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Maltby VE, Scott RJ, Giovannoni G, Hawkes CH, Levy M, Yeh EA, Lechner-Scott J. Where does multiple sclerosis come from? Mult Scler Relat Disord 2024; 85:105575. [PMID: 38574723 DOI: 10.1016/j.msard.2024.105575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
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Petit J, Carroll G, Zhao J, Roper E, Pockney P, Scott RJ. Evaluation of epigenetic methylation biomarkers for the detection of colorectal cancer using droplet digital PCR. Sci Rep 2023; 13:8883. [PMID: 37264006 DOI: 10.1038/s41598-023-35631-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 05/21/2023] [Indexed: 06/03/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. Screening programs allow early diagnosis and have improved the clinical management of this disease. Aberrant DNA methylation is increasingly being explored as potential biomarkers for many types of cancers. In this study we investigate the methylation of ten target genes in 105 CRC and paired normal adjacent colonic tissue samples using a MethylLight droplet digital PCR (ML-ddPCR) assay. Receiver operator characteristic (ROC) curves were used to determine the diagnostic performance of all target genes individually and in combination. All 515 different combinations of genes showed significantly higher levels of methylation in CRC tissue. The combination of multiple target genes into a single test generally resulted in greater diagnostic accuracy when compared to single target genes. Our data confirms that ML-ddPCR is able to reliably detect significant differences in DNA methylation between CRC tissue and normal adjacent colonic tissue in a specific selection of target genes.
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Affiliation(s)
- J Petit
- Division of Surgery, John Hunter Hospital, New Lambton Heights, NSW, Australia.
- Hunter Medical Research Institute, Newcastle, Australia.
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia.
| | - G Carroll
- Division of Surgery, John Hunter Hospital, New Lambton Heights, NSW, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, Newcastle, Australia
| | - J Zhao
- Division of Surgery, John Hunter Hospital, New Lambton Heights, NSW, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia
| | - E Roper
- Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - P Pockney
- Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - R J Scott
- Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
- Pathology North, Newcastle, NSW, Australia
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Connor T, McPhillips M, Hipwell M, Ziolkowski A, Oldmeadow C, Clapham M, Pockney PG, Lis E, Banasiewicz T, Pławski A, Scott RJ. CD36 polymorphisms and the age of disease onset in patients with pathogenic variants within the mutation cluster region of APC. Hered Cancer Clin Pract 2021; 19:25. [PMID: 33926505 PMCID: PMC8086281 DOI: 10.1186/s13053-021-00183-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 04/20/2021] [Indexed: 12/30/2022] Open
Abstract
Background Familial adenomatous polyposis (FAP) is an autosomal dominant condition that predisposes patients to colorectal cancer. FAP is the result of a loss of APC function due to germline pathogenic variants disrupting gene expression. Genotype-phenotype correlations are described for FAP. For example attenuated forms of the disease are associated with pathogenic variants at the 5’ and 3’ ends of APC whilst severe forms of the disease appear to be linked to variants occurring in the mutation cluster region (MCR) of the gene. Variants occurring in the MCR are phenotypically associated with hundreds to thousands of adenomas carpeting the colon and rectum and patients harbouring changes in this region have a high propensity to develop colorectal cancer. Not all patients who carry pathogenic variants in this region have severe disease which may be a result of environmental factors. Alternatively, phenotypic variation observed in these patients could be due to modifier genes that either promote or inhibit disease expression. Mouse models of FAP have provided several plausible candidate modifier genes, but very few of these have survived scrutiny. One such genetic modifier that appears to be associated with disease expression is CD36. We previously reported a weak association between a polymorphism in CD36 and a later age of disease onset on a relatively small FAP patient cohort. Methods In the current study, we enlarged the FAP cohort. 395 patients all carrying pathogenic variants in APC were tested against three CD36 Single Nucleotide Polymorphisms (SNP)s (rs1049673, rs1761667 rs1984112), to determine if any of them were associated with differences in the age of disease expression. Results Overall, there appeared to be a statistically significant difference in the age of disease onset between carriers of the variant rs1984112 and wildtype. Furthermore, test equality of survivor functions for each SNP and mutation group suggested an interaction in the Log Rank, Wilcoxon, and Tarone-Ware methods for rs1049673, rs1761667, and rs1984112, thereby supporting the notion that CD36 modifies disease expression. Conclusions This study supports and strengthens our previous findings concerning CD36 and an association with disease onset in FAP, AFAP and FAP-MCR affected individuals. Knowledge about the role CD36 in adenoma development may provide greater insight into the development of colorectal cancer.
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Affiliation(s)
- T Connor
- School of Biomedical Sciences, Faculty of Health, University of Newcastle, Callaghan Campus, NSW, 2308, Newcastle, Australia
| | - M McPhillips
- Division of Molecular Medicine, NSW Health Pathology North, 2305, New Lambton, NSW, Australia
| | - M Hipwell
- Division of Molecular Medicine, NSW Health Pathology North, 2305, New Lambton, NSW, Australia
| | - A Ziolkowski
- Division of Molecular Medicine, NSW Health Pathology North, 2305, New Lambton, NSW, Australia
| | - C Oldmeadow
- Centre for Clinical Epidemiology and Biostatistics, University of Newcastle, Newcastle, NSW, Australia
| | - M Clapham
- Centre for Clinical Epidemiology and Biostatistics, University of Newcastle, Newcastle, NSW, Australia
| | - P G Pockney
- Department of Surgery, John Hunter Hospital, Newcastle, Australia
| | - E Lis
- Department of General, Endocrinological Surgery and Gastroenterological Oncology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - T Banasiewicz
- Department of General, Endocrinological Surgery and Gastroenterological Oncology, Poznan University of Medical Sciences, Poznan, Poland
| | - A Pławski
- Department of General, Endocrinological Surgery and Gastroenterological Oncology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - R J Scott
- School of Biomedical Sciences, Faculty of Health, University of Newcastle, Callaghan Campus, NSW, 2308, Newcastle, Australia. .,Division of Molecular Medicine, NSW Health Pathology North, 2305, New Lambton, NSW, Australia. .,Hunter Medical Research Institute, John Hunter Hospital, 2305, New Lambton, NSW, Australia.
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Katzman BM, Wockenfus AM, Scott RJ, Bryant SC, Jaffe AS, Karon BS. Estimating short- and long-term reference change values and index of individuality for tests of platelet function. Clin Biochem 2019; 74:54-59. [PMID: 31669512 DOI: 10.1016/j.clinbiochem.2019.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 11/26/2022]
Abstract
BACKGROUND In order to manage risks of bleeding and thrombosis after some surgical procedures, platelet function is often measured repeatedly over days or weeks using laboratory tests of platelet function. To interpret test results in the perioperative period, it is necessary to understand analytical, biological and between-person variation. METHODS We collected three separate blood specimens from 16 healthy volunteers on the first study day, and one additional specimen from each volunteer 1, 2, and 3 months later. Arachidonic acid-induced and adenosine diphosphate (ADP)-induced platelet function were measured in duplicate by whole blood impedance aggregometry using Multiplate (ASPI/ADP tests) and VerifyNow (Aspirin Reaction Units [ARU] and P2Y12 Reaction Units [PRU]). The analytical variation (CVA), within-subject variation (CVI), between-subject variation (CVG), index of individuality (II), and reference change values (RCV) were calculated. RESULTS VerifyNow ARU demonstrated the smallest short-term and long-term variability (CVA, CVI, and CVG ~1%), resulting in short- and long-term RCV values <5%. II was also higher (1.92) for VerifyNow ARU than other platelet function tests. Multiplate ASPI and ADP tests had the highest RCV both short-(19.0% and 25.2%, respectively) and long-term (32.1% and 39.6%, respectively) due to increased CVA (>5%) and CVI (3.9-13.1%). VerifyNow PRU had a lower RCV than Multiplate ADP; but was the only test with II <0.6. CONCLUSIONS VerifyNow ARU results can be interpreted relative to a fixed cut-off or population-based reference interval; or relative to small changes in an individual's previous values. VerifyNow PRU and Multiplate ASPI and ADP tests should only be interpreted based upon relative change; and can only distinguish relatively large (>23%) changes over several weeks.
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Affiliation(s)
- Brooke M Katzman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Amy M Wockenfus
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Renee J Scott
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Sandra C Bryant
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States
| | - Allan S Jaffe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States; Department of Cardiology, Mayo Clinic, Rochester, MN, United States
| | - Brad S Karon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.
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Xavier MJ, Nixon B, Roman SD, Scott RJ, Drevet JR, Aitken RJ. Paternal impacts on development: identification of genomic regions vulnerable to oxidative DNA damage in human spermatozoa. Hum Reprod 2019; 34:1876-1890. [DOI: 10.1093/humrep/dez153] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
Abstract
STUDY QUESTION
Do all regions of the paternal genome within the gamete display equivalent vulnerability to oxidative DNA damage?
SUMMARY ANSWER
Oxidative DNA damage is not randomly distributed in mature human spermatozoa but is instead targeted, with particular chromosomes being especially vulnerable to oxidative stress.
WHAT IS KNOWN ALREADY
Oxidative DNA damage is frequently encountered in the spermatozoa of male infertility patients. Such lesions can influence the incidence of de novo mutations in children, yet it remains to be established whether all regions of the sperm genome display equivalent susceptibility to attack by reactive oxygen species.
STUDY DESIGN, SIZE, DURATION
Human spermatozoa obtained from normozoospermic males (n = 8) were split into equivalent samples and subjected to either hydrogen peroxide (H2O2) treatment or vehicle controls before extraction of oxidized DNA using a modified DNA immunoprecipitation (MoDIP) protocol. Specific regions of the genome susceptible to oxidative damage were identified by next-generation sequencing and validated in the spermatozoa of normozoospermic males (n = 18) and in patients undergoing infertility evaluation (n = 14).
PARTICIPANTS/MATERIALS, SETTING, METHODS
Human spermatozoa were obtained from normozoospermic males and divided into two identical samples prior to being incubated with either H2O2 (5 mm, 1 h) to elicit oxidative stress or an equal volume of vehicle (untreated controls). Alternatively, spermatozoa were obtained from fertility patients assessed as having high basal levels of oxidative stress within their spermatozoa. All semen samples were subjected to MoDIP to selectively isolate oxidized DNA, prior to sequencing of the resultant DNA fragments using a next-generation whole-genomic sequencing platform. Bioinformatic analysis was then employed to identify genomic regions vulnerable to oxidative damage, several of which were selected for real-time quantitative PCR (qPCR) validation.
MAIN RESULTS AND THE ROLE OF CHANCE
Approximately 9000 genomic regions, 150–1000 bp in size, were identified as highly vulnerable to oxidative damage in human spermatozoa. Specific chromosomes showed differential susceptibility to damage, with chromosome 15 being particularly sensitive to oxidative attack while the sex chromosomes were protected. Susceptible regions generally lay outside protamine- and histone-packaged domains. Furthermore, we confirmed that these susceptible genomic sites experienced a dramatic (2–15-fold) increase in their burden of oxidative DNA damage in patients undergoing infertility evaluation compared to normal healthy donors.
LIMITATIONS, REASONS FOR CAUTION
The limited number of samples analysed in this study warrants external validation, as do the implications of our findings. Selection of male fertility patients was based on high basal levels of oxidative stress within their spermatozoa as opposed to specific sub-classes of male factor infertility.
WIDER IMPLICATIONS OF THE FINDINGS
The identification of genomic regions susceptible to oxidation in the male germ line will be of value in focusing future analyses into the mutational load carried by children in response to paternal factors such as age, the treatment of male infertility using ART and paternal exposure to environmental toxicants.
STUDY FUNDING/COMPETING INTEREST(S)
Project support was provided by the University of Newcastle’s (UoN) Priority Research Centre for Reproductive Science. M.J.X. was a recipient of a UoN International Postgraduate Research Scholarship. B.N. is the recipient of a National Health and Medical Research Council of Australia Senior Research Fellowship. Authors declare no conflict of interest.
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Affiliation(s)
- M J Xavier
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - B Nixon
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - S D Roman
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Drug Development, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - R J Scott
- Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Medical Genetics, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- Division of Molecular Medicine, Pathology North, John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - J R Drevet
- GReD Laboratory, CNRS UMR6293—INSERM U1103—Clermont Université, Clermont-Ferrand, France
| | - R J Aitken
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
- Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Medical Genetics, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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Abstract
We report the case of a female found to have mosaicism for mutation in the STK11 gene, with the mutant allele expressed in her gametes, evident by her affected offspring, and in her gastrointestinal tract demonstrated on an excised polyp analysed for diagnosis. Mosaicism for Peutz-Jeghers syndrome (PJS) has been reported in a small number of cases previously but a clinical presentation such as this has not previously been described. This finding of mosaicism was several years after initial investigations failed to identify the same STK11 mutation in this woman whose son was diagnosed with PJS at a young age. This case highlights the importance of considering mosaicism as an explanation for apparent de novo cases of PJS syndrome. It also has implications for genetic counselling, predictive testing and cancer screening.
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Affiliation(s)
| | - A D Spigelman
- Hunter Family Cancer Service, Newcastle, NSW, Australia.,St Vincent's Hospital Clinical School, UNSW, Sydney, NSW, Australia
| | - R J Scott
- Discipline of Medical Genetics, The University of Newcastle, Newcastle, NSW, Australia
| | - R E Vilain
- Division of Anatomical Pathology, NSW Health Pathology (North), John Hunter Hospital, New Lambton, NSW, Australia
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7
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Kelly S, Jahanshad N, Zalesky A, Kochunov P, Agartz I, Alloza C, Andreassen OA, Arango C, Banaj N, Bouix S, Bousman CA, Brouwer RM, Bruggemann J, Bustillo J, Cahn W, Calhoun V, Cannon D, Carr V, Catts S, Chen J, Chen JX, Chen X, Chiapponi C, Cho KK, Ciullo V, Corvin AS, Crespo-Facorro B, Cropley V, De Rossi P, Diaz-Caneja CM, Dickie EW, Ehrlich S, Fan FM, Faskowitz J, Fatouros-Bergman H, Flyckt L, Ford JM, Fouche JP, Fukunaga M, Gill M, Glahn DC, Gollub R, Goudzwaard ED, Guo H, Gur RE, Gur RC, Gurholt TP, Hashimoto R, Hatton SN, Henskens FA, Hibar DP, Hickie IB, Hong LE, Horacek J, Howells FM, Hulshoff Pol HE, Hyde CL, Isaev D, Jablensky A, Jansen PR, Janssen J, Jönsson EG, Jung LA, Kahn RS, Kikinis Z, Liu K, Klauser P, Knöchel C, Kubicki M, Lagopoulos J, Langen C, Lawrie S, Lenroot RK, Lim KO, Lopez-Jaramillo C, Lyall A, Magnotta V, Mandl RCW, Mathalon DH, McCarley RW, McCarthy-Jones S, McDonald C, McEwen S, McIntosh A, Melicher T, Mesholam-Gately RI, Michie PT, Mowry B, Mueller BA, Newell DT, O'Donnell P, Oertel-Knöchel V, Oestreich L, Paciga SA, Pantelis C, Pasternak O, Pearlson G, Pellicano GR, Pereira A, Pineda Zapata J, Piras F, Potkin SG, Preda A, Rasser PE, Roalf DR, Roiz R, Roos A, Rotenberg D, Satterthwaite TD, Savadjiev P, Schall U, Scott RJ, Seal ML, Seidman LJ, Shannon Weickert C, Whelan CD, Shenton ME, Kwon JS, Spalletta G, Spaniel F, Sprooten E, Stäblein M, Stein DJ, Sundram S, Tan Y, Tan S, Tang S, Temmingh HS, Westlye LT, Tønnesen S, Tordesillas-Gutierrez D, Doan NT, Vaidya J, van Haren NEM, Vargas CD, Vecchio D, Velakoulis D, Voineskos A, Voyvodic JQ, Wang Z, Wan P, Wei D, Weickert TW, Whalley H, White T, Whitford TJ, Wojcik JD, Xiang H, Xie Z, Yamamori H, Yang F, Yao N, Zhang G, Zhao J, van Erp TGM, Turner J, Thompson PM, Donohoe G. Widespread white matter microstructural differences in schizophrenia across 4322 individuals: results from the ENIGMA Schizophrenia DTI Working Group. Mol Psychiatry 2018; 23:1261-1269. [PMID: 29038599 PMCID: PMC5984078 DOI: 10.1038/mp.2017.170] [Citation(s) in RCA: 412] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 05/02/2017] [Accepted: 06/07/2017] [Indexed: 12/15/2022]
Abstract
The regional distribution of white matter (WM) abnormalities in schizophrenia remains poorly understood, and reported disease effects on the brain vary widely between studies. In an effort to identify commonalities across studies, we perform what we believe is the first ever large-scale coordinated study of WM microstructural differences in schizophrenia. Our analysis consisted of 2359 healthy controls and 1963 schizophrenia patients from 29 independent international studies; we harmonized the processing and statistical analyses of diffusion tensor imaging (DTI) data across sites and meta-analyzed effects across studies. Significant reductions in fractional anisotropy (FA) in schizophrenia patients were widespread, and detected in 20 of 25 regions of interest within a WM skeleton representing all major WM fasciculi. Effect sizes varied by region, peaking at (d=0.42) for the entire WM skeleton, driven more by peripheral areas as opposed to the core WM where regions of interest were defined. The anterior corona radiata (d=0.40) and corpus callosum (d=0.39), specifically its body (d=0.39) and genu (d=0.37), showed greatest effects. Significant decreases, to lesser degrees, were observed in almost all regions analyzed. Larger effect sizes were observed for FA than diffusivity measures; significantly higher mean and radial diffusivity was observed for schizophrenia patients compared with controls. No significant effects of age at onset of schizophrenia or medication dosage were detected. As the largest coordinated analysis of WM differences in a psychiatric disorder to date, the present study provides a robust profile of widespread WM abnormalities in schizophrenia patients worldwide. Interactive three-dimensional visualization of the results is available at www.enigma-viewer.org.
