.0456; risk ratio, 2.17; 95% confidence interval, 1.02-4.82). These data suggest that PCSK6 CNV is a potential new tumor marker for estimating disease progression in NMIBC.
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Affiliation(s)
- Yoshiaki Yamamoto
- Department of Urology, Graduate School of Medicine, Yamaguchi University, Ube, Yamaguchi 755-8505, Japan
| | - Yutaka Suehiro
- Department of Oncology and Laboratory Medicine, Graduate School of Medicine, Yamaguchi University, Ube, Yamaguchi 755-8505, Japan
| | - Atomu Suzuki
- Department of Urology, Graduate School of Medicine, Yamaguchi University, Ube, Yamaguchi 755-8505, Japan
| | - Ryosuke Nawata
- Department of Urology, Graduate School of Medicine, Yamaguchi University, Ube, Yamaguchi 755-8505, Japan
| | - Yoshihisa Kawai
- Department of Urology, Graduate School of Medicine, Yamaguchi University, Ube, Yamaguchi 755-8505, Japan
| | - Ryo Inoue
- Department of Urology, Graduate School of Medicine, Yamaguchi University, Ube, Yamaguchi 755-8505, Japan
| | - Hiroshi Hirata
- Department of Urology, Graduate School of Medicine, Yamaguchi University, Ube, Yamaguchi 755-8505, Japan
| | - Hiroaki Matsumoto
- Department of Urology, Graduate School of Medicine, Yamaguchi University, Ube, Yamaguchi 755-8505, Japan
| | - Takahiro Yamasaki
- Department of Oncology and Laboratory Medicine, Graduate School of Medicine, Yamaguchi University, Ube, Yamaguchi 755-8505, Japan
| | - Kohsuke Sasaki
- Department of Pathology, Graduate School of Medicine, Yamaguchi University, Ube, Yamaguchi 755-8505, Japan.,Department of Pathology, Shimonoseki Medical Center, Shimonoseki, Yamaguchi 750-0061, Japan
| | - Hideyasu Matsuyama
- Department of Urology, Graduate School of Medicine, Yamaguchi University, Ube, Yamaguchi 755-8505, Japan
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22
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Abstract
Copy number variation (CNV), where a segment of DNA differs in copy number between different individuals, is an extensive and often underappreciated source of genetic variation within species. However, reliably determining copy number of a particular DNA sequence for a large number of samples can be challenging. Here, I describe and review the paralogue ratio test (PRT) in detail. PRT was developed to robustly type the CNV of the beta-defensin locus using small amounts of genomic DNA in a high-throughput manner, and has been applied successfully at many other loci. I discuss the strategies for designing successful PRT assays using both manual and bioinformatics methods, how to optimize experimental conditions, and approaches for analyzing the data. I discuss strengths and weaknesses of the approach, and how to troubleshoot results, as well as the range of problems to which PRT can be a potential solution.
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23
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Prinsen R, Strillacci M, Schiavini F, Santus E, Rossoni A, Maurer V, Bieber A, Gredler B, Dolezal M, Bagnato A. A genome-wide scan of copy number variants using high-density SNPs in Brown Swiss dairy cattle. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.08.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Durán Aguilar M, Román Ponce SI, Ruiz López FJ, González Padilla E, Vásquez Peláez CG, Bagnato A, Strillacci MG. Genome-wide association study for milk somatic cell score in holstein cattle using copy number variation as markers. J Anim Breed Genet 2016; 134:49-59. [PMID: 27578198 DOI: 10.1111/jbg.12238] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 08/03/2016] [Indexed: 12/21/2022]
Abstract
Mastitis, the most common and expensive disease in dairy cows, implies significant losses in the dairy industry worldwide. Many efforts have been made to improve genetic mastitis resistance in dairy populations, but low heritability of this trait made this process not as effective as desired. The purpose of this study was to identify genomic regions explaining genetic variation of somatic cell count using copy number variations (CNVs) as markers in the Holstein population, genotyped with the Illumina BovineHD BeadChip. We found 24 and 47 copy number variation regions significantly associated with estimated breeding values for somatic cell score (SCS_EBVs) using SVS 8.3.1 and PennCNV-CNVRuler software, respectively. The association analysis performed with these two software allowed the identification of 18 candidate genes (TERT, NOTCH1, SLC6A3, CLPTM1L, PPARα, BCL-2, ABO, VAV2, CACNA1S, TRAF2, RELA, ELF3, DBH, CDK5, NF2, FASN, EWSR1 and MAP3K11) that result classified in the same functional cluster. These genes are also part of two gene networks, whose genes share the 'stress', 'cell death', 'inflammation' and 'immune response' GO terms. Combining CNV detection/association analysis based on two different algorithms helps towards a more complete identification of genes linked to phenotypic variation of the somatic cell count.
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Affiliation(s)
- M Durán Aguilar
- Facultad de Estudios Superiores Cuautitlán, UNAM, Cuautitlán Izcalli, México
| | - S I Román Ponce
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, INIFAP, Auchitlán, Querétaro, México
| | - F J Ruiz López
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, INIFAP, Auchitlán, Querétaro, México
| | - E González Padilla
- Departamento de Genética y Bioestadística, Facultad Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México DF, México
| | - C G Vásquez Peláez
- Departamento de Genética y Bioestadística, Facultad Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México DF, México
| | - A Bagnato
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - M G Strillacci
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
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25
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Shrine N, Tobin MD, Schurmann C, Soler Artigas M, Hui J, Lehtimäki T, Raitakari OT, Pennell CE, Ang QW, Strachan DP, Homuth G, Gläser S, Felix SB, Evans DM, Henderson J, Granell R, Palmer LJ, Huffman J, Hayward C, Scotland G, Malarstig A, Musk B, James AL, Wain LV. Genome-wide association study of copy number variation with lung function identifies a novel signal of association near BANP for forced vital capacity. BMC Genet 2016; 17:116. [PMID: 27514831 PMCID: PMC4981989 DOI: 10.1186/s12863-016-0423-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 07/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide association studies of Single Nucleotide Polymorphisms (SNPs) have identified 55 SNPs associated with lung function. However, little is known about the effect of copy number variants (CNVs) on lung function, although CNVs represent a significant proportion of human genetic polymorphism. To assess the effect of CNVs on lung function quantitative traits, we measured copy number at 2788 previously characterised, common copy number variable regions in 6 independent cohorts (n = 24,237) using intensity data from SNP genotyping experiments. We developed a pipeline for genome-wide association analysis and meta-analysis of CNV genotypes measured across multiple studies using SNP genotype array intensity data from different platform technologies. We then undertook cohort-level genome-wide association studies of CNV with lung function in a subset of 4 cohorts (n < =12,403) with lung function measurements and meta-analysed the results. Follow-up was undertaken for CNVs which were well tagged by SNPs, in up to 146,871 individuals. RESULTS We generated robust copy number calls for 1962 out of 2788 (70 %) known CNV regions genome-wide, with 1103 measured with compatible class frequencies in at least 2 cohorts. We report a novel CNV association (discovery P = 0.0007) with Forced Vital Capacity (FVC) downstream of BANP on chromosome 16 that shows evidence of replication by a tag SNP in two independent studies (replication P = 0.004). In addition, we provide suggestive evidence (discovery P = 0.0002) for a role of complex copy number variation at a previously reported lung function locus, containing the rootletin gene CROCC, that is not tagged by SNPs. CONCLUSIONS We demonstrate how common CNV regions can be reliably and consistently called across cohorts, using an existing calling algorithm and rigorous quality control steps, using SNP genotyping array intensity data. Although many common biallelic CNV regions were well-tagged by common SNPs, we also identified associations with untagged mulitallelic CNV regions thereby illustrating the potential of our approach to identify some of the missing heritability of complex traits.
