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Humphries EM, Ahn K, Kember RL, Lopes FL, Mocci E, Peralta JM, Blangero J, Glahn DC, Goes FS, Zandi PP, Kochunov P, Van Hout C, Shuldiner AR, Pollin TI, Mitchell BD, Bucan M, Hong LE, McMahon FJ, Ament SA. Genome-wide significant risk loci for mood disorders in the Old Order Amish founder population. Mol Psychiatry 2023; 28:5262-5271. [PMID: 36882501 PMCID: PMC10483025 DOI: 10.1038/s41380-023-02014-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
Genome-wide association studies (GWAS) of mood disorders in large case-control cohorts have identified numerous risk loci, yet pathophysiological mechanisms remain elusive, primarily due to the very small effects of common variants. We sought to discover risk variants with larger effects by conducting a genome-wide association study of mood disorders in a founder population, the Old Order Amish (OOA, n = 1,672). Our analysis revealed four genome-wide significant risk loci, all of which were associated with >2-fold relative risk. Quantitative behavioral and neurocognitive assessments (n = 314) revealed effects of risk variants on sub-clinical depressive symptoms and information processing speed. Network analysis suggested that OOA-specific risk loci harbor novel risk-associated genes that interact with known neuropsychiatry-associated genes via gene interaction networks. Annotation of the variants at these risk loci revealed population-enriched, non-synonymous variants in two genes encoding neurodevelopmental transcription factors, CUX1 and CNOT1. Our findings provide insight into the genetic architecture of mood disorders and a substrate for mechanistic and clinical studies.
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Affiliation(s)
- Elizabeth M Humphries
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Molecular Epidemiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kwangmi Ahn
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Rachel L Kember
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Fabiana L Lopes
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Evelina Mocci
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Juan M Peralta
- University of Texas Rio Grande Valley, Harlingen, TX, USA
| | - John Blangero
- University of Texas Rio Grande Valley, Harlingen, TX, USA
| | | | - Fernando S Goes
- Departments of Epidemiology and Mental Health, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Peter P Zandi
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Peter Kochunov
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Cristopher Van Hout
- Regeneron Genetics Center, Tarrytown, NY, USA
- Laboratorio Internacional de Investigatión sobre el Genoma Humano, Campus Juriquilla de la Universidad Nacional Autónoma de México, Querétaro, Querétaro, 76230, Mexico
| | - Alan R Shuldiner
- Regeneron Genetics Center, Tarrytown, NY, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Toni I Pollin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maja Bucan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - L Elliot Hong
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Francis J McMahon
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA.
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Xu Z, Wang X, Song X, An Q, Wang D, Zhang Z, Ding X, Yao Z, Wang E, Liu X, Ru B, Xu Z, Huang Y. Association between the copy number variation of CCSER1 gene and growth traits in Chinese Capra hircus (goat) populations. Anim Biotechnol 2023; 34:1377-1383. [PMID: 35108172 DOI: 10.1080/10495398.2022.2025818] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Recently, Coiled-coil serine-rich protein 1 (CCSER1) gene is reported to be related to economic traits in livestock, and become a hotspot. In our study, we detected CCSER1 gene CNV in 693 goats from six breeds (GZB, GZW, AN, BH, HG, TH) by quantitative real-time PCR (qPCR) and the association analysis between the types of CNV and growth traits. Then, CCSER1 gene expression pattern was discovered in seven tissues from NB goats. Our results showed that the CCSER1 gene copy numbers were distributed differently in the aforementioned six breeds. The type of CCSER1 gene CNV was significantly associated with body weight and heart girth traits in GZW goat, in which individuals with deletion type were dominant in body weight trait (P < 0.05), while the normal type individuals were more advantageous in heart girth trait (P < 0.01); and there was a significant association with heart girth in TH goat (P < 0.05), which normal type was the dominant one. The expression profile revealed that CCSER1 gene has the highest level in the lung, followed by the small intestine and heart. In conclusion, our result is dedicated to an in-depth study of the novel CCSER1 gene CNV site and to provide essential information for Chinese goats molecular selective breeding in the future.
