1
|
Ormond C, Ryan NM, Byerley W, Heron EA, Corvin A. Investigating copy number variants in schizophrenia pedigrees using a new consensus pipeline called PECAN. Sci Rep 2024; 14:17518. [PMID: 39080331 PMCID: PMC11289470 DOI: 10.1038/s41598-024-66021-0] [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: 12/19/2023] [Accepted: 06/26/2024] [Indexed: 08/02/2024] Open
Abstract
Copy number variants (CNVs) have been implicated in many human diseases, including psychiatric disorders. Whole genome sequencing offers advantages in CNV calling compared to previous array-based methods. Here we present a robust and transparent CNV calling pipeline, PECAN (PEdigree Copy number vAriaNt calling), for short-read, whole genome sequencing data, comprised of a novel combination of four calling methods and structural variant genotyping. This method is scalable and can incorporate pedigree information to retain lower-confidence CNVs that would otherwise be discarded. We have robustly benchmarked PECAN using gold-standard CNV calls for two well-established evaluation samples, NA12878 and HG002, showing that PECAN performs with high precision and recall on both datasets, outperforming another pedigree-based CNV calling pipeline. As part of this work, we provide a list of high-confidence gold standard CNVs for the NA12878 reference sample, curated from multiple studies. We applied PECAN to a collection of pedigrees multiply affected with schizophrenia and identified a rare deletion that perfectly co-segregates with schizophrenia in one of the pedigrees. The CNV overlaps the gene PITRM1, which has been implicated in a complex phenotype including ataxia, developmental delay, and schizophrenia-like episodes in affected adults.
Collapse
Affiliation(s)
- Cathal Ormond
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity Centre for Health Sciences, Trinity College Dublin, James' Street, Dublin 8, Ireland
| | - Niamh M Ryan
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity Centre for Health Sciences, Trinity College Dublin, James' Street, Dublin 8, Ireland
| | - William Byerley
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, USA
| | - Elizabeth A Heron
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity Centre for Health Sciences, Trinity College Dublin, James' Street, Dublin 8, Ireland
| | - Aiden Corvin
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity Centre for Health Sciences, Trinity College Dublin, James' Street, Dublin 8, Ireland.
| |
Collapse
|
2
|
Lee CC, Ye R, Tubbs JD, Baum L, Zhong Y, Leung SYJ, Chan SC, Wu KYK, Cheng PKJ, Chow LP, Leung PWL, Sham PC. Third-generation genome sequencing implicates medium-sized structural variants in chronic schizophrenia. Front Neurosci 2023; 16:1058359. [PMID: 36711134 PMCID: PMC9874699 DOI: 10.3389/fnins.2022.1058359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/14/2022] [Indexed: 01/13/2023] Open
Abstract
Background Schizophrenia (SCZ) is a heterogeneous psychiatric disorder, with significant contribution from genetic factors particularly for chronic cases with negative symptoms and cognitive deficits. To date, Genome Wide Association Studies (GWAS) and exome sequencing have associated SCZ with a number of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs), but there is still missing heritability. Medium-sized structural variants (SVs) are difficult to detect using SNP arrays or second generation sequencing, and may account for part of the missing heritability of SCZ. Aims and objectives To identify SVs associated with severe chronic SCZ across the whole genome. Study design 10 multiplex families with probands suffering from chronic SCZ with negative symptoms and cognitive deficits were recruited, with all their affected members demonstrating uni-lineal inheritance. Control subjects comprised one affected member from the affected lineage, and unaffected members from each paternal and maternal lineage. Methods Third generation sequencing was applied to peripheral blood samples from 10 probands and 5 unaffected controls. Bioinformatic tools were used to identify SVs from the long sequencing reads, with confirmation of findings in probands by short-read Illumina sequencing, Sanger sequencing and visual manual validation with Integrated Genome Browser. Results In the 10 probands, we identified and validated 88 SVs (mostly in introns and medium-sized), within 79 genes, which were absent in the 5 unaffected control subjects. These 79 genes were enriched in 20 biological pathways which were related to brain development, neuronal migration, neurogenesis, neuronal/synaptic function, learning/memory, and hearing. These identified SVs also showed evidence for enrichment of genes that are highly expressed in the adolescent striatum. Conclusion A substantial part of the missing heritability in SCZ may be explained by medium-sized SVs detectable only by third generation sequencing. We have identified a number of such SVs potentially conferring risk for SCZ, which implicate multiple brain-related genes and pathways. In addition to previously-identified pathways involved in SCZ such as neurodevelopment and neuronal/synaptic functioning, we also found novel evidence for enrichment in hearing-related pathways and genes expressed in the adolescent striatum.
