1
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He KY, Khramtsova EA, Cabrera-Socorro A, Zhang Y, Li S, Sarver BAJ, Smets B, Li QS, De Muynck L, Parrado AR, Lovestone S, Black MH. Characterization of APOE Christchurch carriers in 455,306 UK Biobank participants. Mol Neurodegener 2023; 18:92. [PMID: 38017580 PMCID: PMC10685495 DOI: 10.1186/s13024-023-00684-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/21/2023] [Indexed: 11/30/2023] Open
Affiliation(s)
- Karen Y He
- Population Analytics & Insights, Data Science Analytics & Insights, Janssen R&D, Spring House, PA, USA.
| | - Ekaterina A Khramtsova
- Population Analytics & Insights, Data Science Analytics & Insights, Janssen R&D, Spring House, PA, USA.
| | | | - Yanfei Zhang
- Population Analytics & Insights, Data Science Analytics & Insights, Janssen R&D, Spring House, PA, USA
| | - Shuwei Li
- Population Analytics & Insights, Data Science Analytics & Insights, Janssen R&D, Spring House, PA, USA
| | - Brice A J Sarver
- Population Analytics & Insights, Data Science Analytics & Insights, Janssen R&D, Spring House, PA, USA
| | - Bart Smets
- Neuroscience Data Science, Janssen R&D, Beerse, Belgium
| | - Qingqin S Li
- Neuroscience Data Science, Janssen R&D, Titusville, NJ, USA
| | | | - Antonio R Parrado
- Population Analytics & Insights, Data Science Analytics & Insights, Janssen R&D, Spring House, PA, USA
| | | | - Mary Helen Black
- Population Analytics & Insights, Data Science Analytics & Insights, Janssen R&D, Spring House, PA, USA
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2
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Abdel-Azim G, Patel P, Li S, Guo S, Black MH. Fast multiple-trait genome-wide association analysis for correlated longitudinal measurements. Sci Rep 2023; 13:20603. [PMID: 37996550 PMCID: PMC10667366 DOI: 10.1038/s41598-023-47555-1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023] Open
Abstract
Large-scale longitudinal biobank data can be leveraged to identify genetic variation contributing to human diseases progression and traits trajectories. While methods for genome-wide association studies (GWAS) of multiple correlated traits have been proposed, an efficient multiple-trait approach to model longitudinal phenotypes is not currently available. We developed GAMUT, a genome-wide association approach for multiple longitudinal traits. GAMUT employs a mixed-effects model to fit longitudinal outcomes where a fast algorithm for inversion by recursive partitioning of the random effects submatrix is introduced. To evaluate performance of the algorithms introduced and assess their statistical power and type I error, stochastic simulation was conducted. Consistent with our expectation, power was greater for cross-sectional (CS) than longitudinal (LT) effects, particularly with a diminishing LT/CS ratio. With a minimum minor allele count of 3 within genotype by time categories, observed type I error was roughly equal to theoretical genome-wide significance. Additionally, 28 blood-based biomarkers measured at 2 time points on participants of the UK Biobank were used to compare GAMUT against single-trait standard and longitudinal GWAS (including rate of change). Across all biomarkers, we observed 539 (CS) and 248 (LT) significant independent variants for the GAMUT method, and 513 (CS) and 30 (LT) for single-trait longitudinal GWAS, respectively. Only 37 variants were identified by modeling rates of change using standard GWAS.
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Affiliation(s)
| | - Parth Patel
- Janssen Res. & Dev. (Johnson & Johnson), Spring House, PA, USA
| | - Shuwei Li
- Janssen Res. & Dev. (Johnson & Johnson), Spring House, PA, USA
| | - Shicheng Guo
- Janssen Res. & Dev. (Johnson & Johnson), Spring House, PA, USA
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3
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Sun BB, Chiou J, Traylor M, Benner C, Hsu YH, Richardson TG, Surendran P, Mahajan A, Robins C, Vasquez-Grinnell SG, Hou L, Kvikstad EM, Burren OS, Davitte J, Ferber KL, Gillies CE, Hedman ÅK, Hu S, Lin T, Mikkilineni R, Pendergrass RK, Pickering C, Prins B, Baird D, Chen CY, Ward LD, Deaton AM, Welsh S, Willis CM, Lehner N, Arnold M, Wörheide MA, Suhre K, Kastenmüller G, Sethi A, Cule M, Raj A, Burkitt-Gray L, Melamud E, Black MH, Fauman EB, Howson JMM, Kang HM, McCarthy MI, Nioi P, Petrovski S, Scott RA, Smith EN, Szalma S, Waterworth DM, Mitnaul LJ, Szustakowski JD, Gibson BW, Miller MR, Whelan CD. Plasma proteomic associations with genetics and health in the UK Biobank. Nature 2023; 622:329-338. [PMID: 37794186 PMCID: PMC10567551 DOI: 10.1038/s41586-023-06592-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
The Pharma Proteomics Project is a precompetitive biopharmaceutical consortium characterizing the plasma proteomic profiles of 54,219 UK Biobank participants. Here we provide a detailed summary of this initiative, including technical and biological validations, insights into proteomic disease signatures, and prediction modelling for various demographic and health indicators. We present comprehensive protein quantitative trait locus (pQTL) mapping of 2,923 proteins that identifies 14,287 primary genetic associations, of which 81% are previously undescribed, alongside ancestry-specific pQTL mapping in non-European individuals. The study provides an updated characterization of the genetic architecture of the plasma proteome, contextualized with projected pQTL discovery rates as sample sizes and proteomic assay coverages increase over time. We offer extensive insights into trans pQTLs across multiple biological domains, highlight genetic influences on ligand-receptor interactions and pathway perturbations across a diverse collection of cytokines and complement networks, and illustrate long-range epistatic effects of ABO blood group and FUT2 secretor status on proteins with gastrointestinal tissue-enriched expression. We demonstrate the utility of these data for drug discovery by extending the genetic proxied effects of protein targets, such as PCSK9, on additional endpoints, and disentangle specific genes and proteins perturbed at loci associated with COVID-19 susceptibility. This public-private partnership provides the scientific community with an open-access proteomics resource of considerable breadth and depth to help to elucidate the biological mechanisms underlying proteo-genomic discoveries and accelerate the development of biomarkers, predictive models and therapeutics1.
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Affiliation(s)
- Benjamin B Sun
- Translational Sciences, Research & Development, Biogen, Cambridge, MA, USA.
| | - Joshua Chiou
- Internal Medicine Research Unit, Worldwide Research, Development and Medical, Pfizer, Cambridge, MA, USA
| | - Matthew Traylor
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre Oxford, Oxford, UK
| | | | | | - Tom G Richardson
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre Oxford, Oxford, UK
- Genomic Sciences, GlaxoSmithKline, Stevenage, UK
| | | | | | - Chloe Robins
- Genomic Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | | | - Liping Hou
- Population Analytics, Janssen Research & Development, Spring House, PA, USA
| | | | - Oliver S Burren
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Kyle L Ferber
- Biostatistics, Research and Development, Biogen, Cambridge, MA, USA
| | | | - Åsa K Hedman
- External Science and Innovation Target Sciences, Worldwide Research, Development and Medical, Pfizer, Stockholm, Sweden
| | - Sile Hu
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Tinchi Lin
- Analytics and Data Sciences, Biogen, Cambridge, MA, USA
| | - Rajesh Mikkilineni
- Data Science Institute, Takeda Development Center Americas, Cambridge, MA, USA
| | | | | | - Bram Prins
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Denis Baird
- Translational Sciences, Research & Development, Biogen, Cambridge, MA, USA
| | - Chia-Yen Chen
- Translational Sciences, Research & Development, Biogen, Cambridge, MA, USA
| | - Lucas D Ward
- Alnylam Human Genetics, Discovery & Translational Research, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Aimee M Deaton
- Alnylam Human Genetics, Discovery & Translational Research, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | | | - Carissa M Willis
- Alnylam Human Genetics, Discovery & Translational Research, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Nick Lehner
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - Maria A Wörheide
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | | | - Anil Raj
- Calico Life Sciences, San Francisco, CA, USA
| | | | | | - Mary Helen Black
- Population Analytics, Janssen Research & Development, Spring House, PA, USA
| | - Eric B Fauman
- Internal Medicine Research Unit, Worldwide Research, Development and Medical, Pfizer, Cambridge, MA, USA
| | - Joanna M M Howson
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre Oxford, Oxford, UK
| | | | | | - Paul Nioi
- Alnylam Human Genetics, Discovery & Translational Research, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | | | - Erin N Smith
- Takeda Development Center Americas, San Diego, CA, USA
| | - Sándor Szalma
- Takeda Development Center Americas, San Diego, CA, USA
| | | | | | | | | | - Melissa R Miller
- Internal Medicine Research Unit, Worldwide Research, Development and Medical, Pfizer, Cambridge, MA, USA
| | - Christopher D Whelan
- Translational Sciences, Research & Development, Biogen, Cambridge, MA, USA.
- Neuroscience Data Science, Janssen Research & Development, Cambridge, MA, USA.
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4
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Brown AC, Cohen CJ, Mielczarek O, Migliorini G, Costantino F, Allcock A, Davidson C, Elliott KS, Fang H, Lledó Lara A, Martin AC, Osgood JA, Sanniti A, Scozzafava G, Vecellio M, Zhang P, Black MH, Li S, Truong D, Molineros J, Howe T, Wordsworth BP, Bowness P, Knight JC. Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis. Cell Genom 2023; 3:100306. [PMID: 37388915 PMCID: PMC10300554 DOI: 10.1016/j.xgen.2023.100306] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 01/30/2023] [Accepted: 03/27/2023] [Indexed: 07/01/2023]
Abstract
Ankylosing spondylitis (AS) is a common, highly heritable inflammatory arthritis characterized by enthesitis of the spine and sacroiliac joints. Genome-wide association studies (GWASs) have revealed more than 100 genetic associations whose functional effects remain largely unresolved. Here, we present a comprehensive transcriptomic and epigenomic map of disease-relevant blood immune cell subsets from AS patients and healthy controls. We find that, while CD14+ monocytes and CD4+ and CD8+ T cells show disease-specific differences at the RNA level, epigenomic differences are only apparent upon multi-omics integration. The latter reveals enrichment at disease-associated loci in monocytes. We link putative functional SNPs to genes using high-resolution Capture-C at 10 loci, including PTGER4 and ETS1, and show how disease-specific functional genomic data can be integrated with GWASs to enhance therapeutic target discovery. This study combines epigenetic and transcriptional analysis with GWASs to identify disease-relevant cell types and gene regulation of likely pathogenic relevance and prioritize drug targets.
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Affiliation(s)
- Andrew C. Brown
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Carla J. Cohen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Olga Mielczarek
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Horizon Discovery (PerkinElmer) Cambridge Research Park, 8100 Beach Dr., Waterbeach, Cambridge CB25 9TL, UK
| | - Gabriele Migliorini
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Félicie Costantino
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- UVSQ, INSERM UMR1173, Infection et Inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Paris, France
- Rheumatology Department, AP-HP, Ambroise Paré Hospital, Paris, France
| | - Alice Allcock
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Connor Davidson
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | | | - Hai Fang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Alicia Lledó Lara
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Alice C. Martin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Julie A. Osgood
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Anna Sanniti
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Giuseppe Scozzafava
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Matteo Vecellio
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- Centro Ricerche Fondazione Italiana Ricerca sull’Artrite (FIRA), Fondazione Pisana per la Scienza ONLUS, Via Ferruccio Giovannini 13, 56017 San Giuliano Terme (Pisa), Italy
| | - Ping Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Mary Helen Black
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Shuwei Li
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Dongnhu Truong
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Julio Molineros
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Trevor Howe
- Data Science, External Innovation, Janssen R&D, London W1G 0BG, UK
| | - B. Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Julian C. Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
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5
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Molineros J, Elliott K, Truong DT, Fang H, Hart A, Li S, Waterworth D, Knight JC, Black MH. Leveraging genetic correlation across immune-mediated disease to gain insights into underpowered studies of rare conditions. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.160.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Prevalence of immune mediated disease (IMD) within N. European populations varies from common (atopic dermatitis AD=10%) to rarer (giant cell arteritis-GCA=0.02%; hidradenitis suppurativa-HS=0.77%). This directly affects statistical power to detect genomewide SNP associations and to identify “causal” genes.
Objective
Leverage genetic correlations between differently powered IMD cohorts to study the genetic mechanisms underlying multiple immune-mediated diseases.
We used UK Biobank clinical data to create 18 IMD cohorts and a control set of individuals without any history of autoimmune disease (N=50,136). Using whole genome sequencing data from ~140K participants of the UKB, we performed SNP-level GWAS with REGENIE v2, and prioritized the associated genes using association statistics, in silico annotation, and eQTL information, as implemented in the Priority Index (Pi) algorithm. We used k-means clustering across relative gene rank distances optimized with the elbow method to group IMDs according to similar genetic architectures.
Result
IMD cohort size ranged from 196 to 3,411 cases and were each compared with a common set of controls. Optimal clustering yielded 4 groups, each with 6,5,4 or 3 IMD’s respectively. One cluster of interest contained HS, AD, vitiligo, GCA and Sjogren’s syndrome. This cluster reflects similarity in common “pathogenic” genes across IMD and highlights new candidate genes for further investigation that would otherwise go unnoticed in poorly powered studies of GCA and HS.
In conclusion, our proposed use of genetic associations and clustering of their relative ranks across multiple disease phenotypes identified pathogenic genes in understudied IMDs that would otherwise not have been elucidated.
Supported by Janssen Research & Development
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Affiliation(s)
| | | | | | - Hai Fang
- 2University of Oxford, United Kingdom
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6
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Truong DT, Molineros J, Chen Y, Guan M, Hart A, Keyes B, Seiber KB, Li S, Waterworth D, Black MH. Decoding atopic dermatitis: patient heterogeneity and genetic variation contributing to immune-mediated dermatologic disease in the UK Biobank. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.60.03] [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] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Background
Dupilumab is the only approved biologic used to treat moderate to severe atopic dermatitis (AD) but has a non-response rate of 55–60%. This suggests underlying heterogeneity in AD etiology, requiring alternate therapies for patients.
Study Objective
Identify biomarkers and disease conditions in the UK Biobank that stratify AD patients into homogenous subgroups for genetic characterization.
Methods
We identified 13,137 AD cases and 13,136 age and sex-matched controls using hospital ICD9/10 and primary care codes in the UK Biobank. A total of 94 biomarkers and 1,596 disease PheCodes were used to isolate traits that vary in AD patients relative to controls; K-means (quantitative) and K-modes (binary) clustering was performed to identify subgroups within AD patients. Genetic analysis was performed for subgroups vs. controls using REGENIE.
Results
We observed enrichment of dermatologic, gastrointestinal, and rheumatologic conditions in AD patients, as well as differences in eosinophil percentage, Cystatin C, C-reactive protein, and erythrocyte distribution width relative to controls. There were eight subgroups of AD patients including groups with co-occurring psoriasis, asthma and gastrointestinal problems, penicillin allergy, and AD with no co-morbidities. Genetic analyses revealed novel HLA and non-HLA associations with subgroups, while also replicating known associations with FLG.
Conclusion
There were eight distinct AD subgroups based on co-occurring disease states. Genetic analyses show subgroup-specific factors can contribute to disease pathology—signaling potential utility for differential therapies and highlight mechanisms for targeted therapeutic development in the treatment of AD.
