The impact of hidden copy-number variants to birth defects and rare genetic diseases

Genetic aberrations are the most common cause of first trimester pregnancy losses (> 50%) and constitute the leading cause of birth defects with known etiologies in live-born infants of developed countries. Chromosomal abnormalities such as trisomy 13, 18, 21 and X/Y are found in up to 0.3% of all newborn infants and constitute a significant fraction (~4%) within the group of newborns with birth defects referred for chromosomal studies. Genetic abnormalities are also a relevant contributor to neonatal death: as much as 25% of deceased newborns with congenital defects also present with gross chromosomal abnormalities.

The application of high-resolution molecular techniques revealed that microdeletions and microduplications < 5-10 Mb, usually not visible by classical karyotyping, are also a very important cause of birth defects. Importantly, the variability in detection rate was found to be strongly dependent upon the resolution of the array platform utilized. Higher resolution molecular tools increase the detection rate of pathogenic copy-number variants (CNVs) by at least 4X. Nevertheless, despite the use of higher resolution arrays to detect aneuploidy and CNVs, a large portion of the patients with birth defects suspected to have genetic disorders still do not obtain a molecular diagnosis.

The Carvalho Lab is applying genome sequencing methodologies and developing pipelines to identify CNVs in individuals and families with rare genetic disorders without molecular diagnostic. In collaboration with the GREGoR consortium, this PNRI lab is currently investigating individuals with primary immunodeficiency and multiple individuals with Mendelian disorders of unknown molecular cause with the goal of establishing the impact of CNVs to a diverse range of clinical phenotypes.

b.

c.

d.

Figure – Copy-number variants are an important cause of rare genetic diseases.

a. CNVs may directly impact gene expression of dosage sensitive genes¹ but they can also be formed accompanied by additional genomic and epigenetic alterations such as absence of heterozygosity and imprinting perturbation². 

b. CNV data-processing pipeline incorporates read-depth information from proband with rare diseases and parents. 

c. Pipeline results in a cohort of probands with primary immunodeficiency (PIDD) indicates that majority of inherited CNVs are smaller than 300 kb. About 54% of CNVs are constituted by deletions.

d. Approach described in C. revealed a 12.8 kb heterozygous deletion (log₂ = -1) spanning exon 5 of DOCK8. This exonic deletion in conjunction with an in trans coding variant explains the patient’s phenotype. The window (top to bottom) shows chromosome 9 log₂ ratio plot, followed by zoomed CNV read-depth plots, B-allele frequency plot, structural variant plot, genes plot, segmental duplication and OMIM gene plots, respectively. Unpublished data.