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Nln I, Shum J, Ghodke-Puranik Y, Tipon R, Triese D, Amin S, Makol A, Osborn T, Chowdhary V, Thanarajasingam U, Muskardin TLW, Oke V, Gunnarsson I, Zickert A, Zervou MI, Boumpas DT, Svenungsson E, Goulielmos GN, Niewold TB. Regional European genetic ancestry predicts type I interferon level and risk of severe viral infection. QJM 2024; 117:581-588. [PMID: 38530799 PMCID: PMC11389909 DOI: 10.1093/qjmed/hcae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Viral infection outcomes vary widely between individuals, ranging from mild symptoms to severe organ failure and death, and it is clear that host genetic factors play a role in this variability. Type I interferon (IFN) is a critical anti-viral cytokine, and we have previously noted differences in type I IFN levels between world populations. METHODS In this study, we investigate the interrelationship between regional European genetic ancestry, type I IFN levels and severe viral infection outcomes. RESULTS In cohorts of European ancestry lupus patients living in Europe, we noted higher IFN in the Northwestern populations as compared to Southeastern populations. In an independent cohort of European ancestry lupus patients from the USA with varying proportional regional European genetic admixture, we observed the same Northwest vs. Southeast European ancestry IFN gradient. We developed a model to predict type I IFN level based on regional European ancestry (Area under the curve (AUC) = 0.73, P = 6.1e-6). Examining large databases containing serious viral outcomes data, we found that lower predicted IFN in the corresponding European country was significantly correlated with increased viral infection fatality rate, including Coronavirus Disease 2019 (COVID-19), viral hepatitis and HIV [correlation coefficients: -0.79 (P = 4e-2), -0.94 (P = 6e-3) and -0.96 (P = 8e-2), respectively]. CONCLUSIONS This association between predicted type I IFN level and viral outcome severity suggests a potential causal relationship, as greater intrinsic type I IFN is beneficial in host defense against viruses. Genetic testing could provide insight into individual and population level risk of fatality due to viruses prior to infection, across a wide range of viral pathogens.
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Affiliation(s)
- I Nln
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, USA
| | - J Shum
- Department of Medicine, MarinHealth Medical Center, Kentfield, CA, USA
| | - Y Ghodke-Puranik
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, USA
| | - R Tipon
- The New York Stem Cell Foundation, New York, NY, USA
| | - D Triese
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - S Amin
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - A Makol
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - T Osborn
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - V Chowdhary
- Division of Rheumatology, Yale University, New Haven, CT, USA
| | | | - T L W Muskardin
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, USA
| | - V Oke
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - I Gunnarsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - A Zickert
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - M I Zervou
- Laboratory of Molecular Medicine and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - D T Boumpas
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - E Svenungsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - G N Goulielmos
- Laboratory of Molecular Medicine and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - T B Niewold
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, USA
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2
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Bonilla DA, Orozco CA, Forero DA, Odriozola A. Techniques, procedures, and applications in host genetic analysis. ADVANCES IN GENETICS 2024; 111:1-79. [PMID: 38908897 DOI: 10.1016/bs.adgen.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
This chapter overviews genetic techniques' fundamentals and methodological features, including different approaches, analyses, and applications that have contributed to advancing health and disease. The aim is to describe laboratory methodologies and analyses employed to understand the genetic landscape of different biological contexts, from conventional techniques to cutting-edge technologies. Besides describing detailed aspects of the polymerase chain reaction (PCR) and derived types as one of the principles for many novel techniques, we also discuss microarray analysis, next-generation sequencing, and genome editing technologies such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems. These techniques study several phenotypes, ranging from autoimmune disorders to viral diseases. The significance of integrating diverse genetic methodologies and tools to understand host genetics comprehensively and addressing the ethical, legal, and social implications (ELSI) associated with using genetic information is highlighted. Overall, the methods, procedures, and applications in host genetic analysis provided in this chapter furnish researchers and practitioners with a roadmap for navigating the dynamic landscape of host-genome interactions.
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Affiliation(s)
- Diego A Bonilla
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain; Research Division, Dynamical Business & Science Society-DBSS International SAS, Bogotá, Colombia.
| | - Carlos A Orozco
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá, Colombia
| | - Diego A Forero
- School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Adrián Odriozola
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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3
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Jin S, Huang D, Jin W, Wang Y, Shao H, Gong L, Luo Z, Yang Z, Luan J, Xie D, Ding C. Detection of DNA copy number alterations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of single nucleotide polymorphisms. Clin Chem Lab Med 2022; 60:1543-1550. [PMID: 35938948 DOI: 10.1515/cclm-2022-0511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/20/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Copy number alterations (CNAs) are frequently found in malignant tissues. Different approaches have been used for CNA detection. However, it is not easy to detect a large panel of CNA targets in heterogenous tumors. METHODS We have developed a CNAs detection approach through quantitatively analyzed allelic imbalance by allelotyping single nucleotide polymorphisms (SNPs) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Furthermore, the copy number changes were quantified by real-competitive PCR (rcPCR) to distinguish loss of heterozygosity (LOH) and genomic amplification. The approach was used to validate the CNA regions detected by next generation sequencing (NGS) in early-stage lung carcinoma. RESULTS CNAs were detected in heterogeneous DNA samples where tumor DNA is present at only 10% through the SNP based allelotyping. In addition, two different types of CNAs (loss of heterozygosity and chromosome amplification) were able to be distinguished quantitatively by rcPCR. Validation on a total of 41 SNPs from the selected CNA regions showed that copy number changes did occur, and the tissues from early-stage lung carcinoma were distinguished from normal. CONCLUSIONS CNA detection by MALDI-TOF MS can be used for validating potentially interesting genomic regions identified from next generation sequencing, and for detecting CNAs in tumor tissues consisting of a mixture of neoplastic and normal cells.
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Affiliation(s)
- Shengnan Jin
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Dan Huang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Weijiang Jin
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Yourong Wang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Hengrong Shao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Lisha Gong
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Zhenni Luo
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Zhengquan Yang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Ju Luan
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China; and InnoMed Diagnostics Inc., Wenzhou, P.R. China
| | - Deyao Xie
- Department of Thoracic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Chunming Ding
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
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Li JH, Szczerbinski L, Dawed AY, Kaur V, Todd JN, Pearson ER, Florez JC. A Polygenic Score for Type 2 Diabetes Risk Is Associated With Both the Acute and Sustained Response to Sulfonylureas. Diabetes 2021; 70:293-300. [PMID: 33106254 PMCID: PMC7881853 DOI: 10.2337/db20-0530] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/22/2020] [Indexed: 01/07/2023]
Abstract
There is a limited understanding of how genetic loci associated with glycemic traits and type 2 diabetes (T2D) influence the response to antidiabetic medications. Polygenic scores provide increasing power to detect patterns of disease predisposition that might benefit from a targeted pharmacologic intervention. In the Study to Understand the Genetics of the Acute Response to Metformin and Glipizide in Humans (SUGAR-MGH), we constructed weighted polygenic scores using known genome-wide significant associations for T2D, fasting glucose, and fasting insulin, comprising 65, 43, and 13 single nucleotide polymorphisms, respectively. Multiple linear regression tested for associations between scores and glycemic traits as well as pharmacodynamic end points, adjusting for age, sex, race, and BMI. A higher T2D score was nominally associated with a shorter time to insulin peak, greater glucose area over the curve, shorter time to glucose trough, and steeper slope to glucose trough after glipizide. In replication, a higher T2D score was associated with a greater 1-year hemoglobin A1c reduction to sulfonylureas in the Genetics of Diabetes Audit and Research in Tayside Scotland (GoDARTS) study (P = 0.02). Our findings suggest that individuals with a higher genetic burden for T2D experience a greater acute and sustained response to sulfonylureas.
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Affiliation(s)
- Josephine H Li
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Lukasz Szczerbinski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Adem Y Dawed
- Division of Population Health and Genomics, Ninewells Hospital and School of Medicine, University of Dundee, Dundee, Scotland, U.K
| | - Varinderpal Kaur
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Jennifer N Todd
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, MA
| | - Ewan R Pearson
- Division of Population Health and Genomics, Ninewells Hospital and School of Medicine, University of Dundee, Dundee, Scotland, U.K
| | - Jose C Florez
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
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5
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Yan Y, Jin X, Wang X, Zhang C, Zhang Q, Zheng L, Feng X, Hao S, Gao H, Ma X. Screening of PAH Common Mutations in Chinese Phenylketonuria Patients Using iPLEX MALDI-TOF MS. ACS OMEGA 2020; 5:1805-1812. [PMID: 32039316 PMCID: PMC7003239 DOI: 10.1021/acsomega.9b02955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Phenylketonuria (PKU) is caused by phenylalanine hydroxylase (PAH) gene variants. Previous research has identified some PAH mutation hotspots in Chinese patients with PKU. In this study, we introduce a novel MassArray panel for screening the 29 common PAH gene mutations in Chinese patients using iPLEX MALDI-TOF MS. 105 Patients with PKU and known PAH gene mutations were genotyped using this MassArray panel. All of the 29 mutations screened were detected, and MassArray panel results were consistent with those obtained by Sanger sequencing. Fifty patients newly diagnosed with PKU were recruited in the double-blind experiment. PAH gene variants were detected in these 50 patients using the MassArray panel, and the results were verified with Sanger sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA) methods. Our results show that the mutation detection rate using the MassArray panel with 29 mutations is 74% (95% CI, 65-83%), and the clinical genetic diagnosis rate is 54% (95% CI, 40-68%). This panel can be used as a high throughput, low cost, and rapid method for screening and diagnosing PAH gene mutations. The establishment of this approach provides proof-of-concept for future large-scale PAH mutation carrier screening in areas with high rates of PKU.
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Affiliation(s)
- Yousheng Yan
- National
Research Institute for Family Planning, Beijing 100081, China
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
- Peking
University International Hospital, Beijing 102206, China
| | - Xiaohua Jin
- National
Research Institute for Family Planning, Beijing 100081, China
| | - Xing Wang
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Chuan Zhang
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Qinhua Zhang
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Lei Zheng
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Xuan Feng
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Shengju Hao
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Huafang Gao
- National
Research Institute for Family Planning, Beijing 100081, China
| | - Xu Ma
- National
Research Institute for Family Planning, Beijing 100081, China
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6
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Coates BS, Kozak GM, Seok Kim K, Sun J, Wang Y, Fleischer SJ, Dopman EB, Sappington TW. Influence of host plant, geography and pheromone strain on genomic differentiation in sympatric populations of Ostrinia nubilalis. Mol Ecol 2019; 28:4439-4452. [PMID: 31495004 DOI: 10.1111/mec.15234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/19/2019] [Accepted: 08/05/2019] [Indexed: 12/26/2022]
Abstract
Patterns of mating for the European corn borer (Ostrinia nubilalis) moth depend in part on variation in sex-pheromone blend. The ratio of (E)-11- and (Z)-11-tetradecenyl acetate (E11- and Z11-14:OAc) in the pheromone blend that females produce and males respond to differs between strains of O. nubilalis. Populations also vary in female oviposition preference for and larval performance on maize (C4) and nonmaize (C3) host plants. The relative contributions of sexual and ecological trait variation to the genetic structure of O. nubilalis remains unknown. Host-plant use (13 C/14 C ratios) and genetic differentiation were estimated among sympatric E and Z pheromone strain O. nubilalis males collected in sex-pheromone baited traps at 12 locations in Pennsylvania and New York between 2007 and 2010. Among genotypes at 65 single nucleotide polymorphism marker loci, variance at a position in the pheromone gland fatty acyl-reductase (pgfar) gene at the locus responsible for determining female pheromone ratio (Pher) explained 64% of the total genetic differentiation between males attracted to different pheromones (male response, Resp), providing evidence of sexual inter-selection at these unlinked loci. Principal coordinate, Bayesian clustering, and distance-based redundancy analysis (dbRDA) demonstrate that host plant history or geography does not significantly contribute to population variation or differentiation among males. In contrast, these analyses indicate that pheromone response and pgfar-defined strain contribute significantly to population genetic differentiation. This study suggests that behavioural divergence probably plays a larger role in driving genetic variation compared to host plant-defined ecological adaptation.
