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Balagué-Dobón L, Cáceres A, González JR. Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure. Brief Bioinform 2022; 23:bbac043. [PMID: 35211719 PMCID: PMC8921734 DOI: 10.1093/bib/bbac043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation and the most accessible to genotype in large cohorts. However, they individually explain a small proportion of phenotypic differences between individuals. Ancestry, collective SNP effects, structural variants, somatic mutations or even differences in historic recombination can potentially explain a high percentage of genomic divergence. These genetic differences can be infrequent or laborious to characterize; however, many of them leave distinctive marks on the SNPs across the genome allowing their study in large population samples. Consequently, several methods have been developed over the last decade to detect and analyze different genomic structures using SNP arrays, to complement genome-wide association studies and determine the contribution of these structures to explain the phenotypic differences between individuals. We present an up-to-date collection of available bioinformatics tools that can be used to extract relevant genomic information from SNP array data including population structure and ancestry; polygenic risk scores; identity-by-descent fragments; linkage disequilibrium; heritability and structural variants such as inversions, copy number variants, genetic mosaicisms and recombination histories. From a systematic review of recently published applications of the methods, we describe the main characteristics of R packages, command-line tools and desktop applications, both free and commercial, to help make the most of a large amount of publicly available SNP data.
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Yu Y, Werdyani S, Carey M, Parfrey P, Yilmaz YE, Savas S. A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer. Mol Oncol 2021; 15:3329-3347. [PMID: 34309201 PMCID: PMC8637572 DOI: 10.1002/1878-0261.13067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/29/2021] [Accepted: 07/24/2021] [Indexed: 12/15/2022] Open
Abstract
We aimed to examine the associations of a genome-wide set of single nucleotide polymorphisms (SNPs) and 254 copy number variations (CNVs) and/or insertion/deletions (INDELs) with clinical outcomes in colorectal cancer patients (n = 505). We also aimed to investigate whether their associations changed (e.g., appeared, diminished) over time. Multivariable Cox proportional hazards and piece-wise Cox regression models were used to examine the associations. The Cancer Genome Atlas (TCGA) datasets were used for replication purposes and to examine the gene expression differences between tumor and nontumor tissue samples. A common SNP (WBP11-rs7314075) was associated with disease-specific survival with P-value of 3.2 × 10-8 . Association of this region with disease-specific survival was also detected in the TCGA patient cohort. Two expression quantitative trait loci (eQTLs) were identified in this locus that were implicated in the regulation of ERP27 expression. Interestingly, expression levels of ERP27 and WBP11 were significantly different between colorectal tumors and nontumor tissues. Three SNPs predicted the risk of recurrent disease only after 5 years postdiagnosis. Overall, our study identified novel variants, one of which also showed an association in the TCGA dataset, but no CNVs/INDELs, that associated with outcomes in colorectal cancer. Three SNPs were candidate predictors of long-term recurrence/metastasis risk.
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Affiliation(s)
- Yajun Yu
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Present address:
Division of Biomedical SciencesFaculty of MedicineMemorial UniversitySt. John’sNLCanada
| | - Salem Werdyani
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Present address:
Division of Biomedical SciencesFaculty of MedicineMemorial UniversitySt. John’sNLCanada
| | - Megan Carey
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
| | - Patrick Parfrey
- Discipline of MedicineFaculty of MedicineMemorial UniversitySt. John’sNLCanada
| | - Yildiz E. Yilmaz
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Discipline of MedicineFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Department of Mathematics and StatisticsFaculty of ScienceMemorial UniversitySt. John’sNLCanada
| | - Sevtap Savas
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Discipline of OncologyFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Present address:
Division of Biomedical SciencesFaculty of MedicineMemorial UniversitySt. John’sNLCanada
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Fan DM, Yang X, Huang LM, Ouyang GJ, Yang XX, Li M. Simultaneous detection of target CNVs and SNVs of thalassemia by multiplex PCR and next‑generation sequencing. Mol Med Rep 2019; 19:2837-2848. [PMID: 30720081 DOI: 10.3892/mmr.2019.9896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 12/03/2018] [Indexed: 11/05/2022] Open
Abstract
Thalassemia is caused by complex mechanisms, including copy number variants (CNVs) and single nucleotide variants (SNVs). The CNV types of α‑thalassemia are typically detected by gap‑polymerase chain reaction (PCR). The SNV types are detected by Sanger sequencing. In the present study, a novel method was developed that simultaneously detects CNVs and SNVs by multiplex PCR and next‑generation sequencing (NGS). To detect CNVs, 33 normal samples were used as a cluster of control values to build a baseline, and the A, B, C, and D ratios were developed to evaluate‑SEA, ‑α4.2, ‑α3.7, and compound or homozygous CNVs, respectively. To detect other SNVs, sequencing data were analyzed using the system's software and annotated using Annovar software. In a test of performance, 128 patients with thalassemia were detected using the method developed and were confirmed by Sanger sequencing and gap‑PCR. Four different CNV types were clearly distinguished by the developed algorithm, with ‑SEA, ‑α3.7, ‑α4.2, and compound or homozygous deletions. The sensitivities for each CNV type were 96.72% (59/61), 97.37% (37/38), 83.33% (10/12) and 95% (19/20), and the specificities were 93.94% (32/33), 93.94% (32/33), 100% (33/33) and 100% (33/33), respectively. The SNVs detected were consistent with those of the Sanger sequencing.
