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Mefford JA, Zhao Z, Heilier L, Xu M, Zhou G, Mace R, Sloane KL, Sheppard SM, Glenn S. Varied performance of picture description task as a screening tool across MCI subtypes. PLOS Digit Health 2023; 2:e0000197. [PMID: 36913425 PMCID: PMC10010512 DOI: 10.1371/journal.pdig.0000197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
A picture description task is a component of Miro Health's platform for self-administration of neurobehavioral assessments. Picture description has been used as a screening tool for identification of individuals with Alzheimer's disease and mild cognitive impairment (MCI), but currently requires in-person administration and scoring by someone with access to and familiarity with a scoring rubric. The Miro Health implementation allows broader use of this assessment through self-administration and automated processing, analysis, and scoring to deliver clinically useful quantifications of the users' speech production, vocal characteristics, and language. Picture description responses were collected from 62 healthy controls (HC), and 33 participants with MCI: 18 with amnestic MCI (aMCI) and 15 with non-amnestic MCI (naMCI). Speech and language features and contrasts between pairs of features were evaluated for differences in their distributions in the participant subgroups. Picture description features were selected and combined using penalized logistic regression to form risk scores for classification of HC versus MCI as well as HC versus specific MCI subtypes. A picture-description based risk score distinguishes MCI and HC with an area under the receiver operator curve (AUROC) of 0.74. When contrasting specific subtypes of MCI and HC, the classifiers have an AUROC of 0.88 for aMCI versus HC and and AUROC of 0.61 for naMCI versus HC. Tests of association of individual features or contrasts of pairs of features with HC versus aMCI identified 20 features with p-values below 5e-3 and False Discovery Rates (FDRs) at or below 0.113, and 61 contrasts with p-values below 5e-4 and FDRs at or below 0.132. Findings suggest that performance of picture description as a screening tool for MCI detection will vary greatly by MCI subtype or by the proportion of various subtypes in an undifferentiated MCI population.
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Affiliation(s)
- Joel A. Mefford
- Department of Neurology, University of California, Los Angeles, California, United States of America
| | - Zilong Zhao
- Miro Health, Inc., San Francisco, California, United States of America
| | - Leah Heilier
- Miro Health, Inc., San Francisco, California, United States of America
| | - Man Xu
- Miro Health, Inc., San Francisco, California, United States of America
| | - Guifeng Zhou
- Miro Health, Inc., San Francisco, California, United States of America
| | - Rachel Mace
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kelly L. Sloane
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shannon M. Sheppard
- Department of Communication Sciences & Disorders, Chapman University, Orange, California, United States of America
| | - Shenly Glenn
- Miro Health, Inc., San Francisco, California, United States of America
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2
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Sloane KL, Mefford JA, Zhao Z, Xu M, Zhou G, Fabian R, Wright AE, Glenn S. Validation of a Mobile, Sensor-based Neurobehavioral Assessment With Digital Signal Processing and Machine-learning Analytics. Cogn Behav Neurol 2022; 35:169-178. [PMID: 35749748 DOI: 10.1097/wnn.0000000000000308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/07/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND The Miro Health Mobile Assessment Platform consists of self-administered neurobehavioral and cognitive assessments that measure behaviors typically measured by specialized clinicians. OBJECTIVE To evaluate the Miro Health Mobile Assessment Platform's concurrent validity, test-retest reliability, and mild cognitive impairment (MCI) classification performance. METHOD Sixty study participants were evaluated with Miro Health version V.2. Healthy controls (HC), amnestic MCI (aMCI), and nonamnestic MCI (naMCI) ages 64-85 were evaluated with version V.3. Additional participants were recruited at Johns Hopkins Hospital to represent clinic patients, with wider ranges of age and diagnosis. In all, 90 HC, 21 aMCI, 17 naMCI, and 15 other cases were evaluated with V.3. Concurrent validity of the Miro Health variables and legacy neuropsychological test scores was assessed with Spearman correlations. Reliability was quantified with the scores' intraclass correlations. A machine-learning algorithm combined Miro Health variable scores into a Risk score to differentiate HC from MCI or MCI subtypes. RESULTS In HC, correlations of Miro Health variables with legacy test scores ranged 0.27-0.68. Test-retest reliabilities ranged 0.25-0.79, with minimal learning effects. The Risk score differentiated individuals with aMCI from HC with an area under the receiver operator curve (AUROC) of 0.97; naMCI from HC with an AUROC of 0.80; combined MCI from HC with an AUROC of 0.89; and aMCI from naMCI with an AUROC of 0.83. CONCLUSION The Miro Health Mobile Assessment Platform provides valid and reliable assessment of neurobehavioral and cognitive status, effectively distinguishes between HC and MCI, and differentiates aMCI from naMCI.
