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Hassan EA, Elsaid AM, Abou-Elzahab MM, El-Refaey AM, Elmougy R, Youssef MM. The Potential Impact of MYH9 (rs3752462) and ELMO1 (rs741301) Genetic Variants on the Risk of Nephrotic Syndrome Incidence. Biochem Genet 2024; 62:1304-1324. [PMID: 37594641 DOI: 10.1007/s10528-023-10481-y] [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: 06/04/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023]
Abstract
The kidney lost a lot of protein in the urine when you have nephrotic syndrome (NS). Clinical manifestations mostly common in NS include massive proteinuria, hypoalbuminemia, hyperlipidemia, and edema. Idiopathic nephrotic syndrome is currently classified into steroid-dependent (SDNS) and steroid-resistant (SRNS) based on the initial response to corticosteroid therapy at presentation. Several reports examined the association of the MYH9 gene (rs3752462, C > T) variant and ELMO1 gene (rs741301 G > A) variant as risk factors for Nephrotic Syndrome. This study aimed to determine the potential effect of the MYH9 gene (rs3752462, C > T) and ELMO1 gene (rs741301) variant on the risk of (NS) among Egyptian Children. This study included two hundred participants involving 100 nephrotic syndrome (NS) cases and 100 healthy controls free from nephrotic syndrome (NS). The MYH9 gene (rs3752462, C > T) variant and ELMO1 gene (rs G > A741301) variant were analyzed by ARMS-PCR technique. Nephrotic syndrome cases include 74% SRNS and 26% SDNS. Higher frequencies of the heterozygous carrier (CT) and homozygous variant (TT) genotypes of the MYH9 (rs3752462, C > T) variant were observed in NS patients compared to the controls with p-value < 0.001. The frequencies of the MYH9 (rs3752462, C > T variant indicated a statistically significant elevated risk of NS under various genetic models, including allelic model (OR 2.85, p < 0.001), dominant (OR 3.97, p < 0.001) models, and the recessive model OR 5.94, p < 0.001). Higher frequencies of the heterozygous carrier (GA) and homozygous variant (AA) genotypes of ELMO1gene (rs G > A741301) variant were observed in NS patients compared to the controls with p-value < 0.001. The frequencies of the ELMO1 (rs G > A741301) variant indicated a statistically significant elevated risk of NS under various genetic models, including allelic model (OR 2.15, p < 0.001), dominant models (OR 2.8, p < 0.001), and the recessive model (OR 4.17, p = 0.001). Both MYH9 and ELMO1 gene variants are significantly different in NS in comparison with the control group (p < 0.001). The MYH9 gene (rs3752462, C > T) and ELMO1gene (rs G > A741301) variants were considered independent risk factors for NS among Egyptian Children.
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Affiliation(s)
- Eglal A Hassan
- Biochemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansoura, Egypt.
