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.
Biospecimens 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 | NRGR Studies Included | Samples | Design | Data Type | Platform | File Types | Notes |
|---|---|---|---|---|---|---|---|---|
| Autism | JHU-Autism-1 | 4, 14, 21 | 522 | Family | GWAS Array | Affymetrix 500K | PLINK, CEL | CEL files available via hard drive Data in Autism Dataset 3 |
| Autism | JHU-Autism-2 | 4, 14, 21 | 743 | Family | GWAS Array | Affymetrix 5.0 | PLINK, CEL | CEL files available via hard drive Data in Autism Dataset 3 |
| Autism | AGP/TASC | 65 | 2,893 | Trios | GWAS Array | Illumina 1M | PLINK | 935 Families
Data in Autism Dataset 4 |
| Bipolar | Pritzker | BP0, 29 | 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 | 19 | 2,453 | Case-Control | GWAS Array | Affymetrix 5.0 | PLINK | 955 Cases
Data in Bipolar Dataset 16.01 |
| Bipolar | Colombia/Costa Rica | 71 | 837 | Family | GWAS Array | Illumina Omni 2.5 | PLINK | 26 Families
Samples from BP Study 71
Data in Bipolar Dataset 31 |
| Bipolar | PGC-BP | PGC-Psychiatric GWAS Consortium: Including GAIN (BP0, 1, 40), STEP-BD (19), MGS for controls (SZ0, 6, 29) | 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 | 19 (STEP-BD), 29 (MGS) | 1,698 | Controls Only | GWAS Array | Affymetrix 500K | PLINK, CEL | CEL files available via hard drive Data in Controls Dataset 1 |
| Controls | SICCA | 29 | 26 | Controls Only | GWAS Array | Illumina Omni 2.5M | PLINK | Data in Controls Dataset 3 |
| Depression | STAR*D-1 | 18 | 964 | Cases Only | GWAS Array | Affymetrix 500K | PLINK | Data in Depression Dataset 2 |
| Depression | STAR*D-2 | 18 | 975 | Cases Only | GWAS Array | Affymetrix 5.0 | PLINK | Data in Depression Dataset 3 |
| Depression | GenRED | 52 | 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 | 88 | 922 | Case-Control | RNASeq | Illumina HiSeq2000 | BAM, FASTQ | Data files available via hard drive Data in Depression Dataset 7 |
| Depression | GenRED2/DGN | 52 (GenRED) / 88 (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 | PGC-Psychiatric GWAS Consortium: Including GAIN, GenRED (52), STAR*D (18) | 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 | 17 | 1,492 | Case-Control | GWAS Array | Affymetrix 500K | PLINK | 741 Cases Data in Schizophrenia Dataset 13.01 |
| Schizophrenia | CATIE-2 | 17 | 291 | Cases Only | GWAS Array | Affymetrix 6.0 | PLINK, CEL | Data in Schizophrenia Dataset 27 CEL files available via hard drive |
| Schizophrenia | Tsaung-Exome | SZ0 | 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 | No NRGR study # | 435 | Case-Control | GWAS Array | Affymetrix 5.0 | PLINK | 221 Cases Data in Schizophrenia Dataset 29 |
| Schizophrenia | Sweden-2 | No NRGR study # | 4,417 | Case-Control | GWAS Array | Affymetrix 6.0 | PLINK | 2,076 Cases Data in Schizophrenia Dataset 29 |
| Schizophrenia | Sweden-3 | No NRGR study # | 4,418 | Case-Control | GWAS Array | Illumina OmniExpress | PLINK | 1,801 Cases Data in Schizophrenia Dataset 29 |
| Schizophrenia | Sweden-4 | No NRGR study # | 2,313 | Case-Control | GWAS Array | Illumina OmniExpress | PLINK | 1,094 Cases Data in Schizophrenia Dataset 29 |
| Schizophrenia | CIAC | 94 | 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 | 94 | 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 | 94 | 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 | 90 | 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 | 9 | 1,179 | Case-Control | GWAS Array | Illumina Multiple | PLINK | 532 Cases Samples from SZ Study 9 Data in Schizophrenia Dataset 34 |
| Schizophrenia | CAPS-SZ | 13, 49 | 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 | PGC-Psychiatric GWAS Consortium: Including MGS (SZ0, 6, 29), CATIE (17) | 14,948 | Case-Control | GWAS Array | Multiple | PLINK | 14 cohorts available, some at NRGR 8,004 Total Cases Imputed Genotypes on 2.5M SNPs |