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Affiliation(s)
- S Kelly
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA,Harvard Medical School, Boston, MA, USA,Imaging Genetics Center, Keck School of Medicine, University of Southern California, Marina del Rey, CA 90292, USA. E-mail:
| | - N Jahanshad
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - A Zalesky
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne and Melbourne Health, Carlton South, VIC, Australia
| | - P Kochunov
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - I Agartz
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden,Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
| | - C Alloza
- University of Edinburgh, Edinburgh, UK
| | | | - C Arango
- Child and Adolescent Psychiatry Department, Hospital General Universitario Gregorio Marañón, School of Medicine, Universidad Complutense, IiSGM, CIBERSAM, Madrid, Spain
| | - N Banaj
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - S Bouix
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - C A Bousman
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne and Melbourne Health, Carlton South, VIC, Australia,Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia,Department of General Practice, The University of Melbourne, Parkville, VIC, Australia,Swinburne University of Technology, Melbourne, VIC, Australia
| | - R M Brouwer
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - J Bruggemann
- Neuroscience Research Australia and School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - J Bustillo
- University of New Mexico, Albuquerque, NM, USA
| | - W Cahn
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - V Calhoun
- The Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM, USA,The Mind Research Network, Albuquerque, NM, USA
| | - D Cannon
- Centre for Neuroimaging and Cognitive Genomics (NICOG), Clinical Neuroimaging Laboratory, NCBES Galway Neuroscience Centre, National University of Ireland Galway, Galway, Ireland
| | - V Carr
- Neuroscience Research Australia and School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - S Catts
- Discipline of Psychiatry, School of Medicine, University of Queensland, Herston, QLD, Australia
| | - J Chen
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, USA
| | - J-x Chen
- Beijing Huilongguan Hospital, Beijing, China
| | - X Chen
- Worldwide Research and Development, Pfizer, Cambridge, MA, USA
| | | | - Kl K Cho
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - V Ciullo
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - A S Corvin
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland
| | - B Crespo-Facorro
- University Hospital Marqués de Valdecilla, IDIVAL, Department of Medicine and Psychiatry, School of Medicine, University of Cantabria, Santander, Spain,CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Santander, Spain
| | - V Cropley
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne and Melbourne Health, Carlton South, VIC, Australia
| | - P De Rossi
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy,Department NESMOS, Faculty of Medicine and Psychology, University ‘Sapienza’ of Rome, Rome, Italy,Department of Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy
| | - C M Diaz-Caneja
- Child and Adolescent Psychiatry Department, Hospital General Universitario Gregorio Marañón, School of Medicine, Universidad Complutense, IiSGM, CIBERSAM, Madrid, Spain
| | - E W Dickie
- Center for Addiction and Mental Health, Toronto, ON, Canada
| | - S Ehrlich
- Division of Psychological and Social Medicine and Developmental Neurosciences, Technische Universität Dresden, Faculty of Medicine, University Hospital C.G. Carus, Dresden, Germany
| | - F-m Fan
- Beijing Huilongguan Hospital, Beijing, China
| | - J Faskowitz
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - H Fatouros-Bergman
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden
| | - L Flyckt
- University of New South Wales, School of Psychiatry, Sydney, NSW, Australia,The University of Queensland, Queensland Brain Institute and Centre for Advanced Imaging, Brisbane, QLD, Australia
| | - J M Ford
- University of California, VAMC, San Francisco, CA, USA
| | - J-P Fouche
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - M Fukunaga
- Division of Cerebral Integration, National Institute for Physiological Sciences, Aichi, Japan
| | - M Gill
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland
| | - D C Glahn
- Olin Neuropsychiatric Research Center, Institute of Living, Hartford Hospital and Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - R Gollub
- Harvard Medical School, Boston, MA, USA,Departments of Psychiatry and Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - E D Goudzwaard
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA
| | - H Guo
- Zhumadian Psychiatry Hospital, Henan Province, China
| | - R E Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - R C Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - T P Gurholt
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - R Hashimoto
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan,Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan
| | - S N Hatton
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
| | - F A Henskens
- School of Electrical Engineering and Computer Science, University of Newcastle, Callaghan, NSW, Australia,Health Behaviour Research Group, University of Newcastle, Callaghan, NSW, Australia,Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - D P Hibar
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - I B Hickie
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
| | - L E Hong
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - J Horacek
- National Institute of Mental Health, Klecany, Czech Republic,Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - F M Howells
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - H E Hulshoff Pol
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C L Hyde
- Worldwide Research and Development, Pfizer, Cambridge, MA, USA
| | - D Isaev
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - A Jablensky
- University of Western Australia, Perth, WA, Australia
| | - P R Jansen
- Erasmus University Medical Center, Rotterdam, The Netherlands
| | - J Janssen
- Child and Adolescent Psychiatry Department, Hospital General Universitario Gregorio Marañón, School of Medicine, Universidad Complutense, IiSGM, CIBERSAM, Madrid, Spain,Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - E G Jönsson
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden
| | - L A Jung
- Laboratory for Neuroimaging, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Goethe University, Frankfurt/Main, Germany
| | - R S Kahn
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Z Kikinis
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - K Liu
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne and Melbourne Health, Carlton South, VIC, Australia
| | - P Klauser
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne and Melbourne Health, Carlton South, VIC, Australia,Brain and Mental Health Laboratory, Monash Institute of Cognitive and Clinical Neurosciences, School of Psychological Sciences and Monash Biomedical Imaging, Monash University, Clayton, VIC, Australia,Department of Psychiatry, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland
| | - C Knöchel
- Laboratory for Neuroimaging, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Goethe University, Frankfurt/Main, Germany
| | - M Kubicki
- Departments of Psychiatry and Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - J Lagopoulos
- Sunshine Coast Mind and Neuroscience Institute, University of the Sunshine Coast QLD, Australia, Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
| | - C Langen
- Erasmus University Medical Center, Rotterdam, The Netherlands
| | - S Lawrie
- University of Edinburgh, Edinburgh, UK
| | - R K Lenroot
- Neuroscience Research Australia and School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - K O Lim
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - C Lopez-Jaramillo
- Research Group in Psychiatry (GIPSI), Department of Psychiatry, Faculty of Medicine, Universidad de Antioquia, Mood Disorder Program, Hospital Universitario San Vicente Fundación, Medellín, Colombia
| | - A Lyall
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - R C W Mandl
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - D H Mathalon
- University of California, VAMC, San Francisco, CA, USA
| | | | - S McCarthy-Jones
- Department of Psychiatry, Trinity College Dublin, Dublin, Ireland
| | - C McDonald
- Centre for Neuroimaging and Cognitive Genomics (NICOG), Clinical Neuroimaging Laboratory, NCBES Galway Neuroscience Centre, National University of Ireland Galway, Galway, Ireland
| | - S McEwen
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - T Melicher
- Third Faculty of Medicine, Charles University, Prague, Czech Republic,The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - R I Mesholam-Gately
- Harvard Medical School and Massachusetts Mental Health Center Public Psychiatry Division of the Beth Israel Deaconess, Medical Center, Boston, MA, USA
| | - P T Michie
- Hunter Medical Research Institute, Newcastle, NSW, Australia,The University of Newcastle, Newcastle, NSW, Australia,Schizophrenia Research Institute, Sydney, NSW, Australia
| | - B Mowry
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia and Queensland Centre for Mental Health Research, Brisbane and Queensland Centre for Mental Health Research, Brisbane, QLD, Australia
| | - B A Mueller
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - D T Newell
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - P O'Donnell
- Worldwide Research and Development, Pfizer, Cambridge, MA, USA
| | - V Oertel-Knöchel
- Laboratory for Neuroimaging, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Goethe University, Frankfurt/Main, Germany
| | - L Oestreich
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia and Queensland Centre for Mental Health Research, Brisbane and Queensland Centre for Mental Health Research, Brisbane, QLD, Australia
| | - S A Paciga
- Worldwide Research and Development, Pfizer, Cambridge, MA, USA
| | - C Pantelis
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne and Melbourne Health, Carlton South, VIC, Australia,Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia,Schizophrenia Research Institute, Sydney, NSW, Australia,Centre for Neural Engineering (CfNE), Department of Electrical and Electronic Engineering, University of Melbourne, Parkville, VIC, Australia
| | - O Pasternak
- Departments of Psychiatry and Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - G Pearlson
- Olin Neuropsychiatric Research Center, Institute of Living, Hartford Hospital and Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - G R Pellicano
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - A Pereira
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia
| | | | - F Piras
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy,School of Biomedical Sciences, Faculty of Health, the University of Newcastle, Callaghan, NSW, Australia
| | - S G Potkin
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA
| | - A Preda
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA
| | - P E Rasser
- Hunter Medical Research Institute, Newcastle, NSW, Australia,Priority Centre for Brain and Mental Health Research, The University of Newcastle, Newcastle, NSW, Australia
| | - D R Roalf
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - R Roiz
- University Hospital Marqués de Valdecilla, IDIVAL, Department of Medicine and Psychiatry, School of Medicine, University of Cantabria, Santander, Spain,CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Santander, Spain
| | - A Roos
- SU/UCT MRC Unit on Anxiety and Stress Disorders, Department of Psychiatry, Stellenbosch University, Stellenbosch, South Africa
| | - D Rotenberg
- Center for Addiction and Mental Health, Toronto, ON, Canada
| | - T D Satterthwaite
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - P Savadjiev
- Departments of Psychiatry and Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - U Schall
- Hunter Medical Research Institute, Newcastle, NSW, Australia,Priority Centre for Brain and Mental Health Research, The University of Newcastle, Newcastle, NSW, Australia
| | - R J Scott
- Hunter Medical Research Institute, Newcastle, NSW, Australia,School of Biomedical Sciences, Faculty of Health, the University of Newcastle, Callaghan, NSW, Australia
| | - M L Seal
- Murdoch Childrens Research Institute, The Royal Children’s Hospital, Parkville, VIC, Australia
| | - L J Seidman
- Harvard Medical School, Boston, MA, USA,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA,Harvard Medical School and Massachusetts Mental Health Center Public Psychiatry Division of the Beth Israel Deaconess, Medical Center, Boston, MA, USA
| | - C Shannon Weickert
- Schizophrenia Research Institute, Sydney, NSW, Australia,Neuroscience Research Australia, Sydney, NSW, Australia,School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - C D Whelan
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - M E Shenton
- Departments of Psychiatry and Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA,VA Boston Healthcare System, Boston, MA, USA
| | - J S Kwon
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - G Spalletta
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy,Division of Neuropsychiatry, Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
| | - F Spaniel
- National Institute of Mental Health, Klecany, Czech Republic,Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - E Sprooten
- Olin Neuropsychiatric Research Center, Institute of Living, Hartford Hospital and Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - M Stäblein
- Laboratory for Neuroimaging, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Goethe University, Frankfurt/Main, Germany
| | - D J Stein
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa,Department of Psychiatry and MRC Unit on Anxiety and Stress Disorders, University of Cape Town, Cape Town, South Africa
| | - S Sundram
- Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia,Department of Psychiatry, School of Clinical Sciences, Monash University and Monash Health, Clayton, VIC, Australia
| | - Y Tan
- Beijing Huilongguan Hospital, Beijing, China
| | - S Tan
- Beijing Huilongguan Hospital, Beijing, China
| | - S Tang
- Chongqing Three Gorges Central Hospital, Chongqing, China
| | - H S Temmingh
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - L T Westlye
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Psychology, University of Oslo, Oslo, Norway
| | - S Tønnesen
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - D Tordesillas-Gutierrez
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Santander, Spain,Neuroimaging Unit, Technological Facilities, Valdecilla Biomedical Research Institute IDIVAL, Santander, Spain
| | - N T Doan
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - J Vaidya
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - N E M van Haren
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C D Vargas
- Research Group in Psychiatry (GIPSI), Department of Psychiatry, Faculty of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - D Vecchio
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - D Velakoulis
- Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - A Voineskos
- Kimel Family Translational Imaging-Genetics Research Laboratory, Campbell Family Mental Health Research Institute, CAMH Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - J Q Voyvodic
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Z Wang
- Beijing Huilongguan Hospital, Beijing, China
| | - P Wan
- Zhumadian Psychiatry Hospital, Henan Province, China
| | - D Wei
- Luoyang Fifth People's Hospital, Henan Province, China
| | - T W Weickert
- Schizophrenia Research Institute, Sydney, NSW, Australia,Neuroscience Research Australia, Sydney, NSW, Australia,School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - H Whalley
- University of Edinburgh, Edinburgh, UK
| | - T White
- Erasmus University Medical Center, Rotterdam, The Netherlands
| | - T J Whitford
- University of New South Wales, School of Psychiatry, Sydney, NSW, Australia
| | - J D Wojcik
- Harvard Medical School and Massachusetts Mental Health Center Public Psychiatry Division of the Beth Israel Deaconess, Medical Center, Boston, MA, USA
| | - H Xiang
- Chongqing Three Gorges Central Hospital, Chongqing, China
| | - Z Xie
- Worldwide Research and Development, Pfizer, Cambridge, MA, USA
| | - H Yamamori
- Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan
| | - F Yang
- Beijing Huilongguan Hospital, Beijing, China
| | - N Yao
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - G Zhang
- Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore, MD, USA
| | - J Zhao
- Centre for Neuroimaging and Cognitive Genomics (NICOG), Clinical Neuroimaging Laboratory, NCBES Galway Neuroscience Centre, National University of Ireland Galway, Galway, Ireland,School of Psychology, Shaanxi Normal University and Key Laboratory for Behavior and Cognitive Neuroscience of Shaanxi Province, Xi’an, Shaanxi, China
| | - T G M van Erp
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA
| | - J Turner
- Psychology Department & Neuroscience Institute, Georgia State University, Atlanta, GA, USA
| | - P M Thompson
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - G Donohoe
- Centre for Neuroimaging and Cognitive Genomics (NICOG), Clinical Neuroimaging Laboratory, NCBES Galway Neuroscience Centre, National University of Ireland Galway, Galway, Ireland
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8
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Dymerska D, Gołębiewska K, Kuświk M, Rudnicka H, Scott RJ, Billings R, Pławski A, Boruń P, Siołek M, Kozak-Klonowska B, Szwiec M, Kilar E, Huzarski T, Byrski T, Lubiński J, Kurzawski G. New EPCAM founder deletion in Polish population. Clin Genet 2017; 92:649-653. [PMID: 28369810 DOI: 10.1111/cge.13026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/23/2017] [Accepted: 03/28/2017] [Indexed: 01/30/2023]
Abstract
It is well known that founder mutations associated with cancer risk have useful implications for molecular diagnostics. We report the presence of a founder mutation in EPCAM involved in the etiology of Lynch syndrome (LS). The mutation extends nearly 8.7 kb (c.858 + 2478_*4507del) and is shared by 8 Polish families. Family members suffered almost exclusively from colorectal cancer; however, pancreatic and gastric cancers were also apparent. Next to mutations c. 2041G>A in MLH1 gene and c.942+3A>T in MSH2, the deletion mutation encompassing EPCAM is one of the most common causative changes responsible for LS in Poland.
