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Chi X, Zhang Y, Xue Z, Feng L, Liu H, Wang F, Qi X. Discovery of rare mutations in extensively pooled DNA samples using multiple target enrichment. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:709-717. [PMID: 24602056 PMCID: PMC4265296 DOI: 10.1111/pbi.12174] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/25/2013] [Accepted: 01/16/2014] [Indexed: 05/29/2023]
Abstract
Chemical mutagenesis is routinely used to create large numbers of rare mutations in plant and animal populations, which can be subsequently subjected to selection for beneficial traits and phenotypes that enable the characterization of gene functions. Several next-generation sequencing (NGS)-based target enrichment methods have been developed for the detection of mutations in target DNA regions. However, most of these methods aim to sequence a large number of target regions from a small number of individuals. Here, we demonstrate an effective and affordable strategy for the discovery of rare mutations in a large sodium azide-induced mutant rice population (F2 ). The integration of multiplex, semi-nested PCR combined with NGS library construction allowed for the amplification of multiple target DNA fragments for sequencing. The 8 × 8 × 8 tridimensional DNA sample pooling strategy enabled us to obtain DNA sequences of 512 individuals while only sequencing 24 samples. A stepwise filtering procedure was then elaborated to eliminate most of the false positives expected to arise through sequencing error, and the application of a simple Student's t-test against position-prone error allowed for the discovery of 16 mutations from 36 enriched targeted DNA fragments of 1024 mutagenized rice plants, all without any false calls.
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Affiliation(s)
- Xu Chi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
- Graduate University of Chinese Academy of SciencesBeijing, China
| | - Yingchun Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Zheyong Xue
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Laibao Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Huaqing Liu
- Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural SciencesFuzhou, China
| | - Feng Wang
- Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural SciencesFuzhou, China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
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Plourde M, Vohl MC, Bellis C, Carless M, Dyer T, Dolley G, Marette A, Després JP, Bouchard C, Blangero J, Pérusse L. A variant in the LRRFIP1 gene is associated with adiposity and inflammation. Obesity (Silver Spring) 2013; 21:185-92. [PMID: 23505185 DOI: 10.1002/oby.20242] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 05/17/2012] [Indexed: 01/09/2023]
Abstract
UNLABELLED Inflammation is an important factor linking abdominal obesity with insulin resistance and related cardiometabolic risk. A genome-wide association study of adiposity-related traits performed in the Quebec Family Study (QFS) revealed that a single-nucleotide polymorphism (SNP) in the LRRFIP1 gene (rs11680012) was associated with abdominal adiposity (P = 4.6 × 10(-6)). OBJECTIVE The objective of this study was to assess the relationship between polymorphisms in LRRFIP1 gene and adiposity (BMI, fat mass (FM), waist circumference (WC), and computed tomography-derived areas of total, subcutaneous and visceral abdominal adipose tissue) and markers of inflammation (C-reactive protein (CRP) and interleukin-6 (IL-6)). DESIGN AND METHODS Using Sequenom, 16 tag SNPs in the LRRFIP1 gene, capturing 78% of the genetic variation, were genotyped in 926 participants of the QFS. RESULTS Eight SNPs (rs7575941, rs3769053, rs11689421, rs3820808, rs11680012, rs3806505, rs6739130, and rs11686141) showed evidence of association with at least two adiposity phenotypes and plasma levels of one marker of inflammation. The strongest evidence of association was observed with rs11680012, which explained 1.8-3.4% of the variance in areas of abdominal adiposity and 2.0% of the variation in CRP levels. Carriers of the rare allele of rs11680012 had ≈ 30% more abdominal adiposity (P values between 2.7 × 10(-4) and 3.8 × 10(-6)) and 75% higher CRP levels (P = 1.6 × 10(-4)) than the common allele in age and sex adjusted data. Rs11680012 is a G/C SNP converting an arginine into a threonine and this amino acid substitution may potentially alter exonic splicing. CONCLUSION This gene may therefore represent a potential interesting target to investigate in further functional studies on adiposity and inflammation.