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Affiliation(s)
- Nick Shrine
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP UK
| | - Claudia Schurmann
- Department of Functional Genomics, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, 17475 Greifswald, Germany
| | - María Soler Artigas
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
| | - Jennie Hui
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere and Tampere University Hospital, Tampere, 33521 Finland
| | - Olli T. Raitakari
- Department of Clinical Physiology, Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku University Hospital, Turku, 20521 Finland
| | - Craig E. Pennell
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Australia
| | - Qi Wei Ang
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Australia
| | - David P. Strachan
- Division of Population Health Sciences, St. George’s University of London, London, UK
| | - Georg Homuth
- Department of Functional Genomics, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Greifswald, Germany
| | - Sven Gläser
- Department of Internal Medicine B – Pulmonary Medicine, Weaning and Infectious Diseases and Scientific Division of Pneumology and Pneumological Epidemiology, University Medicine Greifswald, Greifswald, Germany
| | - Stephan B. Felix
- Department of Functional Genomics, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Greifswald, Germany
- Department of Internal Medicine B – Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - David M. Evans
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland Australia
| | - John Henderson
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Raquel Granell
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Lyle J. Palmer
- School of Public Health, University of Adelaide, Adelaide, Australia
| | - Jennifer Huffman
- Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Caroline Hayward
- Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Generation Scotland
- Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | | | - Bill Musk
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Alan L. James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - UK BiLEVE
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP UK
- Department of Functional Genomics, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, 17475 Greifswald, Germany
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere and Tampere University Hospital, Tampere, 33521 Finland
- Department of Clinical Physiology, Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku University Hospital, Turku, 20521 Finland
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Australia
- Division of Population Health Sciences, St. George’s University of London, London, UK
- Department of Internal Medicine B – Pulmonary Medicine, Weaning and Infectious Diseases and Scientific Division of Pneumology and Pneumological Epidemiology, University Medicine Greifswald, Greifswald, Germany
- Department of Internal Medicine B – Cardiology, University Medicine Greifswald, Greifswald, Germany
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland Australia
- School of Public Health, University of Adelaide, Adelaide, Australia
- Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
- Pfizer Worldwide Research and Development, Sollentuna, Sweden
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP UK
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26
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Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression. PLoS Comput Biol 2016; 12:e1004871. [PMID: 27177143 PMCID: PMC4866742 DOI: 10.1371/journal.pcbi.1004871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/14/2016] [Indexed: 11/22/2022] Open
Abstract
By integrating Haar wavelets with Hidden Markov Models, we achieve drastically reduced running times for Bayesian inference using Forward-Backward Gibbs sampling. We show that this improves detection of genomic copy number variants (CNV) in array CGH experiments compared to the state-of-the-art, including standard Gibbs sampling. The method concentrates computational effort on chromosomal segments which are difficult to call, by dynamically and adaptively recomputing consecutive blocks of observations likely to share a copy number. This makes routine diagnostic use and re-analysis of legacy data collections feasible; to this end, we also propose an effective automatic prior. An open source software implementation of our method is available at http://schlieplab.org/Software/HaMMLET/ (DOI: 10.5281/zenodo.46262). This paper was selected for oral presentation at RECOMB 2016, and an abstract is published in the conference proceedings.
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Urnikyte A, Domarkiene I, Stoma S, Ambrozaityte L, Uktveryte I, Meskiene R, Kasiulevičius V, Burokiene N, Kučinskas V. CNV analysis in the Lithuanian population. BMC Genet 2016; 17:64. [PMID: 27142071 PMCID: PMC4855864 DOI: 10.1186/s12863-016-0373-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 04/22/2016] [Indexed: 12/13/2022] Open
Abstract
Background Although copy number variation (CNV) has received much attention, knowledge about the characteristics of CNVs such as occurrence rate and distribution in the genome between populations and within the same population is still insufficient. In this study, Illumina 770 K HumanOmniExpress-12 v1.0 (and v1.1) arrays were used to examine the diversity and distribution of CNVs in 286 unrelated individuals from the two main ethnolinguistic groups of the Lithuanian population (Aukštaičiai and Žemaičiai) (see Additional file 3). For primary data analysis, the Illumina GenomeStudio™ Genotyping Module v1.9 and two algorithms, cnvPartition 3.2.0 and QuantiSNP 2.0, were used to identify high-confidence CNVs. Results A total of 478 autosomal CNVs were detected by both algorithms, and those were clustered in 87 copy number variation regions (CNVRs), spanning ~12.5 Mb of the genome (see Table 1). At least 8.6 % of the CNVRs were unique and had not been reported in the Database of Genomic Variants. Most CNVRs (57.5 %) were rare, with a frequency of <1 %, whereas common CNVRs with at least 5 % frequency made up only 1.1 % of all CNVRs identified. About 49 % of non-singleton CNVRs were shared between Aukštaičiai and Žemaičiai, and the remaining CNVRs were specific to each group. Many of the CNVs detected (66 %) overlapped with known UCSC gene regions. Conclusions The ethnolinguistic groups of the Lithuanian population could not be differentiated based on CNV profiles, which may reflect their geographical proximity and suggest the homogeneity of the Lithuanian population. In addition, putative novel CNVs unique to the Lithuanian population were identified. The results of our study enhance the CNV map of the Lithuanian population. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0373-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A Urnikyte
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Santariskiu St. 2, LT-08661, Vilnius, Lithuania.