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Affiliation(s)
- Brad S Coates
- Corn Insects & Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Genevieve M Kozak
- Department of Biology, University of Massachusetts-Dartmouth, Dartmouth, MA, USA.,Department of Biology, Tufts University, Medford, MA, USA
| | - Kyung Seok Kim
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, USA
| | - Jing Sun
- Department of Entomology, Iowa State University, Ames, IA, USA
| | - Yangzhou Wang
- Jilin Academy of Agricultural Sciences, Changchun, China
| | | | - Erik B Dopman
- Department of Biology, Tufts University, Medford, MA, USA
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7
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Mattes DS, Jung N, Weber LK, Bräse S, Breitling F. Miniaturized and Automated Synthesis of Biomolecules-Overview and Perspectives. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806656. [PMID: 31033052 DOI: 10.1002/adma.201806656] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Chemical synthesis is performed by reacting different chemical building blocks with defined stoichiometry, while meeting additional conditions, such as temperature and reaction time. Such a procedure is especially suited for automation and miniaturization. Life sciences lead the way to synthesizing millions of different oligonucleotides in extremely miniaturized reaction sites, e.g., pinpointing active genes in whole genomes, while chemistry advances different types of automation. Recent progress in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging could match miniaturized chemical synthesis with a powerful analytical tool to validate the outcome of many different synthesis pathways beyond applications in the life sciences. Thereby, due to the radical miniaturization of chemical synthesis, thousands of molecules can be synthesized. This in turn should allow ambitious research, e.g., finding novel synthesis routes or directly screening for photocatalysts. Herein, different technologies are discussed that might be involved in this endeavor. A special emphasis is given to the obstacles that need to be tackled when depositing tiny amounts of materials to many different extremely miniaturized reaction sites.
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Affiliation(s)
- Daniela S Mattes
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Nicole Jung
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Laura K Weber
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Frank Breitling
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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8
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Locked Nucleic Acid Technology for Highly Sensitive Detection of Somatic Mutations in Cancer. Adv Clin Chem 2017; 83:53-72. [PMID: 29304903 DOI: 10.1016/bs.acc.2017.10.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The molecular diagnosis of the cancer mutational status is essential for modern clinical laboratory medicine. Mutations in EGFR, KRAS, BRAF, and PIK3CA genes are widely analyzed in solid tumors such as lung cancer, colorectal cancer, breast cancer, and melanoma. The allele-specific polymerase chain reaction, high-resolution melting, and Sanger sequencing are used for detecting and identifying gene mutations in many clinical laboratories. The locked nucleic acid (LNA) is a class of nucleic acid analogs that contain a methylene bridge connecting the 2' oxygen and 4' carbon in the ribose moiety. This methylene bridge locks the ribose group into a C3'-endo conformation. LNA, including an oligonucleotide, increases the thermal stability of hybrid strands. The use of LNA technology in molecular diagnostic methods improves the specificity and sensitivity of assays. This review describes routinely analyzed mutations and molecular diagnostic methods used in the clinical laboratory along with the performance improvement of mutational analysis with LNA.
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9
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Saxena R, Plenge RM, Bjonnes AC, Dashti HS, Okada Y, Gad El Haq W, Hammoudeh M, Al Emadi S, Masri BK, Halabi H, Badsha H, Uthman IW, Margolin L, Gupta N, Mahfoud ZR, Kapiri M, Dargham SR, Aranki G, Kazkaz LA, Arayssi T. A Multinational Arab Genome‐Wide Association Study Identifies New Genetic Associations for Rheumatoid Arthritis. Arthritis Rheumatol 2017; 69:976-985. [DOI: 10.1002/art.40051] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/17/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Richa Saxena
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, and Broad InstituteCambridge Massachusetts
| | - Robert M. Plenge
- Broad Institute, Cambridge, Massachusetts, and Merck Research Laboratories and Brigham and Women's Hospital, Harvard Medical SchoolBoston Massachusetts
| | - Andrew C. Bjonnes
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, and Broad InstituteCambridge Massachusetts
| | - Hassan S. Dashti
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, and Broad InstituteCambridge Massachusetts
| | - Yukinori Okada
- Tokyo Medical and Dental University Graduate School of Medical and Dental Sciences, Tokyo, Japan, and RikenYokohama Japan
| | | | | | | | | | - Hussein Halabi
- King Faisal Specialist Hospital and Research CenterJeddah Saudi Arabia
| | - Humeira Badsha
- Dr. Humeira Badsha Medical CenterDubai United Arab Emirates
| | | | | | | | | | | | | | - Grace Aranki
- Weill Cornell Medicine–QatarEducation City Doha Qatar
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10
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Lemas DJ, Klimentidis YC, Aslibekyan S, Wiener HW, O'Brien DM, Hopkins SE, Stanhope KL, Havel PJ, Allison DB, Fernandez JR, Tiwari HK, Boyer BB. Polymorphisms in stearoyl coa desaturase and sterol regulatory element binding protein interact with N-3 polyunsaturated fatty acid intake to modify associations with anthropometric variables and metabolic phenotypes in Yup'ik people. Mol Nutr Food Res 2016; 60:2642-2653. [PMID: 27467133 DOI: 10.1002/mnfr.201600170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/09/2016] [Accepted: 07/21/2016] [Indexed: 11/08/2022]
Abstract
SCOPE n-3 polyunsaturated fatty acid (n-3 PUFA) intake is associated with protection from obesity; however, the mechanisms of protection remain poorly characterized. The stearoyl CoA desaturase (SCD), insulin-sensitive glucose transporter (SLC2A4), and sterol regulatory element binding protein (SREBF1) genes are transcriptionally regulated by n-3 PUFA intake and harbor polymorphisms associated with obesity. The present study investigated how consumption of n-3 PUFA modifies associations between SCD, SLC2A4, and SREBF1 polymorphisms and anthropometric variables and metabolic phenotypes. MATERIALS AND METHODS Anthropometric variables and metabolic phenotypes were measured in a cross-sectional sample of Yup'ik individuals (n = 1135) and 33 polymorphisms were tested for main effects and interactions using linear models that account for familial correlations. n-3 PUFA intake was estimated using red blood cell nitrogen stable isotope ratios. SCD polymorphisms were associated with ApoA1 concentration and n-3 PUFA interactions with SCD polymorphisms were associated with reduced fasting cholesterol levels and waist-to-hip ratio. SLC2A4 polymorphisms were associated with hip circumference, high-density lipoprotein and ApoA1 concentrations. SREBF1 polymorphisms were associated with low-density lipoprotein and HOMA-IR and n-3 PUFA interactions were associated with reduced fasting insulin and HOMA-IR levels. CONCLUSION The results suggest that an individual's genotype may interact with dietary n-3 PUFAs in ways that are associated with protection from obesity-related diseases in Yup'ik people.
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Affiliation(s)
- Dominick J Lemas
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA.,Department of Pediatrics, Section of Neonatology, University of Colorado Denver, Aurora, CO, USA
| | - Yann C Klimentidis
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Howard W Wiener
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Diane M O'Brien
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Scarlett E Hopkins
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Kimber L Stanhope
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA.,Department of Nutrition, University of California, Davis, CA, USA
| | - Peter J Havel
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA.,Department of Nutrition, University of California, Davis, CA, USA
| | - David B Allison
- Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.,Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, USA.,Office of Energetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jose R Fernandez
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K Tiwari
- Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Bert B Boyer
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
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11
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Poynter JN, Richardson M, Langer E, Hooten AJ, Roesler M, Hirsch B, Nguyen PL, Cioc A, Warlick E, Ross JA. Association between mitochondrial DNA haplogroup and myelodysplastic syndromes. Genes Chromosomes Cancer 2016; 55:688-93. [PMID: 27121678 DOI: 10.1002/gcc.22370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/22/2016] [Accepted: 04/23/2016] [Indexed: 11/06/2022] Open
Abstract
Polymorphisms in mitochondrial DNA (mtDNA) are used to group individuals into haplogroups reflecting human global migration and are associated with multiple diseases, including cancer. Here, we evaluate the association between mtDNA haplogroup and risk of myelodysplastic syndromes (MDS). Cases were identified by the Minnesota Cancer Surveillance System. Controls were identified through the Minnesota State driver's license/identification card list. Because haplogroup frequencies vary by race and ethnicity, we restricted analyses to non-Hispanic whites. We genotyped 15 mtSNPs that capture common European mitochondrial haplogroup variation. We used SAS v.9.3 (SAS Institute, Cary, NC) to calculate odds ratios (OR) and 95% confidence intervals (CI) overall and stratified by MDS subtype and IPSS-R risk category. We were able to classify 215 cases with confirmed MDS and 522 controls into one of the 11 common European haplogroups. Due to small sample sizes in some subgroups, we combined mt haplogroups into larger bins based on the haplogroup evolutionary tree, including HV (H + V), JT (J + T), IWX (I + W + X), UK (U + K), and Z for comparisons of cases and controls. Using haplogroup HV as the reference group, we found a statistically significant association between haplogroup JT and MDS (OR = 0.58, 95% CI 0.36, 0.92, P = 0.02). No statistically significant heterogeneity was observed in subgroup analyses. In this population-based study of MDS, we observed an association between mtDNA haplogroup JT and risk of MDS. While previously published studies provide biological plausibility for the observed association, further studies of the relationship between mtDNA variation and MDS are warranted in larger sample sizes. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jenny N Poynter
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Michaela Richardson
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Erica Langer
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Anthony J Hooten
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Michelle Roesler
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Betsy Hirsch
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Phuong L Nguyen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Adina Cioc
- VA Medical Center, Minneapolis, Minnesota
| | - Erica Warlick
- Blood and Marrow Transplant Program, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, Minnesota
| | - Julie A Ross
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
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12
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Mondolfi AP, Singh RR. Genotyping of Frequent Mutations in Solid Tumors by PCR-Based Single-Base Extension and MassARRAY Analysis. Methods Mol Biol 2016; 1392:83-101. [PMID: 26843049 DOI: 10.1007/978-1-4939-3360-0_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Over the last decade, cancer genome sequencing has revealed in detail the genomic landscapes of an increasing number of common solid human tumors. This has greatly impacted the clinical care of cancer patients based on the fact that many of these tumors exhibit activating mutations in driver genes that are prone to target therapy, largely impacting cancer management strategies. Genomic heterogeneity of tumors is becoming an increasingly recognized phenomenon relevant to genome-based medicine. Because a large number tumors may display several mutations at the same time, multiplexing has become the preferred approach to reveal the mutational landscape in patient samples and to better design a targeted approach to their illness.
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Affiliation(s)
- Alberto Paniz Mondolfi
- Microbiology Laboratory, Department of Laboratory Medicine,Yale New Haven Hospital, Yale University School of Medicine, New Haven, CT, USA.