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Affiliation(s)
- Kelly L Sloane
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Joel A Mefford
- Department of Neurology, University of California, Los Angeles, California
| | | | - Man Xu
- Miro Health Inc., San Francisco, California
| | | | - Rachel Fabian
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Amy E Wright
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Emami NC, Cavazos TB, Rashkin SR, Cario CL, Graff RE, Tai CG, Mefford JA, Kachuri L, Wan E, Wong S, Aaronson D, Presti J, Habel LA, Shan J, Ranatunga DK, Chao CR, Ghai NR, Jorgenson E, Sakoda LC, Kvale MN, Kwok PY, Schaefer C, Risch N, Hoffmann TJ, Van Den Eeden SK, Witte JS. A Large-Scale Association Study Detects Novel Rare Variants, Risk Genes, Functional Elements, and Polygenic Architecture of Prostate Cancer Susceptibility. Cancer Res 2021; 81:1695-1703. [PMID: 33293427 PMCID: PMC8137514 DOI: 10.1158/0008-5472.can-20-2635] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/27/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022]
Abstract
To identify rare variants associated with prostate cancer susceptibility and better characterize the mechanisms and cumulative disease risk associated with common risk variants, we conducted an integrated study of prostate cancer genetic etiology in two cohorts using custom genotyping microarrays, large imputation reference panels, and functional annotation approaches. Specifically, 11,984 men (6,196 prostate cancer cases and 5,788 controls) of European ancestry from Northern California Kaiser Permanente were genotyped and meta-analyzed with 196,269 men of European ancestry (7,917 prostate cancer cases and 188,352 controls) from the UK Biobank. Three novel loci, including two rare variants (European ancestry minor allele frequency < 0.01, at 3p21.31 and 8p12), were significant genome wide in a meta-analysis. Gene-based rare variant tests implicated a known prostate cancer gene (HOXB13), as well as a novel candidate gene (ILDR1), which encodes a receptor highly expressed in prostate tissue and is related to the B7/CD28 family of T-cell immune checkpoint markers. Haplotypic patterns of long-range linkage disequilibrium were observed for rare genetic variants at HOXB13 and other loci, reflecting their evolutionary history. In addition, a polygenic risk score (PRS) of 188 prostate cancer variants was strongly associated with risk (90th vs. 40th-60th percentile OR = 2.62, P = 2.55 × 10-191). Many of the 188 variants exhibited functional signatures of gene expression regulation or transcription factor binding, including a 6-fold difference in log-probability of androgen receptor binding at the variant rs2680708 (17q22). Rare variant and PRS associations, with concomitant functional interpretation of risk mechanisms, can help clarify the full genetic architecture of prostate cancer and other complex traits. SIGNIFICANCE: This study maps the biological relationships between diverse risk factors for prostate cancer, integrating different functional datasets to interpret and model genome-wide data from over 200,000 men with and without prostate cancer.See related commentary by Lachance, p. 1637.
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Affiliation(s)
- Nima C Emami
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Taylor B Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Clinton L Cario
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Caroline G Tai
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Joel A Mefford
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Eunice Wan
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Simon Wong
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - David Aaronson
- Department of Urology, Kaiser Oakland Medical Center, Oakland, California
| | - Joseph Presti
- Department of Urology, Kaiser Oakland Medical Center, Oakland, California
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Jun Shan
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Dilrini K Ranatunga
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Chun R Chao
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California
| | - Nirupa R Ghai
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Mark N Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Pui-Yan Kwok
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Catherine Schaefer
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Neil Risch
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
- Division of Research, Kaiser Permanente Northern California, Oakland, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Thomas J Hoffmann
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente Northern California, Oakland, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - John S Witte
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California.