Collapse
Affiliation(s)
- Chi Chiu Lee
- Department of Psychiatry, Kwai Chung Hospital, Hong Kong, Hong Kong SAR, China,*Correspondence: Chi Chiu Lee,
| | - Rui Ye
- Department of Psychiatry, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Justin D. Tubbs
- Department of Psychiatry, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Larry Baum
- Department of Psychiatry, The University of Hong Kong, Hong Kong, Hong Kong SAR, China,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yuanxin Zhong
- Department of Psychiatry, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Shuk Yan Joey Leung
- Department of Psychiatry, Kwai Chung Hospital, Hong Kong, Hong Kong SAR, China
| | - Sheung Chun Chan
- Department of Psychiatry, Tai Po Hospital, Hong Kong, Hong Kong SAR, China
| | - Kit Ying Kitty Wu
- Kowloon West Cluster, Hospital Authority, Hong Kong, Hong Kong SAR, China
| | - Po Kwan Jamie Cheng
- Department of Clinical Psychology, Yan Chai Hospital, Hong Kong, Hong Kong SAR, China
| | - Lai Ping Chow
- Department of Psychiatry, Kwai Chung Hospital, Hong Kong, Hong Kong SAR, China
| | - Patrick W. L. Leung
- Department of Psychology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Pak Chung Sham
- Department of Psychiatry, The University of Hong Kong, Hong Kong, Hong Kong SAR, China,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China,Centre for PanorOmic Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China,Pak Chung Sham,
| |
Collapse
|
3
|
Braga LG, Chud TCS, Watanabe RN, Savegnago RP, Sena TM, do Carmo AS, Machado MA, Panetto JCDC, da Silva MVGB, Munari DP. Identification of copy number variations in the genome of Dairy Gir cattle. PLoS One 2023; 18:e0284085. [PMID: 37036840 PMCID: PMC10085049 DOI: 10.1371/journal.pone.0284085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/23/2023] [Indexed: 04/11/2023] Open
Abstract
Studying structural variants that can control complex traits is relevant for dairy cattle production, especially for animals that are tolerant to breeding conditions in the tropics, such as the Dairy Gir cattle. This study identified and characterized high confidence copy number variation regions (CNVR) in the Gir breed genome. A total of 38 animals were whole-genome sequenced, and 566 individuals were genotyped with a high-density SNP panel, among which 36 animals had both sequencing and SNP genotyping data available. Two sets of high confidence CNVR were established: one based on common CNV identified in the studied population (CNVR_POP), and another with CNV identified in sires with both sequence and SNP genotyping data available (CNVR_ANI). We found 10 CNVR_POP and 45 CNVR_ANI, which covered 1.05 Mb and 4.4 Mb of the bovine genome, respectively. Merging these CNV sets for functional analysis resulted in 48 unique high confidence CNVR. The overlapping genes were previously related to embryonic mortality, environmental adaptation, evolutionary process, immune response, longevity, mammary gland, resistance to gastrointestinal parasites, and stimuli recognition, among others. Our results contribute to a better understanding of the Gir breed genome. Moreover, the CNV identified in this study can potentially affect genes related to complex traits, such as production, health, and reproduction.