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Affiliation(s)
- Melanie Plourde
- Institute of Nutraceuticals and Functional Foods (INAF), Quebec City, Québec, Canada
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Fritz KL, McCue ME, Valberg SJ, Rendahl AK, Mickelson JR. Genetic mapping of recurrent exertional rhabdomyolysis in a population of North American Thoroughbreds. Anim Genet 2012; 43:730-8. [PMID: 22497487 DOI: 10.1111/j.1365-2052.2012.02351.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2012] [Indexed: 11/30/2022]
Abstract
Recurrent exertional rhabdomyolysis is a heritable disorder that results in painful skeletal muscle cramping with exercise in up to 10% of all Thoroughbred racehorses. Here, we report a genome-wide association study with 48 282 SNPs analyzed among 48 case and 37 control Thoroughbreds. The most significant SNPs spanned approximately 13 Mb on ECA16, and the P-value of the most significant SNP after correcting for population structure was 8.0 × 10(-6) . This region on ECA16 was further evaluated by genotyping 247 SNPs in both the initial population and a second population of 34 case and 98 control Thoroughbreds. Several SNPs across the 13-Mb region on ECA16 showed significance when each population was analyzed separately; however, the exact positions of the most significant SNPs within this region on ECA16 varied between populations. This variability in location may be attributed to lack of power owing to insufficient sample sizes within each population individually, or to the relative distribution of long, conserved haplotypes, characteristic of the Thoroughbred breed. Future genome-wide association studies with additional horses would likely improve the power to resolve casual loci located on ECA16 and increase the likelihood of detecting any additional loci on other chromosomes contributing to disease susceptibility.
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Affiliation(s)
- K L Fritz
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA.
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Marsden CD, Lee Y, Nieman CC, Sanford MR, Dinis J, Martins C, Rodrigues A, Cornel AJ, Lanzaro GC. Asymmetric introgression between the M and S forms of the malaria vector, Anopheles gambiae, maintains divergence despite extensive hybridization. Mol Ecol 2011; 20:4983-94. [PMID: 22059383 PMCID: PMC3222736 DOI: 10.1111/j.1365-294x.2011.05339.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The suggestion that genetic divergence can arise and/or be maintained in the face of gene flow has been contentious since first proposed. This controversy and a rarity of good examples have limited our understanding of this process. Partially reproductively isolated taxa have been highlighted as offering unique opportunities for identifying the mechanisms underlying divergence with gene flow. The African malaria vector, Anopheles gambiae s.s., is widely regarded as consisting of two sympatric forms, thought by many to represent incipient species, the M and S molecular forms. However, there has been much debate about the extent of reproductive isolation between M and S, with one view positing that divergence may have arisen and is being maintained in the presence of gene flow, and the other proposing a more advanced speciation process with little realized gene flow because of low hybrid fitness. These hypotheses have been difficult to address because hybrids are typically rare (<1%). Here, we assess samples from an area of high hybridization and demonstrate that hybrids are fit and responsible for extensive introgression. Nonetheless, we show that strong divergent selection at a subset of loci combined with highly asymmetric introgression has enabled M and S to remain genetically differentiated despite extensive gene flow. We propose that the extent of reproductive isolation between M and S varies across West Africa resulting in a 'geographic mosaic of reproductive isolation'; a finding which adds further complexity to our understanding of divergence in this taxon and which has considerable implications for transgenic control strategies.