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Affiliation(s)
- D Dymerska
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - K Gołębiewska
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - M Kuświk
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - H Rudnicka
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - R J Scott
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland.,Discipline of Medical Genetics, University of Newcastle, Newcastle, Australia.,Division of Genetics, John Hunter Hospital, Newcastle, Australia
| | - R Billings
- Division of Genetics, John Hunter Hospital, Newcastle, Australia
| | - A Pławski
- Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland.,Department of General, Endocrinological Surgery and Gastroenterological Oncology, Poznan University of Medical Sciences, Poznań, Poland
| | - P Boruń
- Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland
| | - M Siołek
- Department of General, Endocrinological Surgery and Gastroenterological Oncology, Poznan University of Medical Sciences, Poznań, Poland.,Holy Cross Cancer Center, Counselling Unit, Kielce, Poland
| | - B Kozak-Klonowska
- Department of General, Endocrinological Surgery and Gastroenterological Oncology, Poznan University of Medical Sciences, Poznań, Poland.,Holy Cross Cancer Center, Counselling Unit, Kielce, Poland
| | - M Szwiec
- Holy Cross Cancer Center, Counselling Unit, Kielce, Poland.,Regional Oncology Center, Counselling Unit, Opole, Poland
| | - E Kilar
- Regional Oncology Center, Counselling Unit, Opole, Poland.,Regional Oncology Center, Counselling Unit, Świdnica, Poland
| | - T Huzarski
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - T Byrski
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - J Lubiński
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - G Kurzawski
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
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9
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Abdullah N, Abdul Murad NA, Mohd Haniff EA, Syafruddin SE, Attia J, Oldmeadow C, Kamaruddin MA, Abd Jalal N, Ismail N, Ishak M, Jamal R, Scott RJ, Holliday EG. Predicting type 2 diabetes using genetic and environmental risk factors in a multi-ethnic Malaysian cohort. Public Health 2017; 149:31-38. [PMID: 28528225 DOI: 10.1016/j.puhe.2017.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/17/2017] [Accepted: 04/05/2017] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Malaysia has a high and rising prevalence of type 2 diabetes (T2D). While environmental (non-genetic) risk factors for the disease are well established, the role of genetic variations and gene-environment interactions remain understudied in this population. This study aimed to estimate the relative contributions of environmental and genetic risk factors to T2D in Malaysia and also to assess evidence for gene-environment interactions that may explain additional risk variation. STUDY DESIGN This was a case-control study including 1604 Malays, 1654 Chinese and 1728 Indians from the Malaysian Cohort Project. METHODS The proportion of T2D risk variance explained by known genetic and environmental factors was assessed by fitting multivariable logistic regression models and evaluating McFadden's pseudo R2 and the area under the receiver-operating characteristic curve (AUC). Models with and without the genetic risk score (GRS) were compared using the log likelihood ratio Chi-squared test and AUCs. Multiplicative interaction between genetic and environmental risk factors was assessed via logistic regression within and across ancestral groups. Interactions were assessed for the GRS and its 62 constituent variants. RESULTS The models including environmental risk factors only had pseudo R2 values of 16.5-28.3% and AUC of 0.75-0.83. Incorporating a genetic score aggregating 62 T2D-associated risk variants significantly increased the model fit (likelihood ratio P-value of 2.50 × 10-4-4.83 × 10-12) and increased the pseudo R2 by about 1-2% and AUC by 1-3%. None of the gene-environment interactions reached significance after multiple testing adjustment, either for the GRS or individual variants. For individual variants, 33 out of 310 tested associations showed nominal statistical significance with 0.001 < P < 0.05. CONCLUSION This study suggests that known genetic risk variants contribute a significant but small amount to overall T2D risk variation in Malaysian population groups. If gene-environment interactions involving common genetic variants exist, they are likely of small effect, requiring substantially larger samples for detection.
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Affiliation(s)
- N Abdullah
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, NSW, Australia; UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - N A Abdul Murad
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - E A Mohd Haniff
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - S E Syafruddin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - J Attia
- Clinical Research Design, IT and Statistical Support (CReDITSS) Unit, Hunter Medical Research Institute, Newcastle, NSW, Australia; Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, Faculty of Health, University of Newcastle, Newcastle, NSW, Australia
| | - C Oldmeadow
- Clinical Research Design, IT and Statistical Support (CReDITSS) Unit, Hunter Medical Research Institute, Newcastle, NSW, Australia; Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, Faculty of Health, University of Newcastle, Newcastle, NSW, Australia
| | - M A Kamaruddin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - N Abd Jalal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - N Ismail
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - M Ishak
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - R Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - R J Scott
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, NSW, Australia; Hunter Area Pathology Service, John Hunter Hospital, Newcastle, NSW, Australia
| | - E G Holliday
- Clinical Research Design, IT and Statistical Support (CReDITSS) Unit, Hunter Medical Research Institute, Newcastle, NSW, Australia; Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, Faculty of Health, University of Newcastle, Newcastle, NSW, Australia.
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10
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Campbell IG, Thompson ER, Rowely SM, Li N, McInerny S, Devereux L, Wong-Brown MW, Trainer AH, Mitchell G, Scott RJ, James PA. Abstract P2-09-02: Panel testing for familial breast cancer: Tension at the boundary of research and clinical care. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p2-09-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Gene panel sequencing is revolutionizing germline risk assessment for hereditary breast cancer. Despite scant evidence supporting the role of many of these genes in breast cancer predisposition, results are often reported to families as the definitive explanation for their family history. We assessed the frequency of mutations in 18 genes commonly included in hereditary breast cancer panels among 2,000 index cases from breast cancer families and 1,997 population controls. Cases were predominantly breast cancer-affected women referred to specialized familial cancer centers (BRCA1 and BRCA2 wild-type). Controls were cancer-free women from the LifePool study (www.lifepool.org). Sequencing data were filtered for known pathogenic or novel loss of function mutations.
The frequency of pathogenic mutations in BRCA1 and BRCA2 in the control group was 0.2% (4 mutations) and 0.4% (8 mutations), respectively, which is consistent with previous indirect estimates for Caucasian populations but to our knowledge this the largest direct assessment of their prevalence.
Excluding 18 mutations identified in BRCA1 and BRCA2 among the cases and controls, a total of 69 cases (3.5%) and 26 controls (1.3%) were found to carry an "actionable mutation". PALB2 was most frequently mutated (22 cases, 3 controls), while no mutations were identified in PTEN or STK11. Among the remaining genes, loss of function mutations were rare with similar frequency between cases and controls.
The frequency of mutations in most breast cancer panel genes among individuals selected for possible hereditary breast cancer is low and in many cases similar or even lower than that observed among cancer-free population controls. While multi-gene panels can significantly aid in cancer risk management, they equally have the potential to provide clinical misinformation and harm at the individual level if the data is not interpreted cautiously.
Citation Format: Campbell IG, Thompson ER, Rowely SM, Li N, McInerny S, Devereux L, Wong-Brown MW, Trainer AH, Mitchell G, Scott RJ, James PA. Panel testing for familial breast cancer: Tension at the boundary of research and clinical care. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-09-02.
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Affiliation(s)
- IG Campbell
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia; Hunter Area Pathology Service, Newcastle, New South Wales, Australia
| | - ER Thompson
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia; Hunter Area Pathology Service, Newcastle, New South Wales, Australia
| | - SM Rowely
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia; Hunter Area Pathology Service, Newcastle, New South Wales, Australia
| | - N Li
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia; Hunter Area Pathology Service, Newcastle, New South Wales, Australia
| | - S McInerny
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia; Hunter Area Pathology Service, Newcastle, New South Wales, Australia
| | - L Devereux
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia; Hunter Area Pathology Service, Newcastle, New South Wales, Australia
| | - MW Wong-Brown
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia; Hunter Area Pathology Service, Newcastle, New South Wales, Australia
| | - AH Trainer
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia; Hunter Area Pathology Service, Newcastle, New South Wales, Australia
| | - G Mitchell
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia; Hunter Area Pathology Service, Newcastle, New South Wales, Australia
| | - RJ Scott
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia; Hunter Area Pathology Service, Newcastle, New South Wales, Australia
| | - PA James
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia; Hunter Area Pathology Service, Newcastle, New South Wales, Australia
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11
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Ibrahim-Verbaas CA, Bressler J, Debette S, Schuur M, Smith AV, Bis JC, Davies G, Trompet S, Smith JA, Wolf C, Chibnik LB, Liu Y, Vitart V, Kirin M, Petrovic K, Polasek O, Zgaga L, Fawns-Ritchie C, Hoffmann P, Karjalainen J, Lahti J, Llewellyn DJ, Schmidt CO, Mather KA, Chouraki V, Sun Q, Resnick SM, Rose LM, Oldmeadow C, Stewart M, Smith BH, Gudnason V, Yang Q, Mirza SS, Jukema JW, deJager PL, Harris TB, Liewald DC, Amin N, Coker LH, Stegle O, Lopez OL, Schmidt R, Teumer A, Ford I, Karbalai N, Becker JT, Jonsdottir MK, Au R, Fehrmann RSN, Herms S, Nalls M, Zhao W, Turner ST, Yaffe K, Lohman K, van Swieten JC, Kardia SLR, Knopman DS, Meeks WM, Heiss G, Holliday EG, Schofield PW, Tanaka T, Stott DJ, Wang J, Ridker P, Gow AJ, Pattie A, Starr JM, Hocking LJ, Armstrong NJ, McLachlan S, Shulman JM, Pilling LC, Eiriksdottir G, Scott RJ, Kochan NA, Palotie A, Hsieh YC, Eriksson JG, Penman A, Gottesman RF, Oostra BA, Yu L, DeStefano AL, Beiser A, Garcia M, Rotter JI, Nöthen MM, Hofman A, Slagboom PE, Westendorp RGJ, Buckley BM, Wolf PA, Uitterlinden AG, Psaty BM, Grabe HJ, Bandinelli S, Chasman DI, Grodstein F, Räikkönen K, Lambert JC, Porteous DJ, Price JF, Sachdev PS, Ferrucci L, Attia JR, Rudan I, Hayward C, Wright AF, Wilson JF, Cichon S, Franke L, Schmidt H, Ding J, de Craen AJM, Fornage M, Bennett DA, Deary IJ, Ikram MA, Launer LJ, Fitzpatrick AL, Seshadri S, van Duijn CM, Mosley TH. GWAS for executive function and processing speed suggests involvement of the CADM2 gene. Mol Psychiatry 2016; 21:189-197. [PMID: 25869804 PMCID: PMC4722802 DOI: 10.1038/mp.2015.37] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/21/2015] [Accepted: 02/11/2015] [Indexed: 01/20/2023]
Abstract
To identify common variants contributing to normal variation in two specific domains of cognitive functioning, we conducted a genome-wide association study (GWAS) of executive functioning and information processing speed in non-demented older adults from the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) consortium. Neuropsychological testing was available for 5429-32,070 subjects of European ancestry aged 45 years or older, free of dementia and clinical stroke at the time of cognitive testing from 20 cohorts in the discovery phase. We analyzed performance on the Trail Making Test parts A and B, the Letter Digit Substitution Test (LDST), the Digit Symbol Substitution Task (DSST), semantic and phonemic fluency tests, and the Stroop Color and Word Test. Replication was sought in 1311-21860 subjects from 20 independent cohorts. A significant association was observed in the discovery cohorts for the single-nucleotide polymorphism (SNP) rs17518584 (discovery P-value=3.12 × 10(-8)) and in the joint discovery and replication meta-analysis (P-value=3.28 × 10(-9) after adjustment for age, gender and education) in an intron of the gene cell adhesion molecule 2 (CADM2) for performance on the LDST/DSST. Rs17518584 is located about 170 kb upstream of the transcription start site of the major transcript for the CADM2 gene, but is within an intron of a variant transcript that includes an alternative first exon. The variant is associated with expression of CADM2 in the cingulate cortex (P-value=4 × 10(-4)). The protein encoded by CADM2 is involved in glutamate signaling (P-value=7.22 × 10(-15)), gamma-aminobutyric acid (GABA) transport (P-value=1.36 × 10(-11)) and neuron cell-cell adhesion (P-value=1.48 × 10(-13)). Our findings suggest that genetic variation in the CADM2 gene is associated with individual differences in information processing speed.
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Affiliation(s)
- CA Ibrahim-Verbaas
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus
University Medical Center, Rotterdam, The Netherlands,Department of Neurology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - J Bressler
- Human Genetics Center, School of Public Health, University of
Texas Health Science Center at Houston, Houston, TX, USA,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - S Debette
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA,Institut National de la Santé et de la Recherche
Médicale (INSERM), U897, Epidemiology and Biostatistics, University of Bordeaux,
Bordeaux, France,Department of Neurology, Bordeaux University Hospital, Bordeaux,
France,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - M Schuur
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus
University Medical Center, Rotterdam, The Netherlands,Department of Neurology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - AV Smith
- Icelandic Heart Association, Kopavogur, Iceland,Faculty of Medicine, University of Iceland, Reykjavik,
Iceland,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - JC Bis
- Cardiovascular Health Research Unit, Department of Medicine,
University of Washington, Seattle, WA, USA,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - G Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - S Trompet
- Department of Cardiology, Leiden University Medical Center,
Leiden, The Netherlands,Department of Gerontology and Geriatrics, Leiden University
Medical Center, Leiden, The Netherlands
| | - JA Smith
- Department of Epidemiology, University of Michigan, Ann Arbor,
MI, USA
| | - C Wolf
- RG Statistical Genetics, Max Planck Institute of Psychiatry,
Munich, Germany
| | - LB Chibnik
- Program in Translational Neuropsychiatric Genomics, Department
of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Y Liu
- Department of Epidemiology, Wake Forest School of Medicine,
Winston-Salem, NC, USA
| | - V Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular
Medicine, University of Edinburgh, Edinburgh, UK
| | - M Kirin
- Centre for Population Health Sciences, University of Edinburgh,
Edinburgh, UK
| | - K Petrovic
- Department of Neurology, Medical University and General
Hospital of Graz, Graz, Austria
| | - O Polasek
- Department of Public Health, University of Split, Split,
Croatia
| | - L Zgaga
- Department of Public Health and Primary Care, Trinity College
Dublin, Dublin, Ireland
| | - C Fawns-Ritchie
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK
| | - P Hoffmann
- Institute of Neuroscience and Medicine (INM -1), Research
Center Juelich, Juelich, Germany,Division of Medical Genetics, Department of Biomedicine,
University of Basel, Basel, Switzerland,Department of Genomics, Life and Brain Research Center,
Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - J Karjalainen
- Department of Genetics, University Medical Centre Groningen,
University of Groningen, Groningen, The Netherlands
| | - J Lahti
- Institute of Behavioural Sciences, University of Helsinki,
Helsinki, Finland,Folkhälsan Research Centre, Helsinki, Finland
| | - DJ Llewellyn
- Institute of Biomedical and Clinical Sciences, University of
Exeter Medical School, Exeter, UK
| | - CO Schmidt
- Institute for Community Medicine, University Medicine
Greifswald, Greifswald, Germany
| | - KA Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW
Medicine, University of New South Wales, Sydney, Australia
| | - V Chouraki
- Inserm, U1167, Institut Pasteur de Lille, Université
Lille-Nord de France, Lille, France
| | - Q Sun
- Channing Division of Network Medicine, Department of Medicine,
Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - SM Resnick
- Laboratory of Behavioral Neuroscience, National Institute on
Aging, NIH, Baltimore, MD, USA
| | - LM Rose
- Division of Preventive Medicine, Brigham and Women's Hospital,
Boston, MA, USA
| | - C Oldmeadow
- Hunter Medical Research Institute and Faculty of Health,
University of Newcastle, Newcastle, NSW, Australia
| | - M Stewart
- Centre for Population Health Sciences, University of Edinburgh,
Edinburgh, UK
| | - BH Smith
- Medical Research Institute, University of Dundee, Dundee,
UK
| | - V Gudnason
- Icelandic Heart Association, Kopavogur, Iceland,Faculty of Medicine, University of Iceland, Reykjavik,
Iceland
| | - Q Yang
- The National Heart Lung and Blood Institute's Framingham Heart
Study, Framingham, MA, USA,Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
| | - SS Mirza
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The
Netherlands
| | - JW Jukema
