Cytogenomic mapping and bioinformatic mining reveal interacting brain expressed genes for intellectual disability

Abstract

Background: Microarray analysis has been used as the first-tier genetic testing to detect chromosomal imbalances and copy number variants (CNVs) for pediatric patients with intellectual and developmental disabilities (ID/DD). To further investigate the candidate genes and underlying dosage-sensitive mechanisms related to ID, cytogenomic mapping of critical regions and bioinformatic mining of candidate brain-expressed genes (BEGs) and their functional interactions were performed. Critical regions of chromosomal imbalances and pathogenic CNVs were mapped by subtracting known benign CNVs from the Databases of Genomic Variants (DGV) and extracting smallest overlap regions with cases from DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources (DECIPHER). BEGs from these critical regions were revealed by functional annotation using Database for Annotation, Visualization, and Integrated Discovery (DAVID) and by tissue expression pattern from Uniprot. Cross-region interrelations and functional networks of the BEGs were analyzed using Gene Relationships Across Implicated Loci (GRAIL) and Ingenuity Pathway Analysis (IPA).

Results: Of the 1,354 patients analyzed by oligonucleotide array comparative genomic hybridization (aCGH), pathogenic abnormalities were detected in 176 patients including genomic disorders in 66 patients (37.5%), subtelomeric rearrangements in 45 patients (25.6%), interstitial imbalances in 33 patients (18.8%), chromosomal structural rearrangements in 17 patients (9.7%) and aneuploidies in 15 patients (8.5%). Subtractive and extractive mapping defined 82 disjointed critical regions from the detected abnormalities. A total of 461 BEGs was generated from 73 disjointed critical regions. Enrichment of central nervous system specific genes in these regions was noted. The number of BEGs increased with the size of the regions. A list of 108 candidate BEGs with significant cross region interrelation was identified by GRAIL and five significant gene networks involving cell cycle, cell-to-cell signaling, cellular assembly, cell morphology, and gene expression regulations were denoted by IPA.

Conclusions: These results characterized ID related cross-region interrelations and multiple networks of candidate BEGs from the detected genomic imbalances. Further experimental study of these BEGs and their interactions will lead to a better understanding of dosage-sensitive mechanisms and modifying effects of human mental development.

Figure 1

Flowchart for abnormality classification and bioinformatic filtration.

Figure 2

A genome-wide view of detected abnormalities. Detected recurrent genomic disorders, subtelomeric rearrangements, interstitial imbalances, and structural chromosomal abnormalities are shown in its category with genomic location and relative frequency (downward red bar for deletion and upward blue bar for duplication).

Figure 3

The size distribution of genomic disorders, subtelomeric rearrangements and interstitial imbalances. The average sizes for deletions and duplications are 2.2 Mb and 1.4 Mb for genomic disorders, 4.9 Mb and 5.2 Mb for subtelomeric abnormalities (abns), and 6.0 Mb and 6.2 Mb interstitial abnormalities, respectively.

Figure 4

Boxplots showing the permutation-based empirical distributions of the number of BEGs observed in the critical regions of different gene content sizes (measured by gene numbers). For each of the 82 targeted abnormal regions, a set of 10,000 random genomic loci with gene content size defined by the same number of genes as the target regions was drawn from the genome. The X-axis represents the number of genes located in each regions, and the Y-axis stands for the numbers of BEGs observed. The actual numbers of BEGs detected in each abnormal region was shown as big solid red square.

Figure 5

Functional connections between genes at the 73 critical regions inferred by GRAIL. The double circle plots depict the gene relationships across the abnormal regions by GRAIL based on data source PubMed Text. Outer circle represents abnormal regions, of which the G-band regions with '_del' are denoted deletions and the other regions are duplications. The inner circle stands for genes located in the corresponding regions in the outer circle, and for clear visualization only significant genes (p < 0.001) and their connections are shown. The lines represent pair-wise gene connections, with the thickness of the lines indicating the degree functional similarity.

Figure 6

The primary functional network of BEGs identified by the ingenuity pathway analysis. Nodes represent genes and a solid line means a direct interaction between the two genes and a dotted line stands for an indirect relationship. Shaded nodes represent genes within the abnormal regions (genes denoted with underlined G-band position are in the candidate gene list of Table 1)