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Wang H, Kang B, Gao Y, Zhang M, Jiang J, Su J, Zhang B, Zhu B, Liao S. Construction and evaluation of a novel set of 90 microhaplotypes for forensic applications using NGS technology. Forensic Sci Int 2023; 353:111848. [PMID: 37890263 DOI: 10.1016/j.forsciint.2023.111848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/27/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023]
Abstract
Microhaplotypes (MHs), small sets of linked single nucleotide polymorphisms (SNPs), are becoming a valuable tool for paternity testing, personal identification and other different forensic purposes due to their advantages of both short tandem repeats (STRs) and SNPs. However, only a small part of MHs with small segments have been developed and reported so far. And the current population genetic data of MHs are still insufficient. MHs with small segments possess unique advantages in mixture deconvolution, degradation material identification, noninvasive prenatal paternity testing and even medical tumor diagnostic applications. In the present study, a set of 90 autosomal MHs whose PCR amplicon lengths are from 90-150 bp, of which 58 MHs are less than or equal to 100 bp are selected, and assembled into an amplification multiplex system optimized for Ion S5™ System for forensic application. Genetic diversity study of 90 MHs in the populations from different intercontinental regions shows that the polymorphism information content (PIC) values of 83 MHs are greater than 0.4 in populations from East Asia (EAS), and the average PIC value of 90 MHs is greater than 0.5. A total of EAS populations shows the highest cumulative match probability (CMP) and cumulative probability of exclusion (CPE) values in five intercontinental populations. The CMP and CPE values of 90 MHs in EAS are 1.1688 × 10-54 and 0.999999999998954. The informativeness for assignment (In) values of the 90 MHs are calculated based on data from five intercontinental populations, and the In values of 20 MHs have greater than 0.1, indicating that the 20 MHs are high effectiveness in distinguishing different intercontinental populations, which can be used as candidate ancestry informative markers. Further, we have studied the polymorphisms of the 90 MHs based on 224 unrelated individuals of Henan Han population, China, and obtained the frequency data of the 90 MHs. In the Henan Han population, the effective number of alleles (Ae) of the 90 MHs ranges from 1.7649 (MH45) to 3.9792 (MH50), and the Ae values of 10 MHs reach to 3.0; the Ae values of 80 MHs are greater than 2, and the average Ae value for these MHs is 2.422. The average expected heterozygosity, observed heterozygosity, PIC, matching probability, discrimination power and probability of exclusion values of 90 MHs in the Henan Han population are 0.5788, 0.5851, 0.5039, 0.2608, 0.7392 and 0.2806, respectively. The CMP value of 90 MHs in the study population is less than 10-54, and their CPE value reaches 0.999999999999999923. Moreover, the results of the depth of coverage, allele coverage ratio and noise level indicate that the 90 MH amplification system has well sequencing performance, and the sequencing results are reliable. The results indicate the 90 MHs show higher polymorphisms in the study population. The present panel can be well used in paternity testing and individual identification in the study population and even the populations from EAS.
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Affiliation(s)
- Hongdan Wang
- College of Forensic Science, Xi'an Jiaotong University Health Science Center, Xi'an, China; Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China; National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Bing Kang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Yue Gao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Mengting Zhang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Jincheng Jiang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Junxiang Su
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Bo Zhang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Bofeng Zhu
- College of Forensic Science, Xi'an Jiaotong University Health Science Center, Xi'an, China; Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China.