- Department of Cardiology, Leiden University Medical Center,
Leiden, The Netherlands
| | - PL deJager
- Program in Translational Neuropsychiatric Genomics, Department
of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - TB Harris
- Laboratory of Epidemiology and Population Sciences, National
Institute on Aging, Bethesda, MD, USA
| | - DC Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh,
UK
| | - N Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus
University Medical Center, Rotterdam, The Netherlands
| | - LH Coker
- Division of Public Health Sciences and Neurology, Wake Forest
School of Medicine, Winston-Salem, NC, USA
| | - O Stegle
- Max Planck Institute for Developmental Biology, Max Planck
Institute for Intelligent Systems, Tübingen, Germany
| | - OL Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh,
PA, USA
| | - R Schmidt
- Department of Neurology, Medical University and General
Hospital of Graz, Graz, Austria
| | - A Teumer
- Interfaculty Institute for Genetics and Functional Genomics,
University Medicine Greifswald, Greifswald, Germany
| | - I Ford
- Robertson Center for biostatistics, University of Glasgow,
Glasgow, UK
| | - N Karbalai
- RG Statistical Genetics, Max Planck Institute of Psychiatry,
Munich, Germany
| | - JT Becker
- Department of Neurology, University of Pittsburgh, Pittsburgh,
PA, USA,Department of Psychiatry, University of Pittsburgh, Pittsburgh,
PA, USA,Department of Psychology, University of Pittsburgh, Pittsburgh,
PA, USA
| | | | - R Au
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA,The National Heart Lung and Blood Institute's Framingham Heart
Study, Framingham, MA, USA
| | - RSN Fehrmann
- Department of Genetics, University Medical Centre Groningen,
University of Groningen, Groningen, The Netherlands
| | - S Herms
- Division of Medical Genetics, Department of Biomedicine,
University of Basel, Basel, Switzerland,Department of Genomics, Life and Brain Research Center,
Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - M Nalls
- Laboratory of Neurogenetics, National Institute on Aging,
Bethesda, MD, USA
| | - W Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor,
MI, USA
| | - ST Turner
- Division of Nephrology and Hypertension, Department of Internal
Medicine, Mayo Clinic, Rochester, MN, USA
| | - K Yaffe
- Departments of Psychiatry, Neurology and Epidemiology,
University of California, San Francisco and San Francisco VA Medical Center, San Francisco,
CA, USA
| | - K Lohman
- Department of Epidemiology, Wake Forest School of Medicine,
Winston-Salem, NC, USA
| | - JC van Swieten
- Department of Neurology, Erasmus University Medical Center,
Rotterdam, The Netherlands
| | - SLR Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor,
MI, USA
| | - DS Knopman
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - WM Meeks
- Department of Medicine, Division of Geriatrics, University of
Mississippi Medical Center, Jackson, MS, USA
| | - G Heiss
- Department of Epidemiology, Gillings School of Global Public
Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - EG Holliday
- Hunter Medical Research Institute and Faculty of Health,
University of Newcastle, Newcastle, NSW, Australia
| | - PW Schofield
- School of Medicine and Public Health, Faculty of Health,
University of Newcastle, Newcastle, SW, Australia
| | - T Tanaka
- Translational Gerontology Branch, National Institute on Aging,
Baltimore, MD, USA
| | - DJ Stott
- Department of Cardiovascular and Medical Sciences, University
of Glasgow, Glasgow, UK
| | - J Wang
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
| | - P Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital,
Boston, MA, USA
| | - AJ Gow
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh,
UK
| | - A Pattie
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK
| | - JM Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK,Alzheimer Scotland Research Centre, Edinburgh, UK
| | - LJ Hocking
- Division of Applied Medicine, University of Aberdeen, Aberdeen,
UK
| | - NJ Armstrong
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW
Medicine, University of New South Wales, Sydney, Australia,Cancer Research Program, Garvan Institute of Medical Research,
Sydney, NSW, Australia,School of Mathematics & Statistics and Prince of Wales
Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - S McLachlan
- Centre for Population Health Sciences, University of Edinburgh,
Edinburgh, UK
| | - JM Shulman
- Department of Neurology, Baylor College of Medicine, Houston,
TX, USA,Department of Molecular and Human Genetics, The Jan and Dan
Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - LC Pilling
- Epidemiology and Public Health Group, University of Exeter
Medical School, Exeter, UK
| | | | - RJ Scott
- Hunter Medical Research Institute and Faculty of Health,
University of Newcastle, Newcastle, NSW, Australia
| | - NA Kochan
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW
Medicine, University of New South Wales, Sydney, Australia,Neuropsychiatric Institute, The Prince of Wales Hospital,
Sydney, NSW, Australia
| | - A Palotie
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Cambridge, UK,Institute for Molecular Medicine Finland (FIMM), University of
Helsinki, Helsinki, Finland,Department of Medical Genetics, University of Helsinki and
University Central Hospital, Helsinki, Finland
| | - Y-C Hsieh
- School of Public Health, Taipei Medical University, Taipei,
Taiwan
| | - JG Eriksson
- Folkhälsan Research Centre, Helsinki, Finland,Department of General Practice and Primary Health Care,
University of Helsinki, Helsinki, Finland,National Institute for Health and Welfare, Helsinki,
Finland,Helsinki University Central Hospital, Unit of General Practice,
Helsinki, Finland,Vasa Central Hospital, Vasa, Finland
| | - A Penman
- Center of Biostatistics and Bioinformatics, University of
Mississippi Medical Center, Jackson, MS, USA
| | - RF Gottesman
- Department of Neurology, Johns Hopkins University School of
Medicine, Baltimore, MD, USA
| | - BA Oostra
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus
University Medical Center, Rotterdam, The Netherlands
| | - L Yu
- Rush Alzheimer's Disease Center, Rush University Medical
Center, Chicago, IL, USA
| | - AL DeStefano
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA,The National Heart Lung and Blood Institute's Framingham Heart
Study, Framingham, MA, USA,Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
| | - A Beiser
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA,The National Heart Lung and Blood Institute's Framingham Heart
Study, Framingham, MA, USA,Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
| | - M Garcia
- Laboratory of Epidemiology and Population Sciences, National
Institute on Aging, Bethesda, MD, USA
| | - JI Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los
Angeles, CA, USA,Institute for Translational Genomics and Population Sciences,
Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA,
USA,Division of Genetic Outcomes, Department of Pediatrics,
Harbor-UCLA Medical Center, Torrance, CA, USA
| | - MM Nöthen
- Department of Genomics, Life and Brain Research Center,
Institute of Human Genetics, University of Bonn, Bonn, Germany,German Center for Neurodegenerative Diseases (DZNE), Bonn,
Germany
| | - A Hofman
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The
Netherlands
| | - PE Slagboom
- Department of Molecular Epidemiology, Leiden University Medical
Center, Leiden, The Netherlands
| | - RGJ Westendorp
- Leiden Academy of Vitality and Ageing, Leiden, The
Netherlands
| | - BM Buckley
- Department of Pharmacology and Therapeutics, University College
Cork, Cork, Ireland
| | - PA Wolf
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA,The National Heart Lung and Blood Institute's Framingham Heart
Study, Framingham, MA, USA
| | - AG Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The
Netherlands,Department of Internal Medicine, Erasmus University Medical
Center, Rotterdam, The Netherlands
| | - BM Psaty
- Cardiovascular Health Research Unit, Department of Medicine,
University of Washington, Seattle, WA, USA,Department of Epidemiology, University of Washington, Seattle,
WA, USA,Department of Health Services, University of Washington,
Seattle, WA, USA,Group Health Research Institute, Group Health, Seattle, WA,
USA
| | - HJ Grabe
- Department of Psychiatry and Psychotherapy, University Medicine
Greifswald, HELIOS-Hospital Stralsund, Stralsund, Germany
| | - S Bandinelli
- Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - DI Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital,
Boston, MA, USA
| | - F Grodstein
- Channing Division of Network Medicine, Department of Medicine,
Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - K Räikkönen
- Institute of Behavioural Sciences, University of Helsinki,
Helsinki, Finland
| | - J-C Lambert
- Inserm, U1167, Institut Pasteur de Lille, Université
Lille-Nord de France, Lille, France
| | - DJ Porteous
- Centre for Genomic and Experimental Medicine, Institute of
Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | - JF Price
- Centre for Population Health Sciences, University of Edinburgh,
Edinburgh, UK
| | - PS Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW
Medicine, University of New South Wales, Sydney, Australia,Neuropsychiatric Institute, The Prince of Wales Hospital,
Sydney, NSW, Australia
| | - L Ferrucci
- Translational Gerontology Branch, National Institute on Aging,
Baltimore, MD, USA
| | - JR Attia
- Hunter Medical Research Institute and Faculty of Health,
University of Newcastle, Newcastle, NSW, Australia
| | - I Rudan
- Centre for Population Health Sciences, University of Edinburgh,
Edinburgh, UK
| | - C Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular
Medicine, University of Edinburgh, Edinburgh, UK
| | - AF Wright
- MRC Human Genetics Unit, Institute of Genetics and Molecular
Medicine, University of Edinburgh, Edinburgh, UK
| | - JF Wilson
- Centre for Population Health Sciences, University of Edinburgh,
Edinburgh, UK
| | - S Cichon
- Division of Medical Genetics, Department of Biomedicine,
University of Basel, Basel, Switzerland,Department of Genomics, Life and Brain Research Center,
Institute of Human Genetics, University of Bonn, Bonn, Germany,Institute of Neuroscience and Medicine (INM-1), Research Center
Juelich, Juelich, Germany
| | - L Franke
- Department of Genetics, University Medical Centre Groningen,
University of Groningen, Groningen, The Netherlands
| | - H Schmidt
- Department of Neurology, Medical University and General
Hospital of Graz, Graz, Austria
| | - J Ding
- Department of Internal Medicine, Wake Forest University School
of Medicine, Winston-Salem, NC, USA
| | - AJM de Craen
- Department of Gerontology and Geriatrics, Leiden University
Medical Center, Leiden, The Netherlands
| | - M Fornage
- Institute for Molecular Medicine and Human Genetics Center,
University of Texas Health Science Center at Houston, Houston, TX, USA
| | - DA Bennett
- Rush Alzheimer's Disease Center, Rush University Medical
Center, Chicago, IL, USA
| | - IJ Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh,
UK
| | - MA Ikram
- Department of Neurology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The
Netherlands,Department of Radiology, Erasmus University Medical Center,
Rotterdam, The Netherlands
| | - LJ Launer
- Laboratory of Epidemiology and Population Sciences, National
Institute on Aging, Bethesda, MD, USA
| | - AL Fitzpatrick
- Department of Epidemiology, University of Washington, Seattle,
WA, USA
| | - S Seshadri
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA,The National Heart Lung and Blood Institute's Framingham Heart
Study, Framingham, MA, USA
| | - CM van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus
University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The
Netherlands
| | - TH Mosley
- Department of Medicine and Neurology, University of Mississippi
Medical Center, Jackson, MS, USA
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Abdullah N, Abdul Murad NA, Attia J, Oldmeadow C, Mohd Haniff EA, Syafruddin SE, Abd Jalal N, Ismail N, Ishak M, Jamal R, Scott RJ, Holliday EG. Characterizing the genetic risk for Type 2 diabetes in a Malaysian multi-ethnic cohort. Diabet Med 2015; 32:1377-84. [PMID: 25711284 DOI: 10.1111/dme.12735] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/03/2014] [Accepted: 02/20/2015] [Indexed: 12/12/2022]
Abstract
AIMS To characterize the association with Type 2 diabetes of known Type 2 diabetes risk variants in people in Malaysia of Malay, Chinese and Indian ancestry who participated in the Malaysian Cohort project. METHODS We genotyped 1604 people of Malay ancestry (722 cases, 882 controls), 1654 of Chinese ancestry (819 cases, 835 controls) and 1728 of Indian ancestry (851 cases, 877 controls). First, 62 candidate single-nucleotide polymorphisms previously associated with Type 2 diabetes were assessed for association via logistic regression within ancestral groups and then across ancestral groups using a meta-analysis. Second, estimated odds ratios were assessed for excess directional concordance with previously studied populations. Third, a genetic risk score aggregating allele dosage across the candidate single-nucleotide polymorphisms was tested for association within and across ancestral groups. RESULTS After Bonferroni correction, seven individual single-nucleotide polymorphisms were associated with Type 2 diabetes in the combined Malaysian sample. We observed a highly significant excess in concordance of effect directions between Malaysian and previously studied populations. The genetic risk score was strongly associated with Type 2 diabetes in all Malaysian groups, explaining from 1.0 to 1.7% of total Type 2 diabetes risk variance. CONCLUSION This study suggests there is substantial overlap of the genetic risk alleles underlying Type 2 diabetes in Malaysian and other populations.
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Affiliation(s)
- N Abdullah
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, Australia
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - N A Abdul Murad
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - J Attia
- Clinical Research Design, IT and Statistical Support Unit, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, Faculty of Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - C Oldmeadow
- Clinical Research Design, IT and Statistical Support Unit, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, Faculty of Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - E A Mohd Haniff
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - S E Syafruddin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - N Abd Jalal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - N Ismail
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - M Ishak
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - R Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - R J Scott
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Area Pathology Service, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - E G Holliday
- Clinical Research Design, IT and Statistical Support Unit, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, Faculty of Health, University of Newcastle, Newcastle, New South Wales, Australia
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Davies G, Armstrong N, Bis JC, Bressler J, Chouraki V, Giddaluru S, Hofer E, Ibrahim-Verbaas CA, Kirin M, Lahti J, van der Lee SJ, Le Hellard S, Liu T, Marioni RE, Oldmeadow C, Postmus I, Smith AV, Smith JA, Thalamuthu A, Thomson R, Vitart V, Wang J, Yu L, Zgaga L, Zhao W, Boxall R, Harris SE, Hill WD, Liewald DC, Luciano M, Adams H, Ames D, Amin N, Amouyel P, Assareh AA, Au R, Becker JT, Beiser A, Berr C, Bertram L, Boerwinkle E, Buckley BM, Campbell H, Corley J, De Jager PL, Dufouil C, Eriksson JG, Espeseth T, Faul JD, Ford I, Scotland G, Gottesman RF, Griswold ME, Gudnason V, Harris TB, Heiss G, Hofman A, Holliday EG, Huffman J, Kardia SLR, Kochan N, Knopman DS, Kwok JB, Lambert JC, Lee T, Li G, Li SC, Loitfelder M, Lopez OL, Lundervold AJ, Lundqvist A, Mather KA, Mirza SS, Nyberg L, Oostra BA, Palotie A, Papenberg G, Pattie A, Petrovic K, Polasek O, Psaty BM, Redmond P, Reppermund S, Rotter JI, Schmidt H, Schuur M, Schofield PW, Scott RJ, Steen VM, Stott DJ, van Swieten JC, Taylor KD, Trollor J, Trompet S, Uitterlinden AG, Weinstein G, Widen E, Windham BG, Jukema JW, Wright AF, Wright MJ, Yang Q, Amieva H, Attia JR, Bennett DA, Brodaty H, de Craen AJM, Hayward C, Ikram MA, Lindenberger U, Nilsson LG, Porteous DJ, Räikkönen K, Reinvang I, Rudan I, Sachdev PS, Schmidt R, Schofield PR, Srikanth V, Starr JM, Turner ST, Weir DR, Wilson JF, van Duijn C, Launer L, Fitzpatrick AL, Seshadri S, Mosley TH, Deary IJ. Genetic contributions to variation in general cognitive function: a meta-analysis of genome-wide association studies in the CHARGE consortium (N=53949). Mol Psychiatry 2015; 20:183-92. [PMID: 25644384 PMCID: PMC4356746 DOI: 10.1038/mp.2014.188] [Citation(s) in RCA: 260] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/11/2014] [Accepted: 11/24/2014] [Indexed: 01/14/2023]
Abstract
General cognitive function is substantially heritable across the human life course from adolescence to old age. We investigated the genetic contribution to variation in this important, health- and well-being-related trait in middle-aged and older adults. We conducted a meta-analysis of genome-wide association studies of 31 cohorts (N=53,949) in which the participants had undertaken multiple, diverse cognitive tests. A general cognitive function phenotype was tested for, and created in each cohort by principal component analysis. We report 13 genome-wide significant single-nucleotide polymorphism (SNP) associations in three genomic regions, 6q16.1, 14q12 and 19q13.32 (best SNP and closest gene, respectively: rs10457441, P=3.93 × 10(-9), MIR2113; rs17522122, P=2.55 × 10(-8), AKAP6; rs10119, P=5.67 × 10(-9), APOE/TOMM40). We report one gene-based significant association with the HMGN1 gene located on chromosome 21 (P=1 × 10(-6)). These genes have previously been associated with neuropsychiatric phenotypes. Meta-analysis results are consistent with a polygenic model of inheritance. To estimate SNP-based heritability, the genome-wide complex trait analysis procedure was applied to two large cohorts, the Atherosclerosis Risk in Communities Study (N=6617) and the Health and Retirement Study (N=5976). The proportion of phenotypic variation accounted for by all genotyped common SNPs was 29% (s.e.=5%) and 28% (s.e.=7%), respectively. Using polygenic prediction analysis, ~1.2% of the variance in general cognitive function was predicted in the Generation Scotland cohort (N=5487; P=1.5 × 10(-17)). In hypothesis-driven tests, there was significant association between general cognitive function and four genes previously associated with Alzheimer's disease: TOMM40, APOE, ABCG1 and MEF2C.
