Rare variants in neuronal excitability genes influence risk for bipolar disorder

Abstract

We sequenced the genomes of 200 individuals from 41 families multiply affected with bipolar disorder (BD) to identify contributions of rare variants to genetic risk. We initially focused on 3,087 candidate genes with known synaptic functions or prior evidence from genome-wide association studies. BD pedigrees had an increased burden of rare variants in genes encoding neuronal ion channels, including subunits of GABAA receptors and voltage-gated calcium channels. Four uncommon coding and regulatory variants also showed significant association, including a missense variant in GABRA6. Targeted sequencing of 26 of these candidate genes in an additional 3,014 cases and 1,717 controls confirmed rare variant associations in ANK3, CACNA1B, CACNA1C, CACNA1D, CACNG2, CAMK2A, and NGF. Variants in promoters and 5' and 3' UTRs contributed more strongly than coding variants to risk for BD, both in pedigrees and in the case-control cohort. The genes and pathways identified in this study regulate diverse aspects of neuronal excitability. We conclude that rare variants in neuronal excitability genes contribute to risk for BD.

Keywords: GABAA receptor; bipolar disorder; family genomics; regulatory variants; voltage-gated calcium channel.

Fig. 1.

Associations of BD with 5,730 uncommon coding and noncoding SNVs in 3,087 candidate genes. (A) –log10(P values) for the association of individual SNVs with BD, plotted by chromosomal position. P values were calculated using linear mixed models implemented with EMMAX (13). SNVs with significant associations (FDR < 10%) are indicated. (B) Uniform, quantile-quantile plot for the observed vs. null-expectation distribution of P values. Positive deviation from the null indicates the presence of true signal and effective accounting for family and population structure. (C) A missense SNV in the GABA receptor gene GABRA6 was associated with risk for BD (P = 3.0e-5). This SNV was identified in a total of 13 BD cases, 2 major depression cases, and 1 unaffected individual across seven pedigrees. Diamonds below an individual indicate WGS (filled, contains variant; unfilled, does not contain variant). BPI, bipolar disorder, type I; BPII, bipolar disorder, type II; MDDR, major depressive disorder, recurrent; NMI, no mental illness; OTH, other axis I or axis II diagnosis; SA, schizoaffective disorder; SEMD, single episode of major depression; UNK, unknown phenotype (not ascertained).

Fig. 2.

Pathways enriched for rare variants in BD pedigrees. (A) Number of BD (orange) and control (blue) pedigrees in which a fully or nearly fully segregating coding or regulatory variant was found in a gene assigned to the GABA pathway by BioCarta. The 34 control pedigrees used in this analysis were of European ancestry and were matched for similar size and structure to the BD pedigrees. (B) Number of BD (orange) and control (blue) pedigrees in which a fully or nearly fully segregating coding or regulatory variant was found in a gene assigned to the Gene Ontology term “Voltage-Gated Calcium Channel Complex.” (C) Fully and nearly fully segregating coding and regulatory SNVs and indels in the GABA receptor gene GABRA4. Protein-coding regions and UTRs are shown, respectively, by wide and narrow light blue rectangles. Heights of orange and blue bars indicate the number of BD and control pedigrees in which each variant was fully or nearly fully segregating. (D) Number of risk variants identified in each BD case (orange), unaffected individual in a BD pedigree (light blue), or population control (dark blue). For this analysis, we defined as risk variants all SNVs with P < 0.001 and odds ratios > 1 by mixed model analysis (14 SNVs), as well as SNVs with mixed-model P < 0.05, odds ratios > 1, and an annotation to one of the following pathways with an increased burden of rare variants in BD pedigrees (SI Appendix, Table S4): BioCarta GABA pathway (9 SNVs), voltage-gated calcium channel complex (38 SNVs), CaM kinases (10 SNVs), GTPases (88 SNVs), and glycolysis/tricarboxylic acid cycle (13 SNVs). The widths of polygons are proportional to the number of individuals with each variant count.