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Affiliation(s)
- Dongnhu T Truong
- 1Computational Sciences, Population Analytics, Janssen Res. & Develop
| | - Julio Molineros
- 1Computational Sciences, Population Analytics, Janssen Res. & Develop
| | - Yanqing Chen
- 2Immunology, Translational Sciences, Janssen Res. & Develop
| | - Meijian Guan
- 2Immunology, Translational Sciences, Janssen Res. & Develop
| | - Amy Hart
- 2Immunology, Translational Sciences, Janssen Res. & Develop
| | - Bryce Keyes
- 2Immunology, Translational Sciences, Janssen Res. & Develop
| | | | - Shuwei Li
- 1Computational Sciences, Population Analytics, Janssen Res. & Develop
| | | | - Mary Helen Black
- 1Computational Sciences, Population Analytics, Janssen Res. & Develop
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7
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Kamihara J, Zhou J, LaDuca H, Wassner AJ, Dalton E, Garber JE, Black MH. Germline pathogenic variants in cancer risk genes among patients with thyroid cancer and suspected predisposition. Cancer Med 2022; 11:1745-1752. [PMID: 35174967 PMCID: PMC9041070 DOI: 10.1002/cam4.4549] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 12/29/2021] [Accepted: 01/03/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose Multigene panels allow simultaneous testing of genes involved in cancer predisposition. Thyroid cancer (TCa) is a component tumor of several cancer predisposition syndromes, but the complete landscape of germline variants predisposing to TCa remains to be determined. Methods Clinical information and genetic test results were reviewed from over 170,000 individuals who had multigene panel testing for hereditary cancer at a single diagnostic laboratory. Germline pathogenic and likely pathogenic variants (“pathogenic variants”) were examined among individuals with TCa. A cohort with breast cancer (BCa) was examined to serve as a comparison group and to determine the added contribution of TCa to the ascertainment of genetic risk. Results Of 3134 individuals with TCa, 291 (9.3%) were found to have one or more pathogenic variant(s). Among 904 individuals with TCa alone, 7.5% had one or more pathogenic variant(s), similar to those with BCa alone (8.4%). In all groups, CHEK2 was the gene with the highest number of pathogenic variants identified, with a significantly increased frequency among individuals with a history of both thyroid and BCa compared to BCa alone. Conclusions A high prevalence of germline pathogenic variants was observed among individuals with TCa referred for hereditary cancer genetic testing, even in the absence of other cancer diagnoses. These data suggest that TCa may be an under‐recognized component of cancer predisposition syndromes.
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Affiliation(s)
- Junne Kamihara
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Jing Zhou
- Ambry Genetics, Aliso Viejo, California, USA
| | | | - Ari J Wassner
- Boston Children's Hospital Division of Endocrinology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Mary Helen Black
- Boston Children's Hospital Division of Endocrinology, Harvard Medical School, Boston, Massachusetts, USA.,Janssen Research and Development, Spring House, PA, USA
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8
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Srinivasan S, Chen L, Todd J, Divers J, Gidding S, Chernausek S, Gubitosi-Klug RA, Kelsey MM, Shah R, Black MH, Wagenknecht LE, Manning A, Flannick J, Imperatore G, Mercader JM, Dabelea D, Florez JC. Erratum. The First Genome-Wide Association Study for Type 2 Diabetes in Youth: The Progress in Diabetes Genetics in Youth (ProDiGY) Consortium. Diabetes 2021;70:996-1005. Diabetes 2021; 71:db22er01a. [PMID: 34716200 PMCID: PMC8763869 DOI: 10.2337/db22-er01a] [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: 11/13/2022]
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9
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Srinivasan S, Chen L, Todd J, Divers J, Gidding S, Chernausek S, Gubitosi-Klug RA, Kelsey MM, Shah R, Black MH, Wagenknecht LE, Manning A, Flannick J, Imperatore G, Mercader JM, Dabelea D, Florez JC. The First Genome-Wide Association Study for Type 2 Diabetes in Youth: The Progress in Diabetes Genetics in Youth (ProDiGY) Consortium. Diabetes 2021; 70:996-1005. [PMID: 33479058 PMCID: PMC7980197 DOI: 10.2337/db20-0443] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 01/18/2021] [Indexed: 12/16/2022]
Abstract
The prevalence of type 2 diabetes in youth has increased substantially, yet the genetic underpinnings remain largely unexplored. To identify genetic variants predisposing to youth-onset type 2 diabetes, we formed ProDiGY, a multiethnic collaboration of three studies (TODAY, SEARCH, and T2D-GENES) with 3,006 youth case subjects with type 2 diabetes (mean age 15.1 ± 2.9 years) and 6,061 diabetes-free adult control subjects (mean age 54.2 ± 12.4 years). After stratifying by principal component-clustered ethnicity, we performed association analyses on ∼10 million imputed variants using a generalized linear mixed model incorporating a genetic relationship matrix to account for population structure and adjusting for sex. We identified seven genome-wide significant loci, including the novel locus rs10992863 in PHF2 (P = 3.2 × 10-8; odds ratio [OR] = 1.23). Known loci identified in our analysis include rs7903146 in TCF7L2 (P = 8.0 × 10-20; OR 1.58), rs72982988 near MC4R (P = 4.4 × 10-14; OR 1.53), rs200893788 in CDC123 (P = 1.1 × 10-12; OR 1.32), rs2237892 in KCNQ1 (P = 4.8 × 10-11; OR 1.59), rs937589119 in IGF2BP2 (P = 3.1 × 10-9; OR 1.34), and rs113748381 in SLC16A11 (P = 4.1 × 10-8; OR 1.04). Secondary analysis with 856 diabetes-free youth control subjects uncovered an additional locus in CPEB2 (P = 3.2 × 10-8; OR 2.1) and consistent direction of effect for diabetes risk. In conclusion, we identified both known and novel loci in the first genome-wide association study of youth-onset type 2 diabetes.
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Affiliation(s)
- Shylaja Srinivasan
- Division of Pediatric Endocrinology, University of California, San Francisco, San Francisco, CA
| | - Ling Chen
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Jennifer Todd
- Division of Pediatric Endocrinology, University of Vermont, Burlington, VT
| | | | | | - Steven Chernausek
- Pediatric Diabetes and Endocrinology Section, University of Oklahoma College of Medicine, Oklahoma City, OK
| | - Rose A. Gubitosi-Klug
- Pediatric Endocrinology, Diabetes, and Metabolism, Case Western Reserve University and Rainbow Babies and Children’s Hospital, Cleveland, OH
| | - Megan M. Kelsey
- Pediatric Endocrinology, University of Colorado School of Medicine, Aurora, CO
| | - Rachana Shah
- Pediatric Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Alisa Manning
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - Jason Flannick
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA
| | | | - Josep M. Mercader
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Diabetes Research Center, Diabetes Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Dana Dabelea
- Department of Epidemiology, University of Colorado School of Public Health, Aurora, CO
| | - Jose C. Florez
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Diabetes Research Center, Diabetes Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA
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10
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Yao K KA, Clifford J, Li S, LaDuca H, Hulick P, Gutierrez S, Black MH. Prevalence of Germline Pathogenic and Likely Pathogenic Variants in Patients With Second Breast Cancers. JNCI Cancer Spectr 2020; 4:pkaa094. [PMID: 33409458 PMCID: PMC7771422 DOI: 10.1093/jncics/pkaa094] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Background Few studies have examined gene-specific associations with contralateral and/or second breast cancer (SBC). Methods The frequency of pathogenic and likely pathogenic (P/LP) variants in clinically actionable genes (BRCA1, BRCA2, PTEN, TP53, CHEK2, CDH1, ATM, PALB2, NBN, and NF1) was compared between women with a primary breast cancer (PBC) and SBC who underwent multigene panel testing at a single diagnostic testing laboratory. Race- and ethnicity-specific logistic regression burden tests adjusted for age at diagnosis of first breast cancer, histology, presence of first- or second-degree relatives with breast cancer, and prior testing for BRCA1/2 genes were used to test for associations with SBC. All statistical tests were 2-sided. Results The study was comprised of 75 550 women with PBC and 7728 with SBC. Median time between breast cancers for SBC was 11 (interquartile range = 6–17) years. Restricting to women tested for all actionable genes (n = 60 310), there were 4231 (7.8%) carriers of P/LP variants in actionable genes among the controls (PBC) compared with 652 (11.1%) women with SBC (P< .001). Among Caucasians, exclusive of Ashkenazi Jewish women, those carrying a P/LP variant in a clinically actionable gene were 1.44 (95% confidence interval [CI] = 1.30 to 1.60) times as likely to have SBC than noncarriers, after accounting for potential confounders. Among African American and Hispanic women, a P/LP variant in a clinically actionable gene was 1.88 (95% CI = 1.36 to 2.56) and 1.66 (9% CI = 1.02 to 2.58) times as likely to be associated with SBC, respectively (P < .001 and P = .03). Conclusion Women with P/LP variants in breast cancer predisposition genes are more likely to have SBC than noncarriers. Prospective studies are needed confirm these findings.
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Affiliation(s)
- Katharine A Yao K
- Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | | | - Shuwei Li
- Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Peter Hulick
- Department of Medicine, Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL, USA
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11
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Pritzlaff M, Tian Y, Reineke P, Stuenkel AJ, Allen K, Gutierrez S, Jackson M, Dolinsky JS, LaDuca H, Xu J, Black MH, Helfand BT. Diagnosing hereditary cancer predisposition in men with prostate cancer. Genet Med 2020; 22:1517-1523. [PMID: 32439974 PMCID: PMC7462744 DOI: 10.1038/s41436-020-0830-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 12/20/2022] Open
Abstract
PURPOSE We describe the pathogenic variant spectrum and identify predictors of positive results among men referred for clinical genetic testing for prostate cancer. METHODS One thousand eight hundred twelve men with prostate cancer underwent clinical multigene panel testing between April 2012 and September 2017. Stepwise logistic regression determined the most reliable predictors of positive results among clinical variables reported on test requisition forms. RESULTS A yield of 9.4-12.1% was observed among men with no prior genetic testing. In this group, the positive rate of BRCA1 and BRCA2 was 4.6%; the positive rate for the mismatch repair genes was 2.8%. Increasing Gleason score (odds ratio [OR] 1.19; 95% confidence interval [CI] 0.97-1.45); personal history of breast or pancreatic cancer (OR 3.62; 95% CI 1.37-9.46); family history of breast, ovarian, or pancreatic cancer (OR 2.32 95% CI 1.48-3.65); and family history of Lynch syndrome-associated cancers (OR 1.97; 95% CI 1.23-3.15) were predictors of positive results. CONCLUSION These results support multigene panel testing as the primary genetic testing approach for hereditary prostate cancer and are supportive of recommendations for consideration of germline testing in men with prostate cancer. Expanding the criteria for genetic testing should be considered as many pathogenic variants are actionable for treatment of advanced prostate cancer.
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Affiliation(s)
| | - Yuan Tian
- Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | | | | | | | | | | | - Jianfeng Xu
- Division of Urology, Northshore University Health System, Evanston, IL, USA
| | | | - Brian T Helfand
- Division of Urology, Northshore University Health System, Evanston, IL, USA
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12
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Navarro RA, Adams AL, Lin CC, Fleming J, Garcia IA, Lee J, Black MH. Does Knee Arthroscopy for Treatment of Meniscal Damage with Osteoarthritis Delay Knee Replacement Compared to Physical Therapy Alone? Clin Orthop Surg 2020; 12:304-311. [PMID: 32904116 PMCID: PMC7449858 DOI: 10.4055/cios19114] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/25/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUD To determine patient factors that lead to treatment of meniscal tears with osteoarthritis (OA) with knee arthroscopy (KA) or physical therapy only (PT-only); and to assess differences in clinical outcomes including the time to knee arthroplasty. METHODS Patients aged ≥ 45 years with OA at meniscal tear diagnosis were followed up from the date of surgery (KA) or first PT visit (PT-only) until partial/total knee replacement surgery, death, disenrollment, or end of study. Demographic and clinical characteristics were compared and used to derive propensity scores. A Cox proportional hazards model was used to estimate the risk of knee replacement surgery and greater healthcare utilization associated with KA vs. PT-only. RESULTS Among 7,026 patients (KA, 69%; PT-only, 31%), 27% had partial or total knee replacement surgery during follow-up. PT-only patients were older and more likely to be women and had more comorbidities. After accounting for differences between groups, the cumulative incidence of knee replacement was modestly but significantly higher for those who received KA than those who underwent PT-only (hazard ratio, 1.30; 95% confidence interval, 1.17-1.44; p < 0.001), although there was no significant difference in health service utilization, narcotic medication dispenses, or knee injections after initiating treatment. CONCLUSIONS For patients with meniscal damage complicated by OA, those who underwent KA were 30% more likely to have partial or total knee replacement surgery at any given time than those who had PT alone.
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Affiliation(s)
- Ronald A. Navarro
- Department of Orthopaedic Surgery, Kaiser Permanente South Bay Medical Center, Harbor City, CA, USA
| | - Annette L. Adams
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Charles C. Lin
- Department of Orthopedic Surgery, NYU Langone Orthopedic Hospital, New York, NY, USA
| | - John Fleming
- Torrance Orthopaedic and Sports Medicine Group, Torrance, CA, USA
| | - Ivan A. Garcia
- Kaiser Permanente Baldwin Park Medical Center, Baldwin Park, CA, USA
| | - Janet Lee
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Mary Helen Black
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
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13
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Black MH, Li S, LaDuca H, Armasu S, Polley EC, Fitz-Gibbon P, Scott CG, Winham SJ, Olson JE, Ruddy KJ, Vachon CM, Couch FJ. Abstract P5-07-06: Performance of a polygenic risk score combined with clinical assessment for breast cancer risk. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p5-07-06] [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: Polygenic risk scores (PRS) based on a large number of SNPs associated with breast cancer have recently been made available in combination with multigene panel testing for clinical management of breast cancer risk. Breast cancer risk assessment has historically been performed using various non-genetic risk models, which predict lifetime risk of breast cancer in unaffected women based on personal and family history information. While clinical use of PRS in combination with these models continues to increase, the predictive performance of a PRS combined with clinical information in real-world patient populations has not been thoroughly investigated. Methods: We assessed a 100-SNP breast cancer PRS in combination with the Tyrer-Cuzick model-estimated lifetime breast cancer risk in 5,374 Caucasian women from the case-control Mayo Clinic Breast Cancer Study (MCBCS), comprised of 3,373 breast cancer cases and 2,001 unaffected controls seen at Mayo Clinic from 2004 to 2016. Clinical, family history, and demographic information was collected on all MCBCS participants via questionnaires and medical record review. SNPs were selected for the PRS if they exceeded genome-wide significance in ≥2 large-scale breast cancer genome wide association studies (GWAS) in women of European descent. Selected SNPs were then used to construct a population standardized PRS, accounting for per-allele odds ratios reported in the largest GWAS to date and population-specific allele frequencies. PRS and Tyrer-Cuzick model associations with breast cancer and related clinical features were tested using multivariate logistic regression. Results: Among cases and controls, mean±SD age at diagnosis and study enrollment was 56.4±12.4 and 56.2±14.1, respectively. Approximately 36.9% of cases and 16.9% of controls had ≥1 first- or second-degree relative with breast or ovarian cancer, respectively. Among unaffected women, the median (IQR) estimated lifetime risk of breast cancer to age 85 based on Tyrer-Cuzick alone was 8.3% (6.9%), and 2.6% had a clinically actionable lifetime risk of ≥20%. The mean±SD sum of the risk alleles across 100 SNPs was significantly higher for cases vs. controls (94.8±6.3 vs. 92.7±6.2, p<0.001). Compared to women in the lowest quartile of PRS, those in the 2nd, 3rd and 4th quartiles were 1.47 (95% CI: 1.26-1.72), 1.87 (95% CI: 1.60-2.19), and 2.22 (95% CI: 1.89-2.61) times more likely to have breast cancer after adjustment for age and family history. The AUC was 0.59 (95% CI: 0.58-0.61) for PRS and 0.60 (95% CI: 0.58-0.61) for Tyrer-Cuzick model estimated risk alone; but when combined, the model achieved an AUC of 0.63 (95% CI: 0.62-0.65). Among unaffected women, 6.7% had ≥20% lifetime risk of breast cancer based on the combined PRS-clinical model. Conclusions: These findings suggest that the 100-SNP PRS significantly improves estimation of breast cancer risk based on non-genetic models, and can be used to further identify women at increased lifetime risk who would otherwise not be identified by clinical assessment alone.
