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Chen XY, Yu XB, Chen XQ, Chen Y, Liang W. Comparison of tests for detecting Helicobacter pylori in gastric biopsy. Shijie Huaren Xiaohua Zazhi 2018; 26:1499-1504. [DOI: 10.11569/wcjd.v26.i25.1499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To figure out a method to detect Helicobacter pylori (H. pylori) infection that is of high sensitivity and specificity as well as clinically easy-handling by comparing four common H. pylori detection methods.
METHODS Four hundred and ninety gastric mucosa biopsies were tested separately by the rapid urease test (RUT), fluorescence quantitative polymerase chain reaction (qPCR), methylene blue staining, and immunohis-tochemistry (IHC). Positive rates obtained by the different methods were analyzed by the χ2 test.
RESULTS The positive rates of H. pylori obtained by RUT, qPCR, methylene blue staining, and IHC were 18.98%, 63.88%, 32.04%, and 38.16%, respectively, which were statistically different (P < 0.005).
CONCLUSION IHC provides a visual scene for observers, and there is a sharp contrast for IHC images between H. pylori infected and surrounding areas. This feature can facilitate researchers to obtain morphological information with potential clinical value. Furthermore, IHC protocols are friendly to instruments and operators. Hence, we recommend that IHC be used to detect H. pylori in gastric biopsies for diagnosing H. pylori infection and determining H. pylori treatment.
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Affiliation(s)
- Xiao-Yan Chen
- Department of Pathology, Fujian Provincial Hospital, Fuzhou 350001, Fujian Province, China
| | - Xun-Bin Yu
- Department of Pathology, Fujian Provincial Hospital, Fuzhou 350001, Fujian Province, China
| | - Xiao-Qiong Chen
- Provincial Clinical Medical College, Fujian Medical University, Fuzhou 350001, Fujian Province, China
| | - Yong Chen
- Fuzhou Maixin Biotech Co., Ltd, Fuzhou 350001, Fujian Province, China
| | - Wei Liang
- Department of Digestive Endoscopy, Provincial Clinical Medical College, Fujian Medical University, Fujian Provincial Hospital, Fuzhou 350001, Fujian Province, China
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2
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Combs SE, Han G, Mani N, Beruti S, Nerenberg M, Rimm DL. Loss of antigenicity with tissue age in breast cancer. J Transl Med 2016; 96:264-9. [PMID: 26568292 DOI: 10.1038/labinvest.2015.138] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/30/2015] [Indexed: 02/07/2023] Open
Abstract
Archived tumor specimens, particularly those collected by large cooperative groups and trials, provide a wealth of material for post hoc clinical investigation. As these tissues are rigorously collected and preserved for many decades, subsequent use of the specimens to answer clinical questions must rely on the assumption that expression and detection of target biomarkers are not degraded with time. To test this assumption, we measured the expression of estrogen receptor (ER), human epidermal growth receptor 2 (HER2), and Ki67 in human breast carcinoma using quantitative immunofluorescence (QIF) in a series of formalin-fixed paraffin-embedded (FFPE) tissues from 1295 individual patients preserved for 7 to 53 years in four cohorts on tissue microarrays. Protein expression was measured using the automated quantitative analysis method for QIF. Change in quantitative protein expression over time was estimated in positive cases using both Pearson's correlation and a polynomial regression analysis with a random effects model. The average signal decreased with preservation time for all biomarkers measured. For ER and HER2, there was an average of 10% signal loss after 9.9 years and 8.5 years, respectively, compared with the most recent tissue. Detection of Ki67 expression was lost more rapidly, with 10% signal loss in just 4.5 years. Overall, these results demonstrate the need for adjustment of tissue age when studying FFPE biospecimens. The rate of antigenicity loss is biomarker specific and should be considered as an important variable for studies using archived tissues.