| | - I Domarkiene
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Santariskiu St. 2, LT-08661, Vilnius, Lithuania
| | - S Stoma
- Master of Science (MSc), Bioinformatics student, VU University Amsterdam, Amsterdam, Netherlands
| | - L Ambrozaityte
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Santariskiu St. 2, LT-08661, Vilnius, Lithuania
| | - I Uktveryte
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Santariskiu St. 2, LT-08661, Vilnius, Lithuania
| | - R Meskiene
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Santariskiu St. 2, LT-08661, Vilnius, Lithuania
| | - V Kasiulevičius
- Clinics of Internal Diseases, Family Medicine and Oncology, Faculty of Medicine, Vilnius University, Santariskiu St. 2, LT-08661, Vilnius, Lithuania
| | - N Burokiene
- Clinics of Internal Diseases, Family Medicine and Oncology, Faculty of Medicine, Vilnius University, Santariskiu St. 2, LT-08661, Vilnius, Lithuania
| | - V Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Santariskiu St. 2, LT-08661, Vilnius, Lithuania
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Long J. Rapid diagnosis of common deletional α-thalassemia in the Chinese population by qPCR based on identical primer homologous fragments. Clin Chim Acta 2016; 456:93-99. [PMID: 26944566 DOI: 10.1016/j.cca.2016.02.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 02/24/2016] [Accepted: 02/26/2016] [Indexed: 11/16/2022]
Abstract
OBJECTIVE In China, -(SEA), -α(3.7) and -α(4.2) are common deletional α-thalassemia alleles. Gap-PCR is the currently used detection method for these alleles, whose disadvantages include time-consuming procedure and increased potential for PCR product contamination. Therefore, this detection method needs to be improved. Based on identical-primer homologous fragments, a qPCR system was developed for deletional α-thalassemia genotyping, which was composed of a group of quantitatively-related primers and their corresponding probes plus two groups of qualitatively-related primers and their corresponding probes. In order to verify the accuracy of the qPCR system, known genotype samples and random samples are employed. RESULT The standard curve result demonstrated that designed primers and probes all yielded good amplification efficiency. In the tests of known genotype samples and random samples, sample detection results were consistent with verification results. CONCLUSIONS In detecting αα, -(SEA), -α(3.7) and -α(4.2) alleles, deletional α-thalassemia alleles are accurately detected by this method. In addition, this method is provided with a wider detection range, greater speed and reduced PCR product contamination risk when compared with current common gap-PCR detection reagents.
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Affiliation(s)
- Ju Long
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Guangxi 535099, PR China.
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29
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Bagnato A, Strillacci MG, Pellegrino L, Schiavini F, Frigo E, Rossoni A, Fontanesi L, Maltecca C, Prinsen RT, Dolezal MA. Identification and Validation of Copy Number Variants in Italian Brown Swiss Dairy Cattle Using Illumina Bovine SNP50 Beadchip®. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2015.3900] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alessandro Bagnato
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, University of Bologna, Italy
| | - Maria G. Strillacci
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Laura Pellegrino
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Fausta Schiavini
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Erika Frigo
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Attilio Rossoni
- Associazione Nazionale Allevatori Razza Bruna, Bussolengo (VR), Italy
| | - Luca Fontanesi
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, University of Bologna, Italy
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Raphaelle T.M.M. Prinsen
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Marlies A. Dolezal
- Institut für Populationsgenetik Veterinärmedizinische, University of Wien, Austria
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Copy number variation of scavenger-receptor cysteine-rich domains within DMBT1 and Crohn's disease. Eur J Hum Genet 2016; 24:1294-300. [PMID: 26813944 PMCID: PMC4851238 DOI: 10.1038/ejhg.2015.280] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 12/08/2015] [Accepted: 12/09/2015] [Indexed: 12/21/2022] Open
Abstract
Previous work has shown that the gene DMBT1, which encodes a large secreted epithelial glycoprotein known as salivary agglutinin, gp340, hensin or muclin, is an innate immune defence protein that binds bacteria. A deletion variant of DMBT1 has been previously associated with Crohn's disease, and a DMBT1−/− knockout mouse has increased levels of colitis induced by dextran sulphate. DMBT1 has a complex copy number variable structure, with two, independent, rapidly mutating copy number variable regions, called CNV1 and CNV2. Because the copy number variable regions are predicted to affect the number of bacteria-binding domains, different alleles may alter host–microbe interactions in the gut. Our aim was to investigate the role of this complex variation in susceptibility to Crohn's disease by assessing the previously reported association. We analysed the association of both copy number variable regions with presence of Crohn's disease, and its severity, on three case–control cohorts. We also reanalysed array comparative genomic hybridisation data (aCGH) from a large case–control cohort study for both copy number variable regions. We found no association with a linear increase in copy number, nor when the CNV1 is regarded as presence or absence of a deletion allele. Taken together, we show that the DMBT1 CNV does not affect susceptibility to Crohn's disease, at least in Northern Europeans.
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31
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Comparative Genome of GK and Wistar Rats Reveals Genetic Basis of Type 2 Diabetes. PLoS One 2015; 10:e0141859. [PMID: 26529237 PMCID: PMC4631338 DOI: 10.1371/journal.pone.0141859] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/14/2015] [Indexed: 12/12/2022] Open
Abstract
The Goto-Kakizaki (GK) rat, which has been developed by repeated inbreeding of glucose-intolerant Wistar rats, is the most widely studied rat model for Type 2 diabetes (T2D). However, the detailed genetic background of T2D phenotype in GK rats is still largely unknown. We report a survey of T2D susceptible variations based on high-quality whole genome sequencing of GK and Wistar rats, which have generated a list of GK-specific variations (228 structural variations, 2660 CNV amplification and 2834 CNV deletion, 1796 protein affecting SNVs or indels) by comparative genome analysis and identified 192 potential T2D-associated genes. The genes with variants are further refined with prior knowledge and public resource including variant polymorphism of rat strains, protein-protein interactions and differential gene expression. Finally we have identified 15 genetic mutant genes which include seven known T2D related genes (Tnfrsf1b, Scg5, Fgb, Sell, Dpp4, Icam1, and Pkd2l1) and eight high-confidence new candidate genes (Ldlr, Ccl2, Erbb3, Akr1b1, Pik3c2a, Cd5, Eef2k, and Cpd). Our result reveals that the T2D phenotype may be caused by the accumulation of multiple variations in GK rat, and that the mutated genes may affect biological functions including adipocytokine signaling, glycerolipid metabolism, PPAR signaling, T cell receptor signaling and insulin signaling pathways. We present the genomic difference between two closely related rat strains (GK and Wistar) and narrow down the scope of susceptible loci. It also requires further experimental study to understand and validate the relationship between our candidate variants and T2D phenotype. Our findings highlight the importance of sequenced-based comparative genomics for investigating disease susceptibility loci in inbreeding animal models.
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Forni D, Martin D, Abujaber R, Sharp AJ, Sironi M, Hollox EJ. Determining multiallelic complex copy number and sequence variation from high coverage exome sequencing data. BMC Genomics 2015; 16:891. [PMID: 26526070 PMCID: PMC4630827 DOI: 10.1186/s12864-015-2123-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number variation (CNV) is a major component of genomic variation, yet methods to accurately type genomic CNV lag behind methods that type single nucleotide variation. High-throughput sequencing can contribute to these methods by using sequence read depth, which takes the number of reads that map to a given part of the reference genome as a proxy for copy number of that region, and compares across samples. Furthermore, high-throughput sequencing also provides information on the sequence differences between copies within and between individuals. METHODS In this study we use high-coverage phase 3 exome sequences of the 1000 Genomes project to infer diploid copy number of the beta-defensin genomic region, a well-studied CNV that carries several beta-defensin genes involved in the antimicrobial response, signalling, and fertility. We also use these data to call sequence variants, a particular challenge given the multicopy nature of the region. RESULTS We confidently call copy number and sequence variation of the beta-defensin genes on 1285 samples from 26 global populations, validate copy number using Nanostring nCounter and triplex paralogue ratio test data. We use the copy number calls to verify the genomic extent of the CNV and validate sequence calls using analysis of cloned PCR products. We identify novel variation, mostly individually rare, predicted to alter amino-acid sequence in the beta-defensin genes. Such novel variants may alter antimicrobial properties or have off-target receptor interactions, and may contribute to individuality in immunological response and fertility. CONCLUSIONS Given that 81% of identified sequence variants were not previously in dbSNP, we show that sequence variation in multiallelic CNVs represent an unappreciated source of genomic diversity.