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
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4
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Liu X, Mefford JA, Dahl A, He Y, Subramaniam M, Battle A, Price AL, Zaitlen N. GBAT: a gene-based association test for robust detection of trans-gene regulation. Genome Biol 2020; 21:211. [PMID: 32831138 PMCID: PMC7444084 DOI: 10.1186/s13059-020-02120-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/27/2020] [Indexed: 02/07/2023] Open
Abstract
The observation that disease-associated genetic variants typically reside outside of exons has inspired widespread investigation into the genetic basis of transcriptional regulation. While associations between the mRNA abundance of a gene and its proximal SNPs (cis-eQTLs) are now readily identified, identification of high-quality distal associations (trans-eQTLs) has been limited by a heavy multiple testing burden and the proneness to false-positive signals. To address these issues, we develop GBAT, a powerful gene-based pipeline that allows robust detection of high-quality trans-gene regulation signal.
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Affiliation(s)
- Xuanyao Liu
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA USA
- Department of Human Genetics, The University of Chicago, Chicago, IL USA
| | - Joel A. Mefford
- Departments of Neurology and Computational Medicine, University of California Los Angeles, Los Angeles, CA USA
| | - Andrew Dahl
- Departments of Neurology and Computational Medicine, University of California Los Angeles, Los Angeles, CA USA
| | - Yuan He
- Department of Computer Science, Johns Hopkins University, Baltimore, MD USA
| | - Meena Subramaniam
- Departments of Neurology and Computational Medicine, University of California Los Angeles, Los Angeles, CA USA
| | - Alexis Battle
- Department of Computer Science, Johns Hopkins University, Baltimore, MD USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA USA
| | - Noah Zaitlen
- Departments of Neurology and Computational Medicine, University of California Los Angeles, Los Angeles, CA USA
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5
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Lindquist KJ, Paris PL, Hoffmann TJ, Cardin NJ, Kazma R, Mefford JA, Simko JP, Ngo V, Chen Y, Levin AM, Chitale D, Helfand BT, Catalona WJ, Rybicki BA, Witte JS. Mutational Landscape of Aggressive Prostate Tumors in African American Men. Cancer Res 2016; 76:1860-8. [PMID: 26921337 DOI: 10.1158/0008-5472.can-15-1787] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/31/2015] [Indexed: 12/20/2022]
Abstract
Prostate cancer is the most frequently diagnosed and second most fatal nonskin cancer among men in the United States. African American men are two times more likely to develop and die of prostate cancer compared with men of other ancestries. Previous whole genome or exome tumor-sequencing studies of prostate cancer have primarily focused on men of European ancestry. In this study, we sequenced and characterized somatic mutations in aggressive (Gleason ≥7, stage ≥T2b) prostate tumors from 24 African American patients. We describe the locations and prevalence of small somatic mutations (up to 50 bases in length), copy number aberrations, and structural rearrangements in the tumor genomes compared with patient-matched normal genomes. We observed several mutation patterns consistent with previous studies, such as large copy number aberrations in chromosome 8 and complex rearrangement chains. However, TMPRSS2-ERG gene fusions and PTEN losses occurred in only 21% and 8% of the African American patients, respectively, far less common than in patients of European ancestry. We also identified mutations that appeared specific to or more common in African American patients, including a novel CDC27-OAT gene fusion occurring in 17% of patients. The genomic aberrations reported in this study warrant further investigation of their biologic significant role in the incidence and clinical outcomes of prostate cancer in African Americans. Cancer Res; 76(7); 1860-8. ©2016 AACR.
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Affiliation(s)
- Karla J Lindquist
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Pamela L Paris
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California. Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Niall J Cardin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Rémi Kazma
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Joel A Mefford
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Jeffrey P Simko
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Vy Ngo
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Yalei Chen
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | - Dhananjay Chitale
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | - Brian T Helfand
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| | - William J Catalona
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California. Department of Urology, University of California San Francisco, San Francisco, California. Institute for Human Genetics, University of California San Francisco, San Francisco, California. Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California.