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Affiliation(s)
- Susan E Combs
- Yale Pathology Tissue Services, Department of Pathology, Yale University Medical School, New Haven, CT, USA
| | - Gang Han
- Yale Pathology Tissue Services, Department of Pathology, Yale University Medical School, New Haven, CT, USA
| | - Nikita Mani
- Yale Pathology Tissue Services, Department of Pathology, Yale University Medical School, New Haven, CT, USA
| | | | | | - David L Rimm
- Yale Pathology Tissue Services, Department of Pathology, Yale University Medical School, New Haven, CT, USA
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3
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Cantsilieris S, Western PS, Baird PN, White SJ. Technical considerations for genotyping multi-allelic copy number variation (CNV), in regions of segmental duplication. BMC Genomics 2014; 15:329. [PMID: 24885186 PMCID: PMC4035060 DOI: 10.1186/1471-2164-15-329] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 04/22/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Intrachromosomal segmental duplications provide the substrate for non-allelic homologous recombination, facilitating extensive copy number variation in the human genome. Many multi-copy gene families are embedded within genomic regions with high levels of sequence identity (>95%) and therefore pose considerable analytical challenges. In some cases, the complexity involved in analyzing such regions is largely underestimated. Rapid, cost effective analysis of multi-copy gene regions have typically implemented quantitative approaches, however quantitative data are not an absolute means of certainty. Therefore any technique prone to degrees of measurement error can produce ambiguous results that may lead to spurious associations with complex disease. RESULTS In this study we have focused on testing the accuracy and reproducibility of quantitative analysis techniques. With reference to the C-C Chemokine Ligand-3-like-1 (CCL3L1) gene, we performed analysis using real-time Quantitative PCR (QPCR), Multiplex Ligation-dependent Probe Amplification (MLPA) and Paralogue Ratio Test (PRT). After controlling for potential outside variables on assay performance, including DNA concentration, quality, preparation and storage conditions, we find that real-time QPCR produces data that does not cluster tightly around copy number integer values, with variation substantially greater than that of the MLPA or PRT systems. We find that the method of rounding real-time QPCR measurements can potentially lead to mis-scoring of copy number genotypes and suggest caution should be exercised in interpreting QPCR data. CONCLUSIONS We conclude that real-time QPCR is inherently prone to measurement error, even under conditions that would seem favorable for association studies. Our results indicate that potential variability in the physicochemical properties of the DNA samples cannot solely explain the poor performance exhibited by the real-time QPCR systems. We recommend that more robust approaches such as PRT or MLPA should be used to genotype multi-allelic copy number variation in disease association studies and suggest several approaches which can be implemented to ensure the quality of the copy number typing using quantitative methods.
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Affiliation(s)
- Stuart Cantsilieris
- Centre for Genetic Diseases, MIMR-PHI Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton 3168, Victoria, Australia.
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4
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Kim J, Shin JY, Kim JI, Seo JS, Webster MJ, Lee D, Kim S. Somatic deletions implicated in functional diversity of brain cells of individuals with schizophrenia and unaffected controls. Sci Rep 2014; 4:3807. [PMID: 24448323 PMCID: PMC3897957 DOI: 10.1038/srep03807] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 12/27/2013] [Indexed: 12/19/2022] Open
Abstract
While somatic DNA copy number variations (CNVs) have been identified in multiple tissues from normal people, they have not been well studied in brain tissues from individuals with psychiatric disorders. With ultrahigh depth sequencing data, we developed an integrated pipeline for calling somatic deletions using data from multiple tissues of the same individual or a single tissue type taken from multiple individuals. Using the pipelines, we identified 106 somatic deletions in DNA from prefrontal cortex (PFC) and/or cerebellum of two normal controls subjects and/or three individuals with schizophrenia. We then validated somatic deletions in 18 genic and in 1 intergenic region. Somatic deletions in BOD1 and CBX3 were reconfirmed using DNA isolated from non-pyramidal neurons and from cells in white matter using laser capture microdissection (LCM). Our results suggest that somatic deletions may affect metabolic processes and brain development in a region specific manner.