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Affiliation(s)
- Zijie Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xianwei Wang
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Xingya Song
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Qingming An
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou, People's Republic of China
| | - Dahui Wang
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou, People's Republic of China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Xiaoting Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Zhi Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Zejun Xu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
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Finke K, Kourakos M, Brown G, Dang HT, Tan SJS, Simons YB, Ramdas S, Schäffer AA, Kember RL, Bućan M, Mathieson S. Ancestral haplotype reconstruction in endogamous populations using identity-by-descent. PLoS Comput Biol 2021; 17:e1008638. [PMID: 33635861 PMCID: PMC7946327 DOI: 10.1371/journal.pcbi.1008638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 03/10/2021] [Accepted: 12/15/2020] [Indexed: 12/24/2022] Open
Abstract
In this work we develop a novel algorithm for reconstructing the genomes of ancestral individuals, given genotype or sequence data from contemporary individuals and an extended pedigree of family relationships. A pedigree with complete genomes for every individual enables the study of allele frequency dynamics and haplotype diversity across generations, including deviations from neutrality such as transmission distortion. When studying heritable diseases, ancestral haplotypes can be used to augment genome-wide association studies and track disease inheritance patterns. The building blocks of our reconstruction algorithm are segments of Identity-By-Descent (IBD) shared between two or more genotyped individuals. The method alternates between identifying a source for each IBD segment and assembling IBD segments placed within each ancestral individual. Unlike previous approaches, our method is able to accommodate complex pedigree structures with hundreds of individuals genotyped at millions of SNPs. We apply our method to an Old Order Amish pedigree from Lancaster, Pennsylvania, whose founders came to North America from Europe during the early 18th century. The pedigree includes 1338 individuals from the past 12 generations, 394 with genotype data. The motivation for reconstruction is to understand the genetic basis of diseases segregating in the family through tracking haplotype transmission over time. Using our algorithm thread, we are able to reconstruct an average of 224 ancestral individuals per chromosome. For these ancestral individuals, on average we reconstruct 79% of their haplotypes. We also identify a region on chromosome 16 that is difficult to reconstruct—we find that this region harbors a short Amish-specific copy number variation and the gene HYDIN. thread was developed for endogamous populations, but can be applied to any extensive pedigree with the recent generations genotyped. We anticipate that this type of practical ancestral reconstruction will become more common and necessary to understand rare and complex heritable diseases in extended families. When analyzing complex heritable traits, genomic data from many generations of an extended family increases the amount of information available for statistical inference. However, typically only genomic data from the recent generations of a pedigree are available, as ancestral individuals are deceased. In this work we present an algorithm, called thread, for reconstructing the genomes of ancestral individuals, given a complex pedigree and genomic data from the recent generations. Previous approaches have not been able to accommodate large datasets (both in terms of sites and individuals), made simplifying assumptions about pedigree structure, or did not tie reconstructed sequences back to specific individuals. We apply thread to a complex Old Order Amish pedigree of 1338 individuals, 394 with genotype data.
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Affiliation(s)
- Kelly Finke
- Department of Computer Science, Swarthmore College, Swarthmore, Pennsylvania, United States of America
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Michael Kourakos
- Department of Computer Science, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Gabriela Brown
- Department of Computer Science, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Huyen Trang Dang
- Department of Computer Science, Bryn Mawr College, Bryn Mawr, Pennsylvania, United States of America
| | - Shi Jie Samuel Tan
- Department of Computer Science, Haverford College, Haverford, Pennsylvania, United States of America
| | - Yuval B. Simons
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Shweta Ramdas
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alejandro A. Schäffer
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rachel L. Kember
- Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Maja Bućan
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sara Mathieson
- Department of Computer Science, Haverford College, Haverford, Pennsylvania, United States of America
- * E-mail:
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Suga Y, Yoshimoto K, Numata S, Shimodera S, Takamura S, Kamimura N, Sawada K, Kazui H, Ohmori T, Morinobu S. Structural variation in the glycogen synthase kinase 3β and brain-derived neurotrophic factor genes in Japanese patients with bipolar disorders. Neuropsychopharmacol Rep 2019; 40:46-51. [PMID: 31769621 PMCID: PMC7292225 DOI: 10.1002/npr2.12083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/20/2019] [Accepted: 10/21/2019] [Indexed: 01/06/2023] Open