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Li Y, Shi P, Jiang D. Polymorphism rs1801516 (G > A) in the ATM gene is not associated with overall cancer risk: an updated meta-analysis. J Int Med Res 2020; 48:300060520937618. [PMID: 32674635 PMCID: PMC7370572 DOI: 10.1177/0300060520937618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Objective The ataxia telangiectasia mutated (ATM) gene contains a functional single nucleotide polymorphism (SNP) rs1801516 (G > A) that may be associated with cancer risk. This meta-analysis aimed to interrogate the relationship between rs1801516 and cancer occurrence and disease etiology. Methods We retrieved and identified the available case–control studies that met the inclusion criteria from the PubMed, Web of Science, and Embase databases. Odds ratio (OR) and 95% confidence intervals (CIs) were used to measure the association between rs1801516 and cancer risk. Additionally, we performed sensitivity, subgroup, and publication bias analyses. Results After inclusion criteria were met, the meta-analysis included 29 studies, with 9,453 cancer patients (cases) and 14,646 controls. No association was found between rs1801516 and cancer risk (pooled OR = 0.911; 95% CI, 0.740–1.123). Concordantly, no association was found between rs1801516 and cancer risk after subgroup analysis by source of controls, cancer type, or ethnicity, which confirmed the finding of the dominant model that this SNP is not involved in the occurrence of cancer. Conclusions Through this meta-analysis, we found no association between rs1801516 and cancer occurrence as a risk factor. These data provide useful information for future case–control studies on cancer etiology.
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Affiliation(s)
- Yueting Li
- Department of Breast Surgery, Cancer Hospital of China Medical University, Shenyang, Liaoning Province, P.R. China
| | - Pengxu Shi
- Department of Bone Surgery, People's Hospital of Liaoning Province, Shenyang, Liaoning Province, P.R. China
| | - Daqing Jiang
- Department of Breast Surgery, Cancer Hospital of China Medical University, Shenyang, Liaoning Province, P.R. China
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Gu Y, Shi J, Qiu S, Qiao Y, Zhang X, Cheng Y, Liu Y. Association between ATM rs1801516 polymorphism and cancer susceptibility: a meta-analysis involving 12,879 cases and 18,054 controls. BMC Cancer 2018; 18:1060. [PMID: 30384829 PMCID: PMC6211574 DOI: 10.1186/s12885-018-4941-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/11/2018] [Indexed: 01/07/2023] Open
Abstract
Background Ataxia telangiectasia mutated (ATM) gene plays a key role in response to DNA lesions and is related to the invasion and metastasis of malignancy. Epidemiological studies have indicated associations between ATM rs1801516 polymorphism and different types of cancer, but their results are inconsistent. To further evaluate the effect of ATM rs1801516 polymorphism on cancer risk, we conducted this meta-analysis. Methods Studies were identified according to specific inclusion criteria by searching PubMed, Web of Science, and Embase databases. Pooled odds ratios (ORs) and corresponding 95% confidence intervals (CIs) under recessive, dominant, codominant, and overdominant models of inheritance were calculated to estimate the association between rs1801516 polymorphism and cancer risk. Results A total of 37 studies with 12,879 cases and 18,054 controls were included in our study. No significant association was found between rs1801516 polymorphism and cancer risk in overall comparisons (AA vs GG + GA: OR = 0.91, 95% CI, 0.78–1.07; AA+GA vs GG: OR = 1.00, 95% CI, 0.90–1.11; AA vs GG: OR = 0.89, 95% CI, 0.75–1.06; GA vs GG: OR = 1.01, 95% CI, 0.91–1.13; GG + AA vs GA: OR = 1.00, 95% CI, 0.88–1.10). However, after subgroup analyses by region-specified population, significant associations were found in European (AA vs GG + GA: OR = 0.79, 95% CI, 0.65–0.96, P = 0.017; AA vs GG: OR = 0.79, 95% CI, 0.65–0.96, P = 0.017), South American (AA+GA vs GG: OR = 2.15, 95% CI, 1.37–3.38, P = 0.001; GA vs GG: OR = 2.19, 95% CI, 1.38–3.47, P = 0.001; GG + AA vs GA: OR = 0.46, 95% CI, 0.29–0.72, P = 0.001), and Asian (AA vs GG + GA: OR = 7.45, 95% CI, 1.31–42.46, P = 0.024; AA vs GG: OR = 7.40, 95% CI, 1.30–42.19, P = 0.024). Subgroup analyses also revealed that compared with subjects carrying a GG genotype, those carrying a homozygote AA had a decreased risk for breast cancer (AA vs GG: OR = 0.76, 95% CI, 0.59–0.98, P = 0.035), and the homozygote AA was associated with decreased cancer risk in subjects with family history (AA vs GG: OR = 0.68, 95% CI, 0.47–0.98, P = 0.039). Conclusions ATM rs1801516 polymorphism is not associated with overall cancer risk in total population. However, for subgroup analyses, this polymorphism is especially associated with breast cancer risk; in addition, it is associated with overall cancer risk in Europeans, South Americans, Asians, and those with family history. Electronic supplementary material The online version of this article (10.1186/s12885-018-4941-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yulu Gu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Jikang Shi
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Shuang Qiu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Yichun Qiao
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Xin Zhang
- Department of Pharmacy, First Hospital of Jilin University, Changchun, 130021, China
| | - Yi Cheng
- Department of Cardiovascular Center, First Hospital of Jilin University, Changchun, 130021, China
| | - Yawen Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China.
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Zhao Y, Yang L, Wu D, He H, Wang M, Ge T, Liu Y, Tian H, Cui J, Jia L, Wan Z, Han F. Gene-environment interaction for polymorphisms in ataxia telangiectasia-mutated gene and radiation exposure in carcinogenesis: results from two literature-based meta-analyses of 27120 participants. Oncotarget 2018; 7:76867-76881. [PMID: 27764772 PMCID: PMC5363555 DOI: 10.18632/oncotarget.12724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 10/12/2016] [Indexed: 01/02/2023] Open
Abstract
Purpose We conducted two meta-analyses of ATM genetic polymorphisms and cancer risk in individuals with or without radiation exposure to determine whether there was a joint effect between the ATM gene and radiation exposure in carcinogenesis. Results rs1801516, which was the only ATM polymorphism investigated by more than 3 studies of radiation exposure, was eligible for the present study. The meta-analysis of 23333 individuals without radiation exposure from 24 studies showed no association between the rs1801516 polymorphism and cancer risk, without heterogeneity across studies. The meta-analysis of 3787 individuals with radiation exposure from 6 studies showed a significant association between the rs1801516 polymorphism and a decreased cancer risk, with heterogeneity across studies. There was a borderline-significant difference between the ORs of the two meta-analyses (P = 0.066), and the difference was significant when only Caucasians were included (P = 0.011). Materials and methods Publications were identified by searching PubMed, EMBASE, Web of Science, and CNKI databases. Odds ratios (ORs) were calculated to estimate the association between ATM genetic polymorphisms and cancer risk. Tests of interaction were used to compare differences between the ORs of the two meta-analyses. Conclusions Our meta-analyses confirmed the presence of a gene-environment interaction between the rs1801516 polymorphism and radiation exposure in carcinogenesis, whereas no association was found between the rs1801516 polymorphism and cancer risk for individuals without radiation exposure. The heterogeneity observed in the meta-analysis of individuals with radiation exposure might be due to gene-ethnicity or gene-gene interactions. Further studies are needed to elucidate sources of the heterogeneity.