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Affiliation(s)
- Dong-Mei Fan
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Xu Yang
- Clinical Innovation and Research Center, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong 518110, P.R. China
| | - Li-Min Huang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Guo-Jun Ouyang
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, Guangdong 510663, P.R. China
| | - Xue-Xi Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Ming Li
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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Sulovari A, Liu Z, Zhu Z, Li D. Genome-wide meta-analysis of copy number variations with alcohol dependence. THE PHARMACOGENOMICS JOURNAL 2017; 18:398-405. [PMID: 28696413 DOI: 10.1038/tpj.2017.35] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/10/2017] [Accepted: 06/07/2017] [Indexed: 12/26/2022]
Abstract
Genetic association studies and meta-analyses of alcohol dependence (AD) have reported AD-associated single nucleotide polymorphisms (SNPs). These SNPs collectively account for a small portion of estimated heritability in AD. Recent genome-wide copy number variation (CNV) studies have identified CNVs associated with AD and substance dependence, suggesting that a portion of the missing heritability is explained by CNV. We applied PennCNV and QuantiSNP CNV calling algorithms to identify consensus CNVs in five AD cohorts of European and African origins. After rigorous quality control, genome-wide meta-analyses of CNVs were carried out in 3243 well-diagnosed AD cases and 2802 controls. We identified nine CNV regions, including a deletion in chromosome 5q21.3 with a suggestive association with AD (OR=2.15 (1.41-3.29) and P=3.8 × 10-4) and eight nominally significant CNV regions. All regions were replicated with consistent effect sizes across studies and populations. Pathway and gene-drug interaction enrichment analyses based on the resulting genes indicated the mitogen-activated protein kinase signaling pathway and the recombinant insulin and hyaluronidase drugs, which were relevant to AD biology or treatment. To our knowledge, this is the first genome-wide meta-analysis of CNVs with addiction. Further investigation of the AD-associated CNV regions will provide better understanding of the AD genetic mechanism.
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Affiliation(s)
- A Sulovari
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
| | - Z Liu
- Spine Surgery, Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Z Zhu
- Spine Surgery, Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - D Li
- 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
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Mafra F, Mazzotti D, Pellegrino R, Bianco B, Barbosa CP, Hakonarson H, Christofolini D. Copy number variation analysis reveals additional variants contributing to endometriosis development. J Assist Reprod Genet 2016; 34:117-124. [PMID: 27817035 DOI: 10.1007/s10815-016-0822-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/22/2016] [Indexed: 01/21/2023] Open
Abstract
PURPOSE Endometriosis is a gynecological disease influenced by multiple genetic and environmental factors. The aim of the current study was to use SNP-array technology to identify genomic aberrations that may possibly contribute to the development of endometriosis. METHODS We performed an SNP-array genotyping of pooled DNA samples from both patients (n = 100) and controls (n = 50). Copy number variation (CNV) calling and association analyses were performed using PennCNV software. MLPA and TaqMan Copy-Number assays were used for validation of CNVs discovered. RESULTS We detected 49 CNV loci that were present in patients with endometriosis and absent in the control group. After validation procedures, we confirmed six CNV loci in the subtelomeric regions, including 1p36.33, 16p13.3, 19p13.3, and 20p13, representing gains, while 17q25.3 and 20q13.33 showed losses. Among the intrachromosomal regions, our results revealed duplication at 19q13.1 within the FCGBP gene (p = 0.007). CONCLUSIONS We identified CNVs previously associated with endometriosis, together with six suggestive novel loci possibly involved in this disease. The intergenic locus on chromosome 19q13.1 shows strong association with endometriosis and is under further functional investigation.
