Study Report - phs000021.GAIN Schizophrenia.v3.p2.MULTI-2

dbGaP Study Configuration Report
Genome-Wide Association Study of Schizophrenia
Study accession phs000021.v3.p2

Total individuals 5064
Study type Case-Control
NIH sponsor IC / DAC Genetic Association Information Network (GAIN)
Study title Genome-Wide Association Study of Schizophrenia
Study URL http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000021.v3.p2
Data request URL http://view.ncbi.nlm.nih.gov/dbgap-controlled
Participant protection policy URL http://grants.nih.gov/grants/gwas
Weeks before requests unsigned
8
by SO are cancelled
Years before renewal required 1
Dac email gaindac@mail.nih.gov Fax number: 301-435-1580
Display approved non-technical
yes
research summaries?
Display approved research
yes
statements?
Acknowledgement Instructions
http://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=DUC&view_pdf&stacc=phs000021.v3.p2
Data distribution set count: 2
Distribution set number 1 ( Consent code: c1 )

Website label General Research Use
Pdf-424 supplement Dataset Manifest: DAR/sponsors/GAIN/level_3/manifest_phs000021.GAIN_Schizophrenia.v3.p2.c1.GRU.pdf
The data of this distribution set (phs000021.v3.p2.c1) is collected from 4589 participants. The contributing institutions
Set description
have established that the data can be distributed for General Research Use (GRU).
Filename tag for this phs000021.GAIN_Schizophrenia.v3.p2.c1.GRU
distribution set
Distribution set number 2 ( Consent code: c2 )

Website label Schizophrenia and Related Conditions
Pdf-424 supplement Dataset Manifest: DAR/sponsors/GAIN/level_3/manifest_phs000021.GAIN_Schizophrenia.v3.p2.c2.SARC.pdf
The data of this distribution set (phs000021.v3.p2.c2) is collected from 475 participants. The contributing institutions
Set description
have established that the data can be distributed for Schizophrenia and Related Conditions (SARC).
Filename tag for this phs000021.GAIN_Schizophrenia.v3.p2.c2.SARC
distribution set
This dbGaP study configuration report was prepared on 2010-10-28-05:00 UTC. Page: 1
Distribution Set General Research Use

This consent group is released with the filename pattern phs000021.GAIN_Schizophrenia.v3.p2.c1.GRU
Data Use Restrictions
Restriction label General Research Use ( Consent code: c1 )

Full restriction text May be used for any genetic studies.
IRB approval required to
No
use the data
Public link http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000021.v3.p2#restricted-access
Set Information
Distribution set id 1
Number of individuals 4589
The data of this distribution set (phs000021.v3.p2.c1) is collected from 4589 participants. The
Distribution set comments contributing institutions have established that the data can be distributed for General Research Use
(GRU).
Files distributed in this set
Content type : use-contents

Title : Study report for download components
Name : Study_Report.phs000021.GAIN_Schizophrenia.v3.p2.MULTI.pdf
1
Release date : 2010-10-28 Embargo release date : 2010-10-28
File size : 131 kilobytes
Description Master study report describing dbGaP study configuration and data set components by distribution set (informed consent category).

Title : Genome-Wide Association Study of Schizophrenia download component release notes
Name : Release_Notes.phs000021.Schizophrenia.v3.p2.MULTI.pdf
2
Description Release notes describing updates to the download component set
Content type : use-restrictions

Title : Manifest for the data distribution set with consent of General Research Use (GRU)
Name : manifest_phs000021.GAIN_Schizophrenia.v3.p2.c1.GRU.pdf
3 Release date : 2010-10-28 Embargo release date : 2010-10-28
The data distribution set manifest lists the informed consent group use restrictions and specific files that are available to the investigator pending authorized access by the
Description
responsible Data Access Committee (DAC).
Content type : phenotype-data-dictionary

Title : Phenotype Data Dictionary
Name : phs000021.v3.p2.data_dictionary.MULTI.tar.gz
5
Description Phenotype Data Dictionary
Content type : phenotype-variable-report

Title : Phenotype Variable Report
Name : phs000021.v3.p2.variable_report.MULTI.tar.gz
7
Description Phenotype Variable Report
Content type : phenotype-individual-traits

Title : Diagnostic interview of subjects with European ancestry and affected with schizophrenia or schizoaffective disorder
Name : phs000021.v3.pht000067.v2.p2.c1.EA_GAIN_phenotype_cases.GRU.txt.gz ( web-link )
Release date : 2008-02-07 Embargo release date : 2008-11-07 Last update date : 2010-10-28
8
pht000067.v2: (Data distribution set for General Research Use (GRU) consent) Diagnostic interview of subjects with European ancestry and affected with schizophrenia or
Description schizoaffective disorder
Update comment : Variable(s) are changed in this dataset (pht000067.v2) comparing to previous version (pht000067.v1).