Citation Format: Mary Helen Black, Shuwei Li, Holly LaDuca, Sebastian Armasu, Eric C. Polley, Patrick Fitz-Gibbon, Chris G. Scott, Stacey J. Winham, Janet E. Olson, Kathryn J. Ruddy, Celine M. Vachon, Fergus J. Couch. Performance of a polygenic risk score combined with clinical assessment for breast cancer risk [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 P5-07-06.
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Wu Y, Yu H, Li S, Wiley K, Zheng SL, LaDuca H, Gielzak M, Na R, Sarver BAJ, Helfand BT, Walsh PC, Lotan TL, Cooney KA, Black MH, Xu J, Isaacs WB. Rare Germline Pathogenic Mutations of DNA Repair Genes Are Most Strongly Associated with Grade Group 5 Prostate Cancer. Eur Urol Oncol 2020; 3:224-230. [PMID: 31948886 DOI: 10.1016/j.euo.2019.12.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 12/04/2019] [Accepted: 12/16/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Rare germline mutations in several genes, primarily DNA repair genes, have been proposed to predict worse prognosis of prostate cancer (PCa). OBJECTIVE To compare the frequency of germline pathogenic mutations in commonly assayed PCa genes between high- and low-grade PCa in patients initially presenting with clinically localized disease. DESIGN, SETTING, AND PARTICIPANTS A retrospective case-case study of 1694 PCa patients who underwent radical prostatectomy at Johns Hopkins Hospital, including 706 patients with high-grade (grade group [GG] 4 and GG5) and 988 patients with low-grade (GG1) disease. Germline DNA was sequenced for 13 candidate PCa genes using a targeted next-generation sequencing assay by Ambry Genetics. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Carrier rates of pathogenic mutations were compared between high- and low-grade PCa patients using the Fisher's exact test. RESULTS AND LIMITATIONS Overall, the carrier rate of germline pathogenic mutations in the 13 genes was significantly higher in high-grade patients (8.64%) than in low-grade patients (3.54%, p = 9.98 × 10-6). Individually, significantly higher carrier rates for patients with high- versus low-grade PCa were found for three genes: ATM (2.12% and 0.20%, respectively, p = 9.35 × 10-5), BRCA2 (2.55% and 0.20%, respectively, p = 8.99 × 10-6), and MSH2 (0.57% and 0%, respectively, p = 0.03). The mutation carrier rate was significantly higher in patients with GG5 than in patients with GG1 disease for the 13 genes overall (13.07% and 3.54%, respectively, p = 1.27 × 10-9); for the three genes ATM, BRCA2, and MSH2 (7.73% and 0.40%, respectively, p = 3.20 × 10-13); and for the remaining nine DNA repair genes (5.07% and 2.43%, respectively, p = 0.02). CONCLUSIONS In men undergoing treatment for clinically localized disease, pathogenic mutations in 13 commonly assayed genes, especially ATM, BRCA2, and MSH2, are most strongly associated with GG5 PCa. These findings emphasize the importance of genetic testing in men with high-grade PCa, particularly GG5 disease, to inform both treatment decisions and familial risk assessment. PATIENT SUMMARY Prostate cancer in men with inherited mutations in 13 commonly assayed susceptibility genes is more likely to be high-grade, high-risk disease.
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Affiliation(s)
- Yishuo Wu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA; Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Hongjie Yu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Shuwei Li
- Ambry Genetics, Aliso Viejo, CA, USA
| | - Kathleen Wiley
- Department of Urology and the James Buchanan Brady Urologic Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S Lilly Zheng
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | | | - Marta Gielzak
- Department of Urology and the James Buchanan Brady Urologic Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rong Na
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | | | - Brian T Helfand
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Patrick C Walsh
- Department of Urology and the James Buchanan Brady Urologic Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA
| | - Kathleen A Cooney
- Duke University School of Medicine and Duke Cancer Institute, Durham, NC, USA
| | | | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA; Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China.
| | - William B Isaacs
- Department of Urology and the James Buchanan Brady Urologic Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA.
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Tian Y, Pesaran T, Chamberlin A, Fenwick RB, Li S, Gau CL, Chao EC, Lu HM, Black MH, Qian D. REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification. Sci Rep 2019; 9:12752. [PMID: 31484976 PMCID: PMC6726608 DOI: 10.1038/s41598-019-49224-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [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: 01/10/2019] [Accepted: 08/09/2019] [Indexed: 01/07/2023] Open
Abstract
Many in silico predictors of genetic variant pathogenicity have been previously developed, but there is currently no standard application of these algorithms for variant assessment. Using 4,094 ClinVar-curated missense variants in clinically actionable genes, we evaluated the accuracy and yield of benign and deleterious evidence in 5 in silico meta-predictors, as well as agreement of SIFT and PolyPhen2, and report the derived thresholds for the best performing predictor(s). REVEL and BayesDel outperformed all other meta-predictors (CADD, MetaSVM, Eigen), with higher positive predictive value, comparable negative predictive value, higher yield, and greater overall prediction performance. Agreement of SIFT and PolyPhen2 resulted in slightly higher yield but lower overall prediction performance than REVEL or BayesDel. Our results support the use of gene-level rather than generalized thresholds, when gene-level thresholds can be estimated. Our results also support the use of 2-sided thresholds, which allow for uncertainty, rather than a single, binary cut-point for assigning benign and deleterious evidence. The gene-level 2-sided thresholds we derived for REVEL or BayesDel can be used to assess in silico evidence for missense variants in accordance with current classification guidelines.
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Affiliation(s)
- Yuan Tian
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Tina Pesaran
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | | | - R Bryn Fenwick
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Shuwei Li
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Chia-Ling Gau
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Elizabeth C Chao
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA.,Divsion of Genetics and Genomics, University of California, Irvine, CA, 92697, USA
| | - Hsiao-Mei Lu
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | | | - Dajun Qian
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA.
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Fulk K, LaDuca H, Black MH, Qian D, Tian Y, Yussuf A, Espenschied C, Jasperson K. Monoallelic MUTYH carrier status is not associated with increased breast cancer risk in a multigene panel cohort. Fam Cancer 2019; 18:197-201. [PMID: 30582135 DOI: 10.1007/s10689-018-00114-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Whether monoallelic MUTYH mutations increase female breast cancer risk remains controversial. This study aimed to determine if monoallelic MUTYH mutations are associated with increased breast cancer risk in women undergoing multigene panel testing (MGPT). The prevalence of monoallelic MUTYH mutations was compared between Non-Hispanic white female breast cancer cases (n = 30,456) and cancer-free controls (n = 12,289), all of whom underwent MGPT that included MUTYH. We tested breast cancer associations with MUTYH alleles using Fisher's exact test, followed by multivariate logistic regression adjusted for age at testing and MGPT type ordered. Frequencies of the two most common MUTYH founder mutations, p.G396D and p.Y179C, were compared independently between the breast cancer cases and MGPT controls, as well as the healthy UK10K control population (n = 2640). Comparing cases to MGPT controls, no association was observed between female breast cancer and any monoallelic MUTYH carrier status (OR 0.86-1.36, p = 0.21-0.96). Similarly, comparisons to UK10K controls revealed no significant increase in breast cancer risk associated with p.G396D (OR 1.20, p = 0.44) or p.Y179C (OR 1.71, p = 0.24). This study did not find a significant increase in breast cancer risk associated with monoallelic MUTYH mutations.
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Affiliation(s)
- Kelly Fulk
- Ambry Genetics, 92656, Aliso Viejo, CA, USA.
| | | | | | - Dajun Qian
- Ambry Genetics, 92656, Aliso Viejo, CA, USA
| | - Yuan Tian
- Ambry Genetics, 92656, Aliso Viejo, CA, USA
| | | | - Carin Espenschied
- Ambry Genetics, 92656, Aliso Viejo, CA, USA
- Guardant Health, 94063, Redwood City, CA, USA
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17
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Li S, Qian D, Thompson BA, Gutierrez S, Wu S, Pesaran T, LaDuca H, Lu HM, Chao EC, Black MH. Tumour characteristics provide evidence for germline mismatch repair missense variant pathogenicity. J Med Genet 2019; 57:62-69. [PMID: 31391288 DOI: 10.1136/jmedgenet-2019-106096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/28/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Pathogenic variants in mismatch repair (MMR) genes (MLH1, MSH2, MSH6 and PMS2) increase risk for Lynch syndrome and related cancers. We quantified tumour characteristics to assess variant pathogenicity for germline MMR genes. METHODS Among 4740 patients with cancer with microsatellite instability (MSI) and immunohistochemical (IHC) results, we tested MMR pathogenic variant association with MSI/IHC status, and estimated likelihood ratios which we used to compute a tumour characteristic likelihood ratio (TCLR) for each variant. Predictive performance of TCLR in combination with in silico predictors, and a multifactorial variant prediction (MVP) model that included allele frequency, co-occurrence, co-segregation, and clinical and family history information was assessed. RESULTS Compared with non-carriers, carriers of germline pathogenic/likely pathogenic (P/LP) variants were more likely to have abnormal MSI/IHC status (p<0.0001). Among 150 classified missense variants, 73.3% were accurately predicted with TCLR alone. Models leveraging in silico scores as prior probabilities accurately classified >76.7% variants. Adding TCLR as quantitative evidence in an MVP model (MVP +TCLR Pred) increased the proportion of accurately classified variants from 88.0% (MVP alone) to 98.0% and generated optimal performance statistics among all models tested. Importantly, MVP +TCLR Pred resulted in the high yield of predicted classifications for missense variants of unknown significance (VUS); among 193 VUS, 62.7% were predicted as P/PL or benign/likely benign (B/LB) when assessed according to American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines. CONCLUSION Our study demonstrates that when used separately or in conjunction with other evidence, tumour characteristics provide evidence for germline MMR missense variant assessment, which may have important implications for genetic testing and clinical management.
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Affiliation(s)
- Shuwei Li
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Dajun Qian
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Bryony A Thompson
- Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | | | - Sitao Wu
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Tina Pesaran
- Clinical Diagnostics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Holly LaDuca
- Clinical Diagnostics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Hsiao-Mei Lu
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Elizabeth C Chao
- Clinical Diagnostics, Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Mary Helen Black
- Bioinformatics, Ambry Genetics Corp, Aliso Viejo, California, USA
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Xicola RM, Li S, Rodriguez N, Reinecke P, Karam R, Speare V, Black MH, LaDuca H, Llor X. Clinical features and cancer risk in families with pathogenic CDH1 variants irrespective of clinical criteria. J Med Genet 2019; 56:838-843. [DOI: 10.1136/jmedgenet-2019-105991] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 06/05/2019] [Accepted: 06/13/2019] [Indexed: 12/29/2022]
Abstract
BackgroundThe clinical phenotype of CDH1 pathogenic variant carriers has mostly been studied in families that fulfil criteria of hereditary diffuse gastric cancer (HDGC). We aimed at determining cancer phenotype and cancer risk estimation among families with CDH1 pathogenic variants not selected by HDGC clinical criteria.MethodsPatients were all consecutively identified CDH1 pathogenic variant carriers from a clinical laboratory tested with multigene panel testing and from an academic cancer genetics programme. Clinical and demographic features, cancer phenotypes and genotype–phenotype correlations were determined among CDH1 families. Age-specific cumulative cancer risks (penetrance) were calculated based on 38 families with available pedigrees.ResultsWithin the 113 CDH1 pathogenic variant probands and 476 relatives, 113 had gastric cancer, 177 breast cancer and 196 other cancers. Mean age at diagnosis was 47 for gastric and 54 for breast cancer. Forty-six per cent fulfilled criteria of HDGC. While 36% of families had both gastric and breast cancers, 36% had breast but no gastric cancers and 16% had gastric but not breast cancers. Cumulative risk of cancer by age 80 was 37.2% for gastric and 42.9% for breast cancer.ConclusionIn unselected CDH1 pathogenic variant carrier families, gastric cancer risks were lower and age at diagnosis higher than previously reported in families pre-selected for HDGC criteria. A substantial proportion of families did not present with any gastric cancers and their cancers were limited to breast. Thus, clinical criteria for CDH1 testing should be widened, including breast cancer families only, and a consideration for delayed prophylactic gastrectomy/surveillance should be evaluated.