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Affiliation(s)
- Fernanda Mafra
- Collective Health Department, Division of Sexual and Reproductive Health Care and Population Genetics, Faculdade de Medicina do ABC, Santo André, SP, Brazil.
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Diego Mazzotti
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Renata Pellegrino
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bianca Bianco
- Collective Health Department, Division of Sexual and Reproductive Health Care and Population Genetics, Faculdade de Medicina do ABC, Santo André, SP, Brazil
| | - Caio Parente Barbosa
- Collective Health Department, Division of Sexual and Reproductive Health Care and Population Genetics, Faculdade de Medicina do ABC, Santo André, SP, Brazil
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Denise Christofolini
- Collective Health Department, Division of Sexual and Reproductive Health Care and Population Genetics, Faculdade de Medicina do ABC, Santo André, SP, Brazil
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Locke MEO, Milojevic M, Eitutis ST, Patel N, Wishart AE, Daley M, Hill KA. Genomic copy number variation in Mus musculus. BMC Genomics 2015; 16:497. [PMID: 26141061 PMCID: PMC4490682 DOI: 10.1186/s12864-015-1713-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 06/22/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Copy number variation is an important dimension of genetic diversity and has implications in development and disease. As an important model organism, the mouse is a prime candidate for copy number variant (CNV) characterization, but this has yet to be completed for a large sample size. Here we report CNV analysis of publicly available, high-density microarray data files for 351 mouse tail samples, including 290 mice that had not been characterized for CNVs previously. RESULTS We found 9634 putative autosomal CNVs across the samples affecting 6.87% of the mouse reference genome. We find significant differences in the degree of CNV uniqueness (single sample occurrence) and the nature of CNV-gene overlap between wild-caught mice and classical laboratory strains. CNV-gene overlap was associated with lipid metabolism, pheromone response and olfaction compared to immunity, carbohydrate metabolism and amino-acid metabolism for wild-caught mice and classical laboratory strains, respectively. Using two subspecies of wild-caught Mus musculus, we identified putative CNVs unique to those subspecies and show this diversity is better captured by wild-derived laboratory strains than by the classical laboratory strains. A total of 9 genic copy number variable regions (CNVRs) were selected for experimental confirmation by droplet digital PCR (ddPCR). CONCLUSION The analysis we present is a comprehensive, genome-wide analysis of CNVs in Mus musculus, which increases the number of known variants in the species and will accelerate the identification of novel variants in future studies.
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Affiliation(s)
- M Elizabeth O Locke
- Department of Computer Science, The University of Western Ontario, London, ON, N6A 5B7, Canada.
| | - Maja Milojevic
- Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, Canada.
| | - Susan T Eitutis
- Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, Canada.
| | - Nisha Patel
- Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, Canada.
| | - Andrea E Wishart
- Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, Canada.
| | - Mark Daley
- Department of Computer Science, The University of Western Ontario, London, ON, N6A 5B7, Canada.
- Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, Canada.
| | - Kathleen A Hill
- Department of Computer Science, The University of Western Ontario, London, ON, N6A 5B7, Canada.
- Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, Canada.
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Haplotype phasing and inheritance of copy number variants in nuclear families. PLoS One 2015; 10:e0122713. [PMID: 25853576 PMCID: PMC4390228 DOI: 10.1371/journal.pone.0122713] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/12/2015] [Indexed: 11/19/2022] Open
Abstract
DNA copy number variants (CNVs) that alter the copy number of a particular DNA segment in the genome play an important role in human phenotypic variability and disease susceptibility. A number of CNVs overlapping with genes have been shown to confer risk to a variety of human diseases thus highlighting the relevance of addressing the variability of CNVs at a higher resolution. So far, it has not been possible to deterministically infer the allelic composition of different haplotypes present within the CNV regions. We have developed a novel computational method, called PiCNV, which enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data. The algorithm allows to i) phase normal and CNV-carrying haplotypes in the copy number variable regions, ii) resolve the allelic copies of rearranged DNA sequence within the haplotypes and iii) infer the heritability of identified haplotypes in trios or larger nuclear families. To our knowledge this is the first program available that can deterministically phase null, mono-, di-, tri- and tetraploid genotypes in CNV loci. We applied our method to study the composition and inheritance of haplotypes in CNV regions of 30 HapMap Yoruban trios and 34 Estonian families. For 93.6% of the CNV loci, PiCNV enabled to unambiguously phase normal and CNV-carrying haplotypes and follow their transmission in the corresponding families. Furthermore, allelic composition analysis identified the co-occurrence of alternative allelic copies within 66.7% of haplotypes carrying copy number gains. We also observed less frequent transmission of CNV-carrying haplotypes from parents to children compared to normal haplotypes and identified an emergence of several de novo deletions and duplications in the offspring.
