Forms

Dihydrolipoamide Dehydrogenase Deficiency via the DLD Gene

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

NGS Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
7019 DLD$690.00 81406 Add to Order
Pricing Comment

Our most cost-effective testing approach is NextGen sequencing with Sanger sequencing supplemented as needed to ensure sufficient coverage and to confirm NextGen calls that are pathogenic, likely pathogenic or of uncertain significance. If, however, full gene Sanger sequencing only is desired (for purposes of insurance billing or STAT turnaround time for example), please see link below for Test Code, pricing, and turnaround time information.

For Sanger Sequencing click here.
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

Although the sensitivity of this test is difficult to estimate due to the low number of cases reported in the literature, it appears to be high as nearly all reported patients have been found to have two causative DLD variants that are detectable via direct sequencing (Liu et al. 1993; Hong et al. 1996; Elpeleg et al. 1997; Hong et al. 1997; Shaag et al. 1999; Grafakou et al. 2003; Odièvre et al. 2005; Cameron et al. 2006; Quintana et al. 2010; Quinonez and Theone al. 2014; Shany et al 1999).

See More

See Less

Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 DLD$690.00 81479 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

To date, no large deletions or duplications have been reported in the DLD gene.

See More

See Less

Clinical Features

Dihydrolipoamide dehydrogenase (DLD) deficiency, sometimes referred to as maple syrup urine disease (MSUD) type 3, is a disorder caused by defects in the dihydrolipoamide dehydrogenase enzyme. The phenotypic spectrum of DLD deficiency is broad and includes an early-onset neurological form, a mainly hepatic form, and a myopathic form, each described below (Quinonez and Thoene 2014). It should be noted, however, that clinical presentation occurs along a continuum and it may be difficult to differentiate between the different forms.

The initial presentation of the early-onset form of DLD deficiency is generally a lethargic, hypotonic infant with lactic acidosis. Some patients also display a Leigh syndrome phenotype (Quinonez et al. 2013; Carrozzo et al. 2014), and others may exhibit visual impairment (Quinonez and Thoene 2014). The first metabolic decompensation in these infants is often fatal, and others may not survive subsequent metabolic decompensations that occur during the early years of life. Surviving individuals often have growth defects and neurological difficulties, such as seizures, ataxia, spasticity, and intellectual disability (Elpeleg et al. 1997; Quinonez and Thoene 2014). Those with neonatal onset of DLD deficiency generally have a poor prognosis (Carrozzo et al. 2014).

In individuals with the hepatic form of the disease, onset ranges from early in life to as late as the third decade. Symptoms include nausea and emesis, which is followed by signs of liver injury (such as elevated transaminases) and potentially increased liver glycogen content and fibrosis or necrosis. These individuals also suffer from acute metabolic episodes that are often associated with lactic acidosis, hypoglycemia, hyperammonemia and hepatomegaly. Liver failure may occur and can be fatal. These patients do not tend to have neurological symptoms, though they do often experience recurrent attacks of hepatopathy, which are often precipitated by an event such as illness or an extreme dietary change (Brassier et al. 2013; Quinonez and Thoene 2014).

Thus far, few patients with the myopathic form of DLD deficiency have been reported. One individual presented in infancy with photophobia and ptosis, exercise induced fatigability, generalized muscle weakness and cramps, lactic acidosis and elevated plasma creatine kinase (Quintana et al. 2010). A second patient was reported in the second decade of life, presenting with muscle weakness and pain, intermittent lactic acidosis, ketoacidosis, and elevation of creatine kinase (Carrozzo et al. 2014).

These patients may be identified by biochemical testing, which may reveal lactic acidosis, elevated α-ketoglutarate, branched chain keto-acids and branched chain amino acids in the urine, as well as allo-isoleucine in the plasma. Such biochemical signs may be intermittent or absent during testing (Quinonez and Thoene 2014). It should also be noted that the levels of branched chain amino acids are not as high as observed in classical maple syrup urine disease (Robinson 2014).