Title : Demography and epidemiological data collection of mentally healthy subjects with European ancestry
Name : phs000021.v3.pht000068.v1.p2.c1.EA_GAIN_phenotype_controls_main.GRU.txt.gz ( web-link )
pht000068.v1: (Data distribution set for General Research Use (GRU) consent) Demography and epidemiological data collection of mentally healthy subjects with
Description
European ancestry

Title : Diagnostic interview of mentally healthy subjects with European ancestry
Name : phs000021.v3.pht000069.v1.p2.c1.EA_GAIN_phenotype_controls_questionnaire.GRU.txt.gz ( web-link )
12
Description pht000069.v1: (Data distribution set for General Research Use (GRU) consent) Diagnostic interview of mentally healthy subjects with European ancestry

Title : Diagnostic interview of mentally healthy African American subjects
Name : phs000021.v3.pht000287.v1.p2.c1.AA_GAIN_phenotype_controls_questionnaire.GRU.txt.gz ( web-link )
14
Description pht000287.v1: (Data distribution set for General Research Use (GRU) consent) Diagnostic interview of mentally healthy African American subjects

Title : Demography and epidemiological data collection of mentally healthy African American subjects
Name : phs000021.v3.pht000288.v1.p2.c1.AA_GAIN_phenotype_controls_main.GRU.txt.gz ( web-link )
pht000288.v1: (Data distribution set for General Research Use (GRU) consent) Demography and epidemiological data collection of mentally healthy African American
Description
subjects

Title : Diagnostic interview of African American subjects affected with schizophrenia or schizoaffective disorder
Name : phs000021.v3.pht000289.v1.p2.c1.AA_GAIN_phenotype_cases.GRU.txt.gz ( web-link )
pht000289.v1: (Data distribution set for General Research Use (GRU) consent) Diagnostic interview of African American subjects affected with schizophrenia or
Description
schizoaffective disorder
Content type : phenotype-individual-auxiliary

Title : Subjects affected with schizophrenia or schizoaffective disorder
Name : phs000021.v3.pht002001.v1.p2.GAIN_Schizophrenia_Subject.MULTI.txt.gz ( web-link )
20
Description pht002001.v1: Subjects affected with schizophrenia or schizoaffective disorder

Title : Samples obtained from subjects affected with schizophrenia or schizoaffective disorder
Name : phs000021.v3.pht002002.v1.p2.GAIN_Schizophrenia_Sample.MULTI.txt.gz ( web-link )
21
Description pht002002.v1: Samples obtained from subjects affected with schizophrenia or schizoaffective disorder
Content type : genotype-marker-information

Title : phg000013: Affymetrix 6.0 genotypes – marker information - European Ancestry
Name : phg000013.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.MULTI.marker-info.tar.gz
23
File size : 28 megabyte
phg000013.v1.p1: Marker information file: This file name has *.snp extension. Each platform has one file which reports all SNP related information. Each row contains:
Description SNP identifiers (assay ID, dbSNP ss#/rs#);,chromosome,base pair location,allele1,allele2,sequence,strand,genome build. Columns are space delimited. Chromosomes
always defined for mapping purposes are: 1-22, X, and Y, 0 indicating unmapped.
Content type : genotype-calls-filtered-matrix-format

Title : phg000013: Affymetrix 6.0 filtered genotype data (QC filtered). GRU participants. Matrix content = genotypes - European Ancestry
Name : phg000013.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.c1.GRU.filtered.matrixfmt.genotype.update1.tar
25
Genotype files: Provide all called genotypes for 2601 European Ancestry participants with GRU consent. QC filters were applied to the genotypes in this file. Component
contains three sets of individuals: (1) case-controls 2550 individuals; (2) duplicate samples 28 individuals; and (3) parents 23 individuals. Genotype data are provided in 2
Description PLINK matrix formats: binary and text. In text format a single SNP is reported per line, each pair of columns contains all the genotypes for a given individual. Columns are
space-delimited. Genotypes are reported as two letters separated by a space. All chromosomes are included in a single file.
Update comment : Two samples were removed due to consent group changes
Content type : genotype-calls-unfiltered-individual-format

Title : phg000013: Affymetrix 6.0 unfiltered genotype data (QC unfiltered). GRU participants. Individual format. Set 1 of 6 - European Ancestry
Name : phg000013.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.c1.GRU.unfiltered.indfmt.Set1.tar
26 File size : 8 gigabytes WARNING > 2GB: Check applications to ensure you can compute on this file.
phg000013.v1.p1: Genotype file: Provide all called genotypes for 500 samples. No QC filtering was applied to the genotypes in this file. Each file is a unique combination
of: (a) platform (Affymetrix 6.0), (b) consent category GRU (General Research Use),(c) sample. Each file contains header rows indicating Sample ID and Consent Group.
Description
Genotype data rows contain ASSAY_SNP_ID, ss_ID, rs_ID, strand, orig_assay_orient_genotype, genomic_fwd_orient_genotype, confidence, normalized allele1_intensity,
normalized allele2_intensity. ‘GY’ format is used for males genotyped on X chromosome markers.

Description

Name : phg000013.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.c1.GRU.unfiltered.indfmt.Set3.update1.tar
File size : 8 gigabytes WARNING > 2GB: Check applications to ensure you can compute on this file.
29
Genotype file: Provide all called genotypes for 500 samples. No QC filtering was applied to the genotypes in this file. Each file is a unique combination of: (a) platform
(Affymetrix 6.0), (b) consent category GRU (General Research Use),(c) sample. Each file contains header rows indicating Sample ID and Consent Group. Genotype data
Description rows contain ASSAY_SNP_ID, ss_ID, rs_ID, strand, orig_assay_orient_genotype, genomic_fwd_orient_genotype, confidence, normalized allele1_intensity, normalized
allele2_intensity. ‘GY’ format is used for males genotyped on X chromosome markers.

Description

Name : phg000013.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.c1.GRU.unfiltered.indfmt.Set5.update1.tar
32
Genotype file: Provide all called genotypes for 500 samples. No QC filtering was applied to the genotypes in this file. Each file is a unique combination of: (a) platform
(Affymetrix 6.0), (b) consent category GRU (General Research Use),(c) sample. Each file contains header rows indicating Sample ID and Consent Group. Genotype data
Description rows contain ASSAY_SNP_ID, ss_ID, rs_ID, strand, orig_assay_orient_genotype, genomic_fwd_orient_genotype, confidence, normalized allele1_intensity, normalized
allele2_intensity. ‘GY’ format is used for males genotyped on X chromosome markers.

