A neurogenetic model for the study of schizophrenia spectrum disorders: the International 22q11.2 Deletion Syndrome Brain Behavior Consortium

Abstract

Rare copy number variants contribute significantly to the risk for schizophrenia, with the 22q11.2 locus consistently implicated. Individuals with the 22q11.2 deletion syndrome (22q11DS) have an estimated 25-fold increased risk for schizophrenia spectrum disorders, compared to individuals in the general population. The International 22q11DS Brain Behavior Consortium is examining this highly informative neurogenetic syndrome phenotypically and genomically. Here we detail the procedures of the effort to characterize the neuropsychiatric and neurobehavioral phenotypes associated with 22q11DS, focusing on schizophrenia and subthreshold expression of psychosis. The genomic approach includes a combination of whole-genome sequencing and genome-wide microarray technologies, allowing the investigation of all possible DNA variation and gene pathways influencing the schizophrenia-relevant phenotypic expression. A phenotypically rich data set provides a psychiatrically well-characterized sample of unprecedented size (n=1616) that informs the neurobehavioral developmental course of 22q11DS. This combined set of phenotypic and genomic data will enable hypothesis testing to elucidate the mechanisms underlying the pathogenesis of schizophrenia spectrum disorders.

Figure 1

The 22q11.2 region. Cytogenetic representation of chromosome 22 showing the short (p) and long (q) arms with the centromere, which functions to separate both arms. Chromosome 22 is an acrocentric chromosome, as indicated by the two horizontal lines in the p arm. The 22q11.2 deletion occurs on the long arm of one of the two chromosomes, depicted by dashed lines in the 22q11.2 band. The position of the two low-copy repeats (LCRs) on 22q11.2 (LCR22A and LCR22D), which flank the typical 3-Mb deletion, LCR22B and LCR22C and genes (protein-coding and selected non-protein-coding) within the 22q11.2 deletion region, as well as the three typical 22q11.2 deletions that include LCR22A and two nested 22q11.2 deletions that do not include LCR22A (all indicated by blue bars below), are depicted in the inset.

Figure 2

Genomics flow diagram. The figure provides an overview of the ongoing and planned genomics analyses in the IBBC study, beginning with genomic DNA samples available from subjects with 22q11DS from participating international centers. Samples were sent to one laboratory (Albert Einstein College of Medicine, NY) that serves as a central clearinghouse, and provides a unique IBBC identification number to enable linking of genotypic and phenotypic data. Data primarily from studies that pre-dated the IBBC are indicated on a cyan background. The mauve and yellow backgrounds indicate data generated from the IBBC study from WGS and microarray data, respectively. Dotted lines indicate the work flow for microarray data. These provided data for initial analyses, and available for comparison with WGS data, albeit at lower resolution. Red font indicates analyses using the phenotypic data available for subjects with 22q11DS from participating international centers. Main analyses involve comparisons of subjects with 22q11DS and schizophrenia vs those with no psychotic illness at age 25 years and older. See text for details. Quality control measures applied to both WGS and microarray data include checking for duplicate and related samples, for sex and ethnicity using phenotypic data to help detect sample mix-ups, and for 22q11.2 deletion size (assisted by available multiplex ligation dependent probe amplification (MLPA) data and heat-map data generated from microarrays). Additional quality control measures, following transfer of raw WGS data (fastq files) generated at HudsonAlpha Genome Sequencing Center (Huntsville, AL) to the Human Genetics Computational Cluster (Emory U), include checking for mixing of samples, level of genetic variation, base transition to transversion ratios, too many variants in particular regions, and variants that departed from Hardy–Weinberg equilibrium at P<10^−4. The intact haploid 22q11.2 allele requires special computational considerations, thus is analyzed separately from data from the rest of the genome.^,Annotation of structural variation from WGS data is a pioneering area of genomics. Availability of CNV data from standard microarrays in this study will be valuable for comparison purposes.^–Integrated analysis using all variant data, common and rare, sequence and structural, will provide an overview of the genomic architecture of schizophrenia in 22q11DS. Validation studies, for example, polymerase chain reaction for SNV, quantitative polymerase chain reaction for SV, will proceed according to results. CNV, copy number variation; LOF, loss of function; SNP, single-nucleotide polymorphisms (common sequence variants); SNVs, single-nucleotide variants; SV, structural variants; WGS, whole-genome sequencing.