1
|
Han J, Zhuang B, Zou L, Wang D, Jiang L, Wei YL, Zhao L, Zhao L, Li C. A developmental validation of the Quick TargSeq 1.0 integrated system for automated DNA genotyping in forensic science for reference samples. Electrophoresis 2024; 45:814-828. [PMID: 38459798 DOI: 10.1002/elps.202300187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 03/10/2024]
Abstract
Analysis of short tandem repeats (STRs) is a global standard method for human identification. Insertion/Deletion polymorphisms (DIPs) can be used for biogeographical ancestry inference. Current DNA typing involves a trained forensic worker operating several specialized instruments in a controlled laboratory environment, which takes 6-8 h. We developed the Quick TargSeq 1.0 integrated system (hereinafter abbreviated to Quick TargSeq) for automated generation of STR and DIP profiles from buccal swab samples and blood stains. The system fully integrates the processes of DNA extraction, polymerase chain reaction (PCR) amplification, and electrophoresis separation using microfluidic biochip technology. Internal validation studies were performed using RTyper 21 or DIP 38 chip cartridges with single-source reference samples according to the Scientific Working Group for DNA Analysis Methods guidelines. These results indicated that the Quick TargSeq system can process reference samples and generate STR or DIP profiles in approximately 2 h, and the profiles were concordant with those determined using traditional STR or DIP analysis methods. Thus, reproducible and concordant DNA profiles were obtained from reference samples. Throughout the study, no lane-to-lane or run-to-run contamination was observed. The Quick TargSeq system produced full profiles from buccal swabs with at least eight swipes, dried blood spot cards with two 2-mm disks, or 10 ng of purified DNA. Potential PCR inhibitors (i.e., coffee, smoking tobacco, and chewing tobacco) did not appear to affect the amplification reactions of the instrument. The overall success rate and concordance rate of 153 samples were 94.12% and 93.44%, respectively, which is comparable to other commercially available rapid DNA instruments. A blind test initiated by a DNA expert group showed that the system can correctly produce DNA profiles with 97.29% genotype concordance with standard bench-processing methods, and the profiles can be uploaded into the national DNA database. These results demonstrated that the Quick TargSeq system can rapidly generate reliable DNA profiles in an automated manner and has the potential for use in the field and forensic laboratories.
Collapse
Affiliation(s)
- Junping Han
- Technology Department of Chaoyang Sub-bureau, Beijing Public Security Bureau, Beijing, P. R. China
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, P. R. China
| | - Bin Zhuang
- Beijing CapitalBio Technology Ltd. Co., Beijing, P. R. China
| | - Lixin Zou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, P. R. China
| | - Daoyu Wang
- People's Public Security University of China, Beijing, P. R. China
| | - Li Jiang
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, P. R. China
| | - Yi-Liang Wei
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, P. R. China
| | - Lijian Zhao
- Beijing CapitalBio Technology Ltd. Co., Beijing, P. R. China
| | - Lei Zhao
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, P. R. China
| | - Caixia Li
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, P. R. China
| |
Collapse
|
2
|
Simonyte S, Grabauskyte I, Macijauskiene J, Lesauskaite V, Lesauskaite V, Kvaal KS, Stewart R. Associations of the serotonin transporter gene polymorphism, 5-HTTLPR, and adverse life events with late life depression in the elderly Lithuanian population. Sci Rep 2023; 13:12920. [PMID: 37558806 PMCID: PMC10412533 DOI: 10.1038/s41598-023-40215-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/07/2023] [Indexed: 08/11/2023] Open
Abstract
Late-life depression (LLD) is a multifactorial disorder, with susceptibility and vulnerability potentially influenced by gene-environment interaction. The aim of this study was to investigate whether the 5-HTTLPR polymorphism is associated with LLD. The sample of 353 participants aged 65 years and over was randomly selected from the list of Kaunas city inhabitants by Residents' Register Service of Lithuania. Depressive symptoms were ascertained using the EURO-D scale. The List of Threatening Events Questionnaire was used to identify stressful life events that happened over the last 6 months and during lifetime. A 5-HTTLPR and lifetime stressful events interaction was indicated by higher odds of depression in those with s/s genotype who experienced high stress compared to l/l carriers with low or medium stress, while 5-HTTLPR and current stressful events interaction analysis revealed that carriers of either one or two copies of the s allele had increased odds of depressive symptoms associated with stress compared to participants with the l/l genotype not exposed to stressful situations. Although no significant direct association was found between the 5-HTTLPR short allele and depression, our findings demonstrated that lifetime or current stressful life events and their modification by 5-HTTLPR genotype are risk factors for late-life depression.
Collapse
Affiliation(s)
- Sandrita Simonyte
- Institute of Cardiology of Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania.
| | - Ingrida Grabauskyte
- Department of Physics, Mathematics and Biophysics of Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Jurate Macijauskiene
- Department of Geriatrics of Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vita Lesauskaite
- Department of Geriatrics of Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vaiva Lesauskaite
- Institute of Cardiology of Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Kari Sofie Kvaal
- Faculty of Social and Health Sciences, Inland Norway University of Applied Sciences, Lillehammer, Innlandet, Norway
| | - Robert Stewart
- King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK
- South London and Maudsley NHS Foundation Trust, London, UK
| |
Collapse
|
3
|
André J, Diouf M, Martinetti MP, Ortelli O, Gierski F, Fürst F, Pierrefiche O, Naassila M. A new statistical model for binge drinking pattern classification in college-student populations. Front Psychol 2023; 14:1134118. [PMID: 37529316 PMCID: PMC10390312 DOI: 10.3389/fpsyg.2023.1134118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/16/2023] [Indexed: 08/03/2023] Open
Abstract
Background Binge drinking (BD) among students is a frequent alcohol consumption pattern that produces adverse consequences. A widely discussed difficulty in the scientific community is defining and characterizing BD patterns. This study aimed to find homogenous drinking groups and then provide a new tool, based on a model that includes several key factors of BD, to assess the severity of BD regardless of the individual's gender. Methods Using the learning sample (N1 = 1,271), a K-means clustering algorithm and a partial proportional odds model (PPOM) were used to isolate drinking and behavioral key factors, create homogenous groups of drinkers, and estimate the probability of belonging to these groups. Robustness of our findings were evaluated with Two validations samples (N2 = 2,310, N3 = 120) of French university students (aged 18-25 years) were anonymously investigated via demographic and alcohol consumption questionnaires (AUDIT, AUQ, Alcohol Purchase Task for behavioral economic indices). Results The K-means revealed four homogeneous groups, based on drinking profiles: low-risk, hazardous, binge, and high-intensity BD. The PPOM generated the probability of each participant, self-identified as either male or female, to belong to one of these groups. Our results were confirmed in two validation samples, and we observed differences between the 4 drinking groups in terms of consumption consequences and behavioral economic demand indices. Conclusion Our model reveals a progressive severity in the drinking pattern and its consequences and may better characterize binge drinking among university student samples. This model provides a new tool for assessing the severity of binge drinking and illustrates that frequency of drinking behavior and particularly drunkenness are central features of a binge drinking model.
Collapse
Affiliation(s)
- Judith André
- INSERM UMR 1247, Groupe de Recherche sur l’alcool et les Pharmacodépendances, GRAP, Université Picardie Jules Verne, Amiens, France
| | - Momar Diouf
- Biostatistics Unit, Clinical Research Department, Amiens-Picardie University Hospital, Amiens, France
| | - Margaret P. Martinetti
- INSERM UMR 1247, Groupe de Recherche sur l’alcool et les Pharmacodépendances, GRAP, Université Picardie Jules Verne, Amiens, France
- Department of Psychology, The College of New Jersey, Ewing, NJ, United States
| | - Olivia Ortelli
- Department of Psychology, The College of New Jersey, Ewing, NJ, United States
| | - Fabien Gierski
- INSERM UMR 1247, Groupe de Recherche sur l’alcool et les Pharmacodépendances, GRAP, Université Picardie Jules Verne, Amiens, France
- Cognition, Health, Society Laboratory (C2S – EA 6291), University of Reims Champagne Ardenne (URCA), Reims, France
- Fédération Hospitalo-Universitaire A2M2P, Améliore le Pronostic des Troubles Addictifs et Mentaux par une Médecine Personnalisée, Paris, France
- GDR CNRS 3557 Psychiatrie-Addictions, Institut de Psychiatrie, Paris, France
| | - Frederic Fürst
- Laboratoire MIS (Modélisation, Information et Système) UR 4290, Université Picardie Jules Verne, Amiens, France
| | - Olivier Pierrefiche
- INSERM UMR 1247, Groupe de Recherche sur l’alcool et les Pharmacodépendances, GRAP, Université Picardie Jules Verne, Amiens, France
| | - Mickael Naassila
- INSERM UMR 1247, Groupe de Recherche sur l’alcool et les Pharmacodépendances, GRAP, Université Picardie Jules Verne, Amiens, France
- Fédération Hospitalo-Universitaire A2M2P, Améliore le Pronostic des Troubles Addictifs et Mentaux par une Médecine Personnalisée, Paris, France
- GDR CNRS 3557 Psychiatrie-Addictions, Institut de Psychiatrie, Paris, France
| |
Collapse
|
4
|
Shaaban S, Ji Y. Pharmacogenomics and health disparities, are we helping? Front Genet 2023; 14:1099541. [PMID: 36755573 PMCID: PMC9900000 DOI: 10.3389/fgene.2023.1099541] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Pharmacogenomics has been at the forefront of precision medicine during the last few decades. Precision medicine carries the potential of improving health outcomes at both the individual as well as population levels. To harness the benefits of its initiatives, careful dissection of existing health disparities as they relate to precision medicine is of paramount importance. Attempting to address the existing disparities at the early stages of design and implementation of these efforts is the only guarantee of a successful just outcome. In this review, we glance at a few determinants of existing health disparities as they intersect with pharmacogenomics research and implementation. In our opinion, highlighting these disparities is imperative for the purpose of researching meaningful solutions. Failing to identify, and hence address, these disparities in the context of the current and future precision medicine initiatives would leave an already strained health system, even more inundated with inequality.
Collapse
Affiliation(s)
- Sherin Shaaban
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States,ARUP Laboratories, Salt Lake City, Utah, United States,*Correspondence: Sherin Shaaban,
| | - Yuan Ji
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States,ARUP Laboratories, Salt Lake City, Utah, United States
| |
Collapse
|
5
|
Boudeau S, Ramakodi MP, Zhou Y, Liu JC, Ragin C, Kulathinal RJ. Extensive set of African ancestry-informative markers (AIMs) to study ancestry and population health. Front Genet 2023; 14:1061781. [PMID: 36911410 PMCID: PMC9997643 DOI: 10.3389/fgene.2023.1061781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/20/2023] [Indexed: 02/16/2023] Open
Abstract
Introduction: Human populations are often highly structured due to differences in genetic ancestry among groups, posing difficulties in associating genes with diseases. Ancestry-informative markers (AIMs) aid in the detection of population stratification and provide an alternative approach to map population-specific alleles to disease. Here, we identify and characterize a novel set of African AIMs that separate populations of African ancestry from other global populations including those of European ancestry. Methods: Using data from the 1000 Genomes Project, highly informative SNP markers from five African subpopulations were selected based on estimates of informativeness (In) and compared against the European population to generate a final set of 46,737 African ancestry-informative markers (AIMs). The AIMs identified were validated using an independent set and functionally annotated using tools like SIFT, PolyPhen. They were also investigated for representation of commonly used SNP arrays. Results: This set of African AIMs effectively separates populations of African ancestry from other global populations and further identifies substructure between populations of African ancestry. When a subset of these AIMs was studied in an independent dataset, they differentiated people who self-identify as African American or Black from those who identify their ancestry as primarily European. Most of the AIMs were found to be in their intergenic and intronic regions with only 0.6% in the coding regions of the genome. Most of the commonly used SNP array investigated contained less than 10% of the AIMs. Discussion: While several functional annotations of both coding and non-coding African AIMs are supported by the literature and linked these high-frequency African alleles to diseases in African populations, more effort is needed to map genes to diseases in these genetically diverse subpopulations. The relative dearth of these African AIMs on current genotyping platforms (the array with the highest fraction, llumina's Omni 5, harbors less than a quarter of AIMs), further demonstrates a greater need to better represent historically understudied populations.
