1
|
Kim JH, Lee BD, Park JM, Lee YM, Moon E, Suh H, Kim K, Kim YJ, Lee HJ, Oh HY. Family-based genome-wide association analysis of novelty seeking in a Korean schizophrenic population: A pilot study. Medicine (Baltimore) 2024; 103:e38694. [PMID: 38941432 DOI: 10.1097/md.0000000000038694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/30/2024] Open
Abstract
Schizophrenia (SPR) is the most devastating mental illness that causes severe deterioration in social and occupational functioning, but, the etiology remains unknown. The objective of this study is to explore the genetic underpinnings of novelty seeking behavior in schizophrenic family within the Korean population. By conducting a family-based genome-wide association study, we aim to identify potential genetic markers and variations associated with novelty seeking traits in the context of SPR. We have recruited 27 probands (with SPR) with their parents and siblings whenever possible. DNA was extracted from blood sampling of 58 individuals in 27 families and analyzed in an Illumina core exome single nucleotide polymorphism (SNP) array. A family-based association test (qFAM) was used to derive SNP association values across all chromosomes. Although none of the final 800,000 SNPs reached the genome-wide significant threshold of 8.45 × 10-7, the most significant 4 SNPs were within the 10-5 to 10-7. This study identifies genetic associations between novelty seeking behavior and SPR within families. RAPGEF5 emerges as a significant gene, along with other neuropsychiatric-related genes. Noteworthy genes like DRD4 and COMT did not show associations, possibly due to the focus on schizophrenic family. While shedding light on this complex relationship, larger studies are needed for robust conclusions and deeper mechanistic insights.
Collapse
Affiliation(s)
- Ji Hye Kim
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Byung Dae Lee
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
- Department of Psychiatry, Pusan National University College of Medicine, Kyungnam, South Korea
| | - Je Min Park
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
- Department of Psychiatry, Pusan National University College of Medicine, Kyungnam, South Korea
| | - Young Min Lee
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
- Department of Psychiatry, Pusan National University College of Medicine, Kyungnam, South Korea
| | - Eunsoo Moon
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
- Department of Psychiatry, Pusan National University College of Medicine, Kyungnam, South Korea
| | - Hwagyu Suh
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Kyungwon Kim
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Yoo Jun Kim
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Hyun Ji Lee
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Ha Young Oh
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| |
Collapse
|
2
|
Recto K, Kachroo P, Huan T, Van Den Berg D, Lee GY, Bui H, Lee DH, Gereige J, Yao C, Hwang SJ, Joehanes R, Weiss ST, O'Connor GT, Levy D, DeMeo DL. Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthma. EBioMedicine 2023; 95:104758. [PMID: 37598461 PMCID: PMC10462855 DOI: 10.1016/j.ebiom.2023.104758] [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: 03/14/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND Identifying novel epigenetic signatures associated with serum immunoglobulin E (IgE) may improve our understanding of molecular mechanisms underlying asthma and IgE-mediated diseases. METHODS We performed an epigenome-wide association study using whole blood from Framingham Heart Study (FHS; n = 3,471, 46% females) participants and validated results using the Childhood Asthma Management Program (CAMP; n = 674, 39% females) and the Genetic Epidemiology of Asthma in Costa Rica Study (CRA; n = 787, 41% females). Using the closest gene to each IgE-associated CpG, we highlighted biologically plausible pathways underlying IgE regulation and analyzed the transcription patterns linked to IgE-associated CpGs (expression quantitative trait methylation loci; eQTMs). Using prior UK Biobank summary data from genome-wide association studies of asthma and allergy, we performed Mendelian randomization (MR) for causal inference testing using the IgE-associated CpGs from FHS with methylation quantitative trait loci (mQTLs) as instrumental variables. FINDINGS We identified 490 statistically significant differentially methylated CpGs associated with IgE in FHS, of which 193 (39.3%) replicated in CAMP and CRA (FDR < 0.05). Gene ontology analysis revealed enrichment in pathways related to transcription factor binding, asthma, and other immunological processes. eQTM analysis identified 124 cis-eQTMs for 106 expressed genes (FDR < 0.05). MR in combination with drug-target analysis revealed CTSB and USP20 as putatively causal regulators of IgE levels (Bonferroni adjusted P < 7.94E-04) that can be explored as potential therapeutic targets. INTERPRETATION By integrating eQTM and MR analyses in general and clinical asthma populations, our findings provide a deeper understanding of the multidimensional inter-relations of DNA methylation, gene expression, and IgE levels. FUNDING US NIH/NHLBI grants: P01HL132825, K99HL159234. N01-HC-25195 and HHSN268201500001I.
Collapse
Affiliation(s)
- Kathryn Recto
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Priyadarshini Kachroo
- Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, MA 02115, USA
| | - Tianxiao Huan
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - David Van Den Berg
- University of Southern California Methylation Characterization Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Gha Young Lee
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Helena Bui
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Dong Heon Lee
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Jessica Gereige
- Boston University School of Medicine, Pulmonary Center, Boston, MA 02118, USA
| | - Chen Yao
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Shih-Jen Hwang
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Roby Joehanes
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Scott T Weiss
- Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, MA 02115, USA
| | - George T O'Connor
- The Framingham Heart Study, Framingham, MA 01702, USA; Boston University School of Medicine, Pulmonary Center, Boston, MA 02118, USA
| | - Daniel Levy
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA.
| | - Dawn L DeMeo
- Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, MA 02115, USA.
| |
Collapse
|
3
|
Kachroo P, Hecker J, Chawes BL, Ahluwalia TS, Cho MH, Qiao D, Kelly RS, Chu SH, Virkud YV, Huang M, Barnes KC, Burchard EG, Eng C, Hu D, Celedón JC, Daya M, Levin AM, Gui H, Williams LK, Forno E, Mak ACY, Avila L, Soto-Quiros ME, Cloutier MM, Acosta-Pérez E, Canino G, Bønnelykke K, Bisgaard H, Raby BA, Lange C, Weiss ST, Lasky-Su JA. Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children With Asthma. Chest 2019; 156:1068-1079. [PMID: 31557467 PMCID: PMC6904857 DOI: 10.1016/j.chest.2019.08.2202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/02/2019] [Accepted: 08/22/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Asthma is a common respiratory disorder with a highly heterogeneous nature that remains poorly understood. The objective was to use whole genome sequencing (WGS) data to identify regions of common genetic variation contributing to lung function in individuals with a diagnosis of asthma. METHODS WGS data were generated for 1,053 individuals from trios and extended pedigrees participating in the family-based Genetic Epidemiology of Asthma in Costa Rica study. Asthma affection status was defined through a physician's diagnosis of asthma, and most participants with asthma also had airway hyperresponsiveness (AHR) to methacholine. Family-based association tests for single variants were performed to assess the associations with lung function phenotypes. RESULTS A genome-wide significant association was identified between baseline FEV1/FVC ratio and a single-nucleotide polymorphism in the top hit cysteine-rich secretory protein LCCL domain-containing 2 (CRISPLD2) (rs12051168; P = 3.6 × 10-8 in the unadjusted model) that retained suggestive significance in the covariate-adjusted model (P = 5.6 × 10-6). Rs12051168 was also nominally associated with other related phenotypes: baseline FEV1 (P = 3.3 × 10-3), postbronchodilator (PB) FEV1 (7.3 × 10-3), and PB FEV1/FVC ratio (P = 2.7 × 10-3). The identified baseline FEV1/FVC ratio and rs12051168 association was meta-analyzed and replicated in three independent cohorts in which most participants with asthma also had confirmed AHR (combined weighted z-score P = .015) but not in cohorts without information about AHR. CONCLUSIONS These findings suggest that using specific asthma characteristics, such as AHR, can help identify more genetically homogeneous asthma subgroups with genotype-phenotype associations that may not be observed in all children with asthma. CRISPLD2 also may be important for baseline lung function in individuals with asthma who also may have AHR.
Collapse
Affiliation(s)
- Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Julian Hecker
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Bo L Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Tarunveer S Ahluwalia
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Rachel S Kelly
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Su H Chu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Yamini V Virkud
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Department of Pediatrics, Massachusetts General Hospital for Children and Harvard Medical School, Boston, MA
| | - Mengna Huang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Colorado, CO
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Colorado, CO
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI; Center for Bioinformatics, Henry Ford Health System, Detroit, MI
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research, Henry Ford Health System, Detroit, MI; Department of Internal Medicine, Henry Ford Health System, Detroit, MI
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research, Henry Ford Health System, Detroit, MI; Department of Internal Medicine, Henry Ford Health System, Detroit, MI
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA
| | - Angel C Y Mak
- Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Lydiana Avila
- Department of Pediatrics, Hospital Nacional de Niños, San José, Costa Rica
| | | | | | - Edna Acosta-Pérez
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Glorisa Canino
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin A Raby
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA.
| |
Collapse
|
4
|
Lee KY, Lee BD, Park JM, Lee YM, Moon E, Jeong HJ, Kim SY, Suh H, Chung YI, Kim SC. Investigation of Maternal Effects, Maternal-Fetal Interactions, and Parent-of-Origin Effects (Imprinting) for Candidate Genes Positioned on Chromosome 18q21, in Probands with Schizophrenia and their First-Degree Relatives. Psychiatry Investig 2019; 16:450-458. [PMID: 31247704 PMCID: PMC6603700 DOI: 10.30773/pi.2019.04.12] [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: 06/25/2018] [Accepted: 04/12/2019] [Indexed: 12/04/2022] Open
Abstract
OBJECTIVE A popular design for the investigation of such effects, including effects of parent-of-origin (imprinting), maternal genotype, and maternal-fetal genotype interactions, is to collect deoxyribonucleic acid (DNA) from affected offspring and their mothers and to compare with an appropriate control sample. We investigate the effects of estimation of maternal, imprinting and interaction effects using multimodal modeling using parents and their offspring with schizophrenia in Korean population. METHODS We have recruited 27 probands (with schizophrenia) with their parents and siblings whenever possible. We analyzed 20 SNPs of 7 neuronal genes in chromosome 18. We used EMIM analysis program for the estimation of maternal, imprinting and interaction effects using multimodal modeling. RESULTS Of analyzed 20 single nucleotide polymorphisms (SNPs), significant SNP (rs 2276186) was suggested in EMIM analysis for child genetics effects (p=0.0225438044) and child genetic effects allowing for maternal genetic effects (p=0.0209453210) with very stringent multiple comparison Bonferroni correction. CONCLUSION Our results are the pilot study for epigenetic study in mental disorder and help to understanding and use of EMIM statistical genetics analysis program with many limitations including small pedigree numbers.
Collapse
Affiliation(s)
- Kang Yoon Lee
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Byung Dae Lee
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea.,Department of Psychiatry, Pusan National University College of Medicine, Busan, Republic of Korea
| | - Je Min Park
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea.,Department of Psychiatry, Pusan National University College of Medicine, Busan, Republic of Korea
| | - Young Min Lee
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea.,Department of Psychiatry, Pusan National University College of Medicine, Busan, Republic of Korea
| | - Eunsoo Moon
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea.,Department of Psychiatry, Pusan National University College of Medicine, Busan, Republic of Korea
| | - Hee Jeong Jeong
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Soo Yeon Kim
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Hwagyu Suh
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Young In Chung
- Department of Psychiatry, Pusan National University College of Medicine, Busan, Republic of Korea
| | - Seung Chul Kim
- Department of Obstetrics and Gynecology, Pusan National University Hospital, Busan, Republic of Korea
| |
Collapse
|
5
|
Mooney JA, Huber CD, Service S, Sul JH, Marsden CD, Zhang Z, Sabatti C, Ruiz-Linares A, Bedoya G, Freimer N, Lohmueller KE. Understanding the Hidden Complexity of Latin American Population Isolates. Am J Hum Genet 2018; 103:707-726. [PMID: 30401458 PMCID: PMC6218714 DOI: 10.1016/j.ajhg.2018.09.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 09/26/2018] [Indexed: 12/12/2022] Open
Abstract
Most population isolates examined to date were founded from a single ancestral population. Consequently, there is limited knowledge about the demographic history of admixed population isolates. Here we investigate genomic diversity of recently admixed population isolates from Costa Rica and Colombia and compare their diversity to a benchmark population isolate, the Finnish. These Latin American isolates originated during the 16th century from admixture between a few hundred European males and Amerindian females, with a limited contribution from African founders. We examine whole-genome sequence data from 449 individuals, ascertained as families to build mutigenerational pedigrees, with a mean sequencing depth of coverage of approximately 36×. We find that Latin American isolates have increased genetic diversity relative to the Finnish. However, there is an increase in the amount of identity by descent (IBD) segments in the Latin American isolates relative to the Finnish. The increase in IBD segments is likely a consequence of a very recent and severe population bottleneck during the founding of the admixed population isolates. Furthermore, the proportion of the genome that falls within a long run of homozygosity (ROH) in Costa Rican and Colombian individuals is significantly greater than that in the Finnish, suggesting more recent consanguinity in the Latin American isolates relative to that seen in the Finnish. Lastly, we find that recent consanguinity increased the number of deleterious variants found in the homozygous state, which is relevant if deleterious variants are recessive. Our study suggests that there is no single genetic signature of a population isolate.