Abstract
Background Lithium is the first‐line drug for the treatment of bipolar disorders (BDs); however, not all patients responded. Glycogen synthase kinase (GSK) 3β and brain‐derived neurotrophic factor (BDNF) play a role in the therapeutic action of lithium. Since structural variations were reported in these genes, it is possible that these genomic variations may be involved in the therapeutic responses to lithium. Method Fifty patients with BDs and 50 healthy subjects (mean age 55.0 ± 15.0 years; M/F 19/31) participated. We examined structural variation of the GSK3β and BDNF genes by real‐time PCR. We examined the influence of structural variation of these genes on the therapeutic responses to lithium and the occurrence of antidepressant‐emergent affective switch (AEAS). The efficacy of lithium was assessed using the Alda scale, and AEAS was evaluated using Young Mania Rating Scale. Results Although we examined structural variations within intron II and VII of the GSK3® gene and from the end of exon IV to intron IV and within exon IX of the BDNF gene, no structural variation was found in BDs. Whereas 5 of 50 patients exhibited three copies of the genomic region within exon IV of the BDNF gene, all healthy subjects had two copies. No difference in the therapeutic efficacy of lithium was found between patients with three and two copies. No difference in the occurrence of AEAS was found between the two groups. Conclusion The amplification of the BDNF gene influenced neither the therapeutic responses to lithium nor the occurrence of AEAS. Five of 50 patients with bipolar disorders exhibited three copies of the genomic region within exon IV of the BDNF gene. But, 50 healthy subjects had two copies. This amplification did not affect the therapeutic responses to lithium.![]()
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Affiliation(s)
- Yosuke Suga
- Department of Neuropsychiatry, Kochi Medical School, Kochi University, Nankoku, Japan
| | | | - Shusuke Numata
- Department of Psychiatry, Course of Integrated Brain Sciences, Medical Informatics, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | | | | | - Naoto Kamimura
- Department of Neuropsychiatry, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Ken Sawada
- Department of Neuropsychiatry, Kochi Medical School, Kochi University, Nankoku, Japan.,KOKORONO Support Center, Kochi Health Sciences Center, Ike, Japan
| | - Hiromitsu Kazui
- Department of Neuropsychiatry, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Tetsuro Ohmori
- Department of Psychiatry, Course of Integrated Brain Sciences, Medical Informatics, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Shigeru Morinobu
- Department of Neuropsychiatry, Kochi Medical School, Kochi University, Nankoku, Japan.,Department of Occupational Therapy, School of Health Science and Social Welfare, KIBI International University, Takahashi, Japan
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Lunde‐Young R, Ramirez J, Naik V, Orzabal M, Lee J, Konganti K, Hillhouse A, Threadgill D, Ramadoss J. Hippocampal transcriptome reveals novel targets of FASD pathogenesis. Brain Behav 2019; 9:e01334. [PMID: 31140755 PMCID: PMC6625466 DOI: 10.1002/brb3.1334] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/01/2019] [Accepted: 05/06/2019] [Indexed: 01/26/2023] Open
Abstract
INTRODUCTION Prenatal alcohol exposure can contribute to fetal alcohol spectrum disorders (FASD), characterized by a myriad of developmental impairments affecting behavior and cognition. Studies show that many of these functional impairments are associated with the hippocampus, a structure exhibiting exquisite vulnerability to developmental alcohol exposure and critically implicated in learning and memory; however, mechanisms underlying alcohol-induced hippocampal deficits remain poorly understood. By utilizing a high-throughput RNA-sequencing (RNA-seq) approach to address the neurobiological and molecular basis of prenatal alcohol-induced hippocampal functional deficits, we hypothesized that chronic binge prenatal alcohol exposure alters gene expression and global molecular pathways in the fetal hippocampus. METHODS Timed-pregnant Sprague-Dawley rats were randomly assigned to a pair-fed control (PF) or binge alcohol (ALC) treatment group on gestational day (GD) 4. ALC dams acclimatized from GDs 5-10 with a daily treatment of 4.5 g/kg alcohol and subsequently received 6 g/kg on GDs 11-20. PF dams received a once daily maltose dextrin gavage on GDs 5-20, isocalorically matching ALC counterparts. On GD 21, bilateral hippocampi were dissected, flash frozen, and stored at -80° C. Total RNA was then isolated from homogenized tissues. Samples were normalized to ~4nM and pooled equally. Sequencing was performed by Illumina NextSeq 500 on a 75 cycle, single-end sequencing run. RESULTS RNA-seq identified 13,388 genes, of these, 76 genes showed a significant difference (p < 0.05, log2 fold change ≥2) in expression between the PF and ALC groups. Forty-nine genes showed sex-dependent dysregulation; IPA analysis showed among female offspring, dysregulated pathways included proline and citrulline biosynthesis, whereas in males, xenobiotic metabolism signaling and alaninine biosynthesis etc. were altered. CONCLUSION We conclude that chronic binge alcohol exposure during pregnancy dysregulates fetal hippocampal gene expression in a sex-specific manner. Identification of subtle, transcriptome-level dysregulation in hippocampal molecular pathways offers potential mechanistic insights underlying FASD pathogenesis.