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Affiliation(s)
- Junho Kim
- Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Korea
| | - Jong-Yeon Shin
- 1] Genomic Medicine Institute (GMI), Medical Research Center, Seoul National, University, Seoul 110-799, Korea [2] Psoma Therapeutics Inc., Seoul, 153-781, Korea
| | - Jong-Il Kim
- 1] Genomic Medicine Institute (GMI), Medical Research Center, Seoul National, University, Seoul 110-799, Korea [2] Psoma Therapeutics Inc., Seoul, 153-781, Korea [3] Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 110-799, Korea [4] Department of Biochemistry and Molecular Biology, Seoul National University, College of Medicine, Seoul 110-799, Korea
| | - Jeong-Sun Seo
- 1] Genomic Medicine Institute (GMI), Medical Research Center, Seoul National, University, Seoul 110-799, Korea [2] Psoma Therapeutics Inc., Seoul, 153-781, Korea [3] Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 110-799, Korea [4] Department of Biochemistry and Molecular Biology, Seoul National University, College of Medicine, Seoul 110-799, Korea [5] Macrogen Inc., Seoul 153-781, Korea
| | - Maree J Webster
- Stanley Brain Research Laboratory, Stanley Medical Research Institute, 9800 Medical Center Drive, Rockville, MD 20850
| | - Doheon Lee
- Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Korea
| | - Sanghyeon Kim
- Stanley Brain Research Laboratory, Stanley Medical Research Institute, 9800 Medical Center Drive, Rockville, MD 20850
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5
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CNVrd, a read-depth algorithm for assigning copy-number at the FCGR locus: population-specific tagging of copy number variation at FCGR3B. PLoS One 2013; 8:e63219. [PMID: 23646200 PMCID: PMC3640002 DOI: 10.1371/journal.pone.0063219] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 04/04/2013] [Indexed: 01/09/2023] Open
Abstract
The extent of contribution from common gene copy number (CN) variants in human disease is currently unresolved. Part of the reason for this is the technical difficulty in directly measuring CN variation (CNV) using molecular methods, and the lack of single nucleotide polymorphisms (SNPs) that can tag complex CNV that has arisen multiple times on different SNP haplotypes. One CNV locus implicated in human disease is FCGR. Here we aimed to use next-generation sequencing (NGS) data from the 1000 Genomes Project to assign CN at FCGR3A and FCGR3B and to comprehensively assess the ability of SNPs to tag specific CN variants. A read-depth algorithm was developed (CNVrd) and validated on a subset of HapMap samples using CN assignments that had previously been determined using molecular and microarray methods. At 7 out of 9 other complex loci there was >90% concordance with microarray data. However, given that some prior knowledge of CN is required, the generalizability of CNVrd is limited and should be applied to other complex CNV loci with caution. Subsequently, CN was assigned et FCGR3B using CNVrd in a total of 952 samples from the 1000 Genomes Project, using three classes and SNPs that correlated with duplication were identified. The best tag SNP was observed in the Mexican-American sample set for duplication at FCGR3B. This SNP (rs117435514, r2 = 0.79) also tagged similar duplication in Chinese and Japanese (r2 = 0.35–0.60), but not in Caucasian or African. No tag SNP for duplication at FCGR3A or deletion at FCGR3B was identified in any population. We conclude that it is possible to tag CNV at the FCGR locus, but CN and SNPs have to be characterized and correlated on a population-specific basis.
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6
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Soejima M, Koda Y. TaqMan real-time polymerase chain reaction for detection of SEC1-FUT2 hybrid alleles: identification of novel hybrid allele. Clin Chim Acta 2013; 415:59-62. [PMID: 22959923 DOI: 10.1016/j.cca.2012.08.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/14/2012] [Accepted: 08/22/2012] [Indexed: 12/15/2022]
Abstract
BACKGROUND Two hybrid alleles between the secretor type α(1,2)fucosyltransferase gene (FUT2) and a pseudogene of FUT2 (SEC1) have been reported so far; parts of the SEC1 and FUT2 sequences are suggested to be susceptible to recombination. The se(fus), one of the two hybrid alleles, is found in Japanese populations at relative high frequencies. METHODS A TaqMan assay to distinguish SEC1 and SEC1-FUT2 hybrid alleles was designed for the purpose of dealing with large number of samples. RESULTS The results of the present method were fully consistent with those of the previous method for detection of se(fus) in the Japanese population. In addition, a novel SEC1-FUT2-SEC1 hybrid allele, which contains a 35-bp sequence (between positions 418 and 452) that is identical to the FUT2 sequence including a 13-bp FUT2-specific region (between positions 436 and 448), was encountered in an individual of European descent. CONCLUSIONS The present TaqMan assay is a reliable and powerful method for the large scale association study between disease susceptibility and FUT2 genotypes especially in the Japanese populations because of relative high frequency of se(fus). In addition, this method is a useful tool to find novel SEC1-FUT2 hybrid alleles.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, Kurume 830-0011, Japan
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7
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Zakaria Z, Umi S, Mokhtar S, Mokhtar U, Zaiharina M, Aziz A, Hoh B. Methodology An alternate method for DNA and RNA extraction from clotted blood. GENETICS AND MOLECULAR RESEARCH 2013; 12:302-11. [DOI: 10.4238/2013.february.4.4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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8
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Zeng GP, Xiang DS, Cai JZ. A New Trace Analytic Method for the Determination of Sequence-Specific DNA with Fluorescent Probes. ANAL LETT 2012. [DOI: 10.1080/00032719.2012.691591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Cantsilieris S, White SJ. Correlating multiallelic copy number polymorphisms with disease susceptibility. Hum Mutat 2012; 34:1-13. [PMID: 22837109 DOI: 10.1002/humu.22172] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 07/13/2012] [Indexed: 01/20/2023]
Abstract
The human genome contains a significant amount of sequence variation, from single nucleotide polymorphisms to large stretches of DNA that may be present in a range of different copies between individuals. Several such regions are variable in >1% of the population (referred to as copy number polymorphisms or CNPs), and many studies have looked for associations between the copy number of genes within multiallelic CNPs and disease susceptibility. Associations have indeed been described for several genes, including the β-defensins (DEFB4, DEFB103, DEFB104), chemokine ligand 3 like 1 (CCL3L1), Fc gamma receptor 3B (FCGR3B), and complement component C4 (C4). However, follow-up replication in independent cohorts has failed to reproduce a number of these associations. It is clear that replicated associations such as those between C4 and systemic lupus erythematosus, and β-defensin and psoriasis, have used robust genotyping methodologies. Technical issues associated with genotyping sequences of high identity may therefore account for failure to replicate other associations. Here, we compare and contrast the most popular approaches that have been used to genotype CNPs, describe how they have been applied in different situations, and discuss potential reasons for the difficulty in reproducibly linking multiallelic CNPs to complex diseases.
