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Disorders of Fatty Acid Oxidation Sequencing Panel

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
Order Kits
TEST METHODS

NGS Sequencing

Test Code Test Copy GenesCPT Code Copy CPT Codes
4981 ACAD9 81479 Add to Order
ACADL 81479
ACADM 81479
ACADS 81405
ACADSB 81479
ACADVL 81406
ACAT1 81479
CPT1A 81479
CPT2 81404
DECR1 81479
ECHS1 81479
ETFA 81479
ETFB 81479
ETFDH 81479
FLAD1 81479
HADH 81479
HADHA 81406
HADHB 81406
HMGCL 81479
HMGCS2 81479
HSD17B10 81479
LPIN1 81479
MLYCD 81479
PPARG 81479
SLC22A5 81405
SLC25A20 81405
TAZ 81406
Full Panel Price* $1440.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
4981 Genes x (27) $1440.00 81404, 81405(x3), 81406(x4), 81479(x19) Add to Order
Pricing Comment

If you would like to order a subset of these genes contact us to discuss pricing.

Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

Due to the genetic heterogeneity of the fatty acid oxidation disorders, the clinical sensitivity of this specific grouping of genes is difficult to estimate. We are currently unaware of any reports in the literature in which these genes have been sequenced together in a patient cohort with a suspected fatty acid oxidation disorder as the primary indication for testing. The clinical sensitivity of sequencing the individual genes is high in patient groups with biochemical and/or enzymatic diagnoses of the relevant disorders; details are available on the individual gene test descriptions. Analytical sensitivity is expected to be high as the majority of variants reported in these genes are detectable via sequencing.

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 ACADM$690.00 81479 Add to Order
ACADS$690.00 81479
ACADVL$690.00 81479
CPT1A$690.00 81479
CPT2$690.00 81479
ETFA$690.00 81479
ETFB$690.00 81479
ETFDH$690.00 81479
HADH$690.00 81479
HADHA$690.00 81479
HADHB$690.00 81479
HMGCL$690.00 81479
HSD17B10$690.00 81479
LPIN1$690.00 81479
SLC22A5$690.00 81479
SLC25A20$690.00 81404
TAZ$690.00 81479
Full Panel Price* $1290.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (17) $1290.00 81404, 81479(x16) Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

Many of the genes in this panel have no or very few large deletions/duplications reported, indicating clinical sensitivity would be low for this panel. However, the HMGCL and TAZ genes have a higher proportion of gross deletions/duplications reported and could be considered for aCGH testing (Human Gene Mutation Database).

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Clinical Features

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; Baruteau et al. 2013; Murphy et al. 2016; Houten et al. 2016; Nyhan et al. 2017). 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; Nyhan et al. 2017). Additional symptoms associated with specific disorders may also be observed, such as polyneuropathy or retinopathy (Houten et al. 2016).

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; Baruteau et al. 2013; Murphy et al. 2016; Houten et al. 2016; Nyhan et al. 2017).

Treatment may include dietary modification, with particularly careful monitoring of food intake during episodes of decompensation (Murphy et al. 2016; Houten et al. 2016; Nyhan et al. 2017).

Genetics

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 (AR) manner, a few autosomal dominant (AD) and X-linked (XL) disorders are also included. See individual gene test descriptions for information on clinical features and molecular biology of gene products.

Testing Strategy

For this Next Generation Sequencing (NGS) test, sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for any regions not captured or with insufficient number of sequence reads. All reported pathogenic, likely pathogenic, and variants of uncertain significance are confirmed by Sanger sequencing.

For Sanger sequencing, polymerase chain reaction (PCR) is used to amplify targeted regions. After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit. PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer. In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

In addition to the regions described above, this testing includes coverage of the following variants that reside in untranslated or deep intronic regions: the HADH variants c.636+471G>T and c.709+39C>G, HADHB c.442+614A>G, SLC22A5 c.825-52G>A and TAZ c.284+110G>A.

This panel provides full coverage of all coding exons of the genes listed, plus ~20 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads for coding regions and 0-10 bases of flanking DNA, >10X NGS reads for 11-20 bases of flanking DNA, or Sanger sequencing.

Indications for Test

Patients with clinical and/or biochemical features suggestive of a fatty acid oxidation disorder, particularly patients with hypoketotic hypoglycemia and/or an abnormal acylcarnitine profile, are good candidates for this test.

Diseases

Name Inheritance OMIM ID
2-Methyl-3-Hydroxybutyric Aciduria XL 300438
2-Methylbutyryl-CoA Dehydrogenase Deficiency AR 610006
3-Hydroxy-3-Methylglutaryl-CoA Lyase Deficiency AR 246450
3-Methylglutaconic Aciduria Type 2 XL 302060
Alpha-Methylacetoacetic Aciduria AR 203750
Carnitine Palmitoyltransferase I Deficiency AR 255120
Carnitine Palmitoyltransferase II Deficiency, Infantile AR 600649
Carnitine Palmitoyltransferase II Deficiency, Late-Onset AD,AR 255110
Carnitine Palmitoyltransferase II Deficiency, Lethal Neonatal AR 608836
Carnitine-Acylcarnitine Translocase Deficiency AR 212138
Deficiency Of 3-Hydroxyacyl-CoA Dehydrogenase AR 231530
Deficiency Of Butyryl-CoA Dehydrogenase AR 201470
Glutaric Aciduria, Type 2 AR 231680
Lipid Storage Myopathy Due to Flavin Adenine Dinucleotide Synthetase Deficiency AR 255100
Lipodystrophy, Familial Partial, Type 3 AD 604367
Long-Chain 3-Hydroxyacyl-CoA Dehydrogenase Deficiency AR 609016
Malonyl-CoA Decarboxylase Deficiency AR 248360
Medium-Chain Acyl-Coenzyme A Dehydrogenase Deficiency AR 201450
Mitochondrial 3-Hydroxy-3-Methylglutaryl-CoA Synthase Deficiency AR 605911
Mitochondrial Complex I Deficiency due to ACAD9 Deficiency AR 611126
Mitochondrial Short-Chain Enoyl-CoA Hydratase 1 Deficiency AR 616277
Myoglobinuria, Acute Recurrent, Autosomal Recessive AR 268200
Systemic Carnitine Deficiency AR 212140
Trifunctional Protein Deficiency AR 609015
Very Long Chain Acyl-CoA Dehydrogenase Deficiency AR 201475