Collapse
Affiliation(s)
- Samantha Boudeau
- Department of Biology, Temple University, Philadelphia, PA, United States.,Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,African Caribbean Cancer Consortium, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Meganathan P Ramakodi
- Department of Biology, Temple University, Philadelphia, PA, United States.,Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,African Caribbean Cancer Consortium, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Yan Zhou
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Jeffrey C Liu
- Department of Otolaryngology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States.,Department of Surgical Oncology, Fox chase Cancer center, Philadelphia, PA, United States
| | - Camille Ragin
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,African Caribbean Cancer Consortium, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Rob J Kulathinal
- Department of Biology, Temple University, Philadelphia, PA, United States.,African Caribbean Cancer Consortium, Fox Chase Cancer Center, Philadelphia, PA, United States
| |
Collapse
|
6
|
Sun K, Yao Y, Yun L, Zhang C, Xie J, Qian X, Tang Q, Sun L. Application of machine learning for ancestry inference using multi-InDel markers. Forensic Sci Int Genet 2022; 59:102702. [DOI: 10.1016/j.fsigen.2022.102702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 03/22/2022] [Accepted: 03/27/2022] [Indexed: 01/04/2023]
|
7
|
Xu H, Fang Y, Zhao M, Lan Q, Mei S, Liu L, Bai X, Zhu B. Forensic Features and Genetic Structure Analyses of the Beijing Han Nationality Disclosed by a Self-Developed Panel Containing a Series of Ancestry Informative Deletion/Insertion Polymorphism Loci. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.890153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The utilization of the ancestry informative markers to disclose the ancestral composition of a certain population and explore the genetic affinities between diverse populations is beneficial to inferring the biogeographic ancestry of unknown individuals and assisting in case detection, as well as avoiding the impacts of population stratification during genome-wide association analysis studies. In the present study, we applied an in-house ancestry informative deletion/insertion polymorphic multiplex amplification system to investigate the ancestral compositions of the Beijing Han population and analyze the genetic relationships between the Beijing Han population and 31 global reference populations. The results demonstrated that 32 loci of this self-developed panel containing 39 loci significantly contributed to the inference of genetic information for the Beijing Han population. The results of multiple population genetics statistical analyses indicated that the ancestral component and genetic architecture of the Beijing Han population were analogous to the reference East Asian populations, and that the Beijing Han population was genetically close to the reference East Asian populations.
Collapse
|
8
|
Bateman NW, Tarney CM, Abulez TS, Hood BL, Conrads KA, Zhou M, Soltis AR, Teng PN, Jackson A, Tian C, Dalgard CL, Wilkerson MD, Kessler MD, Goecker Z, Loffredo J, Shriver CD, Hu H, Cote M, Parker GJ, Segars J, Al-Hendy A, Risinger JI, Phippen NT, Casablanca Y, Darcy KM, Maxwell GL, Conrads TP, O'Connor TD. Peptide ancestry informative markers in uterine neoplasms from women of European, African, and Asian ancestry. iScience 2021; 25:103665. [PMID: 35036865 PMCID: PMC8753123 DOI: 10.1016/j.isci.2021.103665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/29/2021] [Accepted: 12/17/2021] [Indexed: 02/07/2023] Open
Abstract
Characterization of ancestry-linked peptide variants in disease-relevant patient tissues represents a foundational step to connect patient ancestry with disease pathogenesis. Nonsynonymous single-nucleotide polymorphisms encoding missense substitutions within tryptic peptides exhibiting high allele frequencies in European, African, and East Asian populations, termed peptide ancestry informative markers (pAIMs), were prioritized from 1000 genomes. In silico analysis identified that as few as 20 pAIMs can determine ancestry proportions similarly to >260K SNPs (R2 = 0.99). Multiplexed proteomic analysis of >100 human endometrial cancer cell lines and uterine leiomyoma tissues combined resulted in the quantitation of 62 pAIMs that correlate with patient race and genotype-confirmed ancestry. Candidates include a D451E substitution in GC vitamin D-binding protein previously associated with altered vitamin D levels in African and European populations. pAIMs will support generalized proteoancestry assessment as well as efforts investigating the impact of ancestry on the human proteome and how this relates to the pathogenesis of uterine neoplasms.
Collapse
Affiliation(s)
- Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA,Corresponding author 3289 Woodburn Rd, Suite 375, Annandale, VA 22003;
| | - Christopher M. Tarney
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Tamara S. Abulez
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Brian L. Hood
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Kelly A. Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Ming Zhou
- Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Road, Falls Church, VA 22042, USA
| | - Anthony R. Soltis
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA,The American Genome Center; Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Amanda Jackson
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Clifton L. Dalgard
- The American Genome Center; Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA,Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Matthew D. Wilkerson
- The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA,The American Genome Center; Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA,Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Michael D. Kessler
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Zachary Goecker
- University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jeremy Loffredo
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Craig D. Shriver
- The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Hai Hu
- The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | | | - Glendon J. Parker
- University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - James Segars
- Johns Hopkins University Medical Center, Baltimore, MD 21218, USA
| | - Ayman Al-Hendy
- The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - John I. Risinger
- Department of Obstetrics and Gynecology, Michigan State University, East Lansing, MI 48824, USA
| | - Neil T. Phippen
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Yovanni Casablanca
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Kathleen M. Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - G. Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Road, Falls Church, VA 22042, USA
| | - Thomas P. Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Road, Falls Church, VA 22042, USA
| | - Timothy D. O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA,Program in Personalize and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA,Marlene and Stewart Greenebaum Comprehensive Cancer, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| |
Collapse
|
9
|
Ghaiyed AP, Sutherland H, Lea RA, Gardam T, Chaseling J, James K, Bernie A, Haupt LM, Christie J, Griffiths LR, Wright KM. Evaluation of an ancestry prediction strategy for historical military remains using a World War II-era sample and pedigrees with family-level admixture. AUST J FORENSIC SCI 2021. [DOI: 10.1080/00450618.2021.2005144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- A. P. Ghaiyed
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - H. Sutherland
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - R. A. Lea
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - T. Gardam
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - J. Chaseling
- School of Environment and Science, Griffith University, Nathan, Australia
| | - K. James
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - A. Bernie
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Canberra, Australia
| | - L. M. Haupt
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - J. Christie
- School of Environment and Science, Griffith University, Nathan, Australia
| | - L. R. Griffiths
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - K. M. Wright
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Canberra, Australia
- Royal Australian Air Force (RAAF), Williamtown, Australia
| |
Collapse
|
10
|
Chidambaran V, Mersha TB. A step towards understanding disparities - linking race, ancestry, epigenetics and pain. Epigenomics 2021; 13:1791-1796. [PMID: 34617457 PMCID: PMC8819586 DOI: 10.2217/epi-2021-0354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 09/24/2021] [Indexed: 11/21/2022] Open
Affiliation(s)
- Vidya Chidambaran
- Department of Anesthesiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Tesfaye B Mersha
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| |
Collapse
|
11
|
Flores-Alvarado S, Orellana-Soto M, Moraga M. Ancestry and admixture of a southernmost Chilean population: The reflection of a migratory history. Am J Hum Biol 2021; 34:e23598. [PMID: 33763944 DOI: 10.1002/ajhb.23598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 02/08/2021] [Accepted: 02/25/2021] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES Punta Arenas is a Chilean city situated on ancestral Aönikenk territory. The city was founded by 19th- and 20th-century colonists from Chile (Chiloé) and Europe (Croatia). This work uses uniparental and ancestry-informative markers (AIMs) to explore the effects of historic migratory and admixture patterns on the current genetic composition of Punta Arenas. METHODS We analyzed mitochondrial DNA (mtDNA), Y-chromosome single-nucleotide polymorphisms (SNPs), and 141 AIMs obtained from 129 DNA samples from male residents with regional ancestry. After characterizing uniparental lineages and ancestry proportions, multivariate analysis was used to explore relationships among the various types of data. RESULTS Punta Arenas has an admixed population with three main genetic components: European (56.5%), northern Native (11.3%), and south-central Native (28.6%). The Native component is preponderant in the mtDNA (83.76%), while the foreign component predominates in the Y-chromosome (92.25%). Non-Native mtDNA lineages are associated with European genetic ancestry, and Native mtDNA lineages originated mainly in the southern and southernmost regions of Chile. Most non-Native Y-chromosome SNPs originated in Spain, and secondly, in Croatia. CONCLUSIONS The population of Punta Arenas is mainly of Chilote origin with south-central Native and Spanish ancestral components, as well as some Croatian components. The persistence of local Native lineages is notable, suggesting continuity with the ancestral populations of the region such as the Kawésqar, Aönikenk, Yámana, or Selknam peoples. This study contributes to our knowledge of local history and its links to national and global developments in genetic ancestry.
Collapse
Affiliation(s)
- Sandra Flores-Alvarado
- Programa de Bioestadística, Instituto de Salud Poblacional, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Michael Orellana-Soto
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mauricio Moraga
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| |
Collapse
|
12
|
Caputo M, Amador MA, Sala A, Riveiro Dos Santos A, Santos S, Corach D. Ancestral genetic legacy of the extant population of Argentina as predicted by autosomal and X-chromosomal DIPs. Mol Genet Genomics 2021; 296:581-590. [PMID: 33580820 DOI: 10.1007/s00438-020-01755-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/14/2020] [Indexed: 12/01/2022]
Abstract
Aiming to determine their ancestry diagnostic potential, we selected two sets of nuclear deletion/insertion polymorphisms (DIPs), including 30 located on autosomal chromosomes and 33 on the X chromosome. We analysed over 200 unrelated Argentinean individuals living in urban areas of Argentina. As in most American countries, the extant Argentinean population is the result of tricontinental genetic admixture. The peopling process within the continent was characterised by mating bias involving Native American and enslaved African females and European males. Differential results were detected between autosomal DIPs and X-DIPs. The former showed that the European component was the largest (77.8%), followed by the Native American (17.9%) and African (4.2%) components, in good agreement with the previously published results. In contrast, X-DIPs showed that the European genetic contribution was also predominant but much smaller (52.9%) and considerably larger Native American and African contributions (39.6% and 7.5%, respectively). Genetic analysis revealed continental genetic contributions whose associated phenotypic traits have been mostly lost. The observed differences between the estimated continental genetic contribution proportions based on autosomal DIPs and X-DIPs reflect the effects of autosome and X-chromosome transmission behaviour and their different recombination patterns. This work shows the ability of the tested DIP panels to infer ancestry and confirm mating bias. To the best of our knowledge, this is the first study focusing on ancestry-informative autosomal DIP and X-DIP comparisons performed in a sample representing the entire Argentinean population.
Collapse
Affiliation(s)
- M Caputo
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense Y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina. .,CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina. .,Department of Forensic Genetics and DNA Fingerprinting Service, School of Pharmacy and Biochemistry, Junin 956, 7th floor, C1113AAD, CABA, Argentina.
| | - M A Amador
- Laboratorio de Genética Humana E Médica, Departamento de Patologia, Universidade Federal Do Pará, Belém, Pará, Brazil
| | - A Sala
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense Y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina.,CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina
| | - A Riveiro Dos Santos
- Laboratorio de Genética Humana E Médica, Departamento de Patologia, Universidade Federal Do Pará, Belém, Pará, Brazil
| | - S Santos
- Laboratorio de Genética Humana E Médica, Departamento de Patologia, Universidade Federal Do Pará, Belém, Pará, Brazil
| | - D Corach
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense Y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina.,CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina
| |
Collapse
|
13
|
Oliveira PRS, de Matos LO, Araujo NM, Sant Anna HP, da Silva E Silva DA, Damasceno AKA, Martins de Carvalho L, Horta BL, Lima-Costa MF, Barreto ML, Wiers CE, Volkow ND, Brunialti Godard AL. LRRK2 Gene Variants Associated With a Higher Risk for Alcohol Dependence in Multiethnic Populations. Front Psychiatry 2021; 12:665257. [PMID: 34135785 PMCID: PMC8202767 DOI: 10.3389/fpsyt.2021.665257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/12/2021] [Indexed: 11/22/2022] Open
Abstract
Background: Genetics influence the vulnerability to alcohol use disorders, and among the implicated genes, three previous studies have provided evidences for the involvement of LRRK2 in alcohol dependence (AD). LRRK2 expression is broadly dysregulated in postmortem brain from AD humans, as well as in the brain of mice with alcohol dependent-like behaviors and in a zebrafish model of alcohol preference. The aim of the present study was to evaluate the association of variants in the LRRK2 gene with AD in multiethnic populations from South and North America. Methods: Alcohol-screening questionnaires [such as CAGE and Alcohol Use Disorders Identification Test (AUDIT)] were used to determine individual risk of AD. Multivariate logistic regression analyses were done in three independent populations (898 individuals from Bambuí, Brazil; 3,015 individuals from Pelotas, Brazil; and 1,316 from the United States). Linkage disequilibrium and conditional analyses, as well as in silico functional analyses, were also conducted. Results: Four LRRK2 variants were significantly associated with AD in our discovery cohort (Bambuí): rs4768231, rs4767971, rs7307310, and rs1465527. Two of these variants (rs4768231 and rs4767971) were replicated in both Pelotas and US cohorts. The consistent association signal (at the LRRK2 locus) found in populations with different genetic backgrounds reinforces the relevance of our findings. Conclusion: Taken together, these results support the notion that genetic variants in the LRRK2 locus are risk factors for AD in humans.