Collapse
Affiliation(s)
- Jazlyn A Mooney
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Christian D Huber
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Susan Service
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jae Hoon Sul
- Department of Psychiatry and Biobehavioral Sciences, Semel Center for Informatics and Personalized Genomics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Clare D Marsden
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Zhongyang Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chiara Sabatti
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China; Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - Gabriel Bedoya
- Genética Molecular (GENMOL), Universidad de Antioquia, Medellín, Colombia
| | - Nelson Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kirk E Lohmueller
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
6
|
Healy ME, Hill D, Berwick M, Edgar H, Gross J, Hunley K. Social-group identity and population substructure in admixed populations in New Mexico and Latin America. PLoS One 2017; 12:e0185503. [PMID: 28977000 PMCID: PMC5627912 DOI: 10.1371/journal.pone.0185503] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/13/2017] [Indexed: 12/13/2022] Open
Abstract
We examined the relationship between continental-level genetic ancestry and racial and ethnic identity in an admixed population in New Mexico with the goal of increasing our understanding of how racial and ethnic identity influence genetic substructure in admixed populations. Our sample consists of 98 New Mexicans who self-identified as Hispanic or Latino (NM-HL) and who further categorized themselves by race and ethnic subgroup membership. The genetic data consist of 270 newly-published autosomal microsatellites from the NM-HL sample and previously published data from 57 globally distributed populations, including 13 admixed samples from Central and South America. For these data, we 1) summarized the major axes of genetic variation using principal component analyses, 2) performed tests of Hardy Weinberg equilibrium, 3) compared empirical genetic ancestry distributions to those predicted under a model of admixture that lacked substructure, 4) tested the hypotheses that individuals in each sample had 100%, 0%, and the sample-mean percentage of African, European, and Native American ancestry. We found that most NM-HL identify themselves and their parents as belonging to one of two groups, conforming to a region-specific narrative that distinguishes recent immigrants from Mexico from individuals whose families have resided in New Mexico for generations and who emphasize their Spanish heritage. The “Spanish” group had significantly lower Native American ancestry and higher European ancestry than the “Mexican” group. Positive FIS values, PCA plots, and heterogeneous ancestry distributions suggest that most Central and South America admixed samples also contain substructure, and that this substructure may be related to variation in social identity. Genetic substructure appears to be common in admixed populations in the Americas and may confound attempts to identify disease-causing genes and to understand the social causes of variation in health outcomes and social inequality.
Collapse
Affiliation(s)
- Meghan E. Healy
- Department of Anthropology, University of New Mexico, Albuquerque, NM, United States of America
| | - Deirdre Hill
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM, United States of America
| | - Marianne Berwick
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM, United States of America
| | - Heather Edgar
- Department of Anthropology, University of New Mexico, Albuquerque, NM, United States of America
| | - Jessica Gross
- Department of Anthropology, University of New Mexico, Albuquerque, NM, United States of America
| | - Keith Hunley
- Department of Anthropology, University of New Mexico, Albuquerque, NM, United States of America
- * E-mail:
| |
Collapse
|
7
|
Ancestry variation and footprints of natural selection along the genome in Latin American populations. Sci Rep 2016; 6:21766. [PMID: 26887503 PMCID: PMC4757894 DOI: 10.1038/srep21766] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 01/25/2016] [Indexed: 02/08/2023] Open
Abstract
Latin American populations stem from the admixture of Europeans, Africans and Native Americans, which started over 400 years ago and had lasted for several centuries. Extreme deviation over the genome-wide average in ancestry estimations at certain genomic locations could reflect recent natural selection. We evaluated the distribution of ancestry estimations using 678 genome-wide microsatellite markers in 249 individuals from 13 admixed populations across Latin America. We found significant deviations in ancestry estimations including three locations with more than 3.5 times standard deviations from the genome-wide average: an excess of European ancestry at 1p36 and 14q32, and an excess of African ancestry at 6p22. Using simulations, we could show that at least the deviation at 6p22 was unlikely to result from genetic drift alone. By applying different linguistic groups as well as the most likely ancestral Native American populations as the ancestry, we showed that the choice of Native American ancestry could affect the local ancestry estimation. However, the signal at 6p22 consistently appeared in most of the analyses using various ancestral groups. This study provided important insights for recent natural selection in the context of the unique history of the New World and implications for disease mapping.
Collapse
|
8
|
Cho MJ, Lee BD, Kim C. Pilot study for family-based association analysis of schizophrenia in a Korean population: Analysis for candidate genes positionally on chromosome 18q21. Asia Pac Psychiatry 2015; 7:268-75. [PMID: 25504777 DOI: 10.1111/appy.12167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 10/27/2014] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Schizophrenia is the most devastating mental illness that causes severe deterioration in social and occupational functioning. This is a pilot study for family-based association analysis of schizophrenia in a Korean population to search candidate genes functionally relevant and positionally on chromosome 18. METHODS We have recruited 27 probands (with psychosis) with their parents and siblings whenever possible. We analyzed 20 SNPs (Single Nucleotide Polymorphism) of seven neuronal genes in chromosome 18 for DNA samples that was checked for the data quality and genotype error. For testing of association, we performed family-based association tests analyses with each individual SNP, using the phenotype of psychosis. And then, we performed family-based association tests haplotype analyses with each individual SNP, using the phenotype of psychosis. Finally, we performed linkage disequilibrium analyses for the phenotype of schizophrenia. RESULTS We found one significant SNPs of one neuronal gene in chromosome 18 (P value < 0.05) for the qualitative phenotype of psychosis (rs1893490:MAPK4). We also found significant haplotypes of four SNPs in mitogen-activated protein kinase 4 (MAPK4) gene of chromosome 18 (P value < 0.1) for the phenotype of psychosis (rs1893490-rs3892158-rs3752088-rs3794899). Two SNPS within the MAPK4 gene (rs3794899, rs3794901), plus SNPs within the malic enzyme 2 (rs685533, rs12277), and SMAD4 genes (rs8096092, rs2298617) were in strong linkage disequilibrium with each other (D' > 0.60). DISCUSSION The present findings provide convergent evidence (fine mapping of a chromosomal locus 18q21 associated with schizophrenia) suggesting that a specific MAPK4 could be a candidate gene for causing a spectrum of schizophrenia phenotype.
Collapse
Affiliation(s)
- Min Jung Cho
- Department of Pediatrics, Pusan National University Hospital, Busan, South Korea.,Medical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Byung Dae Lee
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea.,Department of Psychiatry, Pusan National University College of Medicine, Kyungnam, Republic of Korea.,Medical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Choongrak Kim
- Department of Statistics, Pusan National University, Busan, Republic of Korea
| |
Collapse
|
9
|
Peskin VA, Ordóñez A, Mackin RS, Delucchi K, Monge S, McGough JJ, Chavira DA, Berrocal M, Cheung E, Fournier E, Badner JA, Herrera LD, Mathews CA. Neuropsychological and dimensional behavioral trait profiles in Costa Rican ADHD sib pairs: Potential intermediate phenotypes for genetic studies. Am J Med Genet B Neuropsychiatr Genet 2015; 168B:247-57. [PMID: 25832558 PMCID: PMC4437811 DOI: 10.1002/ajmg.b.32305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 02/12/2015] [Indexed: 01/19/2023]
Abstract
Attention deficit hyperactivity disorder (ADHD) is associated with substantial functional impairment in children and in adults. Many individuals with ADHD have clear neurocognitive deficits, including problems with visual attention, processing speed, and set shifting. ADHD is etiologically complex, and although genetic factors play a role in its development, much of the genetic contribution to ADHD remains unidentified. We conducted clinical and neuropsychological assessments of 294 individuals (269 with ADHD) from 163 families (48 multigenerational families created using genealogical reconstruction, 78 affected sib pair families, and 37 trios) from the Central Valley of Costa Rica (CVCR). We used principal components analysis (PCA) to group neurocognitive and behavioral variables using the subscales of the Child Behavior Checklist (CBCL) and 15 neuropsychological measures, and created quantitative traits for heritability analyses. We identified seven cognitive and two behavioral domains. Individuals with ADHD were significantly more impaired than their unaffected siblings on most behavioral and cognitive domains. The verbal IQ domain had the highest heritability (92%), followed by auditory attention (87%), visual processing speed and problem solving (85%), and externalizing symptoms (81%). The quantitative traits identified here have high heritabilities, similar to the reported heritability of ADHD (70-90%), and may represent appropriate alternative phenotypes for genetic studies. The use of multigenerational families from a genetically isolated population may facilitate the identification of ADHD risk genes in the face of phenotypic and genetic heterogeneity.
Collapse
Affiliation(s)
- Viviana A. Peskin
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA
| | - Anna Ordóñez
- Child Psychiatry Branch, National Institute of Mental Health, Bethesda, Maryland
| | - R. Scott Mackin
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA
| | - Kevin Delucchi
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA
| | - Silvia Monge
- Department of Psychiatry, Hospital CIMA, San José, Costa Rica
| | - James J. McGough
- Department of Psychiatry, University of California, Los Angeles, Los Angeles, CA
| | - Denise A. Chavira
- Department of Psychology, University of California, Los Angeles, Los Angeles, CA
| | - Monica Berrocal
- Department of Psychiatry, Hospital CIMA, San José, Costa Rica
| | - Erika Cheung
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA
| | | | - Judith A. Badner
- Departments of Psychiatry and Human Genetics, University of Chicago, Chicago, Illinois
| | | | - Carol A. Mathews
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| |
Collapse
|
10
|
Fears SC, Service SK, Kremeyer B, Araya C, Araya X, Bejarano J, Ramirez M, Castrillón G, Gomez-Franco J, Lopez MC, Montoya G, Montoya P, Aldana I, Teshiba TM, Abaryan Z, Al-Sharif NB, Ericson M, Jalbrzikowski M, Luykx JJ, Navarro L, Tishler TA, Altshuler L, Bartzokis G, Escobar J, Glahn DC, Ospina-Duque J, Risch N, Ruiz-Linares A, Thompson PM, Cantor RM, Lopez-Jaramillo C, Macaya G, Molina J, Reus VI, Sabatti C, Freimer NB, Bearden CE. Multisystem component phenotypes of bipolar disorder for genetic investigations of extended pedigrees. JAMA Psychiatry 2014; 71:375-87. [PMID: 24522887 PMCID: PMC4045237 DOI: 10.1001/jamapsychiatry.2013.4100] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
IMPORTANCE Genetic factors contribute to risk for bipolar disorder (BP), but its pathogenesis remains poorly understood. A focus on measuring multisystem quantitative traits that may be components of BP psychopathology may enable genetic dissection of this complex disorder, and investigation of extended pedigrees from genetically isolated populations may facilitate the detection of specific genetic variants that affect BP as well as its component phenotypes. OBJECTIVE To identify quantitative neurocognitive, temperament-related, and neuroanatomical phenotypes that appear heritable and associated with severe BP (bipolar I disorder [BP-I]) and therefore suitable for genetic linkage and association studies aimed at identifying variants contributing to BP-I risk. DESIGN, SETTING, AND PARTICIPANTS Multigenerational pedigree study in 2 closely related, genetically isolated populations: the Central Valley of Costa Rica and Antioquia, Colombia. A total of 738 individuals, all from Central Valley of Costa Rica and Antioquia pedigrees, participated; among them, 181 have BP-I. MAIN OUTCOMES AND MEASURES Familial aggregation (heritability) and association with BP-I of 169 quantitative neurocognitive, temperament, magnetic resonance imaging, and diffusion tensor imaging phenotypes. RESULTS Of 169 phenotypes investigated, 126 (75%) were significantly heritable and 53 (31%) were associated with BP-I. About one-quarter of the phenotypes, including measures from each phenotype domain, were both heritable and associated with BP-I. Neuroimaging phenotypes, particularly cortical thickness in prefrontal and temporal regions as well as volume and microstructural integrity of the corpus callosum, represented the most promising candidate traits for genetic mapping related to BP based on strong heritability and association with disease. Analyses of phenotypic and genetic covariation identified substantial correlations among the traits, at least some of which share a common underlying genetic architecture. CONCLUSIONS AND RELEVANCE To our knowledge, this is the most extensive investigation of BP-relevant component phenotypes to date. Our results identify brain and behavioral quantitative traits that appear to be genetically influenced and show a pattern of BP-I association within families that is consistent with expectations from case-control studies. Together, these phenotypes provide a basis for identifying loci contributing to BP-I risk and for genetic dissection of the disorder.
