High-impact rare genetic variants in severe schizophrenia

Abstract

Extreme phenotype sequencing has led to the identification of high-impact rare genetic variants for many complex disorders but has not been applied to studies of severe schizophrenia. We sequenced 112 individuals with severe, extremely treatment-resistant schizophrenia, 218 individuals with typical schizophrenia, and 4,929 controls. We compared the burden of rare, damaging missense and loss-of-function variants between severe, extremely treatment-resistant schizophrenia, typical schizophrenia, and controls across mutation intolerant genes. Individuals with severe, extremely treatment-resistant schizophrenia had a high burden of rare loss-of-function (odds ratio, 1.91; 95% CI, 1.39 to 2.63; P = 7.8 × 10^-5) and damaging missense variants in intolerant genes (odds ratio, 2.90; 95% CI, 2.02 to 4.15; P = 3.2 × 10^-9). A total of 48.2% of individuals with severe, extremely treatment-resistant schizophrenia carried at least one rare, damaging missense or loss-of-function variant in intolerant genes compared to 29.8% of typical schizophrenia individuals (odds ratio, 2.18; 95% CI, 1.33 to 3.60; P = 1.6 × 10^-3) and 25.4% of controls (odds ratio, 2.74; 95% CI, 1.85 to 4.06; P = 2.9 × 10^-7). Restricting to genes previously associated with schizophrenia risk strengthened the enrichment with 8.9% of individuals with severe, extremely treatment-resistant schizophrenia carrying a damaging missense or loss-of-function variant compared to 2.3% of typical schizophrenia (odds ratio, 5.48; 95% CI, 1.52 to 19.74; P = 0.02) and 1.6% of controls (odds ratio, 5.82; 95% CI, 3.00 to 11.28; P = 2.6 × 10^-8). These results demonstrate the power of extreme phenotype case selection in psychiatric genetics and an approach to augment schizophrenia gene discovery efforts.

Keywords: genomics; rare variants; schizophrenia; treatment-resistant schizophrenia.

Fig. 1.

Study and analysis workflow. (A) Approximate distribution of illness severity within the schizophrenia spectrum by system of care (numbers not to scale). Typically, patients who do not respond to treatment after several months in community inpatient facilities are transferred to state-funded inpatient facilities and represent a more severe form of schizophrenia. Patients who require very long stays (>5 y) in state-funded inpatient facilities represent the most severe and treatment-resistant subset of the schizophrenia spectrum, which we define as severe, extremely treatment-resistant schizophrenia (SETRS). SCZ: Schizophrenia. (B) Analytic workflow of 112 individuals with SETRS and 4,929 controls. Qualifying missense and loss-of-function variants are analyzed separately in their respective gene sets. SCZ missense enriched: Genes with prior evidence of enrichment for missense variation in the schizophrenia exome meta-analysis (SCHEMA) study of schizophrenia. SCZ loss-of-function enriched: Genes with prior evidence of enrichment for loss-of-function variation in SCHEMA. ASD/DD: combined gene set of 102 genome-wide significant genes associated with autism spectrum disorder and 299 genome-wide significant genes associated with developmental delay. OMIM: All genes associated with Mendelian disorders in the OMIM database. Non-OMIM: Missense and loss-of-function intolerant genes without a known disease association in OMIM. Behavioral OMIM: The subset of OMIM genes with clinical phenotype annotations including “behavioral” manifestations. *P < 0.05; **FDR < 0.1.

Fig. 2.

The burden of rare variants in missense and loss-of-function intolerant genes in 112 individuals with severe, extremely treatment-resistant schizophrenia and 4,929 healthy controls. (A) Missense intolerant genes were those with missense Z > 3.09 and (B) loss-of-function intolerant genes were those with probability of being loss-of-function intolerant (pLI) score > 0.9 as per gnomAD. Unadjusted two-sided Cochran–Mantel–Haenszel exact P values, effect sizes between severe, extremely treatment-resistant schizophrenia and healthy controls represented as odds ratios, and horizontal bars indicating 95% confidence intervals are shown. LoF: Loss-of-Function variants, Miss Dmg Missense Tolerance Ratio (MTR): Damaging missense variants with REVEL score > 0.5 and missense tolerance ratio false discovery rate < 0.1, Miss Dmg: Damaging missense variants with REVEL score > 0.5, Miss Ben: Benign missense variants with REVEL score < 0.15, Syn: Synonymous variants. *False discovery rate < 0.1.

