yu-1011/shared-molecular-neuropathology-across-major-psychiatric-disorders-parallels-polygenic-overlap

Shared-molecular-neuropathology-across-major-psychiatric-disorders-parallels-polygenic-overlap

This repository contains the data, code, and analyses used in Gandal et al., (2017) "Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap" doi: 10.1101/040022

Organization

1. code/ contains the code for normalizing individual datasets and performing cross disroder transcriptome analyess
2. raw_data/ contains individual-level study data for microarray, RNAseq (counts), and GWAS (sum-stats)
3. results/ contains figures and table results from the cross disorder analyses
4. working_data/ contains intermediary files

Microarray datasets used in this study

Disease	# Samples		Brain Region	Platform	Study	Dataset
	Cases	Controls
ASD	29	29	BA9, BA41	Illumina Ref8 v3	Voineagu	GSE28521
	15	18	BA9/46	Illumina Ref8 v3	Chow	GSE28475
	6	6	BA41/42	Affy HG-U133 plus2	Garbett et al., 2008
SCZ	51	50	Parietal cortex	Affy HuGene 1.0 ST	Chen	GSE35978
	15	19	BA46	Affy HG-U133 plus2	Lanz	GSE53987
	28	23	BA10	Affy HG-U133 plus2	Maycox	GSE17612
	35	34	BA46	Affy HG-U133A	Iwamoto	GSE12649
	30	29	BA46	Affy HG-U133 plus2	Narayan	GSE21138
BD	45	Included above (50)	Parietal cortex	Affy HuGene 1.0 ST	Chen	GSE35978
	17	Included above (19)	BA46	Affy HG-U133 plus2	Lanz	GSE53987
	32	Included above (34)	BA46	Affy HG-U133A	Iwamoto	GSE12649
MDD	17	Included above (19)	BA46	Affy HG-U133 plus2	Lanz	GSE53987
	70	70	BA9, BA25	Affy HG-U133 plus2	Sibille	GSE54567
						GSE54568
						GSE54571
						GSE54572
AAD	17	15	Superior frontal cortex	Illumina HumanHT-12 V3	Mayfield	GSE29555
TOTAL	407	293

RNAseq datasets used in this study

Disease	Dataset	# Samples (Cases/Controls)	Brain Region	Library	Sequencer	Data
SCZ	PsychEncode-GVEX	53 / 53	Frontal Cortex	TruSeq / RiboZero	Illumina HiSeq2000	syn4590909
BD	PsychEncode-GVEX	47 / 53 (same)	Frontal Cortex	TruSeq / RiboZero	Illumina HiSeq2000	syn4590909
ASD	ASD-pancortical	53 / 35	BA4/6; BA38; BA7; BA17	TruSeq / RiboZero	Illumina HiSeq 2500	syn11242290
SCZ	CommonMind	262 / 295	DLPFC	TruSeq / RiboZero	Illumina HiSeq 2500	syn2759792
BD	CommonMind	47 / 295 (same)	DLPFC	TruSeq / RiboZero	Illumina HiSeq 2500	syn2759792

GWAS datasets used in this study

Disorder / Trait	Consortium	Dataset	Date	Total Sample Size (Cases)
SCZ	PGC	SCZ2.snp.results.txt.gz	2014	82,315 (35,476)
BD	PGC	pgc.bip.2012-04.zip	2012	16,731 (7,481)
MDD	PGC	pgc.mdd.2012-04.zip	2012	18,759 (9,240)
ASD	iPSYCH	Summary Statistics	2017	28,131 (8,605)
ASD	PGC	PGC.ASD.euro.all.25Mar2015.txt.gz	2015	10,610 (5305)
AAD	AlcGen	Schumann et al., 2011	2011	23,347 (NA)
IBD	IIBDGC	EUR.IBD.gwas.assoc.txt	2015	34,652 (12,882)
Educational Attainment	SSGAC	EduYears_Main.txt.gz	2016	328,917
Subjective Well Being	SSGAC	SWB_Full.txt.gz	2016	298,420
Neuroticism		Neuroticism_Full.txt.gz		170,911
Depressive Symptoms		DS_Full.txt.gz		161,460