Three patients with homozygous familial hypercholesterolemia: Genomic sequencing and kindred analysis

Abstract

BackgroundHomozygous Familial Hypercholesterolemia (HoFH) is an inherited recessive condition associated with extremely high levels of low‐density lipoprotein (LDL) cholesterol in affected individuals. It is usually caused by homozygous or compound heterozygous functional mutations in the LDL receptor (LDLR). A number of mutations causing FH have been reported in literature and such genetic heterogeneity presents great challenges for disease diagnosis.ObjectiveWe aim to determine the likely genetic defects responsible for three cases of pediatric HoFH in two kindreds.MethodsWe applied whole exome sequencing (WES) on the two probands to determine the likely functional variants among candidate FH genes. We additionally applied 10x Genomics (10xG) Linked‐Reads whole genome sequencing (WGS) on one of the kindreds to identify potentially deleterious structural variants (SVs) underlying HoFH. A PCR‐based screening assay was also established to detect the LDLR structural variant in a cohort of 641 patients with elevated LDL.ResultsIn the Caucasian kindred, the FH homozygosity can be attributed to two compound heterozygous LDLR damaging variants, an exon 12 p.G592E missense mutation and a novel 3kb exon 1 deletion. By analyzing the 10xG phased data, we ascertained that this deletion allele was most likely to have originated from a Russian ancestor. In the Mexican kindred, the strikingly elevated LDL cholesterol level can be attributed to a homozygous frameshift LDLR variant p.E113fs.ConclusionsWhile the application of WES can provide a cost‐effective way of identifying the genetic causes of FH, it often lacks sensitivity for detecting structural variants. Our finding of the LDLR exon 1 deletion highlights the broader utility of Linked‐Read WGS in detecting SVs in the clinical setting, especially when HoFH patients remain undiagnosed after WES.

Whole-exome sequencing reveals damaging gene variants associated with hypoalphalipoproteinemia

“…It must also be noted that while the whole-exome sequencing methodology employed here has some power to detect structural variants (CNVs), it often lacks sensitivity. More advanced techniques such as Linked-Read whole-genome sequencing allow for much higher success in structural variant detection as we have recently found in other studies ( 38 , 87 ). A number of the gene loci identified here have significant roles in cell biology and are also associated with cancer and neurodegenerative diseases, providing promising venues for the molecular understanding of these disorders and possible roles for HDL in their etiology.…”

“…Genomic DNA samples were sequenced at the Yale Center for Genome Analysis (n = 192) or at the UCSF Genomics CORE (n = 12) as previously described ( 37 , 38 ).…”

Identification of New Genetic Determinants in Pediatric Patients with Familial Hypercholesterolemia Using a Custom NGS Panel

“…The described aberration is located within a 400-amino acid sequence, formed from three cysteine-rich repeats, in the EGF precursor homology domain [ 28 ]. The localization of a highly-conserved glycine residue, within the fifth repeat of “YWTD”, determines its pathogenicity [ 29 ]. A Polish FH study found that c.1775G>A, as a LOF mutation, reduces LDL receptor activity to 55–15% of wild type values [ 20 ].…”

“…Each LDLR mutation can be assigned to one of five functional groups based on the characteristics of the mutant protein [ 18 ]. Most studies classified c.1775G>A as Group 5, i.e., a defective recycling of the LDLR protein [ 29 , 32 , 33 ]. On the other hand, some authors propose Group 2b, i.e., partially disturbed LDLR protein transport from endoplasmic reticulum to the Golgi apparatus or the plasma membrane [ 20 , 34 , 35 ].…”

APOL1Risk Variants Associate with the Prevalence of Stroke in African American Current and Past Smokers

“…Genomic DNA was extracted using the Wizard purification kit (Qiagen). 24 Both, DNA and plasma aliquots were stored at -80°C.…”