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Affiliation(s)
- G Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - N Armstrong
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia
| | - J C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - J Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - V Chouraki
- Inserm-UMR744, Institut Pasteur de Lille, Unité d'Epidémiologie et de Santé Publique, Lille, France,Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - S Giddaluru
- K.G. Jebsen Centre for Psychosis Research and the Norwegian Centre for Mental Disorders Research (NORMENT), Department of Clinical Science, University of Bergen, Bergen, Norway,Dr Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - E Hofer
- Department of Neurology, Medical University of Graz, Graz, Austria,Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - C A Ibrahim-Verbaas
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands,Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - M Kirin
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - J Lahti
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland,Folkhälsan Research Centre, Helsinki, Finland
| | - S J van der Lee
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - S Le Hellard
- K.G. Jebsen Centre for Psychosis Research and the Norwegian Centre for Mental Disorders Research (NORMENT), Department of Clinical Science, University of Bergen, Bergen, Norway,Dr Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - T Liu
- Max Planck Institute for Human Development, Berlin, Germany,Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - R E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Medical Genetics Section, University of Edinburgh Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - C Oldmeadow
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW, Australia
| | - I Postmus
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - A V Smith
- Icelandic Heart Association, Kopavogur, Iceland,University of Iceland, Reykjavik, Iceland
| | - J A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - A Thalamuthu
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - R Thomson
- Menzies Research Institute, Hobart, Tasmania
| | - V Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - J Wang
- Framingham Heart Study, Framingham, MA, USA,Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - L Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - L Zgaga
- Department of Public Health and Primary Care, Trinity College Dublin, Dublin, Ireland,Andrija Stampar School of Public Health, Medical School, University of Zagreb, Zagreb, Croatia
| | - W Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - R Boxall
- Medical Genetics Section, University of Edinburgh Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - S E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Medical Genetics Section, University of Edinburgh Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - W D Hill
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - D C Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - M Luciano
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - H Adams
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - D Ames
- National Ageing Research Institute, Royal Melbourne Hospital, Melbourne, VIC, Australia,Academic Unit for Psychiatry of Old Age, St George's Hospital, University of Melbourne, Kew, Australia
| | - N Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - P Amouyel
- Inserm-UMR744, Institut Pasteur de Lille, Unité d'Epidémiologie et de Santé Publique, Lille, France
| | - A A Assareh
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - R Au
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA,Framingham Heart Study, Framingham, MA, USA
| | - J T Becker
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA,Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA,Department of Psychology, University of Pittsburgh, Pittsburgh, PA, USA
| | - A Beiser
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA,Framingham Heart Study, Framingham, MA, USA
| | - C Berr
- Inserm, U106, Montpellier, France,Université Montpellier I, Montpellier, France
| | - L Bertram
- Max Planck Institute for Molecular Genetics, Berlin, Germany,Faculty of Medicine, School of Public Health, Imperial College, London, UK
| | - E Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA,Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center at Houston, Houston, TX, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - B M Buckley
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | - H Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - J Corley
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - P L De Jager
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - C Dufouil
- Inserm U708, Neuroepidemiology, Paris, France,Inserm U897, Université Bordeaux Segalen, Bordeaux, France
| | - J G Eriksson
- Folkhälsan Research Centre, Helsinki, Finland,National Institute for Health and Welfare, Helsinki, Finland,Department of General Practice and Primary health Care, University of Helsinki, Helsinki, Finland,Unit of General Practice, Helsinki University Central Hospital, Helsinki, Finland
| | - T Espeseth
- K.G. Jebsen Centre for Psychosis Research, Norwegian Centre For Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Psychology, University of Oslo, Oslo, Norway
| | - J D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - I Ford
- Robertson Center for Biostatistics, Glasgow, UK
| | - Generation Scotland
- Generation Scotland, University of Edinburgh Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - R F Gottesman
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - M E Griswold
- Center of Biostatistics and Bioinformatics, University of Mississippi Medical Center, Jackson, MS, USA
| | - V Gudnason
- Icelandic Heart Association, Kopavogur, Iceland,University of Iceland, Reykjavik, Iceland
| | - T B Harris
- Intramural Research Program National Institutes on Aging, National Institutes of Health, Bethesda, MD, USA
| | - G Heiss
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - A Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - E G Holliday
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW, Australia
| | - J Huffman
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - S L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - N Kochan
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia,Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, NSW, Australia
| | - D S Knopman
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - J B Kwok
- Neuroscience Research Australia, Randwick, NSW, Australia,School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - J-C Lambert
- Inserm-UMR744, Institut Pasteur de Lille, Unité d'Epidémiologie et de Santé Publique, Lille, France
| | - T Lee
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia,Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, NSW, Australia
| | - G Li
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - S-C Li
- Max Planck Institute for Human Development, Berlin, Germany,Technische Universität Dresden, Dresden, Germany
| | - M Loitfelder
- Department of Neurology, Medical University of Graz, Graz, Austria
| | - O L Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - A J Lundervold
- Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway,Kavli Research Centre for Aging and Dementia, Haraldsplass Deaconess Hospital, Bergen, Norway,K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - A Lundqvist
- Umeå Center for Functional Brain Imaging (UFBI), Umeå University, Umeå, Sweden
| | - K A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - S S Mirza
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - L Nyberg
- Umeå Center for Functional Brain Imaging (UFBI), Umeå University, Umeå, Sweden,Department of Radiation Sciences, Umeå University, Umeå, Sweden,Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - B A Oostra
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A Palotie
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland,Department of Medical Genetics, University of Helsinki and University Central Hospital, Helsinki, Finland
| | - G Papenberg
- Max Planck Institute for Human Development, Berlin, Germany,Karolinska Institutet, Aging Research Center, Stockholm University, Stockholm, Sweden
| | - A Pattie
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - K Petrovic
- Department of Neurology, Medical University of Graz, Graz, Austria
| | - O Polasek
- Faculty of Medicine, Department of Public Health, University of Split, Split, Croatia
| | - B M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA,Deparment of Epidemiology, University of Washington, Seattle, WA, USA,Deparment of Health Services, University of Washington, Seattle, WA, USA,Group Health Research Unit, Group Health Cooperative, Seattle, WA, USA
| | - P Redmond
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - S Reppermund
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - J I Rotter
- Institute for Translational Genomics and Population Sciences Los Angeles BioMedical Research Institute, Harbor-UCLA Medical Center, Los Angeles, CA, USA,Division of Genetic Outcomes, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles, CA, USA
| | - H Schmidt
- Department of Neurology, Medical University of Graz, Graz, Austria,Centre for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - M Schuur
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands,Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - P W Schofield
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, Australia
| | - R J Scott
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW, Australia
| | - V M Steen
- K.G. Jebsen Centre for Psychosis Research and the Norwegian Centre for Mental Disorders Research (NORMENT), Department of Clinical Science, University of Bergen, Bergen, Norway,Dr Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - D J Stott
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - J C van Swieten
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - K D Taylor
- Institute for Translational Genomics and Population Sciences Los Angeles BioMedical Research Institute, Harbor-UCLA Medical Center, Los Angeles, CA, USA,Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles, CA, USA
| | - J Trollor
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia,Department of Developmental Disability Neuropsychiatry, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - S Trompet
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands,Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - A G Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands,Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - G Weinstein
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA,Framingham Heart Study, Framingham, MA, USA
| | - E Widen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - B G Windham
- Division of Geriatrics, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - J W Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands,Durrer Center for Cardiogenetic Research, Amsterdam, The Netherlands,Interuniversity Cardiology Institute of the Netherlands, Utrecht, The Netherlands
| | - A F Wright
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - M J Wright
- Neuroimaging Genetics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Q Yang
- Framingham Heart Study, Framingham, MA, USA,Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - H Amieva
- Inserm U897, Université Bordeaux Segalen, Bordeaux, France
| | - J R Attia
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW, Australia
| | - D A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - H Brodaty
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia,Dementia Collaborative Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - A J M de Craen
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - C Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - M A Ikram
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands,Department of Radiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - U Lindenberger
- Max Planck Institute for Human Development, Berlin, Germany
| | - L-G Nilsson
- ARC, Karolinska Institutet, Stockholm and UFBI, Umeå University, Umeå, Sweden
| | - D J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Medical Genetics Section, University of Edinburgh Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK,Generation Scotland, University of Edinburgh Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - K Räikkönen
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland
| | - I Reinvang
- Department of Psychology, University of Oslo, Oslo, Norway
| | - I Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - P S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia,Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, NSW, Australia
| | - R Schmidt
- Department of Neurology, Medical University of Graz, Graz, Austria
| | - P R Schofield
- Neuroscience Research Australia, Sydney, NSW, Australia,Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - V Srikanth
- Menzies Research Institute, Hobart, Tasmania,Stroke and Ageing Research, Medicine, Southern Clinical School, Monash University, Melbourne, VIC, Australia
| | - J M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - S T Turner
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - D R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - J F Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - C van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - L Launer
- Intramural Research Program National Institutes on Aging, National Institutes of Health, Bethesda, MD, USA
| | - A L Fitzpatrick
- Deparment of Epidemiology, University of Washington, Seattle, WA, USA,Department of Global Health, University of Washington, Seattle, WA, USA
| | - S Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA,Framingham Heart Study, Framingham, MA, USA
| | - T H Mosley
- Division of Geriatrics, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - I J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh, UK,Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, Scotland, UK. E-mail:
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14
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Kurlapska A, Serrano-Fernández P, Baszuk P, Gupta S, Starzyńska T, Małecka-Panas E, Dabrowski A, Dębniak T, Kurzawski G, Suchy J, Rogoza-Mateja W, Scott RJ, Lubiński J. Cumulative effects of genetic markers and the detection of advanced colorectal neoplasias by population screening. Clin Genet 2014; 88:234-40. [PMID: 25117299 DOI: 10.1111/cge.12481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 07/25/2014] [Accepted: 08/05/2014] [Indexed: 01/12/2023]
Abstract
Genetic markers associated with colorectal cancer may be used in population screening for the early identification of patients at elevated risk of disease. We genotyped 3059 individuals with no cancer family history for eight markers previously associated with colorectal cancer. After colonoscopy, the genetic profile of cases with advanced colorectal neoplasia (213) was compared with the rest (2846). rs2066847 and rs6983267 were significantly associated with the risk of advanced colorectal neoplasia but with limited effect on their own [odds ratio (OR) 1.59; 95% confidence interval (CI) 1.02-2.41; p = 0.033 and OR 1.45; 95% CI 1.02-2.12; p = 0.044, respectively]. Cumulative effects, in contrast, were associated with high risk: the combination of rs2066847, rs6983267, rs4779584, rs3802842 and rs4939827 minimized the number of markers considered, while maximizing the relative size of the carrier group and the risk associated to it, for example, for at least two cumulated risk markers, OR is 2.57 (95% CI 1.50-4.71; corrected p-value 0.0079) and for three or more, OR is 3.57 (95% CI 1.91-6.96; corrected p-value 0.00074). The identification of cumulative models of - otherwise - low-risk markers could be valuable in defining risk groups, within an otherwise low-risk population (no cancer family history).
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Affiliation(s)
- A Kurlapska
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
| | | | - P Baszuk
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
| | - S Gupta
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
| | - T Starzyńska
- Department of Gastroenterology, Pomeranian Medical University, Szczecin, Poland
| | - E Małecka-Panas
- Department of Digestive Tract Diseases, Faculty of Medicine, Medical University of Łódź, Łódź, Poland
| | - A Dabrowski
- Department of Gastroenterology and Internal Medicine, Medical University of Białystok, Białystok, Poland
| | - T Dębniak
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
| | - G Kurzawski
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
| | - J Suchy
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
| | - W Rogoza-Mateja
- Department of Gastroenterology, Pomeranian Medical University, Szczecin, Poland
| | - R J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - J Lubiński
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
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15
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Graves MC, Benton M, Lea RA, Boyle M, Tajouri L, Macartney-Coxson D, Scott RJ, Lechner-Scott J. Methylation differences at the HLA-DRB1 locus in CD4+ T-Cells are associated with multiple sclerosis. Mult Scler 2013; 20:1033-41. [PMID: 24336351 DOI: 10.1177/1352458513516529] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 10/30/2013] [Indexed: 11/17/2022]
Abstract
BACKGROUND Multiple sclerosis (MS) is thought to be caused by T-cell mediated autoimmune dysfunction. Risk of developing MS is influenced by environmental and genetic factors. Modifiable differences in DNA methylation are recognized as epigenetic contributors to MS risk and may provide a valuable link between environmental exposure and inherited genetic systems. OBJECTIVES AND METHODS To identify methylation changes associated with MS, we performed a genome-wide DNA methylation analysis of CD4+ T cells from 30 patients with relapsing-remitting MS and 28 healthy controls using Illumina 450K methylation arrays. RESULTS A striking differential methylation signal was observed at chr. 6p21, with a peak signal at HLA-DRB1. After prioritisation, we identified a panel of 74 CpGs associated with MS in this cohort. Most notably we found evidence of a major effect CpG island in DRB1 in MS cases (pFDR < 3 × 10(-3)). In addition, we found 55 non-HLA CpGs that exhibited differential methylation, many of which localise to genes previously linked to MS. CONCLUSIONS Our findings provide the first evidence for association of DNA methylation at HLA-DRB1 in relation to MS risk. Further studies are now warranted to validate and understand how these findings are involved in MS pathology.
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Affiliation(s)
- M C Graves
- Centre for Information-Based Medicine, Hunter Medical Research Institute, Australia
| | - M Benton
- Griffith Health Institute, Griffith University, Australia Institute of Environmental Science and Research, New Zealand
| | - R A Lea
- Centre for Information-Based Medicine, Hunter Medical Research Institute, Australia Griffith Health Institute, Griffith University, Australia
| | - M Boyle
- Department of Immunology, Division of Medicine, John Hunter Hospital, Australia
| | - L Tajouri
- Faculty of Health Sciences and Medicine, Bond University, Australia
| | | | - R J Scott
- Centre for Information-Based Medicine, Hunter Medical Research Institute, Australia Division of Molecular Genetics, Hunter Area Pathology Service, Australia
| | - J Lechner-Scott
- Centre for Information-Based Medicine, Hunter Medical Research Institute, Australia Department of Neurology, Division of Medicine, John Hunter Hospital, Australia
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Green MJ, Cairns MJ, Wu J, Dragovic M, Jablensky A, Tooney PA, Scott RJ, Carr VJ. Genome-wide supported variant MIR137 and severe negative symptoms predict membership of an impaired cognitive subtype of schizophrenia. Mol Psychiatry 2013; 18:774-80. [PMID: 22733126 DOI: 10.1038/mp.2012.84] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Progress in determining the aetiology of schizophrenia (Sz) has arguably been limited by a poorly defined phenotype. We sought to delineate empirically derived cognitive subtypes of Sz to investigate the association of a genetic variant identified in a recent genome-wide association study with specific phenotypic characteristics of Sz. We applied Grade of Membership (GoM) analyses to 617 patients meeting ICD-10 criteria for Sz (n=526) or schizoaffective disorder (n=91), using cognitive performance indicators collected within the Australian Schizophrenia Research Bank. Cognitive variables included subscales from the Repeatable Battery for the Assessment of Neuropsychological Status, the Controlled Oral Word Association Test and the Letter Number Sequencing Test, and standardised estimates of premorbid and current intelligence quotient. The most parsimonious GoM solution yielded two subtypes of clinical cases reflecting those with cognitive deficits (CDs; N=294), comprising 47.6% of the sample who were impaired across all cognitive measures, and a cognitively spared group (CS; N=323) made up of the remaining 52.4% who performed relatively well on all cognitive tests. The CD subgroup were more likely to be unemployed, had an earlier illness onset, and greater severity of functional disability and negative symptoms than the CS group. Risk alleles on the MIR137 single-nucleotide polymorphism (SNP) predicted membership of CD subtype only in combination with higher severity of negative symptoms. These findings provide the first evidence for association of the MIR137 SNP with a specific Sz phenotype characterised by severe CDs and negative symptoms, consistent with the emerging role of microRNAs in the regulation of proteins responsible for neural development and function.
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Affiliation(s)
- M J Green
- School of Psychiatry, University of New South Wales, Research Unit for Schizophrenia Epidemiology, St Vincent's Hospital, Darlinghurst, NSW, Australia.
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Paszkowska-Szczur K, Scott RJ, Serrano-Fernandez P, Mirecka A, Gapska P, Górski B, Cybulski C, Maleszka R, Sulikowski M, Nagay L, Lubinski J, Dębniak T. Xeroderma pigmentosum genes and melanoma risk. Int J Cancer 2013; 133:1094-100. [PMID: 23436679 DOI: 10.1002/ijc.28123] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/11/2013] [Indexed: 01/22/2023]
Abstract
Xeroderma pigmentosum is a rare autosomal recessive disease that is associated with a severe deficiency in nucleotide excision repair. The presence of a distinct the nucleotide excision repair (NER) mutation signature in melanoma suggests that perturbations in this critical repair process are likely to be involved with disease risk. We hypothesized that persons with polymorphic NER gene(s) are likely to have reduced NER activity and are consequently at an increased risk of melanoma development. We assessed the association between 94 SNPs within seven XP genes (XPA-XPG) and the melanoma risk in the Polish population. We genotyped 714 unselected melanoma patients and 1,841 healthy adults to determine if there were any polymorphisms differentially represented in the disease group. We found that a significantly decreased risk of melanoma was associated with the Xeroderma pigmentosum complementation (XPC) rs2228000_CT genotype (odds ratio [OR] = 0.15; p < 0.001) and the rs2228000_TT genotype (OR = 0.11; p < 0.001) compared to the reference genotype. Haplotype analysis within XPC revealed the rs2228001_A + G1475A_G + G2061A_A + rs2228000_T + rs3731062_C haplotype (OR = 0.26; p < 0.05) was associated with a significantly decreased disease risk. The haplotype analysis within the Xeroderma pigmentosum group D (XPD) showed a modest association between two haplotypes and a decrease in melanoma risk. There were no major differences between the prevalence of the XP polymorphisms among young or older patients with melanoma. Linkage disequilibrium of XPC: rs2228001, G1475A, G2061A, rs2228000 and rs3731062 was found. The data from our study support the notion that only XPC and XPD genes are associated with melanoma susceptibility.
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Affiliation(s)
- K Paszkowska-Szczur
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland.
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18
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Acikyol B, Graham RM, Trinder D, House MJ, Olynyk JK, Scott RJ, Milward EA, Johnstone DM. Brain transcriptome perturbations in the transferrin receptor 2 mutant mouse support the case for brain changes in iron loading disorders, including effects relating to long-term depression and long-term potentiation. Neuroscience 2013; 235:119-28. [PMID: 23333676 DOI: 10.1016/j.neuroscience.2013.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 12/14/2012] [Accepted: 01/02/2013] [Indexed: 11/16/2022]
Abstract
Iron abnormalities within the brain are associated with several rare but severe neurodegenerative conditions. There is growing evidence that more common systemic iron loading disorders such as hemochromatosis can also have important effects on the brain. To identify features that are common across different forms of hemochromatosis, we used microarray and real-time reverse transcription polymerase chain reaction (RT-PCR) to assess brain transcriptome profiles of transferrin receptor 2 mutant mice (Tfr2(mut)), a model of a rare type of hereditary hemochromatosis, relative to wildtype control mice. The results were compared with our previous findings in dietary iron-supplemented wildtype mice and Hfe(-/-) mice, a model of a common type of hereditary hemochromatosis. For transcripts showing significant changes relative to controls across all three models, there was perfect (100%) directional concordance (i.e. transcripts were increased in all models or decreased in all models). Comparison of the two models of hereditary hemochromatosis, which showed more pronounced changes than the dietary iron-supplemented mice, revealed numerous common molecular effects. Pathway analyses highlighted changes for genes relating to long-term depression (6.8-fold enrichment, p=5.4×10(-7)) and, to a lesser extent, long-term potentiation (3.7-fold enrichment, p=0.01), with generalized reductions in transcription of key genes from these pathways, which are involved in modulating synaptic strength and efficacy and are essential for memory and learning. The agreement across the models suggests the findings are robust and strengthens previous evidence that iron loading disorders affect the brain. Perturbations of brain phenomena such as long-term depression and long-term potentiation might partly explain neurologic symptoms reported for some hemochromatosis patients.