Description
Content type : genotype-calls-unfiltered-matrix-format

Title : phg000013: Affymetrix 6.0 unfiltered genotype data (no QC filters applied). GRU participants. Matrix content = genotypes - European Ancestry
Name : phg000013.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.c1.GRU.unfiltered.matrixfmt.genotype.update1.tar
35 Genotype files: Provide all called genotypes for 2712 European Ancestry participants with GRU consent. Genotype individuals include : (1) case-controls 2659 individuals;
(2) duplicate samples 29 individuals; and (3) parents 24 individuals. For each pair of duplicates one sample is selected as primary based on higher call rate and assigned
a phenotype while the other member of the pair contains “0” for the phenotype. Parents are also assigned a phenotype of “0”; Genotype data are provided in 2 PLINK
Description
matrix formats: binary and text. In text format a single SNP is reported per line, each pair of columns contains all the genotypes for a given individual. Columns are
space-delimited. Genotypes are reported as two letters separated by a space. All chromosomes are included in a single file.
Content type : genotype-individual-information

Title : phg000013: Affymetrix 6.0 genotypes – individual information - European Ancestry
Name : phg000013.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.MULTI.individual-info.update1.tar
39
Individual information file: This file name has *.ind extension. Each platform has one file which reports all individual related information. Each row contains sampleName
(phenotype sample ID), sampleID (genotype plate ID), ind_id (coded to match known duplicates), ped_id, ma_ind_id, pa_ind_id, sex, Sample_type
Description (case/control/parent/duplicate), case_or_control,QC_status,Sample_Consent,Plate,Study_ID to track data source when samples are pooled for a single common analysis.
Columns are space delimited. The file has a header and footer section starting with ‘#’ in column 1. Header rows contain column descriptions.
Content type : genotype-qc

Title : phg000013: Affymetrix 6.0 genotypes – quality assurance data and analysis - European Ancestry
Name : phg000013.Schizophrenia.genotype-qc.Affymetrix6.v1.p1.MULTI.tar
40
This component contains the GAIN genotype working group quality control analysis, results, and summary statistics for all samples and SNPs provided in the GAIN
dataset. Reported SNP statistics include: minor allele frequency, completeness, HWE pvalue, count of Mendel errors, case control chi-square, case control pvalue.
Description Statistics reported per sample include Completeness, Heterozygosity, mendelian error rate, GenderPredictionError, and QC pass/fail status. The file
QC_metrics_all_snps.filtered_list contains a list of the QC passed filtered set of SNP. The files QC_metrics_all_snps.README and Failed_Sample_List.README
describe the quality control process and thresholds used to define the filtered set of SNPs and samples.

Name : phg000013.Schizophrenia.genotype-qc.Affymetrix6.v1.p1.MULTI.tar.gz
41
phg000013.v1.p1: This component contains the GAIN genotype working group quality control analysis, results, and summary statistics for all samples and SNPs provided
in the GAIN dataset. Reported SNP statistics include: minor allele frequency, completeness, HWE pvalue, count of Mendel errors, case control chi-square, case control
Description pvalue. Statistics reported per sample include Completeness, Heterozygosity, mendelian error rate, GenderPredictionError, and QC pass/fail status. The file
Content type : linkage-disequilibrium

Title : phg000013: LD plots - cases only - Schizophrenia - European Ancestry
Name : phg000013.Schizophrenia.linkageplots.cases.Affymetrix6.v1.p1.MULTI.tar
File size : 2 gigabyte
42 phg000013.v1.p1: This component contains linkage disequilibrium plots and data computed from 1351 Schizophrenia EA CASES whose genotypes passed QC filtering.
These sliding-window LD data were computed in 500KB intervals using a single sample without correction for any population substructure. Data files contain the following
columns: rs#, paired-rs#, r-square, and D''''. Images are comprised of 4 horizontal bands. From the top the are (a) mapping information, (b) pretty plot of all individual
Description
genotypes colored by zygosity, (c) SNP density information, and (d) an inverted LD pyramid where hues darken with increasing LD. Files are organized into subdirectories
by chromosome, and each file is named using the convention ChrNumber_StartPosition_EndPosition with *.png and *.dump extensions for image and data file,
respectively.

Title : phg000013: LD plots - controls only - Schizophrenia - European Ancestry
Name : phg000013.Schizophrenia.linkageplots.controls.Affymetrix6.v1.p1.MULTI.tar
43 phg000013.v1.p1: This component contains linkage disequilibrium plots and data computed from 1378 Schizophrenia EA CONTROLS whose genotypes passed QC
filtering. These sliding-window LD data were computed in500KB intervals using a single sample without correction for any population substructure. Data files contain the
following columns: rs#, paired-rs#, r-square, and D''''. Images are comprised of 4 horizontal bands. From the top the are (a) mapping information, (b) pretty plot of all
Description
individual genotypes colored by zygosity, (c) SNP density information, and (d) an inverted LD pyramid where hues darken with increasing LD. Files are organized into
subdirectories by chromosome, and each file is named using the convention ChrNumber_StartPosition_EndPosition with *.png and *.dump extensions for image and data
file, respectively.
Content type : genotype-intensities

Title : phg000013: Affymetrix 6.0 genotype instensity CEL files. GRU participants (Part 1 of 6) European Ancestry
Name : phg000013.Schizophrenia.raw_intensities.Affymetrix6.v1.p1.c1.GRU.Set1.tar
phg000013.v1.p1: This component includes part of the hybridization probe intensity CEL data for one-sixth of the 2712 samples typed with the Affymetrix 6.0 chip.
Description
Samples are identified in the manifest file distributed as part of this component. Files in the tarball are individually compressed with gzip utility.

