Third-generation genome sequencing implicates medium-sized structural variants in chronic schizophrenia

Abstract

Background: Schizophrenia (SCZ) is a heterogeneous psychiatric disorder, with significant contribution from genetic factors particularly for chronic cases with negative symptoms and cognitive deficits. To date, Genome Wide Association Studies (GWAS) and exome sequencing have associated SCZ with a number of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs), but there is still missing heritability. Medium-sized structural variants (SVs) are difficult to detect using SNP arrays or second generation sequencing, and may account for part of the missing heritability of SCZ.

Aims and objectives: To identify SVs associated with severe chronic SCZ across the whole genome.

Study design: 10 multiplex families with probands suffering from chronic SCZ with negative symptoms and cognitive deficits were recruited, with all their affected members demonstrating uni-lineal inheritance. Control subjects comprised one affected member from the affected lineage, and unaffected members from each paternal and maternal lineage.

Methods: Third generation sequencing was applied to peripheral blood samples from 10 probands and 5 unaffected controls. Bioinformatic tools were used to identify SVs from the long sequencing reads, with confirmation of findings in probands by short-read Illumina sequencing, Sanger sequencing and visual manual validation with Integrated Genome Browser.

Results: In the 10 probands, we identified and validated 88 SVs (mostly in introns and medium-sized), within 79 genes, which were absent in the 5 unaffected control subjects. These 79 genes were enriched in 20 biological pathways which were related to brain development, neuronal migration, neurogenesis, neuronal/synaptic function, learning/memory, and hearing. These identified SVs also showed evidence for enrichment of genes that are highly expressed in the adolescent striatum.

Conclusion: A substantial part of the missing heritability in SCZ may be explained by medium-sized SVs detectable only by third generation sequencing. We have identified a number of such SVs potentially conferring risk for SCZ, which implicate multiple brain-related genes and pathways. In addition to previously-identified pathways involved in SCZ such as neurodevelopment and neuronal/synaptic functioning, we also found novel evidence for enrichment in hearing-related pathways and genes expressed in the adolescent striatum.

Keywords: biological pathways; chronic and negative symptoms; intronic; multiplex families; schizophrenia; striatum; structural variants; third generation sequencing.

FIGURE 1

Workflow of the project.

FIGURE 2

Venn diagrams and correlation matrices of structural variations detected by 4 programs from PacBio in 10 probands. DEL, deletion; DUP, duplication; INS, insertion; INV, inversion.

FIGURE 3

Pedigree tree of 10 probands.

FIGURE 4

Kernel density plot in length distribution of SVs from PacBio in 15 samples.

FIGURE 5

Bi-cluster analysis of enriched pathways.

FIGURE 6

Proportion of brain expressed case-specific SV genes annotated to the striatum-expressed gene set vs non-striatum-expressed gene set across development. P-values are from a hypergeometric test for over-representation of case-specific SV genes in the striatum-annotated gene set. Note that these are not the competitive p-values as calculated by ABAEnrichment through permutation. Stage 1 = Prenatal, Stage 2 = Infant, Stage 3 = Child, Stage 4 = Adolescent, Stage 5 = Adult.