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Affiliation(s)
- Clare D. Marsden
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California – Davis, California, USA, 95616
| | - Yoosook Lee
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California – Davis, California, USA, 95616
| | - Catelyn C. Nieman
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California – Davis, California, USA, 95616
| | - Michelle R. Sanford
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California – Davis, California, USA, 95616
| | - Joao Dinis
- National Institute of Public Health (INASA), CP 1013, Bissau, Guinea-Bissau
| | - Cesario Martins
- National Institute of Public Health (INASA), CP 1013, Bissau, Guinea-Bissau
| | - Amabelia Rodrigues
- National Institute of Public Health (INASA), CP 1013, Bissau, Guinea-Bissau
| | - Anthony J. Cornel
- Mosquito Control Research Laboratory, Department of Entomology, University of California - Davis, California, USA, 95616
| | - Gregory C. Lanzaro
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California – Davis, California, USA, 95616
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Beadling C, Heinrich MC, Warrick A, Forbes EM, Nelson D, Justusson E, Levine J, Neff TL, Patterson J, Presnell A, McKinley A, Winter LJ, Dewey C, Harlow A, Barney O, Druker BJ, Schuff KG, Corless CL. Multiplex mutation screening by mass spectrometry evaluation of 820 cases from a personalized cancer medicine registry. J Mol Diagn 2011; 13:504-13. [PMID: 21726664 DOI: 10.1016/j.jmoldx.2011.04.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 03/28/2011] [Accepted: 04/15/2011] [Indexed: 12/25/2022] Open
Abstract
There is an immediate and critical need for a rapid, broad-based genotyping method that can evaluate multiple mutations simultaneously in clinical cancer specimens and identify patients most likely to benefit from targeted agents now in use or in late-stage clinical development. We have implemented a prospective genotyping approach to characterize the frequency and spectrum of mutations amenable to drug targeting present in urothelial, colorectal, endometrioid, and thyroid carcinomas and in melanoma. Cancer patients were enrolled in a Personalized Cancer Medicine Registry that houses both clinical information and genotyping data, and mutation screening was performed using a multiplexed assay panel with mass spectrometry-based analysis to detect 390 mutations across 30 cancer genes. Formalin fixed, paraffin-embedded specimens were evaluated from 820 Registry patients. The genes most frequently mutated across multiple cancer types were BRAF, PIK3CA, KRAS, and NRAS. Less common mutations were also observed in AKT1, CTNNB1, FGFR2, FGFR3, GNAQ, HRAS, and MAP2K1. Notably, 48 of 77 PIK3CA-mutant cases (62%) harbored at least one additional mutation in another gene, most often KRAS. Among melanomas, only 54 of 73 BRAF mutations (74%) were the V600E substitution. These findings demonstrate the diversity and complexity of mutations in druggable targets among the different cancer types and underscore the need for a broad-spectrum, prospective genotyping approach to personalized cancer medicine.
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Affiliation(s)
- Carol Beadling
- Division of Hematology/Oncology, Oregon Health & Science University, Portland, Oregon, USA
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Ibrahem S, Seth R, O'Sullivan B, Fadhil W, Taniere P, Ilyas M. Comparative analysis of pyrosequencing and QMC-PCR in conjunction with high resolution melting for KRAS/BRAF mutation detection. Int J Exp Pathol 2010; 91:500-5. [PMID: 21199003 DOI: 10.1111/j.1365-2613.2010.00733.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mutation detection is important in cancer management. Several methods are available of which high resolution melting (HRM) analysis and pyrosequencing are the most versatile. We undertook a comparative analysis of these techniques. The methods are: To compare the limit of detection (LOD), mutations in KRAS (codon 12/13 hotspot) and BRAF (V600E hotspot) were tested. DNA mixtures containing mutant alleles at a frequency of around 25%/12.5%/6%/3%/ 1.5%/0.8% were analysed. To compare frequency of mutation detection, 22 DNA samples (nine high quality samples from cell lines, 13 low quality samples from formalin-fixed paraffin-embedded tissue) were tested for three hotspots in KRAS (codons 12/13, 61 and 146) and two hotspots in BRAF (V600E and exon 11). HRM analysis of KRAS (codon12/13) and BRAF (V600E) showed that 3% and 1.5% mutant alleles respectively could be reliably detected whilst pyrosequencing reliably detected 6% mutant alleles in each case. Of 110 tests performed on 22 DNA samples, in 109 cases HRM and pyrosequencing gave identical results. Two of the samples tested had previously been called as wild type for KRAS by direct Sanger sequencing but were found to be mutant by both HRM and pyrosequencing. Both HRM and pyrosequencing can detect small numbers of mutant alleles although HRM has a lower limit of detection. Both are suitable for use in mutation detection and are both more sensitive than Sanger sequencing.
