1
|
Yazdani A, Mendez-Giraldez R, Yazdani A, Schaid D, Won Kong S, Hadi M, Samiei A, Wittenbecher C, Lasky-Su J, Clish C, Marotta F, Kosorok M, Mora S, Muehlschlegel J, Chasman D, Larson M, Elsea S. Broadcasters, receivers, functional groups of metabolites and the link to heart failure progression using polygenic factors. Res Sq 2023:rs.3.rs-3246406. [PMID: 37645766 PMCID: PMC10462252 DOI: 10.21203/rs.3.rs-3246406/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
In a prospective study with records of heart failure (HF) incidence, we present metabolite profiling data from individuals without HF at baseline. We uncovered the interconnectivity of metabolites using data-driven and causal networks augmented with polygenic factors. Exploring the networks, we identified metabolite broadcasters, receivers, mediators, and subnetworks corresponding to functional classes of metabolites, and provided insights into the link between metabolomic architecture and regulation in health. We incorporated the network structure into the identification of metabolites associated with HF to control the effect of confounding metabolites. We identified metabolites associated with higher or lower risk of HF incidence, the associations that were not confounded by the other metabolites, such as glycine, ureidopropionic and glycocholic acids, and LPC 18:2. We revealed the underlying relationships of the findings. For example, asparagine directly influenced glycine, and both were inversely associated with HF. These two metabolites were influenced by polygenic factors and only essential amino acids which are not synthesized in the human body and come directly from the diet. Metabolites may play a critical role in linking genetic background and lifestyle factors to HF progression. Revealing the underlying connectivity of metabolites associated with HF strengthens the findings and facilitates a mechanistic understanding of HF progression.
Collapse
Affiliation(s)
| | | | - Akram Yazdani
- Division of Clinical and Translational Sciences, Department of Internal Medicine, at The University of Texas Health Science Center at Houston, McGovern Medical School
| | - Daniel Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55902
| | | | - Mohamad Hadi
- School of Mathematics, University of science and technology of Iran, Tehran
| | - Ahmad Samiei
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA
| | | | | | | | | | | | - Samia Mora
- Brigham and Women's Hospital and Harvard Medical School
| | | | | | | | | |
Collapse
|
2
|
Hui D, Xiao B, Dikilitas O, Freimuth RR, Irvin MR, Jarvik GP, Kottyan L, Kullo I, Limdi NA, Liu C, Luo Y, Namjou B, Puckelwartz MJ, Schaid D, Tiwari H, Wei WQ, Verma S, Kim D, Ritchie MD. Quantifying factors that affect polygenic risk score performance across diverse ancestries and age groups for body mass index. Pac Symp Biocomput 2023; 28:437-448. [PMID: 36540998 PMCID: PMC10018532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Polygenic risk scores (PRS) have led to enthusiasm for precision medicine. However, it is well documented that PRS do not generalize across groups differing in ancestry or sample characteristics e.g., age. Quantifying performance of PRS across different groups of study participants, using genome-wide association study (GWAS) summary statistics from multiple ancestry groups and sample sizes, and using different linkage disequilibrium (LD) reference panels may clarify which factors are limiting PRS transferability. To evaluate these factors in the PRS generation process, we generated body mass index (BMI) PRS (PRSBMI) in the Electronic Medical Records and Genomics (eMERGE) network (N=75,661). Analyses were conducted in two ancestry groups (European and African) and three age ranges (adult, teenagers, and children). For PRSBMI calculations, we evaluated five LD reference panels and three sets of GWAS summary statistics of varying sample size and ancestry. PRSBMI performance increased for both African and European ancestry individuals using cross-ancestry GWAS summary statistics compared to European-only summary statistics (6.3% and 3.7% relative R2 increase, respectively, pAfrican=0.038, pEuropean=6.26x10-4). The effects of LD reference panels were more pronounced in African ancestry study datasets. PRSBMI performance degraded in children; R2 was less than half of teenagers or adults. The effect of GWAS summary statistics sample size was small when modeled with the other factors. Additionally, the potential of using a PRS generated for one trait to predict risk for comorbid diseases is not well understood especially in the context of cross-ancestry analyses - we explored clinical comorbidities from the electronic health record associated with PRSBMI and identified significant associations with type 2 diabetes and coronary atherosclerosis. In summary, this study quantifies the effects that ancestry, GWAS summary statistic sample size, and LD reference panel have on PRS performance, especially in cross-ancestry and age-specific analyses.
Collapse
Affiliation(s)
- Daniel Hui
- Graduate Program in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Brenda Xiao
- Graduate Program in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ozan Dikilitas
- Department of Internal Medicine, Department of Cardiovascular Medicine, Clinician-Investigator Training Program, Mayo Clinic, Rochester MN
| | - Robert R. Freimuth
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Gail P. Jarvik
- Departments of Medicine and Genome Sciences, University of Washington, Seattle WA, USA
| | - Leah Kottyan
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Iftikhar Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Nita A. Limdi
- Department of Neurology & Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Yuan Luo
- Department of Preventive Medicine (Health and Biomedical Informatics), Northwestern University, Chicago, IL USA
| | - Bahram Namjou
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | | | - Daniel Schaid
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Hemant Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shefali Verma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D. Ritchie
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
3
|
Ge T, Irvin MR, Patki A, Srinivasasainagendra V, Lin YF, Tiwari HK, Armstrong ND, Benoit B, Chen CY, Choi KW, Cimino JJ, Davis BH, Dikilitas O, Etheridge B, Feng YCA, Gainer V, Huang H, Jarvik GP, Kachulis C, Kenny EE, Khan A, Kiryluk K, Kottyan L, Kullo IJ, Lange C, Lennon N, Leong A, Malolepsza E, Miles AD, Murphy S, Namjou B, Narayan R, O'Connor MJ, Pacheco JA, Perez E, Rasmussen-Torvik LJ, Rosenthal EA, Schaid D, Stamou M, Udler MS, Wei WQ, Weiss ST, Ng MCY, Smoller JW, Lebo MS, Meigs JB, Limdi NA, Karlson EW. Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations. Genome Med 2022; 14:70. [PMID: 35765100 PMCID: PMC9241245 DOI: 10.1186/s13073-022-01074-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 06/16/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) is a worldwide scourge caused by both genetic and environmental risk factors that disproportionately afflicts communities of color. Leveraging existing large-scale genome-wide association studies (GWAS), polygenic risk scores (PRS) have shown promise to complement established clinical risk factors and intervention paradigms, and improve early diagnosis and prevention of T2D. However, to date, T2D PRS have been most widely developed and validated in individuals of European descent. Comprehensive assessment of T2D PRS in non-European populations is critical for equitable deployment of PRS to clinical practice that benefits global populations. METHODS We integrated T2D GWAS in European, African, and East Asian populations to construct a trans-ancestry T2D PRS using a newly developed Bayesian polygenic modeling method, and assessed the prediction accuracy of the PRS in the multi-ethnic Electronic Medical Records and Genomics (eMERGE) study (11,945 cases; 57,694 controls), four Black cohorts (5137 cases; 9657 controls), and the Taiwan Biobank (4570 cases; 84,996 controls). We additionally evaluated a post hoc ancestry adjustment method that can express the polygenic risk on the same scale across ancestrally diverse individuals and facilitate the clinical implementation of the PRS in prospective cohorts. RESULTS The trans-ancestry PRS was significantly associated with T2D status across the ancestral groups examined. The top 2% of the PRS distribution can identify individuals with an approximately 2.5-4.5-fold of increase in T2D risk, which corresponds to the increased risk of T2D for first-degree relatives. The post hoc ancestry adjustment method eliminated major distributional differences in the PRS across ancestries without compromising its predictive performance. CONCLUSIONS By integrating T2D GWAS from multiple populations, we developed and validated a trans-ancestry PRS, and demonstrated its potential as a meaningful index of risk among diverse patients in clinical settings. Our efforts represent the first step towards the implementation of the T2D PRS into routine healthcare.
Collapse
Affiliation(s)
- Tian Ge
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Amit Patki
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vinodh Srinivasasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yen-Feng Lin
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
- Department of Public Health & Medical Humanities, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Behavioral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicole D Armstrong
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Barbara Benoit
- Mass General Brigham Research Information Science & Computing, Boston, MA, USA
| | - Chia-Yen Chen
- Translational Biology, Biogen Inc., Cambridge, MA, USA
| | - Karmel W Choi
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - James J Cimino
- Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brittney H Davis
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ozan Dikilitas
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Internal Medicine, Mayo Clinician-Investigator Training Program, Mayo Clinic, Rochester, MN, USA
| | - Bethany Etheridge
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yen-Chen Anne Feng
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Vivian Gainer
- Mass General Brigham Research Information Science & Computing, Boston, MA, USA
| | - Hailiang Huang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, USA
| | - Leah Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron Leong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | | | - Ayme D Miles
- Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shawn Murphy
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Renuka Narayan
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Jennifer A Pacheco
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Emma Perez
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Mass General Brigham Personalized Medicine, Boston, MA, USA
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Daniel Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Maria Stamou
- Division of Endocrinology, Massachusetts General Hospital, Boston, MA, USA
| | - Miriam S Udler
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Maggie C Y Ng
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jordan W Smoller
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew S Lebo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Mass General Brigham Personalized Medicine, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - James B Meigs
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nita A Limdi
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Elizabeth W Karlson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Mass General Brigham Personalized Medicine, Boston, MA, USA
| |
Collapse
|
4
|
Glazer AM, Davogustto G, Shaffer CM, Vanoye CG, Desai RR, Farber-Eger EH, Dikilitas O, Shang N, Pacheco JA, Yang T, Muhammad A, Mosley JD, Van Driest SL, Wells QS, Shaffer LL, Kalash OR, Wada Y, Bland S, Yoneda ZT, Mitchell DW, Kroncke BM, Kullo IJ, Jarvik GP, Gordon AS, Larson EB, Manolio TA, Mirshahi T, Luo JZ, Schaid D, Namjou B, Alsaied T, Singh R, Singhal A, Liu C, Weng C, Hripcsak G, Ralston JD, McNally EM, Chung WK, Carrell DS, Leppig KA, Hakonarson H, Sleiman P, Sohn S, Glessner J, Denny J, Wei WQ, George AL, Shoemaker MB, Roden DM. Arrhythmia Variant Associations and Reclassifications in the eMERGE-III Sequencing Study. Circulation 2022; 145:877-891. [PMID: 34930020 PMCID: PMC8940719 DOI: 10.1161/circulationaha.121.055562] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Sequencing Mendelian arrhythmia genes in individuals without an indication for arrhythmia genetic testing can identify carriers of pathogenic or likely pathogenic (P/LP) variants. However, the extent to which these variants are associated with clinically meaningful phenotypes before or after return of variant results is unclear. In addition, the majority of discovered variants are currently classified as variants of uncertain significance, limiting clinical actionability. METHODS The eMERGE-III study (Electronic Medical Records and Genomics Phase III) is a multicenter prospective cohort that included 21 846 participants without previous indication for cardiac genetic testing. Participants were sequenced for 109 Mendelian disease genes, including 10 linked to arrhythmia syndromes. Variant carriers were assessed with electronic health record-derived phenotypes and follow-up clinical examination. Selected variants of uncertain significance (n=50) were characterized in vitro with automated electrophysiology experiments in HEK293 cells. RESULTS As previously reported, 3.0% of participants had P/LP variants in the 109 genes. Herein, we report 120 participants (0.6%) with P/LP arrhythmia variants. Compared with noncarriers, arrhythmia P/LP carriers had a significantly higher burden of arrhythmia phenotypes in their electronic health records. Fifty-four participants had variant results returned. Nineteen of these 54 participants had inherited arrhythmia syndrome diagnoses (primarily long-QT syndrome), and 12 of these 19 diagnoses were made only after variant results were returned (0.05%). After in vitro functional evaluation of 50 variants of uncertain significance, we reclassified 11 variants: 3 to likely benign and 8 to P/LP. CONCLUSIONS Genome sequencing in a large population without indication for arrhythmia genetic testing identified phenotype-positive carriers of variants in congenital arrhythmia syndrome disease genes. As the genomes of large numbers of people are sequenced, the disease risk from rare variants in arrhythmia genes can be assessed by integrating genomic screening, electronic health record phenotypes, and in vitro functional studies. REGISTRATION URL: https://www. CLINICALTRIALS gov; Unique identifier; NCT03394859.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Ning Shang
- Columbia University Irving Medical Center, New York NY
| | | | - Tao Yang
- Vanderbilt University Medical Center, Nashville TN
| | | | | | | | | | | | | | - Yuko Wada
- Vanderbilt University Medical Center, Nashville TN
| | - Sarah Bland
- Vanderbilt University Medical Center, Nashville TN
| | | | | | | | | | - Gail P. Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | | | | | | | | | | | | | - Bahram Namjou
- Cincinnati Children’s Hospital Medical Center, Cincinnati OH
| | - Tarek Alsaied
- Cincinnati Children’s Hospital Medical Center, Cincinnati OH
| | | | | | - Cong Liu
- Columbia University Irving Medical Center, New York NY
| | - Chunhua Weng
- Columbia University Irving Medical Center, New York NY
| | | | - James D. Ralston
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | | | | | | | | | | | | | | | | | | | | | - Wei-Qi Wei
- Vanderbilt University Medical Center, Nashville TN
| | | | | | - Dan M. Roden
- Vanderbilt University Medical Center, Nashville TN
- Correspondence should be addressed to Dan M. Roden, MD, Vanderbilt University Medical Center, 2215B Garland Ave, 1285 MRBIV, Nashville, TN 37232,
| |
Collapse
|
5
|
Veturi Y, Lucas A, Bradford Y, Hui D, Dudek S, Theusch E, Verma A, Miller JE, Kullo I, Hakonarson H, Sleiman P, Schaid D, Stein CM, Edwards DRV, Feng Q, Wei WQ, Medina MW, Krauss R, Hoffmann TJ, Risch N, Voight BF, Rader DJ, Ritchie MD. A unified framework identifies new links between plasma lipids and diseases from electronic medical records across large-scale cohorts. Nat Genet 2021; 53:972-981. [PMID: 34140684 PMCID: PMC8555954 DOI: 10.1038/s41588-021-00879-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/05/2021] [Indexed: 02/05/2023]
Abstract
Plasma lipids are known heritable risk factors for cardiovascular disease, but increasing evidence also supports shared genetics with diseases of other organ systems. We devised a comprehensive three-phase framework to identify new lipid-associated genes and study the relationships among lipids, genotypes, gene expression and hundreds of complex human diseases from the Electronic Medical Records and Genomics (347 traits) and the UK Biobank (549 traits). Aside from 67 new lipid-associated genes with strong replication, we found evidence for pleiotropic SNPs/genes between lipids and diseases across the phenome. These include discordant pleiotropy in the HLA region between lipids and multiple sclerosis and putative causal paths between triglycerides and gout, among several others. Our findings give insights into the genetic basis of the relationship between plasma lipids and diseases on a phenome-wide scale and can provide context for future prevention and treatment strategies.