Collapse
Affiliation(s)
- Larissa G Braga
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Tatiane C S Chud
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | - Rafael N Watanabe
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Rodrigo P Savegnago
- Department of Animal Science, Michigan State University, East Lansing, Michigan, United States of America
| | - Thomaz M Sena
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Adriana S do Carmo
- Departamento de Zootecnia, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | | | | | | | - Danísio P Munari
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| |
Collapse
|
4
|
Yoshikawa A, Kushima I, Miyashita M, Suzuki K, Iino K, Toriumi K, Horiuchi Y, Kawaji H, Ozaki N, Itokawa M, Arai M. Exonic deletions in IMMP2L in schizophrenia with enhanced glycation stress subtype. PLoS One 2022; 17:e0270506. [PMID: 35776734 PMCID: PMC9249242 DOI: 10.1371/journal.pone.0270506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/12/2022] [Indexed: 11/24/2022] Open
Abstract
We previously identified a subtype of schizophrenia (SCZ) characterized by increased plasma pentosidine, a marker of glycation and oxidative stress (PEN-SCZ). However, the genetic factors associated with PEN-SCZ have not been fully clarified. We performed a genome-wide copy number variation (CNV) analysis to identify CNVs associated with PEN-SCZ to provide an insight into the novel therapeutic targets for PEN-SCZ. Plasma pentosidine was measured by high-performance liquid chromatography in 185 patients with SCZ harboring rare CNVs detected by array comparative genomic hybridization. In three patients with PEN-SCZ showing additional autistic features, we detected a novel deletion at 7q31.1 within exons 2 and 3 of IMMP2L, which encodes the inner mitochondrial membrane peptidase subunit 2. The deletion was neither observed in non-PEN-SCZ nor in public database of control subjects. IMMP2L is one of the SCZ risk loci genes identified in a previous SCZ genome-wide association study, and its trans-populational association was recently described. Interestingly, deletions in IMMP2L have been previously linked with autism spectrum disorder. Disrupted IMMP2L function has been shown to cause glycation/oxidative stress in neuronal cells in an age-dependent manner. To our knowledge, this is the first genome-wide CNV study to suggest the involvement of IMMP2L exons 2 and 3 in the etiology of PEN-SCZ. The combination of genomic information with plasma pentosidine levels may contribute to the classification of biological SCZ subtypes that show additional autistic features. Modifying IMMP2L functions may be useful for treating PEN-SCZ if the underlying biological mechanism can be clarified in further studies.
Collapse
Affiliation(s)
- Akane Yoshikawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Setagaya, Tokyo, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Mitsuhiro Miyashita
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Setagaya, Tokyo, Japan
- Department of Psychiatry, Takatsuki Clinic, Akishima, Tokyo, Japan
| | - Kazuhiro Suzuki
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Setagaya, Tokyo, Japan
- Department of Psychiatry, Takatsuki Clinic, Akishima, Tokyo, Japan
| | - Kyoka Iino
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Kazuya Toriumi
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Yasue Horiuchi
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Setagaya, Tokyo, Japan
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Masanari Itokawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Setagaya, Tokyo, Japan
| | - Makoto Arai
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Setagaya, Tokyo, Japan
- * E-mail:
| |
Collapse
|
5
|
Toyama M, Takasaki Y, Branko A, Kimura H, Kato H, Nawa Y, Kushima I, Ishizuka K, Shimamura T, Ogi T, Ozaki N. Exome sequencing of Japanese schizophrenia multiplex families supports the involvement of calcium ion channels. PLoS One 2022; 17:e0268321. [PMID: 35536790 PMCID: PMC9089874 DOI: 10.1371/journal.pone.0268321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 04/27/2022] [Indexed: 11/18/2022] Open
Abstract
Background Most sequencing studies of schizophrenia (SCZ) have focused on de novo genetic variants due to interpretability. However, investigating shared rare variants among patients in the same multiplex family is also important. Relatively large-scale analyses of SCZ multiplex families have been done in Caucasian populations, but whether detected variants are also pathogenic in the Japanese population is unclear because of ethnic differences in rare variants. Materials and methods We performed whole-exome sequencing (WES) of 14 Japanese SCZ multiplex families. After quality control and filtering, we identified rare variants shared among affected persons within the same family. A gene ontology (GO) analysis was performed to identify gene categories possibly affected by these candidate variants. Results We found 530 variants in 486 genes as potential candidate variants from the 14 SCZ multiplex families examined. The GO analysis demonstrated significant enrichment in calcium channel activity. Conclusion This study provides supporting evidence that calcium ion channel activity is involved in SCZ. WES of multiplex families is a potential means of identifying disease-associated rare variants for SCZ.
Collapse
Affiliation(s)
- Miho Toyama
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yuto Takasaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Aleksic Branko
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Hiroki Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- * E-mail:
| | - Hidekazu Kato
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yoshihiro Nawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kanako Ishizuka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| |
Collapse
|
6
|
Baz-Redón N, Soler-Colomer L, Fernández-Cancio M, Benito-Sanz S, Garrido M, Moliné T, Clemente M, Camats-Tarruella N, Yeste D. Novel variant in HHAT as a cause of different sex development with partial gonadal dysgenesis associated with microcephaly, eye defects, and distal phalangeal hypoplasia of both thumbs: Case report. Front Endocrinol (Lausanne) 2022; 13:957969. [PMID: 36303863 PMCID: PMC9592858 DOI: 10.3389/fendo.2022.957969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/15/2022] [Indexed: 11/26/2022] Open
Abstract
The palmitoylation of the Hedgehog (Hh) family of morphogens, named sonic hedgehog (SHH), desert hedgehog (DHH), and Indian hedgehog (IHH), is crucial for effective short- and long-range signaling. The hedgehog acyltransferase (HHAT) attaches the palmitate molecule to the Hh; therefore, variants in HHAT cause a broad spectrum of phenotypes. A missense HHAT novel variant c.1001T>A/p.(Met334Lys) was described in a patient first referred for a 46,XY different sexual development with partial gonadal dysgenesis but with microcephaly, eye defects, and distal phalangeal hypoplasia of both thumbs. The in silico analysis of the variant predicted an affectation of the nearest splicing site. Thus, in vitro minigene studies were carried out, which demonstrated that the variant does not affect the splicing. Subsequent protein in silico studies supported the pathogenicity of the variant, and, in conclusion, this was considered the cause of the patient's phenotype.