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Affiliation(s)
- Salih Ibrahem
- Division of Pathology, School of Molecular Medical Sciences, University of Nottingham, Nottingham, UK
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Annerbrink K, Westberg L, Olsson M, Allgulander C, Andersch S, Sjödin I, Holm G, Eriksson E. Association between the catechol-O-methyltransferase Val158Met polymorphism and panic disorder: a replication. Psychiatry Res 2010; 178:196-8. [PMID: 20457471 DOI: 10.1016/j.psychres.2009.11.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 09/15/2009] [Accepted: 11/20/2009] [Indexed: 11/26/2022]
Abstract
The association between the catechol-O-methyltransferase Val158Met polymorphism and panic disorder was studied in a Swedish sample of 211 patients and 452 controls. We found a significant excess of the Val allele in both male and female patients, the latter but not the former finding being in line with previous studies.
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Affiliation(s)
- Kristina Annerbrink
- Department of Pharmacology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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Falzoi M, Mossa A, Congeddu E, Saba L, Pani L. Multiplex genotyping of CYP3A4, CYP3A5, CYP2C9 and CYP2C19 SNPs using MALDI-TOF mass spectrometry. Pharmacogenomics 2010; 11:559-71. [PMID: 20350138 DOI: 10.2217/pgs.09.172] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Pharmacogenetics is the study of genetic variations that cause alterations in drug level, drug response and adverse drug reactions. SNPs found in CYP450 genes have the greatest genetic influences on interindividual variability in drug bioavailability. The polymorphic nature of these genes may modulate several enzyme levels that affect individual responses to pharmacological treatment. Among them, CYP3A4, CYP3A5, CYP2C9 and CYP2C19 isoforms of CYP450 enzymes are involved in the metabolism of many commonly prescribed drugs. AIMS In this study, we would like to develop a CYP450 genotyping platform that could lead a complete definition of a patient's metabolic genotype in order to improve the clinical outcome of some drug treatments. MATERIALS & METHODS We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) (Sequenom) to develop a SNP genotyping method. RESULTS This MALDI-TOF-based multiplexing system allows the simultaneous and efficient genotyping of a set of CYP450 gene polymorphisms. CONCLUSION The multiple CYP450 gene testing achieved with this application can be used to develop diagnostic tests to predict drug responses and clinical outcomes.
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Affiliation(s)
- Matteo Falzoi
- Istituto Tecnologie Biomediche del Consiglio Nazionale delle Ricerche CNR-ITB, Parco Scientifico e Tecnologico della Sardegna, Ed. 5, Loc. Piscinamanna, 09010 Pula (CA) Italy.
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Chawade A, Sikora P, Bräutigam M, Larsson M, Vivekanand V, Nakash MA, Chen T, Olsson O. Development and characterization of an oat TILLING-population and identification of mutations in lignin and beta-glucan biosynthesis genes. BMC PLANT BIOLOGY 2010; 10:86. [PMID: 20459868 PMCID: PMC3017761 DOI: 10.1186/1471-2229-10-86] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 05/12/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND Oat, Avena sativa is the sixth most important cereal in the world. Presently oat is mostly used as feed for animals. However, oat also has special properties that make it beneficial for human consumption and has seen a growing importance as a food crop in recent decades. Increased demand for novel oat products has also put pressure on oat breeders to produce new oat varieties with specific properties such as increased or improved beta-glucan-, antioxidant- and omega-3 fatty acid levels, as well as modified starch and protein content. To facilitate this development we have produced a TILLING (Targeting Induced Local Lesions IN Genomes) population of the spring oat cultivar SW Belinda. RESULTS Here a population of 2600 mutagenised M2 lines, producing 2550 M3 seed lots were obtained. The M2 population was initially evaluated by visual inspection and a number of different phenotypes were seen ranging from dwarfs to giants, early flowering to late flowering, leaf morphology and chlorosis. Phloroglucinol/HCl staining of M3 seeds, obtained from 1824 different M2 lines, revealed a number of potential lignin mutants. These were later confirmed by quantitative analysis. Genomic DNA was prepared from the M2 population and the mutation frequency was determined. The estimated mutation frequency was one mutation per 20 kb by RAPD-PCR fingerprinting, one mutation per 38 kb by MALDI-TOF analysis and one mutation per 22.4 kb by DNA sequencing. Thus, the overall mutation frequency in the population is estimated to be one mutation per 20-40 kb, depending on if the method used addressed the whole genome or specific genes. During the investigation, 6 different mutations in the phenylalanine ammonia-lyase (AsPAL1) gene and 10 different mutations in the cellulose synthase-like (AsCslF6) beta-glucan biosynthesis gene were identified. CONCLUSION The oat TILLING population produced in this work carries, on average, hundreds of mutations in every individual gene in the genome. It will therefore be an important resource in the development of oat with specific characters. The population (M5) will be available for academic research via Nordgen http://www.nordgen.org as soon as enough seeds are obtained.[Genbank accession number for the cloned AsPAL1 is GQ373155 and GQ379900 for AsCslF6].