Collapse
Affiliation(s)
- Yogasudha Veturi
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anastasia Lucas
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuki Bradford
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Hui
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott Dudek
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth Theusch
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Anurag Verma
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason E. Miller
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iftikhar Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, PA, USA
| | - Patrick Sleiman
- Center for Applied Genomics, Children’s Hospital of Philadelphia, PA, USA
| | - Daniel Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Charles M. Stein
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Digna R. Velez Edwards
- Department of Biomedical Informatics in School of Medicine, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA.,Division of Quantitative Science, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - QiPing Feng
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics in School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Marisa W. Medina
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Ronald Krauss
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Thomas J. Hoffmann
- Institute for Human Genetics, and Department of Epidemiology & Biostatistics, University of California and San Francisco, San Francisco, CA, USA
| | - Neil Risch
- Institute for Human Genetics, and Department of Epidemiology & Biostatistics, University of California and San Francisco, San Francisco, CA, USA
| | - Benjamin F. Voight
- Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J. Rader
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D. Ritchie
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,
| |
Collapse
|
6
|
Thomas M, Sakoda LC, Hoffmeister M, Rosenthal EA, Lee JK, van Duijnhoven FJB, Platz EA, Wu AH, Dampier CH, de la Chapelle A, Wolk A, Joshi AD, Burnett-Hartman A, Gsur A, Lindblom A, Castells A, Win AK, Namjou B, Van Guelpen B, Tangen CM, He Q, Li CI, Schafmayer C, Joshu CE, Ulrich CM, Bishop DT, Buchanan DD, Schaid D, Drew DA, Muller DC, Duggan D, Crosslin DR, Albanes D, Giovannucci EL, Larson E, Qu F, Mentch F, Giles GG, Hakonarson H, Hampel H, Stanaway IB, Figueiredo JC, Huyghe JR, Minnier J, Chang-Claude J, Hampe J, Harley JB, Visvanathan K, Curtis KR, Offit K, Li L, Le Marchand L, Vodickova L, Gunter MJ, Jenkins MA, Slattery ML, Lemire M, Woods MO, Song M, Murphy N, Lindor NM, Dikilitas O, Pharoah PDP, Campbell PT, Newcomb PA, Milne RL, MacInnis RJ, Castellví-Bel S, Ogino S, Berndt SI, Bézieau S, Thibodeau SN, Gallinger SJ, Zaidi SH, Harrison TA, Keku TO, Hudson TJ, Vymetalkova V, Moreno V, Martín V, Arndt V, Wei WQ, Chung W, Su YR, Hayes RB, White E, Vodicka P, Casey G, Gruber SB, Schoen RE, Chan AT, Potter JD, Brenner H, Jarvik GP, Corley DA, Peters U, Hsu L. Response to Li and Hopper. Am J Hum Genet 2021; 108:527-529. [PMID: 33667396 PMCID: PMC8008475 DOI: 10.1016/j.ajhg.2021.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 02/02/2021] [Indexed: 01/15/2023] Open
Affiliation(s)
- Minta Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Elisabeth A Rosenthal
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA
| | - Jeffrey K Lee
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Franzel J B van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen 176700, the Netherlands
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Anna H Wu
- University of Southern California, Preventative Medicine, Los Angeles, CA 90089, USA
| | - Christopher H Dampier
- Department of Surgery, University of Virginia Health System, Charlottesville, VA 22903, USA
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna 1090, Austria
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm 17177, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 17177, Sweden
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona 08007, Spain
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå 90187, Sweden; Wallenberg Centre for Molecular Medicine, Umeå University, Umeå 90187, Sweden
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Qianchuan He
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock 18051, Germany
| | - Corinne E Joshu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - D Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS2 9JT, UK
| | - Daniel D Buchanan
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia; Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Daniel Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - David C Muller
- School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - David Duggan
- Translational Genomics Research Institute - An Affiliate of City of Hope, Phoenix, AZ 85003, USA
| | - David R Crosslin
- Department of Bioinformatics and Medical Education, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02108, USA
| | - Eric Larson
- Kaiser Permanente Washington Research Institute, Seattle, WA 98101, USA
| | - Flora Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Ian B Stanaway
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jessica Minnier
- School of Public Health, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, 69120 Germany; University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg 20246, Germany
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden 01062, Germany
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Keith R Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medical College, NY 10065, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | | | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - Mathieu Lemire
- PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, NL A1B 3R7, Canada
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, AZ 85260, USA
| | - Ozan Dikilitas
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB2 0SR, UK
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA 30303, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona 08007, Spain
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes 44093, France
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 85054, USA
| | - Steven J Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON M5G1X5, Canada
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona 08908, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona 08907, Spain; ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Vicente Martín
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain; Biomedicine Institute (IBIOMED), University of León, León 24071, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wendy Chung
- Office of Research & Development, Department of Veterans Affairs, Washington, DC 20420, USA; Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY 10016, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Centre for Public Health Research, Massey University, Wellington 6140, New Zealand
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA; Genome Sciences, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA.
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
7
|
Thomas M, Sakoda LC, Hoffmeister M, Rosenthal EA, Lee JK, van Duijnhoven FJB, Platz EA, Wu AH, Dampier CH, de la Chapelle A, Wolk A, Joshi AD, Burnett-Hartman A, Gsur A, Lindblom A, Castells A, Win AK, Namjou B, Van Guelpen B, Tangen CM, He Q, Li CI, Schafmayer C, Joshu CE, Ulrich CM, Bishop DT, Buchanan DD, Schaid D, Drew DA, Muller DC, Duggan D, Crosslin DR, Albanes D, Giovannucci EL, Larson E, Qu F, Mentch F, Giles GG, Hakonarson H, Hampel H, Stanaway IB, Figueiredo JC, Huyghe JR, Minnier J, Chang-Claude J, Hampe J, Harley JB, Visvanathan K, Curtis KR, Offit K, Li L, Le Marchand L, Vodickova L, Gunter MJ, Jenkins MA, Slattery ML, Lemire M, Woods MO, Song M, Murphy N, Lindor NM, Dikilitas O, Pharoah PDP, Campbell PT, Newcomb PA, Milne RL, MacInnis RJ, Castellví-Bel S, Ogino S, Berndt SI, Bézieau S, Thibodeau SN, Gallinger SJ, Zaidi SH, Harrison TA, Keku TO, Hudson TJ, Vymetalkova V, Moreno V, Martín V, Arndt V, Wei WQ, Chung W, Su YR, Hayes RB, White E, Vodicka P, Casey G, Gruber SB, Schoen RE, Chan AT, Potter JD, Brenner H, Jarvik GP, Corley DA, Peters U, Hsu L. Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk. Am J Hum Genet 2020; 107:432-444. [PMID: 32758450 PMCID: PMC7477007 DOI: 10.1016/j.ajhg.2020.07.006] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/13/2020] [Indexed: 02/08/2023] Open
Abstract
Accurate colorectal cancer (CRC) risk prediction models are critical for identifying individuals at low and high risk of developing CRC, as they can then be offered targeted screening and interventions to address their risks of developing disease (if they are in a high-risk group) and avoid unnecessary screening and interventions (if they are in a low-risk group). As it is likely that thousands of genetic variants contribute to CRC risk, it is clinically important to investigate whether these genetic variants can be used jointly for CRC risk prediction. In this paper, we derived and compared different approaches to generating predictive polygenic risk scores (PRS) from genome-wide association studies (GWASs) including 55,105 CRC-affected case subjects and 65,079 control subjects of European ancestry. We built the PRS in three ways, using (1) 140 previously identified and validated CRC loci; (2) SNP selection based on linkage disequilibrium (LD) clumping followed by machine-learning approaches; and (3) LDpred, a Bayesian approach for genome-wide risk prediction. We tested the PRS in an independent cohort of 101,987 individuals with 1,699 CRC-affected case subjects. The discriminatory accuracy, calculated by the age- and sex-adjusted area under the receiver operating characteristics curve (AUC), was highest for the LDpred-derived PRS (AUC = 0.654) including nearly 1.2 M genetic variants (the proportion of causal genetic variants for CRC assumed to be 0.003), whereas the PRS of the 140 known variants identified from GWASs had the lowest AUC (AUC = 0.629). Based on the LDpred-derived PRS, we are able to identify 30% of individuals without a family history as having risk for CRC similar to those with a family history of CRC, whereas the PRS based on known GWAS variants identified only top 10% as having a similar relative risk. About 90% of these individuals have no family history and would have been considered average risk under current screening guidelines, but might benefit from earlier screening. The developed PRS offers a way for risk-stratified CRC screening and other targeted interventions.
Collapse
Affiliation(s)
- Minta Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Elisabeth A Rosenthal
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA
| | - Jeffrey K Lee
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Franzel J B van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen 176700, the Netherlands
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Anna H Wu
- University of Southern California, Preventative Medicine, Los Angeles, CA 90089, USA
| | - Christopher H Dampier
- Department of Surgery, University of Virginia Health System, Charlottesville, VA 22903, USA
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna 1090, Austria
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm 17177, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 17177, Sweden
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona 08007, Spain
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå 90187, Sweden; Wallenberg Centre for Molecular Medicine, Umeå University, Umeå 90187, Sweden
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Qianchuan He
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock 18051, Germany
| | - Corinne E Joshu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - D Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS2 9JT, UK
| | - Daniel D Buchanan
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia; Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Daniel Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - David C Muller
- School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - David Duggan
- Translational Genomics Research Institute - An Affiliate of City of Hope, Phoenix, AZ 85003, USA
| | - David R Crosslin
- Department of Bioinformatics and Medical Education, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02108, USA
| | - Eric Larson
- Kaiser Permanente Washington Research Institute, Seattle, WA 98101, USA
| | - Flora Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Ian B Stanaway
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jessica Minnier
- School of Public Health, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, 69120 Germany; University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg 20246, Germany
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden 01062, Germany
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Keith R Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medical College, NY 10065, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | | | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - Mathieu Lemire
- PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, NL A1B 3R7, Canada
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, AZ 85260, USA
| | - Ozan Dikilitas
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB2 0SR, UK
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA 30303, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona 08007, Spain
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes 44093, France
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 85054, USA
| | - Steven J Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON M5G1X5, Canada
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona 08908, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona 08907, Spain; ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Vicente Martín
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain; Biomedicine Institute (IBIOMED), University of León, León 24071, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wendy Chung
- Office of Research & Development, Department of Veterans Affairs, Washington, DC 20420, USA; Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY 10016, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Centre for Public Health Research, Massey University, Wellington 6140, New Zealand
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA; Genome Sciences, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA.
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
8
|
Pruthi S, Kim JO, Schaid D, Cooke A, Kim C, Goldenberg B, Sinnwell J, Grenier D, Couch F, Vachon C. Abstract PD3-03: Impact of the breast cancer polygenic risk score on preventive endocrine therapy adherence and endocrine therapy usage on quality of life - The Genetic Risk Estimate (GENRE) trial. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-pd3-03] [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
Background: Studies demonstrate breast cancer risk reduction of 50-65% with the use of endocrine therapy (ET) and yet drug uptake and adherence in this setting is suboptimal even among high risk women. A Polygenic Risk Score (PRS) comprised of 77 BC genetic susceptibility loci (Single Nucleotide Polymorphisms (SNP)) can provide a personalized risk assessment and potentially influence ET adherence. We assessed ET adherence at 1 year comparing women whose risk estimate increased due to PRS versus women whose risk estimate decreased due to PRS. The effect of ET use on quality of life (hot flashes, night sweats, vaginal dryness, weight gain, joint pain) was evaluated.
