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Homocystinuria Sequencing Panel

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

NGS Sequencing

Test Code Test Copy GenesCPT Code Copy CPT Codes
3277 CBS 81406 Add to Order
MMADHC 81479
MTHFR 81479
MTR 81479
MTRR 81479
Full Panel Price* $1440.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
3277 Genes x (5) $1440.00 81406, 81479(x4) 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. If you would like to order a subset of these genes contact us to discuss pricing.

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 panel is currently unknown, most variants reported for the genes in this panel are of the type which can be detected using direct sequencing methods and thus analytical sensitivity is expected to be high. Based on collective totals of reported patient data, the detection rates for pathogenic variants in the MMADHC, MTR and MTRR genes in this panel are approximately as follows: In the MTRR gene, pathogenic variants were detected in 34 of 36 studied alleles, for an overall detection rate of ~94% (Wilson et al. 1999; Zavadáková et al. 2005); In the MTR gene, pathogenic variants were detected in 36 of 42 studied alleles, for an overall detection rate of ~86% (Watkins et al. 2002); In the MMADHC gene, pathogenic variants were detected in all 20 studied alleles, for an overall detection rate of 100% (Coelho et al. 2008; Miousse et al. 2009).

The clinical sensitivity of MTHFR sequencing is expected to be high as to date, nearly all reported patients have had two pathogenic variants detectable via direct MTHFR sequencing (Goyette et al. 1995; Kluijtmans et al. 1998; Sibani et al. 2000; Sibani et al. 2003; Urreizti et al. 2010; Burda et al. 2015). In these studies, a total of 108 patients were reported with 211 alleles carrying a pathogenic variant, suggesting a clinical sensitivity of ~98%.

Lastly, the sensitivity of this CBS sequencing is also expected to be quite high, as most patients reported to date have been found to have two CBS variants detectable via direct sequencing. The majority of studies with larger patient cohorts have reported pathogenic variant detection via direct sequencing in ~95-98% of patient alleles (Gaustadnes et al. 2002; Kruger et al. 2003; Cozar et al. 2011; Karaca et al. 2014).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 CBS$690.00 81479 Add to Order
MMADHC$690.00 81479
MTHFR$690.00 81479
MTR$690.00 81479
MTRR$690.00 81479
Full Panel Price* $840.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (5) $840.00 81479(x5) 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 gross deletions or insertions have been reported in the MMADHC, MTHFR, MTR or MTRR genes (Human Gene Mutation Database). Therefore, the sensitivity of duplication/deletion testing for these rare disorders, although not precisely known, is low. Large deletions in the CBS gene have been reported, but appear to be a rare cause of disease (Human Gene Mutation Database).

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Clinical Features

Homocystinuria with hypomethioninemia is a genetic disorder caused by inherited inborn errors in the cobalamin, homocysteine or folate metabolic pathways. Clinical symptoms can be severe, and onset is typically during childhood or infancy, although late-onset cases have been reported. Clinically, patients present with megaloblastic anemia, feeding difficulties, lethargy, hypotonia, cerebral atrophy and developmental delay, ectopia lentis and/or severe myopia, skeletal abnormalities which can include thinning and lengthening of the long bones as well as osteoporosis, and vascular disease, including potentially fatal thromboembolisms. Some patients also exhibit ataxia, neonatal seizures and blindness. Biochemically, patients exhibit homocystinuria, hyperhomocystinemia and hypomethioninemia or hypermethioninemia without methylmalonic aciduria. Affected patients may be identified via newborn screening, although this depends on the methods used by the screening laboratory and, for disorders associated with hypomethioninemia, their ability to detect low levels of methionine. Therefore, complementation analysis and/or molecular genetic testing should still be considered for symptomatic individuals, even if newborn screening results are reported to be normal (Kraus et al. 1999; Carrillo-Carrasco et al. 2013; Picker and Levy 2014; Mudd et al. 2014; Watkins and Rosenblatt 2014).