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Affiliation(s)
- Yuguang Zhao
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Lei Yang
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Di Wu
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Hua He
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Mengmeng Wang
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Tingwen Ge
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Yudi Liu
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Huimin Tian
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Jiuwei Cui
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Lin Jia
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Ziqiang Wan
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Fujun Han
- Cancer Center, The First Hospital of Jilin University, Changchun, China
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Ekstrøm PO, Nakken S, Johansen M, Hovig E. Automated amplicon design suitable for analysis of DNA variants by melting techniques. BMC Res Notes 2015; 8:667. [PMID: 26559640 PMCID: PMC4642734 DOI: 10.1186/s13104-015-1624-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 10/26/2015] [Indexed: 05/28/2023] Open
Abstract
Background The technological development of DNA analysis has had tremendous development in recent years, and the present deep sequencing techniques present unprecedented opportunities for detailed and high-throughput DNA variant detection. Although DNA sequencing has had an exponential decrease in cost per base pair analyzed, focused and target-specific methods are however still much in use for analysis of DNA variants. With increasing capacity in the analytical procedures, an equal demand in automated amplicon and primer design has emerged. Results We have constructed a web-based tool that is able to batch design DNA variant assay suitable for analysis by denaturing gel/capillary electrophoresis and high resolution melting. The tool is developed as a computational workflow that implements one of the most widely used primer design tools, followed by validation of primer specificity, as well as calculation and visualization of the melting properties of the resulting amplicon, with or without an artificial high melting domain attached. The tool will be useful for scientists applying DNA melting techniques in analysis of DNA variations. The tool is freely available at http://meltprimer.ous-research.no/. Conclusion Herein, we demonstrate a novel tool with respect to covering the whole amplicon design workflow necessary for groups that use melting equilibrium techniques to separate DNA variants.
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Affiliation(s)
- Per Olaf Ekstrøm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, Oslo, 0310, Norway.
| | - Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, Oslo, 0310, Norway.
| | - Morten Johansen
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, Oslo, 0310, Norway.
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, Oslo, 0310, Norway. .,Institute of Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hosptal, Nydalen, Oslo, 0424, Norway. .,Department of Informatics, University of Oslo, Blindern, Oslo, 0318, Norway.
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Ekstrøm PO, Warren DJ, Thilly WG. Separation principles of cycling temperature capillary electrophoresis. Electrophoresis 2012; 33:1162-8. [PMID: 22539319 DOI: 10.1002/elps.201100550] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
High throughput means to detect and quantify low-frequency mutations (<10(-2) ) in the DNA-coding sequences of human tissues and pathological lesions are required to discover the kinds, numbers, and rates of genetic mutations that (i) confer inherited risk for disease or (ii) arise in somatic tissues as events required for clonal diseases such as cancers and atherosclerotic plaque.While throughput of linear DNA sequencing methods has increased dramatically, such methods are limited by high error rates (>10(-3) ) rendering them unsuitable for the detection of low-frequency risk-conferring mutations among the many neutral mutations carried in the general population or formed in tissue growth and development. In contrast, constant denaturing capillary electrophoresis (CDCE), coupled with high-fidelity PCR, achieved a point mutation detection limit of <10(-5) in exon-sized sequences from human tissue or pooled blood samples. However, increasing CDCE throughput proved difficult due to the need for precise temperature control and the time-consuming optimization steps for each DNA sequence probed. Both of these problems have been solved by the method of cycling temperature capillary electrophoresis (CTCE). The data presented here provide a deeper understanding of the separation principles involved in CTCE and address several elements of a previously presented two-state transport model.
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Affiliation(s)
- Per Olaf Ekstrøm
- Department of Surgical Oncology and Tumor biology, Radiumhospitalet, Oslo University Hospital, Montebello, Oslo, Norway
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Abstract
Analysis and detection of DNA variation is important in any field of biology. Hence, numerous methods have been developed to analyze DNA. A simple yet effective way of analyzing DNA is by denaturant capillary electrophoresis (DCE). The method is in theory applicable to 95% of the human genome. The method involves three steps; fragment design, PCR amplification and allele separation. The allele separation can in principle be performed with any DNA capillary sequencing instrument.