Methods: Eligible women required either a 5 year Gail Model risk of ≥3% or 10 year IBIS ( International Breast Intervention Study or Tyrer-Cuzick model) of ≥5%. Women with a history of breast cancer (BC) or hereditary BC syndrome were excluded. High risk women were counseled at baseline using their Gail and IBIS risk scores and ET options were discussed including benefits and risks. Participants completed a self-reported questionnaire at baseline to assess their understanding of breast cancer risk and decision to take preventive ET. Blood samples were obtained and genotyped for 77 SNPs, and the odds ratio from the SNPs were used to modify the IBIS and Gail risk estimates. The BC -PRS risk estimate information was shared with study participants that reflected the IBIS and Gail risk estimates for 5 year, 10 year, & lifetime BC risk with and without the PRS. Follow up questionnaires at year 1 were administered to assess drug adherence and ET usage on quality of life.
Results: 151 women were enrolled at Mayo Clinic Rochester and CancerCare Manitoba from 2016 to 2017. The median age was 56.1 (range 36-76.4), 35.6% were premenopausal, 98.7% were Caucasian and 64.7% had>1 family member with BC. Median 5yr, 10yr, & lifetime IBIS- PRS risk estimates were 3.8% (2.0-11.5), 7.9% (5.0-23.1), and 25.3% (5.5 to 92.2). At year 1 (n=112 women) 46 % of those with an increase in risk when considering the BC-PRS score and 16 % with a decrease in risk were taking ET ( p< 0.001). Types of ET taken: tamoxifen-18, raloxifene- 3, exemestane -14 and missing-1. Women taking ET reported weight gain ( 19.4% vs 6.7%, p=0.04) and more joint pain ( 27.8 % vs 12%, p=0.04) when compared to women not taking ET.
Conclusion: In high risk women, BC-PRS risk estimates in addition to standard BC risk calculators had a significant impact on preventive ET adherence. ET use was associated with weight gain and joint pain.
Citation Format: Sandhya Pruthi, Julian O Kim, Daniel Schaid, Andrew Cooke, Christina Kim, Benjamin Goldenberg, Jason Sinnwell, Debjani Grenier, Fergus Couch, Celine Vachon. Impact of the breast cancer polygenic risk score on preventive endocrine therapy adherence and endocrine therapy usage on quality of life - The Genetic Risk Estimate (GENRE) trial [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr PD3-03.
Collapse
|
9
|
Chiang T, Liu X, Wu TJ, Hu J, Sedlazeck FJ, White S, Schaid D, Andrade MD, Jarvik GP, Crosslin D, Stanaway I, Carrell DS, Connolly JJ, Hakonarson H, Groopman EE, Gharavi AG, Fedotov A, Bi W, Leduc MS, Murdock DR, Jiang Y, Meng L, Eng CM, Wen S, Yang Y, Muzny DM, Boerwinkle E, Salerno W, Venner E, Gibbs RA. Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel. Genet Med 2019; 21:2135-2144. [PMID: 30890783 PMCID: PMC6752313 DOI: 10.1038/s41436-019-0475-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 09/24/2018] [Accepted: 02/25/2019] [Indexed: 12/24/2022] Open
Abstract
PURPOSE To provide a validated method to confidently identify exon-containing copy-number variants (CNVs), with a low false discovery rate (FDR), in targeted sequencing data from a clinical laboratory with particular focus on single-exon CNVs. METHODS DNA sequence coverage data are normalized within each sample and subsequently exonic CNVs are identified in a batch of samples, when the target log2 ratio of the sample to the batch median exceeds defined thresholds. The quality of exonic CNV calls is assessed by C-scores (Z-like scores) using thresholds derived from gold standard samples and simulation studies. We integrate an ExonQC threshold to lower FDR and compare performance with alternate software (VisCap). RESULTS Thirteen CNVs were used as a truth set to validate Atlas-CNV and compared with VisCap. We demonstrated FDR reduction in validation, simulation, and 10,926 eMERGESeq samples without sensitivity loss. Sixty-four multiexon and 29 single-exon CNVs with high C-scores were assessed by Multiplex Ligation-dependent Probe Amplification (MLPA). CONCLUSION Atlas-CNV is validated as a method to identify exonic CNVs in targeted sequencing data generated in the clinical laboratory. The ExonQC and C-score assignment can reduce FDR (identification of targets with high variance) and improve calling accuracy of single-exon CNVs respectively. We propose guidelines and criteria to identify high confidence single-exon CNVs.
Collapse
Affiliation(s)
- Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - Xiuping Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Tsung-Jung Wu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Daniel Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Gail P Jarvik
- University of Washington Medical Center, Seattle, WA, USA
| | - David Crosslin
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Ian Stanaway
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | | | | | - Emily E Groopman
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY, USA
| | - Alexander Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | | | - David R Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yunyun Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Shu Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,UTHealth School of Public Health, Houston, TX, USA
| | - William Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
10
|
Zhang X, Veturi Y, Verma S, Bone W, Verma A, Lucas A, Hebbring S, Denny JC, Stanaway IB, Jarvik GP, Crosslin D, Larson EB, Rasmussen-Torvik L, Pendergrass SA, Smoller JW, Hakonarson H, Sleiman P, Weng C, Fasel D, Wei WQ, Kullo I, Schaid D, Chung WK, Ritchie MD. Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43,870 individuals from the eMERGE network. Pac Symp Biocomput 2019; 24:272-283. [PMID: 30864329 PMCID: PMC6457436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The link between cardiovascular diseases and neurological disorders has been widely observed in the aging population. Disease prevention and treatment rely on understanding the potential genetic nexus of multiple diseases in these categories. In this study, we were interested in detecting pleiotropy, or the phenomenon in which a genetic variant influences more than one phenotype. Marker-phenotype association approaches can be grouped into univariate, bivariate, and multivariate categories based on the number of phenotypes considered at one time. Here we applied one statistical method per category followed by an eQTL colocalization analysis to identify potential pleiotropic variants that contribute to the link between cardiovascular and neurological diseases. We performed our analyses on ~530,000 common SNPs coupled with 65 electronic health record (EHR)-based phenotypes in 43,870 unrelated European adults from the Electronic Medical Records and Genomics (eMERGE) network. There were 31 variants identified by all three methods that showed significant associations across late onset cardiac- and neurologic- diseases. We further investigated functional implications of gene expression on the detected "lead SNPs" via colocalization analysis, providing a deeper understanding of the discovered associations. In summary, we present the framework and landscape for detecting potential pleiotropy using univariate, bivariate, multivariate, and colocalization methods. Further exploration of these potentially pleiotropic genetic variants will work toward understanding disease causing mechanisms across cardiovascular and neurological diseases and may assist in considering disease prevention as well as drug repositioning in future research.
Collapse
Affiliation(s)
- Xinyuan Zhang
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA*Authors contributed equally to this work
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Safarova M, Austin E, de Andrade M, Bastarache L, Ye Z, Zheng N, Schaid D, Williams M, Ritchie M, Borthwick K, Larson E, Scrol A, Jarvik G, Manolio T, Hebbring S, Denny J, Kullo I. SCANNING THE PHENOME TO UNCOVER PLEIOTROPIC EFFECTS OF PCSK9. J Am Coll Cardiol 2017. [DOI: 10.1016/s0735-1097(17)35950-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
12
|
Ye Z, Austin E, Schaid D, Kullo I. SEX DIFFERENCES IN ABDOMINAL AORTIC ANEURYSM EXPANSION. J Am Coll Cardiol 2016. [DOI: 10.1016/s0735-1097(16)32360-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
13
|
Cropp CD, McDonnell SK, Middha S, DeRycke M, Karyadi DM, Schaid D, Thibodeau SN, Isaacs WB, Ostrander EA, Stanford J, Cooney KA, Bailey-Wilson JE, Carpten JD. Abstract B40: Rare variant discovery in known cancer genes from whole-exome sequencingof African American hereditary prostate cancer families. Cancer Epidemiol Biomarkers Prev 2016. [DOI: 10.1158/1538-7755.disp15-b40] [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] Open
Abstract
Abstract
African American Hereditary Prostate Cancer Study (AAHPC) was developed as a national collaboration to explore the role of genetics in the causation of hereditary prostate cancer (HPC) in African American (AA) men. AAHPC is in partnership with the International Consortium for Prostate Cancer Genetics (ICPCG), which conducts collaborative studies of HPC genetics in multiplex families. As part of an ICPCG sequencing study of 539 affected individuals from 366 HPC pedigrees, we performed whole exome sequencing in 21 ICPCG AA families, of which there were 14 AAHPC affected men from 11 pedigrees. The combined ICPCG AA cohort consisted of N=26 affected members. Post-variant calling quality control (QC) was implemented using Golden Helix SVS 8 software with filters set for removal of variants with Read Depth < 10, Quality Score < 20, Quality Score: Read Depth Ratio < 0.5, Call Rate < 0.75. Variants were additionally filtered by MAF based on the NHLBI ESP650051-V2 exomes variant frequencies for the AA population using a MAF threshold of 5%. Following QC, 176/299 SNVs and 20/39 INDELs remained for further analysis. In these analyses, we focused on 13 known cancer genes (MSR1, AR, BRCA1, BRCA2, BTNL2, EPHB2, CDH1, RNASEL, ELAC2, HOXB13, CHEK2, TP53 and NBN). Three sequenced families had > 1 affected members sequenced (2 or 3 per family) and the remaining 18 families had one member sequenced. Under the dominant model, our preliminary results show that no rare variants in the 13 candidate genes were found in 3/3 affecteds in two families. Rare SNVs in seven candidate genes (AR, CDH1, ELAC2, HOXB13, RNASEL, BRCA2 and EPHB2) were found in 2/3 affecteds for two families and 2/2 affecteds in one family. Several of the remaining 18 affected men (1 sequenced per pedigree) shared the same rare SNV in these candidate genes. For INDELs, rare variants in three candidate genes were found in pedigrees with ≥ 2 affecteds. Several of the remaining 18 affected men (one sequenced per pedigree) shared the same rare INDEL. Additional QC is underway to validate these variants and bioinformatic analyses are being used to predict effects of the variants in an effort to unravel the complex genetic heterogeneity of HPC in AA.
Citation Format: Cheryl D. Cropp, Shannon K. McDonnell, Sumit Middha, Melissa DeRycke, Danielle M. Karyadi, Daniel Schaid, Stephen N. Thibodeau, William B. Isaacs, Elaine A. Ostrander, Janet Stanford, Kathleen A. Cooney, Joan E. Bailey-Wilson, John D. Carpten. Rare variant discovery in known cancer genes from whole-exome sequencingof African American hereditary prostate cancer families. [abstract]. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr B40.
Collapse
Affiliation(s)
- Cheryl D. Cropp
- 1Translational Genomics Research Institute (TGen), Phoenix, AZ,
| | | | | | | | - Danielle M. Karyadi
- 3Cancer Genetics Branch, National Human Genome Research institute, Bethesda, MD,
| | | | | | | | - Elaine A. Ostrander
- 3Cancer Genetics Branch, National Human Genome Research institute, Bethesda, MD,
| | | | | | - Joan E. Bailey-Wilson
- 7Computational and Statistical Genomics Branch, National Human Genome Research Institute, Baltimore, MD
| | - John D. Carpten
- 1Translational Genomics Research Institute (TGen), Phoenix, AZ,
| |
Collapse
|
14
|
Tsuang D, Vardarajan BN, Bird TD, Boeve B, Schaid D, Taner N, Allen M, Barral S, Bennett DA, Cruchaga C, Goate A, Graff-Radford N, Faber K, Farlow MR, Foroud TM, Ottman R, Rosenberg RN, Rumbaugh M, Sano M, Schellenberg GD, Silverman JM, Sweet R, Mayeux R. P1‐059: MAPT haplotypes modify the association between head injury and risk of Alzheimer's disease. Alzheimers Dement 2015. [DOI: 10.1016/j.jalz.2015.06.256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Mary Sano
- Mount Sinai School of MedicineNew YorkNYUSA
| | | | | | | | | | | |
Collapse
|
15
|
Saunders EJ, Dadaev T, Leongamornlert DA, Jugurnauth-Little S, Tymrakiewicz M, Wiklund F, Al Olama AA, Benlloch S, Neal DE, Hamdy FC, Donovan JL, Giles GG, Severi G, Gronberg H, Aly M, Haiman CA, Schumacher F, Henderson BE, Lindstrom S, Kraft P, Hunter DJ, Gapstur S, Chanock S, Berndt SI, Albanes D, Andriole G, Schleutker J, Weischer M, Nordestgaard BG, Canzian F, Campa D, Riboli E, Key TJ, Travis RC, Ingles SA, John EM, Hayes RB, Pharoah P, Khaw KT, Stanford JL, Ostrander EA, Signorello LB, Thibodeau SN, Schaid D, Maier C, Kibel AS, Cybulski C, Cannon-Albright L, Brenner H, Park JY, Kaneva R, Batra J, Clements JA, Teixeira MR, Xu J, Mikropoulos C, Goh C, Govindasami K, Guy M, Wilkinson RA, Sawyer EJ, Morgan A, Easton DF, Muir K, Eeles RA, Kote-Jarai Z. Fine-mapping the HOXB region detects common variants tagging a rare coding allele: evidence for synthetic association in prostate cancer. PLoS Genet 2014; 10:e1004129. [PMID: 24550738 PMCID: PMC3923678 DOI: 10.1371/journal.pgen.1004129] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 12/06/2013] [Indexed: 02/02/2023] Open
Abstract
The HOXB13 gene has been implicated in prostate cancer (PrCa) susceptibility. We performed a high resolution fine-mapping analysis to comprehensively evaluate the association between common genetic variation across the HOXB genetic locus at 17q21 and PrCa risk. This involved genotyping 700 SNPs using a custom Illumina iSelect array (iCOGS) followed by imputation of 3195 SNPs in 20,440 PrCa cases and 21,469 controls in The PRACTICAL consortium. We identified a cluster of highly correlated common variants situated within or closely upstream of HOXB13 that were significantly associated with PrCa risk, described by rs117576373 (OR 1.30, P = 2.62×10(-14)). Additional genotyping, conditional regression and haplotype analyses indicated that the newly identified common variants tag a rare, partially correlated coding variant in the HOXB13 gene (G84E, rs138213197), which has been identified recently as a moderate penetrance PrCa susceptibility allele. The potential for GWAS associations detected through common SNPs to be driven by rare causal variants with higher relative risks has long been proposed; however, to our knowledge this is the first experimental evidence for this phenomenon of synthetic association contributing to cancer susceptibility.
