Hydroxyglutaric Aciduria Panel

The hydroxyglutaric acidurias (HGAs) are a group of organic acidurias that result in the elevation of D-2-hydroxyglutaric acid (D2HG), L-2-hydroxyglutaric acid (L2HG), or both metabolites in the body fluids (urine, plasma and cerebrospinal fluid). It is possible to distinguish D2HG and L2HG biochemically, although additional labwork must be performed to separate these two enantiomers. Onset for the HGAs is mostly in childhood. Common clinical features include developmental delay, hypotonia, and seizures. Additional details regarding each specific HGA are below (Struys et al. 2016):

D-2-hydroxyglutaric aciduria type I (D2HGA-I): this HGA is slowly progressive in many patients, and is mostly non-fatal. Some asymptomatic individuals have been identified. D2HGA-I accounts for ~15% of HGA patients (Kranendijk et al. 2010a; Struys et al. 2016).

D-2-hydroxyglutaric aciduria type II (D2HGA-II): approximately half of these patients also present with cardiomyopathy. Life expectancy is lower than D2HGA-I, with about half of the reported patients having died before adolescence. D2HGA-II also accounts for ~15% of HGA patients (Kranendijk et al. 2010b; Struys et al. 2016).

L-2-hydroxyglutaric aciduria (L2HGA): these patients may also present with intellectual disability, cerebellar ataxia, and a characteristic MRI (see details on individual gene test description). L2HGA patients have been reported to have a tendency to develop central nervous system malignancies. L2HGA accounts for ~60% of HGA patients (Steenweg et al. 2010; Struys et al. 2016).

Combined D2HGA and L2HGA: this is the most severe of the HGAs, having been fatal in two-thirds of reported patients in early childhood. These patients present with severe neonatal epileptic encephalopathy and may require artificial ventilation. They also have highly abnormal MRI findings. Combined D2HGA/L2HGA accounts for <6% of HGA patients (Smith et al. 2016; Struys et al. 2016).

Pathogenic variants in other genes may also lead to increased levels of D2HG or L2HG in body fluids. These genes include IDH1 and possibly ALDH5A1 and ETFA, ETFB and ETFDH (Struys et al. 2006; Struys et al. 2016).

D2HGA-I, L2HGA and combined D2HGA/L2HGA are autosomal recessive disorders caused by pathogenic variants in the D2HGDH, L2HGDH and SLC25A1 genes, respectively. D2HGA-II is an autosomal dominant disorder caused by specific missense variants in the IDH2 gene (p.Arg140Gln and p.Arg140Gly). These variants have been reported to reside in the active site of the enzyme, resulting in a gain of function (Kranendijk et al. 2010b).

Massively parallel sequencing plus Sanger confirmation will detect the vast majority of sequence variants in the D2HGDH, IDH2, L2HGDH and SLC25A1 genes. It should be noted that gross deletions, which may not be detected by direct sequencing, have been reported in the D2HGDH and L2HGDH genes.

See individual gene test descriptions for information on molecular biology of gene products.

Clinical sensitivity of DNA sequencing is generally high for the genes in this sequencing panel. For D2HGDH, clinical sensitivity is estimated at ~46% if diagnosis is based solely on elevated D2HG levels. However, this rose to nearly 100% in patients with confirmed D2HGDH enzyme deficiency (Kranendijk et al. 2010a).

In D2HGA patients with no identified pathogenic mutations in D2HGDH, ~88% were found to have either the p.Arg140Gln or p.Arg140Gly variant in IDH2 (Kranendijk et al. 2010b).

In patients with elevated L2HG, the clinical sensitivity is expected to range from approximately 83% to nearly 100% (Topçu et al. 2004; Vilarinho et al. 2005; Sass et al. 2008; Vilarinho et al. 2010).

Only a small number of patients with combined D2HGA/L2HGA have been reported in the literature. However, all reported patients to date have been homozygous or compound heterozygous for SLC25A1 presumably pathogenic variants, suggesting a clinical sensitivity of near 100% (Edvardson et al. 2013; Nota et al. 2013; Smith et al. 2016).

Together, pathogenic variants in the D2HGDH, IDH2, L2HGDH and SLC25A1 genes are expected to explain nearly 96% of the cases of hydroxyglutaric aciduria (Struys et al. 2016).

In a study of 50 patients with elevated D2HG in body fluids, 24 of the patients were found to be homozygous or compound heterozygous for presumed pathogenic D2HGDH sequence variants. Two of these patients carried unique multi-exonic deletions (Kranendijk et al. 2010a).

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).

In addition to the regions described above, this testing includes coverage of the following variants that reside in untranslated or deep intronic regions: D2HGDH c.293-23A>G and L2HGDH c.906+354G>A.

For the IDH2 gene, this test only includes sequencing of the region of exon 4 containing the c.418 and c.419 nucleotides, plus 20 bp of flanking DNA on each side. At this time, IDH2 sequence variants not located at nucleotides c.418 or c.419 will not be reported (see the IDH2 test description for details).

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).