Collapse
Affiliation(s)
- Scott C Fears
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - Susan K Service
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | | | - Carmen Araya
- Cell and Molecular Biology Research, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Xinia Araya
- Cell and Molecular Biology Research, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Julio Bejarano
- Cell and Molecular Biology Research, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Margarita Ramirez
- Cell and Molecular Biology Research, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | | | - Juliana Gomez-Franco
- Grupo de Investigación en Psiquiatría, Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Maria C Lopez
- Grupo de Investigación en Psiquiatría, Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Gabriel Montoya
- Grupo de Investigación en Psiquiatría, Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Patricia Montoya
- Grupo de Investigación en Psiquiatría, Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Ileana Aldana
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - Terri M Teshiba
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - Zvart Abaryan
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - Noor B Al-Sharif
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - Marissa Ericson
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - Maria Jalbrzikowski
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - Jurjen J Luykx
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles6Department of Psychiatry, ZNA Stuivenberg, Antwerp, Belgium
| | - Linda Navarro
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - Todd A Tishler
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - Lori Altshuler
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - George Bartzokis
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - Javier Escobar
- Department of Psychiatry and Family Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick
| | - David C Glahn
- Department of Psychiatry, Yale University, New Haven, Connecticut9Olin Neuropsychiatric Research Center, Institute of Living, Hartford Hospital, Hartford, Connecticut
| | - Jorge Ospina-Duque
- Grupo de Investigación en Psiquiatría, Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Neil Risch
- Institute for Human Genetics, University of California, San Francisco
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution, and Environment, University College London, London, England
| | - Paul M Thompson
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - Rita M Cantor
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - Carlos Lopez-Jaramillo
- Grupo de Investigación en Psiquiatría, Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia12Mood Disorders Program, Hospital San Vicente Fundacion, Medellín, Colombia
| | - Gabriel Macaya
- Cell and Molecular Biology Research, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Julio Molina
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles13BioCiencias Lab, Guatemala, Guatemala
| | - Victor I Reus
- Department of Psychiatry, University of California, San Francisco
| | - Chiara Sabatti
- Department of Health Research and Policy, Stanford University, Stanford, California
| | - Nelson B Freimer
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| | - Carrie E Bearden
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles
| |
Collapse
|
11
|
Genome-wide association analysis of circulating vitamin D levels in children with asthma. Hum Genet 2012; 131:1495-505. [PMID: 22673963 DOI: 10.1007/s00439-012-1185-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 05/23/2012] [Indexed: 02/06/2023]
Abstract
Vitamin D deficiency is becoming more apparent in many populations. Genetic factors may play a role in the maintenance of vitamin D levels. The objective of this study was to perform a genome-wide analysis (GWAS) of vitamin D levels, including replication of prior GWAS results. We measured 25-hydroxyvitamin D (25(OH)D) levels in serum collected at the time of enrollment and at year 4 in 572 Caucasian children with asthma, who were part of a multi-center clinical trial, the Childhood Asthma Management Program. Replication was performed in a second cohort of 592 asthmatics from Costa Rica and a third cohort of 516 Puerto Rican asthmatics. In addition, we attempted replication of three SNPs that were previously identified in a large GWAS of Caucasian individuals. The setting included data from a clinical trial of childhood asthmatics and two cohorts of asthmatics recruited for genetic studies of asthma. The main outcome measure was circulating 25(OH)D levels. The 25(OH)D levels at the two time-points were only modestly correlated with each other (intraclass correlation coefficient = 0.33) in the CAMP population. We identified SNPs that were nominally associated with 25(OH)D levels at two time-points in CAMP, and replicated four SNPs in the Costa Rican cohort: rs11002969, rs163221, rs1678849, and rs4864976. However, these SNPs were not significantly associated with 25(OH)D levels in a third population of Puerto Rican asthmatics. We were able to replicate the SNP with the strongest effect, previously reported in a large GWAS: rs2282679 (GC), and we were able to replicate another SNP, rs10741657 (CYP2R1), to a lesser degree. We were able to replicate two of three prior significant findings in a GWAS of 25(OH)D levels. Other SNPs may be additionally associated with 25(OH)D levels in certain populations.
Collapse
|
12
|
Segura-Wang M, Raventós H, Escamilla M, Barrantes R. Assessment of genetic ancestry and population substructure in Costa Rica by analysis of individuals with a familial history of mental disorder. Ann Hum Genet 2010; 74:516-24. [PMID: 20946256 DOI: 10.1111/j.1469-1809.2010.00612.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The population of Costa Rica has been considered valuable for locating susceptibility genes of complex disorders because of historical events and a gradual admixture process. We present an assessment of 426 unrelated individuals with a familial history of mental disorder and with ancestors born in the Central Valley, genotyped at 730 microsatellites to evaluate genetic diversity, ancestry, and substructure at the general and regional population levels using quantitative methods. Low population substructure was found. Estimated mean ancestry proportions were 54%, 32%, and 13% for European, Amerindian, and African components, respectively, with some regional variation. The F(ST) values obtained confirm the largest genetic similarity to Europeans. Subdivision of the Amerindians into individual populations revealed strong similarity to Chibchan groups. Analysis of the African ancestry showed high similarity to West and Central African populations. Gene ancestries from other African areas were also detected, probably resulting from ancestral admixture within Africa prior to colonial times. Our analyses show, in an ethnohistorical-genetic context, that gene flow and admixture are important components of Costa Rican population history. The results confirm the need to consider the particular regional genetic structure, the effects of genetic drift and the ancestry when designing and interpreting investigations of genetic traits in this population.
Collapse
|
13
|
Ruiz-Narváez EA, Bare L, Arellano A, Catanese J, Campos H. West African and Amerindian ancestry and risk of myocardial infarction and metabolic syndrome in the Central Valley population of Costa Rica. Hum Genet 2010; 127:629-38. [PMID: 20213474 DOI: 10.1007/s00439-010-0803-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 02/09/2010] [Indexed: 01/28/2023]
Abstract
Genetic ancestry and environmental factors may contribute to the ethnic differences in risk of coronary heart disease (CHD), metabolic syndrome (MS) or its individual components. The population of the Central Valley of Costa Rica offers a unique opportunity to assess the role of genetic ancestry in these chronic diseases because it derived from the admixture of a relatively small number of founders of Southern European, Amerindian, and West African origin. We aimed to determine whether genetic ancestry is associated with risk of myocardial infarction (MI), MS and its individual components in the Central Valley of Costa Rica. We genotyped 39 ancestral informative markers in cases (n = 1,998) with a first non-fatal acute MI and population-based controls (n = 1,998) matched for age, sex, and area of residence, to estimate individual ancestry proportions. Odds ratios (ORs) and 95% confidence intervals (95% CI) were estimated using conditional (MI) and unconditional (MS and its components) logistic regression adjusting for relevant confounders. Mean individual ancestry proportions in cases and controls were 57.5 versus 57.8% for the Southern European, 38.4 versus 38.3% for the Amerindian and 4.1 versus 3.8% for the West African ancestry. Compared with Southern European ancestry, each 10% increase in West African ancestry was associated with a 29% increase in MI, OR (95% CI) = 1.29 (1.07, 1.56), and with a 30% increase on the risk of hypertension, OR (95% CI) = 1.30 (1.00, 1.70). Each 10% increase in Amerindian ancestry was associated with a 14% increase on the risk of MS, OR (95% CI) = 1.14 (1.00, 1.30), and 20% increase on the risk of impaired fasting glucose, OR (95% CI) = 1.20 (1.01, 1.42). These results show that the high variability of admixture proportions in the Central Valley population offers a unique opportunity to uncover the genetic basis of ethnic differences on the risk of disease.
Collapse
|
14
|
Jasinska A, Service S, Jawaheer D, DeYoung J, Levinson M, Zhang Z, Kremeyer B, Muller H, Aldana I, Garcia J, Restrepo G, Lopez C, Palacio C, Duque C, Parra M, Vega J, Ortiz D, Bedoya G, Mathews C, Davanzo P, Fournier E, Bejarano J, Ramirez M, Ortiz CA, Araya X, Molina J, Sabatti C, Reus V, Ospina J, Macaya G, Ruiz-Linares A, Freimer N. A narrow and highly significant linkage signal for severe bipolar disorder in the chromosome 5q33 region in Latin American pedigrees. Am J Med Genet B Neuropsychiatr Genet 2009; 150B:998-1006. [PMID: 19319892 PMCID: PMC4815924 DOI: 10.1002/ajmg.b.30956] [Citation(s) in RCA: 5] [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] [Indexed: 11/09/2022]
Abstract
We previously reported linkage of bipolar disorder to 5q33-q34 in families from two closely related population isolates, the Central Valley of Costa Rica (CVCR) and Antioquia, Colombia (CO). Here we present follow up results from fine-scale mapping in large CVCR and CO families segregating severe bipolar disorder, BP-I, and in 343 population trios/duos from CVCR and CO. Employing densely spaced SNPs to fine map the prior linkage peak region increases linkage evidence and clarifies the position of the putative BP-I locus. We performed two-point linkage analysis with 1134 SNPs in an approximately 9 Mb region between markers D5S410 and D5S422. Combining pedigrees from CVCR and CO yields a LOD score of 4.9 at SNP rs10035961. Two other SNPs (rs7721142 and rs1422795) within the same 94 kb region also displayed LOD scores greater than 4. This linkage peak coincides with our prior microsatellite results and suggests a narrowed BP-I susceptibility regions in these families. To investigate if the locus implicated in the familial form of BP-I also contributes to disease risk in the population, we followed up the family results with association analysis in duo and trio samples, obtaining signals within 2 Mb of the peak linkage signal in the pedigrees; rs12523547 and rs267015 (P = 0.00004 and 0.00016, respectively) in the CO sample and rs244960 in the CVCR sample and the combined sample, with P = 0.00032 and 0.00016, respectively. It remains unclear whether these association results reflect the same locus contributing to BP susceptibility within the extended pedigrees.
Collapse
Affiliation(s)
- A.J. Jasinska
- Center for Neurobehavioral Genetics, University of California, Los Angeles, California
| | - S. Service
- Center for Neurobehavioral Genetics, University of California, Los Angeles, California
| | - D. Jawaheer
- Center for Neurobehavioral Genetics, University of California, Los Angeles, California
| | - J. DeYoung
- Center for Neurobehavioral Genetics, University of California, Los Angeles, California
| | - M. Levinson
- Center for Neurobehavioral Genetics, University of California, Los Angeles, California
| | - Z. Zhang
- Department of Statistics, University of California, Los Angeles, California
| | - B. Kremeyer
- Galton Laboratory, Department of Biology, University College London, London, United Kingdom
| | - H. Muller
- Galton Laboratory, Department of Biology, University College London, London, United Kingdom
| | - I. Aldana
- Center for Neurobehavioral Genetics, University of California, Los Angeles, California
| | - J. Garcia
- Departamento de Psiquiatria, Universidad de Antioquia, Medellin, Colombia, South Carolina
| | - G. Restrepo
- Departamento de Psiquiatria, Universidad de Antioquia, Medellin, Colombia, South Carolina
| | - C. Lopez
- Departamento de Psiquiatria, Universidad de Antioquia, Medellin, Colombia, South Carolina
| | - C. Palacio
- Departamento de Psiquiatria, Universidad de Antioquia, Medellin, Colombia, South Carolina
| | - C. Duque
- Laboratorio de Genetica Molecular, Universidad de Antioquia, Medellin, Colombia, South Carolina
| | - M. Parra
- Laboratorio de Genetica Molecular, Universidad de Antioquia, Medellin, Colombia, South Carolina
| | - J. Vega
- Laboratorio de Genetica Molecular, Universidad de Antioquia, Medellin, Colombia, South Carolina
| | - D. Ortiz
- Laboratorio de Genetica Molecular, Universidad de Antioquia, Medellin, Colombia, South Carolina
| | - G. Bedoya
- Laboratorio de Genetica Molecular, Universidad de Antioquia, Medellin, Colombia, South Carolina
| | - C. Mathews
- Department of Psychiatry, University of California, San Francisco, California
| | - P. Davanzo
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California, Los Angeles, California
| | - E. Fournier
- Cell and Molecular Biology Research Center, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - J. Bejarano
- Cell and Molecular Biology Research Center, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - M. Ramirez
- Cell and Molecular Biology Research Center, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - C. Araya Ortiz
- Cell and Molecular Biology Research Center, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - X. Araya
- Cell and Molecular Biology Research Center, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - J. Molina
- Center for Neurobehavioral Genetics, University of California, Los Angeles, California
| | - C. Sabatti
- Department of Statistics, University of California, Los Angeles, California
- Department of Statistics and Department of Human Genetics, University of California, Los Angeles, California
| | - V. Reus
- Department of Psychiatry, University of California, San Francisco, California
| | - J. Ospina
- Departamento de Psiquiatria, Universidad de Antioquia, Medellin, Colombia, South Carolina
| | - G. Macaya
- Cell and Molecular Biology Research Center, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - A. Ruiz-Linares
- Galton Laboratory, Department of Biology, University College London, London, United Kingdom
| | - N.B. Freimer
- Center for Neurobehavioral Genetics, University of California, Los Angeles, California
| |
Collapse
|
15
|
Verlaan DJ, Berlivet S, Hunninghake GM, Madore AM, Larivière M, Moussette S, Grundberg E, Kwan T, Ouimet M, Ge B, Hoberman R, Swiatek M, Dias J, Lam KC, Koka V, Harmsen E, Soto-Quiros M, Avila L, Celedón JC, Weiss ST, Dewar K, Sinnett D, Laprise C, Raby BA, Pastinen T, Naumova AK. Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease. Am J Hum Genet 2009; 85:377-93. [PMID: 19732864 DOI: 10.1016/j.ajhg.2009.08.007] [Citation(s) in RCA: 230] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 07/31/2009] [Accepted: 08/12/2009] [Indexed: 02/05/2023] Open
Abstract
Common SNPs in the chromosome 17q12-q21 region alter the risk for asthma, type 1 diabetes, primary biliary cirrhosis, and Crohn disease. Previous reports by us and others have linked the disease-associated genetic variants with changes in expression of GSDMB and ORMDL3 transcripts in human lymphoblastoid cell lines (LCLs). The variants also alter regulation of other transcripts, and this domain-wide cis-regulatory effect suggests a mechanism involving long-range chromatin interactions. Here, we further dissect the disease-linked haplotype and identify putative causal DNA variants via a combination of genetic and functional analyses. First, high-throughput resequencing of the region and genotyping of potential candidate variants were performed. Next, additional mapping of allelic expression differences in Yoruba HapMap LCLs allowed us to fine-map the basis of the cis-regulatory differences to a handful of candidate functional variants. Functional assays identified allele-specific differences in nucleosome distribution, an allele-specific association with the insulator protein CTCF, as well as a weak promoter activity for rs12936231. Overall, this study shows a common disease allele linked to changes in CTCF binding and nucleosome occupancy leading to altered domain-wide cis-regulation. Finally, a strong association between asthma and cis-regulatory haplotypes was observed in three independent family-based cohorts (p = 1.78 x 10(-8)). This study demonstrates the requirement of multiple parallel allele-specific tools for the investigation of noncoding disease variants and functional fine-mapping of human disease-associated haplotypes.