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Affiliation(s)
- Diego Forni
- Department of Genetics, University of Leicester, Leicester, UK.,Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio, Parini, Italy
| | - Diana Martin
- Department of Genetics, University of Leicester, Leicester, UK
| | - Razan Abujaber
- Department of Genetics, University of Leicester, Leicester, UK
| | - Andrew J Sharp
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio, Parini, Italy
| | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK.
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Lifestyle Behaviours Add to the Armoury of Treatment Options for Panic Disorder: An Evidence-Based Reasoning. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:7017-43. [PMID: 26095868 PMCID: PMC4483746 DOI: 10.3390/ijerph120607017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/11/2015] [Accepted: 06/12/2015] [Indexed: 11/16/2022]
Abstract
This article presents an evidence-based reasoning, focusing on evidence of an Occupational Therapy input to lifestyle behaviour influences on panic disorder that also provides potentially broader application across other mental health problems (MHP). The article begins from the premise that we are all different. It then follows through a sequence of questions, examining incrementally how MHPs are experienced and classified. It analyses the impact of individual sensitivity at different levels of analysis, from genetic and epigenetic individuality, through neurotransmitter and body system sensitivity. Examples are given demonstrating the evidence base behind the logical sequence of investigation. The paper considers the evidence of how everyday routine lifestyle behaviour impacts on occupational function at all levels, and how these behaviours link to individual sensitivity to influence the level of exposure required to elicit symptomatic responses. Occupational Therapists can help patients by adequately assessing individual sensitivity, and through promoting understanding and a sense of control over their own symptoms. It concludes that present clinical guidelines should be expanded to incorporate knowledge of individual sensitivities to environmental exposures and lifestyle behaviours at an early stage.
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34
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Evolution of the rapidly mutating human salivary agglutinin gene (DMBT1) and population subsistence strategy. Proc Natl Acad Sci U S A 2015; 112:5105-10. [PMID: 25848046 DOI: 10.1073/pnas.1416531112] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The dietary change resulting from the domestication of plant and animal species and development of agriculture at different locations across the world was one of the most significant changes in human evolution. An increase in dietary carbohydrates caused an increase in dental caries following the development of agriculture, mediated by the cariogenic oral bacterium Streptococcus mutans. Salivary agglutinin [SAG, encoded by the deleted in malignant brain tumors 1 (DMBT1) gene] is an innate immune receptor glycoprotein that binds a variety of bacteria and viruses, and mediates attachment of S. mutans to hydroxyapatite on the surface of the tooth. In this study we show that multiallelic copy number variation (CNV) within DMBT1 is extensive across all populations and is predicted to result in between 7-20 scavenger-receptor cysteine-rich (SRCR) domains within each SAG molecule. Direct observation of de novo mutation in multigeneration families suggests these CNVs have a very high mutation rate for a protein-coding locus, with a mutation rate of up to 5% per gamete. Given that the SRCR domains bind S. mutans and hydroxyapatite in the tooth, we investigated the association of sequence diversity at the SAG-binding gene of S. mutans, and DMBT1 CNV. Furthermore, we show that DMBT1 CNV is also associated with a history of agriculture across global populations, suggesting that dietary change as a result of agriculture has shaped the pattern of CNV at DMBT1, and that the DMBT1-S. mutans interaction is a promising model of host-pathogen-culture coevolution in humans.
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35
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D'Apice MR, Novelli A, di Masi A, Biancolella M, Antoccia A, Gullotta F, Licata N, Minella D, Testa B, Nardone AM, Palmieri G, Calabrese E, Biancone L, Tanzarella C, Frontali M, Sangiuolo F, Novelli G, Pallone F. Deletion of REXO1L1 locus in a patient with malabsorption syndrome, growth retardation, and dysmorphic features: a novel recognizable microdeletion syndrome? BMC MEDICAL GENETICS 2015; 16:20. [PMID: 25927938 PMCID: PMC4422118 DOI: 10.1186/s12881-015-0164-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 03/12/2015] [Indexed: 12/27/2022]
Abstract
Background Copy number variations (CNVs) can contribute to genetic variation among individuals and/or have a significant influence in causing diseases. Many studies consider new CNVs’ effects on protein family evolution giving rise to gene duplicates or losses. “Unsuccessful” duplicates that remain in the genome as pseudogenes often exhibit functional roles. So, changes in gene and pseudogene number may contribute to development or act as susceptibility alleles of diseases. Case presentation We report a de novo heterozygous 271 Kb microdeletion at 8q21.2 region which includes the family of REXO1L genes and pseudogenes in a young man affected by global development delay, progeroid signs, and gastrointestinal anomalies. Molecular and cellular analysis showed that the REXO1L1 gene hemizygosity in a patient’s fibroblasts induces genetic instability and increased apoptosis after treatment with different DNA damage-induced agents. Conclusions The present results support the hypothesis that low copy gene number within REXO1L1 cluster could play a significant role in this complex clinical and cellular phenotype.
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Affiliation(s)
| | - Antonio Novelli
- Mendel Institute, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.
| | | | - Michela Biancolella
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy.
| | | | - Francesca Gullotta
- Department of Biology, "Roma Tre" University, Rome, Italy. .,Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy.
| | - Norma Licata
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy. .,Department of Neuroscience, Psychiatry and Anaesthesiology, University of Messina, Messina, Italy.
| | - Daniela Minella
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy.
| | - Barbara Testa
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy.
| | | | | | - Emma Calabrese
- Department of Internal Medicine, Gastrointestinal Unit, Tor Vergata University of Rome, Rome, Italy.
| | - Livia Biancone
- Department of Internal Medicine, Gastrointestinal Unit, Tor Vergata University of Rome, Rome, Italy.
| | | | | | - Federica Sangiuolo
- Fondazione Policlinico Tor Vergata, Rome, Italy. .,Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy.
| | - Giuseppe Novelli
- Fondazione Policlinico Tor Vergata, Rome, Italy. .,Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy. .,San Pietro Fatebenefratelli Hospital, Rome, Italy.
| | - Francesco Pallone
- Department of Internal Medicine, Gastrointestinal Unit, Tor Vergata University of Rome, Rome, Italy.