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Affiliation(s)
- B Acikyol
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
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19
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Wong-Brown MW, McPhillips ML, Hipwell M, Pecenpetelovska G, Dooley S, Meldrum C, Scott RJ. cDNA analysis of the BRCA1 unclassified variant c.5194-12G>A. Clin Genet 2013; 84:505-6. [PMID: 23278966 DOI: 10.1111/cge.12052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 10/29/2012] [Accepted: 10/30/2012] [Indexed: 11/29/2022]
Affiliation(s)
- M W Wong-Brown
- Discipline of Medical Genetics, University of Newcastle, Newcastle, New South Wales, Australia; Centre for Information-Based Medicine, Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia
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20
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Wong-Brown MW, Li S, Wilkins M, Avery-Kiejda KA, Bowden NA, Scott RJ. Abstract P4-10-02: Targeted resequencing of BRCA1 and BRCA2 in inherited breast cancer. Cancer Res 2012. [DOI: 10.1158/0008-5472.sabcs12-p4-10-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Breast cancer is the leading cause of cancer-related deaths in women worldwide, affecting about 13,000 women every year in Australia. Inherited loss-of-function mutations in BRCA1 and BRCA2 predispose to high risk of breast and/or ovarian cancer. Since the discovery of breast cancer susceptibility genes BRCA1 and BRCA2 two decades ago, there have not been any other genes identified that play a significant role in predisposition to inherited breast cancer. A large proportion of individuals with inherited breast cancer are negative for BRCA mutations and despite numerous research efforts, further breast cancer susceptibility genes still remain elusive.
We hypothesize that genetic anomalies are present in the BRCA1 and BRCA2 genes in a subset of individuals with inherited breast cancer where no genetic anomalies where identified using traditional Sanger sequencing. This study aims were to identify genetic anomalies in BRCA1 and BRCA2 by completely re-sequencing 200 kilobases surrounding BRCA1 and BRCA2 using targeted massively parallel sequencing, or next-generation sequencing.
For this study, DNA was used from 10 individuals referred for genetic testing after meeting the criteria for inherited breast cancer, and had been screened for BRCA1 and BRCA2 mutations by the Hunter Area Pathology Service (Newcastle, NSW, Australia). All individuals used for this study did not harbour causative genetic changes in the coding regions of BRCA1 or BRCA2. Targeted next-generation paired-end sequencing of regions containing BRCA1 and BRCA2 was performed using Agilent SureSelect and an Illumina GAIIx (The Ramaciotti Centre for Gene Function Analysis). An average of 50x coverage was achieved across the targeted genomic region for all samples. The sequence data was aligned to the Human Reference Sequence 37.2. Single nucleotide polymorphisms present in dbSNP or the 1000 genomes project were removed from further analyses. Genetic differences in the form of single nucleotide variants (SNVs) and insertions/deletions (indels) were identified in most individuals tested in regions that had previously remained unexplored, such as the non-coding regions of BRCA1 and BRCA2, the 5′ UTR and promoter sites. Structural variations including large deletions, duplications, insertions, inversions and rearrangements were also investigated, but require further analysis and validation for confirmation.
This study has comprehensively investigated BRCA1 and BRCA2 and surrounding genomic regions in a mutation negative inherited breast cancer population. The issue of accuracy of mutation detection by traditional methods, such as Sanger sequencing alone, has also been addressed by this study. The outcome of this study is the increase in current knowledge of the genetic variations that results in the development and/or progression of inherited breast cancer, aid in the management of individuals with breast cancers by providing a more specific diagnosis of disease risk and provide information required for the development of personalized treatment.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-10-02.
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Affiliation(s)
- MW Wong-Brown
- University of Newcastle, NSW, Australia; University of New South Wales, Sydney, NSW, Australia; Hunter Area Pathology Service (HAPS), Newcastle, NSW, Australia
| | - S Li
- University of Newcastle, NSW, Australia; University of New South Wales, Sydney, NSW, Australia; Hunter Area Pathology Service (HAPS), Newcastle, NSW, Australia
| | - M Wilkins
- University of Newcastle, NSW, Australia; University of New South Wales, Sydney, NSW, Australia; Hunter Area Pathology Service (HAPS), Newcastle, NSW, Australia
| | - KA Avery-Kiejda
- University of Newcastle, NSW, Australia; University of New South Wales, Sydney, NSW, Australia; Hunter Area Pathology Service (HAPS), Newcastle, NSW, Australia
| | - NA Bowden
- University of Newcastle, NSW, Australia; University of New South Wales, Sydney, NSW, Australia; Hunter Area Pathology Service (HAPS), Newcastle, NSW, Australia
| | - RJ Scott
- University of Newcastle, NSW, Australia; University of New South Wales, Sydney, NSW, Australia; Hunter Area Pathology Service (HAPS), Newcastle, NSW, Australia
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Jakubowska A, Rozkrut D, Antoniou A, Hamann U, Scott RJ, McGuffog L, Healy S, Sinilnikova OM, Rennert G, Lejbkowicz F, Flugelman A, Andrulis IL, Glendon G, Ozcelik H, Thomassen M, Paligo M, Aretini P, Kantala J, Aroer B, von Wachenfeldt A, Liljegren A, Loman N, Herbst K, Kristoffersson U, Rosenquist R, Karlsson P, Stenmark-Askmalm M, Melin B, Nathanson KL, Domchek SM, Byrski T, Huzarski T, Gronwald J, Menkiszak J, Cybulski C, Serrano P, Osorio A, Cajal TR, Tsitlaidou M, Benítez J, Gilbert M, Rookus M, Aalfs CM, Kluijt I, Boessenkool-Pape JL, Meijers-Heijboer HEJ, Oosterwijk JC, van Asperen CJ, Blok MJ, Nelen MR, van den Ouweland AMW, Seynaeve C, van der Luijt RB, Devilee P, Easton DF, Peock S, Frost D, Platte R, Ellis SD, Fineberg E, Evans DG, Lalloo F, Eeles R, Jacobs C, Adlard J, Davidson R, Eccles D, Cole T, Cook J, Godwin A, Bove B, Stoppa-Lyonnet D, Caux-Moncoutier V, Belotti M, Tirapo C, Mazoyer S, Barjhoux L, Boutry-Kryza N, Pujol P, Coupier I, Peyrat JP, Vennin P, Muller D, Fricker JP, Venat-Bouvet L, Johannsson OT, Isaacs C, Schmutzler R, Wappenschmidt B, Meindl A, Arnold N, Varon-Mateeva R, Niederacher D, Sutter C, Deissler H, Preisler-Adams S, Simard J, Soucy P, Durocher F, Chenevix-Trench G, Beesley J, Chen X, Rebbeck T, Couch F, Wang X, Lindor N, Fredericksen Z, Pankratz VS, Peterlongo P, Bonanni B, Fortuzzi S, Peissel B, Szabo C, Mai PL, Loud JT, Lubinski J. Association of PHB 1630 C>T and MTHFR 677 C>T polymorphisms with breast and ovarian cancer risk in BRCA1/2 mutation carriers: results from a multicenter study. Br J Cancer 2012; 106:2016-24. [PMID: 22669161 PMCID: PMC3388557 DOI: 10.1038/bjc.2012.160] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 03/18/2012] [Accepted: 03/25/2012] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The variable penetrance of breast cancer in BRCA1/2 mutation carriers suggests that other genetic or environmental factors modify breast cancer risk. Two genes of special interest are prohibitin (PHB) and methylene-tetrahydrofolate reductase (MTHFR), both of which are important either directly or indirectly in maintaining genomic integrity. METHODS To evaluate the potential role of genetic variants within PHB and MTHFR in breast and ovarian cancer risk, 4102 BRCA1 and 2093 BRCA2 mutation carriers, and 6211 BRCA1 and 2902 BRCA2 carriers from the Consortium of Investigators of Modifiers of BRCA1 and BRCA2 (CIMBA) were genotyped for the PHB 1630 C>T (rs6917) polymorphism and the MTHFR 677 C>T (rs1801133) polymorphism, respectively. RESULTS There was no evidence of association between the PHB 1630 C>T and MTHFR 677 C>T polymorphisms with either disease for BRCA1 or BRCA2 mutation carriers when breast and ovarian cancer associations were evaluated separately. Analysis that evaluated associations for breast and ovarian cancer simultaneously showed some evidence that BRCA1 mutation carriers who had the rare homozygote genotype (TT) of the PHB 1630 C>T polymorphism were at increased risk of both breast and ovarian cancer (HR 1.50, 95%CI 1.10-2.04 and HR 2.16, 95%CI 1.24-3.76, respectively). However, there was no evidence of association under a multiplicative model for the effect of each minor allele. CONCLUSION The PHB 1630TT genotype may modify breast and ovarian cancer risks in BRCA1 mutation carriers. This association need to be evaluated in larger series of BRCA1 mutation carriers.
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Affiliation(s)
- A Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland.
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Vilain RE, Dudding T, Braye SG, Groombridge C, Meldrum C, Spigelman AD, Ackland S, Ashman L, Scott RJ. Can a familial gastrointestinal tumour syndrome be allelic with Waardenburg syndrome? Clin Genet 2011; 79:554-60. [PMID: 20636395 DOI: 10.1111/j.1399-0004.2010.01489.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Familial gastrointestinal stromal tumours (GISTs) are rare but otherwise well-characterized tumour syndromes, most commonly occurring on a background of germline-activating mutations in the tyrosine kinase receptor c-KIT. The associated clinical spectrum reflects the constitutive activation of this gene product across a number of cell lines, generating gain-of-function phenotypes in interstitial cells of Cajal (GIST and dysphagia), mast cells (mastocytosis) and melanocytes (hyperpigmentation). We report a three-generation kindred harbouring a c-KIT germline-activating mutation resulting in multifocal GISTs, dysphagia and a complex melanocyte hyperpigmentation and hypopigmentation disorder, the latter with features typical of those observed in Waardenburg type 2 syndrome (WS2F). Sequencing of genes known to be causative for WS [microphthalmia transcription factor (MITF), Pax3, Sox10, SNAI2 ] failed to show any candidate mutations to explain this complex cutaneous depigmentation phenotype. Our case report conclusively expands the clinical spectrum of familial GISTs and shows a hitherto unrecognized link to WS. Possible mechanisms responsible for this novel cause of WS2F will be discussed.
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Affiliation(s)
- R E Vilain
- Hunter Area Pathology Service, Hunter New England Health Service, Newcastle, NSW, Australia.
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23
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Dymerska D, Fernández P, Suchy J, Pławski A, Słomski R, Kąklewski K, Scott RJ, Gronwald J, Kładny J, Byrski T, Huzarski T, Lubiński J, Kurzawski G. Combined iPLEX and TaqMan assays to screen for 45 common mutations in Lynch syndrome and FAP patients. Hered Cancer Clin Pract 2011. [PMCID: PMC3108174 DOI: 10.1186/1897-4287-9-s2-a9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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24
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Affiliation(s)
- E G Holliday
- School of Biomedical Sciences, University of Newcastle, Newcastle, New South Wales, Australia
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25
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Abstract
Genomic imprinting, though most extensively studied in mammals, has long been known to perform an important role in seed development in flowering plants. In this chapter, an overview of what is known to date about genomic imprinting in flowering plants and how this knowledge came into being will be given.
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Affiliation(s)
- R Vinkenoog
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
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26
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Baines KJ, Simpson JL, Bowden NA, Scott RJ, Gibson PG. Differential gene expression and cytokine production from neutrophils in asthma phenotypes. Eur Respir J 2009; 35:522-31. [PMID: 19797135 DOI: 10.1183/09031936.00027409] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Asthma is characterised into eosinophilic and non-eosinophilic phenotypes based on inflammatory cell patterns in airway secretions. Neutrophils are important in innate immunity, and are increased in the airways in non-eosinophilic asthma. The present study investigated the activity of neutrophils in asthma phenotypes. Participants with eosinophilic (n = 8) and non-eosinophilic asthma (n = 9) and healthy controls (n = 11) underwent sputum induction and blood collection. Neutrophils were isolated and cultured with or without lipopolysaccharide. Cytokines were measured by ELISA, and gene expression was analysed using a gene expression microarray and quantitative PCR. In non-eosinophilic asthma, blood neutrophils released significantly higher levels of interleukin-8 at rest. Cytokine gene expression and sputum neutrophil protein production did not differ between asthma subtypes. Microarrays demonstrated closely related expression profiles from participants with non-eosinophilic asthma that were significantly distinct from those in eosinophilic asthma. A total of 317 genes were significantly altered in resting neutrophils from participants with non-eosinophilic asthma versus eosinophilic asthma, including genes related to cell motility and regulation of apoptosis. Non-eosinophilic and eosinophilic asthma are associated with specific gene expression profiles, providing further evidence that these phenotypes of asthma involve different molecular mechanisms of disease pathogenesis at the systemic level. The mechanisms of non-eosinophilic asthma may involve enhancement of blood neutrophil chemotaxis and survival.
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Affiliation(s)
- K J Baines
- Level 3, Hunter Medical Research Institute, John Hunter Hospital, Locked Bag 1, Hunter Region Mail Centre, Newcastle, NSW 2310, Australia.
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27
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Abstract
In this study we establish an efficient method for the regeneration for Boechera holboellii via somatic embryogenesis. Immature cotyledons from siliques of 4-6 month-old plants were cultured on MS medium supplemented with plant growth regulators (BA - 6-benzylaminopurine; NAA - alpha-naphthaleneacetic acid; TDZ - 1-phelyl-3-(1,2,3-thiadiazol-5-yl) urea: 2,4 D-2,4-dichlorophenoxy-acetic acid). A high frequency of embryogenic callus was produced after two weeks in culture. The somatic embryos were obtained with a frequency of 10% of explants on MS medium supplemented with 1.34 muM NAA + 8.87 muM BA and 2.68 muM NAA + 17.74 muM BA within 3 weeks in culture. The alternative regime of MS medium supplemented with 1.34 muM NAA + 4.44 muM BA produced somatic embryos at a frequency of 38%.
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Affiliation(s)
- K M Taskin
- Department of Biology, Canakkale Onsekiz Mart University, 17100 Canakkale Turkey.
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28
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Gapska P, Scott RJ, Serrano-Fernandez P, Mirecka A, Rassoud I, Górski B, Cybulski C, Huzarski T, Byrski T, Nagay L, Maleszka R, Sulikowski M, Lubinski J, Debniak T. Vitamin D receptor variants and the malignant melanoma risk: a population-based study. Cancer Epidemiol 2009; 33:103-7. [PMID: 19679055 DOI: 10.1016/j.canep.2009.06.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 06/12/2009] [Accepted: 06/17/2009] [Indexed: 01/07/2023]
Abstract
BACKGROUND There is continuing interest in identifying low-penetrance genes which are associated with an increased susceptibility to common types of cancer, including malignant melanoma. METHODS We sought to examine the association between four VDR common variants (rs1544410, rs731236, rs10735810, rs4516035) and the risk of melanoma in the Polish population. We also determined the prevalence of compound carriers of VDR and known MM genetic risk factors MC1R and CDKN2A (A148T) variants. We examined 763 unselected melanoma cases, 763 healthy adults matched for sex and age with the melanoma cases and 777 newborns. RESULTS None of the VDR variants alone or as compound carriers of two or more of the VDR genotypes were associated with MM risk. There were no major differences between the prevalences of the examined variants among patients with MM on UV-exposed and UV-non exposed skin areas, as well as among early-onset and late-onset cases. We found no association between VDR and MC1R or between VDR and CDKN2A common variants. A statistically significant over-representation of one VDR haplotype: rs731236_A+rs1544410_T (OR=3.2, p=0.02) was detected. Linkage disequilibrium of rs1544410 and rs731236 was confirmed. CONCLUSION To answer the question, whether VDR can be regarded as melanoma susceptibility gene, additional, large multi-center association studies have to be performed.
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Affiliation(s)
- P Gapska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
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29
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Milne E, Royle JA, de Klerk NH, Blair E, Bailey H, Cole C, Attia J, Scott RJ, Armstrong BK. Fetal growth and risk of childhood acute lymphoblastic leukemia: results from an Australian case-control study. Am J Epidemiol 2009; 170:221-8. [PMID: 19478236 DOI: 10.1093/aje/kwp117] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The relation between intrauterine growth and risk of childhood acute lymphoblastic leukemia was investigated in an Australian population-based case-control study that included 347 cases and 762 controls aged <15 years recruited from 2003 to 2006. Information on proportion of optimal birth weight, a measure of the appropriateness of fetal growth, was collected from mothers by questionnaire. Data were analyzed by using logistic regression. Risk of acute lymphoblastic leukemia was positively associated with proportion of optimal birth weight; the odds ratio for a 1-standard-deviation increase in proportion of optimal birth weight was 1.18 (95% confidence interval: 1.04, 1.35) after adjustment for the matching variables and potential confounders. This association was also present among children who did not have a high birth weight, suggesting that accelerated growth, rather than high birth weight per se, is associated with risk of acute lymphoblastic leukemia. Similar associations between proportion of optimal birth weight and acute lymphoblastic leukemia were observed for both sexes and across age groups and leukemia subtypes. Results of this study confirm earlier findings of a positive association between rapidity of fetal growth and subsequent risk of acute lymphoblastic leukemia in childhood, and they are consistent with a role for insulin-like growth factors in the causal pathway.
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Affiliation(s)
- E Milne
- Centre for Child Health Research, Telethon Institute for Child Health Research, University of Western Australia, Perth, Western Australia, Australia.