Collapse
Affiliation(s)
| | - Tokhir Dadaev
- The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | | | | | | | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Cambridge, United Kingdom
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Cambridge, United Kingdom
| | - David E. Neal
- Surgical Oncology (Uro-Oncology: S4), University of Cambridge, Addenbrooke's Hospital, Cambridge and Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Freddie C. Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, and Faculty of Medical Science, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Jenny L. Donovan
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Graham G. Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria, Carlton, Victoria, Australia and Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Gianluca Severi
- Cancer Epidemiology Centre, The Cancer Council Victoria, Carlton, Victoria, Australia and Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Sara Lindstrom
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - David J. Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Susan Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, United States of America
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Demetrius Albanes
- Nutritional Epidemiology Branch, National Cancer Institute, NIH, EPS-3044, Bethesda, Maryland, United States of America
| | - Gerald Andriole
- Division of Urologic Surgery, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Johanna Schleutker
- Department of Medic Biochemistry and Genetics, University of Turku, Turku and Institute of Biomedical Technology and BioMediTech, University of Tampere and FimLab Laboratories, Tampere, Finland
| | - Maren Weischer
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Børge G. Nordestgaard
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniele Campa
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elio Riboli
- Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Tim J. Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Sue A. Ingles
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, California, United States of America, and Stanford University School of Medicine, Stanford, California, United States of America
| | - Richard B. Hayes
- Division of Epidemiology, Department of Population Health, NYU Langone Medical Center, NYU Cancer Institute, New York, New York, United States of America
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Cambridge, United Kingdom
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Janet L. Stanford
- Department of Epidemiology, School of Public Health, University of Washington and Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lisa B. Signorello
- International Epidemiology Institute, Rockville, Maryland, and Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | | | - Daniel Schaid
- Mayo Clinic, Rochester, Minnesota, United States of America
| | - Christiane Maier
- Department of Urology, University Hospital Ulm and Institute of Human Genetics University Hospital Ulm, Ulm, Germany
| | - Adam S. Kibel
- Division of Urologic Surgery, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lisa Cannon-Albright
- Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine and George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, United States of America
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jong Y. Park
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Radka Kaneva
- Molecular Medicine Center and Department of Medical Chemistry and Biochemistry, Medical University - Sofia, Sofia, Bulgaria
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Judith A. Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Manuel R. Teixeira
- Biomedical Sciences Institute (ICBAS), Porto University, Porto, and Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Jianfeng Xu
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | | | - Chee Goh
- The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | | | - Michelle Guy
- The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | | | - Emma J. Sawyer
- The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Angela Morgan
- The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | | | | | | | | | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Cambridge, United Kingdom
| | - Ken Muir
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | | | | |
Collapse
|
16
|
Vardarajan B, Bennett D, Bird T, Boeve B, Farlow M, Foroud T, Goate A, Graff‐Radford N, Ottman R, Rosenberg RN, Schaid D, Sweet R, Tsuang D, Bennett J, Davis B, Faber K, Garland C, Horner K, Kistler D, Kuntz K, Levitch D, Norton J, Pluff L, Reyes D, Rumbaugh M, Sena A, Torneten S, Weamer E, Mayeux R. P3–194: Age‐specific incidence rates of Alzheimer's disease in family members participating in the NIA‐LOAD genetics study. Alzheimers Dement 2013. [DOI: 10.1016/j.jalz.2013.05.1266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | | | - Thomas Bird
- University of Washington Seattle Washington United States
| | | | - Martin Farlow
- Indiana University School of Medicine Indianapolis Washington United States
| | - Tatiana Foroud
- Indiana University School of Medicine Indianapolis Indiana United States
| | - Alison Goate
- Washington University in St. Louis St. Louis Missouri United States
| | | | - Ruth Ottman
- Columbia University New York New York United States
| | | | | | - Robert Sweet
- University of Pittsburgh Pittsburgh Pennsylvania United States
| | - Debby Tsuang
- University of Washington Seattle Washington United States
| | - J. Bennett
- Mayo Clinic Rochester Minnesota United States
| | - Barb Davis
- University of Texas Southwestern Medical Center Dallas Texas United States
| | - Kelley Faber
- Indiana University School of Medicine Indianapolis Indiana United States
| | - Connie Garland
- Indiana University School of Medicine Indianapolis Indiana United States
| | - K. Horner
- Indiana University School of Medicine Indianapolis Indiana United States
| | | | - Karen Kuntz
- Mayo Clinic Rochester Minnesota United States
| | | | - Joanne Norton
- Washington University School of Medicine St. Louis Missouri United States
| | - Lindsay Pluff
- Rush University Medical Center Chicago Illinois United States
| | - Dolly Reyes
- Columbia University New York New York United States
| | - Malia Rumbaugh
- University of Washington Seattle Washington United States
| | - Amanda Sena
- Columbia University New York New York United States
| | | | - Elise Weamer
- University of Pittsburgh Pittsburgh Pennsylvania United States
| | | | | |
Collapse
|
17
|
Xu J, Lange EM, Lu L, Zheng SL, Wang Z, Thibodeau SN, Cannon-Albright LA, Teerlink CC, Camp NJ, Johnson AM, Zuhlke KA, Stanford JL, Ostrander EA, Wiley KE, Isaacs SD, Walsh PC, Maier C, Luedeke M, Vogel W, Schleutker J, Wahlfors T, Tammela T, Schaid D, McDonnell SK, DeRycke MS, Cancel-Tassin G, Cussenot O, Wiklund F, Grönberg H, Eeles R, Easton D, Kote-Jarai Z, Whittemore AS, Hsieh CL, Giles GG, Hopper JL, Severi G, Catalona WJ, Mandal D, Ledet E, Foulkes WD, Hamel N, Mahle L, Moller P, Powell I, Bailey-Wilson JE, Carpten JD, Seminara D, Cooney KA, Isaacs WB. HOXB13 is a susceptibility gene for prostate cancer: results from the International Consortium for Prostate Cancer Genetics (ICPCG). Hum Genet 2013; 132:5-14. [PMID: 23064873 PMCID: PMC3535370 DOI: 10.1007/s00439-012-1229-4] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 09/15/2012] [Indexed: 11/26/2022]
Abstract
Prostate cancer has a strong familial component but uncovering the molecular basis for inherited susceptibility for this disease has been challenging. Recently, a rare, recurrent mutation (G84E) in HOXB13 was reported to be associated with prostate cancer risk. Confirmation and characterization of this finding is necessary to potentially translate this information to the clinic. To examine this finding in a large international sample of prostate cancer families, we genotyped this mutation and 14 other SNPs in or flanking HOXB13 in 2,443 prostate cancer families recruited by the International Consortium for Prostate Cancer Genetics (ICPCG). At least one mutation carrier was found in 112 prostate cancer families (4.6 %), all of European descent. Within carrier families, the G84E mutation was more common in men with a diagnosis of prostate cancer (194 of 382, 51 %) than those without (42 of 137, 30 %), P = 9.9 × 10(-8) [odds ratio 4.42 (95 % confidence interval 2.56-7.64)]. A family-based association test found G84E to be significantly over-transmitted from parents to affected offspring (P = 6.5 × 10(-6)). Analysis of markers flanking the G84E mutation indicates that it resides in the same haplotype in 95 % of carriers, consistent with a founder effect. Clinical characteristics of cancers in mutation carriers included features of high-risk disease. These findings demonstrate that the HOXB13 G84E mutation is present in ~5 % of prostate cancer families, predominantly of European descent, and confirm its association with prostate cancer risk. While future studies are needed to more fully define the clinical utility of this observation, this allele and others like it could form the basis for early, targeted screening of men at elevated risk for this common, clinically heterogeneous cancer.
Collapse
Affiliation(s)
- Jianfeng Xu
- Data Coordinating Center for the ICPCG, Wake Forest University School of Medicine, Winston-Salem, NC USA
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC USA
| | - Ethan M. Lange
- University of Michigan ICPCG Group, University of Michigan Medical School, Ann Arbor, MI USA
- Departments of Genetics and Biostatistics, University of North Carolina, Chapel Hill, NC USA
| | - Lingyi Lu
- Data Coordinating Center for the ICPCG, Wake Forest University School of Medicine, Winston-Salem, NC USA
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC USA
| | - Siqun L. Zheng
- Data Coordinating Center for the ICPCG, Wake Forest University School of Medicine, Winston-Salem, NC USA
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC USA
| | - Zhong Wang
- Data Coordinating Center for the ICPCG, Wake Forest University School of Medicine, Winston-Salem, NC USA
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC USA
| | - Stephen N. Thibodeau
- Mayo Clinic ICPGC Group, Mayo Clinic, Rochester, MN USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Lisa A. Cannon-Albright
- University of Utah ICPCG Group, University of Utah School of Medicine, Salt Lake City, UT USA
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Craig C. Teerlink
- University of Utah ICPCG Group, University of Utah School of Medicine, Salt Lake City, UT USA
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Nicola J. Camp
- University of Utah ICPCG Group, University of Utah School of Medicine, Salt Lake City, UT USA
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Anna M. Johnson
- University of Michigan ICPCG Group, University of Michigan Medical School, Ann Arbor, MI USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI USA
| | - Kimberly A. Zuhlke
- University of Michigan ICPCG Group, University of Michigan Medical School, Ann Arbor, MI USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI USA
| | - Janet L. Stanford
- Fred Hutchinson Cancer Research Center (FHCRC) ICPCG Group, Seattle, WA USA
- Division of Public Health Sciences, FHCRC, Seattle, WA USA
| | - Elaine A. Ostrander
- Fred Hutchinson Cancer Research Center (FHCRC) ICPCG Group, Seattle, WA USA
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD USA
| | - Kathleen E. Wiley
- Johns Hopkins University ICPCG Group, Baltimore, MD USA
- Department of Urology, Johns Hopkins Medical Institutions, Johns Hopkins Hospital, Marburg 115, 600 North Wolfe Street, Baltimore, MD 21287 USA
| | - Sarah D. Isaacs
- Johns Hopkins University ICPCG Group, Baltimore, MD USA
- Department of Urology, Johns Hopkins Medical Institutions, Johns Hopkins Hospital, Marburg 115, 600 North Wolfe Street, Baltimore, MD 21287 USA
| | - Patrick C. Walsh
- Johns Hopkins University ICPCG Group, Baltimore, MD USA
- Department of Urology, Johns Hopkins Medical Institutions, Johns Hopkins Hospital, Marburg 115, 600 North Wolfe Street, Baltimore, MD 21287 USA
| | - Christiane Maier
- University of Ulm ICPCG Group, University of Ulm, Ulm, Germany
- Department of Urology, University of Ulm, Ulm, Germany
| | - Manuel Luedeke
- University of Ulm ICPCG Group, University of Ulm, Ulm, Germany
- Department of Urology, University of Ulm, Ulm, Germany
| | - Walther Vogel
- University of Ulm ICPCG Group, University of Ulm, Ulm, Germany
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Johanna Schleutker
- University of Tampere ICPCG Group, University of Tampere and Fimlab Laboratories, Tampere, Finland
- Institute of Biomedical Technology/BioMediTech, University of Tampere and Fimlab Laboratories, Tampere, Finland
- Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland
| | - Tiina Wahlfors
- University of Tampere ICPCG Group, University of Tampere and Fimlab Laboratories, Tampere, Finland
- Institute of Biomedical Technology/BioMediTech, University of Tampere and Fimlab Laboratories, Tampere, Finland
| | - Teuvo Tammela
- University of Tampere ICPCG Group, University of Tampere and Fimlab Laboratories, Tampere, Finland
