High frequencies of de novo CNVs in bipolar disorder and schizophrenia.

paper Cited Public

Figure 1

Detection, Validation, and Breakpoint Sequencing of De Novo CNVs in BDRepresentative examples of microarray data and sequencing results are provided for deletions detected in two subjects with diagnoses of BD, 410-10142 (panel I) and 410-10127 (panel II).(A) De novo CNVs were identified from whole-genome scans of the child, mother, and father, using the NimbleGen HD2 platform.(B) CNV validation and breakpoint refinement was performed by analysis of the trio using a custom Agilent microarray with dense probe coverage of the target region (~200 bp spacing).(C) Deletion breakpoints were determined by PCR and Sanger sequencing.(D) UCSC genome browser tracks of known genes are shown to scale with a track for de novo deletions displayed in red.

LLM interpretation

This figure presents the detection and validation of de novo copy number variants (CNVs) in two subjects (410-10142 and 410-10127) across four panels. Panels A and B show microarray Log2Ratio plots for the child, mother, and father, where the child exhibits a distinct dip in signal indicating a deletion not present in the parents. Panel C displays Sanger sequencing chromatograms identifying the specific deletion breakpoints, and Panel D uses UCSC genome browser tracks to map these red-highlighted de novo deletions relative to known genes and genomic coordinates.

Figure 2

Detection, Validation, and Breakpoint Sequencing of De Novo CNVs in SCZRepresentative examples of microarray data and sequencing results are provided for deletions detected in two subjects with diagnoses of SCZ, 02-0104 (panel I) and 02-0047 (panel II).(A) De novo CNVs were identified from whole-genome scans of the child, mother, and father, using the NimbleGen HD2 platform.(B) CNV validation and breakpoint refinement was performed by analysis of the trio using a custom Agilent microarray with dense probe coverage of the target region (~200 bp spacing).(C) Deletion breakpoints were determined by PCR and Sanger sequencing.(D) UCSC genome browser tracks of known genes are shown to scale with a track for de novo deletions displayed in red.

LLM interpretation

This figure presents the detection and validation of de novo copy number variants (CNVs) in two subjects with schizophrenia (02-0104 and 02-0047). Panels A and B show microarray Log2Ratio plots across genome order for the child, mother, and father, where a dip in the child's signal indicates a deletion absent in the parents. Panel C displays Sanger sequencing chromatograms identifying specific deletion breakpoints, and Panel D uses UCSC genome browser tracks to map these red-highlighted de novo deletions relative to known genes (e.g., *CSMD3* and *UGT8*).

Figure 3

Survival Analysis of De Novo CNVs and Age at Onset in BD and SCZWe performed a survival analysis/Kaplan-Meier test to analyze the effect of de novo mutations on age at onset in BD(n = 185, panel A) and SCZ (n = 177, panel B). This test determines whether “time to diagnosis” differs systematically between patients who have de novo mutations and those who do not. The test is formalized by performing the Mantel-Haenszel test on the survival curves and reporting the resulting p value.

LLM interpretation

This figure consists of two Kaplan-Meier survival plots (A and B) showing the percentage of subjects not yet diagnosed relative to age at onset for bipolar disorder (BD) and schizophrenia (SCZ). In panel A (BD), subjects with *de novo* mutations (orange line) show an earlier age at onset compared to those without (blue line), with a statistically significant p-value of 0.0368. In panel B (SCZ), the curves for subjects with and without *de novo* mutations overlap significantly, with a non-significant p-value of 0.743.