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 8515 Fannin Street, Houston, TX, 77054, USA.
| | - Rajesh R Singh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 8515 Fannin Street, Houston, TX, 77054, USA.
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13
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Svidnicki MCCM, Silva-Costa SM, Ramos PZ, dos Santos NZP, Martins FTA, Castilho AM, Sartorato EL. Screening of genetic alterations related to non-syndromic hearing loss using MassARRAY iPLEX® technology. BMC MEDICAL GENETICS 2015; 16:85. [PMID: 26399936 PMCID: PMC4581412 DOI: 10.1186/s12881-015-0232-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 09/15/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Recent advances in molecular genetics have enabled to determine the genetic causes of non-syndromic hearing loss, and more than 100 genes have been related to the phenotype. Due to this extraordinary genetic heterogeneity, a large percentage of patients remain without any molecular diagnosis. This condition imply the need for new methodological strategies in order to detect a greater number of mutations in multiple genes. In this work, we optimized and tested a panel of 86 mutations in 17 different genes screened using a high-throughput genotyping technology to determine the molecular etiology of hearing loss. METHODS The technology used in this work was the MassARRAY iPLEX® platform. This technology uses silicon chips and DNA amplification products for accurate genotyping by mass spectrometry of previous reported mutations. The generated results were validated using conventional techniques, as direct sequencing, multiplex PCR and RFLP-PCR. RESULTS An initial genotyping of control subjects, showed failures in 20 % of the selected alterations. To optimize these results, the failed tests were re-designed and new primers were synthesized. Then, the specificity and sensitivity of the panel demonstrated values above 97 %. Additionally, a group of 180 individuals with NSHL without a molecular diagnosis was screened to test the diagnostic value of our panel, and mutations were identified in 30 % of the cases. In 20 % of the individuals, it was possible to explain the etiology of the HL. Mutations in GJB2 gene were the most prevalent, followed by other mutations in in SLC26A4, CDH23, MT-RNR1, MYO15A, and OTOF genes. CONCLUSIONS The MassARRAY technology has the potential for high-throughput identification of genetic variations. However, we demonstrated that optimization is required to increase the genotyping success and accuracy. The developed panel proved to be efficient and cost-effective, being suitable for applications involving the molecular diagnosis of hearing loss.
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Affiliation(s)
- Maria Carolina Costa Melo Svidnicki
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Sueli Matilde Silva-Costa
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Priscila Zonzini Ramos
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Nathalia Zocal Pereira dos Santos
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Fábio Tadeu Arrojo Martins
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Arthur Menino Castilho
- ENT Department, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Edi Lúcia Sartorato
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
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14
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Monnahan PJ, Colicchio J, Kelly JK. A genomic selection component analysis characterizes migration-selection balance. Evolution 2015; 69:1713-27. [PMID: 26082096 DOI: 10.1111/evo.12698] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/22/2015] [Indexed: 12/16/2022]
Abstract
The genetic differentiation of populations in response to local selection pressures has long been studied by evolutionary biologists, but key details about the process remain obscure. How rapidly can local adaptation evolve, how extensive is the process across the genome, and how strong are the opposing forces of natural selection and gene flow? Here, we combine direct measurement of survival and reproduction with whole-genome genotyping of a plant species (Mimulus guttatus) that has recently invaded a novel habitat (the Quarry population). We renovate the classic selection component method to accommodate genomic data and observe selection at SNPs throughout the genome. SNPs showing viability selection in Quarry exhibit elevated divergence from neighboring populations relative to neutral SNPs. We also find that nonsignificant SNPs exhibit a subtle, but still significant, change in allele frequency toward neighboring populations, a predicted effect of gene flow. Given that the Quarry population is most probably only 30-40 generations old, the alleles conferring local advantage are almost certainly older than the population itself. Thus, local adaptation owes to the recruitment of standing genetic variation.
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Affiliation(s)
- Patrick J Monnahan
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045
| | - Jack Colicchio
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045
| | - John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045.
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15
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ZHENG ML, QI XM, TONG H, LIU YL, ZOU BJ, SONG QX, ZHOU GH. Detection of Single Nucleotide Polymorphism Genotyping by Real-time Polymerase Chain Reaction Coupled with High Specific Invader Assay in Single Tube. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1016/s1872-2040(15)60838-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Cheng J, Ondracek RP, Mehedint DC, Kasza KA, Xu B, Gill S, Azabdaftari G, Yao S, Morrison CD, Mohler JL, Marshall JR. Association of fatty-acid synthase polymorphisms and expression with outcomes after radical prostatectomy. Prostate Cancer Prostatic Dis 2015; 18:182-9. [PMID: 25868764 DOI: 10.1038/pcan.2015.11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/24/2015] [Accepted: 02/28/2015] [Indexed: 11/09/2022]
Abstract
BACKGROUND Fatty-acid synthase (FASN), selectively overexpressed in prostate cancer (PCa) cells, has been described as linked to the aggressiveness of PCa. Constitutional genetic variation of the FASN gene and the expression levels of FASN protein in cancer cells could thus be expected to predict outcome after radical prostatectomy (RP). This study evaluates the associations of malignant tissue status, neoadjuvant androgen deprivation therapy (NADT) and single-nucleotide polymorphisms (SNPs) of FASN with FASN protein expression in prostate tissue. The study then examines the associations of FASN SNPs and gene expression with three measures of post-prostatectomy outcome. METHODS Seven tagging FASN SNPs were genotyped in 659 European American men who underwent RP at Roswell Park Cancer Institute between 1993 and 2005. FASN protein expression was assessed using immunohistochemistry. The patients were followed for an average of 6.9 years (range: 0.1-20.6 years). Outcome was assessed using three end points: biochemical failure, treatment failure and development of distant metastatic PCa. Cox proportional hazards analyses were used to evaluate the associations of the tagging SNPs and FASN expression with these end points. Bivariate associations with outcomes were considered; the associations also were controlled for known aggressiveness indicators. RESULTS Overall, no SNPs were associated with any known aggressiveness indicators. FASN staining intensity was stronger in malignant than in benign tissue, and NADT was associated with decreased FASN staining in both benign and malignant tissue. The relationships of FASN SNPs and staining intensity with outcome were less clear. One SNP, rs4246444, showed a weak association with outcome. FASN staining intensity also showed a weak and seemingly contradictory relationship with outcome. CONCLUSIONS Additional study with longer follow-up and populations that include more metastatic patients is warranted.
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Affiliation(s)
- J Cheng
- 1] Department of Cancer Prevention and Population Science, Roswell Park Cancer Institute, Buffalo, NY, USA [2] Department of Pathology, University at Buffalo, Buffalo, NY, USA
| | - R P Ondracek
- Department of Cancer Prevention and Population Science, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - D C Mehedint
- Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - K A Kasza
- Department of Cancer Prevention and Population Science, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - B Xu
- Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - S Gill
- Department of Pathology, University at Buffalo, Buffalo, NY, USA
| | - G Azabdaftari
- Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - S Yao
- Department of Cancer Prevention and Population Science, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - C D Morrison
- Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - J L Mohler
- Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - J R Marshall
- Department of Cancer Prevention and Population Science, Roswell Park Cancer Institute, Buffalo, NY, USA
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17
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The study to understand the genetics of the acute response to metformin and glipizide in humans (SUGAR-MGH): design of a pharmacogenetic resource for type 2 diabetes. PLoS One 2015; 10:e0121553. [PMID: 25812009 PMCID: PMC4374872 DOI: 10.1371/journal.pone.0121553] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 02/13/2015] [Indexed: 12/30/2022] Open
Abstract
Objective Genome-wide association studies have uncovered a large number of genetic variants associated with type 2 diabetes or related phenotypes. In many cases the causal gene or polymorphism has not been identified, and its impact on response to anti-hyperglycemic medications is unknown. The Study to Understand the Genetics of the Acute Response to Metformin and Glipizide in Humans (SUGAR-MGH, NCT01762046) is a novel resource of genetic and biochemical data following glipizide and metformin administration. We describe recruitment, enrollment, and phenotyping procedures and preliminary results for the first 668 of our planned 1,000 participants enriched for individuals at risk of requiring anti-diabetic therapy in the future. Methods All individuals are challenged with 5 mg glipizide × 1; twice daily 500 mg metformin × 2 days; and 75-g oral glucose tolerance test following metformin. Genetic variants associated with glycemic traits and blood glucose, insulin, and other hormones at baseline and following each intervention are measured. Results Approximately 50% of the cohort is female and 30% belong to an ethnic minority group. Following glipizide administration, peak insulin occurred at 60 minutes and trough glucose at 120 minutes. Thirty percent of participants experienced non-severe symptomatic hypoglycemia and required rescue with oral glucose. Following metformin administration, fasting glucose and insulin were reduced. Common genetic variants were associated with fasting glucose levels. Conclusions SUGAR-MGH represents a viable pharmacogenetic resource which, when completed, will serve to characterize genetic influences on pharmacological perturbations, and help establish the functional relevance of newly discovered genetic loci to therapy of type 2 diabetes. Trial Registration ClinicalTrials.gov NCT01762046
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18
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Unique features of mutations revealed by sequentially reprogrammed induced pluripotent stem cells. Nat Commun 2015; 6:6318. [PMID: 25692725 DOI: 10.1038/ncomms7318] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 01/16/2015] [Indexed: 01/06/2023] Open
Abstract
Although viable mice can be generated from induced pluripotent stem cells (iPSCs), the impact of accumulated mutations on the developmental potential of the resulting iPSCs remains to be determined. Here, we demonstrate that all-iPSC mice generated through tetraploid blastocysts complementation can tolerate the accumulation of somatic mutations for up to six generations using a Tet-on inducible reprogramming system. But, the viability of the all-iPS mice decreased with increasing generations. A whole-genome sequencing survey revealed that thousands of single-nucleotide variations (SNVs), including 44 non-synonymous ones, accumulated throughout the sequential reprogramming process. Subsequent analysis provides evidence that these accumulated SNVs account for the gradual reduction in viability of the resultant all-iPSC mice. Unexpectedly, our present reprogramming system revealed that pluripotent stem cells are heterogeneous in terms of possessing a set of copy-number alterations (CNAs). These CNAs are unique for pluripotent cells and subsequently disappear in the differentiating progenies.
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19
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Functional significance of single nucleotide polymorphisms in the lactase gene in diverse US patients and evidence for a novel lactase persistence allele at -13909 in those of European ancestry. J Pediatr Gastroenterol Nutr 2015; 60:182-91. [PMID: 25625576 PMCID: PMC4308731 DOI: 10.1097/mpg.0000000000000595] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVES Recent data from mainly homogeneous European and African populations implicate a 140-bp region 5' to the transcriptional start site of LCT (the lactase gene) as a regulatory site for lactase persistence and nonpersistence. Because there are no studies of US nonhomogeneous populations, we performed genotype/phenotype analysis of the -13910 and -22018 LCT single nucleotide polymorphisms (SNPs) in New England children, mostly of European ancestry. METHODS Duodenal biopsies were processed for disaccharidase activities, RNA quantification by reverse transcription polymerase chain reaction (RT-PCR), allelic expression ratios by PCR, and genotyping and SNP analysis. Results were compared with clinical information. RESULTS Lactase activity and mRNA levels, and sucrase-to-lactase ratios of enzyme activity and mRNA, showed robust correlations with genotype. None of the other LCT SNPs showed as strong a correlation with enzyme or mRNA levels as did -13910. Data were consistent, with the -13910 being the causal sequence variant instead of -22018. Four individuals heterozygous for -13910T/C had allelic expression patterns similar to individuals with -13910C/C genotypes; of these, 2 showed equal LCT expression from the 2 alleles and a novel variant (-13909C>A) associated with lactase persistence. CONCLUSIONS The identification of -13910C/C genotype is likely to predict lactase nonpersistence, consistent with prior published studies. A -13910T/T genotype will frequently, but not perfectly, predict lactase persistence in this mixed European-ancestry population; a -13910T/C genotype will not predict the phenotype. A long, rare haplotype in 2 individuals with -13910T/C genotype but equal allele-specific expression contains a novel lactase persistence allele present at -13909.
