Genome-wide association studies

Study ID # SNPs # Genes Tier Reference Inside Update
CV:GWAScat 560 486 Tier 1 NHGRI-EBI GWAS Catalog SZGR 2.0 page 05/18/2016
CV:GWASdb 560 2130 Tier 1 GWASdb SZGR 2.0 page 05/04/2016
CV:PGC128 128 148 Tier 1 Psychiatric Genomics Consortium (PGC) SZGR 2.0 page 06/01/2016
CV:PheWAS 128 148 Tier 1 PheWAS SZGR 2.0 page 06/01/2016
CV:Ripke_2013 128 27 Tier 1 PubMed 06/01/2016
CV:PGCnp 128 27 Tier 2 Psychiatric Genomics Consortium (PGC) PubMed 06/01/2016

Venn diagram comparing the SNPs among the five Tier 1 SNPs.

Not available

Venn diagram comparing the genes mapped to Tier 1 SNPs within 50kb.

Not available


De novo mutations

Study ID First author Year Journal Sample size Platform Sequencer PMID
DNM:Guipponi_2014 Guipponi 2014 PLoS One 53 Agilent SureSelect Human ALL Exon kits HiSeq 25420024
DNM:Girard_2011 Girard 2011 Nature Genetics 623 Agilent SureSelect Human ALL Exon kits HiSeq 21743468
DNM:Takata_2014 Takata A 2014 Neuron 231 case and 34 control trios Agilent SureSelect v2 (n = 85 trios), NimbleGen SeqCap EZ v2 (n = 180 trios) HiSeq 24853937
DNM:McCarthy_2014 McCarthy 2014 Molecular Psychiatry 57 NimbleGen SeqCap EZ Human Exome Library v2.0 probes HiSeq (101 bp PE reads) 24776741
DNM:Fromer_2014 Fromer 2014 Nature 617 Agilent SureSelect Human All Exon v.2, Nimblegen SeqCap EZ Human Exome Library v2.0, Agilent SureSelect Human All Exon 50MB HiSeq (76 bp, 101 bp, 76 bp PE reads) 24463507
DNM:Gulsuner_2013 Gulsuner 2013 Cell 105 NimbleGen SeqCap EZ Human Exome Library v2.0 HiSeq (101 bp PE reads) 23911319
DNM:Xu_2012 Xu 2012 Nature Genetics 231 Agilent SureSelect v2 (n = 85 trios), NimbleGen SeqCap EZ v2 (n = 180 trios) HiSeq 23042115
DNM:Xu_2011 Xu 2011 Nature Genetics 53 Agilent SureSelect Human All Exon Target Enrichment System HiSeq (50 bp PE reads) 21822266
DNM:Awadalla_2010 Awadalla 2010 AJHG ASD and SCZ cases (n = 285) and 285 controls Targeted sequencing 401 synapse-expressed genes 20797689
Footnote: The data in DNM:Xu_2011 has been included in DNM:Xu_2012.

Differentially expressed genes

Study ID Platform Description # DEGs Tissue In SZGR2 Reference
DEG:Zhao_2015 RNA-sequencing 35 schizophrenia and 35 controls 105 genes Brain Included 25113377
DEG:Sanders_2014 Illumina HT12v4 413 schizophrenia and 446 controls 95 transcripts Lymphoblastoid cell lines Included 23904455

Differentially methylated genes

Study ID Platform # CpGs Description # DMGs Tissue In SZGR2 Reference
DMG:Montano_2016 Illumina HumanMethylation450 BeadChip 456,513 CpG 689 schizophrenia and 645 controls 172 records Included 27074206
DMG:Wockner_2014 Illumina HumanMethylation450 BeadChip 485,000 CpG 24 schizophrenia and 24 controls 4641 Blood Included 26809779
DMG:Nishioka_2013 Illumina Infinium HumanMethylation27 BeadChip 27,578 CpG 18 Japanese FESZ patients (11 males and 7 females); 15 Japanese age-matched healthy controls (10 males and 5 females) 603 Blood Included 23235336
DMG:Jaffe_2016 Illumina HumanMethylation450 BeadChip 485,000 CpG 108 schizophrenia and 136 controls 2104 DLPFC Included 26619358
DMG:vanEijk_2014 Illumina Infinium 27k Human DNA methylation Beadchip v1.2 27,000 CpGs 260 SZ patients and 250 unaffected controls Blood Included 25424713

Copy number variation (CNV) loci in schizophrenia

Locus Studies References Replication # genes
1q21.1 del CNV:Levinson_2011 21285140 Yes 35
CNV:Rees_2014 24311552
2p16.3 CNV:Levinson_2011 21285140 Yes 1
CNV:Rees_2014 24311552
3q29 CNV:Levinson_2011 21285140 Yes 21
CNV:Rees_2014 24311552
7q11.23 CNV:Sanders_2011 21658581 Yes 26
CNV:Rees_2014 24311552
7q36.3 CNV:Levinson_2011 21285140 Yes 1
CNV:Rees_2014 24311552
15q11.2 CNV:Rees_2014 24311552 No 14
AS/PWS dup CNV:Rees_2014 24311552 No 1
15q13.3 del CNV:Levinson_2011 21285140 Yes 16
CNV:Rees_2014 24311552
16p13.11 dup CNV:Rees_2014 21285140 No 9
16p11.2 dup CNV:Levinson_2011 21285140 Yes 27
CNV:Rees_2014 24311552
17q12 del CNV:Levinson_2011 21285140 Yes 17
CNV:Rees_2014 24311552
22q11.21 del CNV:Levinson_2011 21285140 Yes 49
CNV:Rees_2014 24311552