Collapse
Affiliation(s)
- Pablo Rafael Silveira Oliveira
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil.,Centro de Integração de Dados e Conhecimentos para Saúde, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Lorena Oliveira de Matos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Nathalia Matta Araujo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hanaísa P Sant Anna
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Andresa K Andrade Damasceno
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil.,Centro de Integração de Dados e Conhecimentos para Saúde, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Luana Martins de Carvalho
- Department of Psychiatry, Center for Alcohol Research in Epigenetics, University of Illinois, Chicago, IL, United States
| | - Bernardo L Horta
- Programa de Pos-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, Brazil
| | | | - Mauricio Lima Barreto
- Centro de Integração de Dados e Conhecimentos para Saúde, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Corinde E Wiers
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, United States
| | - Nora D Volkow
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, United States
| | - Ana Lúcia Brunialti Godard
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
14
|
Rotroff DM. A Bioinformatics Crash Course for Interpreting Genomics Data. Chest 2020; 158:S113-S123. [PMID: 32658646 PMCID: PMC8176646 DOI: 10.1016/j.chest.2020.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/11/2019] [Accepted: 03/09/2020] [Indexed: 10/23/2022] Open
Abstract
Reductions in genotyping costs and improvements in computational power have made conducting genome-wide association studies (GWAS) standard practice for many complex diseases. GWAS is the assessment of genetic variants across the genome of many individuals to determine which, if any, genetic variants are associated with a specific trait. As with any analysis, there are evolving best practices that should be followed to ensure scientific rigor and reliability in the conclusions. This article presents a brief summary for many of the key bioinformatics considerations when either planning or evaluating GWAS. This review is meant to serve as a guide to those without deep expertise in bioinformatics and GWAS and give them tools to critically evaluate this popular approach to investigating complex diseases. In addition, a checklist is provided that can be used by investigators to evaluate whether a GWAS has appropriately accounted for the many potential sources of bias and generally followed current best practices.
Collapse
Affiliation(s)
- Daniel M Rotroff
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH.
| |
Collapse
|
15
|
Souza AMD, Resende SS, Sousa TND, Brito CFAD. A systematic scoping review of the genetic ancestry of the Brazilian population. Genet Mol Biol 2019; 42:495-508. [PMID: 31188926 PMCID: PMC6905439 DOI: 10.1590/1678-4685-gmb-2018-0076] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 01/16/2019] [Indexed: 12/27/2022] Open
Abstract
The genetic background of the Brazilian population is mainly characterized by
three parental populations: European, African, and Native American. The aim of
this study was to overview the genetic ancestry estimates for different
Brazilian geographic regions and analyze factors involved in these estimates. In
this systematic scoping review were included 51 studies, comprehending 81
populations of 19 states from five regions of Brazil. To reduce the potential of
bias from studies with different sampling methods, we calculated the mean
genetic ancestry weighted by the number of individuals. The weighted mean
proportions of European, African, and Native American ancestries were 68.1%,
19.6%, and 11.6%, respectively. At the regional level, the highest European
contribution occurred in the South, while the highest African and Native
American contributions occurred in the Northeastern and Northern regions,
respectively. Among states in the Northeast region, Bahia and Ceará showed
significant differences, suggesting distinct demographic histories. This review
contributes for a broader understanding of the Brazilian ancestry and indicates
that the ancestry estimates are influenced by the type of molecular marker and
the sampling method.
Collapse
Affiliation(s)
- Aracele Maria de Souza
- Research Group in Molecular Biology and Immunology of Malaria, Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil
| | - Sarah Stela Resende
- Research Group in Molecular Biology and Immunology of Malaria, Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil
| | - Taís Nóbrega de Sousa
- Research Group in Molecular Biology and Immunology of Malaria, Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil
| | | |
Collapse
|
16
|
Lesche D, Mostafa S, Everall I, Pantelis C, Bousman CA. Impact of CYP1A2, CYP2C19, and CYP2D6 genotype- and phenoconversion-predicted enzyme activity on clozapine exposure and symptom severity. THE PHARMACOGENOMICS JOURNAL 2019; 20:192-201. [PMID: 31616047 DOI: 10.1038/s41397-019-0108-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 09/09/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022]
Abstract
Clozapine is an atypical antipsychotic metabolized by CYP1A2, CYP2D6, and CYP2C19 enzymes. Among 66 adult schizophrenia patients treated with clozapine-based combination therapies, we explored the impact of genotype-predicted CYP1A2, CYP2D6, and CYP2C19 activity on dose-adjusted clozapine concentrations and symptom severity, with and without correction for inhibitors and inducers of these enzymes. Uncorrected activity scores were not associated with dose-adjusted clozapine concentrations or symptom severity. CYP1A2 and CYP2D6 activity scores corrected for known inducers (i.e., smoking) and inhibitors (e.g., concomitant medications) were associated with dose-adjusted clozapine levels and in the case of CYP1A2, symptom severity. However, smoking status and certain inhibitors of clozapine metabolism (i.e., esomeprazole) explained significantly more variance in dose-adjusted clozapine levels relative to corrected activity scores. These findings highlight the clinical importance of nongenetic factors (smoking, concomitant medications) and suggest that the added utility of CYP1A2, CYP2D6, and CYP2C19 activity scores to guide clozapine dosing is currently limited.
Collapse
Affiliation(s)
- Dorothea Lesche
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne & Melbourne Health, Melbourne, VIC, Australia
| | - Sam Mostafa
- myDNA Life Australia Limited, South Yarra, VIC, Australia.,Centre for Medicine Use and Safety, Monash University, Parkville, VIC, Australia
| | - Ian Everall
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne & Melbourne Health, Melbourne, VIC, Australia.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.,Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia.,The Cooperative Research Centre (CRC) for Mental Health, VIC, Australia
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne & Melbourne Health, Melbourne, VIC, Australia.,Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia.,The Cooperative Research Centre (CRC) for Mental Health, VIC, Australia
| | - Chad A Bousman
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne & Melbourne Health, Melbourne, VIC, Australia. .,The Cooperative Research Centre (CRC) for Mental Health, VIC, Australia. .,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada. .,Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada. .,Departments of Medical Genetics, Psychiatry, and Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada.
| |
Collapse
|
17
|
Delimitation of the upstream region of NFKBIA gene associated with HTLV-1-associated myelopathy/tropical spastic paraparesis using candidate Tag-SNPs in Peruvian HTLV-1 infected individuals. INFECTION GENETICS AND EVOLUTION 2019; 75:103929. [PMID: 31226330 DOI: 10.1016/j.meegid.2019.103929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/29/2019] [Accepted: 06/18/2019] [Indexed: 11/20/2022]
Abstract
In Peru, it is estimated that about 150 000-400 000 people carry the Human T-lymphotropic virus 1 (HTLV-1). Only 10% of HTLV-1 carries develop complications related to HTLV-1. HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a chronic disabling inflammatory disease affecting the spinal cord. HAM/TSP produces principally weakness in the lower limbs and bladder disturbances, among other complications. In a previous study, our group identified three SNPs (rs3138053, rs2233406, and rs3138045) located in the promoter region of the NFKBIA gene associated with HAM/TSP. This study aimed to analyze the association between four Tag-SNPs (rs10148482, rs17103274, rs17103282, and rs762009) located in the upstream region of the NFKBIA gene and HAM/TSP, and to delimit the linkage disequilibrium zone in the upstream region of the NFBKIA gene associated with HAM/TSP. The tetra-primers ARMS-PCR technique was used to genotype 4 Tag-SNPs on 140 HAM/TSP patients and 258 asymptomatic carriers. The SNP rs17103282 showed a deviation from Hardy-Weinberg equilibrium (p < .0001). Neither of three Tag-SNPs showed an association with HAM/TSP (P > .05). No linkage disequilibrium between four Tag-SNPs evaluated in this study and previous ones was observed. Here we show the region located in the upstream region of the NFKBIA gene highly associated with HAM/TSP disease in patients infected with HTLV-1 from Lima, Peru.
Collapse
|
18
|
Toma TT, Dawson JM, Adjeroh DA. Human ancestry indentification under resource constraints -- what can one chromosome tell us about human biogeographical ancestry? BMC Med Genomics 2018; 11:0. [PMID: 30453954 PMCID: PMC6245491 DOI: 10.1186/s12920-018-0412-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND While continental level ancestry is relatively simple using genomic information, distinguishing between individuals from closely associated sub-populations (e.g., from the same continent) is still a difficult challenge. METHODS We study the problem of predicting human biogeographical ancestry from genomic data under resource constraints. In particular, we focus on the case where the analysis is constrained to using single nucleotide polymorphisms (SNPs) from just one chromosome. We propose methods to construct such ancestry informative SNP panels using correlation-based and outlier-based methods. RESULTS We accessed the performance of the proposed SNP panels derived from just one chromosome, using data from the 1000 Genome Project, Phase 3. For continental-level ancestry classification, we achieved an overall classification rate of 96.75% using 206 single nucleotide polymorphisms (SNPs). For sub-population level ancestry prediction, we achieved an average pairwise binary classification rates as follows: subpopulations in Europe: 76.6% (58 SNPs); Africa: 87.02% (87 SNPs); East Asia: 73.30% (68 SNPs); South Asia: 81.14% (75 SNPs); America: 85.85% (68 SNPs). CONCLUSION Our results demonstrate that one single chromosome (in particular, Chromosome 1), if carefully analyzed, could hold enough information for accurate prediction of human biogeographical ancestry. This has significant implications in terms of the computational resources required for analysis of ancestry, and in the applications of such analyses, such as in studies of genetic diseases, forensics, and soft biometrics.
Collapse
Affiliation(s)
- Tanjin T Toma
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA
| | - Jeremy M Dawson
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA
| | - Donald A Adjeroh
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA.
| |
Collapse
|
19
|
Extended HLA-G genetic diversity and ancestry composition in a Brazilian admixed population sample: Implications for HLA-G transcriptional control and for case-control association studies. Hum Immunol 2018; 79:790-799. [DOI: 10.1016/j.humimm.2018.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/04/2018] [Accepted: 08/09/2018] [Indexed: 12/30/2022]
|
20
|
Association of CamK2A genetic variants with transition time from occasional to regular heroin use in a sample of heroin-dependent individuals. Psychiatr Genet 2018; 29:18-25. [PMID: 30260900 DOI: 10.1097/ypg.0000000000000208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Susceptibility to heroin dependence is strongly influenced by genetic factors with heritability estimates as high as 0.7. A number of genes, as well as environmental factors, are likely to contribute to its etiology. Not all individuals who have ever tried heroin at some stage during their lifetime become dependent on heroin. It has been suggested that genetic factors might be more important in the transition stage to heroin dependence rather than in environmental exposures and experimenting with heroin. As the features of substance dependence and memory formation have been found to be strikingly similar, we have focused on a key enzyme involved in long-term potentiation and synaptic plasticity, namely the calcium-dependent/calmodulin-dependent protein kinase IIα (CAMKIIa). We hypothesized, that CamK2A genetic variation may play a role in the transition from occasional to regular heroin use. MATERIALS AND METHODS Using quantitative trait association analysis, we addressed this hypothesis by correlating the self-reported time interval between occasional and regular heroin use with the frequency of 12 single nucleotide polymorphisms located within the genomic region of the CamK2A gene. A sample of 570 Caucasian patients was available for analysis. RESULTS Single marker association analysis (rs10066581, P=0.007), as well as haplotype analysis (global P=0.005), suggested an association with the quantitative trait 'time interval from occasional to regular heroin use.' CONCLUSION Our results propose that genetic variants located in the genomic region of the CamK2A gene may be involved in transition time from occasional to regular heroin use.