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36
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Li D, Zhao H, Kranzler HR, Li MD, Jensen KP, Zayats T, Farrer LA, Gelernter J. Genome-wide association study of copy number variations (CNVs) with opioid dependence. Neuropsychopharmacology 2015; 40:1016-26. [PMID: 25345593 PMCID: PMC4330517 DOI: 10.1038/npp.2014.290] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 08/18/2014] [Accepted: 08/26/2014] [Indexed: 12/20/2022]
Abstract
Single-nucleotide polymorphisms that have been associated with opioid dependence (OD) altogether account for only a small proportion of the known heritability. Most of the genetic risk factors are unknown. Some of the 'missing heritability' might be explained by copy number variations (CNVs) in the human genome. We used Illumina HumanOmni1 arrays to genotype 5152 African-American and European-American OD cases and screened controls and implemented combined CNV calling methods. After quality control measures were applied, a genome-wide association study (GWAS) of CNVs with OD was performed. For common CNVs, two deletions and one duplication were significantly associated with OD genome-wide (eg, P=2 × 10(-8) and OR (95% CI)=0.64 (0.54-0.74) for a chromosome 18q12.3 deletion). Several rare or unique CNVs showed suggestive or marginal significance with large effect sizes. This study is the first GWAS of OD using CNVs. Some identified CNVs harbor genes newly identified here to be of biological importance in addiction, whereas others affect genes previously known to contribute to substance dependence risk. Our findings augment our specific knowledge of the importance of genomic variation in addictive disorders, and provide an addiction CNV pool for further research. These findings require replication.
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Affiliation(s)
- Dawei Li
- Department of Psychiatry, School of Medicine, Yale University, New Haven, CT, USA
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
- Department of Computer Science, University of Vermont, Burlington, VT, USA
- Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, VT, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
| | - Henry R Kranzler
- Department of Psychiatry, University of Pennsylvania School of Medicine and VISN 4 MIRECC, Philadelphia VAMC, Philadelphia, PA, USA
| | - Ming D Li
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, VA, USA
| | - Kevin P Jensen
- Department of Psychiatry, School of Medicine, Yale University, New Haven, CT, USA
| | - Tetyana Zayats
- Department of Psychiatry, School of Medicine, Yale University, New Haven, CT, USA
| | - Lindsay A Farrer
- Departments of Medicine (Biomedical Genetics), Neurology, Ophthalmology, Genetics and Genomics, Biostatistics, and Epidemiology, Boston University Schools of Medicine and Public Health, Boston, MA, USA
| | - Joel Gelernter
- Department of Psychiatry, School of Medicine, Yale University, New Haven, CT, USA
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
- VA Connecticut Healthcare Center, Department of Neurobiology, Yale University School of Medicine, New Haven, CT, USA
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37
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Ruttens D, Vandermeulen E, Verleden SE, Bellon H, Vos R, Van Raemdonck DE, Dupont LJ, Vanaudenaerde BM, Verleden GM. Role of genetics in lung transplant complications. Ann Med 2015; 47:106-15. [PMID: 25766881 DOI: 10.3109/07853890.2015.1004359] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is increasing knowledge that patients can be predisposed to a certain disease by genetic variations in their DNA. Extensive genetic variation has been described in molecules involved in short- and long-term complications after lung transplantation (LTx), such as primary graft dysfunction (PGD), acute rejection, respiratory infection, chronic lung allograft dysfunction (CLAD), and mortality. Several of these studies could not be confirmed or were not reproduced in other cohorts. However, large multicenter prospective studies need to be performed to define the real clinical consequence and significance of genotyping the donor and receptor of a LTx. The current review presents an overview of genetic polymorphisms (SNP) investigating an association with different complications after LTx. Finally, the major drawbacks, clinical relevance, and future perspectives will be discussed.
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Affiliation(s)
- D Ruttens
- KU Leuven, and UZ Leuven, Department of Clinical and Experimental Medicine, Laboratory of Pneumology, Lung Transplant Unit , Leuven , Belgium
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Park RW, Kim TM, Kasif S, Park PJ. Identification of rare germline copy number variations over-represented in five human cancer types. Mol Cancer 2015; 14:25. [PMID: 25644941 PMCID: PMC4381456 DOI: 10.1186/s12943-015-0292-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 01/08/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Copy number variations (CNVs) are increasingly recognized as significant disease susceptibility markers in many complex disorders including cancer. The availability of a large number of chromosomal copy number profiles in both malignant and normal tissues in cancer patients presents an opportunity to characterize not only somatic alterations but also germline CNVs, which may confer increased risk for cancer. RESULTS We explored the germline CNVs in five cancer cohorts from the Cancer Genome Atlas (TCGA) consisting of 351 brain, 336 breast, 342 colorectal, 370 renal, and 314 ovarian cancers, genotyped on Affymetrix SNP6.0 arrays. Comparing these to ~3000 normal controls from another study, our case-control association study revealed 39 genomic loci (9 brain, 3 breast, 4 colorectal, 11 renal, and 12 ovarian cancers) as potential candidates of tumor susceptibility loci. Many of these loci are new and in some cases are associated with a substantial increase in disease risk. The majority of the observed loci do not overlap with coding sequences; however, several observed genomic loci overlap with known cancer genes including RET in brain cancers, ERBB2 in renal cell carcinomas, and DCC in ovarian cancers, all of which have not been previously associated with germline changes in cancer. CONCLUSIONS This large-scale genome-wide association study for CNVs across multiple cancer types identified several novel rare germline CNVs as cancer predisposing genomic loci. These loci can potentially serve as clinically useful markers conferring increased cancer risk.
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Affiliation(s)
- Richard W Park
- Bioinformatics Program, Boston University, Boston, MA, USA. .,Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA.
| | - Tae-Min Kim
- Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA. .,Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, 137-701, South Korea.
| | - Simon Kasif
- Bioinformatics Program, Boston University, Boston, MA, USA. .,Department of Biomedical Engineering, Boston University, Boston, MA, USA. .,Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA.
| | - Peter J Park
- Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA. .,Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA.
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Dunn EC, Brown RC, Dai Y, Rosand J, Nugent NR, Amstadter AB, Smoller JW. Genetic determinants of depression: recent findings and future directions. Harv Rev Psychiatry 2015; 23:1-18. [PMID: 25563565 PMCID: PMC4309382 DOI: 10.1097/hrp.0000000000000054] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
LEARNING OBJECTIVES After participating in this activity, learners should be better able to: 1. Evaluate current evidence regarding the genetic determinants of depression 2. Assess findings from studies of gene-environment interaction 3. Identify challenges to gene discovery in depression Depression is one of the most prevalent, disabling, and costly mental health conditions in the United States and also worldwide. One promising avenue for preventing depression and informing its clinical treatment lies in uncovering the genetic and environmental determinants of the disorder as well as their interaction (G × E). The overarching goal of this review article is to translate recent findings from studies of genetic association and G × E related to depression, particularly for readers without in-depth knowledge of genetics or genetic methods. The review is organized into three major sections. In the first, we summarize what is currently known about the genetic determinants of depression, focusing on findings from genome-wide association studies (GWAS). In the second section, we review findings from studies of G × E, which seek to simultaneously examine the role of genes and exposure to specific environments or experiences in the etiology of depression. In the third section, we describe the challenges to genetic discovery in depression and promising strategies for future progress.