| | - Afaf M Elsaid
- Genetic Unit, Children Hospital, Mansoura University, Mansoura, Egypt
| | - M M Abou-Elzahab
- Organic Chemistry Division, Chemistry Department, Faculty Of Science, Mansoura University, Mansoura, Egypt
| | - Ahmed M El-Refaey
- Department of Pediatrics, Mansoura University Childrens Hospital, Mansoura University, Mansoura, Egypt
| | - Rehab Elmougy
- Biochemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Magdy M Youssef
- Biochemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansoura, Egypt
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Al-Azzawy MF, Al-Haggar M, ElSaid AM, El-Khawaga OY. Analysis of the association of NPHS2 and ACTN4 genes polymorphism with nephrotic syndrome in Egyptian children. Mol Biol Rep 2023; 50:4481-4490. [PMID: 37014572 PMCID: PMC10147774 DOI: 10.1007/s11033-023-08387-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/14/2023] [Indexed: 04/05/2023]
Abstract
BACKGROUND One of the most common kidney illnesses in developing countries is pediatric nephrotic syndrome (PNS), which is frequently associated with dyslipidemia and edema. The rapid discovery of genes related to NS has aided in the understanding of the molecular mechanics of glomerular filtration. The goal of this study is to determine the relationship between NPHS2 and ACTN4 in PNS youngsters. METHODS A study with 100 NS children and 100 healthy matched volunteers was conducted. Genomic DNA was extracted from peripheral blood. Single-nucleotide polymorphisms were genotyped using ARMS-PCR. RESULTS A substantial decline in the level of albumin was found in NS cases (P < 0.001) Further on, a significantly difference in T.C and TG level between healthy and NS patient. Molecular study showed a highly significant difference of NS patients from controls regarding NPHS2 rs3829795 polymorphic genotypes as the GA heterozygous genotype shows highly significant difference from controls (P < 0.001) as well as GA + AA genotypes (P < 0.001) in comparison with GG genotype. Regarding rs2274625, The GA heterozygous genotype showed no statistically significant difference between genotypes and alleles with NS (P = 0.246). Association of AG haplotype NPHS2 rs3829795-rs2274625 haplotypes found a significant association with the risk of developing NS (P = 0.008). Concerning the ACTN4 rs121908415 SNP, there was no link between this mutation and NS children. CONCLUSION The correlation of AG haplotype NPHS2 rs3829795-rs2274625 haplotypes identified a strong association with the likelihood of getting NS, according to our findings. There was no connection found between the ACTN4 rs121908415 SNP and NS children.
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Affiliation(s)
- Mohammed F Al-Azzawy
- Biochemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Mohammad Al-Haggar
- Genetic Unit, Department of Pediatrics, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Afaf M ElSaid
- Genetic Unit, Department of Pediatrics, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Omali Y El-Khawaga
- Biochemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt.
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Tang YW, Ou CY. Past, present and future molecular diagnosis and characterization of human immunodeficiency virus infections. Emerg Microbes Infect 2012; 1:e19. [PMID: 26038427 PMCID: PMC3630918 DOI: 10.1038/emi.2012.15] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/08/2012] [Accepted: 05/21/2012] [Indexed: 12/31/2022]
Abstract
Substantive and significant advances have been made in the last two decades in the characterization of human immunodeficiency virus (HIV) infections using molecular techniques. These advances include the use of real-time measurements, isothermal amplification, the inclusion of internal quality assurance protocols, device miniaturization and the automation of specimen processing. The result has been a significant increase in the availability of results to a high level of accuracy and quality. Molecular assays are currently widely used for diagnostics, antiretroviral monitoring and drug resistance characterization in developed countries. Simple and cost-effective point-of-care versions are also being vigorously developed with the eventual goal of providing timely healthcare services to patients residing in remote areas and those in resource-constrained countries. In this review, we discuss the evolution of these molecular technologies, not only in the context of the virus, but also in the context of tests focused on human genomics and transcriptomics.
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Affiliation(s)
- Yi-Wei Tang
- Memorial Sloan-Kettering Cancer Center , New York, NY 10065, USA
| | - Chin-Yih Ou
- Centers for Disease Control and Prevention , Atlanta, GA 30333, USA
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Chang HW, Chuang LY, Cheng YH, Hung YC, Wen CH, Gu DL, Yang CH. Prim-SNPing: a primer designer for cost-effective SNP genotyping. Biotechniques 2009; 46:421-31. [PMID: 19480636 DOI: 10.2144/000113092] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Many kinds of primer design (PD) software tools have been developed, but most of them lack a single nucleotide polymorphism (SNP) genotyping service. Here, we introduce the web-based freeware "Prim-SNPing," which, in addition to general PD, provides three kinds of primer design functions for cost-effective SNP genotyping: natural PD, mutagenic PD, and confronting two-pair primers (CTPP) PD. The natural PD and mutagenic PD provide primers and restriction enzyme mining for polymerase chain reaction-restriction fragment of length polymorphism (PCR-RFLP), while CTPP PD provides primers for restriction enzyme-free SNP genotyping. The PCR specificity and efficiency of the designed primers are improved by BLAST searching and evaluating secondary structure (such as GC clamps, dimers, and hairpins), respectively. The length pattern of PCR-RFLP using natural PD is user-adjustable, and the restriction sites of the RFLP enzymes provided by Prim-SNPing are confirmed to be absent within the generated PCR product. In CTPP PD, the need for a separate digestion step in RFLP is eliminated, thus making it faster and cheaper. The output of Prim-SNPing includes the primer list, melting temperature (Tm) value, GC percentage, and amplicon size with enzyme digestion information. The reference SNP (refSNP, or rs) clusters from the Single Nucleotide Polymorphism database (dbSNP) at the National Center for Biotechnology Information (NCBI), and multiple other formats of human, mouse, and rat SNP sequences are acceptable input. In summary, Prim-SNPing provides interactive, user-friendly and cost-effective primer design for SNP genotyping. It is freely available at http://bio.kuas.edu.tw/prim-snping.