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Kasak L, Rull K, Vaas P, Teesalu P, Laan M. Extensive load of somatic CNVs in the human placenta. Sci Rep 2015; 5:8342. [PMID: 25666259 PMCID: PMC4914949 DOI: 10.1038/srep08342] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/15/2015] [Indexed: 11/09/2022] Open
Abstract
Placenta is a temporary, but indispensable organ in mammalian pregnancy. From its basic nature, it exhibits highly invasive tumour-like properties facilitating effective implantation through trophoblast cell proliferation and migration, and a critical role in pregnancy success. We hypothesized that similarly to cancer, somatic genomic rearrangements are promoted in the support of placental function. Here we present the first profiling of copy number variations (CNVs) in human placental genomes, showing an extensive load of somatic CNVs, especially duplications and suggesting that this phenomenon may be critical for normal gestation. Placental somatic CNVs were significantly enriched in genes involved in cell adhesion, immunity, embryonic development and cell cycle. Overrepresentation of imprinted genes in somatic duplications suggests that amplified gene copies may represent an alternative mechanism to support parent-of-origin specific gene expression. Placentas from pregnancy complications exhibited significantly altered CNV profile compared to normal gestations, indicative to the clinical implications of the study.
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Affiliation(s)
- Laura Kasak
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia
| | - Kristiina Rull
- 1] Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia [2] Department of Obstetrics and Gynaecology, University of Tartu, Puusepa St. 8, Tartu 51014, Estonia [3] Women's Clinic of Tartu University Hospital, Puusepa St. 8, Tartu 51014, Estonia
| | - Pille Vaas
- 1] Department of Obstetrics and Gynaecology, University of Tartu, Puusepa St. 8, Tartu 51014, Estonia [2] Women's Clinic of Tartu University Hospital, Puusepa St. 8, Tartu 51014, Estonia
| | - Pille Teesalu
- 1] Department of Obstetrics and Gynaecology, University of Tartu, Puusepa St. 8, Tartu 51014, Estonia [2] Women's Clinic of Tartu University Hospital, Puusepa St. 8, Tartu 51014, Estonia
| | - Maris Laan
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia
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Gamazon E, Cox N, Davis L. Structural architecture of SNP effects on complex traits. Am J Hum Genet 2014; 95:477-89. [PMID: 25307299 DOI: 10.1016/j.ajhg.2014.09.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 09/16/2014] [Indexed: 12/16/2022] Open
Abstract
Despite the discovery of copy-number variation (CNV) across the genome nearly 10 years ago, current SNP-based analysis methodologies continue to collapse the homozygous (i.e., A/A), hemizygous (i.e., A/0), and duplicative (i.e., A/A/A) genotype states, treating the genotype variable as irreducible or unaltered by other colocalizing forms of genetic (e.g., structural) variation. Our understanding of common, genome-wide CNVs suggests that the canonical genotype construct might belie the enormous complexity of the genome. Here we present multiple analyses of several phenotypes and provide methods supporting a conceptual shift that embraces the structural dimension of genotype. We comprehensively investigate the impact of the structural dimension of genotype on (1) GWAS methods, (2) interpretation of rare LOF variants, (3) characterization of genomic architecture, and (4) implications for mapping loci involved in complex disease. Taken together, these results argue for the inclusion of a structural dimension and suggest that some portion of the "missing" heritability might be recovered through integration of the structural dimension of SNP effects on complex traits.