Collapse
|
16
|
Neuropsychological performance as endophenotypes in extended schizophrenia families from the Central Valley of Costa Rica. Psychiatr Genet 2009; 19:45-52. [PMID: 19125108 DOI: 10.1097/ypg.0b013e3283202816] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The understanding of complex heritable psychiatric disorders such as schizophrenia could be clarified by examining endophenotypes within genetically isolated populations, such as the one found in the Central Valley of Costa Rica. The reduction of familial variability within a sample could allow the relationship between the cognitive and symptomatic manifestations of the illness and the genetic underpinnings to become more observable. This study investigates the neuropsychological test performances of 41 family members from four extended multiplex families within the Spanish origin population of the Central Valley of Costa Rica as potential endophenotypes for genetic studies. METHODS Individuals with a diagnosis of schizophrenia or schizoaffective disorder were compared with unaffected relatives and 15 unrelated controls with no family history of schizophrenia. RESULTS Although the sample size is small, the results confirm previous reports in the literature of deficits in working memory, executive function, processing speed, and verbal fluency in individuals with schizophrenia compared with controls and intermediate performance in nonpsychotic family members compared with controls. We also found several suggestive quantitative cognitive trait loci with log of the odds greater than 1.75. CONCLUSION These findings suggest that the cognitive deficits in schizophrenia are consistent aspects of the illness, although their usefulness as endophenotypes for genetic studies remains unclear.
Collapse
|
17
|
Walss-Bass C, Soto-Bernardini MC, Johnson-Pais T, Leach RJ, Ontiveros A, Nicolini H, Mendoza R, Jerez A, Dassori A, Chavarria-Siles I, Escamilla MA, Raventos H. Methionine sulfoxide reductase: a novel schizophrenia candidate gene. Am J Med Genet B Neuropsychiatr Genet 2009; 150B:219-25. [PMID: 18506707 PMCID: PMC3781017 DOI: 10.1002/ajmg.b.30791] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Methionine sulfoxide reductase (MSRA) is an antioxidant enzyme implicated in protection against oxidative stress and protein maintenance. We have previously reported the association of marker D8S542, located within the MSRA gene, with schizophrenia in the Central Valley of Costa Rica (CVCR). By performing fine mapping analysis, we have now identified a potential three-marker at risk haplotype within MSRA in the same CVCR sample, with a global P-value slightly above nominal significance (P = 0.0526). By sequencing the MSRA gene in individuals carrying this haplotype, we identified a novel 4-base pair deletion 1,792 bases upstream of the MSRA transcription start site. This deletion was significantly under-transmitted to schizophrenia patients in the CVCR sample (P = 0.0292) using FBAT, and this was replicated in a large independent sample of 321 schizophrenia families from the Hispanic population (P = 0.0367). These findings suggest a protective effect of the deletion against schizophrenia. Further, MSRA mRNA levels were significantly lower in lymphoblastoid cell lines of individuals homozygous for the deletion compared to carriers of the normal allele (P = 0.0135), although significance was only evident when genotypes were collapsed. This suggests that the deleted sequence may play a role in regulating MSRA expression. In conclusion, this work points towards MSRA as a novel schizophrenia candidate gene. Further studies into the mechanisms by which MSRA is involved in schizophrenia pathophysiology may shed light into the biological underpinnings of this disorder.
Collapse
Affiliation(s)
- Consuelo Walss-Bass
- Department of Psychiatry, The University of Texas Health Science Center at San Antonio, USA.
| | | | - Teresa Johnson-Pais
- Department of Cellular and Structural Biology, The University of Texas Health Science Center at San Antonio, TX, 78229, USA
,Department of Pediatrics, The University of Texas Health Science Center at San Antonio, TX, 78229, USA
| | - Robin J. Leach
- Department of Cellular and Structural Biology, The University of Texas Health Science Center at San Antonio, TX, 78229, USA
,Department of Pediatrics, The University of Texas Health Science Center at San Antonio, TX, 78229, USA
| | - Alfonso Ontiveros
- Center for Investigation, School of Medicine, Division of the Health Sciences ITESM, Institute of Information for the Investigation in Mental Health, Monterrey N.L., Mexico
| | - Humberto Nicolini
- Medical and Family Research Group, Carracci S.C., Mexico D.F. Mexico
| | - Ricardo Mendoza
- Department of Psychiatry, David Geffen School of Medicine at UCLA, Torrence, California
| | - Alvaro Jerez
- International Center for Affective Illnesses and Addictive Conduct (CITACA), Guatemala, Guatemala
| | - Albana Dassori
- Department of Psychiatry, The University of Texas Health Science Center at San Antonio, TX, 78229, USA
| | - Ivan Chavarria-Siles
- Department of Psychiatry, The University of Texas Health Science Center at San Antonio, TX, 78229, USA
| | - Michael A. Escamilla
- Department of Psychiatry, The University of Texas Health Science Center at San Antonio, TX, 78229, USA
| | - Henriette Raventos
- Center for Investigation of Molecular and Cellular Biology, University of Costa Rica, San Jose, Costa Rica
,Genetics Section, School of Biology, University of Costa Rica, San Jose, Costa Rica
| |
Collapse
|
18
|
Sharma S, Murphy AJ, Soto-Quiros ME, Avila L, Klanderman BJ, Sylvia JS, Celedón JC, Raby BA, Weiss ST. Association of VEGF polymorphisms with childhood asthma, lung function and airway responsiveness. Eur Respir J 2009; 33:1287-94. [PMID: 19196819 DOI: 10.1183/09031936.00113008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Vascular endothelial growth factor (VEGF) is an angiogenic factor implicated in asthma severity. The objective of the present study was to determine whether VEGF single nucleotide polymorphisms (SNPs) are associated with asthma, lung function and airway responsiveness. The present authors analysed 10 SNPs in 458 white families in the Childhood Asthma Management Program (CAMP). Tests of association with asthma, lung function and airway responsiveness were performed using PBAT software (Golden Helix, Inc. Bozeman, MT, USA; available at www.goldenhelix.com). Family and population-based, revpeated measures analysis of airflow obstruction were conducted. Replication studies were performed in 412 asthmatic children and their parents from Costa Rica. Associations with asthma, lung function and airway responsiveness were observed in both cohorts. SNP rs833058 was associated with asthma in both cohorts. This SNP was also associated with increased airway responsiveness in both populations. An association of rs4711750 and its haplotype with forced expiratory volume in 1 s (FEV(1))/forced vital capacity (FVC) ratio in both cohorts was observed. Longitudinal analysis in CAMP confirmed an association of rs4711750 with FEV(1)/FVC decline over approximately 4.5 yrs of observation. VEGF polymorphisms are associated with childhood asthma, lung function and airway responsiveness in two populations, suggesting that VEGF polymorphisms influence asthma susceptibility, airflow obstruction and airways responsiveness.
Collapse
Affiliation(s)
- S Sharma
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Channing Laboratory, Harvard Medical School, Boston, MA 02115, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Abstract
Bipolar disorder, especially the most severe type (type I), has a strong genetic component. Family studies suggest that a small number of genes of modest effect are involved in this disorder. Family-based studies have identified a number of chromosomal regions linked to bipolar disorder, and progress is currently being made in identifying positional candidate genes within those regions, À number of candidate genes have also shown evidence of association with bipolar disorder, and genome-wide association studies are now under way, using dense genetic maps. Replication studies in larger or combined datasets are needed to definitively assign a role for specific genes in this disorder. This review covers our current knowledge of the genetics of bipolar disorder, and provides a commentary on current approaches used to identify the genes involved in this complex behavioral disorder.
Collapse
Affiliation(s)
- Michael A Escamilla
- University of Texas Health Science Center at San Antonio, South Texas Medical Genetics Research Center, 1214 Schunior St, Edinburg, TX 78539, USA.
| | | |
Collapse
|
20
|
Hunninghake GM, Soto-Quiros ME, Lasky-Su J, Avila L, Ly NP, Liang C, Klanderman BJ, Raby BA, Gold DR, Weiss ST, Celedon JC. Dust mite exposure modifies the effect of functional IL10 polymorphisms on allergy and asthma exacerbations. J Allergy Clin Immunol 2008; 122:93-8, 98.e1-5. [PMID: 18440625 PMCID: PMC6124308 DOI: 10.1016/j.jaci.2008.03.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Revised: 03/17/2008] [Accepted: 03/20/2008] [Indexed: 12/15/2022]
Abstract
BACKGROUND The allergenicity of dust mite exposure might be dependent on variants in the gene for IL-10 (IL10). OBJECTIVES To evaluate whether dust mite exposure modifies the effect of single nucleotide polymorphisms (SNPs) in IL10 on allergy and asthma exacerbations. METHODS We genotyped 6 SNPs in IL10 in 417 Costa Rican children and 503 white children in the Childhood Asthma Management Program (CAMP) with asthma and their parents. We used family-based and population-based approaches to test for interactions between IL10 SNPs and dust mite allergen on serum IgE to dust mite in Costa Rica and on asthma exacerbations in Costa Rica and CAMP. RESULTS Dust mite exposure significantly modified the relation between 3 SNPs in IL10 (rs1800896, rs3024492, and rs3024496) and IgE to dust mite in Costa Rica (P for interaction, .0004 for SNP rs1800896). For each of these SNPs, homozygosity for the minor allele was associated with increased levels of IgE to dust mite with increased dust mite exposure. Homozygosity for the minor allele of each of the 3 SNPs was associated with increased risk of occurrence (approximately 3-fold to 39-fold increase) and frequency of asthma exacerbations among children exposed to > or = 10 microg/g dust mite allergen in Costa Rica. Similar results were obtained for 2 of these SNPs (rs1800896 and rs3024496) among white children in CAMP. CONCLUSION Our findings suggest that dust mite allergen levels modify the effect of IL10 SNPs on allergy and asthma exacerbations and may partly explain conflicting findings in this field.
Collapse
Affiliation(s)
- Gary M. Hunninghake
- Channing Laboratory, Brigham and Women’s Hospital, Boston
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston
- Harvard Medical School, Boston
| | | | - Jessica Lasky-Su
- Channing Laboratory, Brigham and Women’s Hospital, Boston
- Harvard Medical School, Boston
- Department of Biostatistics, Harvard School of Public Health, Boston
| | - Lydiana Avila
- Division of Pediatric Pulmonology, Hospital Nacional de Ninos, San José
| | - Ngoc P. Ly
- Channing Laboratory, Brigham and Women’s Hospital, Boston
- Harvard Medical School, Boston
- Pediatric Pulmonary Division, Massachusetts General Hospital
| | | | - Barbara J. Klanderman
- Channing Laboratory, Brigham and Women’s Hospital, Boston
- Harvard Medical School, Boston
| | - Benjamin A. Raby
- Channing Laboratory, Brigham and Women’s Hospital, Boston
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston
- Harvard Medical School, Boston
| | - Diane R. Gold
- Channing Laboratory, Brigham and Women’s Hospital, Boston
- Harvard Medical School, Boston
| | - Scott T. Weiss
- Channing Laboratory, Brigham and Women’s Hospital, Boston
- Harvard Medical School, Boston
| | - Juan C. Celedon
- Channing Laboratory, Brigham and Women’s Hospital, Boston
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston
- Harvard Medical School, Boston
| |
Collapse
|
21
|
Chavarría-Siles I, Contreras-Rojas J, Hare E, Walss-Bass C, Quezada P, Dassori A, Contreras S, Medina R, Ramírez M, Salazar R, Raventos H, Escamilla MA. Cannabinoid receptor 1 gene (CNR1) and susceptibility to a quantitative phenotype for hebephrenic schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2008; 147:279-84. [PMID: 18186055 DOI: 10.1002/ajmg.b.30592] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Functional alterations of components of the endogenous cannabinoid system, in particular of the cannabinoid receptor 1 protein (CB1), are hypothetical contributors to many of the symptoms seen in schizophrenia. Variants within the cannabinoid receptor 1 gene (CNR1) have been shown to be directly associated with the hebephrenic form of schizophrenia in a Japanese population. This finding, however, has yet to be replicated. In the present study we sought to study the same (AAT)n-repeat microsatellite of the CNR1 gene which showed association to hebephrenic schizophrenia in Japan, and to investigate whether this microsatellite showed association to a hebephrenic type of schizophrenia in a family-based association study in a population of the Central Valley of Costa Rica. The Lifetime Dimensions of Psychosis Scale and a best estimate consensus process were utilized to identify subjects with schizophrenia who had an elevated lifetime dimensional score for negative and disorganized symptoms, which we used as a proxy for "hebephrenia." Using the Family Based Association Test we found association of these hebephrenic subjects and the (AAT)n-repeat marker of the CNR1 (multi-allelic P = 0.0368). Our hypothesis that an association with the (AAT)n-repeat marker of CNR1 would not be found with the more general type of schizophrenia was also confirmed. Schizophrenic subjects with prominent lifetime scores for disorganization and negative symptoms (dimension for hebephrenia) are associated with the CNR1 gene and present a type of symptomatology that resembles chronic cannabinoid-induced psychosis. The current finding points to the possibility of different genetic and pathophysiologic mechanisms underlying different types of schizophrenia.
Collapse
Affiliation(s)
- Iván Chavarría-Siles
- Department of Psychiatry, Psychiatric Genetics Research Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Lasky-Su J, Lyon HN, Emilsson V, Heid IM, Molony C, Raby BA, Lazarus R, Klanderman B, Soto-Quiros ME, Avila L, Silverman EK, Thorleifsson G, Thorsteinsdottir U, Kronenberg F, Vollmert C, Illig T, Fox CS, Levy D, Laird N, Ding X, McQueen MB, Butler J, Ardlie K, Papoutsakis C, Dedoussis G, O'Donnell CJ, Wichmann HE, Celedón JC, Schadt E, Hirschhorn J, Weiss ST, Stefansson K, Lange C. On the replication of genetic associations: timing can be everything! Am J Hum Genet 2008; 82:849-58. [PMID: 18387595 PMCID: PMC2427263 DOI: 10.1016/j.ajhg.2008.01.018] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 12/10/2007] [Accepted: 01/11/2008] [Indexed: 01/22/2023] Open
Abstract
The failure of researchers to replicate genetic-association findings is most commonly attributed to insufficient statistical power, population stratification, or various forms of between-study heterogeneity or environmental influences.(1) Here, we illustrate another potential cause for nonreplications that has so far not received much attention in the literature. We illustrate that the strength of a genetic effect can vary by age, causing "age-varying associations." If not taken into account during the design and the analysis of a study, age-varying genetic associations can cause nonreplication. By using the 100K SNP scan of the Framingham Heart Study, we identified an age-varying association between a SNP in ROBO1 and obesity and hypothesized an age-gene interaction. This finding was followed up in eight independent samples comprising 13,584 individuals. The association was replicated in five of the eight studies, showing an age-dependent relationship (one-sided combined p = 3.92 x 10(-9), combined p value from pediatric cohorts = 2.21 x 10(-8), combined p value from adult cohorts = 0.00422). Furthermore, this study illustrates that it is difficult for cross-sectional study designs to detect age-varying associations. If the specifics of age- or time-varying genetic effects are not considered in the selection of both the follow-up samples and in the statistical analysis, important genetic associations may be missed.