Name : phg000013.Schizophrenia.raw_intensities.Affymetrix6.v1.p1.c1.GRU.Set2.update1.tar
46
This component includes part of the hybridization probe intensity CEL data for one-sixth of the 2712 samples typed with the Affymetrix 6.0 chip. Samples are identified in
Description the manifest file distributed as part of this component. Files in the tarball are individually compressed with gzip utility.

Description

Name : phg000013.Schizophrenia.raw_intensities.Affymetrix6.v1.p1.c1.GRU.Set4.update1.tar
49
This component includes part of the hybridization probe intensity CEL data for one-sixth of the 2712 samples typed with the Affymetrix 6.0 chip. Samples are identified in
Description the manifest file distributed as part of this component. Files in the tarball are individually compressed with gzip utility.

Description

Description
Content type : genotype-scatterplots

: phg000013: Affymetrix 6.0 genotype scatter plots: QC filtered set, 2737 European Ancestry individuals (2820 samples). Component 1 of 5 containing rs#''''s ending in
Title
000 through 242.
Name : phg000013.Schizophrenia.scatterplots.Affymetrix6.v1.p1-01.MULTI.tar.gz
53 phg000013.v1.p1: This archive contains 218371 of 906600 scatterplots for the GAIN Schizophrenia Disorder study using the Affymetrix 6.0 chip. Scatterplots include 2820
study samples (the 2737 unique participants in the QC filtered genotype set) with genotype QC score >= 2000. These plots do not include 121 samples excluded from the
filtered genotype set. Intensity data for these sampes are available in the genotype files. The scatterplots are used to show the normalized intensities for alleles A and B
Description for each markers of this study. All scatterplots are in PNG format of size 800x900 pixel, and are named using the corresponding RS ID’s (e.g. 223.png). They are stored in
1000 subdirectories numbered from 000-999. SNPs are placed in the subdirectory matching the last 3 digits of the rs#. In each plot. Individuals homozygous for allele A
are shown in red squares, those homozygous for allele B are shown in blue triangles, those with heterozygous alleles are shown are purple circlse, and individuals with at
least one allele failed to call are shown in black x’s. Alleles are shown in genome orientation (NCBI reference assembly 36.2).

Title
243 through 484.

Title
485 through 726.

Title
727 through 969.

Title
970 through 999 and rs_undefined markers.

Title : phg000014: Affymetrix 6.0 genotypes – individual information - African Ancestry
Name : phg000014.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.MULTI.individual-info.tar
58 File size : 133 kilobytes
phg000014.v1.p1: Individual information file: This file name has *.ind extension. Each platform has one file which reports all individual related information. Each row
contains sampleName (phenotype sample ID), sampleID (genotype plate ID), ind_id (coded to match known duplicates), ped_id, ma_ind_id, pa_ind_id, sex, Sample_type
Description
(case/control/parent/duplicate), case_or_control,QC_status,Sample_Consent,Plate,Study_ID to track data source when samples are pooled for a single common analysis.

Title : phg000014: Affymetrix 6.0 genotypes – marker information - African Ancestry
59

Title : phg000014: Affymetrix 6.0 filtered genotype data (QC filtered). GRU participants. Matrix content = genotypes - African Ancestry
Name : phg000014.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.c1.GRU.filtered.matrixfmt.genotype.tar
60 File size : 692 megabyte
phg000014.v1.p1: Genotype files: Provide all called genotypes for 1904 African Ancestry participants with GRU consent. QC filters were applied to the genotypes in this
file. Component contains separate files for three sets of individuals: (1) case-controls – 1875 individuals; (2) duplicate samples– 0 individuals; and (3) parents–29
Description
individuals. Genotype data are provided in 2 PLINK matrix formats: binary and text. In text format a single SNP is reported per line, each pair of columns contains all the
genotypes for a given individual. Columns are space-delimited. Genotypes are reported as two letters separated by a space. All chromosomes are included in a single file.

Title : phg000014: Affymetrix 6.0 unfiltered genotype data (QC unfiltered). GRU participants. Individual format. Set 1 of 4 - African Ancestry
Description

Description

Description

Description

Title : phg000014: Affymetrix 6.0 unfiltered genotype data (no QC filterers applied). GRU participants. Matrix content = genotypes - African Ancestry
Name : phg000014.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.c1.GRU.unfiltered.matrixfmt.genotype.tar
phg000014.v1.p1: Genotype files: Provide all called genotypes for 1983 African Ancestry participants with GRU consent. QC filters were applied to the genotypes in this
file. Component contains separate files for three sets of individuals: (1) case-controls – 1932 individuals; (2) duplicate samples– 19 individuals; and (3) parents–32
Description
individuals. Genotype data are provided in 2 PLINK matrix formats: binary and text. In text format a single SNP is reported per line, each pair of columns contains all the
genotypes for a given individual. Columns are space-delimited. Genotypes are reported as two letters separated by a space. All chromosomes are included in a single file.