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Affiliation(s)
- Aakash Chawade
- Department of Cell and Molecular Biology, Göteborg University, S-40530 Göteborg, Sweden
- Department of Plant and Environmental Sciences, Göteborg University, S-40530, Göteborg, Sweden
| | - Per Sikora
- Department of Plant and Environmental Sciences, Göteborg University, S-40530, Göteborg, Sweden
| | - Marcus Bräutigam
- Department of Cell and Molecular Biology, Göteborg University, S-40530 Göteborg, Sweden
- CropTailorAB, Erik Dahlbergsgatan 11A, SE41126 Göteborg, Sweden
| | - Mikael Larsson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, S-41296, Göteborg, Sweden
| | - Vivekanand Vivekanand
- Department of Plant and Environmental Sciences, Göteborg University, S-40530, Göteborg, Sweden
| | | | - Tingsu Chen
- Department of Cell and Molecular Biology, Göteborg University, S-40530 Göteborg, Sweden
- Current Address: Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Olof Olsson
- Department of Plant and Environmental Sciences, Göteborg University, S-40530, Göteborg, Sweden
- CropTailorAB, Erik Dahlbergsgatan 11A, SE41126 Göteborg, Sweden
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Villani AC, Lemire M, Thabane M, Belisle A, Geneau G, Garg AX, Clark WF, Moayyedi P, Collins SM, Franchimont D, Marshall JK. Genetic risk factors for post-infectious irritable bowel syndrome following a waterborne outbreak of gastroenteritis. Gastroenterology 2010; 138:1502-13. [PMID: 20044998 DOI: 10.1053/j.gastro.2009.12.049] [Citation(s) in RCA: 186] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 11/26/2009] [Accepted: 12/28/2009] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Acute gastroenteritis is the strongest risk factor for irritable bowel syndrome (IBS). In May 2000, >2300 residents of Walkerton, Ontario, developed gastroenteritis from microbial contamination of the municipal water supply; a longitudinal study found that >36.2% of these developed IBS. We used this cohort to study genetic susceptibility to post-infectious (PI)-IBS. METHODS We screened 79 functional variants of genes with products involved in serotoninergic pathways, intestinal epithelial barrier function, and innate immunity and performed fine mapping in regions of interest. We compared data from Walkerton residents who developed gastroenteritis and reported PI-IBS 2 to 3 years after the outbreak (n = 228, cases) with data from residents who developed gastroenteritis but did not develop PI-IBS (n = 581, controls). RESULTS Four variants were associated with PI-IBS, although the association was not significant after correction for the total number of single nucleotide polymorphisms. Two were located in TLR9, which encodes a pattern recognition receptor (rs352139, P545P; P = .0059 and rs5743836, -T1237C; P = .0250; r(2) < 0.14); 1 was in CDH1, which encodes a tight junction protein (rs16260, -C160A; P = .0352); and 1 was in IL6, which encodes a cytokine (rs1800795, -G174C; P = .0420). Denser mapping of these 3 regions revealed 1 novel association in IL6 (rs2069861; P = .0069) and 14 associations that could be accounted for by linkage disequilibrium with the 4 original variants. The TLR9, IL6, and CDH1 variants all persisted as independent risk factors for PI-IBS when controlling for previously identified clinical risk factors. CONCLUSION This is the first descriptive study to assess potential genetic determinants of PI-IBS. Genes that encode proteins involved in epithelial cell barrier function and the innate immune response to enteric bacteria are associated with development of IBS following acute gastroenteritis.