Collapse
Affiliation(s)
- Jessica Lasky-Su
- SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Helen N. Lyon
- Divisions of Genetics and Endocrinology, Program in Genomics, Children's Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Valur Emilsson
- deCode Genetics, IS-101 Reykjavik, Iceland
- Rosetta Inpharmatics, Seattle, WA 98109, USA
| | - Iris M. Heid
- GSF National Research Centre for Environment and Health, Institute of Epidemiology, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry, and Epidemiology, Ludwig-Maximilians-University, 80539 Munich, Germany
| | | | - Benjamin A. Raby
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ross Lazarus
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Barbara Klanderman
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Manuel E. Soto-Quiros
- Division of Pediatric Pulmonology, Hospital Nacional de Niños, PO Box 1654-1000, San José, Costa Rica
| | - Lydiana Avila
- Division of Pediatric Pulmonology, Hospital Nacional de Niños, PO Box 1654-1000, San José, Costa Rica
| | - Edwin K. Silverman
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Caren Vollmert
- GSF National Research Centre for Environment and Health, Institute of Epidemiology, 85764 Neuherberg, Germany
| | - Thomas Illig
- GSF National Research Centre for Environment and Health, Institute of Epidemiology, 85764 Neuherberg, Germany
| | - Caroline S. Fox
- National Heart, Lung, and Blood Institute and its Framingham Heart Study, Framingham, MA 01702, USA
| | - Daniel Levy
- National Heart, Lung, and Blood Institute and its Framingham Heart Study, Framingham, MA 01702, USA
| | - Nan Laird
- Harvard School of Public Health, Boston, MA 02115, USA
| | - Xiao Ding
- Harvard School of Public Health, Boston, MA 02115, USA
| | - Matt B. McQueen
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO 80309, USA
| | - Johannah Butler
- Divisions of Genetics and Endocrinology, Program in Genomics, Children's Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Kristin Ardlie
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - George Dedoussis
- Department of Nutrition and Dietetics, Harokopio University, Athens 17671, Greece
| | - Christopher J. O'Donnell
- National Heart, Lung, and Blood Institute and its Framingham Heart Study, Framingham, MA 01702, USA
| | - H.-Erich Wichmann
- GSF National Research Centre for Environment and Health, Institute of Epidemiology, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry, and Epidemiology, Ludwig-Maximilians-University, 80539 Munich, Germany
| | - Juan C. Celedón
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eric Schadt
- Rosetta Inpharmatics, Seattle, WA 98109, USA
| | - Joel Hirschhorn
- Divisions of Genetics and Endocrinology, Program in Genomics, Children's Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Scott T. Weiss
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Christoph Lange
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard School of Public Health, Boston, MA 02115, USA
| |
Collapse
|
23
|
Wang S, Ray N, Rojas W, Parra MV, Bedoya G, Gallo C, Poletti G, Mazzotti G, Hill K, Hurtado AM, Camrena B, Nicolini H, Klitz W, Barrantes R, Molina JA, Freimer NB, Bortolini MC, Salzano FM, Petzl-Erler ML, Tsuneto LT, Dipierri JE, Alfaro EL, Bailliet G, Bianchi NO, Llop E, Rothhammer F, Excoffier L, Ruiz-Linares A. Geographic patterns of genome admixture in Latin American Mestizos. PLoS Genet 2008; 4:e1000037. [PMID: 18369456 PMCID: PMC2265669 DOI: 10.1371/journal.pgen.1000037] [Citation(s) in RCA: 303] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Accepted: 02/22/2008] [Indexed: 12/27/2022] Open
Abstract
The large and diverse population of Latin America is potentially a powerful resource for elucidating the genetic basis of complex traits through admixture mapping. However, no genome-wide characterization of admixture across Latin America has yet been attempted. Here, we report an analysis of admixture in thirteen Mestizo populations (i.e. in regions of mainly European and Native settlement) from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites. We found extensive variation in Native American and European ancestry (and generally low levels of African ancestry) among populations and individuals, and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women. An admixture analysis allowing for Native American population subdivision revealed a differentiation of the Native American ancestry amongst Mestizos. This observation is consistent with the genetic structure of pre-Columbian populations and with admixture having involved Natives from the area where the Mestizo examined are located. Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region. The history of Latin America has entailed a complex process of population mixture between Native and recent immigrants across a vast geographic region. Few details are known about this process or about how it has shaped the genetic makeup of contemporary Latin American populations. To perform a broad exploration of the genetic diversity of Latin America we carried out genome-wide analyses in 13 mestizo populations sampled from 7 countries across the region. We observe a marked variation in ancestry both within and between mestizo populations. This variation in ancestry correlates with pre-Columbian Native population density in the areas examined and with recent patterns of demographic growth of the sites sampled. We also find evidence that the mixture at the origin of these populations involved mainly immigrant European men and Native and African women. Finally, mestizo populations show a differentiated Amerindian genetic background, consistent with a predominantly local Native ancestry. Mestizos thus still reveal the genetic imprint of the pre-Columbian Native American population diversification. Our study helps delineate the genetic landscape of Latin America and has a number of implications for gene identification analyses in populations from the region.
Collapse
Affiliation(s)
- Sijia Wang
- The Galton Laboratory, Department of Biology, University College London, London, United Kingdom
| | - Nicolas Ray
- Computational and Molecular Population Genetics Laboratory, University of Bern, Bern, Switzerland
| | - Winston Rojas
- Laboratorio de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
| | - Maria V. Parra
- Laboratorio de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
| | - Gabriel Bedoya
- Laboratorio de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Guido Mazzotti
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Kim Hill
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Ana M. Hurtado
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Beatriz Camrena
- Departamento de Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México D.F., México
| | - Humberto Nicolini
- Departamento de Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México D.F., México
| | - William Klitz
- School of Public Health, University of California Berkeley, Berkeley, California, United States of America
- Public Health Institute, Oakland, California, United States of America
| | - Ramiro Barrantes
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | - Julio A. Molina
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Nelson B. Freimer
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil
| | - Francisco M. Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil
| | | | - Luiza T. Tsuneto
- Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - José E. Dipierri
- Instituto de Biología de la Altura, Facultad de Humanidades y Ciencias Sociales, Universidad Nacional de Jujuy, San Salvador de Jujuy, Argentina
| | - Emma L. Alfaro
- Instituto de Biología de la Altura, Facultad de Humanidades y Ciencias Sociales, Universidad Nacional de Jujuy, San Salvador de Jujuy, Argentina
| | - Graciela Bailliet
- Laboratory of Human Molecular Population Genetics, IMBICE, La Plata, Argentina
| | - Nestor O. Bianchi
- Laboratory of Human Molecular Population Genetics, IMBICE, La Plata, Argentina
| | - Elena Llop
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Francisco Rothhammer
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Laboratory, University of Bern, Bern, Switzerland
| | - Andrés Ruiz-Linares
- The Galton Laboratory, Department of Biology, University College London, London, United Kingdom
- * E-mail:
| |
Collapse
|
24
|
Hunninghake GM, Lasky-Su J, Soto-Quirós ME, Avila L, Liang C, Lake SL, Hudson TJ, Spesny M, Fournier E, Sylvia JS, Freimer NB, Klanderman BJ, Raby BA, Celedón JC. Sex-stratified linkage analysis identifies a female-specific locus for IgE to cockroach in Costa Ricans. Am J Respir Crit Care Med 2008; 177:830-6. [PMID: 18244952 DOI: 10.1164/rccm.200711-1697oc] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE The basis for gender influences on allergen-specific IgEs is unclear. OBJECTIVES To perform regular and sex-stratified genomewide linkage analyses of IgE to each of three allergens (Ascaris lumbricoides, Blatella germanica [German cockroach]), and Dermatophagoides pteronyssinus [dust mite]) and to conduct an association study of a candidate gene in a linked genomic region. METHODS Genomewide linkage analyses of allergen-specific IgEs were conducted in 653 members of eight large families of Costa Rican children with asthma. An analysis of the association between single-nucleotide polymorphisms in thymic stromal lymphopoietin (TSLP) and IgE measurements was conducted in 417 parent-child trios in Costa Rica. Significant results were replicated in 470 families of white children in the Childhood Asthma Management Program (CAMP). MEASUREMENTS AND MAIN RESULTS Among all subjects, there was suggestive evidence of linkage (LOD >/= 2.72) to IgE to Ascaris (on chromosome 7q) and IgE to dust mite (on chromosomes 7p and 12q). In a sex-stratified analysis, there was significant evidence of linkage to IgE to cockroach on chromosome 5q23 (peak LOD, 4.14 at 127 cM) in female subjects. TSLP is located within the 1.5 LOD-unit support interval for this linkage peak and has female-specific effects on lung disease in mice. In a sex-stratified analysis, the T allele of single-nucleotide polymorphism rs2289276 in TSLP was associated with reductions in IgE to cockroach (in Costa Rican girls) and total IgE (in girls in Costa Rica and in CAMP; P value for sex-by-genotype interaction, <0.01 in both studies). CONCLUSIONS Consistent with findings in murine models, a variant in TSLP may have female-specific effects on allergic phenotypes.
Collapse
|
25
|
Ly NP, Soto-Quirós ME, Avila L, Hunninghake GM, Raby BA, Laskey D, Sylvia JS, Celedón JC. Paternal asthma, mold exposure, and increased airway responsiveness among children with asthma in Costa Rica. Chest 2007; 133:107-14. [PMID: 17989151 DOI: 10.1378/chest.07-2130] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND Little is known about the determinants of airway hyperresponsiveness (AHR) among children with asthma in Hispanic America. METHODS We examined the relations among selected familial and environmental factors, markers of allergy, spirometric measures of lung function, and AHR in a cross-sectional study of 403 Costa Rican children with asthma between the ages of 6 and 14 years. Study participants completed a protocol that included questionnaires, spirometry, measurements of serum total and allergen-specific IgE, peripheral blood eosinophil count, and body mass index, and the assessment of airway responsiveness to methacholine (ie, a methacholine challenge test [MCT]). AHR to MCT was defined as the provocative dose of methacholine causing a 20% fall in FEV(1). Linear regression was used for the univariate and multivariate analyses. RESULTS Of the 403 asthmatic children who underwent an MCT, 350 (86.8%) had AHR to methacholine. In a multivariate analysis, paternal asthma (p = 0.004), parental report of mold/mildew in the child's home (p = 0.04), FEV(1)/FVC ratio (p < 0.0001), and a positive IgE response to Der p 1 (p = 0.008) were significantly associated with AHR among Costa Rican children with asthma. CONCLUSION Our results suggest that paternal asthma and environmental exposure to mold/mildew are strong determinants of AHR in Costa Rican children with asthma. FEV(1)/FVC ratio may be a useful measure of AHR (a marker of asthma severity) among Costa Ricans and other Hispanic Americans for whom reference values for FEV(1) are not currently available.
Collapse
Affiliation(s)
- Ngoc P Ly
- Channing Laboratory, 181 Longwood Ave, Boston, MA 02115, USA
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Hunninghake GM, Soto-Quiros ME, Avila L, Ly NP, Liang C, Sylvia JS, Klanderman BJ, Silverman EK, Celedón JC. Sensitization to Ascaris lumbricoides and severity of childhood asthma in Costa Rica. J Allergy Clin Immunol 2007; 119:654-61. [PMID: 17336615 DOI: 10.1016/j.jaci.2006.12.609] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Revised: 11/30/2006] [Accepted: 12/04/2006] [Indexed: 10/23/2022]
Abstract
BACKGROUND Little is known about sensitization (defined as a positive IgE) to helminths and disease severity in patients with asthma. OBJECTIVES To examine the relationship between sensitization (defined as a positive IgE) to Ascaris lumbricoides and measures of asthma morbidity and severity in a Costa Rican population with low prevalence of parasitic infection but high prevalence of parasitic exposure. METHODS Cross-sectional study of 439 children (ages 6 to 14 years) with asthma. Linear regression and logistic regression were used for the multivariate statistical analysis. RESULTS After adjustment for parental education and other covariates, sensitization to Ascaris lumbricoides was associated with having at least 1 positive skin test to allergens (odds ratio, 5.15; 95% CI, 2.36-11.21; P < .001), increased total serum IgE and eosinophils in peripheral blood, reductions in FEV(1) and FEV(1)/forced vital capacity, increased airway responsiveness and bronchodilator responsiveness, and hospitalizations for asthma in the previous year (odds ratio, 3.08; 95% CI, 1.23-7.68; P = .02). CONCLUSION Sensitization to Ascaris lumbricoides is associated with increased severity and morbidity of asthma among children in Costa Rica. This association is likely mediated by an increased degree of atopy among children with asthma who are sensitized to Ascaris. CLINICAL IMPLICATIONS In areas with a low prevalence of helminthiasis such as Costa Rica, Ascaris sensitization may be an important marker of severe atopy and disease morbidity in children with asthma.