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Affiliation(s)
- Stuart Cantsilieris
- Centre for Reproduction and Development, Monash Institute of Medical Research, Monash University, Melbourne, Victoria, Australia
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10
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Jackson CB, Gallati S, Schaller A. qPCR-based mitochondrial DNA quantification: influence of template DNA fragmentation on accuracy. Biochem Biophys Res Commun 2012; 423:441-7. [PMID: 22683632 DOI: 10.1016/j.bbrc.2012.05.121] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 05/22/2012] [Indexed: 01/12/2023]
Abstract
Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA (λnDNA) and mtDNA (λmtDNA) we present an approach to possibly correct measurements in degraded samples in the future. To our knowledge this is the first time different degradation impact of the two genomes is demonstrated and which evaluates systematically the impact of DNA degradation on quantification of mtDNA copy number.
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Affiliation(s)
- Christopher B Jackson
- Division of Human Genetics, Departement of Pediatrics, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne, Switzerland.
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11
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McKinney C, Broen JCA, Vonk MC, Beretta L, Hesselstrand R, Hunzelmann N, Riemekasten G, Scorza R, Simeon CP, Fonollosa V, Carreira PE, Ortego-Centeno N, Gonzalez-Gay MA, Airo P, Coenen M, Martin J, Radstake TRDJ, Merriman TR. Evidence that deletion at FCGR3B is a risk factor for systemic sclerosis. Genes Immun 2012; 13:458-60. [PMID: 22551723 DOI: 10.1038/gene.2012.15] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is increasing evidence that gene copy number (CN) variation influences clinical phenotype. The low-affinity Fc receptor 3B (FCGR3B) located in the FCGR gene cluster is a CN polymorphic gene involved in the recruitment of polymorphonuclear neutrophils to sites of inflammation and their activation. Given the genetic overlap between systemic lupus erythematosus and systemic sclerosis (SSc) and the strong evidence for FCGR3B CN in the pathology of SLE, we hypothesised that FCGR3B gene dosage influences susceptibility to SSc. We obtained FCGR3B deletion status in 777 European Caucasian cases and 1000 controls. There was an inverse relationship between FCGR3B CN and disease susceptibility. CN of ≤ 1 was a significant risk factor for SSc (OR=1.55 (1.13-2.14), P=0.007) relative to CN ≥ 2. Although requiring replication, these results suggest that impaired immune complex clearance arising from FCGR3B deficiency contributes to the pathology of SSc, and FCGR3B CN variation is a common risk factor for systemic autoimmunity.
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Affiliation(s)
- C McKinney
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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De novo and inherited CNVs in MZ twin pairs selected for discordance and concordance on Attention Problems. Eur J Hum Genet 2012; 20:1037-43. [PMID: 22490988 PMCID: PMC3449078 DOI: 10.1038/ejhg.2012.49] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Copy number variations (CNVs) have been reported to be causal suspects in a variety of psychopathologic traits. We investigate whether de novo and/or inherited CNVs contribute to the risk for Attention Problems (APs) in children. Based on longitudinal phenotyping, 50 concordant and discordant monozygotic (MZ) twin pairs were selected from a sample of ∼3200 MZ pairs. Two types of de novo CNVs were investigated: (1) CNVs shared by both MZ twins, but not inherited (pre-twinning de novo CNVs), which were detected by comparing copy number (CN) calls between parents and twins and (2) CNVs not shared by co-twins (post-twinning de novo CNVs), which were investigated by comparing the CN calls within MZ pairs. The association between the overall CNV burden and AP was also investigated for CNVs genome-wide, CNVs within genes and CNVs outside of genes. Two de novo CNVs were identified and validated using quantitative PCR: a pre-twinning de novo duplication in a concordant-unaffected twin pair and a post-twinning deletion in the higher scoring twin from a concordant-affected pair. For the overall CNV burden analyses, affected individuals had significantly larger CNVs that overlapped with genes than unaffected individuals (P=0.008). This study suggests that the presence of larger CNVs may increase the risk for AP, because they are more likely to affect genes, and confirms that MZ twins are not always genetically identical.