Collapse
|
21
|
Lee JH, Cho S, Kim MY, Shin DH, Rakha A, Shinde V, Lee SD. Genetic resolution of applied biosystems™ precision ID Ancestry panel for seven Asian populations. Leg Med (Tokyo) 2018; 34:41-47. [PMID: 30153533 DOI: 10.1016/j.legalmed.2018.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 07/23/2018] [Accepted: 08/22/2018] [Indexed: 10/28/2022]
Abstract
Massively parallel sequencing (MPS) offers additional information in cases that lack reference samples for comparison. The HID-Ion AmpliSeq Ancestry Panel is a forensic multiplex platform consisting of 165 autosomal markers designed to provide biogeographic ancestry information. We analyzed seven different population groups from Asia to assess the accuracy and reliability of analysis, using this panel. In this study, we have designated 750 unrelated Asians, from southern China (n = 99), Beijing (n = 100), Japan (n = 101), Korea (n = 100), Vietnam (n = 100), Nepal (n = 100), India (n = 51), and Pakistan (n = 99). The likelihood ratios of 750 Asians were calculated, using the Torrent Server and the HID SNP Genotyper Plugin Version 4.3.2. The results reveal that all Northeast Asians (China, Japan, and Korea), and Vietnamese, were predicted as East Asians with the highest ethnicity likelihood values from reference data. Although the samples from Nepal, India and Pakistan (Southwest Asians), were predominantly predicted as South Asians, there were seven cases of which results revealed as Europeans, with similar likelihood patterns. Population structure analysis indicated that Southwest Asians have a genetic profile that is distinguishable from those of other Asian populations. This panel was validated for potential usefulness in forensic analysis and the findings could be used as a basis for building additional Asian specific reference databases. Nevertheless, additional analyses comprising larger sample sizes will be necessary, especially Southeast Asians, to fully understand the Asian population structure, and to discriminate them with further details.
Collapse
Affiliation(s)
- Ji Hyun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Sohee Cho
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Moon-Young Kim
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Dong Hoon Shin
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea; Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Vasant Shinde
- Department of Archaeology, Deccan University, Pune, India
| | - Soong Deok Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea; Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea.
| |
Collapse
|
22
|
Wiers CE, Towb PC, Hodgkinson CA, Shen PH, Freeman C, Miller G, Lindgren E, Shokri-Kojori E, Demiral ŞB, Kim S, Tomasi D, Sun H, Wang GJ, Goldman D, Volkow ND. Association of genetic ancestry with striatal dopamine D2/D3 receptor availability. Mol Psychiatry 2018; 23:1711-1716. [PMID: 29112197 PMCID: PMC5938168 DOI: 10.1038/mp.2017.208] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 08/20/2017] [Accepted: 08/30/2017] [Indexed: 12/21/2022]
Abstract
Despite ethnic differences in allele frequencies of variants in dopaminergic genes associated with dopamine D2/D3 receptor availability (D2R), no study to date has investigated the relationship between genetic ancestry and striatal D2R. Here, we show that ancestry-informative markers significantly predict dorsal striatal D2R in 117 healthy ethnically diverse residents of the New York metropolitan area using Positron Emission Tomography (PET) with [11C]raclopride (P<0.0001), while correcting for age, sex, BMI, education, smoking status, and estimated socioeconomic status (ZIP codes). Effects of ethnicity on D2R were not driven by variation in dopaminergic candidate genes. Instead, candidate gene associations with striatal D2R were diminished when correcting for ancestry. These findings imply that future studies investigating D2 receptor genes should covary for genetic ancestry or study homogeneous populations. Moreover, ancestry studies on human neurobiology should control for socioeconomic differences between ethnic groups.
Collapse
Affiliation(s)
- Corinde E. Wiers
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20892, Maryland
| | - Par C. Towb
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20892, Maryland
| | - Colin A. Hodgkinson
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20852, Maryland
| | - Pei-Hong Shen
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20852, Maryland
| | - Clara Freeman
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20892, Maryland
| | - Gregg Miller
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20892, Maryland
| | - Elsa Lindgren
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20892, Maryland
| | - Ehsan Shokri-Kojori
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20892, Maryland
| | - Şükrü Barış Demiral
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20892, Maryland
| | - Sunny Kim
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20892, Maryland
| | - Dardo Tomasi
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20892, Maryland
| | - Hui Sun
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20852, Maryland
| | - Gene-Jack Wang
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20892, Maryland
| | - David Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20852, Maryland
| | - Nora D. Volkow
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda 20892, Maryland,National Institute on Drug Abuse, National Institutes of Health, Bethesda 20892, Maryland
| |
Collapse
|
23
|
Chau EJ, Mostaid MS, Cropley V, McGorry P, Pantelis C, Bousman CA, Everall IP. Downregulation of plasma SELENBP1 protein in patients with recent-onset schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 2018; 85:1-6. [PMID: 29577944 DOI: 10.1016/j.pnpbp.2018.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/22/2018] [Accepted: 03/09/2018] [Indexed: 12/19/2022]
Abstract
Upregulation of selenium binding protein 1 (SELENBP1) mRNA expression has been reported in schizophrenia, primarily in the dorsolateral prefrontal cortex. However, peripheral blood studies are limited and results are inconsistent. In this study, we examined SELENBP1 mRNA expression in whole blood and protein expression in plasma from patients with recent-onset schizophrenia (n = 30), treatment-resistant schizophrenia (n = 71) and healthy controls (n = 57). We also examined the effects of SELENBP1 genetic variation on gene and protein expression. We found lower SELENBP1 plasma protein levels in patients with recent-onset schizophrenia (p = 0.042) but not in treatment-resistant schizophrenia (p = 0.81). Measurement of peripheral mRNA levels showed no difference between treatment-resistant schizophrenia and healthy controls (p = 0.234) but clozapine plasma levels (p = 0.036) and duration of illness (p = 0.028) were positively correlated with mRNA levels. Genetic variation was not associated with mRNA or protein expression. Our data represent the first peripheral proteomic study of SELENBP1 in schizophrenia and suggest that plasma SELENBP1 protein is downregulated in patients with recent-onset schizophrenia.
Collapse
Affiliation(s)
- Edith J Chau
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne & Melbourne Health, Carlton South, VIC, Australia
| | - Md Shaki Mostaid
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne & Melbourne Health, Carlton South, VIC, Australia; The Cooperative Research Centre (CRC) for Mental Health, Victoria, Australia
| | - Vanessa Cropley
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne & Melbourne Health, Carlton South, VIC, Australia
| | - Patrick McGorry
- Orygen, The National Centre of Excellence in Youth Mental Health, Parkville, VIC, Australia,; Centre for Youth Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne & Melbourne Health, Carlton South, VIC, Australia; The Cooperative Research Centre (CRC) for Mental Health, Victoria, Australia; Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia; Centre for Neural Engineering, The University of Melbourne, Carlton, VIC, Australia; NorthWestern Mental Health, Melbourne, Victoria, Australia
| | - Chad A Bousman
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne & Melbourne Health, Carlton South, VIC, Australia; The Cooperative Research Centre (CRC) for Mental Health, Victoria, Australia; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada; Departments of Medical Genetics, Psychiatry, and Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
| | - Ian P Everall
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne & Melbourne Health, Carlton South, VIC, Australia; The Cooperative Research Centre (CRC) for Mental Health, Victoria, Australia; Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia; Centre for Neural Engineering, The University of Melbourne, Carlton, VIC, Australia; NorthWestern Mental Health, Melbourne, Victoria, Australia; Institute of Psychiatry, Psychology, and Neuroscience, King's College London, UK.
| |
Collapse
|
24
|
Marini S, Lena UK, Crawford KM, Moomaw CJ, Testai FD, Kittner SJ, James ML, Woo D, Langefeld CD, Rosand J, Anderson CD. Comparison of Genetic and Self-Identified Ancestry in Modeling Intracerebral Hemorrhage Risk. Front Neurol 2018; 9:514. [PMID: 30034361 PMCID: PMC6043667 DOI: 10.3389/fneur.2018.00514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/11/2018] [Indexed: 12/16/2022] Open
Abstract
Background: We sought to determine whether a small pool of ancestry-informative DNA markers (AIMs) improves modeling of intracerebral hemorrhage (ICH) risk in heterogeneous populations, compared with self-identified race/ethnicity (SIRE) alone. Methods: We genotyped 15 preselected AIMs to perform principal component (PC) analysis in the ERICH study (a multi-center case-control study of ICH in whites, blacks, and Hispanics). We used multivariate logistic regression and tests for independent samples to compare associations for genetic ancestry and SIRE with ICH-associated vascular risk factors (VRFs). We then compared the performance of models for ICH risk that included AIMs and SIRE alone. Results: Among 4,935 subjects, 34.7% were non-Hispanic black, 35.1% non-Hispanic white, and 30.2% Hispanic by SIRE. In stratified analysis of these SIRE groups, AIM-defined ancestry was strongly associated with seven of the eight VRFs analyzed (p < 0.001). Within each SIRE group, regression of AIM-derived PCs against VRFs confirmed independent associations of AIMs across at least two race/ethnic groups for seven VRFs. Akaike information criterion (AIC) (6,294 vs. 6,286) and likelihood ratio test (p < 0.001) showed that genetic ancestry defined by AIMs achieved a better ICH risk modeling compared to SIRE alone. Conclusion: Genetically-defined ancestry provides valuable risk exposure information that is not captured by SIRE alone. Particularly among Hispanics and blacks, inclusion of AIMs adds value over self-reported ancestry in controlling for genetic and environmental exposures that influence risk of ICH. While differences are small, this modeling approach may be superior in highly heterogeneous clinical poulations. Additional studies across other ancestries and risk exposures are needed to confirm and extend these findings.