Collapse
Affiliation(s)
- Gary M Hunninghake
- Channing Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Lee BD, Walss-Bass C, Thompson PM, Dassori A, Montero PA, Medina R, Contreras S, Armas R, Ramirez M, Pereira M, Salazar R, Leach RJ, Quezada P, Raventos H, Escamilla MA. Malic enzyme 2 and susceptibility to psychosis and mania. Psychiatry Res 2007; 150:1-11. [PMID: 17258816 DOI: 10.1016/j.psychres.2006.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Revised: 04/12/2006] [Accepted: 06/08/2006] [Indexed: 01/29/2023]
Abstract
Previous studies have identified a putative gene locus for both schizophrenia and bipolar disorder in the chromosome 18q21 region. To identify candidate genes associated with these disorders we completed fine mapping analyses (using microsatellite markers) in 152 families from the Central Valley of Costa Rica (CVCR) (376 total subjects, 151 with a history of psychosis, 97 with a history of mania). Microsatellite analyses showed evidence of association at two contiguous markers, both located at the same genetic distance and spanning approximately 11 known genes. In a corollary gene expression study, one of these genes, malic enzyme 2 (ME2), showed levels of gene expression 5.6-fold lower in anterior cingulate tissue from post-mortem bipolar brains. Subsequent analysis of individual SNPs in strong linkage disequilibrium with the ME2 gene revealed one SNP and one haplotype associated with the phenotype of psychosis in the CVCR sample. ME2 interacts directly with the malate shuttle system, which has been shown to be altered in schizophrenia and bipolar disorder, and has roles in neuronal synthesis of glutamate and gamma-amino butyric acid. The present study suggests that genetic variation in or near the ME2 gene is associated with both psychotic and manic disorders, including schizophrenia and bipolar disorder.
Collapse
Affiliation(s)
- Byung Dae Lee
- Psychiatric Genetics Research Center, Department of Psychiatry, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Raby BA, Soto-Quiros ME, Avila L, Lake SL, Murphy A, Liang C, Fournier E, Spesny M, Sylvia JS, Verner A, Hudson TJ, Klanderman BJ, Freimer NB, Silverman EK, Celedón JC. Sex-specific linkage to total serum immunoglobulin E in families of children with asthma in Costa Rica. Hum Mol Genet 2006; 16:243-53. [PMID: 17142250 DOI: 10.1093/hmg/ddl447] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Serum total immunoglobulin E (IgE) is a critical intermediate phenotype of allergic diseases. Although total IgE exhibits sexual dimorphism in humans (with males demonstrating higher IgE than females), the molecular basis of this difference is unknown. A genome-wide scan of 380 short-tandem repeat (STR) markers was performed in eight extended pedigrees of asthmatic children (n=655) from the Central Valley of Costa Rica. Genome-wide linkage analysis of total IgE was performed by variance component models. Among all subjects, only one genomic region (chromosome 7p15) showed modest evidence of linkage to total IgE (LOD=1.60). In contrast, a sex-stratified analysis revealed distinct genetic architectures of total IgE in males and females and identified significant linkage to total IgE on a novel male-specific locus on chromosome 20p12 (LOD=3.63 at 36 cM). Genotyping of additional STRs on chromosome 20 resulted in improved evidence for linkage (LOD=3.75 at 33 cM) and a 1.5 LOD-unit support interval for the linkage peak between 26 and 38 cM. Three polymorphisms in two genes on chromosome 20p12 (JAG1 and ANKRD5) were then found to be associated with total IgE in 420 nuclear families of Costa Rican children with asthma. Two of these polymorphisms (in JAG1) were significantly associated with total IgE in families of boys (n=264) but not in families of girls (n=156) with asthma. JAG1 is a hematopoetic cell growth factor that may regulate normal B-cell development. This is the first demonstration of a possible genetic basis for differences in total IgE between sexes.
Collapse
Affiliation(s)
- Benjamin A Raby
- Channing Laboratory and Respiratory Disorders Program, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Celedón JC, Soto-Quiros ME, Avila L, Lake SL, Liang C, Fournier E, Spesny M, Hersh CP, Sylvia JS, Hudson TJ, Verner A, Klanderman BJ, Freimer NB, Silverman EK, Weiss ST. Significant linkage to airway responsiveness on chromosome 12q24 in families of children with asthma in Costa Rica. Hum Genet 2006; 120:691-9. [PMID: 17024367 DOI: 10.1007/s00439-006-0255-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Revised: 08/02/2006] [Accepted: 08/28/2006] [Indexed: 01/22/2023]
Abstract
Although asthma is a major public health problem in certain Hispanic subgroups in the United States and Latin America, only one genome scan for asthma has included Hispanic individuals. Because of small sample size, that study had limited statistical power to detect linkage to asthma and its intermediate phenotypes in Hispanic participants. To identify genomic regions that contain susceptibility genes for asthma and airway responsiveness in an isolated Hispanic population living in the Central Valley of Costa Rica, we conducted a genome-wide linkage analysis of asthma (n = 638) and airway responsiveness (n = 488) in members of eight large pedigrees of Costa Rican children with asthma. Nonparametric multipoint linkage analysis of asthma was conducted by the NPL-PAIR allele-sharing statistic, and variance component models were used for the multipoint linkage analysis of airway responsiveness as a quantitative phenotype. All linkage analyses were repeated after exclusion of the phenotypic data of former and current smokers. Chromosome 12q showed some evidence of linkage to asthma, particularly in nonsmokers (P < 0.01). Among nonsmokers, there was suggestive evidence of linkage to airway responsiveness on chromosome 12q24.31 (LOD = 2.33 at 146 cM). After genotyping 18 additional short-tandem repeat markers on chromosome 12q, there was significant evidence of linkage to airway responsiveness on chromosome 12q24.31 (LOD = 3.79 at 144 cM), with a relatively narrow 1.5-LOD unit support interval for the observed linkage peak (142-147 cM). Our results suggest that chromosome 12q24.31 contains a locus (or loci) that influence a critical intermediate phenotype of asthma (airway responsiveness) in Costa Ricans.
Collapse
Affiliation(s)
- Juan C Celedón
- Channing Laboratory, Department of Medicine and Respiratory Disorders Program, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Herzberg I, Jasinska A, García J, Jawaheer D, Service S, Kremeyer B, Duque C, Parra MV, Vega J, Ortiz D, Carvajal L, Polanco G, Restrepo GJ, López C, Palacio C, Levinson M, Aldana I, Mathews C, Davanzo P, Molina J, Fournier E, Bejarano J, Ramírez M, Ortiz CA, Araya X, Sabatti C, Reus V, Macaya G, Bedoya G, Ospina J, Freimer N, Ruiz-Linares A. Convergent linkage evidence from two Latin-American population isolates supports the presence of a susceptibility locus for bipolar disorder in 5q31-34. Hum Mol Genet 2006; 15:3146-53. [PMID: 16984960 DOI: 10.1093/hmg/ddl254] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We performed a whole genome microsatellite marker scan in six multiplex families with bipolar (BP) mood disorder ascertained in Antioquia, a historically isolated population from North West Colombia. These families were characterized clinically using the approach employed in independent ongoing studies of BP in the closely related population of the Central Valley of Costa Rica. The most consistent linkage results from parametric and non-parametric analyses of the Colombian scan involved markers on 5q31-33, a region implicated by the previous studies of BP in Costa Rica. Because of these concordant results, a follow-up study with additional markers was undertaken in an expanded set of Colombian and Costa Rican families; this provided a genome-wide significant evidence of linkage of BPI to a candidate region of approximately 10 cM in 5q31-33 (maximum non-parametric linkage score=4.395, P<0.00004). Interestingly, this region has been implicated in several previous genetic studies of schizophrenia and psychosis, including disease association with variants of the enthoprotin and gamma-aminobutyric acid receptor genes.
Collapse
Affiliation(s)
- Ibi Herzberg
- Galton Laboratory, Department of Biology, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Walss-Bass C, Liu W, Lew DF, Villegas R, Montero P, Dassori A, Leach RJ, Almasy L, Escamilla M, Raventos H. A novel missense mutation in the transmembrane domain of neuregulin 1 is associated with schizophrenia. Biol Psychiatry 2006; 60:548-53. [PMID: 16730337 DOI: 10.1016/j.biopsych.2006.03.017] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 02/28/2006] [Accepted: 03/07/2006] [Indexed: 10/24/2022]
Abstract
BACKGROUND Although genetic factors are known to play an important role in schizophrenia, the identification of genes involved in this disorder has remained elusive. The neuregulin 1 gene is among the few candidate genes to have been implicated in schizophrenia susceptibility in several populations. However, no causal mutations within this gene have been identified. METHODS In attempts to identify polymorphisms within the neuregulin 1 gene, we performed DNA sequencing using 12 subjects with a history of psychosis from the Central Valley of Costa Rica. DNA genotyping and association studies were then performed in an extended cohort of 142 affected individuals and their relatives from the same population. RESULTS We identified a novel missense mutation (Val to Leu) in exon 11, which codes for the transmembrane region of the neuregulin 1 protein. Association analysis by the Family Based Association Test (FBAT) revealed that this mutation is associated with psychosis (p = .0049) and schizophrenia (p = .0191) in this population. CONCLUSIONS We report the finding of a missense mutation in the neuregulin 1 gene associated with schizophrenia. Additional analyses of an independent sample as well as detailed functional studies should be performed to determine the relevance of this novel polymorphism to the pathophysiology of schizophrenia.
Collapse
Affiliation(s)
- Consuelo Walss-Bass
- Department of Psychiatry, University of Texas Health Science Center, San Antonio, Texas, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Walss-Bass C, Montero AP, Armas R, Dassori A, Contreras SA, Liu W, Medina R, Levinson D, Pereira M, Atmella I, NeSmith L, Leach R, Almasy L, Raventos H, Escamilla MA. Linkage disequilibrium analyses in the Costa Rican population suggests discrete gene loci for schizophrenia at 8p23.1 and 8q13.3. Psychiatr Genet 2006; 16:159-68. [PMID: 16829783 DOI: 10.1097/01.ypg.0000218616.27515.67] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Linkage studies using multiplex families have repeatedly implicated chromosome 8 as involved in schizophrenia etiology. The reported areas of linkage, however, span a wide chromosomal region. The present study used the founder population of the Central Valley of Costa Rica and phenotyping strategies alternative to DSM-IV classifications in attempts to further delimitate the areas on chromosome 8 that may harbor schizophrenia susceptibility genes. A linkage disequilibrium screen of chromosome 8 was performed using family trios of individuals with a history of psychosis. Four discrete regions showing evidence of association (nominal P values less than 0.05) to the phenotype of schizophrenia were identified: 8p23.1, 8p21.3, 8q13.3 and 8q24.3. The region of 8p23.1 precisely overlaps a region showing strong evidence of linkage disequilibrium for severe bipolar disorder in Costa Rica. The same chromosomal regions were identified when the broader phenotype definition of all individuals with functional psychosis was used for analyses. Stratification of the psychotic sample by history of mania suggests that the 8q13.3 locus may be preferentially associated with non-manic psychosis. These results may be helpful in targeting specific areas to be analyzed in association-based or linkage disequilibrium-based studies, for researchers who have found evidence of linkage to schizophrenia on chromosome 8 within their previous studies.
Collapse
Affiliation(s)
- Consuelo Walss-Bass
- Department of Psychiatry, University of Texas Health Science Center at San Antonio, and Southwest Foundation for Biomedical Research, San Antonio, Texas 78229-3900, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Service S, Molina J, Deyoung J, Jawaheer D, Aldana I, Vu T, Araya C, Araya X, Bejarano J, Fournier E, Ramirez M, Mathews CA, Davanzo P, Macaya G, Sandkuijl L, Sabatti C, Reus V, Freimer N. Results of a SNP genome screen in a large Costa Rican pedigree segregating for severe bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 2006; 141B:367-73. [PMID: 16652356 DOI: 10.1002/ajmg.b.30323] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have ascertained in the Central Valley of Costa Rica a new kindred (CR201) segregating for severe bipolar disorder (BP-I). The family was identified by tracing genealogical connections among eight persons initially independently ascertained for a genome wide association study of BP-I. For the genome screen in CR201, we trimmed the family down to 168 persons (82 of whom are genotyped), containing 25 individuals with a best-estimate diagnosis of BP-I. A total of 4,690 SNP markers were genotyped. Analysis of the data was hampered by the size and complexity of the pedigree, which prohibited using exact multipoint methods on the entire kindred. Two-point parametric linkage analysis, using a conservative model of transmission, produced a maximum LOD score of 2.78 on chromosome 6, and a total of 39 loci with LOD scores >1.0. Multipoint parametric and non-parametric linkage analysis was performed separately on four sections of CR201, and interesting (nominal P-value from either analysis <0.01), although not statistically significant, regions were highlighted on chromosomes 1, 2, 3, 12, 16, 19, and 22, in at least one section of the pedigree, or when considering all sections together. The difficulties of analyzing genome wide SNP data for complex disorders in large, potentially informative, kindreds are discussed.
