Familial Hypercholesterolemia (FH) Panel

Familial Hypercholesterolemia (FH) is characterized by elevated serum levels of total cholesterol, in particular, elevated levels of low density lipoprotein (LDL) cholesterol (LDL-C) (> 160 mg/dL in persons under 20 years of age, and > 190 mg/dL in adults over 20 years of age, Hopkins et al., 2011. PubMed ID: 21600530). Accumulation of LDL-C can cause early onset atherosclerosis and Coronary Heart Disease (CHD). FH is a genetic cause of premature CHD and is one of the most common diseases of lipid metabolism. By age 50, approximately 45% of male and 20% of female FH patients suffer from coronary artery disease, a causative factor for CHD (Goldstein et al., 2001). The prevalence of heterozygous FH (autosomal dominant FH) is between 1:300 and 1:500 in most countries and is much higher within certain populations, for example, 1:67 in Ashkenazi Jews (Goldstein et al., 1973. PubMed ID: 4718953; Vuorio et al., 1997. PubMed ID: 9409302; Slack, 1979; Kalina et al., 2001. PubMed ID: 11137107; Austin et al., 2004. PubMed ID: 15321837). There are as many as 34 million people with FH worldwide, yet FH remains severely underdiagnosed with some studies suggesting <1% of possible FH patients have been identified in many countries (Sjouke et al., 2015. PubMed ID: 24585268; Nordestgaard et al., 2013. PubMed ID: 23956253). Other symptoms of FH include fatty skin deposits called xanthomas, cholesterol deposits in the eyelids, and chest pains associated with coronary artery disease. FH is present from birth and confers a lifelong risk of atherosclerosis and CHD. Overall, patients with FH respond well to drug treatment making early, accurate diagnosis key factors for reducing risk of atherosclerosis and CHD.

Several genes are reported to be associated with FH, however ~ 86% of patients are found to harbor heterozygous pathogenic variants in one of three genes: LDLR, APOB, or PCSK9. Autosomal recessive forms of FH are associated with variants in the LDLRAP1 gene. Over 1,500 pathogenic variants have been reported in the LDLR gene alone, making variants in LDLR the most common cause of FH, followed by variants in APOB, PCSK9, and LDLRAP1. Patients with homozygous or compound heterozygous variants in LDLR, APOB, or PCSK9 are rare and generally have a severe phenotype with a very early onset of clinical symptoms.

LDLR encodes the LDL receptor that binds LDL-C at the surface of hepatocytes. Loss of function variants in LDLR impede LDL-C binding and endocytosis that result in deposition of cholesterol in cells and arteries and formation of xanthomas and atherosclerotic plaques (Hobbs et al., 1990. PubMed ID: 2088165; Varret et al., 2008. PubMed ID: 18028451). APOB encodes the major protein component of LDL-C particles and serves as a ligand for LDL receptor binding and endocytosis (Hegele, 2009. PubMed ID: 19139765).

Loss of function variants in APOB cause familial defective apolipoprotein B-100 (FDB) (Schmidt et al., 1998. PubMed ID: 9626156) which accounts for a significant portion of dominant FH cases.

A minor fraction of dominant FH cases, <5%, are attributed to gain of function variants in the PCSK9 gene which encodes NARC-1, a protein that influences LDL receptor degradation (Hopkins et al., 2011. PubMed ID: 21600530; Abifadel et al., 2003. PubMed ID: 12730697).

LDLRAP1 encodes an adaptor protein required for LDL uptake in the liver and lymphocytes (Wilund et al., 2002. PubMed ID: 12417523). LDLRAP1 carriers were reported at a frequency of 1:143 in the Sardinian population (Filigheddu et al., 2009. PubMed ID: 19477448), but are likely not as frequent in other populations.

Pathogenic variants in the LDLR, APOB, PCSK9, and LDLRAP1 are found throughout each gene, though most variants in APOB are found in exon 26 (possibly because it is much larger than other exons). Pathogenic variants in LDLR, PCSK9, and LDLRAP1 include nonsense, missense, and splice-site variants. Missense variants are the primary cause of APOB-related FH. Variants resulting in loss of APOB protein are associated with another disorder, Familial Hypobetalipoproteinemia (FHBL), characterized by hypocholesterolemia.

Other genes associated with lipid disorders including ABCG5, ABCG8, LIPA and APOE have been reported to cause hypercholesterolemia and lead to elevated LDL-C levels, early-onset CHD and xanthomas (Rios et al. 2010. PubMed ID: 20719861; Tada et al. 2019. PubMed ID: 31327807; Vinje et al. 2018. PubMed ID: 29196158; Feussner et al. 1996. PubMed ID: 8911609).

Pathogenic variants in LDLR are the most common cause of heterozygous Familial Hypercholesterolemia (FH) followed by variants in APOB, PCSK9, and LDLRAP1. The exact proportion of pathogenic variants within these genes varies among populations, but data from several studies indicate the contribution of LDLR, APOB, and PCSK9 pathogenic variants to FH cases ranges from 37-82%, 0-7%, and 0-3%, respectively (Varret et al., 2008. PubMed ID: 18028451). The frequency of LDLRAP1 / ARH variants in recessive FH is unclear, but the carrier frequency has been reported to be as high as 1:143 in the Sardinian population (Filigheddu et al., 2009. PubMed ID: 19477448).

Over 15% of pathogenic variants reported for the LDLR and LDLRAP1 genes are either large deletions or insertions (Human Gene Mutation Database). Few large deletions or insertions in the APOB and PCSK9 genes have been reported.

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel provides 100% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).