Jump to content

Genomic Data

Overview

Many of the subjects with biomaterials in the NRGR have genomic data (sequence or high density SNP array) available for use by approved researchers. Some of this data is housed at the NRGR, some at collaborating repositories. The NRGR also has genomic datasets from several studies that do not have biomaterials at the NRGR. This section provides information about all subjects with biomaterials and genomic data housed anywhere, as well as all the genomic datasets housed at NRGR, including those without corresponding biomaterials.

Biosamples with Genomic Data

Genomic data is available on over 22,000 NRGR samples. While some of this data is available from Download Data, many of the datasets are housed elsewhere (learn about collaborating repositories). You can search for samples in a disorder collection with genomic data using Data Explorer. Everyone can use Data Explorer to obtain summary counts of numbers of subjects with genomic data. Individuals with approved access to a collection can use Data Explorer to obtain lists of individual samples with associated genomic data.

Collection Data Type Total Data at NRGR Studies Data at dbGaP Studies Notes
ADHD Array 1,786 1,786 25
Autism Array 4,032 1,223 4, 10, 14, 21, 33 2,920 4, 21, 32, 36, 41, 44, 50, 64, 65, 79
Autism Sequence 1,632 1,632 4, 21, 32, 36, 41, 4, 50, 63, 64, 65, 79
Bipolar Array 3,007 1,998 0, 1, 2, 19 1,415 0, 1, 40
Controls Array 4,582 549 19, 29 4,033 19, 29
Controls Sequence 912 912 29
Depression Array 3,172 3,172 18, 52, 88
Depression Sequence 451 451 88 Additional subjects in Controls; RNASeq
OCD Array 1,247 1,247 16, 66
Schizophrenia Array 4,574 741 17 3,833 0, 6, 27, 29
Schizophrenia Sequence 669 455 0, 94 214 22, 27

Genomic Datasets

29 genomic datasets are available via our website. These datasets include high-density SNP array genotypes, RNAseq, and whole exome sequencing. While most are available for download, larger datasets are delivered via shipped hard drive. Everyone can browse the list of files available in each disorder collection in Download Data. Approved users may download or request available datasets. Not all datasets are independent, some may have subject overlap. Most, but not all, of these datasets have subjects with biomaterials at the NRGR. Additional lower-density genetic datasets are available for many samples. Please review the disorder download data pages for details.

Collection Study Name Samples Design Data Type Platform File Types Notes
Autism JHU-Autism-1 522 Family GWAS Array Affymetrix 500K PLINK, CEL
CEL files available via hard drive
Data in Autism Dataset 3
Autism JHU-Autism-2 743 Family GWAS Array Affymetrix 5.0 PLINK, CEL
CEL files available via hard drive
Data in Autism Dataset 3
Autism AGP/TASC 2,893 Trios GWAS Array Illumina 1M PLINK
935 Families
Data in Autism Dataset 4
Bipolar Pritzker 1,956 Case-Control GWAS Array Illumina 550K PLINK, logR/BAF
logR/BAF files available via hard drive
Data in Bipolar Dataset 11
Bipolar STEP-BD 2,453 Case-Control GWAS Array Affymetrix 5.0 PLINK
955 Cases
Data in Bipolar Dataset 16.01
Bipolar Colombia/Costa Rica 837 Family GWAS Array Illumina Omni 2.5 PLINK
26 Families
Samples from BP Study 71
Data in Bipolar Dataset 31
Bipolar PGC-BP 7,274 Case-Control GWAS Array Multiple PLINK
7 cohorts available, some at NRGR
3,803 Total Cases
Imputed Genotypes on 2.5M SNPs
Controls Broad-Controls 1,698 Controls Only GWAS Array Affymetrix 500K PLINK, CEL
CEL files available via hard drive
Data in Controls Dataset 1
Controls SICCA 26 Controls Only GWAS Array Illumina Omni 2.5M PLINK Data in Controls Dataset 3
Depression STAR*D-1 964 Cases Only GWAS Array Affymetrix 500K PLINK Data in Depression Dataset 2
Depression STAR*D-2 975 Cases Only GWAS Array Affymetrix 5.0 PLINK Data in Depression Dataset 3
Depression GenRED 1,103 Cases Only GWAS Array Affymetrix 6.0 PLINK, CEL
CEL files available via hard drive
Data in Depression Dataset 4.02
Depression DGN 922 Case-Control RNASeq Illumina HiSeq2000 BAM, FASTQ
Data files available via hard drive
Data in Depression Dataset 7
Depression GenRED2/DGN 2,226 Case-Control GWAS Array Illumina Omni 1-Quad PLINK, logR/BAF
937 subjects are DGN
Data in Depression Dataset 7
Depression PGC-DP 11,191 Case-Control GWAS Array Multiple PLINK
5 cohorts available, some at NRGR
5,347 Total Cases
Imputed Genotypes on 2.5M SNPs
Schizophrenia CATIE-1 1,492 Case-Control GWAS Array Affymetrix 500K PLINK
741 Cases
Data in Schizophrenia Dataset 13.01
Schizophrenia CATIE-2 291 Cases Only GWAS Array Affymetrix 6.0 PLINK, CEL
Data in Schizophrenia Dataset 27
CEL files available via hard drive
Schizophrenia Tsaung-Exome 12 Family Exome Seq ABI SOLiDv4 BAM
Data files available via hard drive
Samples from SZ Study 0
Data in Schizophrenia Dataset 28
Schizophrenia Sweden-1 435 Case-Control GWAS Array Affymetrix 5.0 PLINK
221 Cases
Data in Schizophrenia Dataset 29
Schizophrenia Sweden-2 4,417 Case-Control GWAS Array Affymetrix 6.0 PLINK
2,076 Cases
Data in Schizophrenia Dataset 29
Schizophrenia Sweden-3 4,418 Case-Control GWAS Array Illumina OmniExpress PLINK
1,801 Cases
Data in Schizophrenia Dataset 29
Schizophrenia Sweden-4 2,313 Case-Control GWAS Array Illumina OmniExpress PLINK
1,094 Cases
Data in Schizophrenia Dataset 29
Schizophrenia CIAC 443 Case-Control Exome Seq Illumina HiSeq2000 VCF
67 Cases
Data files available via hard drive
Samples from SZ Study 94
Data in Schizophrenia Dataset 31
Schizophrenia CIAC 319 Case-Control Exome Array Illumina HumanExome PLINK
113 Cases
Data files available via hard drive
Samples from SZ Study 94
Data in Schizophrenia Dataset 31
Schizophrenia CIAC 384 Case-Control GWAS Array Illumina OmniExpress PLINK
135 Cases
Data files available via hard drive
Samples from SZ Study 94
Data in Schizophrenia Dataset 31
Schizophrenia Ireland 3,400 Case-Control GWAS Array Affymetrix 6.0 PLINK, CEL
1,606 Cases
CEL files available via hard drive
Samples from SZ Study 90
Data in Schizophrenia Dataset 33
Schizophrenia NIMH-SZ 1,179 Case-Control GWAS Array Illumina Multiple PLINK
532 Cases
Samples from SZ Study 9
Data in Schizophrenia Dataset 34
Schizophrenia CAPS-SZ 330 Family GWAS Array Affymetrix Axiom Lat KELVIN, CEL
47 Families
CEL files available via hard drive
Data in Schizophrenia Dataset 36
Schizophrenia PGC-SZ 14,948 Case-Control GWAS Array Multiple PLINK
14 cohorts available, some at NRGR
8,004 Total Cases
Imputed Genotypes on 2.5M SNPs