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Affiliation(s)
- Hsueh-Wei Chang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Taiwan
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Chowdari KV, Bamne M, Wood J, Talkowski ME, Mirnics K, Levitt P, Lewis DA, Nimgaonkar VL. Linkage disequilibrium patterns and functional analysis of RGS4 polymorphisms in relation to schizophrenia. Schizophr Bull 2008; 34:118-26. [PMID: 17515439 PMCID: PMC2632380 DOI: 10.1093/schbul/sbm042] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The regulator of G-protein signaling 4 (RGS4, chromosome 1q23.3) plays a critical role in G-protein function. Four common single-nucleotide polymorphisms (SNPs) localized between the 5' upstream sequence and the first intron, as well as 2 haplotypes derived from these SNPs may confer liability to schizophrenia (SZ). However, the pattern of associations varies among samples. To help clarify the putative associations, we report the following analyses: (1) a comprehensive catalog of common polymorphisms, (2) linkage disequilibrium (LD) and association analyses using these SNPs, and (3) functional analysis based on dual-luciferase promoter assays. We identified 62 SNPs from a 20-kb genomic region spanning RGS4, of which 26 are common polymorphisms with a minor allele frequency (MAF) of >5%. LD analysis suggested 5 clusters of SNPs (r(2) > .8). Association analyses using the novel SNPs were consistent with the prior reports, but further localization was constrained by significant LD across the region. The 2 haplotypes reported to confer liability to SZ had significant promoter activity compared with promoterless constructs, suggesting a functional role for both haplotypes. Further analyses of promoter sequences are warranted to understand transcriptional regulation at RGS4. This information will be useful for further analysis of samples in which genetic association of RGS4 polymorphisms with SZ has been reported.
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Affiliation(s)
- Kodavali V. Chowdari
- Department of Psychiatry, WPIC, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Mikhil Bamne
- Department of Psychiatry, WPIC, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Joel Wood
- Department of Psychiatry, WPIC, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Michael E. Talkowski
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Karoly Mirnics
- Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
| | - Pat Levitt
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
| | - David A. Lewis
- Department of Psychiatry, WPIC, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Vishwajit L. Nimgaonkar
- Department of Psychiatry, WPIC, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
- To whom correspondence should be addressed; Departments of Psychiatry and Human Genetics University of Pittsburgh School of Medicine and Public Health Western Psychiatric Institute and Clinic, Room 441 3811 O'Hara St. Pittsburgh, PA 15213; tel: 412-246-6353, fax: 412-246-6350, e-mail:
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6
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Park HW, Kim IJ, Kang HC, Jang SG, Ahn SA, Lee JS, Shin HR, Park JG. The hOGG1 Ser326Cys polymorphism is not associated with colorectal cancer risk. J Epidemiol 2007; 17:156-60. [PMID: 17827862 PMCID: PMC7058477 DOI: 10.2188/jea.17.156] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Little is known about the genetic risk factors associated with colorectal cancer. Although the Ser326Cys polymorphism of 8-oxoguanine DNA glycosylase (hOGG1) is consistently associated with a range of cancers, there is no consensus regarding this polymorphism and colorectal cancer risk. METHODS In the present study, conducted in a Korean population, we used the TaqMan assay to investigate whether the hOGG1 Ser326Cys polymorphism was associated with colorectal cancer in 439 colorectal cancer patients and 676 healthy normal controls. We also examined whether the hOGG1 Ser326Cys polymorphism is associated with tumor location, microsatellite instability (MSI) status and tumor-node-metastasis (TNM) stage in colorectal cancer. RESULTS We found no significant difference between the cancer and control populations in terms of genotype distribution (CC, CG and GG). In addition, we found no association between the hOGG1 Ser326Cys polymorphism and cancer risk, MSI status, TNM stage or tumor location in colorectal cancer patients. CONCLUSIONS These results suggest that unlike for other cancer types, the hOGG1 Ser326Cys polymorphism is not a major genetic risk factor for colorectal cancer.