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Ashton KA, Proietto A, Otton G, Symonds I, McEvoy M, Attia J, Gilbert M, Hamann U, Scott RJ. Estrogen receptor polymorphisms and the risk of endometrial cancer. BJOG 2009; 116:1053-61. [PMID: 19438492 DOI: 10.1111/j.1471-0528.2009.02185.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE There is evidence that estrogens and some of their metabolites are involved in endometrial cancer pathogenesis. As estrogens mediate their effects via the estrogen receptors, ESR1 and ESR2, the objective of this investigation was to determine whether six single nucleotide polymorphisms (SNPs) in these two genes were over-represented in a population of endometrial cancer patients compared with a healthy matched control population, thereby associating differences in these genes with endometrial cancer. DESIGN The study is a case-control investigation large enough to detect a two-fold increased risk, assuming a dominant genetic model, with P = 0.05 and 80% power. SETTING The study and control populations were all from the Hunter-New England region of New South Wales, Australia collected between the years 1992 and 2005. POPULATION The study consisted of 191 endometrial cancer patients and 291 healthy controls matched for gender and age. METHODS Two SNPs in ESR1 and four SNPs in ESR2 were genotyped using PCR-based restriction fragment length polymorphism analysis and real-time PCR. Odds ratios were calculated using unconditional logistic regression and SIMHAP was used for haplotype analysis, adjusting for potential endometrial cancer risk factors. Kaplan-Meier survival analysis, Cox regression and t tests were used to examine the patient's age of diagnosis of endometrial cancer and genotype. MAIN OUTCOME MEASURES Over-representation of ESR1 and ESR2 polymorphisms in the endometrial cancer population compared with the control population indicates an involvement in the development and/or progression of disease. RESULTS Two ESR1 (rs2234693 and rs9340799) and two ESR2 (rs1255998 and rs944050) polymorphisms were associated with an increased risk of endometrial cancer. Following adjustment for risk factors, the association with the ESR1 and ESR2 polymorphisms (rs2234693, rs1255998 and rs944050) remained highly significant. Haplotype analysis revealed that carriers of the ESR1 haplotype (variant alleles; rs2234693 and rs9340799) and the ESR2 haplotype (variant allele; rs1255998 and wild-type alleles; rs944050, rs4986938 and rs1256049) were at an increased risk (OR 1.862, P = 0.013 and OR 1.918, P = 0.046 respectively). This risk was even greater in women carrying both risk haplotypes (OR 5.041, P = 0.007). CONCLUSIONS Our data suggest that the ESR1 (rs2234693 and rs9340799) and the ESR2 (rs1255998 and rs944050) polymorphisms may be associated with an increased risk of developing endometrial cancer.
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Affiliation(s)
- K A Ashton
- Discipline of Medical Genetics, School of Biomedical Sciences, Faculty of Health, University of Newcastle; and the Hunter Medical Research Institute, Newcastle, NSW, Australia
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Dudding T, Heron J, Thakkinstian A, Nurk E, Golding J, Pembrey M, Ring SM, Attia J, Scott RJ. Factor V Leiden is associated with pre-eclampsia but not with fetal growth restriction: a genetic association study and meta-analysis. J Thromb Haemost 2008; 6:1869-75. [PMID: 18752569 DOI: 10.1111/j.1538-7836.2008.03134.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Adverse pregnancy outcomes have been related to environmental and/or genetic factors. Of interest are genes associated with the clotting system as any perturbation in the balance of thrombotic and thrombolytic cascades could affect the placental circulation and hence the viability of the developing fetus. Several previous reports using relatively small numbers of cases and controls have suggested that there is a relationship between poor pregnancy outcomes and two polymorphisms, one in the factor V gene, the 1691G to A change (rs6025) located on chromosome 1q23 (factor V Leiden, FVL), and the other in the prothrombin gene, 20210G to A change (rs1799963) on chromosome 11p11-q12 (PT). These results, however, are conflicting. METHODS We genotyped 6755 mother/infant pairs from the Avon Longitudinal Study of Parents and Children (ALSPAC) to determine whether maternal or fetal FVL or PT, either alone or in combination, are associated with fetal growth restriction (FGR) or pre-eclampsia (PE). We also added the present results to previous cohort studies using meta-analysis. RESULTS Smoking, primiparity and lower body mass index (BMI) were all associated with FGR, but neither maternal nor fetal FVL or PT, singly or in combination, were associated with FGR in the ALSPAC cohort. Meta-analysis confirmed the lack of association between maternal FVL and FGR with a pooled odds ratio (OR) of 1.15 [95% confidence interval (CI) 0.95-1.39]. High BMI, primiparity, diabetes and chronic hypertension were all associated with pre-eclampsia. Combining ALSPAC results with previous studies in ameta-analysis indicated that maternal FVL is significantly associated with pre-eclampsia, with a pooled OR of 1.49 (95% CI 1.13-1.96). CONCLUSION Neither maternal nor fetal FVL or PT, singly or in combination, are associated with FGR; this contradicts previous case-control studies and meta-analyses based on these studies. In a meta-analysis of all published cohort studies to date, maternal FVL appears to increase the risk of pre-eclampsia by almost 50%. This result is robust, homogeneous and does not appear to be affected by publication bias.
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Affiliation(s)
- T Dudding
- Hunter Genetics, Hunter New England Health Service, NSW, Australia
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Reeves SG, Mossman D, Meldrum CJ, Kurzawski G, Suchy J, Lubinski J, Scott RJ. The -149C>T SNP within the DeltaDNMT3B gene, is not associated with early disease onset in hereditary non-polyposis colorectal cancer. Cancer Lett 2008; 265:39-44. [PMID: 18336997 DOI: 10.1016/j.canlet.2008.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Revised: 01/31/2008] [Accepted: 02/03/2008] [Indexed: 11/29/2022]
Abstract
Hereditary non-polyposis colorectal cancer (HNPCC) is an autosomal dominantly inherited syndrome caused by germline mutations in mismatch repair (MMR) genes. HNPCC patients have a lifetime risk of 80% of developing colorectal cancer (CRC); however the likely age of onset is difficult to predict. A single C>T polymorphism located within the promoter region of the DeltaDNMT3B gene has recently been reported to be associated with a significant increase to the risk of early onset CRC. In this study we determined the DeltaDNMT3B genotype in 404 confirmed HNPCC participants (total of 194 CRC cases) from Australia (203) and Poland (201). From the total number of participants there were 194 diagnosed cases of CRC and 210 healthy MMR gene mutation carriers. The study was undertaken to assess whether the reported effect observed in a previous study of 146 HNPCC patients is consistent in a larger separate and unrelated participant cohort. Through the statistical tests of Kaplan-Meier survival analysis and Cox hazard regression models we did not observe any significant association between the DeltaDNMT3B C>T SNP and early onset CRC in HNPCC patients.
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Affiliation(s)
- S G Reeves
- Discipline of Medical Genetics, Faculty of Health, University of Newcastle, The Hunter Medical Research Institute, NSW, Australia
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Debniak T, Scott RJ, Górski B, Cybulski C, van de Wetering T, Serrano-Fernandez P, Huzarski T, Byrski T, Nagay L, Debniak B, Kowalska E, Jakubowska A, Gronwald J, Wokolorczyk D, Maleszka R, Kładny J, Lubinski J. Common variants of DNA repair genes and malignant melanoma. Eur J Cancer 2007; 44:110-4. [PMID: 18024013 DOI: 10.1016/j.ejca.2007.10.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Revised: 09/12/2007] [Accepted: 10/09/2007] [Indexed: 01/07/2023]
Abstract
In the current study, we evaluated the possible associations of seven common variants of the DNA repair and cell cycle control genes BRCA2 and CHEK2 with malignant melanoma (MM). We genotyped 630 unselected MM patients and over 3700 controls (newborns, age- and sex-matched healthy adults with negative cancer family histories, and the adults selected at random by family doctors) for the prevalence of three common variants of the BRCA2 (T1915M, N991D and N372H) and four common variants of the CHEK2 (1100delC, VS2+1G --> A, I157T and del5395). Our study strongly suggests that the common variant of the BRCA2 gene -- the N991D variant is associated with malignant melanoma risk (OR=1.8, p=0.002 after Bonferroni correction). Patients homozygote for the N991D variant were present in 0.32% of cases and only 0.13% of controls. The other variants studied were not over-represented among MM patients when compared to the general population. In conclusion, we report an increased melanoma risk among carriers of the N991D change of the BRCA2 and no association of the CHEK2 changes with malignant melanoma.
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Affiliation(s)
- T Debniak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland.
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Firbank LG, Rothery P, May MJ, Clark SJ, Scott RJ, Stuart RC, Boffey CWH, Brooks DR, Champion GT, Haughton AJ, Hawes C, Heard MS, Dewar AM, Perry JN, Squire GR. Effects of genetically modified herbicide-tolerant cropping systems on weed seedbanks in two years of following crops. Biol Lett 2007; 2:140-3. [PMID: 17148348 PMCID: PMC1617187 DOI: 10.1098/rsbl.2005.0390] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Farm Scale Evaluations (FSEs) showed that genetically modified herbicide-tolerant (GMHT) cropping systems could influence farmland biodiversity because of their effects on weed biomass and seed production. Recently published results for winter oilseed rape showed that a switch to GMHT crops significantly affected weed seedbanks for at least 2 years after the crops were sown, potentially causing longer-term effects on other taxa. Here, we seek evidence for similar medium-term effects on weed seedbanks following spring-sown GMHT crops, using newly available data from the FSEs. Weed seedbanks following GMHT maize were significantly higher than following conventional varieties for both the first and second years, while by contrast, seedbanks following GMHT spring oilseed rape were significantly lower over this period. Seedbanks following GMHT beet were smaller than following conventional crops in the first year after the crops had been sown, but this difference was much reduced by the second year for reasons that are not clear. These new data provide important empirical evidence for longer-term effects of GMHT cropping on farmland biodiversity.
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Affiliation(s)
- L G Firbank
- Centre for Ecology and Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, UK.
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Hearle N, Schumacher V, Menko FH, Olschwang S, Boardman LA, Gille JJP, Keller JJ, Westerman AM, Scott RJ, Lim W, Trimbath JD, Giardiello FM, Gruber SB, Offerhaus GJA, Rooij FWMDE, Wilson JHP, Hansmann A, Möslein G, Royer-Pokora B, Vogel T, Phillips RKS, Spigelman AD, Houlston RS. STK11 status and intussusception risk in Peutz-Jeghers syndrome. J Med Genet 2006; 43:e41. [PMID: 16882735 PMCID: PMC2564597 DOI: 10.1136/jmg.2005.040535] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Peutz-Jeghers syndrome (PJS) is caused by germline STK11 mutations and characterised by gastrointestinal polyposis. Although small bowel intussusception is a recognised complication of PJS, risk varies between patients. OBJECTIVE To analyse the time to onset of intussusception in a large series of PJS probands. METHODS STK11 mutation status was evaluated in 225 PJS probands and medical histories of the patients reviewed. RESULTS 135 (60%) of the probands possessed a germline STK11 mutation; 109 (48%) probands had a history of intussusception at a median age of 15.0 years but with wide variability (range 3.7 to 45.4 years). Median time to onset of intussusception was not significantly different between those with identified mutations and those with no mutation detected, at 14.7 years and 16.4 years, respectively (log-rank test of difference, chi(2) = 0.58, with 1df; p = 0.45). Similarly no differences were observed between patient groups on the basis of the type or site of STK11 mutation. CONCLUSIONS The risk of intussusception in PJS is not influenced by STK11 mutation status.
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Chow E, Meldrum CJ, Crooks R, Macrae F, Spigelman AD, Scott RJ. An updated mutation spectrum in an Australian series of PJS patients provides further evidence for only one gene locus. Clin Genet 2006; 70:409-14. [PMID: 17026623 DOI: 10.1111/j.1399-0004.2006.00704.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The genetic predisposition Peutz-Jeghers Syndrome (PJS) has been shown to be associated with mutations in the serine threonine kinase 11 (STK11) gene but only a proportion of probands have been shown to harbour changes in the gene. The remaining patients were proposed to be either associated with a second PJS gene or they harboured more cryptic mutations within the STK11 gene itself. With the introduction of the multiplex ligation probe amplification (MLPA) assay, large sequence losses or gains can be more readily identified. In this report we have screened 33 PJS patients from unrelated families, employing a combination of denaturing high-performance liquid chromatography, direct DNA sequencing and the MLPA assay to identify deleterious changes in the STK11 gene. The results revealed that 24 (73%) of patients diagnosed with PJS-harboured pathogenic mutations in the STK11 gene, including 10 (36%) with exonic or whole-gene deletions. No phenotypic differences were identified in patients harbouring large deletions in the STK11 gene compared to patients harbouring missense or nonsense mutations. Mutation analysis in PJS should include techniques such as MLPA to identify large exonic or whole-gene deletions and rearrangements. The high proportion of families with identifiable mutations in the STK11 gene using this range of techniques suggests that most, if not all PJS, is attributable to mutations in the STK11 gene, perhaps including as yet undiscovered changes in promoter or enhancer sequences or other cryptic changes.
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Affiliation(s)
- E Chow
- Royal Melbourne Hospital, Parkville, Victoria, Australia
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Suchy J, Kurzawski G, Jakubowska K, Rać ME, Safranow K, Kładny J, Rzepka-Górska I, Chosia M, Czeszyńska B, Oszurek O, Scott RJ, Lubiński J. Frequency and nature of hMSH6 germline mutations in Polish patients with colorectal, endometrial and ovarian cancers. Clin Genet 2006; 70:68-70. [PMID: 16813607 DOI: 10.1111/j.1399-0004.2006.00630.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Kurzawski G, Suchy J, Lener M, Kłujszo-Grabowska E, Kładny J, Safranow K, Jakubowska K, Jakubowska A, Huzarski T, Byrski T, Debniak T, Cybulski C, Gronwald J, Oszurek O, Oszutowska D, Kowalska E, Góźdź S, Niepsuj S, Słomski R, Pławski A, Łacka-Wojciechowska A, Rozmiarek A, Fiszer-Maliszewska Ł, Bebenek M, Sorokin D, Sasiadek MM, Stembalska A, Grzebieniak Z, Kilar E, Stawicka M, Godlewski D, Richter P, Brozek I, Wysocka B, Limon J, Jawień A, Banaszkiewicz Z, Janiszewska H, Kowalczyk J, Czudowska D, Scott RJ, Lubiński J. Germline MSH2 and MLH1 mutational spectrum including large rearrangements in HNPCC families from Poland (update study). Clin Genet 2006; 69:40-7. [PMID: 16451135 DOI: 10.1111/j.1399-0004.2006.00550.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Germline mutations in the DNA mismatch repair genes MSH2 and MLH1 account for a significant proportion of hereditary non-polyposis colorectal cancer (HNPCC) families. One approach by which development of an efficient DNA-testing procedure can be implemented is to describe the nature and frequency of common mutations in particular ethnic groups. Two hundred and twenty-six patients from families matching the Amsterdam II diagnostic criteria or suspected HNPCC criteria were screened for MSH2 and MLH1 germline mutations. Fifty different pathogenic mutations were found, 25 in MSH2 and 25 in MLH1. Twenty-four of these had not previously been described in other populations. Among our 78 families with MSH2 or MLH1 mutations, 54 (69.2%) were affected by recurrent mutations including 38 found at least twice in our own series. Two of the most frequent alterations were a substitution of A to T at the splice donor site of intron 5 of MSH2 and a missense change (A681T) of MLH1 found in 10 and eight families, respectively. Among large deletions detected by the multiplex ligation-dependent probe amplification assay, exon 9 deletions in the MSH2 gene were found in two families. Our results indicate that a screening protocol specific for the Polish population that is limited to the detection of all reported mutations will result in the identification of the majority of changes present in MLH1 and MSH2 genes in Polish HNPCC kindreds.
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Affiliation(s)
- G Kurzawski
- International Hereditary Cancer Center - Department of Genetics and Pathology, Universit of Szczecin and Pomeranian Medical University, Szczecin, Poland.
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Debniak T, Scott RJ, Huzarski T, Byrski T, Masojć B, van de Wetering T, Serrano-Fernandez P, Górski B, Cybulski C, Gronwald J, Debniak B, Maleszka R, Kładny J, Bieniek A, Nagay L, Haus O, Grzybowska E, Wandzel P, Niepsuj S, Narod SA, Lubinski J. XPD Common Variants and their Association with Melanoma and Breast Cancer Risk. Breast Cancer Res Treat 2006; 98:209-15. [PMID: 16685590 DOI: 10.1007/s10549-005-9151-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Accepted: 12/18/2005] [Indexed: 10/24/2022]
Abstract
There are suggestions in the literature that common variants in the XPD gene may be associated with an altered risk of melanoma and breast cancer. To establish if the XPD common variants Asp312Asn and Lys751Gln are associated with an increased melanoma or breast cancer risk we performed an association study based on genotyping 426 unselected patients with malignant melanoma (MM) and 1830 consecutive breast cancer cases and compared the results to 1262 geographically matched newborns, 621 adults from the region of Szczecin (unselected for age and cancer family history), 421 healthy adults age- and sex-matched with the melanoma cases and 511 healthy controls matched with the breast cancer patients from the region of Szczecin. Additionally we examined the prevalence of three additional XPD variants, Gly156Gly, Leu485Pro and Arg112His amongst the 421 unselected melanoma patients. All of the variants when evaluated singularly were found not to be associated either with melanoma or breast cancer risk in younger or older patients. A modest association was observed with breast cancer risk when the Lys751Gln_CC/Asp312Asn_AA genotype (OR=1.5, p<0.05) segregated together. Individuals harboring the Lys751Gln_CC/Gly156Gly_CC genotype were significantly over-represented among late-onset melanoma cases (OR=1.7, p<0.05). The results of analyses of linkage disequilibrium and haplotype frequency support the thesis that a combination of at least two SNPs (Lys751Gln_CC/Gly156Gly_CC or Lys751Gln_CC/Asp312Asn_AA) inherited as a haplotype was associated with disease. These two pairs of SNPs could therefore be regarded as a single hereditary unit that would have a very small probability of being disrupted by recombination. Additional studies are required to determine whether these particular changes can be associated with an increased risk of other malignancies at different sites of origin.