Collapse
Affiliation(s)
- Sandro Marini
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States.,Medical and Population Genetics, Broad Institute, Cambridge, MA, United States
| | - Umme K Lena
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States.,Medical and Population Genetics, Broad Institute, Cambridge, MA, United States
| | - Katherine M Crawford
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States.,Medical and Population Genetics, Broad Institute, Cambridge, MA, United States
| | - Charles J Moomaw
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Fernando D Testai
- Department of Neurology and Rehabilitation, University of Illinois College of Medicine, Chicago, IL, United States
| | - Steven J Kittner
- Department of Neurology, Baltimore Veterans Administration Medical Center and University of Maryland School of Medicine, Baltimore, MD, United States
| | - Michael L James
- Departments of Anesthesiology and Neurology, Brain Injury Translational Research Center, Duke University, Durham, NC, United States
| | - Daniel Woo
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Carl D Langefeld
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest University, Winston-Salem, NC, United States
| | - Jonathan Rosand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States.,Medical and Population Genetics, Broad Institute, Cambridge, MA, United States.,J. Philip Kistler Stroke Research Center, Massachusetts General Hospital, Boston, MA, United States
| | - Christopher D Anderson
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States.,Medical and Population Genetics, Broad Institute, Cambridge, MA, United States
| |
Collapse
|
25
|
Affiliation(s)
- Tuure Tuunanen
- University of Jyväskylä, Faculty of Information Technology, Jyväskylä, Finland
| | - Ken Peffers
- Lee Business School, Department of Management, Entrepreneurship, and Technology, University of Nevada Las Vegas, Las Vegas, NV, US
| |
Collapse
|
26
|
Elhaik E, Yusuf L, Anderson AIJ, Pirooznia M, Arnellos D, Vilshansky G, Ercal G, Lu Y, Webster T, Baird ML, Esposito U. The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine. Genome Biol Evol 2018; 9:3225-3237. [PMID: 29165562 PMCID: PMC5726468 DOI: 10.1093/gbe/evx237] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2017] [Indexed: 12/11/2022] Open
Abstract
The human population displays wide variety in demographic history, ancestry, content of DNA derived from hominins or ancient populations, adaptation, traits, copy number variation, drug response, and more. These polymorphisms are of broad interest to population geneticists, forensics investigators, and medical professionals. Historically, much of that knowledge was gained from population survey projects. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism genotyping, their design specifications are limited and they do not allow a full exploration of biodiversity. We thereby aimed to design the Diversity of REcent and Ancient huMan (DREAM)—an all-inclusive microarray that would allow both identification of known associations and exploration of standing questions in genetic anthropology, forensics, and personalized medicine. DREAM includes probes to interrogate ancestry informative markers obtained from over 450 human populations, over 200 ancient genomes, and 10 archaic hominins. DREAM can identify 94% and 61% of all known Y and mitochondrial haplogroups, respectively, and was vetted to avoid interrogation of clinically relevant markers. To demonstrate its capabilities, we compared its FST distributions with those of the 1000 Genomes Project and commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, DREAM’s autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. DREAM performances are further illustrated in biogeographical, identical by descent, and copy number variation analyses. In summary, with approximately 800,000 markers spanning nearly 2,000 genes, DREAM is a useful tool for genetic anthropology, forensic, and personalized medicine studies.
Collapse
Affiliation(s)
- Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | - Leeban Yusuf
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | | | - Mehdi Pirooznia
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University
| | - Dimitrios Arnellos
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom.,Department of Biology, Lund University, Sweden
| | | | - Gunes Ercal
- Department of Computer Science, Southern Illinois University Edwardsville
| | - Yontao Lu
- Thermo Fisher Scientific, Santa Clara, California
| | | | | | - Umberto Esposito
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| |
Collapse
|
27
|
Mostaid MS, Lee TT, Chana G, Sundram S, Shannon Weickert C, Pantelis C, Everall I, Bousman C. Elevated peripheral expression of neuregulin-1 (NRG1) mRNA isoforms in clozapine-treated schizophrenia patients. Transl Psychiatry 2017; 7:1280. [PMID: 29225331 PMCID: PMC5802529 DOI: 10.1038/s41398-017-0041-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/13/2017] [Accepted: 09/23/2017] [Indexed: 12/18/2022] Open
Abstract
Differential expression of neuregulin-1 (NRG1) mRNA isoforms and proteins has been reported in schizophrenia, primarily in post-mortem brain tissue. In this study, we examined 12 NRG1 SNPs, eight NRG1 mRNA isoforms (type I, type I(Ig2), type II, type III, type IV, EGFα, EGFβ, pan-NRG1) in whole blood, and NRG1-β1 protein in serum of clozapine-treated schizophrenia patients (N = 71) and healthy controls (N = 57). In addition, using cultured peripheral blood mononuclear cells (PBMC) from 15 healthy individuals, we examined the effect of clozapine on NRG1 mRNA isoform and protein expression. We found elevated levels of NRG1 mRNA, specifically the EGFα (P = 0.0175), EGFβ (P = 0.002) and type I(Ig2) (P = 0.023) containing transcripts, but lower NRG1-β1 serum protein levels (P = 0.019) in schizophrenia patients compared to healthy controls. However, adjusting for smoking status attenuated the difference in NRG1-β1 serum levels (P = 0.050). Examination of clinical factors showed NRG1 EGFα (P = 0.02) and EGFβ (P = 0.02) isoform expression was negatively correlated with age of onset. However, we found limited evidence that NRG1 mRNA isoform or protein expression was associated with current chlorpromazine equivalent dose or clozapine plasma levels, the latter corroborated by our PBMC clozapine exposure experiment. Our SNP analysis found no robust expression quantitative trait loci. Our results represent the first comprehensive investigation of NRG1 isoforms and protein expression in the blood of clozapine-treated schizophrenia patients and suggest levels of some NRG1 transcripts are upregulated in those with schizophrenia.
Collapse
Affiliation(s)
- Md Shaki Mostaid
- 0000 0004 0452 651Xgrid.429299.dMelbourne Neuropsychiatry Center, Department of Psychiatry, The University of Melbourne & Melbourne Health, Parkville, VIC Australia ,The Cooperative Research Center (CRC) for Mental Health, Carlton, VIC Australia
| | - Ting Ting Lee
- 0000 0001 2179 088Xgrid.1008.9Center for Neural Engineering, Department of Electrical and Electronic Engineering, The University of Melbourne, Carlton, VIC Australia
| | - Gursharan Chana
- 0000 0001 2179 088Xgrid.1008.9Center for Neural Engineering, Department of Electrical and Electronic Engineering, The University of Melbourne, Carlton, VIC Australia ,Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC Australia ,0000 0004 0624 1200grid.416153.4Department of Medicine, Royal Melbourne Hospital, Parkville, VIC Australia
| | - Suresh Sundram
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC Australia ,NorthWestern Mental Health, Melbourne, VIC Australia ,0000 0000 9295 3933grid.419789.aDepartment of Psychiatry, School of Clinical Sciences, Monash University and Monash Health, Clayton, VIC Australia
| | - Cynthia Shannon Weickert
- 0000 0000 8696 2171grid.419558.4Schizophrenia Research Institute, Sydney, NSW Australia ,0000 0000 8900 8842grid.250407.4Schizophrenia Research Laboratory, Neuroscience Research Australia, Baker Street, Sydney, NSW Australia ,0000 0004 4902 0432grid.1005.4School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW Australia
| | - Christos Pantelis
- 0000 0004 0452 651Xgrid.429299.dMelbourne Neuropsychiatry Center, Department of Psychiatry, The University of Melbourne & Melbourne Health, Parkville, VIC Australia ,The Cooperative Research Center (CRC) for Mental Health, Carlton, VIC Australia ,0000 0001 2179 088Xgrid.1008.9Center for Neural Engineering, Department of Electrical and Electronic Engineering, The University of Melbourne, Carlton, VIC Australia ,Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC Australia ,NorthWestern Mental Health, Melbourne, VIC Australia
| | - Ian Everall
- 0000 0004 0452 651Xgrid.429299.dMelbourne Neuropsychiatry Center, Department of Psychiatry, The University of Melbourne & Melbourne Health, Parkville, VIC Australia ,The Cooperative Research Center (CRC) for Mental Health, Carlton, VIC Australia ,0000 0001 2179 088Xgrid.1008.9Center for Neural Engineering, Department of Electrical and Electronic Engineering, The University of Melbourne, Carlton, VIC Australia ,Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC Australia ,NorthWestern Mental Health, Melbourne, VIC Australia ,0000 0000 8696 2171grid.419558.4Schizophrenia Research Institute, Sydney, NSW Australia
| | - Chad Bousman
- Melbourne Neuropsychiatry Center, Department of Psychiatry, The University of Melbourne & Melbourne Health, Parkville, VIC, Australia. .,The Cooperative Research Center (CRC) for Mental Health, Carlton, VIC, Australia. .,Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia. .,Departments of Medical Genetics, Psychiatry, and Physiology & Pharmacology, University of Calgary, Calgary, AB, Canada.
| |
Collapse
|
28
|
Shraga R, Yarnall S, Elango S, Manoharan A, Rodriguez SA, Bristow SL, Kumar N, Niknazar M, Hoffman D, Ghadir S, Vassena R, Chen SH, Hershlag A, Grifo J, Puig O. Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening. BMC Genet 2017; 18:99. [PMID: 29179688 PMCID: PMC5704547 DOI: 10.1186/s12863-017-0570-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 11/16/2017] [Indexed: 11/10/2022] Open
Abstract
Background Current professional society guidelines recommend genetic carrier screening be offered on the basis of ethnicity, or when using expanded carrier screening panels, they recommend to compute residual risk based on ethnicity. We investigated the reliability of self-reported ethnicity in 9138 subjects referred to carrier screening. Self-reported ethnicity gathered from test requisition forms and during post-test genetic counseling, and genetic ancestry predicted by a statistical model, were compared for concordance. Results We identified several discrepancies between the two sources of self-reported ethnicity and genetic ancestry. Only 30.3% of individuals who indicated Mediterranean ancestry during consultation self-reported this on requisition forms. Additionally, the proportion of individuals who reported Southeast Asian but were estimated to have a different genetic ancestry was found to depend on the source of self-report. Finally, individuals who reported Latin American demonstrated a high degree of ancestral admixture. As a result, carrier rates and residual risks provided for patient decision-making are impacted if using self-reported ethnicity. Conclusion Our analysis highlights the unreliability of ethnicity classification based on patient self-reports. We recommend the routine use of pan-ethnic carrier screening panels in reproductive medicine. Furthermore, the use of an ancestry model would allow better estimation of carrier rates and residual risks. Electronic supplementary material The online version of this article (10.1186/s12863-017-0570-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Roman Shraga
- Phosphorus, Inc, 25 West 26th St, New York, NY, 10010, USA
| | | | - Sonya Elango
- Sarah Lawrence College, Bronxville, New York, USA
| | | | | | - Sara L Bristow
- Phosphorus, Inc, 25 West 26th St, New York, NY, 10010, USA.,Northwell Fertility, North Shore University Hospital, Manhasset, NY, USA
| | | | | | - David Hoffman
- IVF Florida Reproductive Associates, Margate, FL, USA
| | - Shahin Ghadir
- Department of Obstetrics and Gynecology, The David Geffen School of Medicine at UCLA, California, Los Angeles, USA
| | | | - Serena H Chen
- Institute for Reproductive Medicine and Science, Saint Barnabas Medical Center, Livingston, NJ, USA
| | - Avner Hershlag
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Hofstra Northwell School of Medicine, Manhasset, NY, USA
| | - Jamie Grifo
- Division of Reproductive Endocrinology & Infertility, Department of Obstetrics and Gynecology, NYU Langone, New York, NY, USA
| | - Oscar Puig
- Phosphorus, Inc, 25 West 26th St, New York, NY, 10010, USA.
| |
Collapse
|
29
|
Galán CA, Choe DE, Forbes EE, Shaw DS. The interaction between monoamine oxidase A and punitive discipline in the development of antisocial behavior: Mediation by maladaptive social information processing. Dev Psychopathol 2017; 29:1235-1252. [PMID: 28031080 PMCID: PMC11341723 DOI: 10.1017/s0954579416001279] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Previous studies demonstrate that boys' monoamine oxidase A (MAOA) genotype interacts with adverse rearing environments in early childhood, including punitive discipline, to predict later antisocial behavior. Yet the mechanisms by which MAOA and punitive parenting interact during childhood to amplify risk for antisocial behavior are not well understood. In the present study, hostile attributional bias and aggressive response generation during middle childhood, salient aspects of maladaptive social information processing, were tested as possible mediators of this relation in a sample of 187 low-income men followed prospectively from infancy into early adulthood. Given racial-ethnic variation in MAOA allele frequencies, analyses were conducted separately by race. In both African American and Caucasian men, those with the low-activity MAOA allele who experienced more punitive discipline at age 1.5 generated more aggressive responses to perceived threat at age 10 relative to men with the high-activity variant. In the African American subsample only, formal mediation analyses indicated a marginally significant indirect effect of maternal punitiveness on adult arrest records via aggressive response generation in middle childhood. The findings suggest that maladaptive social information processing may be an important mechanism underlying the association between MAOA × Parenting interactions and antisocial behavior in early adulthood. The present study extends previous work in the field by demonstrating that MAOA and harsh parenting assessed in early childhood interact to not only predict antisocial behavior in early adulthood, but also predict social information processing, a well-established social-cognitive correlate of antisocial behavior.