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Affiliation(s)
- Raine Lunde‐Young
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Josue Ramirez
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Vishal Naik
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Marcus Orzabal
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Jehoon Lee
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Kranti Konganti
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Andrew Hillhouse
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - David Threadgill
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Jayanth Ramadoss
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
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Rediscovering the value of families for psychiatric genetics research. Mol Psychiatry 2019; 24:523-535. [PMID: 29955165 PMCID: PMC7028329 DOI: 10.1038/s41380-018-0073-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/11/2018] [Accepted: 03/26/2018] [Indexed: 01/09/2023]
Abstract
As it is likely that both common and rare genetic variation are important for complex disease risk, studies that examine the full range of the allelic frequency distribution should be utilized to dissect the genetic influences on mental illness. The rate limiting factor for inferring an association between a variant and a phenotype is inevitably the total number of copies of the minor allele captured in the studied sample. For rare variation, with minor allele frequencies of 0.5% or less, very large samples of unrelated individuals are necessary to unambiguously associate a locus with an illness. Unfortunately, such large samples are often cost prohibitive. However, by using alternative analytic strategies and studying related individuals, particularly those from large multiplex families, it is possible to reduce the required sample size while maintaining statistical power. We contend that using whole genome sequence (WGS) in extended pedigrees provides a cost-effective strategy for psychiatric gene mapping that complements common variant approaches and WGS in unrelated individuals. This was our impetus for forming the "Pedigree-Based Whole Genome Sequencing of Affective and Psychotic Disorders" consortium. In this review, we provide a rationale for the use of WGS with pedigrees in modern psychiatric genetics research. We begin with a focused review of the current literature, followed by a short history of family-based research in psychiatry. Next, we describe several advantages of pedigrees for WGS research, including power estimates, methods for studying the environment, and endophenotypes. We conclude with a brief description of our consortium and its goals.
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Genetic pleiotropy between mood disorders, metabolic, and endocrine traits in a multigenerational pedigree. Transl Psychiatry 2018; 8:218. [PMID: 30315151 PMCID: PMC6185949 DOI: 10.1038/s41398-018-0226-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/10/2018] [Accepted: 07/14/2018] [Indexed: 12/15/2022] Open
Abstract
Bipolar disorder (BD) is a mental disorder characterized by alternating periods of depression and mania. Individuals with BD have higher levels of early mortality than the general population, and a substantial proportion of this is due to increased risk for comorbid diseases. To identify the molecular events that underlie BD and related medical comorbidities, we generated imputed whole-genome sequence data using a population-specific reference panel for an extended multigenerational Old Order Amish pedigree (n = 394), segregating BD and related disorders. First, we investigated all putative disease-causing variants at known Mendelian disease loci present in this pedigree. Second, we performed genomic profiling using polygenic risk scores (PRS) to establish each individual's risk for several complex diseases. We identified a set of Mendelian variants that co-occur in individuals with BD more frequently than their unaffected family members, including the R3527Q mutation in APOB associated with hypercholesterolemia. Using PRS, we demonstrated that BD individuals from this pedigree were enriched for the same common risk alleles for BD as the general population (β = 0.416, p = 6 × 10-4). Furthermore, we find evidence for a common genetic etiology between BD risk and polygenic risk for clinical autoimmune thyroid disease (p = 1 × 10-4), diabetes (p = 1 × 10-3), and lipid traits such as triglyceride levels (p = 3 × 10-4) in the pedigree. We identify genomic regions that contribute to the differences between BD individuals and unaffected family members by calculating local genetic risk for independent LD blocks. Our findings provide evidence for the extensive genetic pleiotropy that can drive epidemiological findings of comorbidities between diseases and other complex traits.