Collapse
Affiliation(s)
- Susan Service
- Center for Neurobehavioral Genetics, University of California, Los Angeles, 90095-1761, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Walss-Bass C, Escamilla MA, Raventos H, Montero AP, Armas R, Dassori A, Contreras S, Liu W, Medina R, Balderas TG, Levinson D, Pereira R, Pereira M, Atmella I, Nesmith L, Leach R, Almasy L. Evidence of genetic overlap of schizophrenia and bipolar disorder: linkage disequilibrium analysis of chromosome 18 in the Costa Rican population. Am J Med Genet B Neuropsychiatr Genet 2005; 139B:54-60. [PMID: 16152570 DOI: 10.1002/ajmg.b.30207] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The long-standing concept that schizophrenia (SC) and bipolar disorder (BP) represent two distinct illnesses has been recently challenged by findings of overlap of genetic susceptibility loci for these two diseases. We report here the results of a linkage disequilibrium (LD) analysis of chromosome 18 utilizing subjects with SC from the Central Valley of Costa Rica. Evidence of association (P < 0.05) was obtained in three chromosomal regions: 18p11.31 (D18S63), 18q12.3 (D18S474), and 18q22.3-qter (D18S1161, D18S70), all of which overlap or are in close proximity with loci previously shown to be in LD with BP, type I in this population. Since both the SC and bipolar samples contained cases with a history of mania and almost all cases of SC and BP had a history of psychosis, we performed an alternative phenotyping strategy to determine whether presence or absence of mania, in the context of psychosis, would yield distinct linkage patterns along chromosome 18. To address this issue, a cohort of psychotic patients (including a range of DSMIV diagnoses) was divided into two groups based on the presence or absence of mania. Regions that showed association with SC showed segregation of association when the sample was stratified by history of mania. Our results are compared with previous genetic studies of susceptibility to SC or BP, in Costa Rica as well as in other populations. This study illustrates the importance of detailed phenotype analysis in the search for susceptibility genes influencing complex psychiatric disorders in isolated populations and suggests that subdivision of psychoses by presence or absence of past mania syndromes may be useful to define genetic subtypes of chronic psychotic illness.
Collapse
Affiliation(s)
- Consuelo Walss-Bass
- Psychiatric Genetics Research Center, Department of Psychiatry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Mathews CA, Reus VI, Bejarano J, Escamilla MA, Fournier E, Herrera LD, Lowe TL, McInnes LA, Molina J, Ophoff RA, Raventos H, Sandkuijl LA, Service SK, Spesny M, León PE, Freimer NB. Genetic studies of neuropsychiatric disorders in Costa Rica: a model for the use of isolated populations. Psychiatr Genet 2004; 14:13-23. [PMID: 15091311 DOI: 10.1097/00041444-200403000-00003] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The importance of genetics in understanding the etiology of mental illness has become increasingly clear in recent years, as more evidence has mounted that almost all neuropsychiatric disorders have a genetic component. It has also become clear, however, that these disorders are etiologically complex, and multiple genetic and environmental factors contribute to their makeup. So far, traditional linkage mapping studies have not definitively identified specific disease genes for neuropsychiatric disorders, although some potential candidates have been identified via these methods (e.g. the dysbindin gene in schizophrenia; Straub et al., 2002; Schwab et al., 2003). For this reason, alternative approaches are being attempted, including studies in genetically isolated populations. Because isolated populations have a high degree of genetic homogeneity, their use may simplify the process of identifying disease genes in disorders where multiple genes may play a role. Several areas of Latin America contain genetically isolated populations that are well suited for the study of neuropsychiatric disorders. Genetic studies of several major psychiatric illnesses, including bipolar disorder, major depression, schizophrenia, Tourette Syndrome, alcohol dependence, attention deficit hyperactivity disorder, and obsessive-compulsive disorder, are currently underway in these regions. In this paper we highlight the studies currently being conducted by our groups in the Central Valley of Costa Rica to illustrate the potential advantages of this population for genetic studies.
Collapse
Affiliation(s)
- Carol A Mathews
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093-0810, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Rahman P, Jones A, Curtis J, Bartlett S, Peddle L, Fernandez BA, Freimer NB. The Newfoundland population: a unique resource for genetic investigation of complex diseases. Hum Mol Genet 2003; 12 Spec No 2:R167-72. [PMID: 12915452 DOI: 10.1093/hmg/ddg257] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The population of the province of Newfoundland and Labrador is genetically isolated. This isolation is evidenced by an overabundance of several monogenic disorders. The Newfoundland population, like that of other isolates, is now the focus of interest for identification of genes implicated in common diseases. However, the utility of such populations for this purpose remains unproven. In this paper, we review the current genetic architecture of the province, with respect to geographic isolation, homogeneity, founder effect, genetic drift and extended linkage disequilibrium. Based on these factors, we propose that the population of Newfoundland offers many advantages for genetic mapping of common diseases, compared with admixed populations, and even compared with other isolates.
Collapse
Affiliation(s)
- Proton Rahman
- Department of Medicine, Memorial University of Newfoundland, St Johns, Newfoundland, Canada.
| | | | | | | | | | | | | |
Collapse
|
37
|
Carvajal-Carmona LG, Ophoff R, Service S, Hartiala J, Molina J, Leon P, Ospina J, Bedoya G, Freimer N, Ruiz-Linares A. Genetic demography of Antioquia (Colombia) and the Central Valley of Costa Rica. Hum Genet 2003; 112:534-41. [PMID: 12601469 DOI: 10.1007/s00439-002-0899-8] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2002] [Accepted: 11/26/2002] [Indexed: 10/25/2022]
Abstract
We report a comparative genetic characterization of two population isolates with parallel demographic histories: the Central Valley of Costa Rica (CVCR) and Antioquia (in northwest Colombia). The analysis of mtDNA, Y-chromosome and autosomal polymorphisms shows that Antioquia and the CVCR are genetically very similar, indicating that closely related parental populations founded these two isolates. In both populations, the male ancestry is predominantly European, whereas the female ancestry is mostly Amerind. In agreement with their isolation, the Amerindian mtDNA diversity of Antioquia and the CVCR is typical of ethnically-defined native populations and is markedly lower than in other Latin American populations. A comparison of linkage disequilibrium (LD) at 18 marker pairs in Antioquia and the CVCR shows that markers in LD in both populations are located at short genetic distances (<approximately 1 cM), whereas markers separated by greater distances are in LD only in the CVCR. This difference probably reflects stochastic variation of LD at the limited number of genome regions compared. The genetic similarity of the populations from Antioquia and the CVCR together with differences in LD between them should be exploitable for the identification and fine mapping of shared disease-related gene variants.
Collapse
|
38
|
Sklar P, Gabriel SB, McInnis MG, Bennett P, Lim YM, Tsan G, Schaffner S, Kirov G, Jones I, Owen M, Craddock N, DePaulo JR, Lander ES. Family-based association study of 76 candidate genes in bipolar disorder: BDNF is a potential risk locus. Brain-derived neutrophic factor. Mol Psychiatry 2003; 7:579-93. [PMID: 12140781 DOI: 10.1038/sj.mp.4001058] [Citation(s) in RCA: 460] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2001] [Revised: 10/02/2001] [Accepted: 10/22/2001] [Indexed: 12/13/2022]
Abstract
Identification of the genetic bases for bipolar disorder remains a challenge for the understanding of this disease. Association between 76 candidate genes and bipolar disorder was tested by genotyping 90 single-nucleotide polymorphisms (SNPs) in these genes in 136 parent-proband trios. In this preliminary analysis, SNPs in two genes, brain-derived neurotrophic factor (BDNF) and the alpha subunit of the voltage-dependent calcium channel were associated with bipolar disorder at the P<0.05 level. In view of the large number of hypotheses tested, the two nominally positive associations were then tested in independent populations of bipolar patients and only BDNF remains a potential risk gene. In the replication samples, excess transmission of the valine allele of amino acid 66 of BDNF was observed in the direction of the original result in an additional sample of 334 parent-proband trios (T/U=108/87, P=0.066). Resequencing of 29 kb surrounding the BDNF gene identified 44 additional SNPs. Genotyping eight common SNPs identified three additional markers transmitted to bipolar probands at the P < 0.05 level. Strong LD was observed across this region and all adjacent pairwise haplotypes showed excess transmission to the bipolar proband. Analysis of these haplotypes using TRANSMIT revealed a global P value of 0.03. A single haplotype was identified that is shared by both the original dataset and the replication sample that is uniquely marked by both the rare A allele of the original SNP and a novel allele 11.5 kb 3'. Therefore, this study of 76 candidate genes has identified BDNF as a potential risk allele that will require additional study to confirm.
Collapse
Affiliation(s)
- P Sklar
- Department of Psychiatry, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Abstract
The general population of Costa Rica has sometimes been considered to be the product of an amalgamation of groups of diverse origin. To determine the magnitude of accumulated admixture since Spanish colonization, 11 classic genetic markers were analyzed in a total of 2196 individuals originating from five distinct regions of the country. A maximum likelihood approach was used. The proportions of genes of European, Amerindian and African ancestry were found to be 61%, 30% and 9% of the total population, respectively. Variation was observed at a regional level, with an increased European influence in the North (66%) and Central (65%) regions. Meanwhile an increase in Amerindian ancestry was found in the South (38%), and a higher incidence in the contribution of African genes was detected in the coastal regions (13% in the Atlantic and 14% in the North Pacific). A principal component (PC) analysis showed that 76% of the existing variability can be explained by the first two PCs, which is in agreement with the variations observed in the admixture process by geographic area. It has been concluded that the Costa Rican population is truly trihybrid, similar to populations in other Latin American countries; however, it differs from them fundamentally by the proportion of gene flow from ancestral populations.
Collapse
Affiliation(s)
- B Morera
- Unitat de Biologia Evolutiva, Facultad de Ciencias de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain.
| | | | | |
Collapse
|
40
|
Escamilla MA, Batki S, Reus VI, Spesny M, Molina J, Service S, Vinogradov S, Neylan T, Mathews C, Meza L, Gallegos A, Montero AP, Cruz ML, Neuhaus J, Roche E, Smith L, Leon P, Freimer NB. Comorbidity of bipolar disorder and substance abuse in Costa Rica: pedigree- and population-based studies. J Affect Disord 2002; 71:71-83. [PMID: 12167503 DOI: 10.1016/s0165-0327(01)00373-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND The purpose of this study was to determine the prevalence of substance use disorders (substance abuse or substance dependence: SA/SD) in a large sample of Bipolar Type I (BPI) patients drawn from the Costa Rican population and to describe the effects of SA/SD on the course of their bipolar disorder. METHOD 110 subjects from two high-risk (for BPI) Costa Rican pedigrees and 205 unrelated Costa Rican BPI subjects were assessed using structured interviews and a best estimate process. Chi(2) and survival analyses were performed to assess the effect of gender on comorbidity risk, and the effect of comorbidity on the clinical course of BPI. RESULTS SA/SD (primarily alcohol dependence) occurred in 17% of the BPI patients from the population sample and 35% of the BPI patients from the pedigree sample. Comorbid SA/SD was strongly associated with gender chi(2) = 16.84, P = 0.00004). In comorbid subjects, alcohol dependence tended to predate the first manic episode (chi(2) = 6.54, P < 0.025). History of SA/SD did not significantly alter the prevalence of psychosis or age of onset of mania in BPI subjects. CONCLUSIONS These results suggest that SA/SD comorbidity rates are lower in this type of population than in BPI patient populations in the US. Gender is a strong predictor of comorbidity prevalence in BPI patients from this population. Although SA/SD may be a risk factor for precipitating BPI in those at risk, in this population comorbid BPI subjects do not have a different onset or course of BPI in comparison to BPI patients without comorbidity.
Collapse
Affiliation(s)
- Michael A Escamilla
- Department of Psychiatry, (7792), University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA. escamillam@uthscsa,edu
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Ophoff RA, Escamilla MA, Service SK, Spesny M, Meshi DB, Poon W, Molina J, Fournier E, Gallegos A, Mathews C, Neylan T, Batki SL, Roche E, Ramirez M, Silva S, De Mille MC, Dong P, Leon PE, Reus VI, Sandkuijl LA, Freimer NB. Genomewide linkage disequilibrium mapping of severe bipolar disorder in a population isolate. Am J Hum Genet 2002; 71:565-74. [PMID: 12119601 PMCID: PMC379193 DOI: 10.1086/342291] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2002] [Accepted: 06/11/2002] [Indexed: 11/03/2022] Open
Abstract
Genomewide association studies may offer the best promise for genetic mapping of complex traits. Such studies in outbred populations require very densely spaced single-nucleotide polymorphisms. In recently founded population isolates, however, extensive linkage disequilibrium (LD) may make these studies feasible with currently available sets of short tandem repeat markers, spaced at intervals as large as a few centimorgans. We report the results of a genomewide association study of severe bipolar disorder (BP-I), using patients from the isolated population of the central valley of Costa Rica. We observed LD with BP-I on several chromosomes; the most striking results were in proximal 8p, a region that has previously shown linkage to schizophrenia. This region could be important for severe psychiatric disorders, rather than for a specific phenotype.