Collapse
|
30
|
Barbosa FB, Cagnin NF, Simioni M, Farias AA, Torres FR, Molck MC, Araujo TK, Gil-Da-Silva-Lopes VL, Donadi EA, Simões AL. Ancestry Informative Marker Panel to Estimate Population Stratification Using Genome-wide Human Array. Ann Hum Genet 2017; 81:225-233. [DOI: 10.1111/ahg.12208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/03/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Fernanda B. Barbosa
- Department of Genetics, Ribeirão Preto Medical School; University of São Paulo; Brazil
| | - Natalia F. Cagnin
- Department of Genetics, Ribeirão Preto Medical School; University of São Paulo; Brazil
| | - Milena Simioni
- Department of Medical Genetics, Faculty of Medical Sciences; University of Campinas; Brazil
| | - Allysson A. Farias
- Department of Genetics and Evolutionary Biology, Biosciences Institute; University of São Paulo; Brazil
| | - Fábio R. Torres
- Department of Medical Genetics, Faculty of Medical Sciences; University of Campinas; Brazil
| | - Miriam C. Molck
- Department of Medical Genetics, Faculty of Medical Sciences; University of Campinas; Brazil
| | - Tânia K. Araujo
- Department of Medical Genetics, Faculty of Medical Sciences; University of Campinas; Brazil
| | | | - Eduardo A. Donadi
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School; University of São Paulo; Brazil
| | - Aguinaldo L. Simões
- Department of Genetics, Ribeirão Preto Medical School; University of São Paulo; Brazil
| |
Collapse
|
31
|
Parejo M, Wragg D, Gauthier L, Vignal A, Neumann P, Neuditschko M. Using Whole-Genome Sequence Information to Foster Conservation Efforts for the European Dark Honey Bee, Apis mellifera mellifera. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00140] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
32
|
Rosado J, Morales S, López G, Clark D, Verdonck K, Gotuzzo E, Van Camp G, Talledo M. The FAS‐670 AA genotype is associated with high proviral load in peruvian HAM/TSP patients. J Med Virol 2016; 89:726-731. [DOI: 10.1002/jmv.24681] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Jason Rosado
- Molecular Epidemiology LaboratoryInstitute of Tropical Medicine Alexander von HumboldtUniversidad Peruana Cayetano HerediaLimaPeru
| | - Sandra Morales
- Molecular Epidemiology LaboratoryInstitute of Tropical Medicine Alexander von HumboldtUniversidad Peruana Cayetano HerediaLimaPeru
| | - Giovanni López
- Molecular Epidemiology LaboratoryInstitute of Tropical Medicine Alexander von HumboldtUniversidad Peruana Cayetano HerediaLimaPeru
| | - Daniel Clark
- Laboratories of Research and DevelopmentFaculty of ScienceUniversidad Peruana Cayetano HerediaLimaPeru
| | - Kristien Verdonck
- Department of Public HealthInstitute of Tropical MedicineAntwerpBelgium
| | - Eduardo Gotuzzo
- Faculty of MedicineUniversidad Peruana Cayetano HerediaLimaPeru
- Institute of Tropical Medicine Alexander von HumboldtUniversidad Peruana Cayetano HerediaLimaPeru
| | - Guy Van Camp
- Department of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalAntwerpBelgium
| | - Michael Talledo
- Molecular Epidemiology LaboratoryInstitute of Tropical Medicine Alexander von HumboldtUniversidad Peruana Cayetano HerediaLimaPeru
- Department of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalAntwerpBelgium
| |
Collapse
|
33
|
Eduardoff M, Gross TE, Santos C, de la Puente M, Ballard D, Strobl C, Børsting C, Morling N, Fusco L, Hussing C, Egyed B, Souto L, Uacyisrael J, Syndercombe Court D, Carracedo Á, Lareu MV, Schneider PM, Parson W, Phillips C, Parson W, Phillips C. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™. Forensic Sci Int Genet 2016; 23:178-189. [PMID: 27208666 DOI: 10.1016/j.fsigen.2016.04.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 10/21/2022]
Abstract
The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing.
Collapse
Affiliation(s)
- M Eduardoff
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - T E Gross
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - C Santos
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - D Ballard
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - C Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - L Fusco
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - C Hussing
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - B Egyed
- Department of Genetics, Faculty of Science, Eötvös Loránd University Budapest, Hungary
| | - L Souto
- Department of Biology, University of Aveiro, Aveiro, Portugal
| | - J Uacyisrael
- Fiji Police Forensic Biology and DNA Laboratory, Nasova, Suva, Fiji
| | | | - Á Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - P M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
| | | | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
| |
Collapse
|
34
|
Gitik M, Srivastava V, Hodgkinson CA, Shen PH, Goldman D, Meyerhoff DJ. Association of Superoxide Dismutase 2 (SOD2) Genotype with Gray Matter Volume Shrinkage in Chronic Alcohol Users: Replication and Further Evaluation of an Addiction Gene Panel. Int J Neuropsychopharmacol 2016; 19:pyw033. [PMID: 27207918 PMCID: PMC5043642 DOI: 10.1093/ijnp/pyw033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/01/2016] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Reduction in brain volume, especially gray matter volume, has been shown to be one of the many deleterious effects of prolonged alcohol consumption. High variance in the degree of gray matter tissue shrinkage among alcohol-dependent individuals and a previous neuroimaging genetics report suggest the involvement of environmental and/or genetic factors, such as superoxide dismutase 2 (SOD2). Identification of such underlying factors will help in the clinical management of alcohol dependence. METHODS We analyzed quantitative magnetic resonance imaging and genotype data from 103 alcohol users, including both light drinkers and treatment-seeking alcohol-dependent individuals. Genotyping was performed using a custom gene array that included genes selected from 8 pathways relevant to chronic alcohol-related brain volume loss. RESULTS We replicated a significant association of a functional SOD2 single nucleotide polymorphism with normalized gray matter volume, which had been reported previously in an independent smaller sample of alcohol-dependent individuals. The SOD2-related genetic protection was observed only at the cohort's lower drinking range. Additional associations between normalized gray matter volume and other candidate genes such as alcohol dehydrogenase gene cluster (ADH), GCLC, NOS3, and SYT1 were observed across the entire sample but did not survive corrections for multiple comparisons. CONCLUSION Converging independent evidence for a SOD2 gene association with gray matter volume shrinkage in chronic alcohol users suggests that SOD2 genetic variants predict differential brain volume loss mediated by free radicals. This study also provides the first catalog of genetic variations relevant to gray matter loss in chronic alcohol users. The identified gene-brain structure relationships are functionally pertinent and merit replication.
Collapse
Affiliation(s)
- Miri Gitik
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, NIH, Rockville, Maryland (Drs Gitik, Srivastava, and Hodgkinson, Ms Shen, and Dr Goldman); Department of Radiology and Biomedical Imaging, University of California, San Francisco, California (Dr Meyerhoff); Center for Imaging of Neurodegenerative Diseases, Veterans Administration Medical Center, San Francisco, California (Dr Meyerhoff).Current address (V.S.): Molecular Genetic Technology Program, School of Health Professions, MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030
| | - Vibhuti Srivastava
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, NIH, Rockville, Maryland (Drs Gitik, Srivastava, and Hodgkinson, Ms Shen, and Dr Goldman); Department of Radiology and Biomedical Imaging, University of California, San Francisco, California (Dr Meyerhoff); Center for Imaging of Neurodegenerative Diseases, Veterans Administration Medical Center, San Francisco, California (Dr Meyerhoff).Current address (V.S.): Molecular Genetic Technology Program, School of Health Professions, MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030
| | - Colin A Hodgkinson
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, NIH, Rockville, Maryland (Drs Gitik, Srivastava, and Hodgkinson, Ms Shen, and Dr Goldman); Department of Radiology and Biomedical Imaging, University of California, San Francisco, California (Dr Meyerhoff); Center for Imaging of Neurodegenerative Diseases, Veterans Administration Medical Center, San Francisco, California (Dr Meyerhoff).Current address (V.S.): Molecular Genetic Technology Program, School of Health Professions, MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030
| | - Pei-Hong Shen
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, NIH, Rockville, Maryland (Drs Gitik, Srivastava, and Hodgkinson, Ms Shen, and Dr Goldman); Department of Radiology and Biomedical Imaging, University of California, San Francisco, California (Dr Meyerhoff); Center for Imaging of Neurodegenerative Diseases, Veterans Administration Medical Center, San Francisco, California (Dr Meyerhoff).Current address (V.S.): Molecular Genetic Technology Program, School of Health Professions, MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030
| | - David Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, NIH, Rockville, Maryland (Drs Gitik, Srivastava, and Hodgkinson, Ms Shen, and Dr Goldman); Department of Radiology and Biomedical Imaging, University of California, San Francisco, California (Dr Meyerhoff); Center for Imaging of Neurodegenerative Diseases, Veterans Administration Medical Center, San Francisco, California (Dr Meyerhoff).Current address (V.S.): Molecular Genetic Technology Program, School of Health Professions, MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030
| | - Dieter J Meyerhoff
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, NIH, Rockville, Maryland (Drs Gitik, Srivastava, and Hodgkinson, Ms Shen, and Dr Goldman); Department of Radiology and Biomedical Imaging, University of California, San Francisco, California (Dr Meyerhoff); Center for Imaging of Neurodegenerative Diseases, Veterans Administration Medical Center, San Francisco, California (Dr Meyerhoff).Current address (V.S.): Molecular Genetic Technology Program, School of Health Professions, MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030.
| |
Collapse
|
35
|
A comparison of DMET Plus microarray and genome-wide technologies by assessing population substructure. Pharmacogenet Genomics 2016; 26:147-153. [PMID: 26731477 DOI: 10.1097/fpc.0000000000000200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
OBJECTIVE The capacity of the Affymetrix drug metabolism enzymes and transporters (DMET) Plus pharmacogenomics genotyping chip to estimate population substructure and cryptic relatedness was evaluated. The results were compared with estimates using genome-wide HapMap data for the same individuals. METHODS For 301 unrelated individuals, spanning three continental populations and one admixed population, genotypic data were collected using the Affymetrix DMET Plus microarray. Genome-wide data on these individuals were obtained from HapMap release 3. Population substructure was assessed using Eigenstrat and ADMIXTURE software for both platforms. Cryptic relatedness was explored by inbreeding coefficient estimation. Nonparametric tests were used to determine correlations of the analytical results of the two genotyping platforms. RESULTS Principal components analysis identified population substructure for both datasets, with 15.8 and 16.6% of the total variance explained in the first two principal components for DMET Plus and HapMap data, respectively. ADMIXTURE results correctly identified four subpopulations within each dataset. Nonparametric rank correlations indicated significant associations between analyses with an average ρ=0.7272 (P<10) across the three continental populations and ρ=0.4888 for the admixed population. Concordance correlation coefficients (average ρc=0.9693 across all four subpopulations) strongly indicate concordance between ADMIXTURE results. Inbreeding coefficients were slightly inflated (16 individuals>0.15) using DMET Plus data and no cryptic relatedness was indicated using HapMap data. The inflated inbreeding estimation could be because of the limited number of markers provided by DMET as a random sample of 1832 markers from HapMap also yielded inflated estimates of cryptic relatedness (39 individuals>0.15). Furthermore, use of single nucleotide polymorphisms located in genes involved in metabolism and transport may have different allele frequencies in subpopulations than single nucleotide polymorphisms sampled from the whole genome. CONCLUSION The DMET Plus pharmacogenomics genotyping chip is effective in quantifying population substructure across the three continental populations and inferring the presence of an admixed population. On the basis of our results, these microarrays offer sufficient depth for covariate adjustment of population substructure in genomic association studies.