Title : phg000014: Illumina Infinium 1M genotyping for 96 GRU samples - Final Report and IDAT files
Name : phg000014.Schizophrenia.genotype-calls.Illumina_Infinium_1M_Final_Report_and_IDAT.v1.p1.c1.GRU.unfiltered.matrixfmt.genotype.tar
phg000014.v1.p1: Genotype files: Illumina Final report format and IDAT files are supplied, see the other component
Description
phg000014.Schizophrenia.genotype-calls.Illumina_Infinium_1M_PLINK.v1.p1.c1.GRU.unfiltered.matrixfmt for PLINK files and SNP annotation

Title : phg000014: Illumina Infinium 1M genotyping for 96 GRU samples - PLINK and SNP annotation files
Name : phg000014.Schizophrenia.genotype-calls.Illumina_Infinium_1M_PLINK.v1.p1.c1.GRU.unfiltered.matrixfmt.genotype.tar
phg000014.v1.p1: Genotype files: PLINK format genotypes and SNP descriptions, see the other component
Description
phg000014.Schizophrenia.genotype-calls.Illumina_Infinium_1M_Final_Report_and_IDAT.v1.p1.c1.GRU.unfiltered.matrixfmt for IDAT and final report files

Title : phg000014: Affymetrix 6.0 genotypes – quality assurance data and analysis - African Ancestry
71

Title : phg000014: LD plots - cases only - Schizophrenia - African Ancestry
72 phg000014.v1.p1: This component contains linkage disequilibrium plots and data computed from 921 Schizophrenia AA CASES whose genotypes passed QC filtering.
Description
respectively.

Title : phg000014: LD plots - controls only - Schizophrenia - African Ancestry
73 phg000014.v1.p1: This component contains linkage disequilibrium plots and data computed from 954 Schizophrenia AA CONTROLS whose genotypes passed QC
filtering. These sliding-window LD data were computed in 500KB intervals using a single sample without correction for any population substructure. Data files contain the
Description
file, respectively.

Title : phg000014: Affymetrix 6.0 genotype instensity CEL files. GRU participants (Part 1 of 4) African Ancestry
phg000014.v1.p1: This component includes part of the hybridization probe intensity CEL data for 500 samples typed with the Affymetrix 6.0 chip. Samples are identified in
Description
the manifest file distributed as part of this component. Files in the tarball are individually compressed with gzip utility.

Description

Description

Description

: phg000014: Affymetrix 6.0 genotype scatter plots: QC filtered set, 2196 African Ancestry individuals (2196 samples). Component 1 of 5 containing rs#''''s ending in 000
Title
through 242.
79 phg000014.v1.p1: This archive contains xxx of 906600 scatterplots for the GAIN Schizophrenia Disorder study using the Affymetrix 6.0 chip. Scatterplots include 2196

Title
through 484.

Title
through 726.

: phg000014: Affymetrix 6.0 genotype scatter plots: QC filtered set, 2196 African Ancestry individuals (2196 samples).. Component 4 of 5 containing rs#''''s ending in 727
Title
through 969.

Title
through 999 and rs_undefined markers.
Content type : association-NCBI

Title : Analysis of associations between genotype data and phenotype variables
Name : pha002857.v1.p1.tgz
84
pha002857.v1.p1: Genome-Wide genotyping data has been produced with the Affymetrix 6.0 platform and with the Birdseed calling algorithm. This analysis includes only
the subset of subjects with European ancestry. Data was filtered using criteria: 1) sample heterozygosity range from 0.26-0.285; 2) sample call rate greater than 97%; 3)
Description SNP MAF # 0.01; 4) SNP call rate # 0.95, and HWE pvalue > 0.000001 5) plate effect pvalue test above 10^(-8) for a single plate and/or 10^(-4) for two plates; 4) Less
than 2 discrepancies between SNP calls on duplicated samples. These thresholds resulted in 1378 controls and and 1351 cases genotyped over 729454 SNPs used in
the assoiciation analysis. Genome-wide association scan has been pre-computed by NCBI.

85
the subset of subjects with African American ancestry. Data was filtered using criteria: 1) removal of sample heterozygosity outliers; 2) sample call rate greater than 97%;
Description 3) SNP MAF # 0.01; 4) SNP call rate # 0.95 and HWE p value > 0.000001 5) plate effect p value test above 10^(-8) for a single plate and/or 10^(-4) for two plates; 4) Less
than 2 discrepancies between SNP calls on duplicated samples. These thresholds resulted in 954 controls and 1195 cases genotyped over 845814 SNPs used in the
association analysis. Genome-wide association scan has been pre-computed by NCBI.
Distribution Set Schizophrenia and Related Conditions

This consent group is released with the filename pattern phs000021.GAIN_Schizophrenia.v3.p2.c2.SARC
Data Use Restrictions
Restriction label Schizophrenia and Related Conditions ( Consent code: c2 )

Limited to genetic studies of Schizophrenia and related conditions. Related conditions include
conditions with evidence of genetic relationships to schizophrenia or schizoaffective disorder, such as
Full restriction text
acute psychoses, bipolar disorder, MDD, or "Cluster A" personality disorders (schizotypal, schizoid,
paranoid).
IRB approval required to
No
use the data
Public link http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000021.v3.p2#restricted-access
Set Information
Distribution set id 2
Number of individuals 475
The data of this distribution set (phs000021.v3.p2.c2) is collected from 475 participants. The contributing
Distribution set comments institutions have established that the data can be distributed for Schizophrenia and Related Conditions
(SARC).
Files distributed in this set

Title : Study report for download components
Name : Study_Report.phs000021.GAIN_Schizophrenia.v3.p2.MULTI.pdf
1
Description Master study report describing dbGaP study configuration and data set components by distribution set (informed consent category).