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6
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Mefford JA, Zaitlen NA, Witte JS. Comment: A Human Genetics Perspective. J Am Stat Assoc 2016. [DOI: 10.1080/01621459.2016.1149404] [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: 10/21/2022]
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7
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Tai CG, Graff RE, Liu J, Passarelli MN, Mefford JA, Shaw GM, Hoffmann TJ, Witte JS. Detecting gene-environment interactions in human birth defects: Study designs and statistical methods. ACTA ACUST UNITED AC 2015; 103:692-702. [PMID: 26010994 DOI: 10.1002/bdra.23382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 02/13/2015] [Revised: 03/25/2015] [Accepted: 03/30/2015] [Indexed: 01/12/2023]
Abstract
BACKGROUND The National Birth Defects Prevention Study (NBDPS) contains a wealth of information on affected and unaffected family triads, and thus provides numerous opportunities to study gene-environment interactions (G×E) in the etiology of birth defect outcomes. Depending on the research objective, several analytic options exist to estimate G×E effects that use varying combinations of individuals drawn from available triads. METHODS In this study, we discuss important considerations in the collection of genetic data and environmental exposures. RESULTS We will also present several population- and family-based approaches that can be applied to data from the NBDPS including case-control, case-only, family-based trio, and maternal versus fetal effects. For each, we describe the data requirements, applicable statistical methods, advantages, and disadvantages. CONCLUSION A range of approaches can be used to evaluate potentially important G×E effects in the NBDPS. Investigators should be aware of the limitations inherent to each approach when choosing a study design and interpreting results.
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Affiliation(s)
- Caroline G Tai
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Jinghua Liu
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Michael N Passarelli
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Joel A Mefford
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California.,Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California.,Institute for Human Genetics, University of California San Francisco, San Francisco, California.,Department of Urology, University of California San Francisco, San Francisco, California.,UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
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8
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Goswami S, Yee SW, Stocker S, Mosley JD, Kubo M, Castro R, Mefford JA, Wen C, Liang X, Witte J, Brett C, Maeda S, Simpson MD, Hedderson MM, Davis RL, Roden DM, Giacomini KM, Savic RM. Genetic variants in transcription factors are associated with the pharmacokinetics and pharmacodynamics of metformin. Clin Pharmacol Ther 2014; 96:370-9. [PMID: 24853734 DOI: 10.1038/clpt.2014.109] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 05/07/2014] [Indexed: 12/26/2022]
Abstract
One-third of type 2 diabetes patients do not respond to metformin. Genetic variants in metformin transporters have been extensively studied as a likely contributor to this high failure rate. Here, we investigate, for the first time, the effect of genetic variants in transcription factors on metformin pharmacokinetics (PK) and response. Overall, 546 patients and healthy volunteers contributed their genome-wide, pharmacokinetic (235 subjects), and HbA1c data (440 patients) for this analysis. Five variants in specificity protein 1 (SP1), a transcription factor that modulates the expression of metformin transporters, were associated with changes in treatment HbA1c (P < 0.01) and metformin secretory clearance (P < 0.05). Population pharmacokinetic modeling further confirmed a 24% reduction in apparent clearance in homozygous carriers of one such variant, rs784888. Genetic variants in other transcription factors, peroxisome proliferator-activated receptor-α and hepatocyte nuclear factor 4-α, were significantly associated with HbA1c change only. Overall, our study highlights the importance of genetic variants in transcription factors as modulators of metformin PK and response.
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Affiliation(s)
- S Goswami
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - S W Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - S Stocker
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - J D Mosley
- Department of Pharmacology and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M Kubo
- Center of Genomic Medicine, RIKEN, Yokohama City, Japan
| | - R Castro
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - J A Mefford
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - C Wen
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - X Liang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - J Witte
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - C Brett
- Department of Anesthesiology, University of California, San Francisco, San Francisco, California, USA
| | - S Maeda
- Center of Genomic Medicine, RIKEN, Yokohama City, Japan
| | - M D Simpson
- Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA
| | - M M Hedderson
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - R L Davis
- Center for Health Research Southeast, Kaiser Permanente Georgia, Atlanta, Georgia, USA
| | - D M Roden
- Department of Pharmacology and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - K M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - R M Savic
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
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9
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Kazma R, Mefford JA, Cheng I, Plummer SJ, Levin AM, Rybicki BA, Casey G, Witte JS. Association of the innate immunity and inflammation pathway with advanced prostate cancer risk. PLoS One 2012; 7:e51680. [PMID: 23272139 PMCID: PMC3522730 DOI: 10.1371/journal.pone.0051680] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [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: 08/09/2012] [Accepted: 11/05/2012] [Indexed: 01/13/2023] Open
Abstract
Prostate cancer is the most frequent and second most lethal cancer in men in the United States. Innate immunity and inflammation may increase the risk of prostate cancer. To determine the role of innate immunity and inflammation in advanced prostate cancer, we investigated the association of 320 single nucleotide polymorphisms, located in 46 genes involved in this pathway, with disease risk using 494 cases with advanced disease and 536 controls from Cleveland, Ohio. Taken together, the whole pathway was associated with advanced prostate cancer risk (P = 0.02). Two sub-pathways (intracellular antiviral molecules and extracellular pattern recognition) and four genes in these sub-pathways (TLR1, TLR6, OAS1, and OAS2) were nominally associated with advanced prostate cancer risk and harbor several SNPs nominally associated with advanced prostate cancer risk. Our results suggest that the innate immunity and inflammation pathway may play a modest role in the etiology of advanced prostate cancer through multiple small effects.