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McKinney C, Merriman TR. Meta-analysis confirms a role for deletion in FCGR3B in autoimmune phenotypes. Hum Mol Genet 2012; 21:2370-6. [PMID: 22337955 DOI: 10.1093/hmg/dds039] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although deletion in the low-affinity IgG receptor gene FCGR3B has repeatedly been implicated in systemic autoimmune disease, the role of FCGR3B copy number variation (CNV) in autoimmunity still remains unclear. Factors such as study size, ethnicity, specific disease phenotype and experimental methodology may explain these conflicting results. Here we aimed at using meta-analysis to assess the role for FCGR3B CNV in autoimmunity. We excluded studies using SybrGreen-based genotyping and found strong evidence for association between low (<2) FCGR3B CN and systemic lupus erythematosus [OR = 1.59 (1.32-1.92), P(meta)=9.1 × 10(-7)], but not for rheumatoid arthritis [OR = 1.36 (0.89-2.06), P= 0.15]. However, a combined autoimmune phenotype analysis supports the deletion of FCGR3B as a risk factor for non-organ-specific autoimmunity [OR = 1.44 (1.28-1.62), P(meta)= 2.9 × 10(-9)]. This meta-analysis implicates the clearance of immune complex in the etiology of non-organ-specific autoimmune disease.
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Affiliation(s)
- Cushla McKinney
- Department of Biochemistry, University of Otago, Box 56, Dunedin, New Zealand
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14
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Solassol J, Ramos J, Crapez E, Saifi M, Mangé A, Vianès E, Lamy PJ, Costes V, Maudelonde T. KRAS mutation detection in paired frozen and Formalin-Fixed Paraffin-Embedded (FFPE) colorectal cancer tissues. Int J Mol Sci 2011; 12:3191-204. [PMID: 21686179 PMCID: PMC3116185 DOI: 10.3390/ijms12053191] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 04/11/2011] [Accepted: 05/05/2011] [Indexed: 01/05/2023] Open
Abstract
KRAS mutation has been unambiguously identified as a marker of resistance to cetuximab-based treatment in metastatic colorectal cancer (mCRC) patients. However, most studies of KRAS mutation analysis have been performed using homogenously archived CRC specimens, and studies that compare freshly frozen specimens and formalin-fixed paraffin-embedded (FFPE) specimens of CRC are lacking. The aim of the present study was to evaluate the impact of tissue preservation on the determination of KRAS mutational status. A series of 131 mCRC fresh-frozen tissues were first analyzed using both high-resolution melting (HRM) and direct sequencing. KRAS mutations were found in 47/131 (35.8%) using both approaches. Out of the 47 samples that were positive for KRAS mutations, 33 had available matched FFPE specimens. Using HRM, 2/33 (6%) demonstrated suboptimal template amplification, and 2/33 (6%) expressed an erroneous wild-type KRAS profile. Using direct sequencing, 6/33 (18.1%) displayed a wild-type KRAS status, and 3/33 (9.1%) showed discordant mutations. Finally, the detection of KRAS mutations was lower among the FFPE samples compared with the freshly frozen samples, demonstrating that tissue processing clearly impacts the accuracy of KRAS genotyping.
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Affiliation(s)
- Jérome Solassol
- Department of Cellular Biology, Center Hospital University, Montpellier 34000, France; E-Mails: (A.M.); (E.V.); (T.M.)
- University of Montpellier I, Montpellier 34000, France; E-Mails: (J.R.); (V.C.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-467612412; Fax: +33-467339590
| | - Jeanne Ramos
- University of Montpellier I, Montpellier 34000, France; E-Mails: (J.R.); (V.C.)
- Department of Pathology, Center Hospital University, Montpellier 34000, France; E-Mail:
| | - Evelyne Crapez
- Department of Biology, Centre Lutte Contre Cancer Val d’Aurelle, Montpellier 34000, France; E-Mails: (E.C.); (P.-J.L.)
| | - Majda Saifi
- Department of Pathology, Center Hospital University, Montpellier 34000, France; E-Mail:
| | - Alain Mangé
- Department of Cellular Biology, Center Hospital University, Montpellier 34000, France; E-Mails: (A.M.); (E.V.); (T.M.)