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Affiliation(s)
- Hye-Won Park
- Korean Hereditary Tumor Registry, Cancer Research Institute and Cancer Research Center, Seoul National University
| | - Il-Jin Kim
- Korean Hereditary Tumor Registry, Cancer Research Institute and Cancer Research Center, Seoul National University
| | - Hio Chung Kang
- Korean Hereditary Tumor Registry, Cancer Research Institute and Cancer Research Center, Seoul National University
- Research Institute and Hospital, National Cancer Center
| | - Sang-Geun Jang
- Korean Hereditary Tumor Registry, Cancer Research Institute and Cancer Research Center, Seoul National University
- Research Institute and Hospital, National Cancer Center
| | - Sun-A Ahn
- Korean Hereditary Tumor Registry, Cancer Research Institute and Cancer Research Center, Seoul National University
- Research Institute and Hospital, National Cancer Center
| | - Jin Soo Lee
- Research Institute and Hospital, National Cancer Center
| | - Hai-Rim Shin
- Research Institute and Hospital, National Cancer Center
| | - Jae-Gahb Park
- Korean Hereditary Tumor Registry, Cancer Research Institute and Cancer Research Center, Seoul National University
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7
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Fitzgerald K, Tertyshnikova S, Moore L, Bjerke L, Burley B, Cao J, Carroll P, Choy R, Doberstein S, Dubaquie Y, Franke Y, Kopczynski J, Korswagen H, Krystek SR, Lodge NJ, Plasterk R, Starrett J, Stouch T, Thalody G, Wayne H, van der Linden A, Zhang Y, Walker SG, Cockett M, Wardwell-Swanson J, Ross-Macdonald P, Kindt RM. Chemical genetics reveals an RGS/G-protein role in the action of a compound. PLoS Genet 2006; 2:e57. [PMID: 16683034 PMCID: PMC1440875 DOI: 10.1371/journal.pgen.0020057] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Accepted: 03/01/2006] [Indexed: 12/02/2022] Open
Abstract
We report here on a chemical genetic screen designed to address the mechanism of action of a small molecule. Small molecules that were active in models of urinary incontinence were tested on the nematode Caenorhabditis elegans, and the resulting phenotypes were used as readouts in a genetic screen to identify possible molecular targets. The mutations giving resistance to compound were found to affect members of the RGS protein/G-protein complex. Studies in mammalian systems confirmed that the small molecules inhibit muscarinic G-protein coupled receptor (GPCR) signaling involving G-αq (G-protein alpha subunit). Our studies suggest that the small molecules act at the level of the RGS/G-αq signaling complex, and define new mutations in both RGS and G-αq, including a unique hypo-adapation allele of G-αq. These findings suggest that therapeutics targeted to downstream components of GPCR signaling may be effective for treatment of diseases involving inappropriate receptor activation. The authors have utilized Caenorhabditis elegans, and yeast genetics, combined with mammalian tissue and cell culture experiments to investigate the mechanism of action of a unique set of small molecules. These molecules are active in tissue models of urinary incontinence and allow for increased bladder filling. In the course of studying sensitivity and resistance to these compounds, Fitzgerald et al. uncovered novel alleles of RGS and Gq proteins. Further characterization of one such allele identified that its action conferred a hypo-adaptive phenotype on yeast during pheromone signaling assays. Their data as a whole indicate that these small molecules are able to diminish signaling from G-protein coupled receptors (GPCR) downstream of the receptors themselves. Since GPCR signaling is very important in many diseases in humans, the novel mechanism of these compounds may offer new ways to treat human disease.