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Nagirnaja L, Palta P, Kasak L, Rull K, Christiansen OB, Nielsen HS, Steffensen R, Esko T, Remm M, Laan M. Structural genomic variation as risk factor for idiopathic recurrent miscarriage. Hum Mutat 2014; 35:972-82. [PMID: 24827138 PMCID: PMC4285182 DOI: 10.1002/humu.22589] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 04/23/2014] [Indexed: 12/22/2022]
Abstract
Recurrent miscarriage (RM) is a multifactorial disorder with acknowledged genetic heritability that affects ∼3% of couples aiming at childbirth. As copy number variants (CNVs) have been shown to contribute to reproductive disease susceptibility, we aimed to describe genome-wide profile of CNVs and identify common rearrangements modulating risk to RM. Genome-wide screening of Estonian RM patients and fertile controls identified excessive cumulative burden of CNVs (5.4 and 6.1 Mb per genome) in two RM cases possibly increasing their individual disease risk. Functional profiling of all rearranged genes within RM study group revealed significant enrichment of loci related to innate immunity and immunoregulatory pathways essential for immune tolerance at fetomaternal interface. As a major finding, we report a multicopy duplication (61.6 kb) at 5p13.3 conferring increased maternal risk to RM in Estonia and Denmark (meta-analysis, n = 309/205, odds ratio = 4.82, P = 0.012). Comparison to Estonian population-based cohort (total, n = 1000) confirmed the risk for Estonian female cases (P = 7.9 × 10(-4) ). Datasets of four cohorts from the Database of Genomic Variants (total, n = 5,846 subjects) exhibited similar low duplication prevalence worldwide (0.7%-1.2%) compared to RM cases of this study (6.6%-7.5%). The CNV disrupts PDZD2 and GOLPH3 genes predominantly expressed in placenta and it may represent a novel risk factor for pregnancy complications.
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Affiliation(s)
- Liina Nagirnaja
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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Araujo AN, Moraes L, França MIC, Hakonarson H, Li J, Pellegrino R, Maciel RMB, Cerutti JM. Genome-wide copy number analysis in a family with p.G533C RET mutation and medullary thyroid carcinoma identified regions potentially associated with a higher predisposition to lymph node metastasis. J Clin Endocrinol Metab 2014; 99:E1104-12. [PMID: 24601688 DOI: 10.1210/jc.2013-2993] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
CONTEXT Our group described a p.G533C RET gene mutation in a large family with multiple endocrine neoplasia type 2 syndrome. Clinical heterogeneity, primarily associated with the presence of lymph node metastases, was observed among the p.G533C carriers. OBJECTIVE The aim of this study was to use single-nucleotide polymorphism-array technology to identify copy number variations (CNVs), which are present in the constitutional DNA and associated with the established clinical and pathological features of aggressive medullary thyroid carcinoma (MTC), primarily the presence of lymph node metastasis. DESIGN Fifteen p.G533C carriers with MTC were chosen for the initial screening. The subjects were divided into two groups according the presence (n = 8) or absence (n = 7) of lymph node metastasis. Peripheral blood DNA was independently hybridized using a genome-wide single-nucleotide polymorphism Array 6.0 platform. The results were analyzed using both Genotyping Console and PennCNV software. To identify the possible candidate regions associated with the presence of lymph node metastasis, cases (metastatic MTC) were compared with controls (nonmetastatic MTC). The identified CNVs were validated by quantitative PCR in an extended cohort (n = 32). RESULTS Using two different algorithms, we identified nine CNV regions that may contribute to susceptibility to lymph node metastasis. The validation step confirmed that a CNV loss impacting the FMN2 gene was potentially associated with a greater predisposition to lymph node metastasis in this family (P = .0179). Finally, we sought to investigate whether the development of lymph node metastasis might not depend on a single CNV but rather a combination of various CNVs. These analyses defined a CNV pattern related to a more aggressive phenotype in this family, with CNV deletions being enriched in the metastatic group (P = .0057). CONCLUSION Although hereditable specific RET mutations are important to determine cancer risk, germline CNVs in disease-affected individuals may predispose them to MTC aggressiveness.
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Affiliation(s)
- Aline N Araujo
- Genetic Bases of Thyroid Tumors Laboratory (A.N.A., L.M., J.M.C.), Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, and Laboratory of Molecular and Translational Endocrinology (M.I.C.F., R.M.B.M.), Division of Endocrinology, Department of Medicine, Universidade Federal de São Paulo, São Paulo SP 04039-032, Brazil; Center for Applied Genomics (H.H., J.L., R.P.), The Children's Hospital of Philadelphia, Research Institute; and Department of Pediatrics (H.H.), The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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12
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Castellani CA, Melka MG, Wishart AE, Locke MEO, Awamleh Z, O'Reilly RL, Singh SM. Biological relevance of CNV calling methods using familial relatedness including monozygotic twins. BMC Bioinformatics 2014; 15:114. [PMID: 24750645 PMCID: PMC4021055 DOI: 10.1186/1471-2105-15-114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Studies involving the analysis of structural variation including Copy Number Variation (CNV) have recently exploded in the literature. Furthermore, CNVs have been associated with a number of complex diseases and neurodevelopmental disorders. Common methods for CNV detection use SNP, CNV, or CGH arrays, where the signal intensities of consecutive probes are used to define the number of copies associated with a given genomic region. These practices pose a number of challenges that interfere with the ability of available methods to accurately call CNVs. It has, therefore, become necessary to develop experimental protocols to test the reliability of CNV calling methods from microarray data so that researchers can properly discriminate biologically relevant data from noise. RESULTS We have developed a workflow for the integration of data from multiple CNV calling algorithms using the same array results. It uses four CNV calling programs: PennCNV (PC), Affymetrix® Genotyping Console™ (AGC), Partek® Genomics Suite™ (PGS) and Golden Helix SVS™ (GH) to analyze CEL files from the Affymetrix® Human SNP 6.0 Array™. To assess the relative suitability of each program, we used individuals of known genetic relationships. We found significant differences in CNV calls obtained by different CNV calling programs. CONCLUSIONS Although the programs showed variable patterns of CNVs in the same individuals, their distribution in individuals of different degrees of genetic relatedness has allowed us to offer two suggestions. The first involves the use of multiple algorithms for the detection of the largest possible number of CNVs, and the second suggests the use of PennCNV over all other methods when the use of only one software program is desirable.