#	Section	Preview
0	Introduction	Bipolar disorder (BD, also known as manic-depressive illness) is a severe mood disorder consisting…
1	Introduction	Genes play an important role in risk for BD. The rate of concordance for monozygotic twins is 40%,…
2	Introduction	Genetic risk factors with individually large effects are likely to be rare. Association-based…
3	Introduction	Alternative approaches that focus on rare genetic variants are needed. One genetic approach that has…
4	Introduction	Observations of a similar nature have been made in studies of BD. CNV loci at 16p11.2 (McCarthy et…
5	Introduction	Some of the earliest conclusive evidence for the role of rare CNVs in psychiatric disorders has come…
6	Results	Our study sample included 788 subject-mother-father trios with confirmed parentage. DNA from all…
7	Results	We performed high-resolution genome-wide copy-number scans, using the NimbleGen HD2 array…
8	Results	A total of 23 de novo CNVs were detected and validated in our study sample, including fourteen…
9	Results	About one-third (8/23) of de novo CNVs in our study were flanked by segmental duplications (SDs) at…
10	Results	De novo CNVs were significantly associated with BD and SCZ (Table 2). The rate of de novo mutation…
11	Results	We investigated the influence of age at onset on the frequency of de novo mutations. After…
12	Results	We further reasoned that frequencies of de novo CNVs might be influenced by the presence or lack of…
13	Results	While de novo CNVs might have a stronger effect size, it is quite plausible that inherited CNVs…
14	Results	We sought additional genetic evidence for the loci at which we found de novo CNVs by performing…
15	Results	Previous studies have reported that rare CNVs associated with neuropsychiatric disorders are…
16	Results	Based on the primary analysis using DAVID, eight functional categories were enriched among de novo…
17	Discussion	Here we find strong evidence implicating rare de novo CNVs in genetic risk for bipolar disorder. We…
18	Discussion	Two previous case-control studies have observed an enrichment of rare CNVs in bipolar disorder and…
19	Discussion	The high-density microarray platform used in this study (2.1 million probes) provides good…

Name	Type
15q13.3 deletion	variant
15q13.3 duplication	variant
16p11.2 CNV	variant
1q21.1 duplication	variant
3q29 local	variant
3q29 CNV local	variant
426 control trios local	cohort
45 ASD trios local	cohort
788 trios local	cohort
7q36.3 local	variant
age at onset	phenotype
arrays local	drug
ASD	phenotype
ASD cohort local	cohort
ASD Subjects local	cohort
autism	phenotype
autism spectrum disorder	phenotype
BBID local	drug
BD	phenotype
BD cohort local	cohort
BiGS study local	cohort
BioCarta local	drug
bipolar disorder	phenotype
Bipolar Genome Study local	cohort
bipolar I disorder	phenotype
bipolar II disorder	phenotype
CACNA1C	gene
cases	cohort
children	cohort
CMIP local	gene
CNP	variant
CNV	variant
CNVs	variant
CNVs > 10 kb local	variant
control	cohort
control population	cohort