Title : Genome-Wide Association Study of Schizophrenia download component release notes
Name : Release_Notes.phs000021.Schizophrenia.v3.p2.MULTI.pdf
2
Description Release notes describing updates to the download component set
Content type : use-restrictions

Title : Manifest for the data distribution set with consent of Schizophrenia and Related Conditions (SARC)
Name : manifest_phs000021.GAIN_Schizophrenia.v3.p2.c2.SARC.pdf
The data distribution set manifest lists the informed consent group use restrictions and specific files that are available to the investigator pending authorized access by the
Description
responsible Data Access Committee (DAC).
Content type : phenotype-data-dictionary

Title : Phenotype Data Dictionary
Name : phs000021.v3.p2.data_dictionary.MULTI.tar.gz
5
Description Phenotype Data Dictionary
Content type : phenotype-variable-report

Title : Phenotype Variable Report
Name : phs000021.v3.p2.variable_report.MULTI.tar.gz
7
Description Phenotype Variable Report

Title : Diagnostic interview of subjects with European ancestry and affected with schizophrenia or schizoaffective disorder
Name : phs000021.v3.pht000067.v2.p2.c2.EA_GAIN_phenotype_cases.SARC.txt.gz ( web-link )
9
pht000067.v2: (Data distribution set for Schizophrenia and Related Conditions (SARC) consent) Diagnostic interview of subjects with European ancestry and affected with
Description schizophrenia or schizoaffective disorder
Update comment : Variable(s) are changed in this dataset (pht000067.v2) comparing to previous version (pht000067.v1).

Title : Demography and epidemiological data collection of mentally healthy subjects with European ancestry
Name : phs000021.v3.pht000068.v1.p2.c2.EA_GAIN_phenotype_controls_main.SARC.txt.gz ( web-link )
File size : 204 bytes
pht000068.v1: (Data distribution set for Schizophrenia and Related Conditions (SARC) consent) Demography and epidemiological data collection of mentally healthy
Description
subjects with European ancestry

Title : Diagnostic interview of mentally healthy subjects with European ancestry
Name : phs000021.v3.pht000069.v1.p2.c2.EA_GAIN_phenotype_controls_questionnaire.SARC.txt.gz ( web-link )
13
Description pht000069.v1: (Data distribution set for Schizophrenia and Related Conditions (SARC) consent) Diagnostic interview of mentally healthy subjects with European ancestry

Title : Diagnostic interview of mentally healthy African American subjects
Name : phs000021.v3.pht000287.v1.p2.c2.AA_GAIN_phenotype_controls_questionnaire.SARC.txt.gz ( web-link )
15
Description pht000287.v1: (Data distribution set for Schizophrenia and Related Conditions (SARC) consent) Diagnostic interview of mentally healthy African American subjects

Title : Demography and epidemiological data collection of mentally healthy African American subjects
Name : phs000021.v3.pht000288.v1.p2.c2.AA_GAIN_phenotype_controls_main.SARC.txt.gz ( web-link )
pht000288.v1: (Data distribution set for Schizophrenia and Related Conditions (SARC) consent) Demography and epidemiological data collection of mentally healthy
Description
African American subjects

Title : Diagnostic interview of African American subjects affected with schizophrenia or schizoaffective disorder
Name : phs000021.v3.pht000289.v1.p2.c2.AA_GAIN_phenotype_cases.SARC.txt.gz ( web-link )
pht000289.v1: (Data distribution set for Schizophrenia and Related Conditions (SARC) consent) Diagnostic interview of African American subjects affected with
Description
schizophrenia or schizoaffective disorder

Title : Subjects affected with schizophrenia or schizoaffective disorder
Name : phs000021.v3.pht002001.v1.p2.GAIN_Schizophrenia_Subject.MULTI.txt.gz ( web-link )
20
Description pht002001.v1: Subjects affected with schizophrenia or schizoaffective disorder

Title : Samples obtained from subjects affected with schizophrenia or schizoaffective disorder
Name : phs000021.v3.pht002002.v1.p2.GAIN_Schizophrenia_Sample.MULTI.txt.gz ( web-link )
21
Description pht002002.v1: Samples obtained from subjects affected with schizophrenia or schizoaffective disorder

Title : phg000013: Affymetrix 6.0 genotypes – marker information - European Ancestry
23

Title : phg000013: Affymetrix 6.0 filtered genotype data (QC filtered). SARC participants. Matrix content = genotypes - European Ancestry
Name : phg000013.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.c2.SARC.filtered.matrixfmt.genotype.tar
phg000013.v1.p1: Genotype files: Provide all called genotypes for 219 European Ancestry participants with SARC consent. QC filters were applied to the genotypes in this
file. Component contains three sets o f individuals: (1) case-controls 179 individuals; (2) duplicate samples 2 individuals; and (3) parents 38 individuals. Genotype data are
Description
provided in 2 PLINK matrix formats: binary and text. In text format a single SNP is report ed per line, each pair of columns contains all the genotypes for a given individual.
Columns are space-delimited. Genotypes are reported as two letters separated by a space. All chromosomes are included in a single file.

Title : phg000013: Affymetrix 6.0 unfiltered genotype data (QC unfiltered). SARC participants. Individual format. - European Ancestry
Name : phg000013.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.c2.SARC.unfiltered.indfmt.Set1.tar
of: (a) platform (Affymetrix 6.0), (b) consent category SARC (Schizophrenia and related conditions),(c) sample. Each file contains header rows indicating Sample ID and
Description
Consent Group. Genotype data rows contain ASSAY_SNP_ID, ss_ID, rs_ID, strand, orig_assay_orient_genotype, genomic_fwd_orient_genotype, confidence, normalized
allele1_intensity, normalized allele2_intensity. ‘GY’ format is used for males genotyped on X chromosome markers.