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Identification of rare nonsynonymous variants in SYNE1/CPG2 in bipolar affective disorder. Psychiatr Genet 2018; 27:81-88. [PMID: 28178086 DOI: 10.1097/ypg.0000000000000166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Bipolar affective disorder (BPD) is a severe mood disorder with a prevalence of ∼1.5% in the population. The pathogenesis of BPD is poorly understood; however, a strong heritable component has been identified. Previous genome-wide association studies have indicated a region on 6q25, coding for the SYNE1 gene, which increases disease susceptibility. SYNE1 encodes the synaptic nuclear envelope protein-1, nesprin-1. A brain-specific splice variant of SYNE1, CPG2 encoding candidate plasticity gene 2, has been identified. The intronic single-nucleotide polymorphism with the strongest genome-wide significant association in BPD, rs9371601, is present in both SYNE1 and CPG2. METHODS We screened 937 BPD samples for genetic variation in SYNE1 exons 14-33, which covers the CPG2 region, using high-resolution melt analysis. In addition, we screened two regions of increased transcriptional activity, one of them proposed to be the CPG2 promoter region. RESULTS AND CONCLUSION We identified six nonsynonymous and six synonymous variants. We genotyped three rare nonsynonymous variants, rs374866393, rs148346599 and rs200629713, in a total of 1099 BPD samples and 1056 controls. Burden analysis of these rare variants did not show a significant association with BPD. However, nine patients are compound heterozygotes for variants in SYNE1/CPG2, suggesting that rare coding variants may contribute significantly towards the complex genetic architecture underlying BPD. Imputation analysis in our own whole-genome sequencing sample of 99 BPD individuals identified an additional eight risk variants in the CPG2 region of SYNE1.
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DNA sequence-level analyses reveal potential phenotypic modifiers in a large family with psychiatric disorders. Mol Psychiatry 2018; 23:2254-2265. [PMID: 29880880 PMCID: PMC6294736 DOI: 10.1038/s41380-018-0087-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/30/2018] [Accepted: 04/09/2018] [Indexed: 02/07/2023]
Abstract
Psychiatric disorders are a group of genetically related diseases with highly polygenic architectures. Genome-wide association analyses have made substantial progress towards understanding the genetic architecture of these disorders. More recently, exome- and whole-genome sequencing of cases and families have identified rare, high penetrant variants that provide direct functional insight. There remains, however, a gap in the heritability explained by these complementary approaches. To understand how multiple genetic variants combine to modify both severity and penetrance of a highly penetrant variant, we sequenced 48 whole genomes from a family with a high loading of psychiatric disorder linked to a balanced chromosomal translocation. The (1;11)(q42;q14.3) translocation directly disrupts three genes: DISC1, DISC2, DISC1FP and has been linked to multiple brain imaging and neurocognitive outcomes in the family. Using DNA sequence-level linkage analysis, functional annotation and population-based association, we identified common and rare variants in GRM5 (minor allele frequency (MAF) > 0.05), PDE4D (MAF > 0.2) and CNTN5 (MAF < 0.01) that may help explain the individual differences in phenotypic expression in the family. We suggest that whole-genome sequencing in large families will improve the understanding of the combined effects of the rare and common sequence variation underlying psychiatric phenotypes.
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Bocchetta A, Traccis F. The Sardinian Puzzle: Concentration of Major Psychoses and Suicide in the Same Sub-Regions Across One Century. Clin Pract Epidemiol Ment Health 2017; 13:246-254. [PMID: 29299047 PMCID: PMC5725527 DOI: 10.2174/1745017901713010246] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/03/2017] [Accepted: 11/12/2017] [Indexed: 01/04/2023]
Abstract
BACKGROUND Sardinia, the second largest Mediterranean island has long been considered a privileged observatory for the study of several medical conditions. The peculiar epidemiology of mood disorders and suicide across Sardinian sub-regions has long intrigued clinicians and researchers. OBJECTIVE The principal aim of the present study was to test whether the geographical distribution of suicides committed in Sardinian over the last three decades are comparable with the geographical origin of patients hospitalized up to half a century ago. METHOD The distribution of the municipalities of origin of the patients hospitalized in Sardinia between 1901 and 1964 for schizophrenia, bipolar disorder, and depression was reanalyzed and compared with the distribution of municipalities where suicides were committed between 1980 and 2013. Data were also analyzed by the altitude above the sea level and by the population size of the municipalities. RESULTS There was a significant variation of hospitalization and suicide rates across Sardinian sub-regions. The sub-regions of origin of the patients hospitalized for schizophrenia and bipolar disorder correlated with each other (P = 0.047). Both hospitalizations and suicides were more incident in municipalities with a higher altitude and a smaller population size. The incidence of hospitalizations and suicides correlated significantly with each other both at the municipality (P = 1.86 x 10-7) and at the sub-region level (P = 1.71 x 10-7). CONCLUSION The present study confirms the peculiar geographical distribution of major psychoses and suicide in Sardinia. The two phenomena appear to have been correlated for as long as one century.
