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Familial hypercholesterolemia

Indications

Diagnostic testing:

  • Patient meet eligibility criteria for suspicion of familial hypercholesterolemia:
    • Elevated untreated LDL-cholesterol levels:
      • ≥ 5.0 mmol/L for age 40 and over
      • ≥ 4.5 mmol/L for age 18 to 39
      • ≥ 4.0 mmol/L for age 17 and under
    • AND at least one of the following
      • Tendon xanthomas in patient
      • Known FH-causing DNA variant in a first-degree relative
      • High LDL-cholesterol in patient (≥ 8.5 mmol/L)
      • First-degree relative with high LDL-cholesterol
      • Patient or first-degree relative with early onset atherosclerotic cardiovascular disease (men under 55; women under 65)
Test description

This test detects sequence alterations (SNVs, indels) and copy number variants (CNVs) in the coding exons and flanking intronic regions (+/- 10 bp) of LDLR  (NM_000527.5), APOB  (NM_000384.3), and PCSK9  (NM_174936.4).

Genes for the Familial Hypercholesterolemia Panel
Gene Transcript
APOB

NM_000384.3
LDLR

NM_000527.5
PCSK9

NM_174936.4
Methodology

Targeted regions are enriched using hybridization probes (IDT) and sequencing libraries are prepared using the Illumina DNA Prep with Enrichment kit. Paired-end massively parallel sequencing of 150-bp fragments is performed with an Illumina instrument. Sequences are aligned and compared to reference genome GRCh37. Sample identity is confirmed in parallel using Applied Biosystems™ SNaPshot™ Multiplex Kit. Sequence variants are called using VarDict (PMID: 27060149) and annotated using SnpEff (http://pcingola.github.io/SnpEff/). Copy number variants (CNVs) are detected using a depth of coverage analysis converted to a log2 scale. CNVs are called if at least 3 consecutive probes have less than 1.5 copies (deletion) or more than 2.4 copies (duplication). Variants are interpreted as per standards and guidelines in the field (PMID: 25741868). Clinically relevant copy number variants are confirmed by an orthogonal method (gap-PCR, TaqMan, MLPA or microarray).

Limitations

Based on validation study results, this test achieves >99% analytical sensitivity and specificity for SNVs, indels and CNVs. A negative result does not rule out the possibility that a rare variant not detected by this assay is present in the individual. This test does not detect all possible variants in the genes tested. Unless explicitly specified, only coding exons and flanking intronic regions are covered by this assay. Furthermore, technically challenging variant types, such as large indels, small CNVs, complex rearrangements, low-complexity repeat associated, segmental duplication associated, and postzygotic variants, may not be detected (PMID: 34007000). Interpretation of results is highly dependent on the clinical and demographic information provided.

Clinical interpretation

Only clinically relevant variants are reported. Benign/likely benign variants and variants of uncertain significance with limited evidence for pathogenicity are not reported.

Ordering information

Turnaround time: 4-6 weeks
Specimens accepted: 

  • 2 x 4 mL blood in EDTA tubes (purple top tube)
  • DNA: min 10 ug
  • For any other sample type, contact the laboratory for testing availability

Submit your test request using our molecular genetics requisition.