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Affiliation(s)
- Kevin Fitzgerald
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - Svetlana Tertyshnikova
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - Lisa Moore
- Exelixis Incorporated, South San Francisco, California, United States of America
| | - Lynn Bjerke
- Exelixis Incorporated, South San Francisco, California, United States of America
| | - Ben Burley
- Exelixis Incorporated, South San Francisco, California, United States of America
| | - Jian Cao
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - Pamela Carroll
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - Robert Choy
- Exelixis Incorporated, South San Francisco, California, United States of America
| | - Steve Doberstein
- Exelixis Incorporated, South San Francisco, California, United States of America
| | - Yves Dubaquie
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - Yvonne Franke
- Exelixis Incorporated, South San Francisco, California, United States of America
| | - Jenny Kopczynski
- Exelixis Incorporated, South San Francisco, California, United States of America
| | - Hendrik Korswagen
- Hubrecht Laboratory, Centre for Biomedical Genetics, Utrecht, Netherlands
| | - Stanley R Krystek
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - Nicholas J Lodge
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - Ronald Plasterk
- Hubrecht Laboratory, Centre for Biomedical Genetics, Utrecht, Netherlands
| | - John Starrett
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - Terry Stouch
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - George Thalody
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - Honey Wayne
- Exelixis Incorporated, South San Francisco, California, United States of America
| | | | - Yongmei Zhang
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - Stephen G Walker
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - Mark Cockett
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - Judi Wardwell-Swanson
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
| | - Petra Ross-Macdonald
- Bristol-Myers Squibb Pharmaceutical Research Institute, Pennington, New Jersey, United States of America
- * To whom correspondence should be addressed. E-mail:
| | - Rachel M Kindt
- Exelixis Incorporated, South San Francisco, California, United States of America
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8
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Oberacher H, Niederstätter H, Huber CG, Parson W. Accurate determination of allelic frequencies in mitochondrial DNA mixtures by electrospray ionization time-of-flight mass spectrometry. Anal Bioanal Chem 2006; 384:1155-63. [PMID: 16421710 DOI: 10.1007/s00216-005-0269-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Revised: 12/01/2005] [Accepted: 12/02/2005] [Indexed: 10/25/2022]
Abstract
The mitochondrial locus 16519T/C was used as a model for the evaluation of the benefits of ion-pair reversed-phase high-performance liquid chromatography on-line hyphenated to electrospray ionization time-of-flight mass spectrometry (ICEMS assay) for the determination of allelic frequencies of single nucleotide polymorphisms. This marker has gained interest in forensic science owing to its ability to increase the discrimination power of mitochondrial DNA testing as a consequence of its high variability across various populations. In a first set of experiments, artificial mitochondrial DNA mixtures prepared from all four theoretically possible 16519 alleles served as samples. Any allele occurring at a frequency of as low as 1-5% was unequivocally detectable irrespective of the kind of allelic mixture. Measured and expected allelic frequencies correlated well following correction of observed experimental bias, which was most probably attributable to differential PCR amplification and/or preferential ionization. For thirteen different T/C mixtures with C contents in the range 1.0-99.0%, an average error of 1.2% and a maximum error of 2.2% were observed. Furthermore, ICEMS was applied to the quantitative genotyping of eight selected individuals of which four were heteroplasmic with C contents in the range 1.9-34.1%. To check the reliability of these results, allelic proportions were additionally determined by a cloning assay. The results of the two assays correlated well (R (2)=0.9971). In all cases, deviations were obtained that were smaller than 5.4%. The overall observed assay performance suggests that the described mass spectrometric technique represents one of the most powerful assays for the determination of allelic frequencies available today.
