Disorders of Fatty Acid Oxidation (FAOD) Panel

Fatty acid oxidation (FAO) is required for the generation of energy when glucose supply is limited. A number of clinical disorders have been described that are caused by defects in the enzymes and protein transporters required for FAO. Three main types of clinical presentation are associated with disorders of FAO: (1) a cardiac presentation, which may include cardiomyopathy, arrhythmias and conduction defects, and is often observed in newborns and infants; (2) a hepatic presentation, which includes fasting hypoketotic hypoglycemia with encephalopathy, hepatomegaly and liver dysfunction, and is often first observed during infancy, commonly between ~6-12 months of age; (3) a more mild clinical form that is primarily myopathic in nature, and that can include myalgia, weakness, hypotonia, rhabdomyolysis and myoglobinuria, and may be observed during adolescence and adulthood (Kompare and Rizzo. 2008. PubMed ID: 18708005; Baruteau et al. 2013. PubMed ID: 23053472; Murphy et al. 2016; Houten et al. 2016. PubMed ID: 26474213; Nyhan et al. 2017; Knottnerus et al. 2018. PubMed ID: 29926323; Merritt et al. 2018. PubMed ID: 30740404). In addition, disorders of FAO may first present as sudden infant death syndrome (SIDS), which may later be attributed to a disorder of FAO after a second affected child is identified (van Rijt et al. 2016. PubMed ID: 26907928; Nyhan et al. 2017). Additional symptoms associated with specific disorders may also be observed, such as polyneuropathy or retinopathy (Houten et al. 2016. PubMed ID: 26474213).

Biochemically, patients may be found to have an abnormal acylcarnitine profile, and some patients may also have lactic acidosis, hyperammonemia, elevated liver enzymes, elevated creatine kinase (CK) levels, and/or elevated uric acid. Clinical symptoms are often episodic in nature, and are typically precipitated via some type of stress, such as prolonged exercise, fasting or viral illness. Patients that are treated promptly often fully recover, though they may always be at risk for metabolic decompensation. However, some patients may suffer irreversible neurological damage (Kompare and Rizzo. 2008. PubMed ID: 18708005; Baruteau et al. 2013. PubMed ID: 23053472; Murphy et al. 2016; Houten et al. 2016. PubMed ID: 26474213; Nyhan et al. 2017; Knottnerus et al. 2018. PubMed ID: 29926323; Merritt et al. 2018. PubMed ID: 30740404).

Two of the genes in this panel (HSD17B10, associated with 2-Methyl-3-hydroxybutyryl-CoA dehydrogenase deficiency, and TAFZIN, associated with Barth syndrome) are inherited in an X-linked manner. Both males and females with pathogenic HSD17B10 variants may be affected, although females tend to be more mildly affected and may also be asymptomatic (Zschocke. 2012. PubMed ID: 22127393). Female carriers of TAFAZZIN genes are typically unaffected, although in rare cases females with other X chromosome abnormalities (such as 45,X, structural abnormalities of the X chromosome, or skewed X-inactivation) may be symptomatic (Ferreira et al. 2020. PubMed ID: 25299040; Sabbah. 2020. PubMed ID: 33001359).

The overall incidence of fatty acid oxidation disorders is estimated at 1/5,000 - 10,000 births, although incidence of specific disorders can be quite variable. The most common disorder in Northern European Whites is medium-chain acyl-CoA dehydrogenase deficiency (MCADD), with an estimated prevalence of ~1:20,000 in North America (Merritt et al. 2018. PubMed ID: 30740404). 

Molecular testing is useful to confirm the genetic cause of a clinical diagnosis, which may then be useful for determining appropriate treatment measures, assessment of recurrence risks, and may allow for appropriate screening for potential future symptoms.

This sequencing panel includes genes that have been associated with fatty acid oxidation disorders or disorders with overlapping clinical symptoms. The majority of the disorders due to defects in these genes are inherited in an autosomal recessive manner. The only exceptions are GLUD1, PPARG, and SLC52A1, which exhibit autosomal dominant inheritance, CPT2, which can exhibit both autosomal dominant and recessive inheritance, and HSD17B10 and TAFAZZIN, which exhibit X-linked inheritance. Pathogenic defects in the genes in this panel include missense, nonsense, splicing site variants, small deletions, small insertions/duplications, small indels, and exon-level large deletions (Human Gene Mutation Database).

The genes included in this test are associated with disorders that can be broadly classified into several categories based on the pathways within the cell that are disrupted:

Disorders of Amino Acid or Ketone Metabolism: GLUD1, HMGCL, HMGCS2, HSD17B10

Disorders of Cytoplasmic Triglyceride Metabolism: LPIN1

Disorders of Fatty Acid Oxidation and Transport: ACAD9, ACADM, ACADS, ACADSB, ACADVL, CPT1A, CPT2, ETFA, ETFB, ETFDH, HADH,  HADHA, HADHB, MLYCD, SLC22A5, SLC25A20, TANGO2

Disorders of Niacin, NAD or Riboflavin Metabolism: FLAD1, NADK2, SLC25A32, SLC52A1, SLC52A2, SLC52A3

Disorders of Nuclear Encoded Mitochondrial Genes: TAFAZZIN

Regulation of Adipocyte Development and Function: PPARG

Of the genes included in this test, large copy number variants (gross deletions or duplications/insertions) are only a common cause of disease in TANGO2. For the remainder of the genes on this panel, large copy number variants are a relatively rare cause of disease. It should also be noted that, to our knowledge, de novo variants are not commonly reported for the majority of genes in this panel, although they have been reported in GLUD1, PPARG, SLC52A1 and TAFAZZIN.

See individual gene summaries for more information about molecular biology of gene products and spectra of pathogenic variants.

Due to the genetic heterogeneity of the fatty acid oxidation disorders, the clinical sensitivity of this specific grouping of genes is difficult to estimate. The clinical sensitivity of sequencing the individual genes is high in patient groups with biochemical and/or enzymatic diagnoses of the relevant disorders. 

Clinical sensitivity estimates are available for some of the more commonly reported disorders (see below).

For individuals with a diagnosis of medium-chain acyl-CoA dehydrogenase deficiency (MCADD), ~98% of patients are reported to have pathogenic variants detectable via sequencing (Merritt and Chang. 2019. PubMed ID: 20301597). Of note, the variant c.985A>G (p.Lys304Glu) is found on approximately 70% of pathogenic alleles in individuals of Northern European descent (Merritt et al. 2018. PubMed ID: 30740404).

In one study of individuals with newborn screening results suggestive of very long-chain acyl-CoA dehydrogenase deficiency (VLCADD), 44/46 patients (~96%) had biallelic ACADVL variants (Pena et al. 2016. PubMed ID: 27209629). 

Different detection rates of SLC22A5 causative variants have been reported based on different patient identification methods. In one study, ~70% of 70 infants identified based on a positive newborn screen were found to have at least one SLC22A5 variant. In the same study, ~27% of 52 patients identified based on clinical presentation were found to have at least one SLC22A5 variant (Li et al. 2010. PubMed ID: 20574985). However, in studies of patients with more in-depth biochemical analyses or cellularly confirmed carnitine transport deficiency the detection rate is higher. For example, Rose et al. (2012. PubMed ID: 21922592) reported 54 pathogenic alleles in 28 individuals, while Han et al. (2014. PubMed ID: 25132046) reported 39 pathogenic alleles in 20 patients. Based on these studies, clinical sensitivity would be estimated at ~96-98% in patients with confirmed systemic primary carnitine deficiency (SPCD).

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

This panel typically provides 99.9% 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).