controls	cohort
copy-number polymorphisms local	variant
copy-number variants	variant
CSMD3	gene
DAVID Bioinformatics Resources 6.7 local	drug
deletion	variant
deletion adjacent to UGT8 local	variant
deletion involving CMIP and PLCG2 local	variant
de_novo_CNVs local	variant
de novo variant	variant
depression	phenotype
duplication	variant
early age at onset	phenotype
early-onset bipolar disorder	phenotype
early onset mania local	phenotype
exonic deletion of LINGO2 local	variant
Familial bipolar disorder local	cohort
families	cohort
first-degree relatives	cohort
full sample	cohort
general population	cohort
genomic DNA	drug
GO_BP local	drug
GO_CC local	drug
GO_MF local	drug
Grigoroiu-Serbanescu et al., 2001 local	cohort
Grozeva et al., 2010 local	cohort
healthy controls	cohort
Hindbrain development local	phenotype
inherited CNV local	variant
inherited CNVs	variant
inherited variants local	variant
insertion	variant
intellectual disability	phenotype
Intermediate-size CNVs local	variant
International schizophrenia Consortium	cohort
intronic deletion of CSMD3 local	variant
KEGG	drug
Kelch-type beta propeller local	phenotype
Kirov et al., 2011 local	cohort
Large inherited duplications (≥500 kb) local	variant
late-onset bipolar disorder local	phenotype
Levy2011Controls local	cohort
Levy et al., 2011 local	cohort
LINGO2 local	gene
major depressive disorder	phenotype
mania	phenotype
Marshall et al., 2008 local	cohort
McQuillin et al., 2011 local	cohort
MeZOD local	drug
MGS	anatomy
Molecular Genetics of Schizophrenia local	cohort
mood disorders	phenotype
Mood Disorder Subjects local	cohort
Neural tube development	phenotype
Neurodevelopmental local	phenotype
neuropsychiatric disorders	phenotype
nonallelic homologous recombination local	drug
ODZ4	gene
Our Study Sample local	cohort
Panther pathway database local	drug
parents	cohort
patients with bipolar disorder	phenotype
PCR primers	drug
Pinto et al., 2010 local	cohort
PLCG2 local	gene
Plink	drug
Positive family history of mental illness local	phenotype
present family-based study local	cohort
previous case-control studies local	cohort
Priebe et al., 2011 local	cohort
probe ratio data local	drug
QC filters local	drug
rare alleles of large effect	variant
rare CNV	variant
rare CNVs	variant
Rare CNVs (>100 kb) local	variant
rare copy number variants	variant
reference population	cohort
Response to ethanol local	phenotype
Sanders et al., 2011 local	cohort
schizoaffective disorder	phenotype
schizophrenia	phenotype
Schizophrenia Subjects local	cohort
SCZ	phenotype
SCZ cohort local	cohort
Sebat et al., 2007 local	cohort
segmental duplication local	drug
short interspersed nuclear element local	drug
Sporadic bipolar disorder local	cohort
Sporadic case local	phenotype
sporadic cases	cohort
subjects	cohort
suicide	phenotype
synapse	anatomy
Synaptic local	phenotype
trios	cohort
Twin cohort	cohort
UGT8 local	gene
Vacic et al. 2011 study local	cohort
Xu et al., 2008 local	cohort
Xu et al., 2009 local	cohort
Zhang et al., 2009 local	cohort