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Affiliation(s)
- Rémi Kazma
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Joel A. Mefford
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Iona Cheng
- Epidemiology Program, University of Hawai’i Cancer Center, University of Hawai’i, Honolulu, Hawai’i, United States of America
| | - Sarah J. Plummer
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Albert M. Levin
- Department of Biostatistics and Research Epidemiology, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Benjamin A. Rybicki
- Department of Biostatistics and Research Epidemiology, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Graham Casey
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - John S. Witte
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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10
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Cardin NJ, Mefford JA, Witte JS. Joint association testing of common and rare genetic variants using hierarchical modeling. Genet Epidemiol 2012; 36:642-51. [PMID: 22807252 DOI: 10.1002/gepi.21659] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 04/11/2012] [Accepted: 05/29/2012] [Indexed: 11/11/2022]
Abstract
New sequencing technologies provide an opportunity for assessing the impact of rare and common variants on complex diseases. Several methods have been developed for evaluating rare variants, many of which use weighted collapsing to combine rare variants. Some approaches require arbitrary frequency thresholds below which to collapse alleles, and most assume that effect sizes for each collapsed variant are either the same or a function of minor allele frequency. Some methods also further assume that all rare variants are deleterious rather than protective. We expect that such assumptions will not hold in general, and as a result performance of these tests will be adversely affected. We propose a hierarchical model, implemented in the new program CHARM, to detect the joint signal from rare and common variants within a genomic region while properly accounting for linkage disequilibrium between variants. Our model explores the scale, rather than the center of the odds ratio distribution, allowing for both causative and protective effects. We use cross-validation to assess the evidence for association in a region. We use model averaging to widen the range of disease models under which we will have good power. To assess this approach, we simulate data under a range of disease models with effects at common and/or rare variants. Overall, our method had more power than other well-known rare variant approaches; it performed well when either only rare, or only common variants were causal, and better than other approaches when both common and rare variants contributed to disease.
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Affiliation(s)
- Niall J Cardin
- Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California, San Francisco, California 94158-9001, USA
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Mefford D, Mefford JA. Enumerating the gene sets in breast cancer, a "direct" alternative to hierarchical clustering. BMC Genomics 2010; 11:482. [PMID: 20731868 PMCID: PMC2996978 DOI: 10.1186/1471-2164-11-482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [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: 08/28/2009] [Accepted: 08/23/2010] [Indexed: 11/10/2022] Open
Abstract
Background Two-way hierarchical clustering, with results visualized as heatmaps, has served as the method of choice for exploring structure in large matrices of expression data since the advent of microarrays. While it has delivered important insights, including a typology of breast cancer subtypes, it suffers from instability in the face of gene or sample selection, and an inability to detect small sets that may be dominated by larger sets such as the estrogen-related genes in breast cancer. The rank-based partitioning algorithm introduced in this paper addresses several of these limitations. It delivers results comparable to two-way hierarchical clustering, and much more. Applied systematically across a range of parameter settings, it enumerates all the partition-inducing gene sets in a matrix of expression values. Results Applied to four large breast cancer datasets, this alternative exploratory method detects more than thirty sets of co-regulated genes, many of which are conserved across experiments and across platforms. Many of these sets are readily identified in biological terms, e.g., "estrogen", "erbb2", and 8p11-12, and several are clinically significant as prognostic of either increased survival ("adipose", "stromal"...) or diminished survival ("proliferation", "immune/interferon", "histone",...). Of special interest are the sets that effectively factor "immune response" and "stromal signalling". Conclusion The gene sets induced by the enumeration include many of the sets reported in the literature. In this regard these inventories confirm and consolidate findings from microarray-based work on breast cancer over the last decade. But, the enumerations also identify gene sets that have not been studied as of yet, some of which are prognostic of survival. The sets induced are robust, biologically meaningful, and serve to reveal a finer structure in existing breast cancer microarrays.
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Affiliation(s)
- Dwain Mefford
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California 94107, USA.
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