Genetics

Dihydrolipoamide dehydrogenase (DLD) deficiency is an autosomal recessive disorder caused by pathogenic variants in the DLD gene, which is located on chromosome 7 at 7q31.1. To date, approximately 20 pathogenic variants in the DLD gene have been reported, with the variants being a mix of missense, splicing, small insertion and small deletions (Liu et al. 1993; Hong et al. 1996; Grafakou et al. 2003; Human Gene Mutation Database). Two specific variants (p.Gly229Cys and p.Tyr35*) are common in the Ashkenazi Jewish population (Elpeleg et al. 1997; Shaag et al. 1999; Scott et al. 2010).

The DLD gene encodes the dihydrolipoamide dehydrogenase, which is the E3 subunit of three mitochondrial enzyme complexes: the branched chain α-ketoacid dehydrogenase (BCKDH) complex, the α-ketoglutarate dehydrogenase (aKGDH) complex, and the pyruvate dehydrogenase (PDH) complex (Quinonez and Thoene 2014; Robinson 2014).

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 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.

This test provides full coverage of all coding exons of the DLD gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Candidates for this test are patients with biochemical, enzymatic test results and/or clinical features consistent with dihydrolipoamide dehydrogenase (DLD) deficiency/maple syrup urine disease (MSUD) type III. Testing is also indicated for family members of patients with known DLD mutations. We will also sequence the DLD gene to determine carrier status.

Gene

Official Gene Symbol OMIM ID
DLD 238331
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Dihydrolipoamide dehydrogenase deficiency AR 246900

Related Tests

Name
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Sequencing Panel with CNV Detection
Organic Aciduria Sequencing Panel
Pyruvate Dehydrogenase Complex Deficiency Sequencing Panel with CNV Detection

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Brassier A. et al. 2013. Molecular Genetics and Metabolism. 109: 28-32. PubMed ID: 23478190
  • Cameron J.M. et al. 2006. American Journal of Medical Genetics. Part A. 140: 1542-52. PubMed ID: 16770810
  • Carrozzo R. et al. 2014. Mitochondrion. 18: 49-57. PubMed ID: 25251739
  • Elpeleg O.N. et al. 1997. Human Mutation. 10: 256-7. PubMed ID: 9298831
  • Grafakou O. et al. 2003. European Journal of Pediatrics. 162: 714-8. PubMed ID: 12925875
  • Hong Y.S. et al. 1996. Human Molecular Genetics. 5: 1925–30. PubMed ID: 8968745
  • Hong Y.S. et al. 1997. Biochimica Et Biophysica Acta. 1362: 160-8. PubMed ID: 9540846
  • Human Gene Mutation Database (Bio-base).
  • Liu TC et al. 1993. Proceedings of the National Academy of Sciences. 90: 5186–90. PubMed ID: 8506365
  • Odièvre M.H. et al. 2005. Human Mutation. 25: 323-4. PubMed ID: 15712224
  • Quinonez S.C. et al. 2013. Pediatric Neurology. 48: 67-72. PubMed ID: 23290025
  • Quinonez, S.C. and Thoene, J.G. 2014. Dihydrolipoamide Dehydrogenase Deficiency. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 25032271
  • Quintana E. et al. 2010. Journal of Inherited Metabolic Disease. 33 Suppl 3: S315-9. PubMed ID: 20652410
  • Robinson B.H. 2014. Lactic Acidemia: Disorders of Pyruvate Carboxylase and Pyruvate Dehydrogenase. Online Metabolic & Molecular Bases of Inherited Disease, New York, NY: McGraw-Hill.
  • Scott S.A. et al. 2010. Human Mutation. 31: 1240-50. PubMed ID: 20672374
  • Shaag A. et al. 1999. American Journal of Medical Genetics. 82: 177-82. PubMed ID: 9934985
  • Shany E. et al. 1999. Biochemical and Biophysical Research Communications. 262: 163-6. PubMed ID: 10448086
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.
loading Loading... ×