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20
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Cai W, Yin L, Yang F, Zhang L, Cheng J. Association between Hcy levels and the CBS844ins68 and MTHFR C677T polymorphisms with essential hypertension. Biomed Rep 2014; 2:861-868. [PMID: 25279160 DOI: 10.3892/br.2014.357] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 08/12/2014] [Indexed: 12/27/2022] Open
Abstract
The aim of the present study was to investigate the association between the homocysteine (Hcy) levels and polymorphisms of the CBS844ins68 and MTHFR C677T genes in essential hypertension (EH). The effects of the MTHFR C677T and CBS844ins68 haploid genotypes and the combined genotypes on EH and levels of Hcy were further explored. The polymorphisms of CBS844ins68 and MTHFR C677T genes in 200 EH and 200 normal tensive (NT) patients were detected using polymerase chain reaction-restriction fragment length polymorphism and analysis of the distribution of genotypes. An automated biochemical analyzer was used to measure the plasma Hcy levels and the clinical biochemistry data. The plasma Hcy levels in EH were significantly higher than those of the NT group (P<0.05). There were no significant differences (P>0.05) between males and females. Two genotypes, deletion/deletion (DD) and deletion/insertion (DI), of the CBS844ins68 polymorphism were found in two groups with no clear differences in two genotypes and allele frequency distribution (P>0.05). There were significant differences in the three genotype frequencies (χ2=6.658, χ2=4.410, P<0.05) for MTHFR C677T locus genotypes CC, CT and TT. The Hcy levels in genotypes DD and DI had no significant differences (P>0.05) and the CT and TT types were significantly higher compared to the CC genotype (P<0.05). The CC/DD combined genotype in the two groups was significantly different (P<0.05), and the odds ratio (OR), 0.569 showed that the CC/DD genotype may be a protective factor of hypertension. In the two groups, the Hcy levels for combined genotypes CC/DD, CT/DD, TT/DD and TT/DI were significantly different (P<0.05). The SHEsis software analysis linkage disequilibrium coefficient=0.216, indicates that there is probably a weak linkage for MTHFR C677T and CBS844ins68. Haplotype analysis suggested that the C-D haplotype was negatively correlated with EH (OR, 0.727) and that there was a positive correlation between T-D haplotype and EH (OR, 1.376). MTHFR C677T and CBS844ins68 polymorphisms were present in the populations studied and the CBS844ins68 homozygous mutation was not present. Therefore, there is a correlation between the polymorphisms of the MTHFR C677T gene and EH, and allele T may be one of the predisposing factors. MTHFR C677T and CBS844ins68 may exist with a certain linkage and the T-D haplotype may be a risk factor for EH.
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Affiliation(s)
- Weijuan Cai
- Department of Clinical Laboratory, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, P.R. China
| | - Liang Yin
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, P.R. China
| | - Fang Yang
- Department of Clinical Laboratory, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, P.R. China
| | - Lei Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, P.R. China
| | - Jiang Cheng
- Department of Clinical Laboratory, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, P.R. China
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KLIMENTIDIS YC, LEMAS DJ, WIENER HH, O’BRIEN DM, HAVEL PJ, STANHOPE KL, HOPKINS SE, TIWARI HK, BOYER BB. CDKAL1 and HHEX are associated with type 2 diabetes-related traits among Yup'ik people. J Diabetes 2014; 6:251-9. [PMID: 24112421 PMCID: PMC3964139 DOI: 10.1111/1753-0407.12093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with type 2 diabetes (T2D), mainly among individuals of European ancestry. In the present study, we examined the frequency of these SNPs and their association with T2D-related traits in an Alaska Native study population with a historically low prevalence of T2D. We also investigated whether dietary characteristics that may protect against T2D, such as n-3 polyunsaturated fatty acid (PUFA) intake, modify these associations. METHODS In 1144 Yup'ik people, we examined 17 SNPs repeatedly identified in GWAS for individual and cumulative associations with T2D-related traits. Cumulative associations were evaluated using a genetic risk score (GRS) calculated by summing risk alleles. Associations were tested for interactions with sex, body mass index (BMI), and n-3 PUFA intake. RESULTS The rs7754840 SNP in CDKAL1 is significantly associated with HbA1c (P = 0.00091). The rs5015480 SNP near HHEX is significantly associated (in opposite direction to that in Europeans) with a combined fasting glucose (FG) and HbA1c measure (P = 0.00046) and with homeostatic model assessment of β-cell function (HOMA-B; P = 0.0014). The GRS is significantly associated with FG and combined FG and HbA1c only when the HHEX SNP is dropped from the GRS. Associations are not modified by BMI or n-3 PUFA intake. CONCLUSION Our results highlight the potential importance of CDKAL1 and HHEX in glucose homeostasis in this Alaska Native population with a low prevalence of T2D, and suggest that these loci should be examined in greater detail in this population.
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Affiliation(s)
- Yann C. KLIMENTIDIS
- Mel and Enid Zuckerman College of Public Health, Division of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, 85724
| | - Dominick J. LEMAS
- Department of Pediatrics, Section of Neonatology, University of Colorado Denver, Aurora, CO 80045
| | - Howard H. WIENER
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Diane M. O’BRIEN
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775
| | - Peter J. HAVEL
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616
- Department of Nutrition, University of California, Davis, Davis, CA 95616
| | - Kimber L. STANHOPE
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616
- Department of Nutrition, University of California, Davis, Davis, CA 95616
| | - Scarlett E. HOPKINS
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775
| | - Hemant K. TIWARI
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Bert B. BOYER
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775
- Corresponding author: Yann C. Klimentidis, PhD, Mel and Enid Zuckerman College of Public Health, Division of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, 85724. Phone: 520-621-1047,
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Abstract
Over the last few years, several initiatives have described efforts to combine previously invented techniques in molecular biology with parallel detection principles to sequence or genotype DNA signatures. The Infinium system from Illumina and the Affymetrix GeneChips are two systems suitable for whole-genome scoring of variable positions. However, directed candidate-gene approaches are more cost effective and several academic groups and the private sector provide techniques with moderate typing throughput combined with large sample capacity suiting these needs. Recently, whole-genome sequencing platforms based on the sequencing-by-synthesis principle were presented by 454 Life Sciences and Solexa, showing great potential as alternatives to conventional genotyping approaches. In addition to these sequencing initiatives, many efforts are pursuing novel ideas to facilitate fast and cost-effective whole genome sequencing, such as ligation-based sequencing. Reliable methods for routine re-sequencing of human genomes as a tool for personalized medicine, however, remain to be developed.
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Affiliation(s)
- Max Käller
- AlbaNova University Center, School of Biotechnology, Department of Gene Technology, Royal Institute of Technology, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden.
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23
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Abstract
High-throughput DNA sequencing development for mutation screening and identification is essential to realize the goal of pharmacogenomics and personalized medicine, which will lead to a new era in clinical medicine and healthcare. Molecular engineering approaches to modify the building blocks of DNA by introducing functional groups for purification and detection has led to the development of high-throughput genetic analysis technologies. This review is focused on the following two DNA sequencing approaches. The first approach is based on the use of molecular affinity and mass spectrometry to perform quick and highly accurate mutation screening, heterozygote identification and insertion/deletion detection. The second approach is based on a sequencing-by-synthesis platform that has the potential for generating DNA sequencing data in a massive, parallel manner. The basic principles, fundamental challenges and methods of implementation of these exciting new technologies will be discussed.
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Affiliation(s)
- Xiaopeng Bai
- Columbia University, Department of Chemical Engineering, NY 10027, USA.
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Agunbiade TA, Sun W, Coates BS, Djouaka R, Tamò M, Ba MN, Binso-Dabire C, Baoua I, Olds BP, Pittendrigh BR. Development of reference transcriptomes for the major field insect pests of cowpea: a toolbox for insect pest management approaches in west Africa. PLoS One 2013; 8:e79929. [PMID: 24278221 PMCID: PMC3838393 DOI: 10.1371/journal.pone.0079929] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 09/27/2013] [Indexed: 11/19/2022] Open
Abstract
Cowpea is a widely cultivated and major nutritional source of protein for many people that live in West Africa. Annual yields and longevity of grain storage is greatly reduced by feeding damage caused by a complex of insect pests that include the pod sucking bugs, Anoplocnemis curvipes Fabricius (Hemiptera: Coreidae) and Clavigralla tomentosicollis Stål (Hemiptera: Coreidae); as well as phloem-feeding cowpea aphids, Aphis craccivora Koch (Hemiptera: Aphididae) and flower thrips, Megalurothrips sjostedti Trybom (Thysanoptera: Thripidae). Efforts to control these pests remain a challenge and there is a need to understand the structure and movement of these pest populations in order to facilitate the development of integrated pest management strategies (IPM). Molecular tools have the potential to help facilitate a better understanding of pest populations. Towards this goal, we used 454 pyrosequencing technology to generate 319,126, 176,262, 320,722 and 227,882 raw reads from A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti, respectively. The reads were de novo assembled into 11,687, 7,647, 10,652 and 7,348 transcripts for A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti, respectively. Functional annotation of the resulting transcripts identified genes putatively involved in insecticide resistance, pathogen defense and immunity. Additionally, sequences that matched the primary aphid endosymbiont, Buchnera aphidicola, were identified among A. craccivora transcripts. Furthermore, 742, 97, 607 and 180 single nucleotide polymorphisms (SNPs) were respectively predicted among A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti transcripts, and will likely be valuable tools for future molecular genetic marker development. These results demonstrate that Roche 454-based transcriptome sequencing could be useful for the development of genomic resources for cowpea pest insects in West Africa.
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Affiliation(s)
- Tolulope A. Agunbiade
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
| | - Weilin Sun
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Brad S. Coates
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | | | - Manuele Tamò
- International Institute of Tropical Agriculture, Cotonou, Benin
| | - Malick N. Ba
- Institut de l’Environnement et de Recherches Agricoles, Ouagadougou, Burkina Faso
| | | | - Ibrahim Baoua
- Institut National de la Recherche Agronomique du Niger, Maradi, Niger
| | - Brett P. Olds
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Barry R. Pittendrigh
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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Cagle PT, Allen TC, Olsen RJ. Lung Cancer Biomarkers: Present Status and Future Developments. Arch Pathol Lab Med 2013; 137:1191-8. [DOI: 10.5858/arpa.2013-0319-cr] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The publication of the “Molecular Testing Guideline for Selection of Lung Cancer Patients for EGFR and ALK Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology” has now provided a guideline for biomarker testing for first-generation lung cancer tyrosine kinase inhibitors. Biomarker testing has forever altered the role of pathologists in the management of patients with lung cancer. Current, unresolved issues in the precision medicine of lung cancer will be addressed by the development of new biomarker tests, new drugs, and new test technologies and by improvement in the cost to benefit ratio of biomarker testing.
