Genomic rearrangements and diseases

The human genome contains a diverse array of genomic variants, including single nucleotide polymorphisms (SNPs), length polymorphisms of microsatellite sequences, and several types of structural variations (SVs). SVs comprise dosage-altering variations, such as insertions and deletions, and dosage-invariant rearrangements, such as inversions and translocations. In recent years, copy number variations (CNVs) have been identified by microarray-based genomic profiling technologies in both research and diagnostic settings, thus emerging as major contributors to genomic imbalance disorders.

The ~600 kb deletion/duplication region at 16p11.2 (29.5 to 30.1Mb) is a typical example of such novel genomic imbalances. This region is flanked by 147-kb segmental duplication with 99.5% sequence identity. It has recently been implicated as one of the most significant genetic risk factors for autism spectrum disorders (ASDs) in multiple cohorts, among a variety of other childhood-onset neurodevelopmental and psychiatric conditions, such as mental retardation, language delay, and schizophrenia. Furthermore, it has been recently showed that hemizygosity of this region causes a highly penetrant form of obesity that is often accompanied by hyperphagia, and significant increase in head circumference, while the corresponding reciprocal duplication is associated with being underweight and microcephaly, leading to the hypothesis that these conditions may represent mirror states associated with reciprocal changes in copy number at this locus.

Less frequently, a smaller 220 kb deletion (28.74Mb to 28.95Mb), distal to this 16p11.2 deletion and centered around the SH2B1 gene, previously associated by GWAS with BMI, serum leptin and body fat, has been reported in individuals with developmental delay, autism spectrum disorder, epilepsy, and obesity, thus resembling to a large extent the phenotype of the common proximal deletion at 16p11.2.

Understanding the complex genotype–phenotype correlations involved in genomic disorders is important but very challenging, given that similar phenotypic manifestation could be derived from different and apparently independent genomic imbalances, as in this case.

To allow a better understanding of the molecular mechanism underlying the pathophysiology of these complex disorders, one of the specific aims of my PhD project will consist in the characterization of the three-dimensional (3D) architecture of the 16p locus. Hence, many studies have recently focused on the looping mechanisms of long-range regulatory elements, as the shape of the genome is thought to be structured as a network of interactions between genomic elements, which are supposed to play an important part in the coordination of transcription and other DNA-metabolic processes.

For this purpose, I will use the high-resolution Chromosome Conformation Capture Sequencing (4C-seq) technology with multiple genes as anchor points (“viewpoints”), taken in both the distal and proximal deleted/duplicated region at 16p11.2.

Furthermore, even when the genomic rearrangements (reciprocal deletions and duplications) are seemingly uniform across individuals with a particular genomic imbalance, the clinical phenotypes could also show remarkably variability among them.

Hence, determination of mutations that could be responsible for this heterogeneity is a major goal in genomic medicine.

To address this challenge, massively parallel or next-generation sequencing (NGS) is one of the most effective tool to identify new disease-related genes, usually by sequencing the whole exome or specifically targeted regions. Thus, for which concerns the 16p locus, targeted-capture exome sequencing will be performed to analyze the genomic DNA of individuals carrying the 16p11.2 deletion, in order to allow accurate genetic screening, particularly for those patients in the selected cohorts who show rare and peculiar phenotypic characteristics.