- Department of Urology, Tampere University Hospital, Tampere, Finland
| | - Daniel Schaid
- Mayo Clinic ICPGC Group, Mayo Clinic, Rochester, MN USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Shannon K. McDonnell
- Mayo Clinic ICPGC Group, Mayo Clinic, Rochester, MN USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Melissa S. DeRycke
- Mayo Clinic ICPGC Group, Mayo Clinic, Rochester, MN USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | | | - Olivier Cussenot
- CeRePP ICPCG Group, Paris, France
- Department of Urology, APHP, Hospital Tenon, Paris, France
| | - Fredrik Wiklund
- Karolinska ICPCG Group, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Grönberg
- Karolinska ICPCG Group, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ros Eeles
- ACTANE (Anglo/Canadian/Texan/Australian/Norwegian/EU Biomed) Consortium ICPCG Group, Surrey, UK
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Surrey, UK
| | - Doug Easton
- ACTANE (Anglo/Canadian/Texan/Australian/Norwegian/EU Biomed) Consortium ICPCG Group, Surrey, UK
- Strangeways Laboratory, Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Zsofia Kote-Jarai
- ACTANE (Anglo/Canadian/Texan/Australian/Norwegian/EU Biomed) Consortium ICPCG Group, Surrey, UK
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Surrey, UK
| | - Alice S. Whittemore
- BC/CA/HI ICPCG Group, Stanford School of Medicine, Stanford, CA USA
- Department of Health Research and Policy, Stanford School of Medicine, Stanford, CA USA
- Stanford Comprehensive Cancer Center, Stanford School of Medicine, Stanford, CA USA
| | - Chih-Lin Hsieh
- BC/CA/HI ICPCG Group, Stanford School of Medicine, Stanford, CA USA
- Department of Urology and Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA USA
| | - Graham G. Giles
- ACTANE (Anglo/Canadian/Texan/Australian/Norwegian/EU Biomed) Consortium ICPCG Group, Surrey, UK
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Molecular, Environmental, Genetic and Analytical Epidemiology, University of Melbourne, Melbourne, Australia
| | - John L. Hopper
- ACTANE (Anglo/Canadian/Texan/Australian/Norwegian/EU Biomed) Consortium ICPCG Group, Surrey, UK
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Molecular, Environmental, Genetic and Analytical Epidemiology, University of Melbourne, Melbourne, Australia
| | - Gianluca Severi
- ACTANE (Anglo/Canadian/Texan/Australian/Norwegian/EU Biomed) Consortium ICPCG Group, Surrey, UK
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Molecular, Environmental, Genetic and Analytical Epidemiology, University of Melbourne, Melbourne, Australia
| | - William J. Catalona
- Northwestern University ICPCG Group, Chicago, IL USA
- Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Diptasri Mandal
- Louisiana State University ICPCG Group, New Orleans, LA USA
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA USA
| | - Elisa Ledet
- Louisiana State University ICPCG Group, New Orleans, LA USA
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA USA
| | - William D. Foulkes
- ACTANE (Anglo/Canadian/Texan/Australian/Norwegian/EU Biomed) Consortium ICPCG Group, Surrey, UK
- Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, Montreal, QC Canada
- Research Institute of the McGill University Health Centre, Montreal, QC Canada
| | - Nancy Hamel
- ACTANE (Anglo/Canadian/Texan/Australian/Norwegian/EU Biomed) Consortium ICPCG Group, Surrey, UK
- Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, Montreal, QC Canada
- Research Institute of the McGill University Health Centre, Montreal, QC Canada
| | - Lovise Mahle
- ACTANE (Anglo/Canadian/Texan/Australian/Norwegian/EU Biomed) Consortium ICPCG Group, Surrey, UK
- The Norwegian Radium Hospital, Oslo, Norway
| | - Pal Moller
- ACTANE (Anglo/Canadian/Texan/Australian/Norwegian/EU Biomed) Consortium ICPCG Group, Surrey, UK
- The Norwegian Radium Hospital, Oslo, Norway
| | - Isaac Powell
- African American Hereditary Prostate Cancer ICPCG Group, Detroit, MI USA
- Karmanos Cancer Institute, Wayne State University, Detroit, MI USA
| | - Joan E. Bailey-Wilson
- African American Hereditary Prostate Cancer ICPCG Group, Detroit, MI USA
- Inherited Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD USA
| | - John D. Carpten
- African American Hereditary Prostate Cancer ICPCG Group, Detroit, MI USA
- Genetic Basis of Human Disease Research Division, Translational Genomics Research Institute, Phoenix, AZ USA
| | | | - Kathleen A. Cooney
- University of Michigan ICPCG Group, University of Michigan Medical School, Ann Arbor, MI USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI USA
| | - William B. Isaacs
- Johns Hopkins University ICPCG Group, Baltimore, MD USA
- Department of Urology, Johns Hopkins Medical Institutions, Johns Hopkins Hospital, Marburg 115, 600 North Wolfe Street, Baltimore, MD 21287 USA
| | - International Consortium for Prostate Cancer Genetics
- Data Coordinating Center for the ICPCG, Wake Forest University School of Medicine, Winston-Salem, NC USA
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, NC USA
- University of Michigan ICPCG Group, University of Michigan Medical School, Ann Arbor, MI USA
- Departments of Genetics and Biostatistics, University of North Carolina, Chapel Hill, NC USA
- Mayo Clinic ICPGC Group, Mayo Clinic, Rochester, MN USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
- University of Utah ICPCG Group, University of Utah School of Medicine, Salt Lake City, UT USA
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI USA
- Fred Hutchinson Cancer Research Center (FHCRC) ICPCG Group, Seattle, WA USA
- Division of Public Health Sciences, FHCRC, Seattle, WA USA
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD USA
- Johns Hopkins University ICPCG Group, Baltimore, MD USA
- Department of Urology, Johns Hopkins Medical Institutions, Johns Hopkins Hospital, Marburg 115, 600 North Wolfe Street, Baltimore, MD 21287 USA
- University of Ulm ICPCG Group, University of Ulm, Ulm, Germany
- Department of Urology, University of Ulm, Ulm, Germany
- Institute of Human Genetics, University of Ulm, Ulm, Germany
- University of Tampere ICPCG Group, University of Tampere and Fimlab Laboratories, Tampere, Finland
- Institute of Biomedical Technology/BioMediTech, University of Tampere and Fimlab Laboratories, Tampere, Finland
- Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland
- Department of Urology, Tampere University Hospital, Tampere, Finland
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
- CeRePP ICPCG Group, Paris, France
- Department of Urology, APHP, Hospital Tenon, Paris, France
- CeRePP UPMC University, Paris, France
- Karolinska ICPCG Group, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- ACTANE (Anglo/Canadian/Texan/Australian/Norwegian/EU Biomed) Consortium ICPCG Group, Surrey, UK
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Surrey, UK
- Strangeways Laboratory, Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- BC/CA/HI ICPCG Group, Stanford School of Medicine, Stanford, CA USA
- Department of Health Research and Policy, Stanford School of Medicine, Stanford, CA USA
- Stanford Comprehensive Cancer Center, Stanford School of Medicine, Stanford, CA USA
- Department of Urology and Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA USA
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Molecular, Environmental, Genetic and Analytical Epidemiology, University of Melbourne, Melbourne, Australia
- Northwestern University ICPCG Group, Chicago, IL USA
- Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Louisiana State University ICPCG Group, New Orleans, LA USA
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA USA
- Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, Montreal, QC Canada
- Research Institute of the McGill University Health Centre, Montreal, QC Canada
- The Norwegian Radium Hospital, Oslo, Norway
- African American Hereditary Prostate Cancer ICPCG Group, Detroit, MI USA
- Karmanos Cancer Institute, Wayne State University, Detroit, MI USA
- Inherited Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD USA
- Genetic Basis of Human Disease Research Division, Translational Genomics Research Institute, Phoenix, AZ USA
- National Cancer Institute, NIH, Bethesda, MD USA
| |
Collapse
|
18
|
Liu M, Wang L, Schaid D, Wickerham DL, Costantino JP, Goetz MP, Ames MM, Vogel VG, Paik S, Batzler A, Wolmark N, Nakamura Y, Kubo M, Kamatani N, Ingle JN, Weinshilboum RM. Abstract 4727: Breast cancer prevention and selective estrogen response modulators (SERMs): Pharmacogenomics and differential estrogen and SERM regulation of BRCA1 and BRCA2 expression. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-4727] [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
Introduction: The NSABP P-1 and P-2 breast cancer prevention trials have demonstrated that the SERMs tamoxifen and raloxifene can reduce the risk of breast cancer in high risk women.
Methods: We performed a nested matched case-control GWAS utilizing DNA from participants enrolled in P-1 and P-2. 592 participants developed invasive breast cancer or ductal carcinoma in situ, and were matched with 1171 controls who did not. Genome-wide genotyping with the Illumina 610-Quad chip and CYP2D6 genotyping for pertinent alleles were performed. Functional genomic studies involved the use of cultured cells, with siRNA knockdown, followed by qRT-PCR and Western blot analyses.
Results: Eleven SNPs with p-values < 3E-05 were identified. Twenty one additional SNPs with p < 4E-05 were identified by imputation around the genotyped SNPs on chromosomes (Chrs) 4, 8, 9, 13, 16 and 22, which were then genotyped with the Invader platform. Initial functional genomic studies focused on 6 SNPs on Chr16 (p-values 1.81-9.55E-06), all of which were in ZNF423, a gene encoding a putative zinc-finger protein. The Chr16 minor variant SNP sequences had less risk than the common variant (OR=0.7). Our functional studies showed that incubation of Hs578T cells stably transfected with estrogen receptor (ER) α with 0.1 nM estradiol (E2) induced expression of ZNF423, BRCA1/2 for WT but not variant SNP sequences. There was also a striking difference between E2-induced ZNF423, BRCA1/2 expression for variant and WT SNPs in lymphoblastoid cell lines (LCLs) stably transfected with ERα, with only WT showing induction. ChIP assay showed that ZNF423 could bind to the 5’-flanking region of BRCA1, and reporter gene assays showed that ZNF423 could regulate BRCA1/2 transcription. In LCLs stably transfected with ERα and genotyped for ZNF423 SNPs, estrogen-dependent expression of all 3 genes occurred only in the presence of the WT, but not variant ZNF423 SNP sequences. Blockade of ERα with 4-OH tamoxifen prevented induction of expression in cells with WT sequences, but resulted in gene dose-dependent increases in BRCA1/2 expression in cells with variant SNP sequences-suggested that the minor variant has a “protective” effect during clinical SERM therapy and verified by ChIP assays.
Conclusions: The SNPs in ZNF423 identified during GWAS were associated with differential E2-dependent induction of ZNF423, BRCA1 and BRCA2-implying that ZNF423 is “upstream” for the estrogen-dependent induction of BRCA1/2 expression. However, LCLs with variant SNP sequences showed greatly enhanced expression of ZNF423, BRCA1/2 during 4-OH tamoxifen exposure, while cells with WT sequences did not. These results may reveal a novel mechanism for SERM-dependent regulation of BRCA1/2 expression and may have implications for patient selection for SERM therapy.
Funded by U10-CA37377, U10-CA69974 and U14-GM61388.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4727. doi:10.1158/1538-7445.AM2011-4727
Collapse
|
19
|
Ji Y, Hebbring S, Zhu H, Jenkins GD, Biernacka J, Snyder K, Drews M, Fiehn O, Zeng Z, Schaid D, Mrazek DA, Kaddurah-Daouk R, Weinshilboum RM. Glycine and a glycine dehydrogenase (GLDC) SNP as citalopram/escitalopram response biomarkers in depression: pharmacometabolomics-informed pharmacogenomics. Clin Pharmacol Ther 2010; 89:97-104. [PMID: 21107318 DOI: 10.1038/clpt.2010.250] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Major depressive disorder (MDD) is a common psychiatric disease. Selective serotonin reuptake inhibitors (SSRIs) are an important class of drugs used in the treatment of MDD. However, many patients do not respond adequately to SSRI therapy. We used a pharmacometabolomics-informed pharmacogenomic research strategy to identify citalopram/escitalopram treatment outcome biomarkers. Metabolomic assay of plasma samples from 20 escitalopram remitters and 20 nonremitters showed that glycine was negatively associated with treatment outcome (P = 0.0054). This observation was pursued by genotyping tag single-nucleotide polymorphisms (SNPs) for genes encoding glycine synthesis and degradation enzymes, using 529 DNA samples from SSRI-treated MDD patients. The rs10975641 SNP in the glycine dehydrogenase (GLDC) gene was associated with treatment outcome phenotypes. Genotyping for rs10975641 was carried out in 1,245 MDD patients in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study, and its presence was significant (P = 0.02) in DNA taken from these patients. These results highlight a possible role for glycine in SSRI response and illustrate the use of pharmacometabolomics to "inform" pharmacogenomics.