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In this knowledge base

Title	Year	PMID
Genetics of Alcohol Use Disorder: A Role for Induced Pluripotent Stem Cells?	2018	29897633
Divergent Levels of Marker Chromosomes in an hiPSC-Based Model of Psychosis.	2017	28216146
Characterization of bipolar disorder patient-specific induced pluripotent stem cells from a family reveals neurodevelopmental and mRNA expression abnormalities.	2015	25733313
Genetic determinants of depression: recent findings and future directions.	2015	25563565
Genetics and genomics of psychiatric disease.	2015	26404826
Assessing the utility of intermediate phenotypes for genetic mapping of psychiatric disease.	2014	25216981
Copy number variation in obsessive-compulsive disorder and tourette syndrome: a cross-disorder study.	2014	25062598
Synaptic dysregulation in a human iPS cell model of mental disorders.	2014	25132547
Distribution of disease-associated copy number variants across distinct disorders of cognitive development.	2013	23582872
CNVs: harbingers of a rare variant revolution in psychiatric genetics.	2012	22424231
Genetic architectures of psychiatric disorders: the emerging picture and its implications.	2012	22777127

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High-resolution copy number variation analysis of schizophrenia in Japan.	Kushima I et al.	—	2017	→
Prenatal genetic counselling for psychiatric disorders.	Inglis A et al.	—	2017	→
Rare damaging variants in DNA repair and cell cycle pathways are associated with hippocampal and cognitive dysfunction: a combined genetic imaging study in first-episode treatment-naive patients with schizophrenia.	Yang Z et al.	—	2017	→
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A Case for Returning to Multiplex Families for Further Understanding the Heritability of Schizophrenia: A Psychiatrist's Perspective.	DeLisi LE	—	2016	→
A novel 3q29 deletion associated with autism, intellectual disability, psychiatric disorders, and obesity.	Biamino E et al.	—	2016	→
Array-based molecular karyotyping in fetuses with isolated brain malformations identifies disease-causing CNVs.	Schumann M et al.	—	2016	→
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CUB and Sushi multiple domains 3 regulates dendrite development.	Mizukami T et al.	—	2016	→
Differential sensory fMRI signatures in autism and schizophrenia: Analysis of amplitude and trial-to-trial variability.	Haigh SM et al.	—	2016	→
Exome sequencing for bipolar disorder points to roles of de novo loss-of-function and protein-altering mutations.	Kataoka M et al.	—	2016	→
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SALM5 trans-synaptically interacts with LAR-RPTPs in a splicing-dependent manner to regulate synapse development.	Choi Y et al.	—	2016	→
Uncovering obsessive-compulsive disorder risk genes in a pediatric cohort by high-resolution analysis of copy number variation.	Gazzellone MJ et al.	—	2016	→
A genome-wide copy number variant study of suicidal behavior.	Gross JA et al.	—	2015	→
Age-related sperm DNA methylation changes are transmitted to offspring and associated with abnormal behavior and dysregulated gene expression.	Milekic MH et al.	—	2015	→
Assessing the Power of Exome Chips.	Page CM et al.	—	2015	→
Assessment of copy number variations in the brain genome of schizophrenia patients.	Sakai M et al.	—	2015	→
Characterization of bipolar disorder patient-specific induced pluripotent stem cells from a family reveals neurodevelopmental and mRNA expression abnormalities.	Madison JM et al.	—	2015	→
Childhood-onset schizophrenia case with 2.2 Mb deletion at chromosome 3p12.2-p12.1 and two large chromosomal abnormalities at 16q22.3-q24.3 and Xq23-q28.	Rudd D et al.	—	2015	→
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Genetic and genomic analyses as a basis for new diagnostic nosologies.	Gershon ES et al.	—	2015	→
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Genomic structural variation in affective, anxiety, and stress-related disorders.	Ono S et al.	—	2015	→
Imaging Brain Development: Benefiting from Individual Variability.	Sharda M et al.	—	2015	→
Novel Findings from CNVs Implicate Inhibitory and Excitatory Signaling Complexes in Schizophrenia.	Pocklington AJ et al.	—	2015	→
Recent genetic findings in schizophrenia and their therapeutic relevance.	Harrison PJ	—	2015	→
Regulation of recombination and genomic maintenance.	Heyer WD	—	2015	→
Spatiotemporal 16p11.2 protein network implicates cortical late mid-fetal brain development and KCTD13-Cul3-RhoA pathway in psychiatric diseases.	Lin GN et al.	—	2015	→