Title : phg000013: Affymetrix 6.0 unfiltered genotype data (no QC filters applied). SARC participants. Matrix content = genotypes - European Ancestry
Name : phg000013.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.c2.SARC.unfiltered.matrixfmt.genotype.tar
phg000013.v1.p1: Genotype files: Provide all called genotypes for 229 European Ancestry participants with SARC consent. No QC filters were applied to the genotypes in
this file. Component contain three set s of individuals: (1) case-controls 187 individuals; (2) duplicate samples 2 individuals; and (3) parents 40 individuals. Genotype data
Description
are provided in 2 PLINK matrix formats: binary and text. In text format a single SNP is rep orted per line, each pair of columns contains all the genotypes for a given
individual. Columns are space-delimited. Genotypes are reported as two letters separated by a space. All chromosomes are included in a single file.

Title : phg000013: Affymetrix 6.0 genotypes – individual information - European Ancestry
Name : phg000013.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.MULTI.individual-info.update1.tar
39
Individual information file: This file name has *.ind extension. Each platform has one file which reports all individual related information. Each row contains sampleName
(phenotype sample ID), sampleID (genotype plate ID), ind_id (coded to match known duplicates), ped_id, ma_ind_id, pa_ind_id, sex, Sample_type
Description (case/control/parent/duplicate), case_or_control,QC_status,Sample_Consent,Plate,Study_ID to track data source when samples are pooled for a single common analysis.

Name : phg000013.Schizophrenia.genotype-qc.Affymetrix6.v1.p1.MULTI.tar
40
This component contains the GAIN genotype working group quality control analysis, results, and summary statistics for all samples and SNPs provided in the GAIN
dataset. Reported SNP statistics include: minor allele frequency, completeness, HWE pvalue, count of Mendel errors, case control chi-square, case control pvalue.
Description Statistics reported per sample include Completeness, Heterozygosity, mendelian error rate, GenderPredictionError, and QC pass/fail status. The file

41

Title : phg000013: LD plots - cases only - Schizophrenia - European Ancestry
42 phg000013.v1.p1: This component contains linkage disequilibrium plots and data computed from 1351 Schizophrenia EA CASES whose genotypes passed QC filtering.
Description
respectively.

Title : phg000013: LD plots - controls only - Schizophrenia - European Ancestry
43 phg000013.v1.p1: This component contains linkage disequilibrium plots and data computed from 1378 Schizophrenia EA CONTROLS whose genotypes passed QC
filtering. These sliding-window LD data were computed in500KB intervals using a single sample without correction for any population substructure. Data files contain the
Description
file, respectively.

Title : phg000013: Affymetrix 6.0 genotype instensity CEL files. SARC participants (Part 1 of 1) European Ancestry
Name : phg000013.Schizophrenia.raw_intensities.Affymetrix6.v1.p1.c2.SARC.Set1.tar
phg000013.v1.p1: This component includes part of the hybridization probe intensity CEL data for the 229 samples typed with the Affymetrix 6.0 chip. Samples are
Description
identified in the manifest file distributed as part of this component. Files in the tarball are individually compressed with gzip utility.

Title
000 through 242.

Title
243 through 484.

Title
485 through 726.

Title
727 through 969.

Title
970 through 999 and rs_undefined markers.

Title : phg000014: Affymetrix 6.0 genotypes – individual information - African Ancestry
Name : phg000014.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.MULTI.individual-info.tar
58 File size : 133 kilobytes
phg000014.v1.p1: Individual information file: This file name has *.ind extension. Each platform has one file which reports all individual related information. Each row
contains sampleName (phenotype sample ID), sampleID (genotype plate ID), ind_id (coded to match known duplicates), ped_id, ma_ind_id, pa_ind_id, sex, Sample_type
Description
(case/control/parent/duplicate), case_or_control,QC_status,Sample_Consent,Plate,Study_ID to track data source when samples are pooled for a single common analysis.

Title : phg000014: Affymetrix 6.0 genotypes – marker information - African Ancestry
59

Title : phg000014: Affymetrix 6.0 filtered genotype data (QC filtered). SARC participants. Matrix content = genotypes - African Ancestry
Name : phg000014.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.c2.SARC.filtered.matrixfmt.genotype.tar
phg000014.v1.p1: Genotype files: Provide all called genotypes for 288 individuals with SARC consent. QC filters were applied to the genotypes in this file. Component
contains separate files for three sets of individuals: (1) case-controls – 274 individuals; (2) duplicate samples– 0 individuals; and (3) parents–14 individuals. Genotype data
Description
are provided in 2 PLINK matrix formats: binary and text. In text format a single SNP is reported per line, each pair of columns contains all the genotypes for a given

Title : phg000014: Affymetrix 6.0 unfiltered genotype data (QC unfiltered). SARC participants. Individual format. - African Ancestry
Name : phg000014.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.c2.SARC.unfiltered.indfmt.Set1.tar
of: (a) platform (Affymetrix 6.0), (b) consent category SARC (Schizophrenia and related conditions),(c) sample. Each file contains header rows indicating Sample ID and
Description
Consent Group. Genotype data rows contain ASSAY_SNP_ID, ss_ID, rs_ID, strand, orig_assay_orient_genotype, genomic_fwd_orient_genotype, confidence, normalized
allele1_intensity, normalized allele2_intensity. ‘GY’ format is used for males genotyped on X chromosome markers.