Four genetic causes of homocystinuria with hypomethionimemia have been identified: cblD variant 1, cblE and cblG types, and homocystinuria due to MTHFR enzyme deficiency. The cblG type of homocystinuria is caused by pathogenic variants in the MTR gene, while the cblE type is caused by pathogenic variants in the MTRR gene. The cblE and cblG disorders are clinically indistinguishable, although the specific diagnosis can be confirmed by enzymatic or cellular complementation assays, as well as molecular genetic studies. The cblE and cblG types of cobalamin metabolic deficiencies can be difficult to distinguish from the cblD variant 1 cobalamin disorder, which is caused by pathogenic variants in the MMADHC gene. Depending on the type and location of the variants found in the MMADHC gene, patients can present with classic cblD type (combined homocystinuria and methylmalonic aciduria), cblD variant 1 (isolated homocystinuria) or cblD variant 2 (isolated methylmalonic aciduria). In addition to symptoms mentioned above, cblD variant 1 patients have also been reported to present with a marfanoid appearance, venous thrombosis, and/or hydrocephalus (Carrillo-Carrasco et al. 2013; Watkins and Rosenblatt 2014). Lastly, pathogenic variants in the MTHFR gene can also cause homocystinuria with low to normal levels of methionine in the plasma (Watkins and Rosenblatt 2014; Froese et al. 2016). It should be noted that MTHFR deficient patients typically do not present with megaloblastic anemia (Watkins and Rosenblatt 2014).

Homocystinuria can also be caused by defects in the CBS (cystathionine beta-synthase) gene. CBS deficiency can typically be biochemically distinguished from the cblD variant 1, cblE and cblG disorders and MTHFR deficiency because hypermethioninemia is observed rather than hypomethioninemia (Mudd et al. 2014). Defects in the CBS enzyme are the most commonly observed cause of homocystinuria without associated methylmalonic aciduria (Picker and Levy 2014; Mudd et al. 2014). Biochemically, patients with this disorder are found to have greatly increased concentrations of plasma and urine homocysteine, total homocysteine, and marked hypermethioninemia (Picker and Levy 2014). Age of onset and expressivity of clinical features displayed by CBS deficienct patients varies widely, even within sibships, and can range from affected newborns to adults who were previously asymptomatic first presenting with a thromboembolytic event (Carrillo-Carrasco et al. 2013; Picker and Levy 2014; Mudd et al. 2014).

For additional information, please see the individual test descriptions for the MTR, MTRR, MMADHC, MTHFR and CBS genes.

Genetics

The cblD variant 1, cblE and cblG types of homocystinuria, as well as MTHFR deficiency and classical CBS deficiency homocystinuria, are all autosomal recessive disorders.

The cblD variant 1 type is caused by variants in the MMADHC gene, and the type and location of the variant(s) affects whether the individual presents with classic cblD, cblD variant 1 or cblD variant 2. The exact function of the MMADHC protein is not known, although it is thought to play a role in the generation or transport of both Adenosylcobalamin (AdoCbl; required by the Methylmalonyl CoA Mutase enzyme) and Methylcobalamin (MeCbl; required by the Methionine Synthase enzyme). To date, fewer than 20 pathogenic variants have been reported in the MMADHC gene. They are a mix of missense, nonsense, small deletion and small insertion variants (Human Gene Mutation Database).

The cblG type of homocystinuria is caused by pathogenic variants in the MTR gene, which encodes the Methionine Synthase enzyme. The cblE type is caused by pathogenic variants in the MTRR gene, which encodes the Methionine Synthase Reductase enzyme which is responsible for ensuring the continued function of Methionine Synthase. The MeCbl-dependent Methionine Synthase enzyme is responsible for the conversion of homocysteine to methionine. Over 20 causative variants have been reported in both MTR and MTRR. The majority of reported pathogenic variants are missense and small deletions that lead to premature protein termination, although splice variants, small insertions and indels, and small and gross insertions have also been reported (Human Gene Mutation Database).

MTHFR deficiency and classical CBS deficiency homocystinuria are more commonly reported, with over 100 MTHFR and nearly 200 CBS causative variants documented in the literature (Human Gene Mutation Database). The majority of variants reported in both genes are missense, although protein truncating variants, and in CBS, large deletions, have been reported as well (Human Gene Mutation Database).

