Six years’ experience with LipidSeq: clinical and research learnings from a hybrid, targeted sequencing panel for dyslipidemias

Abstract

Background: In 2013, our laboratory designed a targeted sequencing panel, "LipidSeq", to study the genetic determinants of dyslipidemia and metabolic disorders. Over the last 6 years, we have analyzed 3262 patient samples obtained from our own Lipid Genetics Clinic and international colleagues. Here, we highlight our findings and discuss research benefits and clinical implications of our panel. Methods: LipidSeq targets 69 genes and 185 single-nucleotide polymorphisms (SNPs) either causally related or associated with dyslipidemia and metabolic disorders. This design allows us to simultaneously evaluate monogenic-caused by rare single-nucleotide variants (SNVs) or copy-number variants (CNVs)-and polygenic forms of dyslipidemia. Polygenic determinants were assessed using three polygenic scores, one each for low-density lipoprotein cholesterol, triglyceride, and high-density lipoprotein cholesterol. Results: Among 3262 patient samples evaluated, the majority had hypertriglyceridemia (40.1%) and familial hypercholesterolemia (28.3%). Across all samples, we identified 24,931 unique SNVs, including 2205 rare variants predicted disruptive to protein function, and 77 unique CNVs. Considering our own 1466 clinic patients, LipidSeq results have helped in diagnosis and improving treatment options. Conclusions: Our LipidSeq design based on ontology of lipid disorders has enabled robust detection of variants underlying monogenic and polygenic dyslipidemias. In more than 50 publications related to LipidSeq, we have described novel variants, the polygenic nature of many dyslipidemias-some previously thought to be primarily monogenic-and have uncovered novel mechanisms of disease. We further demonstrate several tangible clinical benefits of its use.

Genetics of Hypertriglyceridemia

“…Recently, in a cohort of 563 patients with TG ≥10 mmol/L (≥885 mg/dL), we reported that 1.1% had rare biallelic variants indicating FCS (16). Furthermore, our clinical experience integrating DNA sequencing data with clinical assessments (11) confirms that FCS patients are exceedingly rare. Specifically, in our lipid clinic, we have molecularly identified a similar number of patients with FCS and homozygous FH (HoFH) (9).…”

“…Because both common and rare variants, including SNVs and CNVs, are involved in the pathogenesis of hypertriglyceridemia, an optimal diagnostic method must be able to detect all possible variant types and bioinformatically process them en route to reporting them for potential clinical or research applications. In our experience, this is best accomplished using a targeted next-generation sequencing panel for hypertriglyceridemia, such as the LipidSeq panel (11); this panel can be used to account for different variant types disrupting the main genes involved in the TG metabolic pathway, as well as non-coding polygenic contributors.…”

Next-generation sequencing to confirm clinical familial hypercholesterolemia

“…As diagnostic resources in many countries are limited and FH-causing variants in one of the three culprit genes are not always identified in patients with severe hypercholesterolemia, [11][12][13] the selection of FH patients who are deemed eligible for molecular testing is mostly based on clinical FH criteria such as the DLCN criteria. 14 Moreover, the yield of FH sequencing is proportionally related to the severity of the FH phenotype (i.e.…”

Genetic testing in dyslipidemia: A scientific statement from the National Lipid Association

“…Genetic testing 23 includes the following methods: 1) genotype only previously described DNA variants (eg, DNA microarrays or TaqMan genotyping) and/or 2) scan all DNA nucleotide positions within a single gene, a panel of selected genes, or exome of genome (see glossary), enabling detection of both previously known and newly discovered DNA variants (eg, Sanger or capillary electrophoresis sequencing, targeted next-generation gene sequencing panels, exome sequencing [ES], or genome sequencing [GS]). 23 Some targeted sequencing panels for dyslipidemia have been clinically validated 30,31 and are the current gold standard for diagnosis in dyslipidemias, 32 for example, targeted panels for FH genes, or ''pandyslipidemia'' panels for all monogenic dyslipidemias. 7,30 The same result from a targeted panel can be achieved by performing ES or GS analysis and then masking most results, reporting only findings from genes of interest.…”

“…23 Some targeted sequencing panels for dyslipidemia have been clinically validated 30,31 and are the current gold standard for diagnosis in dyslipidemias, 32 for example, targeted panels for FH genes, or ''pandyslipidemia'' panels for all monogenic dyslipidemias. 7,30 The same result from a targeted panel can be achieved by performing ES or GS analysis and then masking most results, reporting only findings from genes of interest.…”