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Rana HQ, Clifford J, Hoang L, LaDuca H, Black MH, Li S, McGoldrick K, Speare V, Dolinsky JS, Gau CL, Garber JE. Genotype–phenotype associations among panel-based TP53+ subjects. Genet Med 2019; 21:2478-2484. [DOI: 10.1038/s41436-019-0541-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/30/2019] [Indexed: 11/09/2022] Open
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Salvador MU, Truelson MR, Mason C, Souders B, LaDuca H, Dougall B, Black MH, Fulk K, Profato J, Gutierrez S, Jasperson K, Tippin-Davis B, Lu HM, Gray P, Shah S, Chao EC, Ghahramani N, Landsverk M, Gau CL, Chen D, Pronold M. Comprehensive Paired Tumor/Germline Testing for Lynch Syndrome: Bringing Resolution to the Diagnostic Process. J Clin Oncol 2019; 37:647-657. [PMID: 30702970 PMCID: PMC6494248 DOI: 10.1200/jco.18.00696] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2018] [Indexed: 12/11/2022] Open
Abstract
PURPOSE The current diagnostic testing algorithm for Lynch syndrome (LS) is complex and often involves multiple follow-up germline and somatic tests. We aimed to describe the results of paired tumor/germline testing performed on a large cohort of patients with colorectal cancer (CRC) and endometrial cancer (EC) to better determine the utility of this novel testing methodology. MATERIALS AND METHODS We retrospectively reviewed a consecutive series of patients with CRC and EC undergoing paired tumor/germline analysis of the LS genes at a clinical diagnostic laboratory (N = 702). Microsatellite instability, MLH1 promoter hypermethylation, and germline testing of additional genes were performed if ordered. Patients were assigned to one of five groups on the basis of prior tumor screening and germline testing outcomes. Results for each group are described. RESULTS Overall results were informative regarding an LS diagnosis for 76.1% and 60.8% of patients with mismatch-repair-deficient (MMRd) CRC and EC without and with prior germline testing, respectively. LS germline mutations were identified in 24.8% of patients in the group without prior germline testing, and interestingly, in 9.5% of patients with previous germline testing; four of these were discordant with prior tumor screening. Upon excluding patients with MLH1 promoter hypermethylation and germline mutations, biallelic somatic inactivation was seen in approximately 50% of patients with MMRd tumors across groups. CONCLUSION Paired testing identified a cause for MMRd tumors in 76% and 61% of patients without and with prior LS germline testing, respectively. Findings support inclusion of tumor sequencing as well as comprehensive LS germline testing in the LS testing algorithm. Paired testing offers a complete, convenient evaluation for LS with high diagnostic resolution.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Elizabeth C. Chao
- Ambry Genetics, Aliso Viejo, CA
- University of California, Irvine, School of Medicine, Irvine, CA
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Yao K, Clifford J, Li S, LaDuca H, Hulick PJ, Xu J, Gutierrez S, Black MH. Abstract P1-09-02: Prevalence of genetic mutations in patients with second primary breast cancers. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p1-09-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Women newly diagnosed with primary breast cancer (PBC) often undergo multi-gene panel testing to determine their contralateral breast cancer (BC) risk and whether a contralateral prophylactic mastectomy is warranted. However, with the exception of BRCA1/2, gene-specific associations with contralateral or second PBC (SPBC) have not been established. Methods: The study sample was comprised of 83,278 women with BC referred to a single diagnostic laboratory for multi-gene panel testing. The frequency of pathogenic/likely pathogenic variants in clinically-actionable genes (CAG), including highly penetrant genes (HPG: BRCA1, BRCA2, TP53, PTEN) and moderately penetrant genes (MPG: ATM, CHEK2, PALB2, CDH1, NBN, NF1) was compared between women with a PBC and SPBC. Women with a SPBC <1 year from their first diagnosis were excluded. Logistic regression burden tests were used to test for associations between mutated genes and SPBC adjusting for age at diagnosis of first BC, histology, presence of first- or second-degree relative with BC, and race/ethnicity. Results: The study included 75,550 women with PBC and 7,728 with SPBC. The median (IQR) time between primaries for the SPBC group was 11 (6,17) years . Women with SPBC were slightly more likely to be Caucasian (67.8% vs. 63.4%; p<0.001), older when referred for genetic testing (mean difference 9.7 years, p<0.001), slightly younger at first BC diagnosis (mean difference 2.1 years, p<0.001) and slightly more likely to have >1 first or second degree relative with BC (62.2% vs. 60.8%; p=0.004) than PBC. Among women tested for all CAGs, 4,883 (8.1%) were carriers of pathogenic/likely pathogenic variants (11.1% SPBC vs. 7.8% PBC). CHEK2 was the most frequently mutated gene (3.4% SPBC vs. 2.3% PBC), followed by BRCA1 (2.7% SPBC vs.1.6% PBC), BRCA2 (2.2% SPBC vs. 1.8% PBC), and PALB2 (1.4% SPBC vs. 0.9% PBC). In fully adjusted models, women with SPBC were 1.38 times as likely (p=<0.0001) as women with PBC to test positive for a CAG (OR=1.35 for HPG and 1.34 for MPG). BRCA1 (OR=1.49; p<0.0001), followed by CHEK2 (OR=1.36; p<0.0001) and PALB2 (OR=1.53; p<0.001) were most significantly associated with SPBC. TP53, BARD1, ATM and BRCA2 were marginally associated with SPBC (p=0.01 to 0.06). When results were stratified by race/ethnicity, ORs among Caucasians were similar to those observed overall. Among African Americans, women with SPBC were 1.76 times as likely to carry a CAG (p<0.001) than their PBC counterparts. PALB2 (OR=2.69; p=0.002), BRCA2 (OR=1.85; p=.004), and TP53 (OR=3.88; p=.009) were most significantly associated with SPBC followed by BRCA1 (OR=1.63; p=.002). Analysis of gene associations for other racial/ethnic groups was limited by small sample size. Conclusions: There is a significantly higher prevalence of CAG mutations among women with SPBC, even after adjusting for age at diagnosis and family history. These findings support SPBC as a standalone indication for multigene panel testing. Additional studies aimed to assess cumulative risk of SPBC for CAG beyond BRCA1/2 are needed to help guide clinical management decisions for mutation carriers.
Citation Format: Yao K, Clifford J, Li S, LaDuca H, Hulick PJ, Xu J, Gutierrez S, Black MH. Prevalence of genetic mutations in patients with second primary breast cancers [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-09-02.
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Affiliation(s)
- K Yao
- NorthShore University HealthSystem, Evanston, IL; Ambry Genetics, Aliso Viejo, CA
| | - J Clifford
- NorthShore University HealthSystem, Evanston, IL; Ambry Genetics, Aliso Viejo, CA
| | - S Li
- NorthShore University HealthSystem, Evanston, IL; Ambry Genetics, Aliso Viejo, CA
| | - H LaDuca
- NorthShore University HealthSystem, Evanston, IL; Ambry Genetics, Aliso Viejo, CA
| | - PJ Hulick
- NorthShore University HealthSystem, Evanston, IL; Ambry Genetics, Aliso Viejo, CA
| | - J Xu
- NorthShore University HealthSystem, Evanston, IL; Ambry Genetics, Aliso Viejo, CA
| | - S Gutierrez
- NorthShore University HealthSystem, Evanston, IL; Ambry Genetics, Aliso Viejo, CA
| | - MH Black
- NorthShore University HealthSystem, Evanston, IL; Ambry Genetics, Aliso Viejo, CA
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Reading SR, Black MH, Singer DE, Go AS, Fang MC, Udaltsova N, Harrison TN, Wei RX, Liu ILA, Reynolds K. Risk factors for medication non-adherence among atrial fibrillation patients. BMC Cardiovasc Disord 2019; 19:38. [PMID: 30744554 PMCID: PMC6371431 DOI: 10.1186/s12872-019-1019-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
Background Atrial fibrillation (AF) patients are routinely prescribed medications to prevent and treat complications, including those from common co-occurring comorbidities. However, adherence to such medications may be suboptimal. Therefore, we sought to identify risk factors for general medication non-adherence in a population of patients with atrial fibrillation. Methods Data were collected from a large, ethnically-diverse cohort of Kaiser Permanente Northern and Southern California adult members with incident diagnosed AF between January 1, 2006 and June 30, 2009. Self-reported questionnaires were completed between May 1, 2010 and September 30, 2010, assessing patient socio-demographics, health behaviors, health status, medical history and medication adherence. Medication adherence was assessed using a previously validated 3-item questionnaire. Medication non-adherence was defined as either taking medication(s) as the doctor prescribed 75% of the time or less, or forgetting or choosing to skip one or more medication(s) once per week or more. Electronic health records were used to obtain additional data on medical history. Multivariable logistic regression analyses examined the associations between patient characteristics and self-reported general medication adherence among patients with complete questionnaire data. Results Among 12,159 patients with complete questionnaire data, 6.3% (n = 771) reported medication non-adherence. Minority race/ethnicity versus non-Hispanic white, not married/with partner versus married/with partner, physical inactivity versus physically active, alcohol use versus no alcohol use, any days of self-reported poor physical health, mental health and/or sleep quality in the past 30 days versus 0 days, memory decline versus no memory decline, inadequate versus adequate health literacy, low-dose aspirin use versus no low-dose aspirin use, and diabetes mellitus were associated with higher adjusted odds of non-adherence, whereas, ages 65–84 years versus < 65 years of age, a Charlson Comorbidity Index score ≥ 3 versus 0, and hypertension were associated with lower adjusted odds of non-adherence. Conclusions Several potentially preventable and/or modifiable risk factors related to medication non-adherence and a few non-modifiable risk factors were identified. These risk factors should be considered when assessing medication adherence among patients diagnosed with AF.
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Affiliation(s)
- Stephanie R Reading
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., 2nd floor, Pasadena, CA, 91101, USA
| | - Mary Helen Black
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., 2nd floor, Pasadena, CA, 91101, USA
| | - Daniel E Singer
- Department of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alan S Go
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Departments of Epidemiology, Biostatistics and Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Margaret C Fang
- Division of Hospital Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Natalia Udaltsova
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Teresa N Harrison
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., 2nd floor, Pasadena, CA, 91101, USA
| | - Rong X Wei
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., 2nd floor, Pasadena, CA, 91101, USA
| | - In-Lu Amy Liu
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., 2nd floor, Pasadena, CA, 91101, USA
| | - Kristi Reynolds
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., 2nd floor, Pasadena, CA, 91101, USA.
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Fulk K, Milam MR, Li S, Yussuf A, Black MH, Chao EC, LaDuca H, Stany MP. Women with breast and uterine cancer are more likely to harbor germline mutations than women with breast or uterine cancer alone: A case for expanded gene testing. Gynecol Oncol 2019; 152:612-617. [PMID: 30612783 DOI: 10.1016/j.ygyno.2018.12.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 12/24/2022]
Abstract
OBJECTIVE We explored the germline mutation spectrum and prevalence among 1650 women with breast and uterine cancer (BUC) who underwent multi-gene hereditary cancer panel testing at a single commercial laboratory. METHODS The combined frequency of mutations in 23 BC and/or UC genes was compared between BUC cases and control groups with (1) no personal cancer history; (2) BC only; and (3) UC only using logistic regression. RESULTS Fourteen percent (n = 231) of BUC cases tested positive for mutations in BC and/or UC genes and were significantly more likely to test positive than individuals with BC only (P < 0.001), UC only (P < 0.01), or unaffected controls (P < 0.001). Analysis of gene-specific mutation frequencies revealed that MSH6, CHEK2, BRCA1, BRCA2, ATM, PMS2, PALB2 and MSH2 were most frequently mutated among BUC cases. Compared to BC only, BRCA1, MLH1, MSH2, MSH6, PMS2 and PTEN mutations were more frequent among BUC; however, only ATM mutations were more frequent among BUC compared to UC only. All of the more commonly mutated genes have published management guidelines to guide clinical care. Of patients with a single mutation in a gene with established testing criteria (n = 152), only 81.6% met their respective criteria, and 65.8% met criteria for multiple syndromes. CONCLUSIONS Women with BUC are more likely to carry hereditary cancer gene mutations than women with breast or uterine cancer alone, potentially warranting expanded genetic testing for these women. Most mutations found via multi-gene panel testing in women with BUC have accompanying published management guidelines and significant implications for clinical care.
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Affiliation(s)
- Kelly Fulk
- Ambry Genetics, Aliso Viejo, CA, United States of America.
| | | | - Shuwei Li
- Ambry Genetics, Aliso Viejo, CA, United States of America
| | - Amal Yussuf
- Ambry Genetics, Aliso Viejo, CA, United States of America
| | | | - Elizabeth C Chao
- Ambry Genetics, Aliso Viejo, CA, United States of America; University of California Irvine, Irvine, CA, United States of America
| | - Holly LaDuca
- St Thomas Health, Nashville, TN, United States of America
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Affiliation(s)
| | - Shuwei Li
- Ambry Genetics, Aliso Viejo, California
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25
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Lu HM, Li S, Black MH, Lee S, Hoiness R, Wu S, Mu W, Huether R, Chen J, Sridhar S, Tian Y, McFarland R, Dolinsky J, Tippin Davis B, Mexal S, Dunlop C, Elliott A. Association of Breast and Ovarian Cancers With Predisposition Genes Identified by Large-Scale Sequencing. JAMA Oncol 2019; 5:51-57. [PMID: 30128536 PMCID: PMC6439764 DOI: 10.1001/jamaoncol.2018.2956] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/04/2018] [Indexed: 12/21/2022]
Abstract
Importance Since the discovery of BRCA1 and BRCA2, multiple high- and moderate-penetrance genes have been reported as risk factors for hereditary breast cancer, ovarian cancer, or both; however, it is unclear whether these findings represent the complete genetic landscape of these cancers. Systematic investigation of the genetic contributions to breast and ovarian cancers is needed to confirm these findings and explore potentially new associations. Objective To confirm reported and identify additional predisposition genes for breast or ovarian cancer. Design, Setting, and Participants In this sample of 11 416 patients with clinical features of breast cancer, ovarian cancer, or both who were referred for genetic testing from 1200 hospitals and clinics across the United States and of 3988 controls who were referred for genetic testing for noncancer conditions between 2014 and 2015, whole-exome sequencing was conducted and gene-phenotype associations were examined. Case-control analyses using the Genome Aggregation Database as a set of reference controls were also conducted. Main Outcomes and Measures Breast cancer risk associated with pathogenic variants among 625 cancer predisposition genes; association of identified predisposition breast or ovarian cancer genes with the breast cancer subtypes invasive ductal, invasive lobular, hormone receptor-positive, hormone receptor-negative, and male, and with early-onset disease. Results Of 9639 patients with breast cancer, 3960 (41.1%) were early-onset cases (≤45 years at diagnosis) and 123 (1.3%) were male, with men having an older age at diagnosis than women (mean [SD] age, 61.8 [12.8] vs 48.6 [11.4] years). Of 2051 women with ovarian cancer, 445 (21.7%) received a diagnosis at 45 years or younger. Enrichment of pathogenic variants were identified in 4 non-BRCA genes associated with breast cancer risk: ATM (odds ratio [OR], 2.97; 95% CI, 1.67-5.68), CHEK2 (OR, 2.19; 95% CI, 1.40-3.56), PALB2 (OR, 5.53; 95% CI, 2.24-17.65), and MSH6 (OR, 2.59; 95% CI, 1.35-5.44). Increased risk for ovarian cancer was associated with 4 genes: MSH6 (OR, 4.16; 95% CI, 1.95-9.47), RAD51C (OR, not estimable; false-discovery rate-corrected P = .004), TP53 (OR, 18.50; 95% CI, 2.56-808.10), and ATM (OR, 2.85; 95% CI, 1.30-6.32). Neither the MRN complex genes nor CDKN2A was associated with increased breast or ovarian cancer risk. The findings also do not support previously reported breast cancer associations with the ovarian cancer susceptibility genes BRIP1, RAD51C, and RAD51D, or mismatch repair genes MSH2 and PMS2. Conclusions and Relevance The results of this large-scale exome sequencing of patients and controls shed light on both well-established and controversial non-BRCA predisposition gene associations with breast or ovarian cancer reported to date and may implicate additional breast or ovarian cancer susceptibility gene candidates involved in DNA repair and genomic maintenance.
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Affiliation(s)
| | - Shuwei Li
- Ambry Genetics, Aliso Viejo, California
| | | | - Shela Lee
- Ambry Genetics, Aliso Viejo, California
- Now with Simcere Pharmaceutical, Jiangsu, China
| | | | - Sitao Wu
- Ambry Genetics, Aliso Viejo, California
| | - Wenbo Mu
- Ambry Genetics, Aliso Viejo, California
| | - Robert Huether
- Ambry Genetics, Aliso Viejo, California
- Tempus, Chicago, Illinois
| | | | - Srijani Sridhar
- Ambry Genetics, Aliso Viejo, California
- Intellia Therapeutics, Cambridge, Massachusetts
| | - Yuan Tian
- Ambry Genetics, Aliso Viejo, California
| | - Rachel McFarland
- Ambry Genetics, Aliso Viejo, California
- Department of Epidemiology, School of Medicine,
University of California, Irvine
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Mu W, Li B, Wu S, Chen J, Sain D, Xu D, Black MH, Karam R, Gillespie K, Farwell Hagman KD, Guidugli L, Pronold M, Elliott A, Lu HM. Detection of structural variation using target captured next-generation sequencing data for genetic diagnostic testing. Genet Med 2018; 21:1603-1610. [PMID: 30563988 PMCID: PMC6752280 DOI: 10.1038/s41436-018-0397-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 05/26/2018] [Accepted: 11/28/2018] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Structural variation (SV) is associated with inherited diseases. Next-generation sequencing (NGS) is an efficient method for SV detection because of its high-throughput, low cost, and base-pair resolution. However, due to lack of standard NGS protocols and a limited number of clinical samples with pathogenic SVs, comprehensive standards for SV detection, interpretation, and reporting are to be established. METHODS We performed SV assessment on 60,000 clinical samples tested with hereditary cancer NGS panels spanning 48 genes. To evaluate NGS results, NGS and orthogonal methods were used separately in a blinded fashion for SV detection in all samples. RESULTS A total of 1,037 SVs in coding sequence (CDS) or untranslated regions (UTRs) and 30,847 SVs in introns were detected and validated. Across all variant types, NGS shows 100% sensitivity and 99.9% specificity. Overall, 64% of CDS/UTR SVs were classified as pathogenic/likely pathogenic, and five deletions/duplications were reclassified as pathogenic using breakpoint information from NGS. CONCLUSION The SVs presented here can be used as a valuable resource for clinical research and diagnostics. The data illustrate NGS as a powerful tool for SV detection. Application of NGS and confirmation technologies in genetic testing ensures delivering accurate and reliable results for diagnosis and patient care.