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Affiliation(s)
- T Debniak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland.
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Scott RJ, Spielman M. Genomic imprinting in plants and mammals: how life history constrains convergence. Cytogenet Genome Res 2006; 113:53-67. [PMID: 16575163 DOI: 10.1159/000090815] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Accepted: 08/02/2005] [Indexed: 12/25/2022] Open
Abstract
In both flowering plants and mammals, DNA methylation is involved in silencing alleles of imprinted genes, but surprising differences in imprinting control are emerging between the two taxa which may be traced to differences in their life cycles. Imprinted gene expression in plants occurs in the endosperm, a separate fertilisation product which transmits nutrients to the embryo and does not contribute a genome to the next generation. Regulation of expression of the known imprinted genes in Arabidopsis involves a cascade of gene expression beginning in the gametophyte, a haploid life phase interposed between the meiotic products and the gametes, which evolved from free-living organisms that constitute the dominant life phase of lower plants. Although the gametophytes of flowering plants are highly reduced they still express large numbers of genes, perhaps reflecting their evolutionary legacy, and which may now be recruited for control of imprinting. Strikingly, the genes at the top of the expression cascade appear to be specifically activated by demethylation, rather than targeted for silencing. Unlike in mammals, there is no evidence for global resetting of methylation in plants, and although imprinting involves the activity of a maintenance methyltransferase, de novo methyltransferases do not appear to be required. Plants do not set aside a germline; instead the cells that undergo meiosis to produce gametophytes differentiate in the adult plant during flower development. Both the late differentiation of the lineage producing germ cells, and the extent of gene expression during the haploid phase, may be incompatible with global resetting of methylation. Resetting may be unnecessary in any case because the adult plant expresses imprinted loci either biallelically or not at all, suggesting there is no chromosomal memory of parent-of-origin in the lineage that produces the gametophytes. Thus several features of the plant life cycle may account for the different strategies used by plants and animals to regulate parent-specific gene expression.
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Affiliation(s)
- R J Scott
- Department of Biology and Biochemistry, University of Bath, Bath, UK.
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Thompson E, Meldrum CJ, Crooks R, McPhillips M, Thomas L, Spigelman AD, Scott RJ. Hereditary non-polyposis colorectal cancer and the role of hPMS2 and hEXO1 mutations. Clin Genet 2004; 65:215-25. [PMID: 14756672 DOI: 10.1111/j.1399-0004.2004.00214.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hereditary non-polyposis colorectal cancer (HNPCC) is an autosomal dominant, inherited condition that is characterized primarily by the development of early-onset colorectal cancer and a number of other epithelial malignancies. The underlying genetic basis of the disease is associated with a breakdown of DNA-mismatch repair. There are many genes involved in DNA-mismatch repair, and five of them have been implicated in HNPCC. Two of the genes (hMSH2 and hMLH1) account for the majority of HNPCC families (approximately 60%), and it is not known what the exact contributions of the remaining three genes (hPMS1, hPMS2, and hMSH6) are in relation to this condition. In addition, a sixth gene (hEXO1) has been associated with a disease phenotype that is consistent with HNPCC. Current estimates suggest that all four of these genes, combined, may account for up to 5% of families. In this report, we examine the contribution of hPMS2 and hEXO1 to a well-defined set of families that fulfill the diagnostic criteria for HNPCC. The genes, hPMS2 and hEXO1, were studied by denaturing high performance liquid chromatography (DHPLC) analysis in 21 families that have previously been determined not to have mutations in hMSH2 or hMLH1. hPMS2 accounts for a small proportion of HNPCC families, and none were deemed to be associated with hEXO1. Mutations in hPMS2 appear to account for a small proportion of families adhering to the Amsterdam II criteria, whereas hEXO1 does not appear to be associated with HNPCC.
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Affiliation(s)
- E Thompson
- Discipline of Medical Genetics, Faculty of Health, University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
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Spigelman A, Burgess B, Groombridge C, Scott RJ. Genetic testing: a round table conversation. Intern Med J 2004; 34:587-8; author reply 588-9. [PMID: 15482283 DOI: 10.1111/j.1445-5994.2004.00679.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Koch KM, Corrigan BW, Manzo J, James CD, Scott RJ, Stead AG, Kersey KE. Alosetron repeat dose pharmacokinetics, effects on enzyme activities, and influence of demographic factors. Aliment Pharmacol Ther 2004; 20:223-30. [PMID: 15233703 DOI: 10.1111/j.1365-2036.2004.02031.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIM To assess the pharmacokinetics of alosetron, its effect on in vivo enzyme activities, and influence of demographic factors during repeated dosing. METHODS Thirty healthy men and women received 1 mg oral alosetron twice-daily for 29.5 days and a single oral dose of a metabolic probe cocktail before and on the last day of alosetron dosing. Serum alosetron concentrations were measured on days 1, 8, 15, 22 and 29. Probe-substrate and metabolite concentrations were measured after each cocktail dose. RESULTS Alosetron accumulation in serum was negligible. Exposure to alosetron did not alter probe-metabolite/substrate ratios associated with CYP2C19, 2E1, 2C9, or 3A4 activity, but modestly decreased those associated with CYP1A2 and N-acetyltransferase activity. Systemic exposure to alosetron was higher in women, positively correlated with age and body mass index, and negatively correlated with CYP1A2 activity. Incidence of constipation was higher in women, but not associated with alosetron concentration. CONCLUSIONS Single dose data can reliably predict the pharmacokinetics of alosetron after repeated doses. Alosetron exhibits limited potential for inhibition of cytochrome P450-mediated metabolism. Interindividual differences in alosetron pharmacokinetics associated with demographic factors may be related to strong dependence on metabolism by CYP1A2.
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Affiliation(s)
- K M Koch
- Department of Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Research Triangle Park, NC, USA.
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Affiliation(s)
- R J Scott
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom.
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Heard MS, Hawes C, Champion GT, Clark SJ, Firbank LG, Haughton AJ, Parish AM, Perry JN, Rothery P, Scott RJ, Skellern MP, Squire GR, Hill MO. Weeds in fields with contrasting conventional and genetically modified herbicide-tolerant crops. I. Effects on abundance and diversity. Philos Trans R Soc Lond B Biol Sci 2003; 358:1819-32. [PMID: 14561316 PMCID: PMC1693279 DOI: 10.1098/rstb.2003.1402] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We compared the seedbanks, seed rains, plant densities and biomasses of weeds under two contrasting systems of management in beet, maize and spring oilseed rape. Weed seedbank and plant density were measured at the same locations in two subsequent seasons. About 60 fields were sown with each crop. Each field was split, one half being sown with a conventional variety managed according to the farmer's normal practice, the other half being sown with a genetically modified herbicide-tolerant (GMHT) variety, with weeds controlled by a broad-spectrum herbicide. In beet and rape, plant densities shortly after sowing were higher in the GMHT treatment. Following weed control in conventional beet, plant densities were approximately one-fifth of those in GMHT beet. In both beet and rape, this effect was reversed after the first application of broad-spectrum herbicide, so that late-season plant densities were lower in the GMHT treatments. Biomass and seed rain in GMHT crops were between one-third and one-sixth of those in conventional treatments. The effects of differing weed-seed returns in these two crops persisted in the seedbank: densities following the GMHT treatment were about 20% lower than those following the conventional treatment. The effect of growing maize was quite different. Weed density was higher throughout the season in the GMHT treatment. Late-season biomass was 82% higher and seed rain was 87% higher than in the conventional treatment. The difference was not subsequently detectable in the seedbank because the total seed return was low after both treatments. In all three crops, weed diversity was little affected by the treatment, except for transient effects immediately following herbicide application.
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Affiliation(s)
- M S Heard
- NERC Centre for Ecology and Hydrology, Monks Wood, Abbots Ripton, Huntingdon, Cambridgeshire PE28 2LS, UK.
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Heard MS, Hawes C, Champion GT, Clark SJ, Firbank LG, Haughton AJ, Parish AM, Perry JN, Rothery P, Roy DB, Scott RJ, Skellern MP, Squire GR, Hill MO. Weeds in fields with contrasting conventional and genetically modified herbicide-tolerant crops. II. Effects on individual species. Philos Trans R Soc Lond B Biol Sci 2003; 358:1833-46. [PMID: 14561317 PMCID: PMC1693275 DOI: 10.1098/rstb.2003.1401] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We compared the effects of the management of genetically modified herbicide-tolerant (GMHT) and conventional beet, maize and spring oilseed rape on 12 weed species. We sampled the seedbank before and after cropping. During the season we counted plants and measured seed rain and biomass. Ratios of densities were used to calculate emergence, survival, reproduction and seedbank change. Treatments significantly affected the biomass of six species in beet, eight in maize and five in spring oilseed rape. The effects were generally consistent, with biomass lower in GMHT beet and spring oilseed rape and higher in GMHT maize. With few exceptions, emergence was higher in GMHT crops. Subsequent survival was significantly lowered for eight species in beet and six in spring oilseed rape in the GMHT treatments. It was increased for five species in maize and one in spring oilseed rape. Significant effects on seedbank change were found for four species. However, for many species in beet and spring oilseed rape (19 out of 24 cases), seed densities were lower in the seedbank after GMHT cropping. These differences compounded over time would result in large decreases in population densities of arable weeds. In maize, populations may increase.
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Affiliation(s)
- M S Heard
- NERC Centre for Ecology and Hydrology, Monks Wood, Abbots Ripton, Huntingdon, Cambridgeshire PE28 2LS, UK.
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Haughton AJ, Champion GT, Hawes C, Heard MS, Brooks DR, Bohan DA, Clark SJ, Dewar AM, Firbank LG, Osborne JL, Perry JN, Rothery P, Roy DB, Scott RJ, Woiwod IP, Birchall C, Skellern MP, Walker JH, Baker P, Browne EL, Dewar AJG, Garner BH, Haylock LA, Horne SL, Mason NS, Sands RJN, Walker MJ. Invertebrate responses to the management of genetically modified herbicide-tolerant and conventional spring crops. II. Within-field epigeal and aerial arthropods. Philos Trans R Soc Lond B Biol Sci 2003; 358:1863-77. [PMID: 14561319 PMCID: PMC1693277 DOI: 10.1098/rstb.2003.1408] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The effects of the management of genetically modified herbicide-tolerant (GMHT) crops on the abundances of aerial and epigeal arthropods were assessed in 66 beet, 68 maize and 67 spring oilseed rape sites as part of the Farm Scale Evaluations of GMHT crops. Most higher taxa were insensitive to differences between GMHT and conventional weed management, but significant effects were found on the abundance of at least one group within each taxon studied. Numbers of butterflies in beet and spring oilseed rape and of Heteroptera and bees in beet were smaller under the relevant GMHT crop management, whereas the abundance of Collembola was consistently greater in all GMHT crops. Generally, these effects were specific to each crop type, reflected the phenology and ecology of the arthropod taxa, were indirect and related to herbicide management. These results apply generally to agriculture across Britain, and could be used in mathematical models to predict the possible long-term effects of the widespread adoption of GMHT technology. The results for bees and butterflies relate to foraging preferences and might or might not translate into effects on population densities, depending on whether adoption leads to forage reductions over large areas. These species, and the detritivore Collembola, may be useful indicator species for future studies of GMHT management.
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Affiliation(s)
- A J Haughton
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
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Brooks DR, Bohan DA, Champion GT, Haughton AJ, Hawes C, Heard MS, Clark SJ, Dewar AM, Firbank LG, Perry JN, Rothery P, Scott RJ, Woiwod IP, Birchall C, Skellern MP, Walker JH, Baker P, Bell D, Browne EL, Dewar AJG, Fairfax CM, Garner BH, Haylock LA, Horne SL, Hulmes SE, Mason NS, Norton LR, Nuttall P, Randle Z, Rossall MJ, Sands RJN, Singer EJ, Walker MJ. Invertebrate responses to the management of genetically modified herbicide-tolerant and conventional spring crops. I. Soil-surface-active invertebrates. Philos Trans R Soc Lond B Biol Sci 2003; 358:1847-62. [PMID: 14561318 PMCID: PMC1693272 DOI: 10.1098/rstb.2003.1407] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The effects of herbicide management of genetically modified herbicide-tolerant (GMHT) beet, maize and spring oilseed rape on the abundance and diversity of soil-surface-active invertebrates were assessed. Most effects did not differ between years, environmental zones or initial seedbanks or between sugar and fodder beet. This suggests that the results may be treated as generally applicable to agricultural situations throughout the UK for these crops. The direction of the effects was evenly balanced between increases and decreases in counts in the GMHT compared with the conventional treatment. Most effects involving a greater capture in the GMHT treatments occurred in maize, whereas most effects involving a smaller capture were in beet and spring oilseed rape. Differences between GMHT and conventional crop herbicide management had a significant effect on the capture of most surface-active invertebrate species and higher taxa tested in at least one crop, and these differences reflected the phenology and ecology of the invertebrates. Counts of carabids that feed on weed seeds were smaller in GMHT beet and spring oilseed rape but larger in GMHT maize. In contrast, collembolan detritivore counts were significantly larger under GMHT crop management.
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Affiliation(s)
- D R Brooks
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
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Roy DB, Bohan DA, Haughton AJ, Hill MO, Osborne JL, Clark SJ, Perry JN, Rothery P, Scott RJ, Brooks DR, Champion GT, Hawes C, Heard MS, Firbank LG. Invertebrates and vegetation of field margins adjacent to crops subject to contrasting herbicide regimes in the Farm Scale Evaluations of genetically modified herbicide-tolerant crops. Philos Trans R Soc Lond B Biol Sci 2003; 358:1879-98. [PMID: 14561320 PMCID: PMC1693278 DOI: 10.1098/rstb.2003.1404] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The effects of management of genetically modified herbicide-tolerant (GMHT) crops on adjacent field margins were assessed for 59 maize, 66 beet and 67 spring oilseed rape sites. Fields were split into halves, one being sown with a GMHT crop and the other with the equivalent conventional non-GMHT crop. Margin vegetation was recorded in three components of the field margins. Most differences were in the tilled area, with fewer smaller effects mirroring them in the verge and boundary. In spring oilseed rape fields, the cover, flowering and seeding of plants were 25%, 44% and 39% lower, respectively, in the GMHT uncropped tilled margins. Similarly, for beet, flowering and seeding were 34% and 39% lower, respectively, in the GMHT margins. For maize, the effect was reversed, with plant cover and flowering 28% and 67% greater, respectively, in the GMHT half. Effects on butterflies mirrored these vegetation effects, with 24% fewer butterflies in margins of GMHT spring oilseed rape. The likely cause is the lower nectar supply in GMHT tilled margins and crop edges. Few large treatment differences were found for bees, gastropods or other invertebrates. Scorching of vegetation by herbicide-spray drift was on average 1.6% on verges beside conventional crops and 3.7% beside GMHT crops, the difference being significant for all three crops.
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Affiliation(s)
- D B Roy
- NERC Centre for Ecology and Hydrology, Monks Wood, Abbots Ripton, Huntingdon, Cambridgeshire PE28 2LS, UK.
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Champion GT, May MJ, Bennett S, Brooks DR, Clark SJ, Daniels RE, Firbank LG, Haughton AJ, Hawes C, Heard MS, Perry JN, Randle Z, Rossall MJ, Rothery P, Skellern MP, Scott RJ, Squire GR, Thomas MR. Crop management and agronomic context of the Farm Scale Evaluations of genetically modified herbicide-tolerant crops. Philos Trans R Soc Lond B Biol Sci 2003; 358:1801-18. [PMID: 14561315 PMCID: PMC1693273 DOI: 10.1098/rstb.2003.1405] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Farm Scale Evaluations of genetically modified herbicide-tolerant crops (GMHT) were conducted in the UK from 2000 to 2002 on beet (sugar and fodder), spring oilseed rape and forage maize. The management of the crops studied is described and compared with current conventional commercial practice. The distribution of field sites adequately represented the areas currently growing these crops, and the sample contained sites operated at a range of management intensities, including low intensity. Herbicide inputs were audited, and the active ingredients used and the rates and the timings of applications compared well with current practice for both GMHT and conventional crops. Inputs on sugar beet were lower than, and inputs on spring oilseed rape and forage maize were consistent with, national averages. Regression analysis of herbicide-application strategies and weed emergence showed that inputs applied by farmers increased with weed densities in beet and forage maize. GMHT crops generally received only one herbicide active ingredient per crop, later and fewer herbicide sprays and less active ingredient (for beet and maize) than the conventional treatments. The audit of inputs found no evidence of bias.
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Affiliation(s)
- G T Champion
- Broom's Barn Research Station, Higham, Bury St Edmunds, Suffolk IP28 6NP, UK.
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