Collapse
Affiliation(s)
- Y Ji
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Ingle J, Schaid D, Goss P, Mushiroda T, Chapman J, Kubo M, Jenkins G, Batzler A, Liu M, Shepherd L, Ellis M, Flockhart D, Nakamura Y, Weinshilboum R. A Genome-Wide Association Study in Patients Experiencing Musculoskeletal Adverse Events on Aromatase Inhibitors as Adjuvant Therapy in Early Breast Cancer Entered on NCIC CTG Trial MA.27. A Pharmacogenetics Research Network-RIKEN Collaboration. Cancer Res 2009. [DOI: 10.1158/0008-5472.sabcs-09-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
Background: The third-generation aromatase inhibitors (AIs) are established adjuvant therapy for postmenopausal women with early stage breast cancer. Musculoskeletal adverse events (MS AE) have become increasingly recognized as an issue for many women receiving AIs resulting in decreased quality of life and, in some instances, discontinuation of the AI. MA.27 is an ongoing randomized clinical trial comparing anastrozole with exemestane that accrued 7576 patients (pts), including 6827 from North America, about 79% of whom provided DNA and consent for genetic testing. A review of withdrawals related to adverse events revealed that the most common cause was MS AE. The hypothesis for our study was that a genome-wide association (GWA) case control study would identify single nucleotide polymorphisms (SNPs) associated with MS AE.Methods: Cases were defined as pts with grade 3 or 4 MS AE (NCI CTCAE v3.0) or who went off treatment for any grade MS AE within the first 2 years and were matched to 2 controls based on treatment arm, length of follow-up, prior chemotherapy, age and prior celecoxib (at least 3 months prior to MS AE). The study was restricted to the 94% of pts self-identified as Caucasian. Genotyping was performed with the Illumina Human610-Quad. Genotype quality control prior to analysis required call rates ≥98%. Eigenstrat analyses were performed to control for population stratification.Results: The GWA study included 293 cases and 586 controls with 6 pts (0.7%) (4 cases, 2 controls) excluded for call rates <98%. 551,358 SNPs were used in the analyses after removing 29,439 for a minor allele frequency <1% and 82 with Hardy Weinberg Equilibrium p-values <10-6. Eigenvectors did not impact the results when used as covariates. Four SNPs with the lowest p-values (3.3-8.2 x 10-6, Armitage test), 3 in high LD (r2>.8) on chromosome (ch) 14 (rs7158782, rs7159713, rs2369049) and 1 on the X ch (rs6637820) were identified. The gene closest (4000-7000 bp) to the 3 SNPs on ch 14 was T-Cell Leukemia 1A (TCL1A), encoding a protein known to augment AKT kinase activity. Expression array data from lymphoblastoid cell lines from 300 subjects of 3 ethnicities revealed that all 3 SNPs were associated with decreased TCL1A expression after adjusting for ethnicity using 2 probe sets (p=0.006 to 0.03). Electromobility shift assay (EMSA) showed that 2 of these SNPs (rs7158782, rs7159713) displayed a shift and the former SNP showed substantially less binding for variant than wild type. The gene closest to the X ch SNP was Immunoglobulin Superfamily 1 (IGSF1), but EMSA did not show a shift for this SNP.Conclusions: MS AEs represent a major impediment to optimal use of AIs in women with breast cancer and this GWA study identified SNPs on ch 14 that provide a focus for further research to identify pts at risk for, and means to ameliorate, this adverse event.(Supported in part by NIH grants U01GM61388, U01GM63173, P50CA116201 and U10CA77202)
Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 15.
Collapse
Affiliation(s)
| | | | | | | | | | - M. Kubo
- 3RIKEN Center for Genomic Medicine, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Kote-Jarai Z, Easton DF, Stanford JL, Ostrander EA, Schleutker J, Ingles SA, Schaid D, Thibodeau S, Dörk T, Neal D, Donovan J, Hamdy F, Cox A, Maier C, Vogel W, Guy M, Muir K, Lophatananon A, Kedda MA, Spurdle A, Steginga S, John EM, Giles G, Hopper J, Chappuis PO, Hutter P, Foulkes WD, Hamel N, Salinas CA, Koopmeiners JS, Karyadi DM, Johanneson B, Wahlfors T, Tammela TL, Stern MC, Corral R, McDonnell SK, Schürmann P, Meyer A, Kuefer R, Leongamornlert DA, Tymrakiewicz M, Liu JF, O'Mara T, Gardiner RAF, Aitken J, Joshi AD, Severi G, English DR, Southey M, Edwards SM, Al Olama AA, Eeles RA. Multiple novel prostate cancer predisposition loci confirmed by an international study: the PRACTICAL Consortium. Cancer Epidemiol Biomarkers Prev 2008; 17:2052-61. [PMID: 18708398 DOI: 10.1158/1055-9965.epi-08-0317] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [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] Open
Abstract
A recent genome-wide association study found that genetic variants on chromosomes 3, 6, 7, 10, 11, 19 and X were associated with prostate cancer risk. We evaluated the most significant single-nucleotide polymorphisms (SNP) in these loci using a worldwide consortium of 13 groups (PRACTICAL). Blood DNA from 7,370 prostate cancer cases and 5,742 male controls was analyzed by genotyping assays. Odds ratios (OR) associated with each genotype were estimated using unconditional logistic regression. Six of the seven SNPs showed clear evidence of association with prostate cancer (P = 0.0007-P = 10(-17)). For each of these six SNPs, the estimated per-allele OR was similar to those previously reported and ranged from 1.12 to 1.29. One SNP on 3p12 (rs2660753) showed a weaker association than previously reported [per-allele OR, 1.08 (95% confidence interval, 1.00-1.16; P = 0.06) versus 1.18 (95% confidence interval, 1.06-1.31)]. The combined risks associated with each pair of SNPs were consistent with a multiplicative risk model. Under this model, and in combination with previously reported SNPs on 8q and 17q, these loci explain 16% of the familial risk of the disease, and men in the top 10% of the risk distribution have a 2.1-fold increased risk relative to general population rates. This study provides strong confirmation of these susceptibility loci in multiple populations and shows that they make an important contribution to prostate cancer risk prediction.
Collapse
Affiliation(s)
- Zsofia Kote-Jarai
- Section of Cancer Genetics Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Li L, Fridley B, Kalari K, Jenkins G, Batzler A, Safgren S, Hildebrandt M, Ames M, Schaid D, Wang L. Gemcitabine and cytosine arabinoside cytotoxicity: association with lymphoblastoid cell expression. Cancer Res 2008; 68:7050-8. [PMID: 18757419 DOI: 10.1158/0008-5472.can-08-0405] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Two cytidine analogues, gemcitabine (dFdC) and 1-beta-d-arabinofuranosylcytosine (AraC), show significant therapeutic effect in a variety of cancers. However, response to these drugs varies widely. Evidence from tumor biopsy samples shows that expression levels for genes involved in the cytidine transport, metabolism, and bioactivation pathway contribute to this variation in response. In the present study, we set out to test the hypothesis that variation in gene expression both within and outside of this "pathway" might influence sensitivity to gemcitabine and AraC. Specifically, Affymetrix U133 Plus 2.0 GeneChip and cytotoxicity assays were performed to obtain basal mRNA expression and IC(50) values for both drugs in 197 ethnically defined Human Variation Panel lymphoblastoid cell lines. Genes with a high degree of association with IC(50) values were involved mainly in cell death, cancer, cell cycle, and nucleic acid metabolism pathways. We validated selected significant genes by performing real-time quantitative reverse transcription-PCR and selected two representative candidates, NT5C3 (within the pathway) and FKBP5 (outside of the pathway), for functional validation. Those studies showed that down-regulation of NT5C3 and FKBP5 altered tumor cell sensitivity to both drugs. Our results suggest that cell-based model system studies, when combined with complementary functional characterization, may help to identify biomarkers for response to chemotherapy with these cytidine analogues.
Collapse
Affiliation(s)
- Liang Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Ji Y, Olson J, Zhang J, Hildebrandt M, Wang L, Ingle J, Fredericksen Z, Sellers T, Miller W, Dixon JM, Brauch H, Eichelbaum M, Justenhoven C, Hamann U, Ko Y, Brüning T, Chang-Claude J, Wang-Gohrke S, Schaid D, Weinshilboum R. Breast cancer risk reduction and membrane-bound catechol O-methyltransferase genetic polymorphisms. Cancer Res 2008; 68:5997-6005. [PMID: 18632656 DOI: 10.1158/0008-5472.can-08-0043] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Catechol O-methyltransferase (COMT)-catalyzed methylation of catecholestrogens has been proposed to play a protective role in estrogen-induced genotoxic carcinogenesis. We have taken a comprehensive approach to test the hypothesis that genetic variation in COMT might influence breast cancer risk. Fifteen COMT single nucleotide polymorphisms (SNPs) selected on the basis of in-depth resequencing of the COMT gene were genotyped in 1,482 DNA samples from a Mayo Clinic breast cancer case control study. Two common SNPs in the distal promoter for membrane-bound (MB) COMT, rs2020917 and rs737865, were associated with breast cancer risk reduction in premenopausal women in the Mayo Clinic study, with allele-specific odds ratios (OR) of 0.70 [95% confidence interval (CI), 0.52-0.95] and 0.68 (95% CI, 0.51-0.92), respectively. These two SNPs were then subjected to functional genomic analysis and were genotyped in an additional 3,683 DNA samples from two independent case control studies (GENICA and GESBC). Functional genomic experiments showed that these SNPs could up-regulate transcription and that they altered DNA-protein binding patterns. Furthermore, substrate kinetic and exon array analyses suggested a role for MB-COMT in catecholestrogen inactivation. The GENICA results were similar to the Mayo case control observations, with ORs of 0.85 (95% CI, 0.72-1.00) and 0.85 (95% CI, 0.72-1.01) for the two SNPs. No significant effect was observed in the GESBC study. These studies showed that two SNPs in the COMT distal promoter were associated with breast cancer risk reduction in two of three case control studies, compatible with the results of functional genomic experiments, suggesting a role for MB-COMT in breast cancer risk.
Collapse
Affiliation(s)
- Yuan Ji
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Schaid D. Genome Wide Association Studies of Complex Diseases. Am J Epidemiol 2006. [DOI: 10.1093/aje/163.suppl_11.s79-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
25
|
Ma CX, Adjei AA, Salavaggione OE, Coronel J, Pelleymounter L, Wang L, Eckloff BW, Schaid D, Wieben ED, Adjei AA, Weinshilboum RM. Human aromatase: gene resequencing and functional genomics. Cancer Res 2005; 65:11071-82. [PMID: 16322257 DOI: 10.1158/0008-5472.can-05-1218] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [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: 11/16/2022]
Abstract
Aromatase [cytochrome P450 19 (CYP19)] is a critical enzyme for estrogen biosynthesis, and aromatase inhibitors are of increasing importance in the treatment of breast cancer. We set out to identify and characterize genetic polymorphisms in the aromatase gene, CYP19, as a step toward pharmacogenomic studies of aromatase inhibitors. Specifically, we "resequenced" all coding exons, all upstream untranslated exons plus their presumed core promoter regions, all exon-intron splice junctions, and a portion of the 3'-untranslated region of CYP19 using 240 DNA samples from four ethnic groups. Eighty-eight polymorphisms were identified, resulting in 44 haplotypes. Functional genomic studies were done with the four nonsynonymous coding single nucleotide polymorphisms (cSNP) that we observed, two of which were novel. Those cSNPs altered the following amino acids: Trp39Arg, Thr201Met, Arg264Cys, and Met364Thr. The Cys264, Thr364, and double variant Arg39Cys264 allozymes showed significant decreases in levels of activity and immunoreactive protein when compared with the wild-type (WT) enzyme after transient expression in COS-1 cells. A slight decrease in protein level was also observed for the Arg39 allozyme, whereas Met201 displayed no significant changes in either activity or protein level when compared with the WT enzyme. There was also a 4-fold increase in apparent K(m) value for Thr364 with androstenedione as substrate. Of the recombinant allozymes, only the double mutant (Arg39Cys264) displayed a significant change from the WT enzyme in inhibitor constant for the aromatase inhibitors exemestane and letrozole. These observations indicate that genetic variation in CYP19 might contribute to variation in the pathophysiology of estrogen-dependent disease.
Collapse
Affiliation(s)
- Cynthia X Ma
- Department of Medical Oncology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Shrestha S, Strathdee SA, Galai N, Oleksyk T, Fallin MD, Mehta S, Schaid D, Vlahov D, O'Brien SJ, Smith MW. Behavioral risk exposure and host genetics of susceptibility to HIV-1 infection. J Infect Dis 2005; 193:16-26. [PMID: 16323127 DOI: 10.1086/498532] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [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] [Received: 05/11/2005] [Accepted: 06/29/2005] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Some individuals are readily infected with low human immunodeficiency virus type 1 (HIV-1) exposure, whereas others appear less susceptible, suggesting that host genetics plays a role in the viral entry pathway. The matched case-control study design with measured risk exposures provides an avenue for discovering genes involved in susceptibility to infection. METHODS We conducted a nested case-control study of African Americans (266 HIV-1 seroconverter cases and 532 seronegative controls from the AIDS Link to Intravenous Experience cohort), to examine the association between 50 single-nucleotide polymorphisms (SNPs) in 9 candidate genes (CCR5, CCR2, RANTES, MIP1A, MCP2, IL10, IFNG, MCSF, and IL2) and susceptibility to HIV-1 infection. To account for differential exposure propensities, risk behavior self-reported during semiannual visits was used to estimate a standardized cumulative risk exposure (SCRE). Individual SNPs were evaluated using conditional logistic-regression models, and the inferred haplotypes were assessed in the haplotype trend regression analyses after adjusting for age and SCRE. RESULTS Four SNPs (CCR2-V64I, CCR5-2459, MIP1A+954, and IL2+3896) and specific haplotypes in the IL2 and CCR2/CCR5 regions were significantly associated with HIV-1 infection susceptibility in different genetic models. CONCLUSIONS Our results suggest that genetic variants in associated host genes may play an important role in susceptibility to HIV-1 infection.