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Affiliation(s)
- Wenbo Mu
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Bing Li
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sitao Wu
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | | | - Divya Sain
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Dong Xu
- Ambry Genetics, Aliso Viejo, CA 92656, USA
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Black MH, Almabruk T, Albrecht MA, Chen NT, Lipp OV, Tan T, Bolte S, Girdler S. Altered Connectivity in Autistic Adults during Complex Facial Emotion Recognition: A Study of EEG Imaginary Coherence. Annu Int Conf IEEE Eng Med Biol Soc 2018; 2018:2752-2755. [PMID: 30440971 DOI: 10.1109/embc.2018.8512802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Difficulties in Facial Emotion Recognition (FER) are commonly associated with individuals diagnosed with Autism Spectrum Disorder (ASD). However, the mechanisms underlying these impairments remain inconclusive. While atypical cortical connectivity has been observed in autistic individuals, there is a paucity of investigation during cognitive tasks such as FER. It is possible that atypical cortical connectivity may underlie FER impairments in this population. Electroencephalography (EEG) Imaginary Coherence was examined in 22 autistic adults and 23 typically developing (TD) matched controls during a complex, dynamic FER task. Autistic adults demonstrated reduced coherence between both short and long range inter-hemispheric electrodes. By contrast, short range intra-hemispheric connectivity was increased in frontal and occipital regions during FER. These findings suggest altered network functioning in ASD.
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Goldstein RF, Abell SK, Ranasinha S, Misso ML, Boyle JA, Harrison CL, Black MH, Li N, Hu G, Corrado F, Hegaard H, Kim YJ, Haugen M, Song WO, Kim MH, Bogaerts A, Devlieger R, Chung JH, Teede HJ. Gestational weight gain across continents and ethnicity: systematic review and meta-analysis of maternal and infant outcomes in more than one million women. BMC Med 2018; 16:153. [PMID: 30165842 PMCID: PMC6117916 DOI: 10.1186/s12916-018-1128-1] [Citation(s) in RCA: 248] [Impact Index Per Article: 41.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/13/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The association between Institute of Medicine (IOM) guidelines and pregnancy outcomes across ethnicities is uncertain. We evaluated the associations of gestational weight gain (GWG) outside 2009 IOM guidelines, with maternal and infant outcomes across the USA, western Europe and east Asia, with subgroup analyses in Asia. The aim was to explore ethnic differences in maternal prepregnancy body mass index (BMI), GWG and health outcomes across these regions. METHODS Systematic review, meta-analysis and meta-regression of observational studies were used for the study. MEDLINE, MEDLINE In-Process, Embase and all Evidence-Based Medicine (EBM) Reviews were searched from 1999 to 2017. Studies were stratified by prepregnancy BMI category and total pregnancy GWG. Odds ratio (ORs) 95% confidence intervals (CI) applied recommended GWG within each BMI category as the reference. Primary outcomes were small for gestational age (SGA), preterm birth and large for gestational age (LGA). Secondary outcomes were macrosomia, caesarean section and gestational diabetes. RESULTS Overall, 5874 studies were identified and 23 were included (n = 1,309,136). Prepregnancy overweight/obesity in the USA, Europe and Asia was measured at 42%, 30% and 10% respectively, with underweight 5%, 3% and 17%. GWG below guidelines in the USA, Europe and Asia was 21%, 18% and 31%, and above was 51%, 51% and 37% respectively. Applying regional BMI categories in Asia showed GWG above guidelines (51%) was similar to that in the USA and Europe. GWG below guidelines was associated with a higher risk of SGA (USA/Europe [OR 1.51; CI 1.39, 1.63]; Asia [1.63; 1.45, 1.82]) and preterm birth (USA/Europe [1.35; 1.17, 1.56]; Asia [1.06; 0.78, 1.44]) than GWG within guidelines. GWG above guidelines was associated with a higher risk of LGA (USA/Europe [1.93; 1.81, 2.06]; Asia [1.68; 1.51 , 1.87]), macrosomia (USA/Europe [1.87; 1.70, 2.06]; Asia [2.18; 1.91, 2.49]) and caesarean (USA/Europe [1.26; 1.21, 1.33]; Asia [1.37; 1.30, 1.45]). Risks remained elevated when regional BMI categories were applied for GWG recommendations. More women in Asia were categorised as having GWG below guidelines using World Health Organization (WHO) (60%) compared to regional BMI categories (16%), yet WHO BMI was not accompanied by increased risks of adverse outcomes. CONCLUSIONS Women in the USA and western Europe have higher prepregnancy BMI and higher rates of GWG above guidelines than women in east Asia. However, when using regional BMI categories in east Asia, rates of GWG above guidelines are similar across the three continents. GWG outside guidelines is associated with adverse outcomes across all regions. If regional BMI categories are used in east Asia, IOM guidelines are applicable in the USA, western Europe and east Asia.
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Affiliation(s)
- Rebecca F. Goldstein
- Monash Centre for Health Research and Implementation, Monash University, Clayton, VIC Australia
- Monash Diabetes and Endocrine Units, Monash Health, Locked Bag 29, Clayton Rd, Clayton, VIC 3168 Australia
| | - Sally K. Abell
- Monash Centre for Health Research and Implementation, Monash University, Clayton, VIC Australia
- Monash Diabetes and Endocrine Units, Monash Health, Locked Bag 29, Clayton Rd, Clayton, VIC 3168 Australia
| | - Sanjeeva Ranasinha
- Monash Centre for Health Research and Implementation, Monash University, Clayton, VIC Australia
| | - Marie L. Misso
- Monash Centre for Health Research and Implementation, Monash University, Clayton, VIC Australia
| | - Jacqueline A. Boyle
- Monash Centre for Health Research and Implementation, Monash University, Clayton, VIC Australia
| | - Cheryce L. Harrison
- Monash Centre for Health Research and Implementation, Monash University, Clayton, VIC Australia
| | | | - Nan Li
- Tianjin Women’s and Children’s Health Center, Tianjin, China
| | - Gang Hu
- Pennington Biomedical Research Center, Baton Rouge, LA USA
| | | | - Hanne Hegaard
- Copenhagen University Hospital, Righospitalet, Copenhagen, Denmark
| | - Young Ju Kim
- Department of Obstetrics and Gynecology, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | | | - Won O. Song
- Michigan State University, East Lansing, MI USA
| | - Min Hyoung Kim
- Cheil Genetal Hospital and Women’s Healthcare Centre Dankook University College of Medicine, Seoul, South Korea
| | - Annick Bogaerts
- Department of Development and Regeneration KU Leuven, University of Leuven, Leuven, Belgium
- Faculty of Medicine and Health Sciences, Centre for Research and Innovation in Care (CRIC), University of Antwerp, Antwerp, Belgium
- Faculty of Health and Social Work, Research unit Healthy Living, UC Leuven-Limburg, Leuven, Belgium
| | - Roland Devlieger
- Department of Obstetrics and Gynaecology, University Hospitals KU Leuven, Leuven, Belgium
- Department of Obstetrics, Gynaecology and Fertility, GZA Campus Sint-Augustinus, Wilrijk, Belgium
| | | | - Helena J. Teede
- Monash Centre for Health Research and Implementation, Monash University, Clayton, VIC Australia
- Monash Diabetes and Endocrine Units, Monash Health, Locked Bag 29, Clayton Rd, Clayton, VIC 3168 Australia
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Xiang AH, Black MH, Shu YH, Wu J, MacKay A, Koebnick C, Watanabe RM, Buchanan TA. Association of weight gain and fifteen adipokines with declining beta-cell function in Mexican Americans. PLoS One 2018; 13:e0201568. [PMID: 30102726 PMCID: PMC6089433 DOI: 10.1371/journal.pone.0201568] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 04/11/2018] [Accepted: 07/17/2018] [Indexed: 01/22/2023] Open
Abstract
Obesity and adipokines are associated with development of type 2 diabetes. However, limited longitudinal studies have examined their roles on declining β-cell function over time. This report assessed three adiposity measures (BMI, percent body fat, trunk fat), insulin resistance, and fifteen adipokines in relationship to longitudinal change in β-cell function measured by disposition index (DI) from frequently-sampled-intravenous-glucose-tolerance testing. The results showed that three factors were significantly and independently associated with rate of change in DI over time: rate of change in BMI (negative), rate of change in IL-6 (negative), and baseline adiponectin (positive). The association was the strongest for changing BMI and was largely explained by changing insulin resistance; the association with changing IL-6 was also largely explained by changing insulin resistance. Baseline adiponectin remained positively associated after adjustment for changing insulin resistance, suggesting an independent effect of adiponectin to preserve or improve β-cell function. These findings provide evidence and potential mechanisms for the role of obesity in promoting β-cell dysfunction, highlighting the potential importance of mitigating obesity and its metabolic effects in preventing and treating type 2 diabetes.
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Affiliation(s)
- Anny H. Xiang
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States of America
- * E-mail:
| | - Mary Helen Black
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States of America
| | - Yu-Hsiang Shu
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States of America
| | - Jun Wu
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States of America
| | - Adrienne MacKay
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, United States of America
- Diabetes and Obesity Research Institute, University of Southern California, Los Angeles, CA, United States of America
| | - Corinna Koebnick
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States of America
| | - Richard M. Watanabe
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, United States of America
- Diabetes and Obesity Research Institute, University of Southern California, Los Angeles, CA, United States of America
| | - Thomas A. Buchanan
- Diabetes and Obesity Research Institute, University of Southern California, Los Angeles, CA, United States of America
- Department of Medicine, Keck School of Medicine of USC, Los Angeles, CA, United States of America
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Brand R, Borazanci E, Speare V, Dudley B, Karloski E, Peters MLB, Stobie L, Bahary N, Zeh H, Zureikat A, Hogg M, Lee K, Tsung A, Rhee J, Ohr J, Sun W, Lee J, Moser AJ, DeLeonardis K, Krejdovsky J, Dalton E, LaDuca H, Dolinsky J, Colvin A, Lim C, Black MH, Tung N. Prospective study of germline genetic testing in incident cases of pancreatic adenocarcinoma. Cancer 2018; 124:3520-3527. [PMID: 30067863 DOI: 10.1002/cncr.31628] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/07/2018] [Accepted: 05/29/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND The objective of this study was to investigate the prevalence of pathogenic germline variants (PGVs) in 32 cancer susceptibility genes in individuals with newly diagnosed pancreatic ductal adenocarcinoma (PDAC). A key secondary objective was to evaluate how often PGVs would have been undetected with existing genetic testing criteria. METHODS From May 2016 through May 2017, this multicenter cohort study enrolled consecutive patients aged 18 to 89 years with histologically confirmed PDAC diagnosed within the previous 12 weeks. Demographics, medical histories, and 3-generation pedigrees were collected from participants who provided samples for germline DNA analysis. RESULTS Four hundred nineteen patients were deemed eligible, 302 were enrolled, and 298 were included in the final cohort. Clinically actionable variants were reported in 29 PDAC patients (9.7%), with 23 (7.7%) having a PGV associated with an increased risk for PDAC. Six of 23 individuals (26%) with PDAC-associated gene mutations did not meet currently established genetic testing criteria. According to guideline-based genetic testing, only 11 of the 23 PGVs (48%) in known PDAC genes would have been detected. Six additional patients (2%) had PGVs associated with an increased risk for other cancers. CONCLUSIONS These findings support the significant prevalence of PGVs associated with PDAC and the limitations of current paradigms for selecting patients for genetic testing, and they thereby lend support for universal germline multigene genetic testing in this population.
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Affiliation(s)
- Randall Brand
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | | | | | - Beth Dudley
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Eve Karloski
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | | | - Lindsey Stobie
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Nathan Bahary
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Herbert Zeh
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Amer Zureikat
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Melissa Hogg
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Kenneth Lee
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Allan Tsung
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - John Rhee
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - James Ohr
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Weijing Sun
- Division of Medical Oncology, University of Kansas, Kansas City, Kansas
| | - James Lee
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - A James Moser
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | | | | | | | | | | | | | | | - Nadine Tung
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
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Hu C, LaDuca H, Shimelis H, Polley EC, Lilyquist J, Hart SN, Na J, Thomas A, Lee KY, Davis BT, Black MH, Pesaran T, Goldgar DE, Dolinsky JS, Couch FJ. Multigene Hereditary Cancer Panels Reveal High-Risk Pancreatic Cancer Susceptibility Genes. JCO Precis Oncol 2018; 2:PO.17.00291. [PMID: 31497750 PMCID: PMC6731034 DOI: 10.1200/po.17.00291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PURPOSE The relevance of inherited pathogenic mutations in cancer predisposition genes in pancreatic cancer is not well understood. We aimed to assess the characteristics of patients with pancreatic cancer referred for hereditary cancer genetic testing and to estimate the risk of pancreatic cancer associated with mutations in panel-based cancer predisposition genes in this high-risk population. METHODS Patients with pancreatic cancer (N = 1,652) were identified from a 140,000-patient cohort undergoing multigene panel testing of predisposition genes between March 2012 and June 2016. Gene-level mutation frequencies relative to Exome Aggregation Consortium and Genome Aggregation Database reference controls were assessed. RESULTS The frequency of germline cancer predisposition gene mutations among patients with pancreatic cancer was 20.73%. Mutations in ATM, BRCA2, CDKN2A, MSH2, MSH6, PALB2, and TP53 were associated with high pancreatic cancer risk (odds ratio, > 5), and mutations in BRCA1 were associated with moderate risk (odds ratio, > 2). In a logistic regression model adjusted for age at diagnosis and family history of cancer, ATM and BRCA2 mutations were associated with personal history of breast or pancreatic cancer, whereas PALB2 mutations were associated with family history of breast or pancreatic cancer. CONCLUSION These findings provide insight into the spectrum of mutations expected in patients with pancreatic cancer referred for cancer predisposition testing. Mutations in eight genes confer high or moderate risk of pancreatic cancer and may prove useful for risk assessment for pancreatic and other cancers. Family and personal histories of breast cancer are strong predictors of germline mutations.