Title : phg000014: Affymetrix 6.0 unfiltered genotype data (no QC filters applied). SARC participants. Matrix content = genotypes - African Ancestry
Name : phg000014.Schizophrenia.genotype-calls.Affymetrix6.v1.p1.c2.SARC.unfiltered.matrixfmt.genotype.tar
phg000014.v1.p1: Genotype files: Provide all called genotypes for 306 individuals with SARC consent. QC filters were applied to the genotypes in this file. Component
contains separate files for three sets of individuals: (1) case-controls – 288 individuals; (2) duplicate samples– 3 individuals; and (3) parents–15 individuals. Genotype data
Description
are provided in 2 PLINK matrix formats: binary and text. In text format a single SNP is reported per line, each pair of columns contains all the genotypes for a given

Title : phg000014: Affymetrix 6.0 genotypes – quality assurance data and analysis - African Ancestry
71

Title : phg000014: LD plots - cases only - Schizophrenia - African Ancestry
72 phg000014.v1.p1: This component contains linkage disequilibrium plots and data computed from 921 Schizophrenia AA CASES whose genotypes passed QC filtering.
Description
respectively.

Title : phg000014: LD plots - controls only - Schizophrenia - African Ancestry
73 phg000014.v1.p1: This component contains linkage disequilibrium plots and data computed from 954 Schizophrenia AA CONTROLS whose genotypes passed QC
filtering. These sliding-window LD data were computed in 500KB intervals using a single sample without correction for any population substructure. Data files contain the
Description
file, respectively.

Title : phg000014: Affymetrix 6.0 genotype instensity CEL files. SARC participants (Part 1 of 1) African Ancestry
Name : phg000014.Schizophrenia.raw_intensities.Affymetrix6.v1.p1.c2.SARC.Set1.tar
phg000014.v1.p1: This component includes part of the hybridization probe intensity CEL data for the 306 samples typed with the Affymetrix 6.0 chip. Samples are
Description
identified in the manifest file distributed as part of this component. Files in the tarball are individually compressed with gzip utility.

Title
through 242.

Title
through 484.

Title
through 726.

: phg000014: Affymetrix 6.0 genotype scatter plots: QC filtered set, 2196 African Ancestry individuals (2196 samples).. Component 4 of 5 containing rs#''''s ending in 727
Title
through 969.

Title
through 999 and rs_undefined markers.

84
the subset of subjects with European ancestry. Data was filtered using criteria: 1) sample heterozygosity range from 0.26-0.285; 2) sample call rate greater than 97%; 3)
Description SNP MAF # 0.01; 4) SNP call rate # 0.95, and HWE pvalue > 0.000001 5) plate effect pvalue test above 10^(-8) for a single plate and/or 10^(-4) for two plates; 4) Less
than 2 discrepancies between SNP calls on duplicated samples. These thresholds resulted in 1378 controls and and 1351 cases genotyped over 729454 SNPs used in
the assoiciation analysis. Genome-wide association scan has been pre-computed by NCBI.

85
the subset of subjects with African American ancestry. Data was filtered using criteria: 1) removal of sample heterozygosity outliers; 2) sample call rate greater than 97%;
Description 3) SNP MAF # 0.01; 4) SNP call rate # 0.95 and HWE p value > 0.000001 5) plate effect p value test above 10^(-8) for a single plate and/or 10^(-4) for two plates; 4) Less
than 2 discrepancies between SNP calls on duplicated samples. These thresholds resulted in 954 controls and 1195 cases genotyped over 845814 SNPs used in the
association analysis. Genome-wide association scan has been pre-computed by NCBI.

Study Report - phs000021.GAIN Schizophrenia.v3.p2.MULTI-2

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dbGaP Study Configuration Report

Genome-Wide Association Study of Schizophrenia

Study accession phs000021.v3.p2

Data distribution set count: 2

Distribution set number 1 ( Consent code: c1 )

Distribution set number 2 ( Consent code: c2 )

Distribution Set General Research Use

Data Use Restrictions

Restriction label General Research Use ( Consent code: c1 )

Files distributed in this set

Content type : use-contents

Content type : use-contents

Content type : use-restrictions

Content type : phenotype-data-dictionary

Content type : phenotype-variable-report

Content type : phenotype-individual-traits

Content type : phenotype-individual-traits

Content type : phenotype-individual-traits

Content type : phenotype-individual-traits

Content type : phenotype-individual-traits

Content type : phenotype-individual-traits

Content type : phenotype-individual-auxiliary

Content type : phenotype-individual-auxiliary

Content type : genotype-marker-information

Content type : genotype-calls-filtered-matrix-format

Content type : genotype-calls-unfiltered-individual-format

Content type : genotype-calls-unfiltered-individual-format

Content type : genotype-calls-unfiltered-individual-format

Content type : genotype-calls-unfiltered-individual-format

Content type : genotype-calls-unfiltered-individual-format

Content type : genotype-calls-unfiltered-individual-format

Content type : genotype-calls-unfiltered-matrix-format

Content type : genotype-individual-information

Content type : genotype-qc

Content type : genotype-qc

Content type : linkage-disequilibrium

Content type : linkage-disequilibrium

Content type : genotype-intensities

Content type : genotype-intensities

Content type : genotype-intensities

Content type : genotype-intensities

Content type : genotype-intensities

Content type : genotype-intensities

Content type : genotype-scatterplots

Content type : genotype-scatterplots

Content type : genotype-scatterplots

Content type : genotype-scatterplots

Content type : genotype-scatterplots

Content type : genotype-individual-information

Content type : genotype-marker-information

Content type : genotype-calls-filtered-matrix-format

Content type : genotype-calls-unfiltered-individual-format

Content type : genotype-calls-unfiltered-individual-format

Content type : genotype-calls-unfiltered-individual-format

Content type : genotype-calls-unfiltered-individual-format

Content type : genotype-calls-unfiltered-matrix-format

Content type : genotype-calls-unfiltered-matrix-format