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Affiliation(s)
- Philip T. Cagle
- From the Department of Pathology and Genomic Medicine, The Methodist Hospital, Houston, Texas, and the Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York (Drs Cagle and Olsen); and
- the Department of Pathology, The University of Texas Health Science Center at Tyler (Dr Allen)
| | - Timothy Craig Allen
- From the Department of Pathology and Genomic Medicine, The Methodist Hospital, Houston, Texas, and the Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York (Drs Cagle and Olsen); and
- the Department of Pathology, The University of Texas Health Science Center at Tyler (Dr Allen)
| | - Randall J. Olsen
- From the Department of Pathology and Genomic Medicine, The Methodist Hospital, Houston, Texas, and the Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York (Drs Cagle and Olsen); and
- the Department of Pathology, The University of Texas Health Science Center at Tyler (Dr Allen)
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Nishida N, Tokunaga K, Mizokami M. Genome-Wide Association Study Reveals Host Genetic Factors for Liver Diseases. J Clin Transl Hepatol 2013; 1:45-50. [PMID: 26357606 PMCID: PMC4521269 DOI: 10.14218/jcth.2013.010xx] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/13/2013] [Accepted: 05/22/2013] [Indexed: 12/11/2022] Open
Abstract
A number of disease-associated genetic markers for common liver diseases have been identified using genome-wide association studies (GWASs). The GWAS strategy is based on genome-wide single-nucleotide polymorphism typing technologies, which are now commercially available, accompanied by statistical methods to identify host genetic factors that are associated with target diseases or complex genetic traits. One of the most striking features of the GWAS strategy is the ability to identify unexpected disease-associated genetic markers across the entire human genome. Here, we describe the technological aspects of the GWAS strategy with examples from actual GWAS reports related to hepatitis research, including drug response for patients with chronic hepatitis C, susceptibility to primary biliary cirrhosis, and hepatitis-B-related hepatocellular carcinoma.
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Affiliation(s)
- Nao Nishida
- The Research Center for Hepatitis & Immunology, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
- Department of Human Genetics, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masashi Mizokami
- The Research Center for Hepatitis & Immunology, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
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Mitjans M, Serretti A, Fabbri C, Gastó C, Catalán R, Fañanás L, Arias B. Screening genetic variability at the CNR1 gene in both major depression etiology and clinical response to citalopram treatment. Psychopharmacology (Berl) 2013; 227:509-19. [PMID: 23407780 DOI: 10.1007/s00213-013-2995-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 01/08/2013] [Indexed: 11/30/2022]
Abstract
RATIONALE The endocannabinoid system has been implicated in the pathogenesis of major depression (MD) as well as in the mediation of antidepressant drug effects. OBJECTIVES To analyze CNR1 gene variants in MD and clinical response to citalopram (selective serotonin re-uptake inhibitors [SSRI]). METHODS The role of CNR1 gene (rs806368, rs1049353, rs806371, rs806377 and rs1535255) was investigated in 319 outpatients with MD and 150 healthy individuals. A subsample of 155 depressive patients were treated with citalopram and evaluated for response (fourth week) and remission (12th week) by the 21-item Hamilton Depression Rating Scale (HDRS). RESULTS We observed a higher frequency of rs806371 G carriers in MD patients with both presence of melancholia (p = 0.018) and psychotic symptoms (p = 0.007) than in controls. Haplotype frequency distributions between MD sample and controls showed a significant difference for Block 1 (rs806368-rs1049353-rs806371) (p = 0.008). This haplotype finding was consistent when we compared controls with MD subsample stratified by melancholia (p = 0.0009) and psychotic symptoms (p = 0.014). The TT homozygous of the rs806368 and rs806371 presented more risk of no Remission than the C carriers (p = 0.008 and 0.012, respectively). Haplotype frequency distributions according to Remission status showed a significant difference for Block 1 (p = 0.032). Also, we observed significant effect of time-sex-genotype interaction for the rs806368, showing that the C carrier men presented a better response to antidepressant treatment throughout the follow-up than TT homozygous men and women group (p = 0.026). CONCLUSIONS These results suggest an effect of CNR1 gene in the etiology of MD and clinical response to citalopram.
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Affiliation(s)
- Marina Mitjans
- Unitat d'Antropologia, Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona/Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal, 643 2on pis, 08028 Barcelona, Spain
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Lee ST, Gong SP, Yum KE, Lee EJ, Lee CH, Choi JH, Kim DY, Han H, Kim KS, Hysolli E, Ahn JY, Park IH, Han JY, Jeong JW, Lim JM. Transformation of somatic cells into stem cell-like cells under a stromal niche. FASEB J 2013; 27:2644-56. [PMID: 23580613 DOI: 10.1096/fj.12-223065] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To study the genomic plasticity of somatic cells without ectopic genetic manipulation, we cultured mouse fibroblasts with ovarian cells, embryonic fibroblasts of different strains, and parthenogenetic embryonic stem cells (ESCs). Of 41 trials, cell aggregation resembling nascent ESC colony from inner cell mass was detected in 9 cases (22%), and 6 cases (67%) yielded fibroblast-derived colonies with ESC morphology. Cells used in coculture provided the critical (P=0.0061) inducing factor for the aggregation. These colony-forming fibroblasts (CFFs) showed similar characteristics to those in ESCs and induced pluripotent stem cells (iPSCs), including pluripotency gene expression, in vitro differentiation, and teratoma formation. Furthermore, CFFs produced somatic chimera, although none showed germline chimerism. CFFs had a tetraploid-like karyotype, and their imprinting patterns differed from parthenogenetic ESCs, thereby confirming their nongermline transmissibility. We observed dysregulation of cell cycle-related proteins, as well as both homologous and heterologous recombination of genomic single-nucleotide polymorphisms in CFFs. Our observations provide information on somatic cell plasticity, resulting in stemness or tumorigenesis, regardless of colony-forming cell progenitors in the fibroblast population. The plasticity of somatic genomes under environmental influences, as well as acquisition of pluripotency by cell fusion, is also implicated.
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Affiliation(s)
- Seung Tae Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
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Lemas DJ, Klimentidis YC, Wiener HH, O'Brien DM, Hopkins SE, Allison DB, Fernandez JR, Tiwari HK, Boyer BB. Obesity polymorphisms identified in genome-wide association studies interact with n-3 polyunsaturated fatty acid intake and modify the genetic association with adiposity phenotypes in Yup'ik people. GENES AND NUTRITION 2013; 8:495-505. [PMID: 23526194 DOI: 10.1007/s12263-013-0340-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/26/2013] [Indexed: 11/26/2022]
Abstract
n-3 Polyunsaturated fatty acids (n-3 PUFAs) have anti-obesity effects that may modulate risk of obesity, in part, through interactions with genetic factors. Genome-wide association studies (GWAS) have identified genetic variants associated with body mass index (BMI); however, the extent to which these variants influence adiposity through interactions with n-3 PUFAs remains unknown. We evaluated 10 highly replicated obesity GWAS single nucleotide polymorphisms (SNPs) for individual and cumulative associations with adiposity phenotypes in a cross-sectional sample of Yup'ik people (n = 1,073) and evaluated whether genetic associations with obesity were modulated by n-3 PUFA intake. A genetic risk score (GRS) was calculated by adding the BMI-increasing alleles across all 10 SNPs. Dietary intake of n-3 PUFAs was estimated using nitrogen stable isotope ratio (δ(15)N) of red blood cells, and genotype-phenotype analyses were tested in linear models accounting for familial correlations. GRS was positively associated with BMI (p = 0.012), PBF (p = 0.022), ThC (p = 0.025), and waist circumference (p = 0.038). The variance in adiposity phenotypes explained by the GRS included BMI (0.7 %), PBF (0.3 %), ThC (0.7 %), and WC (0.5 %). GRS interactions with n-3 PUFAs modified the association with adiposity and accounted for more than twice the phenotypic variation (~1-2 %), relative to GRS associations alone. Obesity GWAS SNPs contribute to adiposity in this study population of Yup'ik people and interactions with n-3 PUFA intake potentiated the risk of fat accumulation among individuals with high obesity GRS. These data suggest the anti-obesity effects of n-3 PUFAs among Yup'ik people may, in part, be dependent upon an individual's genetic predisposition to obesity.
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Affiliation(s)
- Dominick J Lemas
- Institute of Arctic Biology, Center for Alaska Native Health Research, University of Alaska Fairbanks, 311 Irving I Building, PO Box 757000, Fairbanks, AK, 99775-7000, USA,
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30
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Chitta KS, Paulus A, Ailawadhi S, Foster BA, Moser MT, Starostik P, Masood A, Sher T, Miller KC, Iancu DM, Conroy J, Nowak NJ, Sait SN, Personett DA, Coleman M, Furman RR, Martin P, Ansell SM, Lee K, Chanan-Khan AA. Development and characterization of a novel human Waldenström macroglobulinemia cell line: RPCI-WM1, Roswell Park Cancer Institute - Waldenström Macroglobulinemia 1. Leuk Lymphoma 2013; 54:387-96. [PMID: 22812491 PMCID: PMC4406272 DOI: 10.3109/10428194.2012.713481] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Understanding the biology of Waldenström macroglobulinemia is hindered by a lack of preclinical models. We report a novel cell line, RPCI-WM1, from a patient treated for WM. The cell line secretes human immunoglobulin M (h-IgM) with κ-light chain restriction identical to the primary tumor. The cell line has a modal chromosomal number of 46 and harbors chromosomal changes such as deletion of 6q21, monoallelic deletion of 9p21 (CDKN2A), 13q14 (RB1) and 18q21 (BCL-2), with a consistent amplification of 14q32 (immunoglobulin heavy chain; IgH) identical to its founding tumor sample. The clonal relationship is confirmed by identical CDR3 length and single nucleotide polymorphisms as well as a matching IgH sequence of the cell line and founding tumor. Both also harbor a heterozygous, non-synonymous mutation at amino acid 265 in the MYD88 gene (L265P). The cell line expresses most of the cell surface markers present on the parent cells. Overall, RPCI-WM1 represents a valuable model to study Waldenström macroglobulinemia.
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Affiliation(s)
- Kasyapa S Chitta
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL 32224, USA.
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Kilpinen H, Barrett JC. How next-generation sequencing is transforming complex disease genetics. Trends Genet 2013; 29:23-30. [DOI: 10.1016/j.tig.2012.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 09/25/2012] [Accepted: 10/01/2012] [Indexed: 02/02/2023]
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Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon. Comp Funct Genomics 2012; 2012:628204. [PMID: 23326209 PMCID: PMC3544263 DOI: 10.1155/2012/628204] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/29/2012] [Accepted: 11/09/2012] [Indexed: 11/28/2022] Open
Abstract
Domesticated animals provide a unique opportunity to identify genomic targets of artificial selection to the captive environment. Here, we screened three independent domesticated/captive Atlantic salmon (Salmo salar) strains and their wild progenitor populations in an effort to detect potential signals of domestication selection by typing of 261 SNPs and 70 microsatellite loci. By combining information from four different neutrality tests, in total ten genomic regions showed signs of directional selection based on multiple sources of evidence. Most of the identified candidate regions were rather small ranging from zero to a few centimorgans (cM) in the female Atlantic salmon linkage map. We also evaluated how adaptation from standing variation affects adjacent SNP and microsatellite variation along the chromosomes and, by using forward simulations with strong selection, we were able to generate genetic differentiation patterns comparable to the observed data. This study highlights the significance of standing genetic variation during the early stages of adaptation and represents a useful step towards identifying functional variants involved in domestication of Atlantic salmon.