Collapse
Affiliation(s)
- Sadeep Shrestha
- Laboratory of Genomic Diversity, National Cancer Institute at Frederick, National Institutes of Health, MD 21702, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Sinclair CS, Adem C, Naderi A, Soderberg CL, Johnson M, Wu K, Wadum L, Couch VL, Sellers TA, Schaid D, Slezak J, Fredericksen Z, Ingle JN, Hartmann L, Jenkins RB, Couch FJ. TBX2 is preferentially amplified in BRCA1- and BRCA2-related breast tumors. Cancer Res 2002; 62:3587-91. [PMID: 12097257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The chromosome 17q23 region is frequently amplified in breast tumors. Gain of the region is present in 50% of BRCA1-associated breast tumors and 87% of BRCA2-associated breast tumors. The amplification frequency of the RPS6KB1 and TBX2 oncogenes from this amplicon was compared in 27 BRCA1 and BRCA2 mutant breast tumors, 15 breast tumors from high-risk patients with no BRCA1 or BRCA2 mutations, and 62 matched sporadic breast tumor controls. TBX2 was determined to be preferentially amplified and overexpressed in BRCA1 and BRCA2 mutant tumors, whereas RPS6KB1 was not, suggesting a role for TBX2 amplification in the development of BRCA1- and BRCA2-associated breast tumors.
Collapse
Affiliation(s)
- Colleen S Sinclair
- Department of Laboratory Medicine and Pathology, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Weinshenker BG, Hebrink D, Kantarci OH, Schaefer-Klein J, Atkinson E, Schaid D, McMurray CM. Genetic variation in the transforming growth factor beta1 gene in multiple sclerosis. J Neuroimmunol 2001; 120:138-45. [PMID: 11694328 DOI: 10.1016/s0165-5728(01)00424-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [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: 10/27/2022]
Abstract
Transforming growth factor beta1 (TGFbeta1) is a Th2 cytokine encoded on chromosome 19q13, a region possibly linked to multiple sclerosis (MS). TGFbeta1 exerts favorable effects on experimental allergic encephalomyelitis. We performed a comprehensive search for genetic variants in this gene in 122 population-based sporadic cases of MS. We detected six variants, including three missense variants. We tested for association of the variants with susceptibility and course of MS and for linkage and transmission disequilibrium in a family series consisting of 395 samples in 59 pedigrees. Genetic variation in TGFB1 does not appear to contribute in a major way to susceptibility to MS.
Collapse
Affiliation(s)
- B G Weinshenker
- Department of Neurology, Mayo Clinic and Mayo Foundation, 200 First Street SW, Rochester, MN 55905, USA.
| | | | | | | | | | | | | |
Collapse
|
29
|
Blaszyk H, Hartmann A, Cunningham JM, Schaid D, Wold LE, Kovach JS, Sommer SS. A prospective trial of midwest breast cancer patients: a p53 gene mutation is the most important predictor of adverse outcome. Int J Cancer 2000. [PMID: 10719728 DOI: 10.1002/(sici)1097-0215(20000120)89:1<32::aid-ijc6>3.0.co;2-g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Several retrospective studies have suggested p53 gene mutation as an adverse prognostic indicator in breast cancer patients, based on a selective growth advantage of p53 mutant cancer cells and their presumed resistance to current adjuvant therapy regimens. A cohort of 90 Caucasian midwestern breast cancer patients was analyzed prospectively (60 months of follow-up) with a rigorous mutation detection methodology. The presence of a p53 gene mutation was the single most adverse prognostic indicator for recurrence (p = 0.0032) and death (p = 0.0001), and was associated with poor response to both adjuvant (p = 0.0001) and palliative (p = 0.006) therapy. Analysis of the p53 gene with appropriate mutation detection methodology markedly improves the prediction of early recurrence, treatment failure, and death in breast cancer patients.
Collapse
Affiliation(s)
- H Blaszyk
- Department of Oncology, Mayo Clinic and Mayo Foundation, Rochester, MN, USA
| | | | | | | | | | | | | |
Collapse
|
30
|
Sinclair CS, Berry R, Schaid D, Thibodeau SN, Couch FJ. BRCA1 and BRCA2 have a limited role in familial prostate cancer. Cancer Res 2000; 60:1371-5. [PMID: 10728701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Epidemiological studies have suggested that the breast cancer susceptibility genes, BRCA1 and BRCA2, may be involved in the development of prostate cancer. Several studies have screened prostate cancer populations for the presence of BRCA1 and BRCA2 mutations, with few mutations identified. In this study, 22 high-risk prostate cancer families (at least three cases of prostate cancer) were screened by conformation-sensitive gel electrophoresis (CSGE) for mutations in BRCA1 and BRCA2. To maximize the chance of finding mutations in these two genes, families were also selected for the presence of at least two cases of breast and/or ovarian cancer. We identified one previously reported BRCA2 missense mutation and two previously unreported BRCA2 intron polymorphisms. No BRCA1 or BRCA2 truncating mutations were detected. Thus, BRCA1 and BRCA2 appear to have a limited role in familial prostate cancer, and families with both prostate and breast cancer may result from mutations in other predisposition genes.
Collapse
Affiliation(s)
- C S Sinclair
- Department of Laboratory Medicine and Pathology, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
| | | | | | | | | |
Collapse
|
31
|
Blaszyk H, Hartmann A, Cunningham JM, Schaid D, Wold LE, Kovach JS, Sommer SS. A prospective trial of midwest breast cancer patients: a p53 gene mutation is the most important predictor of adverse outcome. Int J Cancer 2000; 89:32-8. [PMID: 10719728 DOI: 10.1002/(sici)1097-0215(20000120)89:1<32::aid-ijc6>3.0.co;2-g] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [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: 12/15/2022]
Abstract
Several retrospective studies have suggested p53 gene mutation as an adverse prognostic indicator in breast cancer patients, based on a selective growth advantage of p53 mutant cancer cells and their presumed resistance to current adjuvant therapy regimens. A cohort of 90 Caucasian midwestern breast cancer patients was analyzed prospectively (60 months of follow-up) with a rigorous mutation detection methodology. The presence of a p53 gene mutation was the single most adverse prognostic indicator for recurrence (p = 0.0032) and death (p = 0.0001), and was associated with poor response to both adjuvant (p = 0.0001) and palliative (p = 0.006) therapy. Analysis of the p53 gene with appropriate mutation detection methodology markedly improves the prediction of early recurrence, treatment failure, and death in breast cancer patients.
Collapse
Affiliation(s)
- H Blaszyk
- Department of Oncology, Mayo Clinic and Mayo Foundation, Rochester, MN, USA
| | | | | | | | | | | | | |
Collapse
|
32
|
Schaid D. Mathematical and Statistical Methods for Genetic Analysis. Am J Hum Genet 1999. [DOI: 10.1086/302430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
|
33
|
Xu J, Meyers D, Freije D, Isaacs S, Wiley K, Nusskern D, Ewing C, Wilkens E, Bujnovszky P, Bova G, Walsh P, Isaacs W, Schleutker J, Matikainen M, Tammela T, Visakorpi T, Kallioniemi OP, Berry R, Schaid D, French A, McDonnell S, Schroeder J, Blute M, Thibodeau S, Gronberg H, Emanuelsson M, Damber JE, Bergh A, Jonsson BA, Smith J, Bailey-Wilson J, Carpten J, Stephan D, Gillanders E, Amundson I, Kainu T, Freas-Lutz D, Baffoe-Bonnie A, Van Aucken A, Sood R, Collins F, Brownstein M, Trent J. Evidence for a Prostate Cancer Susceptibility Locus on the X Chromosome. J Urol 1999. [DOI: 10.1016/s0022-5347(01)61689-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- J. Xu
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - D. Meyers
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - D. Freije
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - S. Isaacs
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - K. Wiley
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - D. Nusskern
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - C. Ewing
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - E. Wilkens
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - P. Bujnovszky
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - G.S. Bova
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - P. Walsh
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - W. Isaacs
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - J. Schleutker
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - M. Matikainen
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - T. Tammela
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - T. Visakorpi
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - O.-P. Kallioniemi
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - R. Berry
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - D. Schaid
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - A. French
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - S. McDonnell
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - J. Schroeder
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - M. Blute
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - S. Thibodeau
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - H. Gronberg
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - M. Emanuelsson
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - J.-E. Damber
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - A. Bergh
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - B.-A. Jonsson
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - J. Smith
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - J. Bailey-Wilson
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - J. Carpten
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - D. Stephan
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - E. Gillanders
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - I. Amundson
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - T. Kainu
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - D. Freas-Lutz
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - A. Baffoe-Bonnie
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - A. Van Aucken
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - R. Sood
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - F. Collins
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - M. Brownstein
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| | - J. Trent
- Center for Genetics of Asthma and Complex Diseases, University of Maryland and Departments of Urology, Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore and Prostate Cancer Investigation Group, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland, Departments of Laboratory Medicine and Pathology, Health
| |
Collapse
|
34
|
Santos JL, Schaid D, Pérez-Bravo F, Carrasco E, Calvillán M, Albala C. Applicability of the case-parent design in the etiological research of Type 1 diabetes in Chile and other genetically mixed populations. Diabetes Res Clin Pract 1999; 43:143-6. [PMID: 10221667 DOI: 10.1016/s0168-8227(98)00128-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 11/25/2022]
Abstract
In case-control studies, spurious associations between Human Leukocyte Antigen (HLA) alleles and Type 1 diabetes could arise as a result of population stratification, if there are ethnic differences between cases and non-related controls. The Chilean population has several unique features which make it ideal for the study of the effect of stratification by ethnicity on genetic epidemiological research. The incidence rates of Type 1 diabetes in Chilean Aboriginal populations are very low compared to Caucasian populations, while the frequency of the alleles in HLA loci also vary across ethnic groups. In order to avoid the confounding effect of ethnicity, one possible remedy would be the use of cases and their parents in place of non-related controls. The case-parent design offers an adequate framework for the study of the association between HLA polymorphisms and Type 1 diabetes in the Chilean population and can also be applicable to other genetically mixed populations especially in the Americas.
Collapse
Affiliation(s)
- J L Santos
- Department of Nutritional Epidemiology, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago.
| | | | | | | | | | | |
Collapse
|
35
|
Poland GA, Jacobson RM, Schaid D, Moore SB, Jacobsen SJ. The association between HLA class I alleles and measles vaccine-induced antibody response: evidence of a significant association. Vaccine 1998; 16:1869-71. [PMID: 9795394 DOI: 10.1016/s0264-410x(98)00017-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [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: 10/18/2022]
Abstract
While the Moraten strain measles vaccine is an excellent, safe, and immunogenic vaccine, vaccine failure occurs, presumably when an individual develops an inadequate immune response. In this study, we examined the association of HLA class I genes and measles vaccine-induced antibody levels. We found that the allele distribution of HLA-B alleles differed between non-responders and hyper-responders (p = 0.002). Several class I alleles were associated with non-response (HLA-B13, -B44, and -C5); whereas several other alleles were associated with hyper-response (HLA-B7 and -B51). In addition, non-responders were more likely to be HLA-B homozygous than normal responders (odds ratio 2.1), and more likely to be homozygous than hyper-responders (odds ratio 3.7, p = 0.031 Mantel-Haenzel for trend). Finally, we found evidence of an allele dose-response phenomenon for HLA-B7. We conclude that there are important associations between class I HLA genes and measles antibody levels following immunization.
Collapse
Affiliation(s)
- G A Poland
- Mayo Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | | |
Collapse
|
36
|
Xu J, Meyers D, Freije D, Isaacs S, Wiley K, Nusskern D, Ewing C, Wilkens E, Bujnovszky P, Bova GS, Walsh P, Isaacs W, Schleutker J, Matikainen M, Tammela T, Visakorpi T, Kallioniemi OP, Berry R, Schaid D, French A, McDonnell S, Schroeder J, Blute M, Thibodeau S, Grönberg H, Emanuelsson M, Damber JE, Bergh A, Jonsson BA, Smith J, Bailey-Wilson J, Carpten J, Stephan D, Gillanders E, Amundson I, Kainu T, Freas-Lutz D, Baffoe-Bonnie A, Van Aucken A, Sood R, Collins F, Brownstein M, Trent J. Evidence for a prostate cancer susceptibility locus on the X chromosome. Nat Genet 1998; 20:175-9. [PMID: 9771711 DOI: 10.1038/2477] [Citation(s) in RCA: 414] [Impact Index Per Article: 15.9] [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: 11/09/2022]
Abstract
Over 200,000 new prostate cancer cases are diagnosed in the United States each year, accounting for more than 35% of all cancer cases affecting men, and resulting in 40,000 deaths annually. Attempts to characterize genes predisposing to prostate cancer have been hampered by a high phenocopy rate, the late age of onset of the disease and, in the absence of distinguishing clinical features, the inability to stratify patients into subgroups relative to suspected genetic locus heterogeneity. We previously performed a genome-wide search for hereditary prostate cancer (HPC) genes, finding evidence of a prostate cancer susceptibility locus on chromosome 1 (termed HPC1; ref. 2). Here we present evidence for the location of a second prostate cancer susceptibility gene, which by heterogeneity estimates accounts for approximately 16% of HPC cases. This HPC locus resides on the X chromosome (Xq27-28), a finding consistent with results of previous population-based studies suggesting an X-linked mode of HPC inheritance. Linkage to Xq27-28 was observed in a combined study population of 360 prostate cancer families collected at four independent sites in North America, Finland and Sweden. A maximum two-point lod score of 4.60 was observed at DXS1113, theta=0.26, in the combined data set. Parametric multipoint and non-parametric analyses provided results consistent with the two-point analysis. Significant evidence for genetic locus heterogeneity was observed, with similar estimates of the proportion of linked families in each separate family collection. Genetic mapping of the locus represents an important initial step in the identification of an X-linked gene implicated in the aetiology of HPC.