Fig. 3.

Rare variant burden analyses in schizophrenia relevant gene sets. Enrichment of qualifying missense (A) and loss-of-function variants (B) across gene sets of relevance to schizophrenia in individuals with severe, extremely treatment-resistant schizophrenia compared to healthy controls. Unadjusted exact two-sided Cochran–Mantel–Haenszel P values, effect sizes between severe, extremely treatment-resistant schizophrenia and healthy controls represented as odds ratios, and horizontal bars indicating 95% CIs are shown. Gene sets are described in detail in Fig. 1 and SI Appendix. All OMIM: All genes associated with Mendelian disorders in the OMIM database. Non-OMIM: Missense and loss-of-function intolerant genes without a known disease association in OMIM. Behav OMIM: The subset of OMIM genes with clinical phenotype annotations including “behavioral” manifestations. SCHEMA Miss Intol: Genes with prior evidence of enrichment for missense variation in the schizophrenia exome meta-analysis (SCHEMA) study of schizophrenia. SCHEMA LoF Intol: Genes with prior evidence of enrichment for loss-of-function variation in SCHEMA. ASD/DD: combined gene set of 102 genome-wide significant genes associated with autism spectrum disorder and 299 genome-wide significant genes associated with developmental delay. All gene sets ending with “Miss Intol” are restricted to include only those overlapping intolerant genes with a missense Z > 3.09 and those ending in “LoF Intol” overlapping genes with probability of loss-of-function intolerance (pLI) score > 0.9. *FDR < 0.1.

Fig. 4.

Overall burden of rare variants in severe, extremely treatment-resistant schizophrenia compared to typical schizophrenia and control individuals. (A) No difference observed between severe, extremely treatment-resistant schizophrenia, typical schizophrenia, and controls for benign missense variants in missense intolerant genes (Mis Z > 3.09, n = 956 genes). (B) Increased burden of damaging missense MTR variants in severe, extremely treatment-resistant schizophrenia compared to typical schizophrenia in missense intolerant genes (Mis Z > 3.09, n = 956 genes). (C) Increased burden of loss-of-function variants in severe, extremely treatment-resistant schizophrenia compared to typical schizophrenia in loss-of-function (LoF) intolerant genes (pLI > 0.9, n = 3,063). (D) Increased burden of damaging missense MTR variants in severe, extremely treatment-resistant schizophrenia compared to typical schizophrenia in missense intolerant schizophrenia exome meta-analysis (SCHEMA) genes (n = 45 genes). (E) Nonsignificant increase in burden of loss-of-function variants in severe, extremely treatment-resistant schizophrenia compared to typical schizophrenia in loss-of-function intolerant SCHEMA genes (n = 75 genes). (F) Increased burden of damaging missense MTR and loss-of-function in severe, extremely treatment-resistant schizophrenia compared to typical schizophrenia in intolerant SCHEMA genes (n = 45 for missense intolerant and n = 75 for loss-of-function intolerant SCHEMA genes). Odds ratios (OR) and P values shown are based on a comparison of typical schizophrenia individuals to controls and severe, extremely treatment-resistant schizophrenia individuals to typical schizophrenia using one-sided Cochran–Mantel–Haenszel test. Benign missense: missense variants with REVEL score < 0.15, Missense damaging MTR: missense variants with REVEL score > 0.5 and missense tolerance ratio false discovery rate < 0.1. SCZ: schizophrenia, SETRS: severe, extremely treatment-resistant schizophrenia.