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Affiliation(s)
- Chunling Hu
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - Holly LaDuca
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - Hermela Shimelis
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - Eric C. Polley
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - Jenna Lilyquist
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - Steven N. Hart
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - Jie Na
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - Abigail Thomas
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - Kun Y. Lee
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - Brigette Tippin Davis
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - Mary Helen Black
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - Tina Pesaran
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - David E. Goldgar
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - Jill S. Dolinsky
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
| | - Fergus J. Couch
- Chunling Hu, Hermela Shimelis, Eric C. Polley, Jenna Lilyquist, Steven N. Hart, Jie Na, Abigail Thomas, Kun Y. Lee, and Fergus J. Couch, Mayo Clinic, Rochester, MN; Holly LaDuca, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, and Jill S. Dolinsky, Ambry Genetics, Aliso Viejo, CA; and David E. Goldgar, University of Utah, Salt Lake City, UT
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Black MH, Li S, LaDuca H, Chen J, Hoiness R, Gutierrez S, Lu HM, Dolinsky JS, Xu J, Vachon C, Couch F, Tippin Davis B. Polygenic risk score for breast cancer in high-risk women. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.1508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Celine Vachon
- Mayo Clinic, Health Sciences Research, Rochester, MN
| | - Fergus Couch
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN
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Black MH, Shu YH, Wu J, Koebnick C, MacKay A, Watanabe RM, Buchanan TA, Xiang AH. Longitudinal Increases in Adiposity Contribute to Worsening Adipokine Profile over Time in Mexican Americans. Obesity (Silver Spring) 2018; 26:703-712. [PMID: 29427376 PMCID: PMC6021026 DOI: 10.1002/oby.22128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/02/2018] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Limited studies have assessed the relationship between longitudinal changes in adiposity and changes in multiple adipokines over time. This study examined changes in BMI, total body fat, and trunk fat associated with changes in 16 circulating adipokines in Mexican Americans at risk for type 2 diabetes. METHODS Participants included 1,213 individuals with cross-sectional data and a subset of 368 individuals with follow-up measures (mean 4.6 ± 1.5 years from baseline). Joint multivariate associations between 3 adiposity measures and 16 adipokines were assessed by canonical correlation analysis. RESULTS Longitudinal increases in adiposity were most strongly associated with increasing leptin, C-reactive protein (CRP), and interleukin 1 receptor antagonist (IL-1Ra) and decreasing adiponectin and secreted frizzled protein 5 (SFRP5) over time. Participants with BMI ≥ 30 kg/m2 at baseline had greater increases in leptin, CRP, IL-1Ra, and interleukin 6 (IL-6) and greater decreases in adiponectin and SFRP5, associated with increasing adiposity over follow-up, than those with BMI < 30 kg/m2 . Associations between adiposity and adipokines were most accounted for by leptin; adjustment for leptin greatly reduced the magnitude of all associations between adiposity and remaining adipokines. CONCLUSIONS Increasing adiposity contributes to a worsening imbalance of pro- and anti-inflammatory adipokines over time, in which leptin may have an important role as a key mediator of metabolic disease risk in Mexican Americans.
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Affiliation(s)
- Mary Helen Black
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA
| | - Yu-Hsiang Shu
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA
| | - Jun Wu
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA
| | - Corinna Koebnick
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA
| | - Adrienne MacKay
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA
| | - Richard M. Watanabe
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA
- USC Diabetes and Obesity Research Institute, Los Angeles, CA
- Department of Physiology & Biophysics, Keck School of Medicine of USC, Los Angeles, CA
| | - Thomas A. Buchanan
- USC Diabetes and Obesity Research Institute, Los Angeles, CA
- Department of Physiology & Biophysics, Keck School of Medicine of USC, Los Angeles, CA
- Department of Medicine, Keck School of Medicine of USC, Los Angeles, CA
| | - Anny H. Xiang
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA
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Norheim EP, Black MH, Ngor EW, Shi JM, Safran MR, Navarro RA. Cervical spine disease in surgeons performing arthroscopy or laparoscopy. Arch Environ Occup Health 2017; 74:206-214. [PMID: 29035681 DOI: 10.1080/19338244.2017.1392277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/06/2017] [Indexed: 06/07/2023]
Abstract
Minimal research exists regarding cervical spine disorders in surgeons who perform endoscopy. A confidential on-line survey regarding neck pain (NP), spine disease (SD), and radiculopathy/myelopathy (R/M) was sent to 722 surgeons from a managed, group-based health care system. 415 responded. 361 had endoscopy experience, of whom 24.4% had NP, 20.8% SD, and 3.9% R/M. Most respondents were less than 50 years of age (62.3%), and male (65.7%). Significant risk factors for NP included older age and female, whereas OB/Gyn specialty, increased age and job stress were for SD. After adjusting for age and gender, significant risk factors for NP and SD included greater surgeon experience. After also adjusting for job stress, significant risk factors for SD included increased surgeon experience and higher frequency of endoscopies. No association was found between use of digital OR. Endoscopy appears to place surgeons at higher risk of cervical disease. Level of Evidence: Level 3.
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Affiliation(s)
- Elizabeth P Norheim
- a Southern California Permanente Medical Group, Kaiser Permanente, Downey Medical Center, Spine Surgery , Downey , California , USA
| | | | - Eunis W Ngor
- b Kaiser Foundation Health Plan , Pasadena , California , USA
| | - Jiaxiao M Shi
- b Kaiser Foundation Health Plan , Pasadena , California , USA
| | - Marc R Safran
- c Stanford Hospital and Clinics , Stanford , California , USA
| | - Ronald A Navarro
- d Southern California Permanente Medical Group, Kaiser Permanente, South Bay Medical Center , Harbor City , California , USA
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Black MH, Li S, Pesaran T, LaDuca H, Karam R, Clifford J, Smith B, Pilarski R. PTEN Promoter Variants Are Not Associated With Common Cancers: Implications for Multigene Panel Testing. JCO Precis Oncol 2017; 1:1-7. [DOI: 10.1200/po.17.00108] [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: 11/20/2022] Open
Abstract
Purpose PTEN mutations are associated with breast, colon, endometrial, kidney, and thyroid cancers. Most PTEN promoter alterations, however, are characterized as variants of unknown significance, and their contribution to cancer risk is unclear. Materials and Methods Personal and family histories of 88,333 patients undergoing PTEN analysis as part of multigene panel testing (MGPT) were retrospectively reviewed. Cases (n = 59,784) were individuals with personal history of PTEN-related cancer. Controls (n = 28,549) had no personal history of cancer. Individuals were categorized as positive for one or more mutations (PATHO), without mutations but carrying one or more promoter variant (PROM), or negative for alterations (WT). Multivariable logistic regression was used to assess PTEN associations with phenotypes, adjusted for race/ethnicity, age, sex, and MGPT. Results Overall, 79 (0.09%) patients were PATHO and 791 (0.9%) were PROM carriers. Compared with WT, PATHOs were 2.30 (95% CI, 1.19 to 4.72) times as likely to have breast, 7.23 (95% CI, 2.74 to 19.14) times as likely to have bilateral/multiple primary breast, and 7.56 (95% CI, 1.97 to 23.98) times as likely to have uterine/endometrial cancer. PROMs were not significantly more likely than WT to have cancer (all 0.84 < odds ratio < 1.15; P > .05). Conclusion PTEN promoter variants were not associated with cancer. These results do not support the inclusion of PTEN promoter sequencing in MGPT.
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Affiliation(s)
- Mary Helen Black
- Mary Helen Black, Shuwei Li, Tina Pesaran, Holly LaDuca, Rachid Karam, Jacob Clifford, and Brandon Smith, Ambry Genetics, Aliso Viejo, CA; and Robert Pilarski, The Ohio State University, Columbus, OH
| | - Shuwei Li
- Mary Helen Black, Shuwei Li, Tina Pesaran, Holly LaDuca, Rachid Karam, Jacob Clifford, and Brandon Smith, Ambry Genetics, Aliso Viejo, CA; and Robert Pilarski, The Ohio State University, Columbus, OH
| | - Tina Pesaran
- Mary Helen Black, Shuwei Li, Tina Pesaran, Holly LaDuca, Rachid Karam, Jacob Clifford, and Brandon Smith, Ambry Genetics, Aliso Viejo, CA; and Robert Pilarski, The Ohio State University, Columbus, OH
| | - Holly LaDuca
- Mary Helen Black, Shuwei Li, Tina Pesaran, Holly LaDuca, Rachid Karam, Jacob Clifford, and Brandon Smith, Ambry Genetics, Aliso Viejo, CA; and Robert Pilarski, The Ohio State University, Columbus, OH
| | - Rachid Karam
- Mary Helen Black, Shuwei Li, Tina Pesaran, Holly LaDuca, Rachid Karam, Jacob Clifford, and Brandon Smith, Ambry Genetics, Aliso Viejo, CA; and Robert Pilarski, The Ohio State University, Columbus, OH
| | - Jacob Clifford
- Mary Helen Black, Shuwei Li, Tina Pesaran, Holly LaDuca, Rachid Karam, Jacob Clifford, and Brandon Smith, Ambry Genetics, Aliso Viejo, CA; and Robert Pilarski, The Ohio State University, Columbus, OH
| | - Brandon Smith
- Mary Helen Black, Shuwei Li, Tina Pesaran, Holly LaDuca, Rachid Karam, Jacob Clifford, and Brandon Smith, Ambry Genetics, Aliso Viejo, CA; and Robert Pilarski, The Ohio State University, Columbus, OH
| | - Robert Pilarski
- Mary Helen Black, Shuwei Li, Tina Pesaran, Holly LaDuca, Rachid Karam, Jacob Clifford, and Brandon Smith, Ambry Genetics, Aliso Viejo, CA; and Robert Pilarski, The Ohio State University, Columbus, OH
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LaDuca H, Hu C, Shimelis H, Polley E, Lilyquist J, Black MH, Davis BT, Goldgar DE, Dolinsky J, Couch FJ. Abstract 4286: What have we learned from pancreatic cancer patients undergoing multigene panel testing. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4286] [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
Purpose: The relevance of inherited pathogenic variants in cancer predisposition genes to pancreatic cancer (PC) is not well understood. Several small studies have identified pathogenic variants in 4% to 14% of unselected PC patients using multigene panels of predisposition genes, but only BRCA2, ATM, and PALB2 have been clearly implicated in this disease. We aimed to assess the clinical and molecular characteristics of PC patients referred for hereditary cancer genetic testing, and to estimate the risk of PC associated with pathogenic variants in panel-based cancer predisposition genes.
Methods: PC patients (n=1,819) were ascertained from a large cohort of over 140,000 patients undergoing multigene panel testing (MGPT) of predisposition genes between March 2012 and June 2016 at a single diagnostic laboratory. Clinical histories and molecular results were reviewed and summarized. Gene-level variant frequencies among PC cases were compared to those from the Exome Aggregation Consortium (ExAC) to calculate gene-specific pancreatic cancer risk ratios.
Results: PC patients were predominantly Caucasian (76.5%) and female (58.9%), with a median age at diagnosis of 61 years (51.7). Of these, 33.5% reported additional cancer primaries, and 44.8% reported a family history of PC. Overall, 15.4% of PC patients were found to have at least one pathogenic/likely pathogenic variant in panel-based predisposition genes. Genes with the highest frequencies of pathogenic/likely pathogenic variants included BRCA2 (3.9%), ATM (3.6%), CHEK2 (excluding p.Ile157Thr) (2.0%), PALB2 (1.5%), VHL (1.4%), CDKN2A (1.2%), BRCA1 (0.8%), and MSH6 (0.8%). 21.8% of BRCA1 and BRCA2 carriers did not meet BRCA1/2 testing criteria and 61.5% of MSH6 carriers did not meet Lynch syndrome testing criteria. No CDKN2A families met diagnostic criteria for familial atypical multiple mole melanoma syndrome, and 44% did not report any personal or family history of melanoma. To estimate associations between pathogenic variants and pancreatic cancer, Caucasian PC cases were compared to non-Finnish European, non-TCGA ExAC reference controls. Pathogenic variants in ATM, BRCA2, CDKN2A, MSH6, and PALB2 were significantly associated with high PC risks. Pathogenic variants in BRCA1 were associated with a moderate risk of PC (RR=2.7).
Conclusions: These findings shed light on the spectrum of mutations that can be expected for PC patients referred for cancer predisposition testing. The results confirm the associations of CDKN2A and BRCA2 variants with PC, and expand on the phenotypic spectrum associated with these variants. Furthermore, these results suggest that ATM, PALB2, and MSH6 may be high-risk PC genes, warranting further investigation in case-control and family-based studies.
Citation Format: Holly LaDuca, Chunling Hu, Hermela Shimelis, Eric Polley, Jenna Lilyquist, Mary Helen Black, Brigette Tippin Davis, David E. Goldgar, Jill Dolinsky, Fergus J. Couch. What have we learned from pancreatic cancer patients undergoing multigene panel testing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4286. doi:10.1158/1538-7445.AM2017-4286
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Goldstein RF, Abell SK, Ranasinha S, Misso M, Boyle JA, Black MH, Li N, Hu G, Corrado F, Rode L, Kim YJ, Haugen M, Song WO, Kim MH, Bogaerts A, Devlieger R, Chung JH, Teede HJ. Association of Gestational Weight Gain With Maternal and Infant Outcomes: A Systematic Review and Meta-analysis. JAMA 2017; 317:2207-2225. [PMID: 28586887 PMCID: PMC5815056 DOI: 10.1001/jama.2017.3635] [Citation(s) in RCA: 944] [Impact Index Per Article: 134.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
IMPORTANCE Body mass index (BMI) and gestational weight gain are increasing globally. In 2009, the Institute of Medicine (IOM) provided specific recommendations regarding the ideal gestational weight gain. However, the association between gestational weight gain consistent with theIOM guidelines and pregnancy outcomes is unclear. OBJECTIVE To perform a systematic review, meta-analysis, and metaregression to evaluate associations between gestational weight gain above or below the IOM guidelines (gain of 12.5-18 kg for underweight women [BMI <18.5]; 11.5-16 kg for normal-weight women [BMI 18.5-24.9]; 7-11 kg for overweight women [BMI 25-29.9]; and 5-9 kg for obese women [BMI ≥30]) and maternal and infant outcomes. DATA SOURCES AND STUDY SELECTION Search of EMBASE, Evidence-Based Medicine Reviews, MEDLINE, and MEDLINE In-Process between January 1, 1999, and February 7, 2017, for observational studies stratified by prepregnancy BMI category and total gestational weight gain. DATA EXTRACTION AND SYNTHESIS Data were extracted by 2 independent reviewers. Odds ratios (ORs) and absolute risk differences (ARDs) per live birth were calculated using a random-effects model based on a subset of studies with available data. MAIN OUTCOMES AND MEASURES Primary outcomes were small for gestational age (SGA), preterm birth, and large for gestational age (LGA). Secondary outcomes were macrosomia, cesarean delivery, and gestational diabetes mellitus. RESULTS Of 5354 identified studies, 23 (n = 1 309 136 women) met inclusion criteria. Gestational weight gain was below or above guidelines in 23% and 47% of pregnancies, respectively. Gestational weight gain below the recommendations was associated with higher risk of SGA (OR, 1.53 [95% CI, 1.44-1.64]; ARD, 5% [95% CI, 4%-6%]) and preterm birth (OR, 1.70 [1.32-2.20]; ARD, 5% [3%-8%]) and lower risk of LGA (OR, 0.59 [0.55-0.64]; ARD, -2% [-10% to -6%]) and macrosomia (OR, 0.60 [0.52-0.68]; ARD, -2% [-3% to -1%]); cesarean delivery showed no significant difference (OR, 0.98 [0.96-1.02]; ARD, 0% [-2% to 1%]). Gestational weight gain above the recommendations was associated with lower risk of SGA (OR, 0.66 [0.63-0.69]; ARD, -3%; [-4% to -2%]) and preterm birth (OR, 0.77 [0.69-0.86]; ARD, -2% [-2% to -1%]) and higher risk of LGA (OR, 1.85 [1.76-1.95]; ARD, 4% [2%-5%]), macrosomia (OR, 1.95 [1.79-2.11]; ARD, 6% [4%-9%]), and cesarean delivery (OR, 1.30 [1.25-1.35]; ARD, 4% [3%-6%]). Gestational diabetes mellitus could not be evaluated because of the nature of available data. CONCLUSIONS AND RELEVANCE In this systematic review and meta-analysis of more than 1 million pregnant women, 47% had gestational weight gain greater than IOM recommendations and 23% had gestational weight gain less than IOM recommendations. Gestational weight gain greater than or less than guideline recommendations, compared with weight gain within recommended levels, was associated with higher risk of adverse maternal and infant outcomes.
