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Table 2 Six gene-sets showing enrichment for rare duplications in the schizophrenia-LIQ group compared to the schizophrenia-average IQ group

From: Impact of IQ on the diagnostic yield of chromosomal microarray in a community sample of adults with schizophrenia

  Schizophrenia-LIQ (n = 162)a Schizophrenia-average IQ (n = 278)a Analyses
  Participants   Participants
Gene-set name Total genes (n) CNVs (n) n % CNVs (n) n % p BH-FDR OR
GO Nervous system development 1874 44 35 18.5 29 28 10.1 0.013 0.0783 1.7
Union inclusive 2874 56 45 23.8 43 41 14.7 0.058 0.1554 1.4
NMDARb 62 4 4 2.1 0 0 0 0.078 0.1554 Inf
Targets of FMR1, Darnell et al. (2012) 840 25 24 12.7 21 20 7.2 0.371 0.5563 1.3
GO Synaptic 622 15 15 8.5 11 11 4.0 0.471 0.5650 1.2
GO Nervous system transmission 716 18 17 9.0 10 10 3.6 0.761 0.7605 1.1
  1. aAll rare (< 0.1%) autosomal CNVs > 10 kb were included in the analysis; see “Methods” for details. Sample sizes represent those individuals with one or more rare CNVs overlapping at least 1 bp of coding sequence, according to RefSeq annotations, in each group (162/192, or 84.3%, of the schizophrenia-LIQ group; 278/325, or 85.5%, of the schizophrenia-average IQ group)
  2. bThe CNVs comprised four pathogenic 16p11.2 duplications in four individuals, for which the contributing gene for this gene-set result was MAPK3
  3. LIQ low IQ, GO gene ontology, CNV copy number variation, p statistical result when all rare autosomal CNVs are included; BH-FDR Benjamini–Hochberg false discovery rate, Inf infinity, NMDAR N-methyl-D-aspartate receptor components