Collapse
|
36
|
Dalvie S, King A, Fein G, Ramesar R, Stein DJ. Possible involvement of the circadian pathway in alcohol use disorder in a South African adolescent cohort. Metab Brain Dis 2016; 31:75-80. [PMID: 26446021 PMCID: PMC5478278 DOI: 10.1007/s11011-015-9744-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/04/2015] [Indexed: 11/26/2022]
Abstract
Alcoholism has an estimated heritability of between 40 and 60% and it is thought that several genes of small effect may contribute to the risk of developing this disorder. Studies of the genetics of alcohol use disorder (AUD) may, however, be confounded by issues of comorbidity. The aim of this investigation was to assess associations between variants in a range of candidate genes and AUD in a unique sample of adolescents without comorbidity. Our cohort consisted of 80 adolescents with an AUD diagnosis and 80 matched controls of mixed ancestry ethnicity. An Illumina Infinium iSelect custom 6000 bead chip was used to genotype 5348 SNPs in 378 candidate genes. Association analysis, gene-based analysis and polygenic scoring were performed. There was no statistical association between any of the investigated SNPs and AUD after correction for multiple testing. However, from the gene-based analysis it was found that the circadian rhythm genes NR1D1 and BHLHE41 are associated with AUD. While preliminary, these data provide some evidence that the circadian pathway may be relevant to the pathophysiology of AUD. Study of early onset non-comorbid populations with AUD may be useful in identifying target genes for study in larger more representative samples.
Collapse
Affiliation(s)
- Shareefa Dalvie
- MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
| | - Anthony King
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - George Fein
- Neurobehavioral Research Inc., Honolulu, HI, USA
| | - Raj Ramesar
- MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Dan J Stein
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
37
|
Webb C, Gunn JM, Potiriadis M, Everall IP, Bousman CA. The Brain-Derived Neurotrophic Factor Val66Met Polymorphism Moderates the Effects of Childhood Abuse on Severity of Depressive Symptoms in a Time-Dependent Manner. Front Psychiatry 2016; 7:151. [PMID: 27621711 PMCID: PMC5002876 DOI: 10.3389/fpsyt.2016.00151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 08/17/2016] [Indexed: 01/27/2023] Open
Abstract
Cross-sectional studies have demonstrated that the brain-derived neurotrophic factor (BDNF) Val66Met single-nucleotide polymorphism moderates the association between exposure to negative life events and depression outcomes. Yet, it is currently unclear whether this moderating effect is applicable to positive life events and if the moderating effect is stable over time. To address these gaps in the literature, we examined clinical and BDNF genotypic data from a 5-year prospective cohort of 310 primary care attendees. Primary care attendees were selected based on existence of depressive symptoms at screening. Depressive symptoms were assessed at baseline and annually for 5 years post-baseline using the Primary Care Evaluation of Mental Disorders Patient Health Questionnaire-9 (PHQ-9). Linear mixed models assessed differences in depressive symptom severity over the 5-year follow-up period by BDNF Val66Met and history of life events, both negative and positive. Analysis identified a novel three-way interaction between the BDNF Val66Met polymorphism, history of severe childhood abuse, and time. Post hoc analysis stratified by time showed a two-way interaction between Val66Met and severe childhood abuse at baseline that was not detectable at any other time point. An interaction between Val66Met and positive life events was not detected. Our longitudinal results suggest that the BDNF Val66Met polymorphism moderates the depressive symptom severity experienced by those with a history of severe childhood abuse but does so in a time-dependent manner. Our results further support the notion that gene-environment-depression interactions are dynamic and highlight the importance of longitudinal assessment of these interactions. Given these novel longitudinal findings; replication is required.
Collapse
Affiliation(s)
- Caitlin Webb
- Department of Psychiatry, The University of Melbourne , Parkville, VIC , Australia
| | - Jane M Gunn
- Department of General Practice, The University of Melbourne , Parkville, VIC , Australia
| | - Maria Potiriadis
- Department of General Practice, The University of Melbourne , Parkville, VIC , Australia
| | - Ian P Everall
- Department of Psychiatry, The University of Melbourne, Parkville, VIC, Australia; NorthWestern Mental Health, Melbourne, VIC, Australia; Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Chad A Bousman
- Department of Psychiatry, The University of Melbourne, Parkville, VIC, Australia; Department of General Practice, The University of Melbourne, Parkville, VIC, Australia; Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia; Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorne, VIC, Australia
| |
Collapse
|
38
|
Weeland J, Overbeek G, de Castro BO, Matthys W. Underlying Mechanisms of Gene-Environment Interactions in Externalizing Behavior: A Systematic Review and Search for Theoretical Mechanisms. Clin Child Fam Psychol Rev 2015; 18:413-42. [PMID: 26537239 PMCID: PMC4637001 DOI: 10.1007/s10567-015-0196-4] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the last decade, several candidate genes (i.e., MAOA, DRD4, DRD2, DAT1, 5-HTTLPR, and COMT) have been extensively studied as potential moderators of the detrimental effects of postnatal family adversity on child externalizing behaviors, such as aggression and conduct disorder. Many studies on such candidate gene by environment interactions (i.e., cG × E) have been published, and the first part of this paper offers a systematic review and integration of their findings (n = 53). The overview shows a set of heterogeneous findings. However, because of large differences between studies in terms of sample composition, conceptualizations, and power, it is difficult to determine if different findings indeed illustrate inconsistent cG × E findings or if findings are simply incomparable. In the second part of the paper, therefore, we argue that one way to help resolve this problem is the development of theory-driven a priori hypotheses on which biopsychosocial mechanisms might underlie cG × E. Such a theoretically based approach can help us specify our research strategies, create more comparable findings, and help us interpret different findings between studies. In accordance, we describe three possible explanatory mechanisms, based on extant literature on the concepts of (1) emotional reactivity, (2) reward sensitivity, and (3) punishment sensitivity. For each mechanism, we discuss the link between the putative mechanism and externalizing behaviors, the genetic polymorphism, and family adversity. Possible research strategies to test these mechanisms, and implications for interventions, are discussed.
Collapse
Affiliation(s)
- Joyce Weeland
- Utrecht Centre for Child and Adolescent Studies, Utrecht University, PO Box 15.804, 1001 NH, Amsterdam, The Netherlands.
- Research Institute of Child Development and Education, University of Amsterdam, Amsterdam, The Netherlands.
| | - Geertjan Overbeek
- Research Institute of Child Development and Education, University of Amsterdam, Amsterdam, The Netherlands
| | - Bram Orobio de Castro
- Utrecht Centre for Child and Adolescent Studies, Utrecht University, PO Box 15.804, 1001 NH, Amsterdam, The Netherlands
| | - Walter Matthys
- Department of Child and Adolescent Studies, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
39
|
Guo G, Li Y, Wang H, Cai T, Duncan G. Peer Influence, Genetic Propensity, and Binge Drinking: A Natural Experiment and a Replication. AJS; AMERICAN JOURNAL OF SOCIOLOGY 2015; 121:914-54. [PMID: 26900620 PMCID: PMC6650272 DOI: 10.1086/683224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The authors draw data from the College Roommate Study (ROOM) and the National Longitudinal Study of Adolescent Health to investigate gene-environment interaction effects on youth binge drinking. In ROOM, the environmental influence was measured by the precollege drinking behavior of randomly assigned roommates. Random assignment safeguards against friend selection and removes the threat of gene-environment correlation that makes gene-environment interaction effects difficult to interpret. On average, being randomly assigned a drinking peer as opposed to a nondrinking peer increased college binge drinking by 0.5-1.0 episodes per month, or 20%-40% the average amount of binge drinking. However, this peer influence was found only among youths with a medium level of genetic propensity for alcohol use; those with either a low or high genetic propensity were not influenced by peer drinking. A replication of the findings is provided in data drawn from Add Health. The study shows that gene-environment interaction analysis can uncover social-contextual effects likely to be missed by traditional sociological approaches.
Collapse
Affiliation(s)
- Guang Guo
- Department of Sociology, University of North Carolina at Chapel Hill, NC 27599
- Carolina Center for Genomic Sciences, University of North Carolina at Chapel Hill, NC 27599
| | - Yi Li
- Department of Sociology, University of North Carolina at Chapel Hill, NC 27599
| | - Hongyu Wang
- Department of Sociology, University of Macau, Av. Padre Tomás Pereira, Taipa, Macau
| | - Tianji Cai
- Department of Sociology, University of Macau, Av. Padre Tomás Pereira, Taipa, Macau
| | - Greg Duncan
- Department of Education, University of California, Irvine 2001 Berkeley Place Irvine, CA 92697-5500
| |
Collapse
|
40
|
Nguyen TB, Gunn JM, Potiriadis M, Everall IP, Bousman CA. Serotonin transporter polymorphism ( 5HTTLPR), severe childhood abuse and depressive symptom trajectories in adulthood. BJPsych Open 2015; 1:104-109. [PMID: 27703731 PMCID: PMC4998927 DOI: 10.1192/bjpo.bp.115.000380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 07/02/2015] [Accepted: 08/19/2015] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Cross-sectional studies suggest that the serotonin transporter promoter region polymorphism (5-HTT gene-linked polymorphic region, 5HTTLPR) moderates the relationship between childhood abuse and major depressive disorder. AIMS To examine whether the 5HTTLPR polymorphism moderates the effect childhood abuse has on 5-year depressive symptom severity trajectories in adulthood. METHOD At 5-year follow-up, DNA from 333 adult primary care attendees was obtained and genotyped for the 5HTTLPR polymorphism. Linear mixed models were used to test for a genotype × childhood abuse interaction effect on 5-year depressive symptom severity trajectories. RESULTS After covariate adjustment, homozygous s allele carriers with a history of severe childhood abuse had significantly greater depressive symptom severity at baseline compared with those without a history of severe childhood abuse and this effect persisted throughout the 5-year period of observation. CONCLUSIONS The 5HTTLPR s/s genotype robustly moderates the effects of severe childhood abuse on depressive symptom severity trajectories in adulthood. DECLARATION OF INTEREST None. COPYRIGHT AND USAGE © The Royal College of Psychiatrists 2015. This is an open access article distributed under the terms of the Creative Commons Non-Commercial, No Derivatives (CC BY-NC-ND) licence.
Collapse
Affiliation(s)
- Timothy B Nguyen
- , BS, MD, Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia
| | - Jane M Gunn
- , PhD, MBBS, Department of General Practice, The University of Melbourne, Parkville, Victoria, Australia
| | - Maria Potiriadis
- , BAppSc, GDip Clin Epi, M Prim HlthCare, Department of General Practice, The University of Melbourne, Parkville, Victoria, Australia
| | - Ian P Everall
- , BSC (Hons), MB ChB (Hons), PhD, DSc, FRCPsych, FRANZCP, FRCPath, Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia, NorthWestern Mental Health, Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Chad A Bousman
- , BS, MPH, PhD, Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia, Department of General Practice, The University of Melbourne, Parkville, Victoria, Australia, Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia and Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorne, Victoria, Australia
| |
Collapse
|
41
|
Bello L, Kesari A, Gordish-Dressman H, Cnaan A, Morgenroth LP, Punetha J, Duong T, Henricson EK, Pegoraro E, McDonald CM, Hoffman EP. Genetic modifiers of ambulation in the Cooperative International Neuromuscular Research Group Duchenne Natural History Study. Ann Neurol 2015; 77:684-96. [PMID: 25641372 PMCID: PMC4403971 DOI: 10.1002/ana.24370] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/30/2014] [Accepted: 01/21/2015] [Indexed: 12/11/2022]
Abstract
Objective We studied the effects of LTBP4 and SPP1 polymorphisms on age at loss of ambulation (LoA) in a multiethnic Duchenne muscular dystrophy (DMD) cohort. Methods We genotyped SPP1 rs28357094 and LTBP4 haplotype in 283 of 340 participants in the Cooperative International Neuromuscular Research Group Duchenne Natural History Study (CINRG-DNHS). Median ages at LoA were compared by Kaplan–Meier analysis and log-rank test. We controlled polymorphism analyses for concurrent effects of glucocorticoid corticosteroid (GC) treatment (time-varying Cox regression) and for population stratification (multidimensional scaling of genome-wide markers). Results Hispanic and South Asian participants (n = 18, 41) lost ambulation 2.7 and 2 years earlier than Caucasian subjects (p = 0.003, <0.001). The TG/GG genotype at SPP1 rs28357094 was associated to 1.2-year-earlier median LoA (p = 0.048). This difference was greater (1.9 years, p = 0.038) in GC-treated participants, whereas no difference was observed in untreated subjects. Cox regression confirmed a significant effect of SPP1 genotype in GC-treated participants (hazard ratio = 1.61, p = 0.016). LTBP4 genotype showed a direction of association with age at LoA as previously reported, but it was not statistically significant. After controlling for population stratification, we confirmed a strong effect of LTBP4 genotype in Caucasians (2.4 years, p = 0.024). Median age at LoA with the protective LTBP4 genotype in this cohort was 15.0 years, 16.0 for those who were treated with GC. Interpretation SPP1 rs28357094 acts as a pharmacodynamic biomarker of GC response, and LTBP4 haplotype modifies age at LoA in the CINRG-DNHS cohort. Adjustment for GC treatment and population stratification appears crucial in assessing genetic modifiers in DMD.