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Ekstrøm PO, Khrapko K, Li-Sucholeiki XC, Hunter IW, Thilly WG. Analysis of mutational spectra by denaturing capillary electrophoresis. Nat Protoc 2008; 3:1153-66. [PMID: 18600220 PMCID: PMC2742298 DOI: 10.1038/nprot.2008.79] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The point mutational spectrum over nearly any 75- to 250-bp DNA sequence isolated from cells, tissues or large populations may be discovered using denaturing capillary electrophoresis (DCE). A modification of the standard DCE method that uses cycling temperature (e.g., +/-5 degrees C), CyDCE, permits optimal resolution of mutant sequences using computer-defined target sequences without preliminary optimization experiments. The protocol consists of three steps: computer design of target sequence including polymerase chain reaction (PCR) primers, high-fidelity DNA amplification by PCR and mutant sequence separation by CyDCE and takes about 6 h. DCE and CyDCE have been used to define quantitative point mutational spectra relating to errors of DNA polymerases, human cells in development and carcinogenesis, common gene-disease associations and microbial populations. Detection limits are about 5 x 10(-3) (mutants copies/total copies) but can be as low as 10(-6) (mutants copies/total copies) when DCE is used in combination with fraction collection for mutant enrichment. No other technological approach for unknown mutant detection and enumeration offers the sensitivity, generality and efficiency of the approach described herein.
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Affiliation(s)
- Per O Ekstrøm
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA. or
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Ekstrøm PO, Bjørheim J. Evaluation of sieving matrices used to separate alleles by cycling temperature capillary electrophoresis. Electrophoresis 2006; 27:1878-85. [PMID: 16619298 DOI: 10.1002/elps.200500642] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Denaturing CE (DCE) is a powerful tool for analysis of DNA variation. The development of commercial multi-CE instruments allows large-scale studies of DNA variation (many samples and many fragments). However, the cost of consumables like capillary arrays and sieving matrix might limit the use of DCE in such studies. Thus, we have tested 72 different in-house formulated sieving matrices' ability to suppress EOF and separate PCR-amplified alleles with the DCE variant, cycling temperature CE (CTCE). The data herein demonstrate that alleles can be baseline-separated by use of PVP and poly(N,N-dimethyl acrylamide) polymers at various percentages and pH. Allele separation by CTCE is matrix-independent and consequently applicable to any capillary instrument used for DNA separation. Formulation of sieving matrix for CTCE was done by dissolving appropriate amount of polymer powder into the running buffers. Allele separation was observed at different pH (7.5-8.5), concentrations and molecular size of the polymer, without compromising the separation and reproducibility. Finally, the cost reduction of homemade matrices is more than 1000-fold as compared to commercial sieving matrices.
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Affiliation(s)
- Per Olaf Ekstrøm
- Department of Surgical Oncology, The Norwegian Radium Hospital, Oslo, Norway.
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Harbo HF, Ekstrøm PO, Lorentzen AR, Sundvold-Gjerstad V, Celius EG, Sawcer S, Spurkland A. Coding region polymorphisms in T cell signal transduction genes. Prevalence and association to development of multiple sclerosis. J Neuroimmunol 2006; 177:40-5. [PMID: 16764945 DOI: 10.1016/j.jneuroim.2006.04.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Revised: 03/31/2006] [Accepted: 04/26/2006] [Indexed: 01/22/2023]
Abstract
We systematically assessed 53 genes involved in T cell signaling, among which 72 SNPs in 32 genes were reported in databases as causing non-synonymous amino acid substitutions. Screening of 41 of these SNPs in DNA pools from 4000 Norwegian controls showed that only 12 SNPs (29%) were polymorphic. These were tested for association to MS in DNA pools from 364 Norwegian MS patients. To eliminate sources of variance introduced by DNA pooling, the SNPs in the best-ranked PLCG1 as well as the PTPN22 gene were thereafter genotyped in individual MS and control samples, however, without finding evidence for association to MS.
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Affiliation(s)
- Hanne F Harbo
- Institute of Immunology, University of Oslo, Oslo, Norway.