Collapse
Affiliation(s)
- Noelia Baz-Redón
- Growth and Development Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, Barcelona, Spain
- Pediatrics, Obstetrics and Gynecology and Preventive Medicine Department, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Soler-Colomer
- Pediatric Endocrinology Section, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Mónica Fernández-Cancio
- Growth and Development Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, Barcelona, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Sara Benito-Sanz
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autonóma de Madrid, Madrid, Spain
| | - Marta Garrido
- Department of Pathology, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Teresa Moliné
- Department of Pathology, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - María Clemente
- Growth and Development Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, Barcelona, Spain
- Pediatrics, Obstetrics and Gynecology and Preventive Medicine Department, Universitat Autònoma de Barcelona, Barcelona, Spain
- Pediatric Endocrinology Section, Hospital Universitari Vall d’Hebron, Barcelona, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Núria Camats-Tarruella
- Growth and Development Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, Barcelona, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- *Correspondence: Núria Camats-Tarruella,
| | - Diego Yeste
- Growth and Development Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, Barcelona, Spain
- Pediatrics, Obstetrics and Gynecology and Preventive Medicine Department, Universitat Autònoma de Barcelona, Barcelona, Spain
- Pediatric Endocrinology Section, Hospital Universitari Vall d’Hebron, Barcelona, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| |
Collapse
|
7
|
Historical pursuits of the language pathway hypothesis of schizophrenia. NPJ SCHIZOPHRENIA 2021; 7:53. [PMID: 34753947 PMCID: PMC8578658 DOI: 10.1038/s41537-021-00182-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/13/2021] [Indexed: 12/21/2022]
|
8
|
Pol-Fuster J, Cañellas F, Ruiz-Guerra L, Medina-Dols A, Bisbal-Carrió B, Ortega-Vila B, Llinàs J, Hernandez-Rodriguez J, Lladó J, Olmos G, Strauch K, Heine-Suñer D, Vives-Bauzà C, Flaquer A. The conserved ASTN2/BRINP1 locus at 9q33.1-33.2 is associated with major psychiatric disorders in a large pedigree from Southern Spain. Sci Rep 2021; 11:14529. [PMID: 34267256 PMCID: PMC8282839 DOI: 10.1038/s41598-021-93555-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/21/2021] [Indexed: 11/11/2022] Open
Abstract
We investigated the genetic causes of major mental disorders (MMDs) including schizophrenia, bipolar disorder I, major depressive disorder and attention deficit hyperactive disorder, in a large family pedigree from Alpujarras, South of Spain, a region with high prevalence of psychotic disorders. We applied a systematic genomic approach based on karyotyping (n = 4), genotyping by genome-wide SNP array (n = 34) and whole-genome sequencing (n = 12). We performed genome-wide linkage analysis, family-based association analysis and polygenic risk score estimates. Significant linkage was obtained at chromosome 9 (9q33.1–33.2, LOD score = 4.11), a suggestive region that contains five candidate genes ASTN2, BRINP1, C5, TLR4 and TRIM32, previously associated with MMDs. Comprehensive analysis associated the MMD phenotype with genes of the immune system with dual brain functions. Moreover, the psychotic phenotype was enriched for genes involved in synapsis. These results should be considered once studying the genetics of psychiatric disorders in other families, especially the ones from the same region, since founder effects may be related to the high prevalence.