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Affiliation(s)
| | | | | | | | | | | | - Shiva M Singh
- Department of Biology, The University of Western Ontario, London N6A 5B7, ON, Canada.
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Copy number variation distribution in six monozygotic twin pairs discordant for schizophrenia. Twin Res Hum Genet 2014; 17:108-20. [PMID: 24556202 DOI: 10.1017/thg.2014.6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have evaluated copy number variants (CNVs) in six monozygotic twin pairs discordant for schizophrenia. The data from Affymetrix® Human SNP 6.0 arrays™ were analyzed using Affymetrix® Genotyping Console™, Partek® Genomics Suite™, PennCNV, and Golden Helix SVS™. This yielded both program-specific and overlapping results. Only CNVs called by Affymetrix Genotyping Console, Partek Genomics Suite, and PennCNV were used in further analysis. This analysis included an assessment of calls in each of the six twin pairs towards identification of unique CNVs in affected and unaffected co-twins. Real time polymerase chain reaction (PCR) experiments confirmed one CNV loss at 7q11.21 that was found in the affected patient but not in the unaffected twin. The results identified CNVs and genes that were previously implicated in mental abnormalities in four of the six twin pairs. It included PYY (twin pairs 1 and 5), EPHA3 (twin pair 3), KIAA1211L (twin pair 4), and GPR139 (twin pair 5). They represent likely candidate genes and CNVs for the discordance of four of the six monozygotic twin pairs for this heterogeneous neurodevelopmental disorder. An explanation for these differences is ontogenetic de novo events that differentiate in the monozygotic twins during development.
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Uckun FM, Ma H, Ishkhanian R, Arellano M, Shahidzadeh A, Termuhlen A, Gaynon PS, Qazi S. Constitutive function of the Ikaros transcription factor in primary leukemia cells from pediatric newly diagnosed high-risk and relapsed B-precursor ALL patients. PLoS One 2013; 8:e80732. [PMID: 24278314 PMCID: PMC3835424 DOI: 10.1371/journal.pone.0080732] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 10/05/2013] [Indexed: 11/18/2022] Open
Abstract
We examined the constitutive function of the Ikaros (IK) transcription factor in blast cells from pediatric B-precursor acute lymphoblastic leukemia (BPL) patients using multiple assay platforms and bioinformatics tools. We found no evidence of diminished IK expression or function for primary cells from high-risk BPL patients including a Philadelphia chromosome (Ph)+ subset. Relapse clones as well as very aggressive in vivo clonogenic leukemic B-cell precursors isolated from spleens of xenografted NOD/SCID mice that developed overt leukemia after inoculation with primary leukemic cells of patients with BPL invariably and abundantly expressed intact IK protein. These results demonstrate that a lost or diminished IK function is not a characteristic feature of leukemic cells in Ph+ or Ph- high-risk BPL.