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Affiliation(s)
- Alberto Bocchetta
- Department of Biomedical Sciences, Section of Neurosciences and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Francesco Traccis
- Department of Biomedical Sciences, Section of Neurosciences and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
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11
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Rao AR, Yourshaw M, Christensen B, Nelson SF, Kerner B. Rare deleterious mutations are associated with disease in bipolar disorder families. Mol Psychiatry 2017; 22:1009-1014. [PMID: 27725659 PMCID: PMC5388596 DOI: 10.1038/mp.2016.181] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 06/19/2016] [Accepted: 08/01/2016] [Indexed: 12/18/2022]
Abstract
Bipolar disorder (BD) is a common, complex and heritable psychiatric disorder characterized by episodes of severe mood swings. The identification of rare, damaging genomic mutations in families with BD could inform about disease mechanisms and lead to new therapeutic interventions. To determine whether rare, damaging mutations shared identity-by-descent in families with BD could be associated with disease, exome sequencing was performed in multigenerational families of the NIMH BD Family Study followed by in silico functional prediction. Disease association and disease specificity was determined using 5090 exomes from the Sweden-Schizophrenia (SZ) Population-Based Case-Control Exome Sequencing study. We identified 14 rare and likely deleterious mutations in 14 genes that were shared identity-by-descent among affected family members. The variants were associated with BD (P<0.05 after Bonferroni's correction) and disease specificity was supported by the absence of the mutations in patients with SZ. In addition, we found rare, functional mutations in known causal genes for neuropsychiatric disorders including holoprosencephaly and epilepsy. Our results demonstrate that exome sequencing in multigenerational families with BD is effective in identifying rare genomic variants of potential clinical relevance and also disease modifiers related to coexisting medical conditions. Replication of our results and experimental validation are required before disease causation could be assumed.
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Affiliation(s)
- Aliz R Rao
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Yourshaw
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Stanley F Nelson
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry and Biobehavioral Sciences at the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Berit Kerner
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Guzman-Parra J, Rivas F, Strohmaier J, Forstner A, Streit F, Auburger G, Propping P, Orozco-Diaz G, González MJ, Gil-Flores S, Cabaleiro-Fabeiro FJ, Del Río-Noriega F, Perez-Perez F, Haro-González J, de Diego-Otero Y, Romero-Sanchiz P, Moreno-Küstner B, Cichon S, Nöthen MM, Rietschel M, Mayoral F. The Andalusian Bipolar Family (ABiF) Study: Protocol and sample description. REVISTA DE PSIQUIATRIA Y SALUD MENTAL 2017; 11:199-207. [PMID: 28619597 DOI: 10.1016/j.rpsm.2017.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 01/29/2017] [Accepted: 03/23/2017] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Here, we present the first description of the Andalusian Bipolar Family (ABiF) Study. This longitudinal investigation of families from Andalusia, Spain commenced in 1997 with the aim of elucidating the molecular genetic causes of bipolar affective disorder. The cohort has since contributed to a number of key genetic findings, as reported in international journals. However, insight into the genetic underpinnings of the disorder in these families remains limited. METHOD In the initial 1997-2003 study phase, 100 multiplex bipolar disorder and other mood disorder families were recruited. The ongoing second phase of the project commenced in 2013, and involves follow-up of a subgroup of the originally recruited families. The aim of the follow-up investigation is to generate: i) longitudinal clinical data; ii) results from detailed neuropsychological assessments; and iii) a more extensive collection of biomaterials for future molecular biological studies. RESULTS The ABiF Study will thus generate a valuable resource for future investigations into the aetiology of bipolar affective disorder; in particular the causes of high disease loading within multiply affected families. DISCUSSION We discuss the value of this approach in terms of new technologies for the identification of high-penetrance genetic factors. These new technologies include exome and whole genome sequencing, and the use of induced pluripotent stem cells or model organisms to determine functional consequences.