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Affiliation(s)
- Rebecca F. Goldstein
- Monash Centre for Health Research and Implementation, Monash University, Victoria, Australia
- Monash Diabetes and Endocrine Units, Monash Health, Victoria, Australia
| | - Sally K. Abell
- Monash Centre for Health Research and Implementation, Monash University, Victoria, Australia
- Monash Diabetes and Endocrine Units, Monash Health, Victoria, Australia
| | - Sanjeeva Ranasinha
- Monash Centre for Health Research and Implementation, Monash University, Victoria, Australia
| | - Marie Misso
- Monash Centre for Health Research and Implementation, Monash University, Victoria, Australia
| | - Jacqueline A. Boyle
- Monash Centre for Health Research and Implementation, Monash University, Victoria, Australia
| | - Mary Helen Black
- Kaiser Permanente, Southern California, Los Angeles
- Ambry Genetics, Aliso Viejo, California
| | - Nan Li
- Tianjin Women’s and Children’s Health Center, Tianjin, China
| | - Gang Hu
- Pennington Biomedical Research Center, Baton Rouge, Louisiana
| | | | - Line Rode
- Department of Biochemistry, Copenhagen University Hospital, Righospitalet, Copenhagen, Denmark
| | - Young Ju Kim
- Department of Obstetrics and Gynecology, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | | | | | - Min Hyoung Kim
- Dankook University College of Medicine, Seoul, Republic of Korea
| | - Annick Bogaerts
- Department of Development and Regeneration KU Leuven, University of Leuven, Leuven, Belgium
- Faculty of Medicine and Health Sciences, Centre for Research and Innovation in Care, University of Antwerp, Antwerp, Belgium
- Faculty of Health and Social Work, Research Unit Healthy Living, UC Leuven-Limburg, Leuven, Belgium
| | - Roland Devlieger
- Department of Obstetrics and Gynaecology, University Hospitals KU Leuven, Leuven, Belgium
- Department of Obstetrics, Gynaecology and Fertility, GZA Campus Sint-Augustinus, Wilrijk, Belgium
| | | | - Helena J. Teede
- Monash Centre for Health Research and Implementation, Monash University, Victoria, Australia
- Monash Diabetes and Endocrine Units, Monash Health, Victoria, Australia
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Abstract
1581 Background: Thyroid cancers are known component tumors of both well-described and emerging hereditary cancer syndromes. To assess the contribution of germline variants in thyroid cancer predisposition, we examined the prevalence of germline mutations among individuals with a history of thyroid cancer, compared to those with thyroid and breast cancer or breast cancer alone. Methods: Clinical histories and molecular results were reviewed for individuals with a history of thyroid and/or breast cancer, ascertained from a cohort of > 140,000 patients who underwent hereditary cancer multigene panel testing at a single commercial laboratory. Clinical history information was obtained from test requisition forms completed by ordering clinicians and from pedigrees/clinic notes, if provided. Results: Among 2,678 thyroid cancer patients, the majority were Caucasian (66.9%), female (92.3%), and/or had an additional cancer primary (71.9%), with nearly half reporting an additional breast cancer primary (49.1%). Among those with available pathology information, 4.1% had medullary thyroid cancer. The median (IQR) age at diagnosis was 38 (26,48) years, and while 94.1% had a family history of cancer, 78.8% had at least one affected 1st degree relative. Overall, 11.1% were identified as mutation carriers, defined as ≥1 pathogenic or likely pathogenic variant. Among those with thyroid cancer alone, 9.7% had a mutation, similar to those with breast cancer alone (9.7%) and those with breast and thyroid cancer only (10.5%). Genes most frequently mutated in the thyroid only group included CHEK2 (3.1%), MUTYH (monoallelic) (2.4%), APC (2.0%), ATM (1.6%), and PALB2 (1.2%). CHEK2 was the most frequently mutated gene observed in all groups, with a higher frequency seen among those with thyroid and breast cancer (5.5%) compared to breast cancer (2.5%) or thyroid cancer (3.1%) alone (p < 0.001). Conclusions: A high rate of germline mutations is observed among individuals with thyroid cancer presenting for clinical genetic testing, even in the absence of other primary cancer diagnoses. Thyroid cancer may be an under-recognized component tumor of hereditary cancer predisposition syndromes suggesting the need for further investigation.
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Peters MLB, Brand R, Borazanci EH, Stobie L, Dudley B, Karloski E, Moser AJ, Colvin A, Lim C, Bahary N, Sun W, Rhee JC, Lembersky BC, Stoller RG, LaDuca H, Dolinsky JS, Dalton E, Speare V, Black MH, Tung NM. Germline genetic testing in unselected pancreatic ductal adenocarcinoma (PDAC) patients. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.1501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1501 Background: The aim of this study is to assess the prevalence of known heritable germline mutations in unselected PDAC patients and to determine how well current guidelines for genetic testing identify mutation carriers. Methods: Consecutive, unselected patients with recently diagnosed PDAC from three centers were enrolled from May to December 2016 in an ongoing prospective study. A three-generation pedigree was obtained. Germline mutations in 12 genes associated with PDAC risk ( APC, ATM, BRCA1, BRCA2, CDKN2A, EPCAM, MLH1, MSH2, PALB2, PMS2, STK11, TP53) and in 19 genes related to other cancer risks were screened for by NGS. American College of Gastroenterology and NCCN criteria for genetic testing for BRCA1/2, Lynch syndrome, and Familial Pancreatic Cancer (FPC) were assessed. Results: Among 183 patients, 46% are female, 79% are Caucasian and 10% are Ashkenazi Jewish, with median (IQR) age 68 (62,75) years at diagnosis. 41% of patients met ³1 criteria for genetic testing (35.5% BRCA1/2, 2.7% Lynch, 9.3% FPC). Twenty patients (11%) were found to have a total of 21 pathogenic mutations (table). Mutation status was not associated with age at diagnosis, sex, or personal history of cancer (all p > 0.05). Six mutation carriers (30% of positives) did not meet current criteria for genetic testing. Conclusions: Preliminary results show that 6.6% of unselected PDAC patients carry a germline mutation in a gene known to increase PDAC risk and 4.3% have a mutation in genes not previously linked to PDAC. Existing testing criteria did not identify 30% of carriers. Continued refinement of guidelines is necessary to align genetic testing with inherited PDAC risk. Clinical trial information: NCT02790944. [Table: see text]
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Affiliation(s)
| | | | | | | | - Beth Dudley
- University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Eve Karloski
- University of Pittsburgh Medical Center, Pittsburgh, PA
| | | | | | | | - Nathan Bahary
- University of Pittsburgh Medical Center Cancer Center Pavilion, Pittsburgh, PA
| | | | - John C. Rhee
- University of Pittsburgh Medical Center Cancer Center Pavilion, Pittsburgh, PA
| | - Barry C. Lembersky
- University of Pittsburgh Medical Center Cancer Center Pavilion, Pittsburgh, PA
| | - Ronald G. Stoller
- University of Pittsburgh Medical Center Cancer Center Pavilion, Pittsburgh, PA
| | | | | | | | | | | | - Nadine M. Tung
- Beth Israel Deaconess Medical Center and Dana-Farber Harvard Cancer Center, Boston, MA
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Abstract
Background Atrial fibrillation (AF) is the most common clinically significant arrhythmia in adults and a major risk factor for ischemic stroke. Nonetheless, previous research suggests that many individuals diagnosed with AF lack awareness about their diagnosis and inadequate health literacy may be an important contributing factor to this finding. Methods and Results We examined the association between health literacy and awareness of an AF diagnosis in a large, ethnically diverse cohort of Kaiser Permanente Northern and Southern California adults diagnosed with AF between January 1, 2006 and June 30, 2009. Using self‐reported questionnaire data completed between May 1, 2010 and September 30, 2010, awareness of an AF diagnosis was evaluated using the question “Have you ever been told by a doctor or other health professional that you have a heart rhythm problem called atrial fibrillation or atrial flutter?” and health literacy was assessed using a validated 3‐item instrument examining problems because of reading, understanding, and filling out medical forms. Of the 12 517 patients diagnosed with AF, 14.5% were not aware of their AF diagnosis and 20.4% had inadequate health literacy. Patients with inadequate health literacy were less likely to be aware of their AF diagnosis compared with patients with adequate health literacy (prevalence ratio=0.96; 95% CI [0.94, 0.98]), adjusting for sociodemographics, health behaviors, and clinical characteristics. Conclusions Lower health literacy is independently associated with less awareness of AF diagnosis. Strategies designed to increase patient awareness of AF and its complications are warranted among individuals with limited health literacy.
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Affiliation(s)
- Stephanie R Reading
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA
| | - Alan S Go
- Division of Research, Kaiser Permanente Northern California, Oakland, CA
| | - Margaret C Fang
- Division of Hospital Medicine, University of California San Francisco, San Francisco, CA
| | - Daniel E Singer
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - In-Lu Amy Liu
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA
| | - Mary Helen Black
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA
| | - Natalia Udaltsova
- Division of Research, Kaiser Permanente Northern California, Oakland, CA
| | - Kristi Reynolds
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA
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Dabelea D, Stafford JM, Mayer-Davis EJ, D'Agostino R, Dolan L, Imperatore G, Linder B, Lawrence JM, Marcovina SM, Mottl AK, Black MH, Pop-Busui R, Saydah S, Hamman RF, Pihoker C. Association of Type 1 Diabetes vs Type 2 Diabetes Diagnosed During Childhood and Adolescence With Complications During Teenage Years and Young Adulthood. JAMA 2017; 317:825-835. [PMID: 28245334 PMCID: PMC5483855 DOI: 10.1001/jama.2017.0686] [Citation(s) in RCA: 392] [Impact Index Per Article: 56.0] [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: 12/15/2022]
Abstract
IMPORTANCE The burden and determinants of complications and comorbidities in contemporary youth-onset diabetes are unknown. OBJECTIVE To determine the prevalence of and risk factors for complications related to type 1 diabetes vs type 2 diabetes among teenagers and young adults who had been diagnosed with diabetes during childhood and adolescence. DESIGN, SETTING, AND PARTICIPANTS Observational study from 2002 to 2015 in 5 US locations, including 2018 participants with type 1 and type 2 diabetes diagnosed at younger than 20 years, with single outcome measures between 2011 and 2015. EXPOSURES Type 1 and type 2 diabetes and established risk factors (hemoglobin A1c level, body mass index, waist-height ratio, and mean arterial blood pressure). MAIN OUTCOMES AND MEASURES Diabetic kidney disease, retinopathy, peripheral neuropathy, cardiovascular autonomic neuropathy, arterial stiffness, and hypertension. RESULTS Of 2018 participants, 1746 had type 1 diabetes (mean age, 17.9 years [SD, 4.1]; 1327 non-Hispanic white [76.0%]; 867 female patients [49.7%]), and 272 had type 2 (mean age, 22.1 years [SD, 3.5]; 72 non-Hispanic white [26.5%]; 181 female patients [66.5%]). Mean diabetes duration was 7.9 years (both groups). Patients with type 2 diabetes vs those with type 1 had higher age-adjusted prevalence of diabetic kidney disease (19.9% vs 5.8%; absolute difference [AD], 14.0%; 95% CI, 9.1%-19.9%; P < .001), retinopathy (9.1% vs 5.6%; AD, 3.5%; 95% CI, 0.4%-7.7%; P = .02), peripheral neuropathy (17.7% vs 8.5%; AD, 9.2%; 95% CI, 4.8%-14.4%; P < .001), arterial stiffness (47.4% vs 11.6%; AD, 35.9%; 95% CI, 29%-42.9%; P < .001), and hypertension (21.6% vs 10.1%; AD, 11.5%; 95% CI, 6.8%-16.9%; P < .001), but not cardiovascular autonomic neuropathy (15.7% vs 14.4%; AD, 1.2%; 95% CI, -3.1% to 6.5; P = .62). After adjustment for established risk factors measured over time, participants with type 2 diabetes vs those with type 1 had significantly higher odds of diabetic kidney disease (odds ratio [OR], 2.58; 95% CI, 1.39-4.81; P=.003), retinopathy (OR, 2.24; 95% CI, 1.11-4.50; P = .02), and peripheral neuropathy (OR, 2.52; 95% CI, 1.43-4.43; P = .001), but no significant difference in the odds of arterial stiffness (OR, 1.07; 95% CI, 0.63-1.84; P = .80) and hypertension (OR, 0.85; 95% CI, 0.50-1.45; P = .55). CONCLUSIONS AND RELEVANCE Among teenagers and young adults who had been diagnosed with diabetes during childhood or adolescence, the prevalence of complications and comorbidities was higher among those with type 2 diabetes compared with type 1, but frequent in both groups. These findings support early monitoring of youth with diabetes for development of complications.
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Affiliation(s)
- Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, Aurora
| | - Jeanette M Stafford
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | | | - Ralph D'Agostino
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Lawrence Dolan
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Giuseppina Imperatore
- Division of Diabetes Translation, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Barbara Linder
- Division of Diabetes, Endocrinology and Metabolic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
| | - Jean M Lawrence
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena
| | | | - Amy K Mottl
- UNC Division of Nephrology and Hypertension, University of North Carolina School of Medicine, Chapel Hill
| | - Mary Helen Black
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena
| | - Rodica Pop-Busui
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor
| | - Sharon Saydah
- Division of Diabetes Translation, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Richard F Hamman
- Department of Epidemiology, Colorado School of Public Health, Aurora
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Nandi-Munshi D, Afkarian M, Whitlock KB, Crandell JL, Bell RA, D’Agostino R, Saydah S, Mottl AK, Dabelea D, Black MH, Mayer-Davis EJ, Pihoker C. Vitamin D and Albuminuria in Youth with and without Type 1 Diabetes. Horm Res Paediatr 2017; 87:385-395. [PMID: 28554178 PMCID: PMC5568007 DOI: 10.1159/000475711] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/12/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND/AIMS In adults, lower vitamin D has been associated with increased albuminuria. This association has not been extensively studied in youth with or without type 1 diabetes. METHODS We examined the cross-sectional association between vitamin D and albuminuria (urine albumin to creatinine ratio ≥30 mg/g) in 8,789 participants of the National Health and Nutrition Survey 2001-2006 (NHANES), who were 6-19 years old. Further, we examined the association between vitamin D and albuminuria in 938 participants from the SEARCH Nutritional Ancillary Study (SNAS), a longitudinal cohort of youth with type 1 diabetes. RESULTS Of the NHANES participants, 5.3, 19.5, and 53.7% had vitamin D levels <30, 50 and 80 nmol/L, respectively. Albuminuria was present in 12.8% and was more common in younger children, females, non-Hispanic whites, non-obese children, and children with hypertension. After adjustments, there was no association between vitamin D and albuminuria. Among the SNAS participants with type 1 diabetes, we also found no association between baseline vitamin D and subsequent albuminuria in unadjusted or adjusted analyses. CONCLUSION We did not find an association between serum vitamin D and albuminuria in either non-diabetic youth or those with type 1 diabetes. Further research is needed to more fully understand this relationship.