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Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, 6020 Innsbruck, Austria.
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9
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Rickert AM, Borodina TA, Kuhn EJ, Lehrach H, Sperling S. Refinement of single-nucleotide polymorphism genotyping methods on human genomic DNA: amplifluor allele-specific polymerase chain reaction versus ligation detection reaction-TaqMan. Anal Biochem 2005; 330:288-97. [PMID: 15203335 DOI: 10.1016/j.ab.2004.03.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Indexed: 11/26/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) have proven to be powerful genetic markers for a variety of genetic applications, e.g., association studies leading to dissection of both monogenetic and complex diseases. However, no single SNP genotyping method has been broadly accepted. In the present study, we compared and refined two promising methods with potential for research and for diagnostic SNP genotyping: Amplifluor allele-specific polymerase chain reaction (PCR) and ligation detection reaction (LDR)-TaqMan. The methods are based on allele-specific primer extension and allele-specific ligation, respectively. Since LDR-TaqMan had previously been tested on just Arabidopsis thaliana, we adjusted the method for the more complex human genome. Amplifluor allele-specific PCR has a single-step and closed-tube format, whereas the LDR-TaqMan assay comprises two simple steps. Contrary to the primer-extension-based method, the ligation-based method can be multiplexed. Refining the LDR-TaqMan technique, we successfully replaced a previously suggested three-step multiplexing procedure with a less laborious two-step approach. Comparing refined LDR-TaqMan with Amplifluor allele-specific PCR in a family-based study, both techniques appeared similar with respect to high robustness and accuracy. As both approaches utilize primers with common tails, all SNPs can be assayed with the same couple of fluorescence reporting reagents, ensuring low establishing and running expenses.
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Ramanathan A, Huff EJ, Lamers CC, Potamousis KD, Forrest DK, Schwartz DC. An integrative approach for the optical sequencing of single DNA molecules. Anal Biochem 2005; 330:227-41. [PMID: 15203328 DOI: 10.1016/j.ab.2004.03.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2003] [Indexed: 11/18/2022]
Abstract
A new approach for optically sequencing ensembles of single DNA molecules using DNA polymerase to mediate the consecutive incorporation of fluorochrome-labeled nucleotides into an array of large single DNA molecules is presented. The approach utilizes cycles of labeled fluorochrome addition, detection to count incorporations, and bleaching to reset the counter. These additions are imaged and analyzed to estimate the number of labeled additions and to correlate them on a per-locus basis along DNA backbones. Initial studies used precisely labeled polymerase chain reaction products to aid the development and validation of simple models of fluorochrome point spread functions within the imaging system. In complementary studies, nucleotides labeled with the fluorochrome R110 were incorporated into surface-elongated lambda DNA, and fluorescent signals corresponding to the addition of R110-dUTP were counted and assigned precise loci along DNA backbones. The labeled DNAs were then subjected to photobleaching and to a second cycle of addition of R110-labeled nucleotides-a second round of additions was correlated with the first to establish strings of addition histories among the ensemble of largely double-stranded templates. These results confirm the basic operational validity of this approach and point the way to the development of a practical system for optical sequencing.