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Civit L, Fragoso A, O’Sullivan CK. Evaluation of techniques for generation of single-stranded DNA for quantitative detection. Anal Biochem 2012; 431:132-8. [DOI: 10.1016/j.ab.2012.09.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 08/31/2012] [Accepted: 09/01/2012] [Indexed: 11/30/2022]
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Robinson N, Sahoo PK, Baranski M, Das Mahapatra K, Saha JN, Das S, Mishra Y, Das P, Barman HK, Eknath AE. Expressed sequences and polymorphisms in rohu carp (Labeo rohita, Hamilton) revealed by mRNA-seq. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:620-633. [PMID: 22298294 DOI: 10.1007/s10126-012-9433-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 12/23/2011] [Indexed: 05/31/2023]
Abstract
Expressed genes and polymorphisms were identified in lines of rohu Labeo rohita selected for resistance or susceptibility to Aeromonas hydrophila, an important bacterial pathogen causing aeromoniasis. All animals were grown in a common environment and RNA from ten individuals from each line pooled for Illumina mRNA-seq. De novo transcriptome assembly produced 137,629 contigs with 40× average coverage.Forty-four percent of the assembled sequences were annotated with gene names and ontology terms. Of these, 3,419 were assigned biological process terms related to "stress response" and 1,939 "immune system". Twenty-six contigs containing 38 single nucleotide polymorphisms (SNPs) were found to map to the Cyprinus carpio mitochondrial genome and over 26,000 putative SNPs and 1,700 microsatellite loci were detected. Seventeen percent of the 100 transcripts with coverage data most indicative of higher-fold expression(>5.6 fold) in the resistant line pool showed homology to major histocompatibility (MH), heat shock proteins (HSP)30, 70 and 90, glycoproteins or serum lectin genes with putative functions affecting immune response. Forty-one percent of these 100 transcripts showed no or low homology to known genes. Of the SNPs identified, 96 showing the highest allele frequency differences between susceptible and resistant line fish included transcripts with homology to MH class I and galactoside-binding soluble lectin, also with putative functions affecting innate and acquired immune response. A comprehensive sequence resource for L. rohita, including annotated microsatellites and SNPs from a mixture of A. hydrophila-susceptible and -resistant individuals, was created for subsequent experiments aiming to identify genes associated with A. hydrophila resistance.
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Florez JC, Jablonski KA, McAteer JB, Franks PW, Mason CC, Mather K, Horton E, Goldberg R, Dabelea D, Kahn SE, Arakaki RF, Shuldiner AR, Knowler WC. Effects of genetic variants previously associated with fasting glucose and insulin in the Diabetes Prevention Program. PLoS One 2012; 7:e44424. [PMID: 22984506 PMCID: PMC3439414 DOI: 10.1371/journal.pone.0044424] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 08/03/2012] [Indexed: 11/19/2022] Open
Abstract
Common genetic variants have been recently associated with fasting glucose and insulin levels in white populations. Whether these associations replicate in pre-diabetes is not known. We extended these findings to the Diabetes Prevention Program, a clinical trial in which participants at high risk for diabetes were randomized to placebo, lifestyle modification or metformin for diabetes prevention. We genotyped previously reported polymorphisms (or their proxies) in/near G6PC2, MTNR1B, GCK, DGKB, GCKR, ADCY5, MADD, CRY2, ADRA2A, FADS1, PROX1, SLC2A2, GLIS3, C2CD4B, IGF1, and IRS1 in 3,548 Diabetes Prevention Program participants. We analyzed variants for association with baseline glycemic traits, incident diabetes and their interaction with response to metformin or lifestyle intervention. We replicated associations with fasting glucose at MTNR1B (P<0.001), G6PC2 (P = 0.002) and GCKR (P = 0.001). We noted impaired β-cell function in carriers of glucose-raising alleles at MTNR1B (P<0.001), and an increase in the insulinogenic index for the glucose-raising allele at G6PC2 (P<0.001). The association of MTNR1B with fasting glucose and impaired β-cell function persisted at 1 year despite adjustment for the baseline trait, indicating a sustained deleterious effect at this locus. We also replicated the association of MADD with fasting proinsulin levels (P<0.001). We detected no significant impact of these variants on diabetes incidence or interaction with preventive interventions. The association of several polymorphisms with quantitative glycemic traits is replicated in a cohort of high-risk persons. These variants do not have a detectable impact on diabetes incidence or response to metformin or lifestyle modification in the Diabetes Prevention Program.
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Affiliation(s)
- Jose C. Florez
- Center for Human Genetic Research and Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (DPPRG); (JCF)
| | - Kathleen A. Jablonski
- The Biostatistics Center, George Washington University, Rockville, Maryland, United States of America
| | - Jarred B. McAteer
- Center for Human Genetic Research and Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Paul W. Franks
- Lund University Diabetes Center, Department of Clinical Sciences, Lund University, Malmö, Sweden
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Clinton C. Mason
- Diabetes Epidemiology and Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, United States of America
| | - Kieren Mather
- Division of Endocrinology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Edward Horton
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Joslin Diabetes Center, Boston, Massachusetts, United States of America
| | - Ronald Goldberg
- Lipid Disorders Clinic, Division of Endocrinology, Diabetes, and Metabolism, and the Diabetes Research Institute, Leonard M. Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Dana Dabelea
- Department of Preventive Medicine and Biometrics, University of Colorado at Denver and Health Sciences Center, Denver, Colorado, United States of America
| | - Steven E. Kahn
- Division of Metabolism, Endocrinology and Nutrition, Department of Medicine, VA Puget Sound Health Care System and University of Washington, Seattle, Washington, United States of America
| | - Richard F. Arakaki
- Department of Medicine Clinical Research, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Alan R. Shuldiner
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - William C. Knowler
- Diabetes Epidemiology and Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, United States of America
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Florez JC, Jablonski KA, Taylor A, Mather K, Horton E, White NH, Barrett-Connor E, Knowler WC, Shuldiner AR, Pollin TI. The C allele of ATM rs11212617 does not associate with metformin response in the Diabetes Prevention Program. Diabetes Care 2012; 35:1864-7. [PMID: 22751958 PMCID: PMC3425006 DOI: 10.2337/dc11-2301] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE The C allele at the rs11212617 polymorphism in the ataxia-telangiectasia-mutated (ATM) gene has been associated with greater clinical response to metformin in people with type 2 diabetes. We tested whether this variant modified the effect of metformin in the Diabetes Prevention Program (DPP), in which metformin reduced diabetes incidence by 31% in volunteers with impaired glucose tolerance. RESEARCH DESIGN AND METHODS We genotyped rs11212617 in 2,994 DPP participants and analyzed its effects on diabetes incidence and related traits. RESULTS Contrary to expectations, C carriers enjoyed no preventive advantage on metformin; their hazard ratio, compared with A carriers, was 1.17 ([95% CI 0.96-1.42], P = 0.13) under metformin. There were no significant differences by genotype in metformin's effects on insulin sensitivity, fasting glucose, glycated hemoglobin, or disposition index. CONCLUSIONS The reported association of rs11212617 with metformin response was not confirmed for diabetes prevention or for effects on relevant physiologic parameters in the DPP.
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Genetic modulation of lipid profiles following lifestyle modification or metformin treatment: the Diabetes Prevention Program. PLoS Genet 2012. [PMID: 22951888 PMCID: PMC3431328 DOI: 10.1371/journal.pgen.1002895] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Weight-loss interventions generally improve lipid profiles and reduce cardiovascular disease risk, but effects are variable and may depend on genetic factors. We performed a genetic association analysis of data from 2,993 participants in the Diabetes Prevention Program to test the hypotheses that a genetic risk score (GRS) based on deleterious alleles at 32 lipid-associated single-nucleotide polymorphisms modifies the effects of lifestyle and/or metformin interventions on lipid levels and nuclear magnetic resonance (NMR) lipoprotein subfraction size and number. Twenty-three loci previously associated with fasting LDL-C, HDL-C, or triglycerides replicated (P = 0.04–1×10−17). Except for total HDL particles (r = −0.03, P = 0.26), all components of the lipid profile correlated with the GRS (partial |r| = 0.07–0.17, P = 5×10−5–1×10−19). The GRS was associated with higher baseline-adjusted 1-year LDL cholesterol levels (β = +0.87, SEE±0.22 mg/dl/allele, P = 8×10−5, Pinteraction = 0.02) in the lifestyle intervention group, but not in the placebo (β = +0.20, SEE±0.22 mg/dl/allele, P = 0.35) or metformin (β = −0.03, SEE±0.22 mg/dl/allele, P = 0.90; Pinteraction = 0.64) groups. Similarly, a higher GRS predicted a greater number of baseline-adjusted small LDL particles at 1 year in the lifestyle intervention arm (β = +0.30, SEE±0.012 ln nmol/L/allele, P = 0.01, Pinteraction = 0.01) but not in the placebo (β = −0.002, SEE±0.008 ln nmol/L/allele, P = 0.74) or metformin (β = +0.013, SEE±0.008 nmol/L/allele, P = 0.12; Pinteraction = 0.24) groups. Our findings suggest that a high genetic burden confers an adverse lipid profile and predicts attenuated response in LDL-C levels and small LDL particle number to dietary and physical activity interventions aimed at weight loss. The study included 2,993 participants from the Diabetes Prevention Program, a randomized clinical trial of intensive lifestyle intervention, metformin treatment, and placebo control. We examined associations between 32 gene variants that have been reproducibly associated with dyslipidemia and concentrations of lipids and NMR lipoprotein particle sizes and numbers. We also examined whether genetic background influences a person's response to cardioprotective interventions on lipid levels. Our analysis, which focused on determining whether common genetic variants impact the effects of cardioprotective interventions on lipid and lipoprotein particle size, shows that in persons with a high genetic risk score the benefit of intensive lifestyle intervention on LDL and small LDL particle levels is substantially diminished; this information may be informative for the targeted prevention of dyslipidemia, as it suggests that genetics might help identify persons in whom lifestyle intervention is likely to be an effective treatment for elevated lipids and lipoproteins. The NMR subfraction analyses provide novel insight into the biology of dyslipidemia by illustrating how numerous genetic variants that have previously been associated with lipid levels also modulate NMR lipoprotein particle sizes and number. This information may be informative for the targeted prevention of cardiovascular disease.
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Papageorgiou EA, Patsalis PC. Non-invasive prenatal diagnosis of aneuploidies: new technologies and clinical applications. Genome Med 2012; 4:46. [PMID: 22640877 PMCID: PMC3506912 DOI: 10.1186/gm345] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2012] [Indexed: 12/11/2022] Open
Abstract
Non-invasive prenatal diagnosis (NIPD) has substantial medical importance as it targets the development of safer and more effective methods to avoid the risk of fetal loss associated with currently used invasive methods. Several approaches have been demonstrated as being proof-of concept for NIPD of chromosomal aneuploidies. These approaches include cell-based and cell-free detection methods, involving the investigation of fetal cells in the maternal circulation, formaldehyde treatment of maternal plasma, DNA methylation studies using sodium bisulfite or restriction enzymes, protein-based studies, identification of fetal-specific mRNAs and digital polymerase chain reaction (PCR) approaches, and recently next-generation sequencing and methylated DNA immunoprecipitation real-time quantitative PCR-based approaches. Although all these NIPD methods have both advantages and limitations, some are moving closer to clinical implementation. Biotechnology companies dedicated to the development of NIPD tests such as the sequencing- or methylation-based approaches are finalizing large clinical trials. It is expected that these new technologies will facilitate safer, more sensitive and accurate prenatal diagnostic tests in the near future. In this review, we highlight the most recent advances in methods for NIPD of aneuploidies, and we discuss their future implications in clinical practice.