Collapse
Affiliation(s)
- Roel A. Ophoff
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michael A. Escamilla
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Susan K. Service
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Mitzi Spesny
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Dar B. Meshi
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Wingman Poon
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Julio Molina
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Eduardo Fournier
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Alvaro Gallegos
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Carol Mathews
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas Neylan
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Steven L. Batki
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Erin Roche
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Margarita Ramirez
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sandra Silva
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Melissa C. De Mille
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Penny Dong
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pedro E. Leon
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Victor I. Reus
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Lodewijk A. Sandkuijl
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Nelson B. Freimer
- Neurogenetics Laboratory, Department of Psychiatry, Veterans Administration Medical Center, Department of Psychiatry, San Francisco General Hospital, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco; Centro de Biologia Molecular y Celular de la Universidad de Costa Rica, Hospital Calderon Guardia, and Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica; Centro Internacional de Control de Estres, Guatemala City, Guatemala; Applied Biosystems, Foster City, CA; and Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
42
|
DeLisi LE, Mesen A, Rodriguez C, Bertheau A, LaPrade B, Llach M, Riondet S, Razi K, Relja M, Byerley W, Sherrington R. Genome-wide scan for linkage to schizophrenia in a Spanish-origin cohort from Costa Rica. AMERICAN JOURNAL OF MEDICAL GENETICS 2002; 114:497-508. [PMID: 12116183 DOI: 10.1002/ajmg.10538] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genetic isolates have been useful cohorts in which to search for genes underlying disorders of unknown pathology. One such cohort is thought to exist in the Central Valley of Costa Rica surrounding the city of San Jose. Previous investigators identified a rare dominant gene for hereditary deafness in this population, and a suggestive linkage of severe bipolar psychosis has been reported in another study. Ninety-nine families with at least one pair of siblings affected with schizophrenia or a schizophrenia-spectrum diagnosis had clinical evaluations and DNA collected for genotyping. The Marshfield Medical Research Foundation (NHLBI) Mammalian Genotyping Service performed all genotyping using 404 short-tandem repeat polymorphic markers (STRPs) spaced on average 10 cM apart. Data were analyzed using the nonparametric program, GeneHunterPlus. The population structure was investigated using the STRUCT program. No region was found with genome-wide significance for linkage. Using a phenotype of schizophrenia plus schizoaffective disorder, the highest maximum likelihood score (MLS) observed was 1.78 (P < 0.004) at 176.6 cM from pter on chromosome 5q, an area previously implicated by some other groups. In addition, five regions on chromosomes 1p, 2p, 2q, 14p, and 8p had MLSs above 1.0. All other regions produced scores below 1.0. Population genetic analysis reveals no evidence for population substructure, for admixture with other populations, such as Amerindians, or for inbreeding in the parental generation. The latter casts some doubt on this population being an isolate, although there was evidence of inbreeding among the offspring.
Collapse
MESH Headings
- Chromosome Mapping
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 14/genetics
- Chromosomes, Human, Pair 2/genetics
- Chromosomes, Human, Pair 5/genetics
- Chromosomes, Human, Pair 8/genetics
- Cohort Studies
- Costa Rica
- DNA/genetics
- Family Health
- Female
- Genome, Human
- Homozygote
- Humans
- Lod Score
- Male
- Nuclear Family
- Phenotype
- Schizophrenia/genetics
- Spain/ethnology
Collapse
Affiliation(s)
- Lynn E DeLisi
- Department of Psychiatry, New York University, Millhauser Laboratories, New York, New York 10016, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Abstract
OBJECTIVES Population isolates offer several advantages for those hoping to identify predisposition genes for bipolar disorder (BP). In this review article, the rationale for performing gene mapping studies in this type of population and the results of genetic mapping studies performed to date in population isolates are presented. METHODS This article begins with a brief review of the concepts involved in mapping genes for BP. The concept of populations that show some degree of historical isolation and their special utility for certain types of gene mapping is presented. Methods of statistical analysis particularly relevant for gene mapping of complex diseases like BP are presented. Finally, several BP gene studies conducted to date in several population isolates are reviewed. RESULTS Genetic mapping studies of BP have occurred thus far in several isolates or sub-isolates, including the Amish population, Costa Ricans, Finnish, and Canadians (in Quebec), and significant linkage scores have been identified in the latter three isolates. CONCLUSIONS Possible greater homogeneity and greater consistency of diagnosis are factors that have been cited in several studies of BP done in isolates to date. Another special advantage of working in certain types of population isolate is their appropriateness for using certain types of association or linkage disequilibrium-based approaches at both the genome screening and fine mapping stages. These tests include mapping by linkage disequilibrium analyses, an approach that allows mapping to occur at the population, rather than the pedigree, level.
Collapse
Affiliation(s)
- M A Escamilla
- Neurogenetics Laboratory, Department of Psychiatry, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA.
| |
Collapse
|
44
|
McInnes LA, Service SK, Reus VI, Barnes G, Charlat O, Jawahar S, Lewitzky S, Yang Q, Duong Q, Spesny M, Araya C, Araya X, Gallegos A, Meza L, Molina J, Ramirez R, Mendez R, Silva S, Fournier E, Batki SL, Mathews CA, Neylan T, Glatt CE, Escamilla MA, Luo D, Gajiwala P, Song T, Crook S, Nguyen JB, Roche E, Meyer JM, Leon P, Sandkuijl LA, Freimer NB, Chen H. Fine-scale mapping of a locus for severe bipolar mood disorder on chromosome 18p11.3 in the Costa Rican population. Proc Natl Acad Sci U S A 2001; 98:11485-90. [PMID: 11572994 PMCID: PMC58756 DOI: 10.1073/pnas.191519098] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2000] [Indexed: 11/18/2022] Open
Abstract
We have searched for genes predisposing to bipolar disorder (BP) by studying individuals with the most extreme form of the affected phenotype, BP-I, ascertained from the genetically isolated population of the Central Valley of Costa Rica (CVCR). The results of a previous linkage analysis on two extended CVCR BP-I pedigrees, CR001 and CR004, and of linkage disequilibrium (LD) analyses of a CVCR population sample of BP-I patients implicated a candidate region on 18p11.3. We further investigated this region by creating a physical map and developing 4 new microsatellite and 26 single-nucleotide polymorphism markers for typing in the pedigree and population samples. We report the results of fine-scale association analyses in the population sample, as well as evaluation of haplotypes in pedigree CR001. Our results suggest a candidate region containing six genes but also highlight the complexities of LD mapping of common disorders.
Collapse
Affiliation(s)
- L A McInnes
- Neurogenetics Laboratory, Center for Neurobiology and Psychiatry, and Department of Psychiatry, University of California, San Francisco, CA 94143, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
DeLisi LE, Mesen A, Rodriguez C, Bertheau A, LaPrade B, Llach M, Riondet S, Razi K. Clinical characteristics of schizophrenia in multiply affected Spanish origin families from Costa Rica. Psychiatr Genet 2001; 11:145-52. [PMID: 11702056 DOI: 10.1097/00041444-200109000-00006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Sixty-six families from Costa Rica with multiply ill sets of siblings were examined in detailed clinical evaluations and compared with 59 similarly evaluated families from the USA. Eighty-six unrelated Costa Rican individuals with a schizophrenia spectrum diagnosis and no other ill siblings were an additional comparison group. This study was undertaken to examine whether schizophrenia in Costa Rica has similar clinical and demographic characteristics to that in the USA, whether a homogeneous population such as that in Costa Rica might harbor a specific definable subtype, and whether singletons have similar or differing characteristics from individuals in multiplex families. Overall, schizophrenia in Costa Rica is similar to that in any other geographic location. The same symptoms, sex ratio and age of onset characteristics predominate. However, there was significantly less prevalence of affective symptoms (depression and mania) and drug abuse among the Costa Rican multiplex families by comparison with those from the USA. The families with only one ill member from Costa Rica had significantly more alcohol abuse than the multiply affected families. Within multiplex families (both USA and Costa Rica), age of onset was found to have a familial component. Family sibship size was significantly greater in Costa Rica than the USA for the generation with illness studied. However, these siblings had overall fewer children. In Costa Rica, the male but not the female siblings with schizophrenia had reduced fecundity compared with their well siblings. These families from Costa Rica will be used in further molecular genetic studies to determine whether the illness etiology can be traced to one or more specific genetic linkages.
Collapse
Affiliation(s)
- L E DeLisi
- Department of Psychiatry, New York University, New York, USA.
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Degn B, Lundorf MD, Wang A, Vang M, Mors O, Kruse TA, Ewald H. Further evidence for a bipolar risk gene on chromosome 12q24 suggested by investigation of haplotype sharing and allelic association in patients from the Faroe Islands. Mol Psychiatry 2001; 6:450-5. [PMID: 11443532 DOI: 10.1038/sj.mp.4000882] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2000] [Revised: 01/16/2001] [Accepted: 01/18/2001] [Indexed: 11/09/2022]
Abstract
A number of studies have strongly suggested a susceptibility locus for bipolar affective disorder on chromosome 12q24. The present study investigates for a shared chromosomal segment among distantly related patients with bipolar affective disorder from the Faroe Islands, using 17 microsatellite markers covering 24 cM in the previously suggested region on chromosome 12q24. D12S342 showed possible allelic association to bipolar affective disorder (P-value using CLUMP below 0.01). Increased sharing among cases of two-marker haplotypes were suggested at D12S1614--D12S342 (P-values using CLUMP below 0.01), and D12S2075--D12S1675 (P-values using CLUMP around 0.001). The region of most interest is around 6 cM and bounded by markers D12S1614 and D12S1675 as suggested by the interesting two-marker haplotypes. This area contains the minimum interesting region between D12S342 and D12S1658 suggested by the previously reported haplotypes in the two Danish families with bipolar affective disorder.
Collapse
Affiliation(s)
- B Degn
- Department of Biological Psychiatry, Institute for Basic Psychiatric Research, Psychiatric Hospital in Aarhus, DK-8240 Risskov, Denmark
| | | | | | | | | | | | | |
Collapse
|
47
|
Mathews CA, Herrera Amighetti LD, Lowe TL, van de Wetering BJ, Freimer NB, Reus VI. Cultural influences on diagnosis and perception of Tourette syndrome in Costa Rica. J Am Acad Child Adolesc Psychiatry 2001; 40:456-63. [PMID: 11314572 DOI: 10.1097/00004583-200104000-00015] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
BACKGROUND AND OBJECTIVES Tourette syndrome (TS) is a neuropsychiatric disorder in which the pattern of symptom presentation can vary greatly between individuals. Although globally described, TS has not been well characterized in many parts of the world. Differences in individual and cultural perceptions of TS may impact its expression and recognition in some countries, confounding the identification of affected individuals. This study examines the phenomenology and presentation of TS in Costa Rica. METHOD Clinical data on 85 Costa Rican subjects with TS (aged 5-29 years) initially recruited for a genetic study between 1996 and early 2000 were obtained by direct interview and review of medical records. RESULTS The clinical characteristics of TS were similar to that found elsewhere. The gender ratio was 4.6:1, the mean age of onset was 6.1 years, and 20% of subjects had coprolalia. However, the perceived impact of TS was different. Many subjects denied that their TS caused impairment or distress, even when objective evidence of impairment was available. CONCLUSIONS TS in Costa Rica is phenomenologically similar to TS seen in other parts of the world, but differs in perceived impairment. In other countries where cultural forces affect disease definition, close scrutiny of symptom expression and possible adjustment of phenotype definition may be important.
Collapse
Affiliation(s)
- C A Mathews
- Department of Psychiatry, University of California at San Francisco, 401 Parnassus Avenue, Box NGL-0984, San Francisco, CA 94143, USA.
| | | | | | | | | | | |
Collapse
|
48
|
Escamilla MA, McInnes LA, Service SK, Spesny M, Reus VI, Molina J, Gallegos A, Fournier E, Batki S, Neylan T, Matthews C, Vinogradov S, Roche E, Tyler DJ, Shimayoshi N, Mendez R, Ramirez R, Ramirez M, Araya C, Araya X, Leon PE, Sandkuijl LA, Freimer NB. Genome screening for linkage disequilibrium in a Costa Rican sample of patients with bipolar-I disorder: a follow-up study on chromosome 18. AMERICAN JOURNAL OF MEDICAL GENETICS 2001; 105:207-13. [PMID: 11304838 DOI: 10.1002/ajmg.1205] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Linkage disequilibrium (LD) methods offer great promise for mapping complex traits, but have thus far been applied sparingly. In this paper we describe an LD mapping study of severe bipolar disorder (BP-I) in the genetically isolated population of the Central Valley of Costa Rica. This study provides the first complete screen of a chromosome for a complex trait using LD mapping and presents the first application of a new LD mapping statistic (ancestral haplotype reconstruction (AHR)) that evaluates haplotype sharing among affected individuals. The results of this chromosome-wide analysis are instructive for genome-wide LD mapping in isolated populations. Furthermore, the analysis continues to support a possible BP-I locus on 18pter, suggested by previous analyses in this population. Evidence for a possible BP-I locus on 18q12.2 is also described.
Collapse
Affiliation(s)
- M A Escamilla
- Neurogenetics Laboratory, University of California at San Francisco, San Francisco, California, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Levinson DF, Kirby A, Slepner S, Nolte I, Spijker GT, te Meerman G. Simulation studies of detection of a complex disease in a partially isolated population. ACTA ACUST UNITED AC 2001. [DOI: 10.1002/1096-8628(20010108)105:1<65::aid-ajmg1064>3.0.co;2-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
50
|
Tishkoff SA, Pakstis AJ, Ruano G, Kidd KK. The accuracy of statistical methods for estimation of haplotype frequencies: an example from the CD4 locus. Am J Hum Genet 2000; 67:518-22. [PMID: 10859209 PMCID: PMC1287198 DOI: 10.1086/303000] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2000] [Accepted: 05/25/2000] [Indexed: 12/28/2022] Open
Abstract
Haplotype analysis has become increasingly important for the study of human disease as well as for reconstruction of human population histories. Computer programs have been developed to estimate haplotype frequencies statistically from marker phenotypes in unrelated individuals. However, there currently are few empirical reports on the accuracy of statistical estimates that must infer linkage phase. We have analyzed haplotypes at the CD4 locus on chromosome 12 that consist of a short tandem-repeat polymorphism and an Alu insertion/deletion polymorphism located 9.8 kb apart, in 398 individuals from 10 geographically diverse sub-Saharan African populations. Haplotype frequency estimates obtained using gene counting based on molecularly haplotyped (phase-known) data were compared with haplotype frequency estimates obtained using the expectation-maximization algorithm. We show that the estimated frequencies of common haplotypes do not differ significantly with the use of phase-known versus phase-unknown data. However, rare haplotypes are occasionally miscalled when their presence/absence must be inferred. Thus, for those research questions for which the common haplotypes are most important, frequency estimates based on the phase-unknown marker-typing results from unrelated individuals will be sufficient. However, in cases where knowledge of rare haplotypes is critical, molecular haplotyping will be necessary to determine linkage phase unambiguously.
Collapse
Affiliation(s)
- S A Tishkoff
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | | | | |
Collapse
|