Collapse
Affiliation(s)
- Josep Pol-Fuster
- Department of Biology, University of Balearic Islands (UIB), Institut Universitari d'Investigacions en Ciències de la Salut (IUNICS), Palma, Spain.,Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain
| | - Francesca Cañellas
- Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain.,Department of Psychiatry, HUSE, IdISBa, Palma, Spain
| | - Laura Ruiz-Guerra
- Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain
| | - Aina Medina-Dols
- Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain
| | - Bàrbara Bisbal-Carrió
- Department of Biology, University of Balearic Islands (UIB), Institut Universitari d'Investigacions en Ciències de la Salut (IUNICS), Palma, Spain.,Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain
| | - Bernat Ortega-Vila
- Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain.,Molecular Diagnostics and Clinical Genetics Unit (UDMGC) and Genomics of Health Research Group, Hospital Universitari Son Espases (HUSE) and Institut d'Investigacions Sanitaries de Balears (IDISBA), Palma, Spain
| | - Jaume Llinàs
- Department of Biology, University of Balearic Islands (UIB), Institut Universitari d'Investigacions en Ciències de la Salut (IUNICS), Palma, Spain
| | - Jessica Hernandez-Rodriguez
- Molecular Diagnostics and Clinical Genetics Unit (UDMGC) and Genomics of Health Research Group, Hospital Universitari Son Espases (HUSE) and Institut d'Investigacions Sanitaries de Balears (IDISBA), Palma, Spain
| | - Jerònia Lladó
- Department of Biology, University of Balearic Islands (UIB), Institut Universitari d'Investigacions en Ciències de la Salut (IUNICS), Palma, Spain.,Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain
| | - Gabriel Olmos
- Department of Biology, University of Balearic Islands (UIB), Institut Universitari d'Investigacions en Ciències de la Salut (IUNICS), Palma, Spain.,Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain
| | - Konstantin Strauch
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany.,Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, LMU Munich, Munich, Germany
| | - Damià Heine-Suñer
- Molecular Diagnostics and Clinical Genetics Unit (UDMGC) and Genomics of Health Research Group, Hospital Universitari Son Espases (HUSE) and Institut d'Investigacions Sanitaries de Balears (IDISBA), Palma, Spain
| | - Cristòfol Vives-Bauzà
- Department of Biology, University of Balearic Islands (UIB), Institut Universitari d'Investigacions en Ciències de la Salut (IUNICS), Palma, Spain. .,Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain.
| | - Antònia Flaquer
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany.,Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, LMU Munich, Munich, Germany
| |
Collapse
|
9
|
Abstract
Advances in next-generation sequencing technology have enabled whole genome sequencing (WGS) to be widely used for identification of causal variants in a spectrum of genetic-related disorders, and provided new insight into how genetic polymorphisms affect disease phenotypes. The development of different bioinformatics pipelines has continuously improved the variant analysis of WGS data. However, there is a necessity for a systematic performance comparison of these pipelines to provide guidance on the application of WGS-based scientific and clinical genomics. In this study, we evaluated the performance of three variant calling pipelines (GATK, DRAGEN and DeepVariant) using the Genome in a Bottle Consortium, "synthetic-diploid" and simulated WGS datasets. DRAGEN and DeepVariant show better accuracy in SNP and indel calling, with no significant differences in their F1-score. DRAGEN platform offers accuracy, flexibility and a highly-efficient execution speed, and therefore superior performance in the analysis of WGS data on a large scale. The combination of DRAGEN and DeepVariant also suggests a good balance of accuracy and efficiency as an alternative solution for germline variant detection in further applications. Our results facilitate the standardization of benchmarking analysis of bioinformatics pipelines for reliable variant detection, which is critical in genetics-based medical research and clinical applications.
Collapse
|
10
|
Zhao S, Agafonov O, Azab A, Stokowy T, Hovig E. Accuracy and efficiency of germline variant calling pipelines for human genome data. Sci Rep 2020; 10:20222. [PMID: 33214604 PMCID: PMC7678823 DOI: 10.1038/s41598-020-77218-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 11/02/2020] [Indexed: 12/30/2022] Open
Abstract
Advances in next-generation sequencing technology have enabled whole genome sequencing (WGS) to be widely used for identification of causal variants in a spectrum of genetic-related disorders, and provided new insight into how genetic polymorphisms affect disease phenotypes. The development of different bioinformatics pipelines has continuously improved the variant analysis of WGS data. However, there is a necessity for a systematic performance comparison of these pipelines to provide guidance on the application of WGS-based scientific and clinical genomics. In this study, we evaluated the performance of three variant calling pipelines (GATK, DRAGEN and DeepVariant) using the Genome in a Bottle Consortium, "synthetic-diploid" and simulated WGS datasets. DRAGEN and DeepVariant show better accuracy in SNP and indel calling, with no significant differences in their F1-score. DRAGEN platform offers accuracy, flexibility and a highly-efficient execution speed, and therefore superior performance in the analysis of WGS data on a large scale. The combination of DRAGEN and DeepVariant also suggests a good balance of accuracy and efficiency as an alternative solution for germline variant detection in further applications. Our results facilitate the standardization of benchmarking analysis of bioinformatics pipelines for reliable variant detection, which is critical in genetics-based medical research and clinical applications.