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Qiu C, Kumar S, Guo J, Lu J, Shi S, Kalachikov SM, Russo JJ, Naini AB, Schon EA, Ju J. Mitochondrial single nucleotide polymorphism genotyping by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using cleavable biotinylated dideoxynucleotides. Anal Biochem 2012; 427:202-10. [PMID: 22579594 DOI: 10.1016/j.ab.2012.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 04/19/2012] [Accepted: 05/02/2012] [Indexed: 10/28/2022]
Abstract
Characterization of mitochondrial DNA (mtDNA) single nucleotide polymorphisms (SNPs) and mutations is crucial for disease diagnosis, which requires accurate and sensitive detection methods and quantification due to mitochondrial heteroplasmy. We report here the characterization of mutations for myoclonic epilepsy with ragged red fibers syndrome using chemically cleavable biotinylated dideoxynucleotides and a mass spectrometry (MS)-based solid phase capture (SPC) single base extension (SBE) assay. The method effectively eliminates unextended primers and primer dimers, and the presence of cleavable linkers between the base and biotin allows efficient desalting and release of the DNA products from solid phase for MS analysis. This approach is capable of high multiplexing, and the use of different length linkers for each of the purines and each of the pyrimidines permits better discrimination of the four bases by MS. Both homoplasmic and heteroplasmic genotypes were accurately determined on different mtDNA samples. The specificity of the method for mtDNA detection was validated by using mitochondrial DNA-negative cells. The sensitivity of the approach permitted detection of less than 5% mtDNA heteroplasmy levels. This indicates that the SPC-SBE approach based on chemically cleavable biotinylated dideoxynucleotides and MS enables rapid, accurate, and sensitive genotyping of mtDNA and has broad applications for genetic analysis.
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Affiliation(s)
- Chunmei Qiu
- Columbia Genome Center, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
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Menke A, Sämann P, Kloiber S, Czamara D, Lucae S, Hennings J, Heck A, Kohli MA, Czisch M, Müller-Myhsok B, Holsboer F, Binder EB. Polymorphisms within the metabotropic glutamate receptor 1 gene are associated with depression phenotypes. Psychoneuroendocrinology 2012; 37:565-75. [PMID: 21962378 DOI: 10.1016/j.psyneuen.2011.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 07/07/2011] [Accepted: 09/07/2011] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Glutamate has been implicated in the pathophysiology and treatment of mood disorders possibly by affecting the regulation of the hypothalamus-pituitary-adrenocortical (HPA) axis. Growing evidence suggests an important role of the metabotropic glutamate receptor 1 (mGlu1) in depression-related phenotypes. To test whether these findings can also be supported by human genetics data, we explored polymorphisms within the metabotropic glutamate receptor 1 gene (GRM1) for their association with unipolar depression (UPD) as well as with biological phenotypes of this disorder. METHODS We first tested the association of 43 tag-SNPs covering the GRM1 locus with UPD in 350 patients and 370 matched controls. We then investigated the effects of the associated SNPs on hippocampal glutamate levels estimated using ¹H-MR-spectroscopy (¹H-MRS) and on endocrine measures from the combined dexamethasone-suppression/CRH stimulation (dex/CRH) test. RESULTS Within the GRM1 locus, 22 SNPs showed nominally significant association with UPD, of which 6 withstood corrections for multiple testing (rs2268666 with best allelic p=7.0×10⁻⁵). Supportive evidence for an association with UPD was gained from a second independent sample with 904 patients and 1012 controls. Furthermore, patients homozygous for the non-risk genotypes showed reduced hippocampal glutamate levels as measured by ¹H-MRS, a more pronounced normalization of HPA-axis hyperactivity as well as a better antidepressant treatment outcome. CONCLUSIONS These results suggest that the combination of genetic and biological markers may allow to subgroup patients into etiopathogenetically more relevant subcategories which could guide clinicians in their antidepressant treatment choices.
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Affiliation(s)
- Andreas Menke
- Max Planck Institute of Psychiatry, Kraepelinstr. 10, D-80804 Munich, Germany.
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Menke A, Domschke K, Czamara D, Klengel T, Hennings J, Lucae S, Baune BT, Arolt V, Müller-Myhsok B, Holsboer F, Binder EB. Genome-wide association study of antidepressant treatment-emergent suicidal ideation. Neuropsychopharmacology 2012; 37:797-807. [PMID: 22030708 PMCID: PMC3260972 DOI: 10.1038/npp.2011.257] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 09/09/2011] [Accepted: 09/26/2011] [Indexed: 11/08/2022]
Abstract
Emergence of suicidal ideation (TESI) during treatment with antidepressants in major depression led to a black box warning. We performed a genome-wide association study to identify genetic markers, which increase the risk for this serious side effect. TESI was evaluated in depressed in-patients (N=397) and defined by an emergence of suicidal thoughts during hospitalization without suicidal thoughts at admission using the suicide item (3) of the Hamilton Depression Rating Scale. Genotype distribution of 405.383 single-nucleotide polymorphisms (SNPs) in patients with TESI (N=32/8.1%) was compared to patients without increase in suicidal ideation (N=329/82.9%) and to a subgroup never reported suicidal ideation (N=79/19.9%). Top results were analyzed in an independent sample (N=501). None variant reached genome-wide significance, the best associated SNP was rs1630535 (p-value=1.3 × 10(-7)). The top 79 SNPs could be analyzed in an independent sample, and 14 variants showed nominal significant association with the same risk allele in the replication sample. A discriminant analysis classifying patients using these 79 SNPs revealed a 91% probability to classify TESI vs non-TESI cases correctly in the replication sample. Although our data need to be interpreted carefully owing to the small numbers in both cohorts, they suggest that a combination of genetic markers might indeed be used to identify patients at risk for TESI.
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Affiliation(s)
- Andreas Menke
- Max Planck Institute of Psychiatry, Munich, Germany.
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Lemas DJ, Wiener HW, O'Brien DM, Hopkins S, Stanhope KL, Havel PJ, Allison DB, Fernandez JR, Tiwari HK, Boyer BB. Genetic polymorphisms in carnitine palmitoyltransferase 1A gene are associated with variation in body composition and fasting lipid traits in Yup'ik Eskimos. J Lipid Res 2011; 53:175-84. [PMID: 22045927 DOI: 10.1194/jlr.p018952] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Variants of carnitine palmitoyltransferase 1A (CPT1A), a key hepatic lipid oxidation enzyme, may influence how fatty acid oxidation contributes to obesity and metabolic outcomes. CPT1A is regulated by diet, suggesting interactions between gene variants and diet may influence outcomes. The objective of this study was to test the association of CPT1A variants with body composition and lipids, mediated by consumption of polyunsaturated fatty acids (PUFA). Obesity phenotypes and fasting lipids were measured in a cross-sectional sample of Yup'ik Eskimo individuals (n = 1141) from the Center of Alaska Native Health Research (CANHR) study. Twenty-eight tagging CPT1A SNPs were evaluated with outcomes of interest in regression models accounting for family structure. Several CPT1A polymorphisms were associated with HDL-cholesterol and obesity phenotypes. The P479L (rs80356779) variant was associated with all obesity-related traits and fasting HDL-cholesterol. Interestingly, the association of P479L with HDL-cholesterol was still significant after correcting for body mass index (BMI), percentage body fat (PBF), or waist circumference (WC). Our findings are consistent with the hypothesis that the L479 allele of the CPT1A P479L variant confers a selective advantage that is both cardioprotective (through increased HDL-cholesterol) and associated with reduced adiposity.
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Affiliation(s)
- Dominick J Lemas
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
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A single major QTL controls expression of larval Cry1F resistance trait in Ostrinia nubilalis (Lepidoptera: Crambidae) and is independent of midgut receptor genes. Genetica 2011; 139:961-72. [DOI: 10.1007/s10709-011-9590-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 06/09/2011] [Indexed: 12/11/2022]
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McCaffery JM, Jablonski KA, Franks PW, Dagogo-Jack S, Wing RR, Knowler WC, Delahanty L, Dabelea D, Hamman R, Shuldiner AR, Florez JC. TCF7L2 polymorphism, weight loss and proinsulin:insulin ratio in the diabetes prevention program. PLoS One 2011; 6:e21518. [PMID: 21814547 PMCID: PMC3144193 DOI: 10.1371/journal.pone.0021518] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 06/02/2011] [Indexed: 01/17/2023] Open
Abstract
Aims TCF7L2 variants have been associated with type 2 diabetes, body mass index (BMI), and deficits in proinsulin processing and insulin secretion. Here we sought to test whether these effects were apparent in high-risk individuals and modify treatment responses. Methods We examined the potential role of the TCF7L2 rs7903146 variant in predicting resistance to weight loss or a lack of improvement of proinsulin processing during 2.5-years of follow-up participants (N = 2,994) from the Diabetes Prevention Program (DPP), a randomized controlled trial designed to prevent or delay diabetes in high-risk adults. Results We observed no difference in the degree of weight loss by rs7903146 genotypes. However, the T allele (conferring higher risk of diabetes) at rs7903146 was associated with higher fasting proinsulin at baseline (P<0.001), higher baseline proinsulin∶insulin ratio (p<0.0001) and increased proinsulin∶insulin ratio over a median of 2.5 years of follow-up (P = 0.003). Effects were comparable across treatment arms. Conclusions The combination of a lack of impact of the TCF7L2 genotypes on the ability to lose weight, but the presence of a consistent effect on the proinsulin∶insulin ratio over the course of DPP, suggests that high-risk genotype carriers at this locus can successfully lose weight to counter diabetes risk despite persistent deficits in insulin production.
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Affiliation(s)
- Jeanne M McCaffery
- The Biostatistics Center, The George Washington University, Rockville, Maryland, United States of America.
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Margam VM, Coates BS, Bayles DO, Hellmich RL, Agunbiade T, Seufferheld MJ, Sun W, Kroemer JA, Ba MN, Binso-Dabire CL, Baoua I, Ishiyaku MF, Covas FG, Srinivasan R, Armstrong J, Murdock LL, Pittendrigh BR. Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae). PLoS One 2011; 6:e21388. [PMID: 21754987 PMCID: PMC3130784 DOI: 10.1371/journal.pone.0021388] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 05/26/2011] [Indexed: 01/31/2023] Open
Abstract
The legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), is an insect pest species of crops grown by subsistence farmers in tropical regions of Africa. We present the de novo assembly of 3729 contigs from 454- and Sanger-derived sequencing reads for midgut, salivary, and whole adult tissues of this non-model species. Functional annotation predicted that 1320 M. vitrata protein coding genes are present, of which 631 have orthologs within the Bombyx mori gene model. A homology-based analysis assigned M. vitrata genes into a group of paralogs, but these were subsequently partitioned into putative orthologs following phylogenetic analyses. Following sequence quality filtering, a total of 1542 putative single nucleotide polymorphisms (SNPs) were predicted within M. vitrata contig assemblies. Seventy one of 1078 designed molecular genetic markers were used to screen M. vitrata samples from five collection sites in West Africa. Population substructure may be present with significant implications in the insect resistance management recommendations pertaining to the release of biological control agents or transgenic cowpea that express Bacillus thuringiensis crystal toxins. Mutation data derived from transcriptome sequencing is an expeditious and economical source for genetic markers that allow evaluation of ecological differentiation.