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Affiliation(s)
- Arvind Ramanathan
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, UW-Biotechnology Center, 425 Henry Mall, Madison, WI 53706, USA
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11
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Silander K, Mohlke KL, Scott LJ, Peck EC, Hollstein P, Skol AD, Jackson AU, Deloukas P, Hunt S, Stavrides G, Chines PS, Erdos MR, Narisu N, Conneely KN, Li C, Fingerlin TE, Dhanjal SK, Valle TT, Bergman RN, Tuomilehto J, Watanabe RM, Boehnke M, Collins FS. Genetic variation near the hepatocyte nuclear factor-4 alpha gene predicts susceptibility to type 2 diabetes. Diabetes 2004; 53:1141-9. [PMID: 15047633 DOI: 10.2337/diabetes.53.4.1141] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Finland-United States Investigation Of NIDDM Genetics (FUSION) study aims to identify genetic variants that predispose to type 2 diabetes by studying affected sibling pair families from Finland. Chromosome 20 showed our strongest initial evidence for linkage. It currently has a maximum logarithm of odds (LOD) score of 2.48 at 70 cM in a set of 495 families. In this study, we searched for diabetes susceptibility variant(s) at 20q13 by genotyping single nucleotide polymorphism (SNP) markers in case and control DNA pools. Of 291 SNPs successfully typed in a 7.5-Mb interval, the strongest association confirmed by individual genotyping was with SNP rs2144908, located 1.3 kb downstream of the primary beta-cell promoter P2 of hepatocyte nuclear factor-4 alpha (HNF4A). This SNP showed association with diabetes disease status (odds ratio [OR] 1.33, 95% CI 1.06-1.65, P = 0.011) and with several diabetes-related traits. Most of the evidence for linkage at 20q13 could be attributed to the families carrying the risk allele. We subsequently found nine additional associated SNPs spanning a 64-kb region, including the P2 and P1 promoters and exons 1-3. Our results and the independent observation of association of SNPs near the P2 promoter with diabetes in a separate study population of Ashkenazi Jewish origin suggests that variant(s) located near or within HNF4A increases susceptibility to type 2 diabetes.
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Affiliation(s)
- Kaisa Silander
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
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Rickert AM, Kim JH, Meyer S, Nagel A, Ballvora A, Oefner PJ, Gebhardt C. First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genome. PLANT BIOTECHNOLOGY JOURNAL 2003; 1:399-410. [PMID: 17134399 DOI: 10.1046/j.1467-7652.2003.00036.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A panel of 17 tetraploid and 11 diploid potato genotypes was screened by comparative sequence analysis of polymerase chain reaction (PCR) products for single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), in regions of the potato genome where genes for qualitative and/or quantitative resistance to different pathogens have been localized. Most SNP and InDel markers were derived from bacterial artificial chromosome (BAC) insertions that contain sequences similar to the family of plant genes for pathogen resistance having nucleotide-binding-site and leucine-rich-repeat domains (NBS-LRR-type genes). Forty-four such NBS-LRR-type genes containing BAC-insertions were mapped to 14 loci, which tag most known resistance quantitative trait loci (QTL) in potato. Resistance QTL not linked to known resistance-gene-like (RGL) sequences were tagged with other markers. In total, 78 genomic DNA fragments with an overall length of 31 kb were comparatively sequenced in the panel of 28 genotypes. 1498 SNPs and 127 InDels were identified, which corresponded, on average, to one SNP every 21 base pairs and one InDel every 243 base pairs. The nucleotide diversity of the tetraploid genotypes (pi = 0.72 x 10(-3)) was lower when compared with diploid genotypes (pi = 2.31 x 10(-3)). RGL sequences showed higher nucleotide diversity when compared with other sequences, suggesting evolution by divergent selection. Information on sequences, sequence similarities, SNPs and InDels is provided in a database that can be queried via the Internet.
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Affiliation(s)
- Andreas M Rickert
- Max-Planck-Institute for Breeding Research, Carl-von-Linne-Weg 10, 50829 Cologne, Germany
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Weber M, Hagège H, Lutfalla G, Dandolo L, Brunel C, Cathala G, Forné T. A real-time polymerase chain reaction assay for quantification of allele ratios and correction of amplification bias. Anal Biochem 2003; 320:252-8. [PMID: 12927831 DOI: 10.1016/s0003-2697(03)00396-8] [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] [Indexed: 10/27/2022]
Abstract
Allele-specific epigenetic modifications are crucial for several important biological functions, including genomic imprinting and X-inactivation in mammals. Consequently, an ever increasing number of investigations requires accurate quantification of the relative abundance of parental alleles of a specific sequence in a DNA sample. Here, combining the use of polymorphic restriction sites with real-time polymerase chain reaction (PCR) amplification, we describe a simple and quantitative assay to measure allele ratios. The efficiency of the assay was assessed on genomic DNA for several polymorphic restriction sites located in the mouse Igf2/H19 imprinted locus. The assay was also successfully applied to quantify allele ratio in cDNA samples. In addition, we provide an experimental procedure for detection and correction of potential PCR amplification bias which significantly extends the range of application of the assay.