Collapse
Affiliation(s)
- Sen Zhao
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0310, Oslo, Norway
| | | | - Abdulrahman Azab
- Center for Bioinformatics, Department of Informatics, University of Oslo, 0316, Oslo, Norway
- Division of Research Computing, University Center for Information Technology (USIT), University of Oslo, 0316, Oslo, Norway
| | - Tomasz Stokowy
- Computational Biology Unit, Institute of Informatics, University of Bergen, 5008, Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0310, Oslo, Norway.
- Center for Bioinformatics, Department of Informatics, University of Oslo, 0316, Oslo, Norway.
| |
Collapse
|
11
|
Schwab SG. Dissecting the molecular biology of schizophrenia: A call for emphasising genetic and phenotypic heterogeneity: commentary on Torrey and Yolken (this issue). Psychiatry Res 2020; 287:112430. [PMID: 31200949 DOI: 10.1016/j.psychres.2019.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 06/03/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Sibylle G Schwab
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine & Health, University of Wollongong, NSW, 2522, Australia; Illawarra Health and Medical Research Institute, Australia.
| |
Collapse
|
12
|
Rhoades R, Jackson F, Teng S. Discovery of rare variants implicated in schizophrenia using next-generation sequencing. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2019; 3:1-20. [PMID: 33981965 PMCID: PMC8112455 DOI: 10.20517/jtgg.2018.26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Schizophrenia is a highly heritable psychiatric disorder that affects 1% of the population. Genome-wide association studies have identified common variants in candidate genes associated with schizophrenia, but the genetics mechanisms of this disorder have not yet been elucidated. The discovery of rare genetic variants that contribute to schizophrenia symptoms promises to help explain the missing heritability of the disease. Next generation sequencing techniques are revolutionizing the field of psychiatric genetics. Various statistical approaches have been developed for rare variant association testing in case-control and family studies. Targeted resequencing, whole exome sequencing and whole genome sequencing combined with these computational tools are used for the discovery of rare genetic variations in schizophrenia. The findings provide useful information for characterizing the rare mutations and elucidating the genetic mechanisms by which the variants cause schizophrenia.
Collapse
Affiliation(s)
- Raina Rhoades
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Fatimah Jackson
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Shaolei Teng
- Department of Biology, Howard University, Washington, DC 20059, USA
| |
Collapse
|
13
|
Supernat A, Vidarsson OV, Steen VM, Stokowy T. Comparison of three variant callers for human whole genome sequencing. Sci Rep 2018; 8:17851. [PMID: 30552369 PMCID: PMC6294778 DOI: 10.1038/s41598-018-36177-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/13/2018] [Indexed: 12/30/2022] Open
Abstract
Testing of patients with genetics-related disorders is in progress of shifting from single gene assays to gene panel sequencing, whole-exome sequencing (WES) and whole-genome sequencing (WGS). Since WGS is unquestionably becoming a new foundation for molecular analyses, we decided to compare three currently used tools for variant calling of human whole genome sequencing data. We tested DeepVariant, a new TensorFlow machine learning-based variant caller, and compared this tool to GATK 4.0 and SpeedSeq, using 30×, 15× and 10× WGS data of the well-known NA12878 DNA reference sample. According to our comparison, the performance on SNV calling was almost similar in 30× data, with all three variant callers reaching F-Scores (i.e. harmonic mean of recall and precision) equal to 0.98. In contrast, DeepVariant was more precise in indel calling than GATK and SpeedSeq, as demonstrated by F-Scores of 0.94, 0.90 and 0.84, respectively. We conclude that the DeepVariant tool has great potential and usefulness for analysis of WGS data in medical genetics.
Collapse
Affiliation(s)
- Anna Supernat
- Laboratory of Cell Biology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | | | - Vidar M Steen
- NORMENT & K.J. Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Dr. E. Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Tomasz Stokowy
- Computational Biology Unit, Institute of Informatics, University of Bergen, Bergen, Norway.
- NORMENT & K.J. Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Dr. E. Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| |
Collapse
|