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Affiliation(s)
- Venu M. Margam
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
| | - Brad S. Coates
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Darrell O. Bayles
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Richard L. Hellmich
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Tolulope Agunbiade
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Manfredo J. Seufferheld
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Weilin Sun
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Jeremy A. Kroemer
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Malick N. Ba
- Institut de l'Environnement et de Recherches Agricoles (INERA), Station de Kamboinsé, Ouagadougou, Burkina Faso
| | - Clementine L. Binso-Dabire
- Institut de l'Environnement et de Recherches Agricoles (INERA), Station de Kamboinsé, Ouagadougou, Burkina Faso
| | - Ibrahim Baoua
- Institut National de Recherche Agronomique du Niger, Maradi, Niger
| | - Mohammad F. Ishiyaku
- Department of Plant Science, Institute for Agricultural Research, Ahmadu Bello University, Zaria, Nigeria
| | | | | | - Joel Armstrong
- Ecosystem Sciences, The Commonwealth Scientific and Industrial Research Organization, Black Mountain, Australian Capital Territory, Australia
| | - Larry L. Murdock
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
| | - Barry R. Pittendrigh
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
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Coates BS, Bayles DO, Wanner KW, Robertson HM, Hellmich RL, Sappington TW. The application and performance of single nucleotide polymorphism markers for population genetic analyses of lepidoptera. Front Genet 2011; 2:38. [PMID: 22303334 PMCID: PMC3268592 DOI: 10.3389/fgene.2011.00038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 06/10/2011] [Indexed: 01/19/2023] Open
Abstract
Microsatellite markers are difficult to apply within lepidopteran studies due to the lack of locus-specific PCR amplification and the high proportion of “null” alleles, such that erroneous estimations of population genetic parameters often result. Herein single nucleotide polymorphism (SNP) markers are developed from Ostrinia nubilalis (Lepidoptera: Crambidae) using next generation expressed sequence tag (EST) data. A total of 2742 SNPs were predicted within a reference assembly of 7414 EST contigs, and a subset of 763 were incorporated into 24 multiplex PCR reactions. To validate this pipeline, 5 European and North American sample sites were genotyped at 178 SNP loci, which indicated 84 (47.2%) were in Hardy–Weinberg equilibrium. Locus-by-locus FST, analysis of molecular variance, and STRUCTURE analyses indicate significant genetic differentiation may exist between European and North American O. nubilalis. The observed genetic diversity was significantly lower among European sites, which may result from genetic drift, natural selection, a genetic bottleneck, or ascertainment bias due to North American origin of EST sequence data. SNPs are an abundant source of mutation data for molecular genetic marker development in non-model species, with shared ancestral SNPs showing application within closely related species. These markers offer advantages over microsatellite markers for genetic and genomic analyses of Lepidoptera, but the source of mutation data may affect the estimation of population parameters and likely need to be considered in the interpretation of empirical data.
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Affiliation(s)
- Brad Steven Coates
- Corn Insects and Crop Genetics Research Unit, Agricultural Research Service, United States Department of Agriculture Ames, IA, USA
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Andersen Ø, De Rosa MC, Pirolli D, Tooming-Klunderud A, Petersen PE, André C. Polymorphism, selection and tandem duplication of transferrin genes in Atlantic cod (Gadus morhua)--conserved synteny between fish monolobal and tetrapod bilobal transferrin loci. BMC Genet 2011; 12:51. [PMID: 21612617 PMCID: PMC3125230 DOI: 10.1186/1471-2156-12-51] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 05/25/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The two homologous iron-binding lobes of transferrins are thought to have evolved by gene duplication of an ancestral monolobal form, but any conserved synteny between bilobal and monolobal transferrin loci remains unexplored. The important role played by transferrin in the resistance to invading pathogens makes this polymorphic gene a highly valuable candidate for studying adaptive divergence among local populations. RESULTS The Atlantic cod genome was shown to harbour two tandem duplicated serum transferrin genes (Tf1, Tf2), a melanotransferrin gene (MTf), and a monolobal transferrin gene (Omp). Whereas Tf1 and Tf2 were differentially expressed in liver and brain, the Omp transcript was restricted to the otoliths. Fish, chicken and mammals showed highly conserved syntenic regions in which monolobal and bilobal transferrins reside, but contrasting with tetrapods, the fish transferrin genes are positioned on three different linkage groups. Sequence alignment of cod Tf1 cDNAs from Northeast (NE) and Northwest (NW) Atlantic populations revealed 22 single nucleotide polymorphisms (SNP) causing the replacement of 16 amino acids, including eight surface residues revealed by the modelled 3D-structures, that might influence the binding of pathogens for removal of iron. SNP analysis of a total of 375 individuals from 14 trans-Atlantic populations showed that the Tf1-NE variant was almost fixed in the Baltic cod and predominated in the other NE Atlantic populations, whereas the NW Atlantic populations were more heterozygous and showed high frequencies of the Tf-NW SNP alleles. CONCLUSIONS The highly conserved synteny between fish and tetrapod transferrin loci infers that the fusion of tandem duplicated Omp-like genes gave rise to the modern transferrins. The multiple nonsynonymous substitutions in cod Tf1 with putative structural effects, together with highly divergent allele frequencies among different cod populations, strongly suggest evidence for positive selection and local adaptation in trans-Atlantic cod populations.
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Urban PL, Amantonico A, Zenobi R. Lab-on-a-plate: extending the functionality of MALDI-MS and LDI-MS targets. MASS SPECTROMETRY REVIEWS 2011; 30:435-478. [PMID: 21254192 DOI: 10.1002/mas.20288] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We review the literature that describes how (matrix-assisted) laser desorption/ionization (MA)LDI target plates can be used not only as sample supports, but beyond that: as functional parts of analytical protocols that incorporate detection by MALDI-MS or matrix-free LDI-MS. Numerous steps of analytical procedures can be performed directly on the (MA)LDI target plates prior to the ionization of analytes in the ion source of a mass spectrometer. These include homogenization, preconcentration, amplification, purification, extraction, digestion, derivatization, synthesis, separation, detection with complementary techniques, data storage, or other steps. Therefore, we consider it helpful to define the "lab-on-a-plate" as a format for carrying out extensive sample treatment as well as bioassays directly on (MA)LDI target plates. This review introduces the lab-on-plate approach and illustrates it with the aid of relevant examples from the scientific and patent literature.
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Affiliation(s)
- Pawel L Urban
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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Hivert MF, Jablonski KA, Perreault L, Saxena R, McAteer JB, Franks PW, Hamman RF, Kahn SE, Haffner S, Meigs JB, Altshuler D, Knowler WC, Florez JC. Updated genetic score based on 34 confirmed type 2 diabetes Loci is associated with diabetes incidence and regression to normoglycemia in the diabetes prevention program. Diabetes 2011; 60:1340-8. [PMID: 21378175 PMCID: PMC3064108 DOI: 10.2337/db10-1119] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Over 30 loci have been associated with risk of type 2 diabetes at genome-wide statistical significance. Genetic risk scores (GRSs) developed from these loci predict diabetes in the general population. We tested if a GRS based on an updated list of 34 type 2 diabetes-associated loci predicted progression to diabetes or regression toward normal glucose regulation (NGR) in the Diabetes Prevention Program (DPP). RESEARCH DESIGN AND METHODS We genotyped 34 type 2 diabetes-associated variants in 2,843 DPP participants at high risk of type 2 diabetes from five ethnic groups representative of the U.S. population, who had been randomized to placebo, metformin, or lifestyle intervention. We built a GRS by weighting each risk allele by its reported effect size on type 2 diabetes risk and summing these values. We tested its ability to predict diabetes incidence or regression to NGR in models adjusted for age, sex, ethnicity, waist circumference, and treatment assignment. RESULTS In multivariate-adjusted models, the GRS was significantly associated with increased risk of progression to diabetes (hazard ratio [HR] = 1.02 per risk allele [95% CI 1.00-1.05]; P = 0.03) and a lower probability of regression to NGR (HR = 0.95 per risk allele [95% CI 0.93-0.98]; P < 0.0001). At baseline, a higher GRS was associated with a lower insulinogenic index (P < 0.001), confirming an impairment in β-cell function. We detected no significant interaction between GRS and treatment, but the lifestyle intervention was effective in the highest quartile of GRS (P < 0.0001). CONCLUSIONS A high GRS is associated with increased risk of developing diabetes and lower probability of returning to NGR in high-risk individuals, but a lifestyle intervention attenuates this risk.
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Affiliation(s)
- Marie-France Hivert
- Division of Endocrinology, Department of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | | | - Leigh Perreault
- Department of Medicine, Division of Endocrinology, Metabolism and Diabetes, University of Colorado at Denver School of Medicine, Aurora, Colorado
| | - Richa Saxena
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Jarred B. McAteer
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Paul W. Franks
- Department of Public Health and Clinical Medicine, Division of Medicine, Genetic Epidemiology and Clinical Research Group, Umeå University Hospital, Umeå, Sweden
- Department of Clinical Sciences, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - Richard F. Hamman
- Department of Epidemiology, Colorado School of Public Health, University of Colorado at Denver, Aurora, Colorado
| | - Steven E. Kahn
- Division of Metabolism, Endocrinology and Nutrition, Veterans’ Affairs Puget Sound Health Care System and the University of Washington, Seattle, Washington
| | | | | | - James B. Meigs
- General Medicine Unit, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - David Altshuler
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - William C. Knowler
- Diabetes Epidemiology and Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona
| | - Jose C. Florez
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Corresponding author: Jose C. Florez, and
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The efficacy of detecting variants with small effects on the Affymetrix 6.0 platform using pooled DNA. Hum Genet 2011; 130:607-21. [PMID: 21424828 DOI: 10.1007/s00439-011-0974-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 03/06/2011] [Indexed: 01/10/2023]
Abstract
Genome-wide genotyping of a cohort using pools rather than individual samples has long been proposed as a cost-saving alternative for performing genome-wide association (GWA) studies. However, successful disease gene mapping using pooled genotyping has thus far been limited to detecting common variants with large effect sizes, which tend not to exist for many complex common diseases or traits. Therefore, for DNA pooling to be a viable strategy for conducting GWA studies, it is important to determine whether commonly used genome-wide SNP array platforms such as the Affymetrix 6.0 array can reliably detect common variants of small effect sizes using pooled DNA. Taking obesity and age at menarche as examples of human complex traits, we assessed the feasibility of genome-wide genotyping of pooled DNA as a single-stage design for phenotype association. By individually genotyping the top associations identified by pooling, we obtained a 14- to 16-fold enrichment of SNPs nominally associated with the phenotype, but we likely missed the top true associations. In addition, we assessed whether genotyping pooled DNA can serve as an inexpensive screen as the second stage of a multi-stage design with a large number of samples by comparing the most cost-effective 3-stage designs with 80% power to detect common variants with genotypic relative risk of 1.1, with and without pooling. Given the current state of the specific technology we employed and the associated genotyping costs, we showed through simulation that a design involving pooling would be 1.07 times more expensive than a design without pooling. Thus, while a significant amount of information exists within the data from pooled DNA, our analysis does not support genotyping pooled DNA as a means to efficiently identify common variants contributing small effects to phenotypes of interest. While our conclusions were based on the specific technology and study design we employed, the approach presented here will be useful for evaluating the utility of other or future genome-wide genotyping platforms in pooled DNA studies.
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