Splicing-Dependent Trans-synaptic SALM3-LAR-RPTP Interactions Regulate Excitatory Synapse Development and Locomotion.	Li Y et al.	—	2015	→
S-SCAM, a rare copy number variation gene, induces schizophrenia-related endophenotypes in transgenic mouse model.	Zhang N et al.	—	2015	→
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Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells.	McCole RB et al.	—	2014	→
A genome-wide association analysis of a broad psychosis phenotype identifies three loci for further investigation.	Psychosis Endophenotypes International Consortium et al.	—	2014	→
An inherited duplication at the gene p21 Protein-Activated Kinase 7 (PAK7) is a risk factor for psychosis.	Morris DW et al.	—	2014	→
An inherited small microdeletion at 15q13.3 in a patient with early-onset obsessive-compulsive disorder.	Cappi C et al.	—	2014	→
Assessing the utility of intermediate phenotypes for genetic mapping of psychiatric disease.	Flint J et al.	—	2014	→
Chronic desipramine treatment rescues depression-related, social and cognitive deficits in Engrailed-2 knockout mice.	Brielmaier J et al.	—	2014	→
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Copy number variant study of bipolar disorder in Canadian and UK populations implicates synaptic genes.	Noor A et al.	—	2014	→
Copy number variation in obsessive-compulsive disorder and tourette syndrome: a cross-disorder study.	McGrath LM et al.	—	2014	→
Copy number variation in schizophrenia in Sweden.	Szatkiewicz JP et al.	—	2014	→
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De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability.	McCarthy SE et al.	—	2014	→
De novo mutations in schizophrenia implicate synaptic networks.	Fromer M et al.	—	2014	→
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Evolutionary conservation in genes underlying human psychiatric disorders.	Ogawa LM et al.	—	2014	→
Excess of rare novel loss-of-function variants in synaptic genes in schizophrenia and autism spectrum disorders.	Kenny EM et al.	—	2014	→
Exome sequencing in 53 sporadic cases of schizophrenia identifies 18 putative candidate genes.	Guipponi M et al.	—	2014	→
Explaining additional genetic variation in complex traits.	Robinson MR et al.	—	2014	→
Genetic relationships between schizophrenia, bipolar disorder, and schizoaffective disorder.	Cardno AG et al.	—	2014	→
Genome-wide copy number variation analysis in adult attention-deficit and hyperactivity disorder.	Ramos-Quiroga JA et al.	—	2014	→
Genomic insights into the overlap between psychiatric disorders: implications for research and clinical practice.	Doherty JL et al.	—	2014	→
Identification of pathways for bipolar disorder: a meta-analysis.	Nurnberger JI et al.	—	2014	→
Identification of structural variation in mouse genomes.	Keane TM et al.	—	2014	→
Identifying Potential Regions of Copy Number Variation for Bipolar Disorder.	Chen YH et al.	—	2014	→
Large-scale genomics unveils the genetic architecture of psychiatric disorders.	Gratten J et al.	—	2014	→
Long-term depression-inducing stimuli promote cleavage of the synaptic adhesion molecule NGL-3 through NMDA receptors, matrix metalloproteinases and presenilin/γ-secretase.	Lee H et al.	—	2014	→
Loss-of-function variants in schizophrenia risk and SETD1A as a candidate susceptibility gene.	Takata A et al.	—	2014	→
Neuroanatomical phenotypes in a mouse model of the 22q11.2 microdeletion.	Ellegood J et al.	—	2014	→
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Proteomic analysis of rat prefrontal cortex after chronic valproate treatment.	Thangavel M et al.	—	2014	→
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Scan statistic-based analysis of exome sequencing data identifies FAN1 at 15q13.3 as a susceptibility gene for schizophrenia and autism.	Ionita-Laza I et al.	—	2014	→
Synaptic dysregulation in a human iPS cell model of mental disorders.	Wen Z et al.	—	2014	→
The phenotypic manifestations of rare CNVs in schizophrenia.	Merikangas AK et al.	—	2014	→
The role of F-actin in modulating Clathrin-mediated endocytosis: Lessons from neurons in health and neuropsychiatric disorder.	Loebrich S	—	2014	→
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A common 56-kilobase deletion in a primate-specific segmental duplication creates a novel butyrophilin-like protein.	Aigner J et al.	—	2013	→
A high-resolution enhancer atlas of the developing telencephalon.	Visel A et al.	—	2013	→
Alterations in mitochondrial DNA copy number and the activities of electron transport chain complexes and pyruvate dehydrogenase in the frontal cortex from subjects with autism.	Gu F et al.	—	2013	→
An emerging role for Wnt and GSK3 signaling pathways in schizophrenia.	Singh KK	—	2013	→