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Affiliation(s)
- Erin C. Dunn
- Center for Human Genetic Research, Massachusetts General Hospital
- Department of Psychiatry, Harvard Medical School
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT
| | - Ruth C. Brown
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University
| | - Yael Dai
- Center for Human Genetic Research, Massachusetts General Hospital
| | - Jonathan Rosand
- Center for Human Genetic Research, Massachusetts General Hospital
- Department of Neurology, Massachusetts General Hospital
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT
| | - Nicole R. Nugent
- Department of Psychiatry and Human Behavior, Alpert Brown Medical School
| | - Ananda B. Amstadter
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University
| | - Jordan W. Smoller
- Center for Human Genetic Research, Massachusetts General Hospital
- Department of Psychiatry, Harvard Medical School
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT
- Center on the Developing Child, Harvard University
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Johnson JO, Stevanin G, van de Leemput J, Hernandez DG, Arepalli S, Forlani S, Zonozi R, Gibbs JR, Brice A, Durr A, Singleton AB. A 7.5-Mb duplication at chromosome 11q21-11q22.3 is associated with a novel spastic ataxia syndrome. Mov Disord 2014; 30:262-6. [PMID: 25545641 DOI: 10.1002/mds.26059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 07/28/2014] [Accepted: 08/25/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The autosomal dominant spinocerebellar ataxias are most commonly caused by nucleotide repeat expansions followed by base-pair changes in functionally important genes. Structural variation has recently been shown to underlie spinocerebellar ataxia types 15 and 20. METHODS We applied single-nucleotide polymorphism (SNP) genotyping to determine whether structural variation causes spinocerebellar ataxia in a family from France. RESULTS We identified an approximately 7.5-megabasepair duplication on chromosome 11q21-11q22.3 that segregates with disease. This duplication contains an estimated 44 genes. Duplications at this locus were not found in control individuals. CONCLUSIONS We have identified a new spastic ataxia syndrome caused by a genomic duplication, which we have denoted as spinocerebellar ataxia type 39. Finding additional families with this phenotype will be important to identify the genetic lesion underlying disease.
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Affiliation(s)
- Janel O Johnson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Department of Molecular Neuroscience and Reta Lila Weston Institute of Neurological Studies, Institute of Neurology, University College London, Queen Square, London, UK
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Narang A, Jha P, Kumar D, Kutum R, Mondal AK, Dash D, Mukerji M. Extensive copy number variations in admixed Indian population of African ancestry: potential involvement in adaptation. Genome Biol Evol 2014; 6:3171-81. [PMID: 25398783 PMCID: PMC4986450 DOI: 10.1093/gbe/evu250] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation.
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Affiliation(s)
- Ankita Narang
- G.N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
| | - Pankaj Jha
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
| | - Dhirendra Kumar
- G.N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rintu Kutum
- G.N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
| | - Anupam Kumar Mondal
- G.N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Debasis Dash
- G.N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mitali Mukerji
- G.N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India Genomics and Molecular Medicine, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
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Park CH, Rha SY, Ahn JB, Shin SJ, Kwon WS, Kim TS, An S, Kim NK, Yang WI, Chung HC. PINCH-2 presents functional copy number variation and suppresses migration of colon cancer cells by paracrine activity. Int J Cancer 2014; 136:2273-83. [PMID: 25346044 DOI: 10.1002/ijc.29273] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/30/2014] [Indexed: 01/15/2023]
Abstract
In recent years, characterization of cancer and its environment has become necessary. However, studies of the cancer microenvironment remain insufficient. Copy number variations (CNVs) occur in 40% of cancer-related genes, but few studies have reported the correlation between CNVs in morphologically normal tissues adjacent to cancer and cancer progression. In this study, we evaluated cancer cell migration and invasion according to the genetic differences between cancer tissues and their surrounding normal tissues. To study the field cancerization effect, we screened 89 systemic metastasis-related CNVs from morphologically normal tissues adjacent to colon cancers. Among these CNVs, LIM and senescent cell antigen-like domain 2 (PINCH-2) showed copy number amplification and upregulation of mRNA in the nonrelapsed group compared to the systemic relapse group. PINCH-2 expression in colon cancer cells was lower than that in normal epithelial colon cells at both the protein and mRNA levels. Suppression of PINCH-2 resulted in decreased formation of the PINCH-2-IPP (PINCH-2, integrin-linked kinase and α-parvin) complex and reciprocally increased formation of the PINCH-1-IPP complex. Although PINCH-2 expression of survival pathway-related proteins (Akt and phospho-Akt) did not change upon suppression of PINCH-2 expression, cell migration-related proteins [matrix-metalloproteinase (MMP)-9 and -11] were upregulated through autocrine and paracrine activation. Thus, PINCH-2 participates in decreased systemic recurrence by competitively regulating IPP complex formation with PINCH-1, thereby suppressing autocrine and paracrine effects on motility in colon cancer. This genetic change in morphologically normal tissue suggests a field cancerization effect of the tumor microenvironment in cancer progression.
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Affiliation(s)
- Chan Hee Park
- National Biochip Research Center, Yonsei University College of Medicine, Yonsei University Health System, Seoul, Korea; Cancer Metastasis Research Center, Yonsei University College of Medicine, Yonsei University Health System, Seoul, Korea; Yonsei Cancer Research Institute, Yonsei University College of Medicine, Yonsei University Health System, Seoul, Korea
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Tan YT, McPherson GE, Peretz I, Berkovic SF, Wilson SJ. The genetic basis of music ability. Front Psychol 2014; 5:658. [PMID: 25018744 PMCID: PMC4073543 DOI: 10.3389/fpsyg.2014.00658] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 06/08/2014] [Indexed: 01/18/2023] Open
Abstract
Music is an integral part of the cultural heritage of all known human societies, with the capacity for music perception and production present in most people. Researchers generally agree that both genetic and environmental factors contribute to the broader realization of music ability, with the degree of music aptitude varying, not only from individual to individual, but across various components of music ability within the same individual. While environmental factors influencing music development and expertise have been well investigated in the psychological and music literature, the interrogation of possible genetic influences has not progressed at the same rate. Recent advances in genetic research offer fertile ground for exploring the genetic basis of music ability. This paper begins with a brief overview of behavioral and molecular genetic approaches commonly used in human genetic analyses, and then critically reviews the key findings of genetic investigations of the components of music ability. Some promising and converging findings have emerged, with several loci on chromosome 4 implicated in singing and music perception, and certain loci on chromosome 8q implicated in absolute pitch and music perception. The gene AVPR1A on chromosome 12q has also been implicated in music perception, music memory, and music listening, whereas SLC6A4 on chromosome 17q has been associated with music memory and choir participation. Replication of these results in alternate populations and with larger samples is warranted to confirm the findings. Through increased research efforts, a clearer picture of the genetic mechanisms underpinning music ability will hopefully emerge.
