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Updated: Apr 5, 2026
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
Targeted next-generation sequencing to diagnose disorders of HDL cholesterol
Singh N Sadananda1, Jia Nee Foo2, Meng Tiak Toh1
1Translational Laboratory in Genetic Medicine, Agency for Science Technology and Research (ASTAR) and National University of Singapore, Singapore.
Insights
Identifying genetic causes for extreme HDL cholesterol (HDL-C) is crucial for cardiovascular risk assessment. A targeted next-generation sequencing (NGS) assay successfully identified molecular abnormalities in a significant portion of patients with low HDL-C.
Area of Science:
- Genetics
- Cardiovascular Medicine
- Biochemistry
Background:
- Low high-density lipoprotein cholesterol (HDL-C) is a significant cardiovascular risk factor.
- Genetic mutations in specific genes can cause extreme HDL-C levels, but molecular diagnosis is infrequently performed.
- Identifying these genetic underpinnings is essential for personalized risk assessment and management.
Purpose of the Study:
- To evaluate the accuracy and diagnostic yield of a targeted next-generation sequencing (NGS) assay for identifying genetic causes of extreme HDL-C levels.
- To assess the utility of NGS in clinical practice for patients with dyslipidemia.
- To discover novel genetic variants associated with HDL-C metabolism.
Main Methods:
- Development of a targeted NGS panel covering 26 genes critical for plasma lipid levels.
- Sequencing of 141 patients with extreme HDL-C (very low or very high).
- Variant prioritization using established medical genetics guidelines and functional validation of identified variants.
Main Results:
- A molecular diagnosis was established in 35.9% of patients with low HDL-C and 5.2% of patients with high HDL-C.
- Thirty-five pathogenic or probably pathogenic variants were identified in HDL genes, including 21 novel variants.
- All prioritized variants detected by NGS were confirmed via Sanger sequencing, demonstrating high assay accuracy.
Conclusions:
- Targeted NGS is an accurate and effective method for identifying molecular diagnoses in patients with extreme HDL-C levels, particularly those with low HDL-C.
- This approach can significantly improve the understanding of genetic contributions to dyslipidemia and cardiovascular risk.
- The findings support the clinical implementation of targeted NGS for genetic evaluation of extreme HDL-C phenotypes.
Abstract:
A low level of HDL cholesterol (HDL-C) is a common clinical scenario and an important marker for increased cardiovascular risk. Many patients with very low or very high HDL-C have a rare mutation in one of several genes, but identification of the molecular abnormality in patients with extreme HDL-C is rarely performed in clinical practice. We investigated the accuracy and diagnostic yield of a targeted next-generation sequencing (NGS) assay for extreme levels of HDL-C. We developed a targeted NGS panel to capture the exons, intron/exon boundaries, and untranslated regions of 26 genes with highly penetrant effects on plasma lipid levels. We sequenced 141 patients with extreme HDL-C levels and prioritized variants in accordance with medical genetics guidelines. We identified 35 pathogenic and probably pathogenic variants in HDL genes, including 21 novel variants, and performed functional validation on a subset of these. Overall, a molecular diagnosis was established in 35.9% of patients with low HDL-C and 5.2% with high HDL-C, and all prioritized variants identified by NGS were confirmed by Sanger sequencing. Our results suggest that a molecular diagnosis can be identified in a substantial proportion of patients with low HDL-C using targeted NGS.
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