A proposal for reframing schizophrenia research.	Molina V et al.	—	2013	→
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Consideration of plausible genetic architectures for schizophrenia and implications for analytic approaches in the era of next generation sequencing.	Curtis D	—	2013	→
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Genetics of psychiatric disorders in the GWAS era: an update on schizophrenia.	Schwab SG et al.	—	2013	→
Human spermatogenic failure purges deleterious mutation load from the autosomes and both sex chromosomes, including the gene DMRT1.	Lopes AM et al.	—	2013	→
Identification of rare copy number variants in high burden schizophrenia families.	Van Den Bossche MJ et al.	—	2013	→
Impacts of variation in the human genome on gene regulation.	Haraksingh RR et al.	—	2013	→
LAR-RPTPs: synaptic adhesion molecules that shape synapse development.	Um JW et al.	—	2013	→
Multiple variants aggregate in the neuregulin signaling pathway in a subset of schizophrenia patients.	Hatzimanolis A et al.	—	2013	→
Neurodevelopmental disorders: mechanisms and boundary definitions from genomes, interactomes and proteomes.	Mullin AP et al.	—	2013	→
Phenotypic impact of genomic structural variation: insights from and for human disease.	Weischenfeldt J et al.	—	2013	→
Protein tyrosine phosphatases PTPδ, PTPσ, and LAR: presynaptic hubs for synapse organization.	Takahashi H et al.	—	2013	→
Rare exonic deletions implicate the synaptic organizer Gephyrin (GPHN) in risk for autism, schizophrenia and seizures.	Lionel AC et al.	—	2013	→
Reconsideration of bipolar disorder as a developmental disorder: importance of the time of onset.	Geoffroy PA et al.	—	2013	→
Reduced burden of very large and rare CNVs in bipolar affective disorder.	Grozeva D et al.	—	2013	→
Risk counselling for family members in bipolar disorder and schizophrenia.	Gershon ES	—	2013	→
The dynamics of DNA methylation in schizophrenia and related psychiatric disorders.	Grayson DR et al.	—	2013	→
The emerging spectrum of allelic variation in schizophrenia: current evidence and strategies for the identification and functional characterization of common and rare variants.	Mowry BJ et al.	—	2013	→
The genomics of schizophrenia: update and implications.	Giusti-Rodríguez P et al.	—	2013	→
A genetic model for neurodevelopmental disease.	Coe BP et al.	—	2012	→
Assessment between Dopamine Receptor D2 (DRD2) Polymorphisms and Schizophrenia in Korean Population.	Cho AR et al.	—	2012	→
CNVs: harbingers of a rare variant revolution in psychiatric genetics.	Malhotra D et al.	—	2012	→
De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia.	Xu B et al.	—	2012	→
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De novo mutations in neurological and psychiatric disorders: effects, diagnosis and prevention.	Gauthier J et al.	—	2012	→
Diverse types of genetic variation converge on functional gene networks involved in schizophrenia.	Gilman SR et al.	—	2012	→
Genetic architectures of psychiatric disorders: the emerging picture and its implications.	Sullivan PF et al.	—	2012	→
Genetics of bipolar disorder: where we are and where we are going.	Nurnberger JI	—	2012	→
Genomic structural variation in psychiatric disorders.	Rucker JJ et al.	—	2012	→
Hybridization and amplification rate correction for affymetrix SNP arrays.	Wang Q et al.	—	2012	→
Identification of a CACNA2D4 deletion in late onset bipolar disorder patients and implications for the involvement of voltage-dependent calcium channels in psychiatric disorders.	Van Den Bossche MJ et al.	—	2012	→
Implications of genetic findings for understanding schizophrenia.	Owen MJ	—	2012	→
Potential opposite roles of the extracellular signal-regulated kinase (ERK) pathway in autism spectrum and bipolar disorders.	Kalkman HO	—	2012	→
Quantitative proteomic and genetic analyses of the schizophrenia susceptibility factor dysbindin identify novel roles of the biogenesis of lysosome-related organelles complex 1.	Gokhale A et al.	—	2012	→
Rare copy number variants in neuropsychiatric disorders: Specific phenotype or not?	Van Den Bossche MJ et al.	—	2012	→
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The genetic variability and commonality of neurodevelopmental disease.	Coe BP et al.	—	2012	→
The hunt for gene effects pertinent to behavioral traits and psychiatric disorders: from mouse to human.	Wahlsten D	—	2012	→
Whole-genome sequencing in autism identifies hot spots for de novo germline mutation.	Michaelson JJ et al.	—	2012	→
De novo CNVs in bipolar disorder: recurrent themes or new directions?	Girirajan S et al.	—	2011	→