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Affiliation(s)
- Alexandra-Chloé Villani
- Division of Gastroenterology, Department of Medicine, McGill University, Montréal, Québec, Canada.
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Genetic variation in brain-derived neurotrophic factor is associated with serotonin transporter but not serotonin-1A receptor availability in men. Biol Psychiatry 2009; 66:477-85. [PMID: 19500776 DOI: 10.1016/j.biopsych.2009.04.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2008] [Revised: 03/23/2009] [Accepted: 04/02/2009] [Indexed: 12/15/2022]
Abstract
BACKGROUND The serotonergic system, including the serotonin transporter (5-HTT), which is the target of many antidepressants, seems to be influenced by brain-derived neurotrophic factor (BDNF). METHODS Positron emission tomography (PET) was used to address, in 25 and 53 healthy volunteers, respectively, the possible association between six polymorphisms in the gene encoding BDNF and the availability of two proteins expressed by serotonergic neurons: the 5-HTT, measured with the radioligand [(11)C]MADAM, and the serotonin-1A (5-HT1A) receptor, measured with [(11)C]WAY-100635. RESULTS Several single nucleotide polymorphisms were associated with [(11)C]MADAM binding potential (BP) in most brain regions, male carriers of the valine/valine genotype of the Val66Met polymorphism displaying higher availability. Effect sizes ranged from a 50% to a threefold increase. In contrast, there was no association for [(11)C]WAY-100635 BP. The observation that BDNF polymorphisms were associated with 5-HTT availability could be partly replicated in an independent population comprising nine male suicide attempters and nine matched control subjects, in which transporter availability had been measured with single photon emission computed tomography with (123)I-beta-CIT as ligand. CONCLUSIONS Our results suggest that genetic variation in BDNF influences 5-HTT but not 5-HT1A receptor density in the human brain.
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Delvaeye M, Noris M, De Vriese A, Esmon CT, Esmon NL, Ferrell G, Del-Favero J, Plaisance S, Claes B, Lambrechts D, Zoja C, Remuzzi G, Conway EM. Thrombomodulin mutations in atypical hemolytic-uremic syndrome. N Engl J Med 2009; 361:345-57. [PMID: 19625716 PMCID: PMC3530919 DOI: 10.1056/nejmoa0810739] [Citation(s) in RCA: 399] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND The hemolytic-uremic syndrome consists of the triad of microangiopathic hemolytic anemia, thrombocytopenia, and renal failure. The common form of the syndrome is triggered by infection with Shiga toxin-producing bacteria and has a favorable outcome. The less common form of the syndrome, called atypical hemolytic-uremic syndrome, accounts for about 10% of cases, and patients with this form of the syndrome have a poor prognosis. Approximately half of the patients with atypical hemolytic-uremic syndrome have mutations in genes that regulate the complement system. Genetic factors in the remaining cases are unknown. We studied the role of thrombomodulin, an endothelial glycoprotein with anticoagulant, antiinflammatory, and cytoprotective properties, in atypical hemolytic-uremic syndrome. METHODS We sequenced the entire thrombomodulin gene (THBD) in 152 patients with atypical hemolytic-uremic syndrome and in 380 controls. Using purified proteins and cell-expression systems, we investigated whether thrombomodulin regulates the complement system, and we characterized the mechanisms. We evaluated the effects of thrombomodulin missense mutations associated with atypical hemolytic-uremic syndrome on complement activation by expressing thrombomodulin variants in cultured cells. RESULTS Of 152 patients with atypical hemolytic-uremic syndrome, 7 unrelated patients had six different heterozygous missense THBD mutations. In vitro, thrombomodulin binds to C3b and factor H (CFH) and negatively regulates complement by accelerating factor I-mediated inactivation of C3b in the presence of cofactors, CFH or C4b binding protein. By promoting activation of the plasma procarboxypeptidase B, thrombomodulin also accelerates the inactivation of anaphylatoxins C3a and C5a. Cultured cells expressing thrombomodulin variants associated with atypical hemolytic-uremic syndrome had diminished capacity to inactivate C3b and to activate procarboxypeptidase B and were thus less protected from activated complement. CONCLUSIONS Mutations that impair the function of thrombomodulin occur in about 5% of patients with atypical hemolytic-uremic syndrome.