Collapse
Affiliation(s)
- Luca Bello
- Children's National Medical Center, Washington, DC; Department of Neuroscience (Neurological, Psychiatric, Sensory, Reconstructive, Rehabilitative Science), University of Padua, Padua, Italy
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Handelman SK, Aaronson JM, Seweryn M, Voronkin I, Kwiek JJ, Sadee W, Verducci JS, Janies DA. Cladograms with Path to Event (ClaPTE): a novel algorithm to detect associations between genotypes or phenotypes using phylogenies. Comput Biol Med 2015; 58:1-13. [PMID: 25577610 PMCID: PMC4331246 DOI: 10.1016/j.compbiomed.2014.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 12/09/2014] [Accepted: 12/15/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Associations between genotype and phenotype provide insight into the evolution of pathogenesis, drug resistance, and the spread of pathogens between hosts. However, common ancestry can lead to apparent associations between biologically unrelated features. The novel method Cladograms with Path to Event (ClaPTE) detects associations between character-pairs (either a pair of mutations or a mutation paired with a phenotype) while adjusting for common ancestry, using phylogenetic trees. METHODS ClaPTE tests for character-pairs changing close together on the phylogenetic tree, consistent with an associated character-pair. ClaPTE is compared to three existing methods (independent contrasts, mixed model, and likelihood ratio) to detect character-pair associations adjusted for common ancestry. Comparisons utilize simulations on gene trees for: HIV Env, HIV promoter, and bacterial DnaJ and GuaB; and case studies for Oseltamavir resistance in Influenza, and for DnaJ and GuaB. Simulated data include both true-positive/associated character-pairs, and true-negative/not-associated character-pairs, used to assess type I (frequency of p-values in true-negatives) and type II (sensitivity to true-positives) error control. RESULTS AND CONCLUSIONS ClaPTE has competitive sensitivity and better type I error control than existing methods. In the Influenza/Oseltamavir case study, ClaPTE reports no new permissive mutations but detects associations between adjacent (in primary sequence) amino acid positions which other methods miss. In the DnaJ and GuaB case study, ClaPTE reports more frequent associations between positions both from the same protein family than between positions from different families, in contrast to other methods. In both case studies, the results from ClaPTE are biologically plausible.
Collapse
Affiliation(s)
- Samuel K Handelman
- Department of Pharmacology, Ohio State University College of Medicine, 5072 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, United States; Mathematical Biosciences Institute, The Ohio State University, Jennings Hall 3rd Floor, 1735 Neil Avenue, Columbus, OH 43210, United States.
| | - Jacob M Aaronson
- Department of Biomedical Informatics, Ohio State University College of Medicine, 3190 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, United States
| | - Michal Seweryn
- Mathematical Biosciences Institute, The Ohio State University, Jennings Hall 3rd Floor, 1735 Neil Avenue, Columbus, OH 43210, United States
| | - Igor Voronkin
- Department of Biomedical Informatics, Ohio State University College of Medicine, 3190 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, United States
| | - Jesse J Kwiek
- Department of Microbial Infection & Immunity and Department of Microbiology, The Ohio State University, 788 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210, United States
| | - Wolfgang Sadee
- Department of Pharmacology, Ohio State University College of Medicine, 5072 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, United States
| | - Joseph S Verducci
- Department of Statistics, The Ohio State University, 404 Cockins Hall, 1958 Neil Avenue, Columbus, OH 43210-1247, United States
| | - Daniel A Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223-0001, United States
| |
Collapse
|
43
|
Liu H, Li Y, Guo G. Gene by Social-Environment Interaction for Youth Delinquency and Violence: Thirty-Nine Aggression-related Genes. ACTA ACUST UNITED AC 2014; 93:881-903. [PMID: 25755300 DOI: 10.1093/sf/sou086] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Complex human traits are likely to be affected by many environmental and genetic factors, and the interactions among them. However, previous gene-environment interaction (G×E) studies have typically focused on one or only a few genetic variants at a time. To provide a broader view of G×E, this study examines the relationship between 403 genetic variants from 39 genes and youth delinquency and violence. We find evidence that low social control is associated with greater genetic risk for delinquency and violence and high/moderate social control with smaller genetic risk for delinquency and violence. Our findings are consistent with prior G×E studies based on a small number of genetic variants, and, more importantly, we show that these findings still hold when a large number of genetic variants are considered simultaneously. A key implication of these findings is that the expression of multiple genes related to delinquency depends on the social environment: gene expression is likely to be amplified in low-social-control environments but, tends to be suppressed in high/moderate-social-control environments. This study not only deepens our understanding of how the social environment shapes individual behavior, but also provides important conceptual and methodological insights for future G×E research on complex human traits.
Collapse
Affiliation(s)
- Hexuan Liu
- Department of Sociology, the University of North Carolina at Chapel Hill ; Carolina Population Center, the University of North Carolina at Chapel Hill
| | - Yi Li
- Department of Sociology, the University of North Carolina at Chapel Hill
| | - Guang Guo
- Department of Sociology, the University of North Carolina at Chapel Hill ; Carolina Center for Genome Sciences, the University of North Carolina at Chapel Hill ; Carolina Population Center, the University of North Carolina at Chapel Hill
| |
Collapse
|
44
|
Guo G, Fu Y, Lee H, Cai T, Mullan Harris K, Li Y. Genetic bio-ancestry and social construction of racial classification in social surveys in the contemporary United States. Demography 2014; 51:141-72. [PMID: 24019100 DOI: 10.1007/s13524-013-0242-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Self-reported race is generally considered the basis for racial classification in social surveys, including the U.S. census. Drawing on recent advances in human molecular genetics and social science perspectives of socially constructed race, our study takes into account both genetic bio-ancestry and social context in understanding racial classification. This article accomplishes two objectives. First, our research establishes geographic genetic bio-ancestry as a component of racial classification. Second, it shows how social forces trump biology in racial classification and/or how social context interacts with bio-ancestry in shaping racial classification. The findings were replicated in two racially and ethnically diverse data sets: the College Roommate Study (N = 2,065) and the National Longitudinal Study of Adolescent Health (N = 2,281).
Collapse
Affiliation(s)
- Guang Guo
- Department of Sociology and Carolina Population Center, University of North Carolina, CB#3210, Chapel Hill, NC, 27599-3210, USA,
| | | | | | | | | | | |
Collapse
|
45
|
Kennedy AE, Kamdar KY, Lupo PJ, Okcu MF, Scheurer ME, Dorak MT. Genetic markers in a multi-ethnic sample for childhood acute lymphoblastic leukemia risk. Leuk Lymphoma 2014; 56:169-74. [DOI: 10.3109/10428194.2014.910662] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
46
|
Progress toward an efficient panel of SNPs for ancestry inference. Forensic Sci Int Genet 2014; 10:23-32. [DOI: 10.1016/j.fsigen.2014.01.002] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 01/31/2023]
|
47
|
Nelson BD, Bishop JR, Sarapas C, Kittles RA, Shankman SA. Asians demonstrate reduced sensitivity to unpredictable threat: a preliminary startle investigation using genetic ancestry in a multiethnic sample. ACTA ACUST UNITED AC 2014; 14:615-23. [PMID: 24708496 DOI: 10.1037/a0035776] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Research has indicated that individuals of Asian descent, relative to other racial groups, demonstrate reduced emotional responding and lower prevalence rates of several anxiety disorders. It is unclear though whether these group differences extend to biomarkers of anxiety disorders and whether genetic differences play a role. This study compared self-identified Caucasian, Latino, and Asian persons (total N = 174) on startle response during a baseline period and while anticipating unpredictable threat-a putative biomarker for certain anxiety disorders--as well as predictable threat. In addition, the association between genetic ancestry and startle response was examined within each racial group to determine potential genetic influences on responding. For the baseline period, Asian participants exhibited a smaller startle response relative to Caucasian and Latino participants, who did not differ. Within each racial group, genetic ancestry was associated with baseline startle. Furthermore, genetic ancestry mediated racial group differences in baseline startle. For the threat conditions, a Race × Condition interaction indicated that Asian participants exhibited reduced startle potentiation to unpredictable, but not predicable, threat relative to Caucasian and Latino participants, who did not differ. However, genetic ancestry was not associated with threat-potentiated startle in any racial group. This study adds to the growing literature on racial differences in emotional responding and provides preliminary evidence suggesting that genetic ancestry may play an important role. Moreover, reduced sensitivity to unpredictable threat may reflect a mechanism for why individuals of Asian descent are at less risk for particular anxiety disorders relative to other racial groups.
Collapse
|
48
|
Levran O, Peles E, Randesi M, Shu X, Ott J, Shen PH, Adelson M, Kreek MJ. Association of genetic variation in pharmacodynamic factors with methadone dose required for effective treatment of opioid addiction. Pharmacogenomics 2014; 14:755-68. [PMID: 23651024 DOI: 10.2217/pgs.13.58] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AIM The interindividual variability in the dose required for effective methadone maintenance treatment (MMT) for opioid addiction may be influenced in part by genetic variations in genes encoding pharmacodynamic factors of methadone. This study was conducted to identify some of these variants. MATERIALS & METHODS This study focused on 11 genes encoding components of the opioidergic (OPRM1, POMC and ARRB2), the dopaminergic (ANKK1 and DRD2) and the glutamatergic pathways (GRIN1 and GRIN2A), as well as the neurotrophin system (NGFB, BDNF, NTRK1 and NTRK2). The study includes 227 Israeli patients undergoing stable MMT. RESULTS Out of the 110 variants analyzed, 12 SNPs (in BDNF, NTRK2, OPRM1, DRD2 and ANKK1) were associated with methadone dose (nominal p < 0.05). Of these SNPs, ANKK1 rs7118900 and DRD2 rs2283265 are known to affect gene expression. Logistic regression of five representative SNPs discriminated between individuals requiring a methadone dose of >120 mg/day and <120 mg/day (p = 0.019), and showed moderate sensitivity and specificity (AUC of 0.63 in receiver operating characteristic analysis). CONCLUSION This data should stimulate further research on the potential influence and clinical significance of these variants on MMT.
Collapse
Affiliation(s)
- Orna Levran
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, NY, USA.
| | | | | | | | | | | | | | | |
Collapse
|
49
|
The promise of immunogenomics at the bedside: genetic risk of intra-abdominal candidiasis*. Crit Care Med 2014; 42:1019-20. [PMID: 24633117 DOI: 10.1097/ccm.0000000000000252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
50
|
Li Y, Guo G. Data quality control in social surveys using genetic information. BIODEMOGRAPHY AND SOCIAL BIOLOGY 2014; 60:212-228. [PMID: 25343368 PMCID: PMC6642059 DOI: 10.1080/19485565.2014.953029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This article introduces a novel way of taking advantage of genetic data in social surveys for the purposes of data quality control. Genetic information could detect and repair data issues such as missing data, reporting errors, differences in measures of the same variable, and flawed data. Using data from two surveys, the College Roommate Study (ROOM) and the National Longitudinal Study of Adolescent Health (Add Health), we show that proportion identical by descent score (a measure of genetic relationships) can identify "misreported" and unreported sibling type and detect misrepresented participants, bio-ancestry score (a measure of ancestral population memberships) can repair and recover missing race and discrepancies among different measures of self-reported race, and sex chromosomal information may help cross-check self-reported sex. This article represents an initial effort to utilize genetic data for the purposes of data quality control. As genetic data become increasingly available, researchers may explore more approaches to improving data quality.
Collapse
Affiliation(s)
- Yi Li
- Department of Sociology, University of North Carolina at Chapel Hill
| | - Guang Guo
- Department of Sociology, University of North Carolina at Chapel Hill
- Carolina Population Center, University of North Carolina at Chapel Hill
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill
| |
Collapse
|