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Affiliation(s)
- Jose Guzman-Parra
- Unidad de Salud Mental, Hospital Regional Universitario de Málaga, Instituto de Biomedicina de Málaga (IBIMA), Málaga, España.
| | - Fabio Rivas
- Unidad de Salud Mental, Hospital Regional Universitario de Málaga, Instituto de Biomedicina de Málaga (IBIMA), Málaga, España
| | - Jana Strohmaier
- Departamento de Epidemiología Genética en Psiquiatría, Instituto Central de Salud Mental, Facultad de Medicina de Mannheim, Universidad de Heidelberg, Mannheim, Alemania
| | - Andreas Forstner
- Instituto de Genética Humana, Universidad de Bonn, Bonn, Alemania; Departamento de Genómica, Life & Brain Center, Universidad de Bonn, Bonn, Alemania
| | - Fabian Streit
- Departamento de Epidemiología Genética en Psiquiatría, Instituto Central de Salud Mental, Facultad de Medicina de Mannheim, Universidad de Heidelberg, Mannheim, Alemania
| | - Georg Auburger
- Clínica de Neurología, Universidad de Frankfurt, Frankfurt, Alemania
| | - Peter Propping
- Instituto de Genética Humana, Universidad de Bonn, Bonn, Alemania; Departamento de Genómica, Life & Brain Center, Universidad de Bonn, Bonn, Alemania
| | - Guillermo Orozco-Diaz
- Unidad de Gestión Clínica del Dispositivo de Cuidados Críticos y Urgencias Coin-Gudalhorce, Málaga, España
| | - Maria José González
- Unidad de Salud Mental, Hospital Regional Universitario de Málaga, Instituto de Biomedicina de Málaga (IBIMA), Málaga, España
| | - Susana Gil-Flores
- Departamento de Salud Mental, Universidad Hospital Reina Sofía, Córdoba, España
| | | | | | - Fermin Perez-Perez
- Departamento de Salud Mental, Hospital de Puerto Real, Puerto Real, Cádiz, España
| | - Jesus Haro-González
- Departamento de Salud Mental, Hospital Punta de Europa, Algeciras, Cádiz, España
| | - Yolanda de Diego-Otero
- Unidad de Salud Mental, Hospital Regional Universitario de Málaga, Instituto de Biomedicina de Málaga (IBIMA), Málaga, España
| | - Pablo Romero-Sanchiz
- Unidad de Salud Mental, Hospital Regional Universitario de Málaga, Instituto de Biomedicina de Málaga (IBIMA), Málaga, España
| | - Berta Moreno-Küstner
- Departamento de Personalidad, Evaluación y Tratamiento Psicológico, Universidad de Málaga, Málaga, España
| | - Sven Cichon
- Departamento de Biomedicina, Universidad de Basel, Basel, Suiza
| | - Markus M Nöthen
- Unidad de Salud Mental, Hospital Regional Universitario de Málaga, Instituto de Biomedicina de Málaga (IBIMA), Málaga, España; Departamento de Genómica, Life & Brain Center, Universidad de Bonn, Bonn, Alemania
| | - Marcella Rietschel
- Departamento de Epidemiología Genética en Psiquiatría, Instituto Central de Salud Mental, Facultad de Medicina de Mannheim, Universidad de Heidelberg, Mannheim, Alemania
| | - Fermin Mayoral
- Unidad de Salud Mental, Hospital Regional Universitario de Málaga, Instituto de Biomedicina de Málaga (IBIMA), Málaga, España
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Blum K, Febo M, Badgaiyan RD, Demetrovics Z, Simpatico T, Fahlke C, Li M, Dushaj K, Gold MS. Common Neurogenetic Diagnosis and Meso-Limbic Manipulation of Hypodopaminergic Function in Reward Deficiency Syndrome (RDS): Changing the Recovery Landscape. Curr Neuropharmacol 2017; 15:184-194. [PMID: 27174576 PMCID: PMC5327445 DOI: 10.2174/1570159x13666160512150918] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 04/11/2016] [Accepted: 04/21/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In 1990, Blum and associates provided the first confirmed genetic link between the DRD2 polymorphisms and alcoholism. This finding was based on an earlier conceptual framework, which served as a blueprint for their seminal genetic association discovery they termed "Brain Reward Cascade." These findings were followed by a new way of understanding all addictive behaviors (substance and non-substance) termed "Reward Deficiency Syndrome" (RDS). RDS incorporates a complex multifaceted array of inheritable behaviors that are polygenic. OBJECTIVE In this review article, we attempt to clarify these terms and provide a working model to accurately diagnose and treat these unwanted behaviors. METHOD We are hereby proposing the development of a translational model we term "Reward Deficiency Solution System™" that incorporates neurogenetic testing and meso-limbic manipulation of a "hypodopaminergic" trait/state, which provides dopamine agonistic therapy (DAT) as well as reduced "dopamine resistance," while embracing "dopamine homeostasis." RESULT The result is better recovery and relapse prevention, despite DNA antecedents, which could impact the recovery process and relapse. Understanding the commonality of mental illness will transform erroneous labeling based on symptomatology, into a genetic and anatomical etiology. WC: 184.