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Affiliation(s)
- Yi Ting Tan
- Melbourne Conservatorium of Music, University of Melbourne Parkville, VIC, Australia
| | - Gary E McPherson
- Melbourne Conservatorium of Music, University of Melbourne Parkville, VIC, Australia
| | - Isabelle Peretz
- International Laboratory for Brain, Music and Sound Research and Department of Psychology, Université de Montréal Montreal, QC, Canada
| | - Samuel F Berkovic
- Department of Medicine, Epilepsy Research Centre, University of Melbourne Heidelberg, VIC, Australia
| | - Sarah J Wilson
- Department of Medicine, Epilepsy Research Centre, University of Melbourne Heidelberg, VIC, Australia ; Melbourne School of Psychological Sciences, University of Melbourne Parkville, VIC, Australia
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Bharuthram A, Paximadis M, Picton ACP, Tiemessen CT. Comparison of a quantitative Real-Time PCR assay and droplet digital PCR for copy number analysis of the CCL4L genes. INFECTION GENETICS AND EVOLUTION 2014; 25:28-35. [PMID: 24727646 DOI: 10.1016/j.meegid.2014.03.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/25/2014] [Accepted: 03/24/2014] [Indexed: 02/02/2023]
Abstract
The controversy surrounding the findings that copy number variation, of the CCL3 encoding genes, influences HIV-1 infection and disease progression has been in part attributed to the variable results obtained from methods used for copy number evaluation. Like CCL3, the genes encoding the CC chemokine CCL4, also a natural ligand of the CCR5 receptor, are found to occur in population-specific multiple copy number and have been shown to play a protective role against HIV-1. This study evaluated the standard method of quantitative Real-Time PCR (qPCR) and droplet digital PCR (ddPCR) for CCL4L gene copy number determination. The CCL4 encoding genes are CCL4, occurring in two copies per diploid genome (pdg), and the non-allelic CCL4L genes, comprised of CCL4L1 and CCL4L2, which are both found in multiple copies pdg. Copy number of CCL4L, CCL4L1 and CCL4L2 was determined in a cohort of HIV-1-uninfected individuals from the South African Black (n=23) and Caucasian (n=32) population groups using qPCR and ddPCR. A stronger correlation between the number of CCL4L copies and the sum of CCL4L1 and CCL4L2 copies generated by ddPCR (r=0.99, p<0.0001) compared to qPCR (r=0.87, p<0.0001) was observed. Real-Time qPCR exhibited greater inaccuracy at higher copy numbers which is particularly relevant to our cohort of Black individuals who have a higher range of CCL4L copies (3-6) compared to Caucasians (0-4) and a higher population median (4 and 2, respectively). Medians and ranges of CCL4L1 (Black: 2, 0-4, Caucasian: 0, 0-2) and CCL4L2 (Black: 2, 1-5, Caucasian: 2, 0-3) were also higher in the Black population. Droplet digital PCR was shown to be a far superior method to qPCR for assessment of CCL4 gene copy number variation, the accuracy of which is essential for studies of the contribution of variable gene copy number to phenotypic outcomes of host infection and disease course.
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Affiliation(s)
- Avani Bharuthram
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Anabela C P Picton
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Abernathy J, Li X, Jia X, Chou W, Lamont SJ, Crooijmans R, Zhou H. Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization. Anim Genet 2014; 45:400-11. [DOI: 10.1111/age.12141] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2014] [Indexed: 12/25/2022]
Affiliation(s)
- J. Abernathy
- Department of Animal Science; University of California; Davis CA 95616 USA
| | - X. Li
- College of Animal Science and Technology; Shandong Agricultural University; Taian Shandong 271018 China
- Department of Poultry Science; Texas A&M University; College Station TX 77843 USA
| | - X. Jia
- Department of Animal Science; University of California; Davis CA 95616 USA
- College of Animal Science and Technology; China Agricultural University; Beijing 100193 China
| | - W. Chou
- Department of Poultry Science; Texas A&M University; College Station TX 77843 USA
| | - S. J. Lamont
- Department of Animal Science; Iowa State University; Ames IA 50011 USA
| | - R. Crooijmans
- Animal Breeding and Genomics Centre; Wageningen University; Wageningen the Netherlands
| | - H. Zhou
- Department of Animal Science; University of California; Davis CA 95616 USA
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Wain LV, Odenthal-Hesse L, Abujaber R, Sayers I, Beardsmore C, Gaillard EA, Chappell S, Dogaru CM, McKeever T, Guetta-Baranes T, Kalsheker N, Kuehni CE, Hall IP, Tobin MD, Hollox EJ. Copy number variation of the beta-defensin genes in europeans: no supporting evidence for association with lung function, chronic obstructive pulmonary disease or asthma. PLoS One 2014; 9:e84192. [PMID: 24404154 PMCID: PMC3880289 DOI: 10.1371/journal.pone.0084192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/13/2013] [Indexed: 12/23/2022] Open
Abstract
Lung function measures are heritable, predict mortality and are relevant in diagnosis of chronic obstructive pulmonary disease (COPD). COPD and asthma are diseases of the airways with major public health impacts and each have a heritable component. Genome-wide association studies of SNPs have revealed novel genetic associations with both diseases but only account for a small proportion of the heritability. Complex copy number variation may account for some of the missing heritability. A well-characterised genomic region of complex copy number variation contains beta-defensin genes (DEFB103, DEFB104 and DEFB4), which have a role in the innate immune response. Previous studies have implicated these and related genes as being associated with asthma or COPD. We hypothesised that copy number variation of these genes may play a role in lung function in the general population and in COPD and asthma risk. We undertook copy number typing of this locus in 1149 adult and 689 children using a paralogue ratio test and investigated association with COPD, asthma and lung function. Replication of findings was assessed in a larger independent sample of COPD cases and smoking controls. We found evidence for an association of beta-defensin copy number with COPD in the adult cohort (OR = 1.4, 95%CI:1.02-1.92, P = 0.039) but this finding, and findings from a previous study, were not replicated in a larger follow-up sample(OR = 0.89, 95%CI:0.72-1.07, P = 0.217). No robust evidence of association with asthma in children was observed. We found no evidence for association between beta-defensin copy number and lung function in the general populations. Our findings suggest that previous reports of association of beta-defensin copy number with COPD should be viewed with caution. Suboptimal measurement of copy number can lead to spurious associations. Further beta-defensin copy number measurement in larger sample sizes of COPD cases and children with asthma are needed.