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Affiliation(s)
| | - Maryam Afkarian
- Nephrology Division, Department of Medicine, University of California, Davis, CA
| | - Kathryn B. Whitlock
- Core for Biomedical Statistics, Center for Clinical & Translational Research, Seattle Children’s Research Institute, Seattle, WA
| | - Jamie L. Crandell
- Department of Biostatistics and School of Nursing, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ronny A. Bell
- Department of Public Health, Brody School of Medicine, East Carolina University, Greenville, NC
| | - Ralph D’Agostino
- Department of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Sharon Saydah
- Centers for Disease Control and Prevention, Division of Diabetes Translation
| | - Amy K. Mottl
- Division of Nephrology and Hypertension, University of North Carolina, Chapel Hill, NC
| | - Dana Dabelea
- Colorado School Of Public Health, University of Colorado Denver, Aurora, CO
| | | | - Elizabeth J Mayer-Davis
- Departments of Nutrition and Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Black MH, Navarro RA, Adams AL. Evaluation of Knee Arthroscopy as a Low-Value Intervention for Treatment of Meniscal Damage in Patients With Osteoarthritis. J Patient Cent Res Rev 2015. [DOI: 10.17294/2330-0698.1085] [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: 11/04/2022] Open
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Tomer Y, Dolan LM, Kahaly G, Divers J, D'Agostino RB, Imperatore G, Dabelea D, Marcovina S, Black MH, Pihoker C, Hasham A, Hammerstad SS, Greenberg DA, Lotay V, Zhang W, Monti MC, Matheis N. Genome wide identification of new genes and pathways in patients with both autoimmune thyroiditis and type 1 diabetes. J Autoimmun 2015; 60:32-9. [PMID: 25936594 DOI: 10.1016/j.jaut.2015.03.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/27/2015] [Accepted: 03/29/2015] [Indexed: 12/17/2022]
Abstract
Autoimmune thyroid diseases (AITD) and Type 1 diabetes (T1D) frequently occur in the same individual pointing to a strong shared genetic susceptibility. Indeed, the co-occurrence of T1D and AITD in the same individual is classified as a variant of the autoimmune polyglandular syndrome type 3 (designated APS3v). Our aim was to identify new genes and mechanisms causing the co-occurrence of T1D + AITD (APS3v) in the same individual using a genome-wide approach. For our discovery set we analyzed 346 Caucasian APS3v patients and 727 gender and ethnicity matched healthy controls. Genotyping was performed using the Illumina Human660W-Quad.v1. The replication set included 185 APS3v patients and 340 controls. Association analyses were performed using the PLINK program, and pathway analyses were performed using the MAGENTA software. We identified multiple signals within the HLA region and conditioning studies suggested that a few of them contributed independently to the strong association of the HLA locus with APS3v. Outside the HLA region, variants in GPR103, a gene not suggested by previous studies of APS3v, T1D, or AITD, showed genome-wide significance (p < 5 × 10(-8)). In addition, a locus on 1p13 containing the PTPN22 gene showed genome-wide significant associations. Pathway analysis demonstrated that cell cycle, B-cell development, CD40, and CTLA-4 signaling were the major pathways contributing to the pathogenesis of APS3v. These findings suggest that complex mechanisms involving T-cell and B-cell pathways are involved in the strong genetic association between AITD and T1D.
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Affiliation(s)
- Yaron Tomer
- Division of Endocrinology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA.
| | - Lawrence M Dolan
- Division of Pediatric Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - George Kahaly
- Thyroid Research Laboratory, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Jasmin Divers
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ralph B D'Agostino
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Giuseppina Imperatore
- Division of Diabetes Translation, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dana Dabelea
- Colorado School of Public Health, University of Colorado, Denver, CO, USA
| | - Santica Marcovina
- Northwest Lipid Metabolism and Diabetes Research Laboratories, University of Washington, Seattle, WA, USA
| | - Mary Helen Black
- Kaiser Permanente Southern California, Department of Research and Evaluation, Pasadena, CA, USA
| | - Catherine Pihoker
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Alia Hasham
- Division of Endocrinology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - David A Greenberg
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Vaneet Lotay
- The Charles Bronfman Institute for Personalized Medicine, Department of Medicine Bioinformatics Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Weijia Zhang
- The Charles Bronfman Institute for Personalized Medicine, Department of Medicine Bioinformatics Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maria Cristina Monti
- Department of Public Health, Neurosciences, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Nina Matheis
- Thyroid Research Laboratory, Johannes Gutenberg University Medical Center, Mainz, Germany
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Black MH, Wu J, Takayanagi M, Wang N, Taylor KD, Haritunians T, Trigo E, Lawrence JM, Watanabe RM, Buchanan TA, Xiang AH. Variation in PPARG is associated with longitudinal change in insulin resistance in Mexican Americans at risk for type 2 diabetes. J Clin Endocrinol Metab 2015; 100:1187-95. [PMID: 25584717 PMCID: PMC4333029 DOI: 10.1210/jc.2014-3246] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 11/19/2022]
Abstract
CONTEXT Peroxisome proliferator-activated receptor gamma (PPARG) is a susceptibility locus for type 2 diabetes mellitus (T2DM). Although cross-sectional associations have been reported, primarily for Pro12Ala, few longitudinal studies in nondiabetic populations have been conducted. OBJECTIVE This study aimed to examine whether and to what extent variation in PPARG is associated with longitudinal changes in anthropometric and metabolic traits in Mexican Americans at risk for T2DM. SETTING AND DESIGN Subjects were participants of BetaGene, a family-based study of obesity, insulin resistance, and β-cell function, who completed a baseline and follow-up study visit (n = 378; mean followup, 4.6 ± 1.5 y). Phenotypes included body fat assessed by dual-energy x-ray absorptiometry; insulin sensitivity (SI), acute insulin response, and β-cell function (disposition index; DI) were estimated from iv glucose tolerance tests with Minimal Model analysis. Eighteen tag single nucleotide polymorphisms (SNPs) capturing variation in a 156-kb region surrounding PPARG were tested for association with changes in longitudinal traits. P-values were Bonferroni-corrected for multiple testing. RESULTS Six SNPs (rs2972164, rs11128598, rs17793951, rs1151996, rs1175541, rs3856806) were significantly associated with rate of change in SI after adjustment for age, sex, and body fat percentage, but not with changes in adiposity. rs17793951 also had a significant effect on change in DI over time. Association between rs1175541 and change in SI varied by changes in adiposity such that only carriers of the minor allele who reduced body fat over followup improved SI. rs1306470 (captured Pro12Ala, r(2) = 0.9) was not associated with rates of change in any traits and its effects were not modified by changes in adiposity. CONCLUSIONS Variation in PPARG, but not Pro12Ala, contributes to declining SI and concomitant deterioration in β-cell function in Mexican Americans at risk for T2DM.
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Affiliation(s)
- Mary Helen Black
- Department of Research & Evaluation (M.H.B., J.W., M.T., J.M.L., A.H.X.), Kaiser Permanente Southern California, Pasadena, California; Department of Preventive Medicine (N.W., R.M.W., T.A.B.), Keck School of Medicine of University of Southern California (USC), Los Angeles, California; Medical Genetics Institute (K.D.T., T.H.), Cedars-Sinai Medical Center, Los Angeles, California; Department of Medicine (E.T.), Keck School of Medicine of USC, Los Angeles, California; USC Diabetes and Obesity Research Institute (R.M.W., T.A.B.), Los Angeles, California; Department of Physiology & Biophysics (R.M.W., T.A.B.), Keck School of Medicine of USC, Los Angeles, California
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Xiang AH, Black MH, Li BH, Martinez MP, Sacks DA, Lawrence JM, Buchanan TA, Jacobsen SJ. Racial and ethnic disparities in extremes of fetal growth after gestational diabetes mellitus. Diabetologia 2015; 58:272-81. [PMID: 25341460 DOI: 10.1007/s00125-014-3420-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 09/25/2014] [Indexed: 12/22/2022]
Abstract
AIMS/HYPOTHESIS The aim of this study was to assess and compare risks of having large- or small-for gestational age (LGA and SGA, respectively) infants born to women with gestational diabetes mellitus (GDM) from ten racial/ethnic groups. METHODS LGA and SGA were defined as birthweight >90th and <10th percentile, respectively, specific to each racial/ethnic population and infant sex. Risks of LGA and SGA were compared among a retrospective cohort of 29,544 GDM deliveries from Hispanic, non-Hispanic white (NHW), non-Hispanic black (NHB), Filipino, Chinese, Asian Indian, Vietnamese, Korean, Japanese and Pacific Islander (PI) groups of women. RESULTS Unadjusted LGA and SGA risks varied among the ten groups. For LGA, the highest risk was in infants born to NHB women (17.2%), followed by those born to PI (16.2%), Hispanic (14.5%), NHW (13.1%), Asian Indian (12.8%), Filipino (11.6%) and other Asian (9.6-11.1%) women (p < 0.0001). Compared with NHW, the LGA risk was significantly greater for NHB women with GDM (RR 1.25 [95% CI 1.11-1.40]; p = 0.0001 after adjustment for maternal characteristics). Further adjustment for maternal pre-pregnancy BMI and gestational weight gain in the sub-cohort with available data (n = 8,553) greatly attenuated the elevated LGA risk for NHB women. For SGA, the risks ranged from 5.6% to 11.3% (p = 0.003) where most groups (8/10) had risks that were lower than the population-expected 10% and risks were not significantly different from those in NHW women. CONCLUSIONS/INTERPRETATION These data suggest that variation in extremes of fetal growth associated with GDM deliveries across race/ethnicity can be explained by maternal characteristics, maternal obesity and gestational weight gain. Women should be advised to target a normal weight and appropriate weight gain for pregnancies; this is particularly important for NHB women.
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Affiliation(s)
- Anny H Xiang
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles, 5th Floor, Pasadena, CA, 91101, USA,
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Lamichhane AP, Liese AD, Urbina EM, Crandell JL, Jaacks LM, Dabelea D, Black MH, Merchant AT, Mayer-Davis EJ. Associations of dietary intake patterns identified using reduced rank regression with markers of arterial stiffness among youth with type 1 diabetes. Eur J Clin Nutr 2014; 68:1327-33. [PMID: 24865480 DOI: 10.1038/ejcn.2014.96] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 03/03/2014] [Accepted: 03/24/2014] [Indexed: 02/07/2023]
Abstract
BACKGROUND/OBJECTIVES Youth with type 1 diabetes (T1DM) are at substantially increased risk for adverse vascular outcomes, but little is known about the influence of dietary behavior on cardiovascular disease (CVD) risk profile. We aimed to identify dietary intake patterns associated with CVD risk factors and evaluate their impact on arterial stiffness (AS) measures collected thereafter in a cohort of youth with T1DM. SUBJECTS/METHODS Baseline diet data from a food frequency questionnaire and CVD risk factors (triglycerides, low density lipoprotein-cholesterol, systolic blood pressure, hemoglobin A1c, C-reactive protein and waist circumference) were available for 1153 youth aged ⩾10 years with T1DM from the SEARCH for Diabetes in Youth Study. A dietary intake pattern was identified using 33 food groups as predictors and six CVD risk factors as responses in reduced rank regression (RRR) analysis. Associations of this RRR-derived dietary pattern with AS measures (augmentation index (AIx75), n=229; pulse wave velocity, n=237; and brachial distensibility, n=228) were then assessed using linear regression. RESULTS The RRR-derived pattern was characterized by high intakes of sugar-sweetened beverages (SSB) and diet soda, eggs, potatoes and high-fat meats and low intakes of sweets/desserts and low-fat dairy; major contributors were SSB and diet soda. This pattern captured the largest variability in adverse CVD risk profile and was subsequently associated with AIx75 (β=0.47; P<0.01). The mean difference in AIx75 concentration between the highest and the lowest dietary pattern quartiles was 4.3% in fully adjusted model. CONCLUSIONS Intervention strategies to reduce consumption of unhealthy foods and beverages among youth with T1DM may significantly improve CVD risk profile and ultimately reduce the risk for AS.
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Affiliation(s)
- A P Lamichhane
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - A D Liese
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - E M Urbina
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - J L Crandell
- Departments of Nursing and Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - L M Jaacks
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - D Dabelea
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - M H Black
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - A T Merchant
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - E J Mayer-Davis
- 1] Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA [2] School of Medicine, University of North Carolina, Chapel Hill, NC, USA
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Jacobsen JJ, Black MH, Li BH, Reynolds K, Lawrence JM. Race/ethnicity and measures of glycaemia in the year after diagnosis among youth with type 1 and type 2 diabetes mellitus. J Diabetes Complications 2014; 28:279-85. [PMID: 24581944 DOI: 10.1016/j.jdiacomp.2014.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [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] [Received: 05/02/2013] [Revised: 01/14/2014] [Accepted: 01/15/2014] [Indexed: 11/18/2022]
Abstract
AIMS To assess associations between race/ethnicity, glycated hemoglobin (HbA1c), and glycemic control among youth with type 1 (T1D) or type 2 diabetes (T2D). METHODS The study sample was youth<20years old from the SEARCH California Center diagnosed from 2002 to 2009 who remained insured for at least one year. HbA1c at one year was from clinical data; HbA1c at diagnosis was from clinical data (81%) or imputed (19%). Multivariable logistic and linear regression models were used to examine associations between race/ethnicity and poor glycemic control (≥9.5%), HbA1c at one-year, and change in HbA1c. RESULTS The study included 1162 Hispanic (52.3%), non-Hispanic White (NHW, 28.4%), African American (15.1%) and Asian/Pacific Islander (4.1%) youth. Among T1D youth (n=789), Hispanics were 1.60 times as likely (95% CI 1.01-2.53) to have poor control at one year compared to NHWs, after adjustments. Among T2D youth (n=373), only African American youth were significantly more likely (OR=4.85; 95% CI 1.49-15.77) to have poor control at one year, after adjustments. HbA1c at one year and change in HbA1c did not differ by race/ethnicity. CONCLUSION Poor glycemic control was evident one year after diagnosis in some minority youth with T1D or T2D in an integrated managed health care setting.
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Affiliation(s)
- Joanna J Jacobsen
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena CA, USA
| | - Mary Helen Black
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena CA, USA
| | - Bonnie H Li
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena CA, USA
| | - Kristi Reynolds
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena CA, USA
| | - Jean M Lawrence
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena CA, USA.
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Koebnick C, Black MH, Wu J, Martinez M, Smith N, Kuizon B, Cuan D, Young D, Lawrence J, Jacobsen S. High blood pressure in overweight and obese adolescents (641.18). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.641.18] [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: 11/11/2022]
Affiliation(s)
- Corinna Koebnick
- Research and Evaluation Kaisser Permanente Southern CaliforniaPasadenaCAUnited States
| | - Mary Helen Black
- Research and Evaluation Kaisser Permanente Southern CaliforniaPasadenaCAUnited States
| | - Jun Wu
- Research and Evaluation Kaisser Permanente Southern CaliforniaPasadenaCAUnited States
| | - Mayra Martinez
- Research and Evaluation Kaisser Permanente Southern CaliforniaPasadenaCAUnited States
| | - Ning Smith
- Center for Health Research Kaisser Permanente NorthwestPortlandORUnited States
| | - Beatriz Kuizon
- Research and Evaluation Kaiser Permanente Southern CaliforniaLos AngelesCAUnited States
| | - David Cuan
- Pediatrics Kaisser Permanente Southern CaliforniaRiversideCAUnited States
| | - Deborah Young
- Research and Evaluation Kaisser Permanente Southern CaliforniaPasadenaCAUnited States
| | - Jean Lawrence
- Research and Evaluation Kaisser Permanente Southern CaliforniaPasadenaCAUnited States
| | - Steven Jacobsen
- Research and Evaluation Kaiser Permanente Southern CaliforniaPasadenaCAUnited States
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Adams AL, Black MH, Zhang JL, Shi JM, Jacobsen SJ. Proton-pump inhibitor use and hip fractures in men: a population-based case-control study. Ann Epidemiol 2014; 24:286-90. [DOI: 10.1016/j.annepidem.2014.01.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 12/20/2013] [Accepted: 01/02/2014] [Indexed: 12/25/2022]
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