Table 1.

TE copy number, DNA methylation and expression in neurodevelopmental and psychiatric disorders.

Disorder	Tissue/samplea	Sample size	Method	TE copy number	TE DNA methylation	TE expression	Reference
Rett syndrome	Neural progenitor cells derived from induced pluripotent stem cells	Rhett syndrome: n = 5 Control: n = 5	L1 5′UTR-Luciferase plasmid	Increased L1 retrotransposition			Muotri et al. (2010)
Ataxia telangiectasia (Louis-Bar syndrome)	Post-mortem hippocampal tissue	Ataxia telangiectasia: n = 7 Control: n = 7	Taqman q-PCR	Increased L1 ORF2 copy number			Coufal et al. (2011)
Rett syndrome, Ataxia telangiectasia, tuberous sclerosis complex, nonsyndromic autism	Post-mortem cerebellar, occipital, and frontal cortex tissue	Pathologic: n = 17 Non-pathologic: n = 5 (various areas)	Whole-genome mapping	Increased L1 and Alu retrotransposition			Jacobs-Hirsh et al. (2018)
ASD	Peripheral blood	ASD: n = 28 Control: n = 28	PCR amplification, gel electrophoresis for presence/absence detection			More individuals with ERV-H and HERV-W expression	Balestrier et al. (2012)
ASD	Post-mortem cerebellum, BA9, BA22, and BA24	ASD: n = 13 Control: n = 13	Taqman q-PCR			Higher L1 in cerebellum, no difference in other regions	Shpyleva et al. (2018)
ASD	Existing peripheral blood transcriptome data from NCBI Gene Expression Omnibus DataSets	ASD: n = 465 Control: n = 256	Ingenuity Pathway Analysis of differentially expressed genes	Increased L1 insertions near genes involved in sex hormone receptor signaling and axon guidance			Tangsuwansri et al. (2018)
ASD	Existing peripheral blood transcriptome data from NCBI Gene Expression Omnibus DataSets	ASD: n = 36 Control: n = 20	Ingenuity Pathway Analysis of differentially expressed genes		Alu methylation varied by ASD subtype		Saeliw et al. (2018)
ASD with severe language impairment	Lymphoblastoid cell lines	ASD: n = 36 Control: n = 20	Combined bisulfite restriction analysis, qPCR		L1 hypomethylation	L1 methylation negatively associated with L1 expression	Tangsuwansri et al. (2018)
Schizophrenia	Cell-free cerebrospinal fluid, postmortem frontal cortex	Schizophrenia (CFS): n = 55 Control (CFS): n = 12 Schizophrenia (brain): n = 5 Control (brain): n = 6	Nested PCR & gel electrophoresis visualization, sequencing			More individuals with HERV-W expression in CFS, increased HERV-W expression in frontal cortex	Karlsson et al. (2001)
Schizophrenia & Bipolar disorder	Peripheral blood	Bipolar disorder: n = 110 Schizophrenia: n = 59 control: n = 105	Taqman q-PCR, sequencing	Decreased HERV-W copy number		Elevated ERV-W expression	Perron et al. (2012)
Schizophrenia	Serum	Schizophrenia: n = 118 Control: n = 106	Nested PCR & gel electrophoresis visualization, sequencing			More individuals with HERV-W evn expression	Huang et al. (2011)
Schizophrenia	Peripheral blood	Schizophrenia: n = 58 Control: n = 38	Nested PCR & gel electrophoresis visualization, sequencing			More individuals with ERV9 pol expression	Huang et al. (2006)
Schizophrenia	Postmortem dorsolateral PFC tissue	Schizophrenia: n = 13, n = 35 Control: n = 13, n = 34	Taqman q-PCR	Increased L1 copy number			Bundo et al. (2014)
PolyI:C maternal immune activation (mice), chronic epidermal growth factor (macaque) models of schizophrenia	PFC	PolyI:C (mice): n = 8 Control (mice): n = 8 EGF (macaques): n = 2 Control (macaques): n = 3	SYBR green q-PCR	Increased L1 copy number			Bundo et al. (2014)
Schizophrenia	Postmortem dorsolateral PFC tissue	Schizophrenia: n = 36 Controls: n = 26	L1-seq	Increased L1 insertions near genes involved in cell projection and post-synaptic membrane			Doyle et al. (2017)
Schizophrenia with childhood trauma	Peripheral blood leukocytes	Schizophrenia w/trauma: n = 18 Schizophrenia w/o trauma: n = 18 Control: n = 46	Combined bisulfite restriction analysis, PCR, gel electrophoresis visualization		L1 hypomethylation		Misiak et al. (2015)
Schizophrenia	Peripheral blood, Han Chinese cohort	Schizophrenia: n = 92 Control: n = 92	Bisulfite conversion-specific one-label extension		L1 hypomethylation		Li et al. (2018)
PTSD	Serum, military service members	PTSD: n = 75 Control: n = 75	Pyrosequencing		L1 hypomethylation post-deployment, Alu hypermethylation pre-deployment		Rusiecki et al. (2012)
Stress-enhanced fear learning model of PTSD	Rat basolateral amygdala	n = 7–8	Transcriptomic network analysis			Higher expression of elements containing L1 domains	Ponomarev et al. (2010)
Bipolar disorder	Peripheral blood, Han Chinese cohort	Bipolar: n = 99 Control: n = 92	Bisulfite conversion-specific one-label extension		L1 hypomethylation		Li et al. (2018)
Major depressive disorder	Postmortem dorsolateral PFC tissue	MDD: n = 12 Control: n = 13	Taqman q-PCR	Non-significant increase in L1 copy number			Bundo et al. (2014)
Major depressive disorder	Peripheral blood	MDD: n = 105 Control: 105	Taqman q-PCR, methylation sensitive restriction enzymes		L1 hypomethylation	Higher L1 expression	Liu et al. (2016)
Chronic unpredictable mild stress model of depression	Peripheral blood, PFC, hippocampus, nucleus accumbans, paraventricular nucleus of hypothalamus of mice	Depression model: n = 22 Control: n = 12	SYBR green q-PCR	L1 copy number increased in blood, reduced in PFC, unaffected in other areas			Liu et al. (2016)
Major depressive disorder	Peripheral blood	MDD: n = 122 Control: n = 176	Bisulfite conversion, PCR amplification, sequencing		AluJb element in serotonin transporter promoter hypomethylation		Schneider et al. (2018)

^aAll tissues are human unless otherwise specified.