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Affiliation(s)
- Fatih M. Uckun
- Systems Immunobiology Laboratory and Developmental Therapeutics Program, Children’s Center for Cancer and Blood Diseases, Children’s Hospital Los Angeles, Los Angeles, California, United States of America
- Department of Pediatrics, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
- Developmental Therapeutics Program, USC Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
- * E-mail:
| | - Hong Ma
- Systems Immunobiology Laboratory and Developmental Therapeutics Program, Children’s Center for Cancer and Blood Diseases, Children’s Hospital Los Angeles, Los Angeles, California, United States of America
| | - Rita Ishkhanian
- Systems Immunobiology Laboratory and Developmental Therapeutics Program, Children’s Center for Cancer and Blood Diseases, Children’s Hospital Los Angeles, Los Angeles, California, United States of America
| | - Martha Arellano
- Systems Immunobiology Laboratory and Developmental Therapeutics Program, Children’s Center for Cancer and Blood Diseases, Children’s Hospital Los Angeles, Los Angeles, California, United States of America
| | - Anoush Shahidzadeh
- Systems Immunobiology Laboratory and Developmental Therapeutics Program, Children’s Center for Cancer and Blood Diseases, Children’s Hospital Los Angeles, Los Angeles, California, United States of America
| | - Amanda Termuhlen
- Department of Pediatrics, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
- Jonathan Jaques Cancer Center, Miller Children’s Hospital, Long Beach, California, United States of America
| | - Paul S. Gaynon
- Department of Pediatrics, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Sanjive Qazi
- Systems Immunobiology Laboratory and Developmental Therapeutics Program, Children’s Center for Cancer and Blood Diseases, Children’s Hospital Los Angeles, Los Angeles, California, United States of America
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Masson AL, Talseth-Palmer BA, Evans TJ, Grice DM, Duesing K, Hannan GN, Scott RJ. Copy number variation in hereditary non-polyposis colorectal cancer. Genes (Basel) 2013; 4:536-55. [PMID: 24705261 PMCID: PMC3927572 DOI: 10.3390/genes4040536] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/02/2013] [Accepted: 09/11/2013] [Indexed: 12/12/2022] Open
Abstract
Hereditary non-polyposis colorectal cancer (HNPCC) is the commonest form of inherited colorectal cancer (CRC) predisposition and by definition describes families which conform to the Amsterdam Criteria or reiterations thereof. In ~50% of patients adhering to the Amsterdam criteria germline variants are identified in one of four DNA Mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2. Loss of function of any one of these genes results in a failure to repair DNA errors occurring during replication which can be most easily observed as DNA microsatellite instability (MSI)—a hallmark feature of this disease. The remaining 50% of patients without a genetic diagnosis of disease may harbour more cryptic changes within or adjacent to MLH1, MSH2, MSH6 or PMS2 or elsewhere in the genome. We used a high density cytogenetic array to screen for deletions or duplications in a series of patients, all of whom adhered to the Amsterdam/Bethesda criteria, to determine if genomic re-arrangements could account for a proportion of patients that had been shown not to harbour causative mutations as assessed by standard diagnostic techniques. The study has revealed some associations between copy number variants (CNVs) and HNPCC mutation negative cases and further highlights difficulties associated with CNV analysis.
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Affiliation(s)
- Amy L. Masson
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, 2308, Australia
| | - Bente A. Talseth-Palmer
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, 2308, Australia
| | - Tiffany-Jane Evans
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, 2308, Australia
| | - Desma M. Grice
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- CSIRO Preventative Health Flagship and Division of Animal, Food and Health Sciences, North Ryde, New South Wales, 2113, Australia; E-Mails: (K.D.); (G.N.H.)
| | - Konsta Duesing
- CSIRO Preventative Health Flagship and Division of Animal, Food and Health Sciences, North Ryde, New South Wales, 2113, Australia; E-Mails: (K.D.); (G.N.H.)
| | - Garry N. Hannan
- CSIRO Preventative Health Flagship and Division of Animal, Food and Health Sciences, North Ryde, New South Wales, 2113, Australia; E-Mails: (K.D.); (G.N.H.)