- University of Montpellier I, Montpellier 34000, France; E-Mails: (J.R.); (V.C.)
| | - Evelyne Vianès
- Department of Cellular Biology, Center Hospital University, Montpellier 34000, France; E-Mails: (A.M.); (E.V.); (T.M.)
| | - Pierre-Jean Lamy
- Department of Biology, Centre Lutte Contre Cancer Val d’Aurelle, Montpellier 34000, France; E-Mails: (E.C.); (P.-J.L.)
| | - Valérie Costes
- University of Montpellier I, Montpellier 34000, France; E-Mails: (J.R.); (V.C.)
- Department of Pathology, Center Hospital University, Montpellier 34000, France; E-Mail:
| | - Thierry Maudelonde
- Department of Cellular Biology, Center Hospital University, Montpellier 34000, France; E-Mails: (A.M.); (E.V.); (T.M.)
- University of Montpellier I, Montpellier 34000, France; E-Mails: (J.R.); (V.C.)
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Fode P, Jespersgaard C, Hardwick RJ, Bogle H, Theisen M, Dodoo D, Lenicek M, Vitek L, Vieira A, Freitas J, Andersen PS, Hollox EJ. Determination of beta-defensin genomic copy number in different populations: a comparison of three methods. PLoS One 2011; 6:e16768. [PMID: 21364933 PMCID: PMC3043064 DOI: 10.1371/journal.pone.0016768] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 12/24/2010] [Indexed: 01/13/2023] Open
Abstract
Background There have been conflicting reports in the literature on association of gene copy number with disease, including CCL3L1 and HIV susceptibility, and β-defensins and Crohn's disease. Quantification of precise gene copy numbers is important in order to define any association of gene copy number with disease. At present, real-time quantitative PCR (QPCR) is the most commonly used method to determine gene copy number, however the Paralogue Ratio Test (PRT) is being used in more and more laboratories. Findings In this study we compare a Pyrosequencing-based Paralogue Ratio Test (PPRT) for determining beta-defensin gene copy number with two currently used methods for gene copy number determination, QPCR and triplex PRT by typing five different cohorts (UK, Danish, Portuguese, Ghanaian and Czech) of DNA from a total of 576 healthy individuals. We found a systematic measurement bias between DNA cohorts revealed by QPCR, but not by the PRT-based methods. Using PRT, copy number ranged from 2 to 9 copies, with a modal copy number of 4 in all populations. Conclusions QPCR is very sensitive to quality of the template DNA, generating systematic biases that could produce false-positive or negative disease associations. Both triplex PRT and PPRT do not show this systematic bias, and type copy number within the correct range, although triplex PRT appears to be a more precise and accurate method to type beta-defensin copy number.
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Affiliation(s)
- Peder Fode
- Department for Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Cathrine Jespersgaard
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Robert J. Hardwick
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Helen Bogle
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Michael Theisen
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Daniel Dodoo
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Martin Lenicek
- Department of Clinical Biochemistry and Laboratory Diagnostics, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- 4th Department of Internal Medicine, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Libor Vitek
- Department of Clinical Biochemistry and Laboratory Diagnostics, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- 4th Department of Internal Medicine, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ana Vieira
- Department of Gastroenterology, Hospital Garcia de Orta, Almada, Portugal
| | - Joao Freitas
- Department of Gastroenterology, Hospital Garcia de Orta, Almada, Portugal
| | - Paal Skytt Andersen
- Department for Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Edward J. Hollox
- Department of Genetics, University of Leicester, Leicester, United Kingdom
- * E-mail:
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16
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McKinney C, Fanciulli M, Merriman ME, Phipps-Green A, Alizadeh BZ, Koeleman BPC, Dalbeth N, Gow PJ, Harrison AA, Highton J, Jones PB, Stamp LK, Steer S, Barrera P, Coenen MJH, Franke B, van Riel PLCM, Vyse TJ, Aitman TJ, Radstake TRDJ, Merriman TR. Association of variation in Fcgamma receptor 3B gene copy number with rheumatoid arthritis in Caucasian samples. Ann Rheum Dis 2010; 69:1711-6. [PMID: 20472591 PMCID: PMC3670580 DOI: 10.1136/ard.2009.123588] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVE There is increasing evidence that variation in gene copy number (CN) influences clinical phenotype. The low-affinity Fcgamma receptor 3B (FCGR3B) located in the FCGR gene cluster is a CN polymorphic gene involved in the recruitment to sites of inflammation and activation of polymorphonuclear neutrophils (PMNs). Given recent evidence that low FCGR3B CN is a risk factor for systemic but not organ-specific autoimmune disease and the potential importance of PMN in the pathophysiology of rheumatoid arthritis (RA), the authors hypothesised that FCGR3B gene dosage influences susceptibility to RA. METHODS FCGR3B CN was measured in 643 cases of RA and 461 controls from New Zealand (NZ), with follow-up analysis in 768 cases and 702 controls from the Netherlands and 250 cases and 211 controls from the UK. All subjects were of Caucasian ancestry. RESULTS Significant evidence for an association between CN <2 and RA was observed in the Dutch cohort (OR 2.01 (95% CI 1.37 to 2.94), p=3 x 10-4) but not in the two smaller cohorts (OR 1.45 (95% CI 0.92 to 2.26), p=0.11 and OR 1.33 (95% CI 0.58 to 3.02), p=0.50 for the NZ and UK populations, respectively). The association was evident in a meta-analysis which included a previously published Caucasian sample set (OR 1.67 (95% CI 1.28 to 2.17), p=1.2 x 10-4). CONCLUSIONS One possible mechanism to explain the association between reduced FCGR3B CN and RA is the reduced clearance of immune complex during inflammation. However, it is not known whether the association between RA and FCGR3B CN is aetiological or acts as a proxy marker for another biologically relevant variant. More detailed examination of genetic variation within the FCGR gene cluster is required.