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Affiliation(s)
- Michaël Weber
- Institut de Génétique Moléculaire, UMR 5535 CNRS-Université Montpellier 2, IFR 24, 34293 Montpellier Cedex 5, France
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14
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Bataller R, North KE, Brenner DA. Genetic polymorphisms and the progression of liver fibrosis: a critical appraisal. Hepatology 2003; 37:493-503. [PMID: 12601343 DOI: 10.1053/jhep.2003.50127] [Citation(s) in RCA: 264] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Liver fibrosis is a highly dynamic process in which multiple genes interact with environmental factors. Recent human epidemiologic studies have identified possible polymorphisms in a number of candidate genes that influence the progression of liver fibrosis. These genetic factors could explain the broad spectrum of responses to the same etiologic agent found in patients with chronic liver diseases. Polymorphisms in genes encoding immunoregulatory proteins, proinflammatory cytokines, and fibrogenic factors may influence disease progression in patients with alcohol-induced liver disease, primary biliary cirrhosis, or chronic hepatitis C. However, some of the studies have yielded contradictory results. For example, conflicting results have been obtained in studies assessing the role of mutations in the hemochromatosis gene on fibrosis progression in patients with chronic hepatitis C. Large-scale, well-designed studies are required to clarify the actual role of this factor and other genetic variants in liver fibrosis.
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Affiliation(s)
- Ramón Bataller
- Department of Medicine, Biochemistry and Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599, USA
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Kirk BW, Feinsod M, Favis R, Kliman RM, Barany F. Single nucleotide polymorphism seeking long term association with complex disease. Nucleic Acids Res 2002; 30:3295-311. [PMID: 12140314 PMCID: PMC137089 DOI: 10.1093/nar/gkf466] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2002] [Revised: 04/02/2002] [Accepted: 06/12/2002] [Indexed: 12/16/2022] Open
Abstract
Successful investigation of common diseases requires advances in our understanding of the organization of the genome. Linkage disequilibrium provides a theoretical basis for performing candidate gene or whole-genome association studies to analyze complex disease. However, to constructively interrogate SNPs for these studies, technologies with sufficient throughput and sensitivity are required. A plethora of suitable and reliable methods have been developed, each of which has its own unique advantage. The characteristics of the most promising genotyping and polymorphism scanning technologies are presented. These technologies are examined both in the context of complex disease investigation and in their capacity to face the unique physical and molecular challenges (allele amplification, loss of heterozygosity and stromal contamination) of solid tumor research.
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Affiliation(s)
- Brian W Kirk
- Department of Microbiology, Box 62, Hearst Microbiology Research Center, Joan and Sanford I. Weill Medical College of Cornell University, Room B-406, 1300 York Avenue, New York, NY 10021, USA
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Nissum M, Preuss D, Harig A, Lieberwirth U, Betz C, Neumann S, Deravanessian E, Bock M, Wehmeier L, Bonk T. High-throughput genetic screening using matrix-assisted laser desorption/ionization mass spectrometry. Psychiatr Genet 2002; 12:109-17. [PMID: 12131763 DOI: 10.1097/00041444-200206000-00008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has become a powerful and widespread analytical tool in all fields of life science. Compared with other techniques, its high accuracy and sensitivity makes it a superior method, especially for the analysis of nucleic acids. Recent problems in the analysis of nucleic acids by MALDI-TOF MS can be solved using an automated MALDI-compatible sample-preparation system. Together with the reliable minisequencing assay, high-throughput genotyping of single nucleotide polymorphisms by MALDI-TOF MS is able to become a routine method in research, clinical genetics and diagnostics.
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