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Affiliation(s)
- Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | | | - Razan Abujaber
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Ian Sayers
- Division of Respiratory Medicine, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Caroline Beardsmore
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
- Institute for Lung Health, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Erol A. Gaillard
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
- Institute for Lung Health, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Sally Chappell
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Cristian M. Dogaru
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Tricia McKeever
- School of Community Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - Noor Kalsheker
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Claudia E. Kuehni
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Ian P. Hall
- Division of Respiratory Medicine, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- Department of Genetics, University of Leicester, Leicester, United Kingdom
- Institute for Lung Health, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Edward J. Hollox
- Department of Genetics, University of Leicester, Leicester, United Kingdom
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Moriya H, Saito K, Helsby N, Hayashi N, Sugino S, Yamakage M, Sawaguchi T, Takasaki M, Takahashi M, Kurosawa N. Single-nucleotide polymorphisms and copy number variations of the FCGR2A and FCGR3A genes in healthy Japanese subjects. Biomed Rep 2013; 2:265-269. [PMID: 24649108 DOI: 10.3892/br.2013.210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 11/18/2013] [Indexed: 01/31/2023] Open
Abstract
FcγRII and FcγRIII are low-affinity Fcγ receptors that are encoded by the FCGR2A and FCGR3A genes, respectively. These genes contain functional single-nucleotide polymorphisms (SNPs), which alter the binding affinities of these receptors for the γ chain of the Fc fragment of immunoglobulin G. The known SNPs in FCGR2A and FCGR3A are rs1801274 (A>G; H131R) and rs396991 (T>G; F158V), respectively. It is also known that there are copy number variations (CNVs) in the genetic locus (1q23) where FCGR2A and FCGR3A are located. However, the frequencies of these SNPs and CNVs have not been determined in the Japanese population. The aim of this study was to investigate SNPs and CNVs in FCGR2A and FCGR3A among 113 healthy individuals. The SNPs and CNVs in FCGR2A and FCGR3A were determined using the TaqMan® SNP Genotyping and the TaqMan® Copy Number assays. Our results revealed that the incidence of FCGR2A (rs1801274) genotypes were as follows: A/A, 69.9%; A/G, 29.2%; and G/G, 0.9%. The incidence of the FCGR3A (rs396991) genotypes were as follows: T/T, 56.7%; T/G, 38.9%; and G/G, 4.4%). No CNVs were detected for FCGR2A. To the best of our knowledge, this finding has not been previously reported in the Japanese population. By contrast, CNVs were observed in FCGR3A (3 subjects were found to harbour a gene deletion and 5 subjects had 3 copies of the gene). Using simple commercially available assays we were able to confirm previous findings regarding FCGR2A and FCGR3A alleles and CNVs. These assays may provide a basis for the investigation of the role of these genes in the efficacy of antibody-based drugs, such as trastuzumab and rituximab, in Japanese subjects.
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Affiliation(s)
- Hiroyuki Moriya
- Department of Pharmacy, Hokkaido Pharmaceutical University School of Pharmacy, Otaru, Hokkaido 047-0264, Japan
| | - Katsuhiko Saito
- Department of Pharmacy, Hokkaido Pharmaceutical University School of Pharmacy, Otaru, Hokkaido 047-0264, Japan ; Department of Pharmacy, Sapporo Hokuyu Hospital, Sapporo, Hokkaido 003-0006, Japan
| | - Nuala Helsby
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1142, New Zealand, Japan
| | - Naomi Hayashi
- Department of Pharmacy, Hokkaido Pharmaceutical University School of Pharmacy, Otaru, Hokkaido 047-0264, Japan
| | - Shigekazu Sugino
- Department of Anesthesiology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8543, Japan
| | - Michiaki Yamakage
- Department of Anesthesiology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8543, Japan
| | - Takeru Sawaguchi
- Department of Pharmacy, National Hospital Organization Hokkaido Cancer Center, Sapporo, Hokkaido 003-0804, Japan
| | - Masahiko Takasaki
- Department of Pharmacy, National Hospital Organization Hokkaido Cancer Center, Sapporo, Hokkaido 003-0804, Japan
| | - Masato Takahashi
- Department of Breast Surgery, National Hospital Organization Hokkaido Cancer Center, Sapporo, Hokkaido 003-0804, Japan
| | - Nahoko Kurosawa
- Department of Pharmacy, Hokkaido Pharmaceutical University School of Pharmacy, Otaru, Hokkaido 047-0264, Japan
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Short copy number variations potentially associated with tonic immobility responses in newly hatched chicks. PLoS One 2013; 8:e80205. [PMID: 24282524 PMCID: PMC3839970 DOI: 10.1371/journal.pone.0080205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/29/2013] [Indexed: 11/19/2022] Open
Abstract
Introduction Tonic immobility (TI) is fear-induced freezing that animals may undergo when confronted by a threat. It is principally observed in prey species as defence mechanisms. In our preliminary research, we detected large inter-individual variations in the frequency and duration of freezing behavior among newly hatched domestic chicks (Gallus gallus). In this study we aim to identify the copy number variations (CNVs) in the genome of chicks as genetic candidates that underlie the behavioral plasticity to fearful stimuli. Methods A total of 110 domestic chicks were used for an association study between TI responses and copy number polymorphisms. Array comparative genomic hybridization (aCGH) was conducted between chicks with high and low TI scores using an Agilent 4×180 custom microarray. We specifically focused on 3 genomic regions (>60 Mb) of chromosome 1 where previous quantitative trait loci (QTL) analysis showed significant F-values for fearful responses. Results ACGH successfully detected short CNVs within the regions overlapping 3 QTL peaks. Eleven of these identified loci were validated by real-time quantitative polymerase chain reaction (qPCR) as copy number polymorphisms. Although there wkas no significant p value in the correlation analysis between TI scores and the relative copy number within each breed, several CNV loci showed significant differences in the relative copy number between 2 breeds of chicken (White Leghorn and Nagoya) which had different quantitative characteristics of fear-induced responses. Conclusion Our data shows the potential CNVs that may be responsible for innate fear response in domestic chicks.
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Aklillu E, Odenthal-Hesse L, Bowdrey J, Habtewold A, Ngaimisi E, Yimer G, Amogne W, Mugusi S, Minzi O, Makonnen E, Janabi M, Mugusi F, Aderaye G, Hardwick R, Fu B, Viskaduraki M, Yang F, Hollox EJ. CCL3L1 copy number, HIV load, and immune reconstitution in sub-Saharan Africans. BMC Infect Dis 2013; 13:536. [PMID: 24219137 PMCID: PMC3829100 DOI: 10.1186/1471-2334-13-536] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 10/28/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The role of copy number variation of the CCL3L1 gene, encoding MIP1α, in contributing to the host variation in susceptibility and response to HIV infection is controversial. Here we analyse a sub-Saharan African cohort from Tanzania and Ethiopia, two countries with a high prevalence of HIV-1 and a high co-morbidity of HIV with tuberculosis. METHODS We use a form of quantitative PCR called the paralogue ratio test to determine CCL3L1 gene copy number in 1134 individuals and validate our copy number typing using array comparative genomic hybridisation and fiber-FISH. RESULTS We find no significant association of CCL3L1 gene copy number with HIV load in antiretroviral-naïve patients prior to initiation of combination highly active anti-retroviral therapy. However, we find a significant association of low CCL3L1 gene copy number with improved immune reconstitution following initiation of highly active anti-retroviral therapy (p = 0.012), replicating a previous study. CONCLUSIONS Our work supports a role for CCL3L1 copy number in immune reconstitution following antiretroviral therapy in HIV, and suggests that the MIP1α -CCR5 axis might be targeted to aid immune reconstitution.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Edward J Hollox
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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Romero I, Sun CC, Wong KK, Bast RC, Gershenson DM. Low-grade serous carcinoma: New concepts and emerging therapies. Gynecol Oncol 2013; 130:660-6. [DOI: 10.1016/j.ygyno.2013.05.021] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/09/2013] [Accepted: 05/16/2013] [Indexed: 11/29/2022]
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