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Bjørheim J, Ekstrøm PO. Review of denaturant capillary electrophoresis in DNA variation analysis. Electrophoresis 2005; 26:2520-30. [PMID: 15934053 DOI: 10.1002/elps.200410403] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Analyses of germline and somatic single-nucleotide DNA variations are important in both population genetics research and clinical practice. Reliable and inexpensive methods that are flexible and designed for automation are required for these analyses. Present day DNA sequencing technology is too expensive for testing all 22-25 000 human genes in populations genetics studies or in scanning large numbers of tumors for novel mutations. Denaturant capillary electrophoresis (DCE) has the potential to meet the need for large-scale analysis of DNA variants. Several different analyses can be performed by DCE, including mutation analysis, single-nucleotide polymorphism (SNP) discovery in individual and pooled samples, detection of allelic imbalance, and determination of microhaplotypes. Here we review the theoretical background of the method, its sensitivity, specificity, detection limit, throughput, and repeatability in the light of current literature in the field.
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Affiliation(s)
- Jens Bjørheim
- Section for Immunotherapy, Department of Immunology, Institute for Cancer Research, University of Oslo, Oslo, Norway
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Szantai E, Ronai Z, Szilagyi A, Sasvari-Szekely M, Guttman A. Haplotyping by capillary electrophoresis. J Chromatogr A 2005; 1079:41-9. [PMID: 16038289 DOI: 10.1016/j.chroma.2005.03.078] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The investigation of the genetic background and phenotype structures of complex diseases, such as cardiovascular or psychiatric disorders and tumors, is one of the most scrutinized fields of the post genomic era. Besides the multiplex analysis of genetic markers and polymorphisms throughout the whole genome, more and more attention is focused on the interaction between the etiological factors of these traits. Haplotype determination, rather than multiplex genotyping seems to be one of the first building blocks of this endeavor. This review focuses on the importance and theoretical background of haplotyping, and summarizes the recent examples of novel and emerging haplotyping techniques by capillary gel electrophoresis based DNA fragment analysis, a powerful tool for the examination of the inheritance of complex traits.
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Affiliation(s)
- Eszter Szantai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
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Li-Sucholeiki XC, Tomita-Mitchell A, Arnold K, Glassner BJ, Thompson T, Murthy JV, Berk L, Lange C, Leong-Morgenthaler PM, MacDougall D, Munro J, Cannon D, Mistry T, Miller A, Deka C, Karger B, Gillespie KM, Ekstrøm PO, Todd JA, Thilly WG. Detection and frequency estimation of rare variants in pools of genomic DNA from large populations using mutational spectrometry. Mutat Res 2005; 570:267-80. [PMID: 15708585 DOI: 10.1016/j.mrfmmm.2004.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Accepted: 11/29/2004] [Indexed: 11/21/2022]
Abstract
DNA variants underlying the inheritance of risk for common diseases are expected to have a wide range of population allele frequencies. The detection and scoring of the rare alleles (at frequencies of <0.01) presents significant practical problems, including the requirement for large sample sizes and the limitations inherent in current methodologies for allele discrimination. In the present report, we have applied mutational spectrometry based on constant denaturing capillary electrophoresis (CDCE) to DNA pools from large populations in order to improve the prospects of testing the role of rare variants in common diseases on a large scale. We conducted a pilot study of the cytotoxic T lymphocyte-associated antigen-4 gene (CTLA4) in type 1 diabetes (T1D). A total of 1228 bp, comprising 98% of the CTLA4 coding sequence, all adjacent intronic mRNA splice sites, and a 3' UTR sequence were scanned for unknown point mutations in pools of genomic DNA from a control population of 10,464 young American adults and two T1D populations, one American (1799 individuals) and one from the United Kingdom (2102 individuals). The data suggest that it is unlikely that rare variants in the scanned regions of CTLA4 represent a significant proportion of T1D risk and illustrate that CDCE-based mutational spectrometry of DNA pools offers a feasible and cost-effective means of testing the role of rare variants in susceptibility to common diseases.
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