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Affiliation(s)
- Cushla McKinney
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Manuela Fanciulli
- MRC Clinical Sciences Centre and Division of Medicine, Imperial College London, London, UK
| | | | | | - Behrooz Z Alizadeh
- Complex Genetics Section, Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Bobby P C Koeleman
- Complex Genetics Section, Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Nicola Dalbeth
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Peter J Gow
- Department of Rheumatology, Middlemore Hospital, Auckland, New Zealand
| | - Andrew A Harrison
- Department of Medicine, University of Otago, Wellington, New Zealand
| | - John Highton
- Department of Medicine, University of Otago, Dunedin, New Zealand
| | - Peter B Jones
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Lisa K Stamp
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Sophia Steer
- Kings’ College Hospital NHS Foundation Trust, London, UK
| | - Pilar Barrera
- Department of Rheumatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Marieke J H Coenen
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Barbara Franke
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Piet L C M van Riel
- Department of Rheumatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Tim J Vyse
- Division of Medicine, Imperial College London, London, UK
| | - Tim J Aitman
- MRC Clinical Sciences Centre and Division of Medicine, Imperial College London, London, UK
| | - Timothy R D J Radstake
- Department of Rheumatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Tony R Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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17
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Morris DL, Roberts AL, Witherden AS, Tarzi R, Barros P, Whittaker JC, Cook TH, Aitman TJ, Vyse TJ. Evidence for both copy number and allelic (NA1/NA2) risk at the FCGR3B locus in systemic lupus erythematosus. Eur J Hum Genet 2010; 18:1027-31. [PMID: 20442749 DOI: 10.1038/ejhg.2010.56] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The Fcgamma-receptor locus on chromosome 1q23 shows copy-number variation (CNV), and it has previously been shown that individuals with reduced numbers of copies of the Fcgamma-receptor-IIIB gene (FCGR3B) have an increased risk of developing systemic lupus erythematosus (SLE). It is not understood whether the association arises from FCGR3B (CD16b) itself, is observed because of linkage disequilibrium with actual causal alleles and/or is an effect of CNV on flanking FCGR genes. Thus, we extended this previous work by genotyping the FCGR3B alleles NA1/NA2 and re-assaying CNV using a paralogue ratio test assay in a family study (365 families). We have developed a novel case/pseudo-control approach to analyse family data, as the phase of copy number (CN) is not known in parents and cannot always be inferred in offspring. The results, obtained by fitting logistic regression models, confirm the association of low CN of FCGR3B with SLE (P=0.04). The risk conferred by low copies (<2) was contingent on FCGR3B allotype, being greater for deletion of NA1 than the for lower-affinity NA2. The simpler model with just CN was rejected in favour of the biallelic-CN model (P=0.03). We observed a correlation (R(2)=0.75, P<0.0001) between FCGR3B CNV and neutrophil expression in both healthy controls and patients with SLE. Our results suggest that one mechanism by which CNV at this locus confers disease risk is directly as a result of reduced FcgammaRIIIb function, either because of reduced expression (related to CNV) or because of reduced affinity for its ligand (NA1/NA2 allotype).