Related Tests

Name
β-Ketothiolase Deficiency via the ACAT1 Gene
3-Hydroxy-3-MethylGlutaryl-CoA Lyase Deficiency via the HMGCL Gene
3-Hydroxyacyl-CoA Dehydrogenase Deficiency via the HADH Gene
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Sequencing Panel with CNV Detection
Barth Syndrome via the TAZ Gene
Carnitine Palmitoyltransferase 1A Deficiency via the CPT1A Gene
Carnitine Palmitoyltransferase II Deficiency via the CPT2 Gene
Carnitine-Acylcarnitine Translocase Deficiency via the SLC25A20 Gene
Coenzyme Q10 Ubiquinone Deficiency Sequencing Panel
Comprehensive Cardiology Sequencing Panel with CNV Detection
Congenital Hyperinsulinism Sequencing Panel
Glutaric Acidemia Type II Sequencing Panel
Glutaric Acidemia Type II via the ETFA Gene
Glutaric Acidemia Type II via the ETFB Gene
Glutaric Acidemia Type II via the ETFDH Gene
Hyperammonemia Sequencing Panel
Hypoparathyroidism Sequencing Panel
Left Ventricular Noncompaction (LVNC) Sequencing Panel with CNV Detection
Malonyl-CoA Decarboxylase Deficiency via the MLYCD Gene
Medium Chain Acyl-CoA Dehydrogenase Deficiency via the ACADM Gene
Metabolic Hypoglycemia Sequencing Panel
Metabolic Myopathies, Rhabdomyolysis and Exercise Intolerance Sequencing Panel
Methylmalonic Acidemia Sequencing Panel
Mitochondrial Complex I Deficiency Sequencing Panel with CNV Detection (Nuclear Genes)
Mitochondrial Trifunctional Protein Deficiency and Long-Chain 3-Hydroxyacyl CoA Dehydrogenase Deficiency via the HADHA Gene
Organic Aciduria Sequencing Panel
Paroxysmal Paralytic Rhabdomyolysis via the LPIN1 Gene
Paroxysmal Paralytic Rhabdomyolysis via the LPIN1 Gene, Exons 18-19 Deletion Test
Short Chain Acyl-CoA Dehydrogenase Deficiency via the ACADS Gene
Systemic Primary Carnitine Deficiency via the SLC22A5 Gene
Very Long Chain Acyl-CoA Dehydrogenase Deficiency via the ACADVL Gene
X-Linked Intellectual Disability Sequencing Panel with CNV Detection

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Baruteau J. et al. 2013. Journal of Inherited Metabolic Disease. 36: 795-803. PubMed ID: 23053472
  • Houten S.M. et al. 2016. Annual Review of Physiology. 78: 23-44. PubMed ID: 26474213
  • Human Gene Mutation Database (Bio-base).
  • Kompare M., Rizzo W.B. 2008. Seminars in Pediatric Neurology. 15: 140-9. PubMed ID: 18708005
  • Murphy E., Nadjar Y., Vianey-Saban C. 2016. Fatty Acid Oxidation, Electron Transfer and Riboflavin Metabolism Defects. In: Hollak C.E.M. and Lachmann R.H., editors. Inherited Metabolic Disease in Adults: A Clinical Guide. New York: Oxford University Press, p 55-67.
  • Nyhan W.L., Kolker S., Hoffmann G.F. 2017. Approach to the Child Suspected of Having a Disorder of Fatty Acid Oxidation. In: Hoffmann G.F., Nyhan W.L. and Zschocke J., editors. Inherited Metabolic Diseases: A Clinical Approach. Berlin: Springer, p 107-111.
  • van Rijt W.J. et al. 2016. Neonatology. 109: 297-302. PubMed ID: 26907928
Order Kits
TEST METHODS

NextGen Sequencing using PG-Select Capture Probes

Test Procedure

We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~20 bases of non-coding DNA flanking each exon.  As required, genomic DNA is extracted from the patient specimen.  For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes.  Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA).  Regions with insufficient coverage by NGS are covered by Sanger sequencing.  All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

For Sanger sequencing, Polymerase Chain Reaction (PCR) is used to amplify targeted regions.  After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).

(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign, Common Variants

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (http://www.hgvs.org).  Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.

Analytical Validity

As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.

In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable.   

Analytical Limitations

Interpretation of the test results is limited by the information that is currently available.  Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.

When Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles.  Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion.   In these cases, the report will contain no information about the second allele.  Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).

We sequence all coding exons for each given transcript, plus ~20 bp of flanking non-coding DNA for each exon.  Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.

In most cases, we are unable to determine the phase of sequence variants.  In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants due to somatic mosaicism is limited.  Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes from whole blood).   Test reports contain no information about the DNA sequence in other cell-types.

We cannot be certain that the reference sequences are correct.

Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.

We have confidence in our ability to track a specimen once it has been received by PreventionGenetics.  However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options


myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
REQUISITION FORM
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.

CELL CULTURE

(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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