Table 3.
SNP and CNV data sets
| Data set | Sourcea | Platform | # Subjects | # Families | # Markers |
|---|---|---|---|---|---|
| SNP data sets | |||||
| Primary | AGRE-NIMH | Affymetrix 5.0 | 1756 | 1033 multiplex | 345 429 |
| Replication | AGP-1M | Illumina 1M | 1330 | 1369 simplex and multiplex | 842 215 |
| SSC-V1 | Illumina 1M | 691 | 698 simplex | 839 246 | |
| Meta-analysis | Imputed | Mixed microarray | 4222 | 3444 simplex and multiplex | 634 151 |
| Control | NHGRI-VU | Illumina 1M | 769 | Case–control | 1 199 187 |
| Data set | Sourceb | Platform | # Subjects | # Families | |
| CNV data sets | |||||
| Primary | AGP-10K | Affymetrix 10K | 196 | 173 multiplex | |
| CIHR | Affymetrix 550K | 427 | 427 simplex and multiplex | ||
| AGRE-ACC (exonic) | Illumina 550 | 2542 | 1802 simplex and multiplex | ||
| AGRE | Illumina 550 | 1683 | 943 simplex and multiplex | ||
| AGP-1M | Illumina 1M | 996 | 876 simplex and multiplex | ||
| SSC | Illumina 1M | 1124 | 1124 simplex | ||
| ACRD | Mixed microarray | – | – | ||
| Control | DGV | Mixed microarray | – | – | |
| WTSI | Agilent 105K | 450 | – | ||
Five SNP data sets were used for common polymorphism association analysis. The genotyping platform, number of subjects, number of families and number of high quality markers are shown. Seven autism and two control CNV data sets were used for rare variant association analysis. The genotyping platform, number of subjects and number of families are shown.
aAGRE-NIMH: combined data sets from AGRE (Autism Genetic Resource Exchange, www.agre.org) and NIMH (National Institute for Mental Health, collections of DNA from multiplex and simplex families with ASD by the NIMH Autism Genetics Initiative) (17). AGP-1M: Autism Genome Project (http://www.autismgenome.org/) (20). SSC-V1: Simons Simplex Collection V1 Public Cohort (https://sfari.org/simons-simplex-collection) (83). Imputed: imputed data sets based on AGRE-NIMH, AGP, SSC-V1 and AGRE-CHOP. NHGRI-VU: Vanderbilt University NUgene Project type 2 diabetes SNP data set (dbGap: phs000237.v1.p1)) (89).
bAGP-10K: Autism Genome Project CNV data set (15); CIHR: Marshall et al. CNV data set (13); AGRE-ACC: Bucan et al. CNV data set (14); AGRE: Autism Genetic Resource Exchange CNV data set identified by PennCNV (82); AGP-1M: Pinto et al. CNV data set (23); SSC: Sanders et al. CNV data set (12); ACRD: CNV data set from the Autism Chromosome Rearrangement Database (ACRD) (84); DGV: CNV control data set from the DGV (86); WTSI: Conrad et al. CNV control data set (29).