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Affiliation(s)
- Kenneth Blum
- Department of Psychiatry, University of Florida College of Medicine and McKnight Brain Institute, Gainesville, FL, USA
- Department of Nutrigenomics, RDSolutions, Inc., Salt Lake City, UT, USA
- Department of Psychology, Eotvos Lorand University, Budapest, Hungary
- PATH Foundation NY, New York, NY, USA
- Division of Neuroscience Research and Addiction Therapy, The Shores Treatment and Recovery, Port Saint Lucie, FL, USA
| | - Marcelo Febo
- Department of Psychiatry, University of Florida College of Medicine and McKnight Brain Institute, Gainesville, FL, USA
| | - Rajendra D. Badgaiyan
- Division of Neuroimaging, Department of Psychiatry, University of Minnesota College of Medicine, Minneapolis, MN, USA;
| | - Zsolt Demetrovics
- Department of Psychology, Eotvos Lorand University, Budapest, Hungary
| | - Thomas Simpatico
- Department of Psychiatry, University of Vermont, Burlington, VT, USA
| | - Claudia Fahlke
- Department of Psychology, University of Gothenburg, Göteborg, Sweden;
| | - Oscar-Berman M
- Departments of Psychiatry and Anatomy & Neurobiology, Boston University School of Medicine and Boston VA Healthcare System, Boston, MA, USA
| | - Mona Li
- PATH Foundation NY, New York, NY, USA
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Commonalities in Development of Pure Breeds and Population Isolates Revealed in the Genome of the Sardinian Fonni's Dog. Genetics 2016; 204:737-755. [PMID: 27519604 PMCID: PMC5068859 DOI: 10.1534/genetics.116.192427] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/10/2016] [Indexed: 12/30/2022] Open
Abstract
The island inhabitants of Sardinia have long been a focus for studies of complex human traits due to their unique ancestral background and population isolation reflecting geographic and cultural restriction. Population isolates share decreased genomic diversity, increased linkage disequilibrium, and increased inbreeding coefficients. In many regions, dogs and humans have been exposed to the same natural and artificial forces of environment, growth, and migration. Distinct dog breeds have arisen through human-driven selection of characteristics to meet an ideal standard of appearance and function. The Fonni's Dog, an endemic dog population on Sardinia, has not been subjected to an intensive system of artificial selection, but rather has developed alongside the human population of Sardinia, influenced by geographic isolation and unregulated selection based on its environmental adaptation and aptitude for owner-desired behaviors. Through analysis of 28 dog breeds, represented with whole-genome sequences from 13 dogs and ∼170,000 genome-wide single nucleotide variants from 155 dogs, we have produced a genomic illustration of the Fonni's Dog. Genomic patterns confirm within-breed similarity, while population and demographic analyses provide spatial identity of Fonni's Dog to other Mediterranean breeds. Investigation of admixture and fixation indices reveals insights into the involvement of Fonni's Dogs in breed development throughout the Mediterranean. We describe how characteristics of population isolates are reflected in dog breeds that have undergone artificial selection, and are mirrored in the Fonni's Dog through traditional isolating factors that affect human populations. Lastly, we show that the genetic history of Fonni's Dog parallels demographic events in local human populations.
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