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Affiliation(s)
- Mieke Delvaeye
- VIB-K.U.Leuven Vesalius Research Center, Leuven, Belgium
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Villani AC, Lemire M, Fortin G, Louis E, Silverberg MS, Collette C, Baba N, Libioulle C, Belaiche J, Bitton A, Gaudet D, Cohen A, Langelier D, Fortin PR, Wither JE, Sarfati M, Rutgeerts P, Rioux JD, Vermeire S, Hudson TJ, Franchimont D. Common variants in the NLRP3 region contribute to Crohn's disease susceptibility. Nat Genet 2008; 41:71-6. [PMID: 19098911 DOI: 10.1038/ng.285] [Citation(s) in RCA: 391] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Accepted: 10/02/2008] [Indexed: 01/11/2023]
Abstract
We used a candidate gene approach to identify a set of SNPs, located in a predicted regulatory region on chromosome 1q44 downstream of NLRP3 (previously known as CIAS1 and NALP3) that are associated with Crohn's disease. The associations were consistently replicated in four sample sets from individuals of European descent. In the combined analysis of all samples (710 father-mother-child trios, 239 cases and 107 controls), these SNPs were strongly associated with risk of Crohn's disease (P(combined) = 3.49 x 10(-9), odds ratio = 1.78, confidence interval = 1.47-2.16 for rs10733113), reaching a level consistent with the stringent significance thresholds imposed by whole-genome association studies. In addition, we observed significant associations between SNPs in the associated regions and NLRP3 expression and IL-1beta production. Mutations in NLRP3 are known to be responsible for three rare autoinflammatory disorders. These results suggest that the NLRP3 region is also implicated in the susceptibility of more common inflammatory diseases such as Crohn's disease.
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Affiliation(s)
- Alexandra-Chloé Villani
- Division of Gastroenterology, McGill University Health Centre, Montreal General Hospital, Montréal, Québec, Canada.
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Affiliation(s)
- Estelle Espinos
- Inserm U563, centre de physiopathologie de Toulouse Purpan, 31059 Toulouse cedex, France
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Schroeder C, Walter M, Berg D, Leitner P, Bauer P, Kohl Z, Winkler J, Riess O, Bonin M. High-throughput homogeneous mass cleave assay technology for the diagnosis of autosomal recessive Parkinson's disease. J Mol Diagn 2008; 10:217-24. [PMID: 18403612 DOI: 10.2353/jmoldx.2008.070100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To date, 11 gene loci that contribute to familial Parkinson's disease (PD) are known. Of these, mutations in six genes have been identified, allowing genetic testing and more accurate phenotypic characterization of genetically defined disease subtypes. In particular, mutations in Parkin, DJ-1, and Pink1 genes are associated with autosomal recessive PD and may also play a major role in early onset PD (EOPD). However, genetic testing for sequence alterations in these genes remains laborious. Therefore, our aim was to develop a flexible, rapid, high-throughput screening procedure using matrix-assisted laser desorption ionization/time of flight technology and homogeneous mass cleave assays. Using this novel approach, we screened all 27 coding exons of the Parkin, DJ-1, and Pink1 genes in 31 patients with EOPD, a total of 367,195 nucleotides. Four positive controls with known autosomal recessive PD mutations that had previously been screened by denaturing high performance liquid chromatography in combination with sequencing were also tested. All known alterations were detected by matrix-assisted laser desorption ionization/time of flight mass spectrometer, as well as additional polymorphisms in formerly unscreened regions. Overall, two previously described mutations in three patients with EOPD, 27 known polymorphisms with 386 occurrences, and eight unknown variants with 21 occurrences were detected. In total, we identified 410 sequence alterations in 31 patients with EOPD. In conclusion, this is the first study using matrix-assisted laser desorption ionization/time of flight mass spectrometry and homogeneous mass cleave assay for high-throughput mutation screening.
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