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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

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