Collapse
Affiliation(s)
- J Xu
- Center for the Genetics of Asthma and Complex Diseases, University of Maryland, Baltimore 21201, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Weinshenker BG, Santrach P, Bissonet AS, McDonnell SK, Schaid D, Moore SB, Rodriguez M. Major histocompatibility complex class II alleles and the course and outcome of MS: a population-based study. Neurology 1998; 51:742-7. [PMID: 9748020 DOI: 10.1212/wnl.51.3.742] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.4] [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: 01/16/2023] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) has been consistently associated with susceptibility to MS and the course of several other human autoimmune diseases. A putative association between the course and severity of MS and the MHC remains controversial. METHODS DR and DQ genotyping by either restriction fragment length polymorphism or sequence-specific PCR-based typing in 119 patients representing 73.4% of the population with MS evaluated in a cross-sectional disability survey and 100 healthy controls from Olmsted County, Minnesota. RESULTS We found a positive association between MS susceptibility and the DR15-DQ6 and DR13-DQ7 haplotypes, and we found a negative association with the DR1-DQ5 haplotype. We found a trend to a positive association of primary progressive MS with DR4-DQ8 and DR1-DQ5 and an association of "bout onset" MS with DR17-DQ2. We did not find an association with disease severity, as defined by EDSS/duration. CONCLUSION Lack of consistency between different studies may be due to regional variation in MS and limitations of power but likely indicate a minor effect of MHC class II genes on the course and severity of MS.
Collapse
Affiliation(s)
- B G Weinshenker
- Department of Neurology, Mayo Clinic and Mayo Foundation, Rochester, MN 55905, USA
| | | | | | | | | | | | | |
Collapse
|
38
|
Abstract
OBJECTIVE The repertoire of T cells in patients with rheumatoid arthritis (RA) is characterized by clonal expansion of selected CD4+ T cells, which are autoreactive and lack the expression of the functionally important CD28 molecule. The goal of this study was to determine the contribution of these unusual lymphocytes to the disease process. METHODS RA patients (n = 108) and normal controls (n = 53) were examined for the expression of CD4+ CD28- T cells by 2-color fluorescence-activated cell sorter analysis. Clinical data were ascertained by retrospective chart review. RESULTS The frequencies of CD4+ CD28- T cells displayed a bimodal distribution, defining carriers and noncarriers in normal subjects and RA patients. In longitudinal studies, the noncarrier and carrier phenotypes were stable over time. Carriers of CD4+ CD28- T cells accumulated in the RA population (64% versus 45%; P = 0.02). The expansion of CD4+ CD28- T cells correlated with extraarticular involvement, but not with disease duration, antirheumatic treatment, or severity of joint destruction. The patient subsets with nodular disease (P = 0.02) and rheumatoid organ disease (P = 0.04) had the highest proportion of CD4+ CD28- T cell carriers. The size of the CD4+ CD28- compartment correlated with extraarticular progression of RA (P = 0.001 in nodular RA, P = 0.003 in rheumatoid organ disease). CONCLUSION The bimodality of distribution of CD4+ CD28- T cell frequencies is compatible with genetic control of the generation of these unusual T cells. In RA patients, CD4+ CD28- T cells are not an epiphenomenon of the disease process, but predispose patients to developing inflammatory lesions in extraarticular tissues.
Collapse
Affiliation(s)
- P B Martens
- Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
| | | | | | | |
Collapse
|
39
|
Kovach JS, Hartmann A, Blaszyk H, Cunningham J, Schaid D, Sommer SS. Mutation detection by highly sensitive methods indicates that p53 gene mutations in breast cancer can have important prognostic value. Proc Natl Acad Sci U S A 1996; 93:1093-6. [PMID: 8577720 PMCID: PMC40036 DOI: 10.1073/pnas.93.3.1093] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.5] [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: 01/31/2023] Open
Abstract
Human cancer cells with a mutated p53 tumor-suppressor gene have a selective growth advantage and may exhibit resistance to ionizing radiation and certain chemotherapeutic agents. To examine the prognostic value of mutations in the p53 gene, a cohort of 90 Midwestern Caucasian breast cancer patients were analyzed with methodology that detects virtually 100% of all mutations. The presence of a p53 gene mutation was by far the single most predictive indicator for recurrence and death (relative risks of 4.7 and 23.2, respectively). Direct detection of p53 mutations had substantially greater prognostic value than immunohistochemical detection of p53 overexpression. Analysis of p53 gene mutations may permit identification of a subset of breast cancer patients who, despite lack of conventional indicators of poor prognosis, are at high risk of early recurrence and death.
Collapse
Affiliation(s)
- J S Kovach
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | | | | |
Collapse
|
40
|
Abstract
Based on evaluation of 59 probands and their families, we previously demonstrated that over 20% of patients with idiopathic dilated cardiomyopathy (DCM) have familial disease. We acquired 36 additional probands and found familial disease in 24.2% of the 95 probands in this expanded consecutively ascertained cohort. The family history, as reported by the patient and relatives, is often an unreliable indicator of familial disease because patients may be unaware of the significance of a family history of sudden death, arrhythmia or stroke. We demonstrate that careful family history with review of medical records identifies more familial cases than merely asking the patient if there is a family history of DCM. However, even such a careful family history does not identify all familial cases. Some familial cases are identified only by echocardiographic investigation of asymptomatic relatives. We found no clinical attributes of probands, other than family history, which predicted familial disease.
Collapse
Affiliation(s)
- J B Goerss
- Department of Medical Genetics, Mayo Clinic/Mayo Foundation, Rochester, Minnesota 55905, USA
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Saitoh S, Cunningham J, De Vries EM, McGovern RM, Schroeder JJ, Hartmann A, Blaszyk H, Wold LE, Schaid D, Sommer SS. p53 gene mutations in breast cancers in midwestern US women: null as well as missense-type mutations are associated with poor prognosis. Oncogene 1994; 9:2869-75. [PMID: 8084591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We determined the pattern of mutations in exons 2-11 and adjacent intronic regions in breast cancers from Midwestern US white women. Twenty-one mutations were detected in 53 tumors (39.6%). Comparisons of the pattern of mutations within exons 5-9 showed that the frequency of missense mutations (44%) was lower in breast cancers of US Midwestern women than in most tumor types including breast cancers in other populations. Compared to breast cancers reported in a Scottish population, US women had a high frequency of G:C-->T:A transversions (P = 0.046). These findings suggest that environmental or endogenous factors contribute to p53 mutagenesis in mammary tissue to different extents among different populations. With a median follow-up of 19 months, the presence of a mutation was associated with shorter time to disease recurrence (P = 0.05) and shorter survival (P = 0.003). Putative dominant negative missense-type mutations (missense and in-frame microdeletions; P = 0.001) and null mutations (hemizygous nonsense and frameshift mutations; P = 0.007) were equally ominous. Thus, tumors with missense p53 mutations resulting in over-expression of a dysfunctional but otherwise intact protein have a clinical outcome similar to tumors with null mutations resulting in a truncated or garbled protein.
Collapse
Affiliation(s)
- S Saitoh
- Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905
| | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Blaszyk H, Vaughn CB, Hartmann A, McGovern RM, Schroeder JJ, Cunningham J, Schaid D, Sommer SS, Kovach JS. Novel pattern of p53 gene mutations in an American black cohort with high mortality from breast cancer. Lancet 1994; 343:1195-7. [PMID: 7909871 DOI: 10.1016/s0140-6736(94)92403-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The pattern of acquired mutations in the p53 gene can be used to study differences in factors contributing to carcinogenesis. We investigated mutations in exons 5-9 and adjacent intronic regions in 47 breast cancers of black women from Michigan, a population with the highest breast-cancer mortality in the US. The 16 mutations detected differed from those of other populations. In particular, the black women had an excess of A:T-->G:C transitions compared with rural white US midwest women. While the causes of the different pattern of acquired mutation remain to be determined, this molecular epidemiological approach detects the consequences of mutagenic processes in specific populations. Mutation patterns will constrain hypotheses to mechanisms consistent with the observed biochemical alterations.
Collapse
Affiliation(s)
- H Blaszyk
- Department of Oncology, Mayo Clinic and Foundation, Rochester, MN 55905
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Abstract
Colorectal tumor DNA was examined for somatic instability at (CA)n repeats on human chromosomes 5q, 15q, 17p, and 18q. Differences between tumor and normal DNA were detected in 25 of the 90 (28 percent) tumors examined. This instability appeared as either a substantial change in repeat length (often heterogeneous in nature) or a minor change (typically two base pairs). Microsatellite instability was significantly correlated with the tumor's location in the proximal colon (P = 0.003), with increased patient survival (P = 0.02), and, inversely, with loss of heterozygosity for chromosomes 5q, 17p, and 18q. These data suggest that some colorectal cancers may arise through a mechanism that does not necessarily involve loss of heterozygosity.
Collapse
MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Chromosomes, Human, Pair 15
- Chromosomes, Human, Pair 17
- Chromosomes, Human, Pair 18
- Chromosomes, Human, Pair 5
- Colonic Neoplasms/genetics
- Colorectal Neoplasms/genetics
- DNA, Neoplasm/genetics
- DNA, Satellite/genetics
- Female
- Heterozygote
- Humans
- Male
- Middle Aged
- Mutation
- Polymerase Chain Reaction
- Repetitive Sequences, Nucleic Acid
Collapse
Affiliation(s)
- S N Thibodeau
- Molecular Genetics Laboratory, Mayo Clinic, Rochester, MN 55905
| | | | | |
Collapse
|
44
|
Patterson MN, Bell MV, Bloomfield J, Flint T, Dorkins H, Thibodeau SN, Schaid D, Bren G, Schwartz CE, Wieringa B. Genetic and physical mapping of a novel region close to the fragile X site on the human X chromosome. Genomics 1989; 4:570-8. [PMID: 2744766 DOI: 10.1016/0888-7543(89)90281-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [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: 01/02/2023]
Abstract
We report the isolation and characterization of a novel DNA marker (1A1) in Xqter in the region of the fragile X. Genetic studies in families segregating for the fragile X syndrome suggest that 1A1 lies between the disease mutation and the distal locus, DXS52. Studies in normal and fragile X families show that 1A1 is tightly linked to DXS52 (Zmax = 17.20; theta max = 0.03) and F8 (Zmax = 7.01; theta max = 0.08). Multipoint mapping of families supports the order Xcen-DXS105-FRAXA-1A1-DXS52-(F8, DXS115)-Xqter. Pulsed-field gel electrophoresis (PFGE) studies demonstrate that 1A1 defines a new region of at least 2 Mb of DNA not physically linked to DXS52 or F8, thus extending the physical map of Xq27-qter to over 4 Mb. Complex partial digestion PFGE patterns, probably due to differing degrees of methylation, are observed with 1A1 in unrelated normal and fragile-X-positive individuals, whereas other distal markers give uniform digestion profiles. Physical data suggest that 1A1 lies in a region less CpG rich than other distal markers in Xq27-qter.
Collapse
Affiliation(s)
- M N Patterson
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford, England
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Patterson M, Gitschier J, Bloomfield J, Bell M, Dorkins H, Froster-Iskenius U, Sommer S, Sobell J, Schaid D, Thibodeau S. An intronic region within the human factor VIII gene is duplicated within Xq28 and is homologous to the polymorphic locus DXS115 (767). Am J Hum Genet 1989; 44:679-85. [PMID: 2565080 PMCID: PMC1715651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The genomic sequences recognized by the anonymous probe 767 (DXS115) are localized to two sites within Xq28. One site lies within intron 22 of the factor VIII gene (FBC). Physical mapping suggests that the second site lies within 1.2 megabases of the F8C gene. The RFLPs detected by 767 are located within the second site. Genetic data suggest that F8C and DXS115 are tightly linked (theta max = .04; Zmax = 8.30). Recombination events in meioses informative for DXS52 (St14), DXS115, and F8C suggest that DXS115 and F8C lie distal to DXS52.
Collapse
Affiliation(s)
- M Patterson
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford, England
| | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Abstract
Androgen-induced changes in laryngeal growth patterns were studied using a sheep animal model. Forty-eight lambs were divided into eight treatment groups. Lambs in seven of the groups were castrated at birth, while lambs in the eighth group served as an intact (noncastrated) control. Six groups were then treated with varying doses of testosterone and dihydrotestosterone, while the seventh served as a castrated, nontreated control. All animals were killed and gross dissections of the larynges were performed. Thirty-four linear and angular measurements were obtained from each larynx. The mean superior thyroid horn separation showed the most dramatic androgen-induced effect (p = 0.023). Laryngeal anterior-posterior diameter, superior thyroid horn height, posterior thyroid cartilage width, thyroid cartilage angle, and vocal process to arytenoid base distances all demonstrated positive dose-response relationships. Hypoandrogenic levels appeared to have an inhibitory effect upon laryngeal growth when compared to castrated controls.
Collapse
|