| | - Rodney J. Scott
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, 2308, Australia
- Division of Molecular Medicine, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, New South Wales, 2305, Australia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +61-2-4921-4974; Fax: +61-2-4921-4253
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Falola MI, Wiener HW, Wineinger NE, Cutter GR, Kimberly RP, Edberg JC, Arnett DK, Kaslow RA, Tang J, Shrestha S. Genomic copy number variants: evidence for association with antibody response to anthrax vaccine adsorbed. PLoS One 2013; 8:e64813. [PMID: 23741398 PMCID: PMC3669407 DOI: 10.1371/journal.pone.0064813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 04/09/2013] [Indexed: 01/09/2023] Open
Abstract
Background Anthrax and its etiologic agent remain a biological threat. Anthrax vaccine is highly effective, but vaccine-induced IgG antibody responses vary widely following required doses of vaccinations. Such variation can be related to genetic factors, especially genomic copy number variants (CNVs) that are known to be enriched among genes with immunologic function. We have tested this hypothesis in two study populations from a clinical trial of anthrax vaccination. Methods We performed CNV-based genome-wide association analyses separately on 794 European Americans and 200 African-Americans. Antibodies to protective antigen were measured at week 8 (early response) and week 30 (peak response) using an enzyme-linked immunosorbent assay. We used DNA microarray data (Affymetrix 6.0) and two CNV detection algorithms, hidden markov model (PennCNV) and circular binary segmentation (GeneSpring) to determine CNVs in all individuals. Multivariable regression analyses were used to identify CNV-specific associations after adjusting for relevant non-genetic covariates. Results Within the 22 autosomal chromosomes, 2,943 non-overlapping CNV regions were detected by both algorithms. Genomic insertions containing HLA-DRB5, DRB1 and DQA1/DRA genes in the major histocompatibility complex (MHC) region (chromosome 6p21.3) were moderately associated with elevated early antibody response (β = 0.14, p = 1.78×10−3) among European Americans, and the strongest association was observed between peak antibody response and a segmental insertion on chromosome 1, containing NBPF4, NBPF5, STXMP3, CLCC1, and GPSM2 genes (β = 1.66, p = 6.06×10−5). For African-Americans, segmental deletions spanning PRR20, PCDH17 and PCH68 genes on chromosome 13 were associated with elevated early antibody production (β = 0.18, p = 4.47×10−5). Population-specific findings aside, one genomic insertion on chromosome 17 (containing NSF, ARL17 and LRRC37A genes) was associated with elevated peak antibody response in both populations. Conclusion Multiple CNV regions, including the one consisting of MHC genes that is consistent with earlier research, can be important to humoral immune responses to anthrax vaccine adsorbed.
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Affiliation(s)
- Michael I. Falola
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Howard W. Wiener
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Nathan E. Wineinger
- Scripps Translational Science Institute, La Jolla, California, United States of America
| | - Gary R. Cutter
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Robert P. Kimberly
- Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jeffrey C. Edberg
- Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Donna K. Arnett
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Richard A. Kaslow
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Sadeep Shrestha
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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Talseth-Palmer BA, Holliday EG, Evans TJ, McEvoy M, Attia J, Grice DM, Masson AL, Meldrum C, Spigelman A, Scott RJ. Continuing difficulties in interpreting CNV data: lessons from a genome-wide CNV association study of Australian HNPCC/lynch syndrome patients. BMC Med Genomics 2013; 6:10. [PMID: 23531357 PMCID: PMC3626775 DOI: 10.1186/1755-8794-6-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 03/18/2013] [Indexed: 01/13/2023] Open
Abstract
Background Hereditary non-polyposis colorectal cancer (HNPCC)/Lynch syndrome (LS) is a cancer syndrome characterised by early-onset epithelial cancers, especially colorectal cancer (CRC) and endometrial cancer. The aim of the current study was to use SNP-array technology to identify genomic aberrations which could contribute to the increased risk of cancer in HNPCC/LS patients. Methods Individuals diagnosed with HNPCC/LS (100) and healthy controls (384) were genotyped using the Illumina Human610-Quad SNP-arrays. Copy number variation (CNV) calling and association analyses were performed using Nexus software, with significant results validated using QuantiSNP. TaqMan Copy-Number assays were used for verification of CNVs showing significant association with HNPCC/LS identified by both software programs. Results We detected copy number (CN) gains associated with HNPCC/LS status on chromosome 7q11.21 (28% cases and 0% controls, Nexus; p = 3.60E-20 and QuantiSNP; p < 1.00E-16) and 16p11.2 (46% in cases, while a CN loss was observed in 23% of controls, Nexus; p = 4.93E-21 and QuantiSNP; p = 5.00E-06) via in silico analyses. TaqMan Copy-Number assay was used for validation of CNVs showing significant association with HNPCC/LS. In addition, CNV burden (total CNV length, average CNV length and number of observed CNV events) was significantly greater in cases compared to controls. Conclusion A greater CNV burden was identified in HNPCC/LS cases compared to controls supporting the notion of higher genomic instability in these patients. One intergenic locus on chromosome 7q11.21 is possibly associated with HNPCC/LS and deserves further investigation. The results from this study highlight the complexities of fluorescent based CNV analyses. The inefficiency of both CNV detection methods to reproducibly detect observed CNVs demonstrates the need for sequence data to be considered alongside intensity data to avoid false positive results.
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Affiliation(s)
- Bente A Talseth-Palmer
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia.
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