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Affiliation(s)
- David L Morris
- Section of Rheumatology, Hammersmith Hospital, Imperial College London, London, UK
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18
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Barnes MR, Breen G. A short primer on the functional analysis of copy number variation for biomedical scientists. Methods Mol Biol 2010; 628:119-35. [PMID: 20238079 DOI: 10.1007/978-1-60327-367-1_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Recent studies have highlighted the potential prevalence of copy number variation (CNV) in mammalian genomes, including the human genome. These studies suggest that CNVs may play a potentially important role in human phenotypic diversity and disease susceptibility. Here, we consider some of the in silico challenges of characterizing genomic structural variants. While the phenotypic impact of the vast majority of CNVs is likely to be neutral, some CNVs will clearly impact phenotype. Here, we review some of the key databases hosting CNV data and discuss some of the caveats in the analysis of CNV data. The task is now to translate some of the initial associations between CNVs and disease into causal variants.
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Affiliation(s)
- Michael R Barnes
- Medicines Research Centre, GlaxoSmithKline Research & Development Limited, Stevenage, Hertfordshire, UK
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19
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Targeted KRAS mutation assessment on patient tumor histologic material in real time diagnostics. PLoS One 2009; 4:e7746. [PMID: 19888477 PMCID: PMC2768905 DOI: 10.1371/journal.pone.0007746] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 10/13/2009] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Testing for tumor specific mutations on routine formalin-fixed paraffin-embedded (FFPE) tissues may predict response to treatment in Medical Oncology and has already entered diagnostics, with KRAS mutation assessment as a paradigm. The highly sensitive real time PCR (Q-PCR) methods developed for this purpose are usually standardized under optimal template conditions. In routine diagnostics, however, suboptimal templates pose the challenge. Herein, we addressed the applicability of sequencing and two Q-PCR methods on prospectively assessed diagnostic cases for KRAS mutations. METHODOLOGY/PRINCIPAL FINDINGS Tumor FFPE-DNA from 135 diagnostic and 75 low-quality control samples was obtained upon macrodissection, tested for fragmentation and assessed for KRAS mutations with dideoxy-sequencing and with two Q-PCR methods (Taqman-minor-groove-binder [TMGB] probes and DxS-KRAS-IVD). Samples with relatively well preserved DNA could be accurately analyzed with sequencing, while Q-PCR methods yielded informative results even in cases with very fragmented DNA (p<0.0001) with 100% sensitivity and specificity vs each other. However, Q-PCR efficiency (Ct values) also depended on DNA-fragmentation (p<0.0001). Q-PCR methods were sensitive to detect<or=1% mutant cells, provided that samples yielded cycle thresholds (Ct)<29, but this condition was met in only 38.5% of diagnostic samples. In comparison, FFPE samples (>99%) could accurately be analyzed at a sensitivity level of 10% (external validation of TMGB results). DNA quality and tumor cell content were the main reasons for discrepant sequencing/Q-PCR results (1.5%). CONCLUSIONS/SIGNIFICANCE Diagnostic targeted mutation assessment on FFPE-DNA is very efficient with Q-PCR methods in comparison to dideoxy-sequencing. However, DNA fragmentation/amplification capacity and tumor DNA content must be considered for the interpretation of Q-PCR results in order to provide accurate information for clinical decision making.
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20
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Gnanapragasam VJ. Unlocking the molecular archive: the emerging use of formalin-fixed paraffin-embedded tissue for biomarker research in urological cancer. BJU Int 2009; 105:274-8. [PMID: 19519763 DOI: 10.1111/j.1464-410x.2009.08665.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Rapid developments have been made in identifying predictive and prognostic markers in urological cancers. Most biomarker profiling has been primarily conducted in fresh-frozen tissue taken at the time of diagnosis or surgery. The disadvantage of this process is that the sampled tissue might not be entirely representative of the tumour and there is a lack of adequate numbers and follow-up to make clear conclusions as to a biomarker's prognostic potential. Formalin fixation and paraffin embedding (FFPE) is the clinical standard for preparing samples for histopathological assessment; this preserves tissue architecture and allows the storage of diagnostic and surplus tissue in archival banks. This resource represents a vast repository of tissue material with a long-term clinical follow-up. With the advent of high-throughput profiling technologies, there is a unique opportunity to screen and comprehensively evaluate many biomarkers. Such studies require the large sample numbers and outcome data which is a key feature of archival FFPE tissue. However, the process of FFPE induces chemical changes and degradation in tissue DNA, RNA and protein, which can make subsequent analysis unreliable. Recently, several technical advances have been made to overcome the degrading effects of FFPE. This review highlights the key advances that are beginning to allow the use of FFPE archives for molecular biomarker profiling.
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Affiliation(s)
- Vincent J Gnanapragasam
- Uro-oncology Group, Department of Oncology, Hutchison MRC Research Centre, University of Cambridge, UK.
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