Please see individual test descriptions for additional information on the molecular biology of each gene.

Testing Strategy

For this NextGen test, the full coding regions, plus ~20 bp of non-coding DNA flanking each exon, are sequenced for each of the genes listed below. Sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization method, 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 pathogenic, undocumented and questionable variant calls are confirmed by Sanger sequencing.

Please note that as recommended by the ACMG, ACOG and AHA, we do not offer testing specifically for the MTHFR common polymorphisms c.665C>T and c.1286A>C (also known as C677T and A1298C) due to the limited clinical utility of such testing (Hickey et al. 2013; Levin and Varga 2016). 

This panel provides 100% coverage of the aforementioned regions of the indicated genes. We define coverage as > 20X NGS reads for exons and 0-10 bases of flanking DNA, > 10X NGS reads for 11-20 bases of flanking DNA, or Sanger sequencing.

Indications for Test

Individuals with a positive newborn screening result for homocystinuria are good candidates for this test. Additionally, individuals that exhibit biochemical and clinical symptoms of the cblD variant 1, cblE or cblG disorders, CBS or MTHFR deficiency, are good candidates.

Genes

Official Gene Symbol OMIM ID
CBS 613381
MMADHC 611935
MTHFR 607093
MTR 156570
MTRR 602568
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Tests

Name
Disorders of Folate Metabolism and Transport Sequencing Panel
Homocystinuria via the CBS Gene
Homocystinuria, cblE Type, via the MTRR Gene
Homocystinuria, cblG Type, via the MTR Gene
Methylmalonic Aciduria and Homocystinuria, cblD type, via the MMADHC Gene
Severe MTHFR Deficiency via the MTHFR Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Burda P. et al. 2015. Human Mutation. 36: 611-21. PubMed ID: 25736335
  • Carrillo-Carrasco N. et al. 2013. Disorders of Intracellular Cobalamin Metabolism. 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: 20301503
  • Coelho D. et al. 2008. The New England Journal of Medicine. 358: 1454-64.  PubMed ID: 18385497
  • Cozar M. et al. 2011. Human Mutation. 32: 835-42. PubMed ID: 21520339
  • Froese D.S. et al. 2016. Human Mutation. 37: 427-38. PubMed ID: 26872964
  • Gaustadnes M. et al. 2002. Human Mutation. 20: 117-26. PubMed ID: 12124992
  • Goyette P. et al. 1995. American Journal of Human Genetics. 56: 1052-9. PubMed ID: 7726158
  • Hickey S.E. et al. 2013. Genetics in Medicine. 15: 153-6. PubMed ID: 23288205
  • Human Gene Mutation Database (Bio-base).
  • Karaca M. et al. 2014. Gene. 534: 197-203. PubMed ID: 24211323
  • Kluijtmans L.A. et al. 1998. European Journal of Human Genetics. 6: 257-65. PubMed ID: 9781030
  • Kraus J.P. et al. 1999. Human Mutation. 13: 362-75.  PubMed ID: 10338090
  • Kruger W.D. et al. 2003. Human Mutation. 22: 434-41. PubMed ID: 14635102
  • Levin B.L., Varga E. 2016. Journal of Genetic Counseling. 25: 901-11. PubMed ID: 27130656
  • Miousse I.R. et al. 2009. The Journal of Pediatrics. 154: 551-6.  PubMed ID: 19058814
  • Mudd H.S. et al. 2014. Disorders of Transsulfuration. In: Valle D, Beaudet AL, Vogelstein B, et al., editors.New York, NY: McGraw-Hill. OMMBID. 
  • Picker J.D. and Levy H.L. 2014. Homocystinuria Caused by Cystathionine Beta-Synthase 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: 20301697
  • Sibani S. et al. 2000. Human Mutation. 15: 280-7. PubMed ID: 10679944
  • Sibani S. et al. 2003. Human Mutation. 21: 509-20. PubMed ID: 12673793
  • Urreizti R. et al. 2010. Clinical Genetics. 78: 441-8. PubMed ID: 20236116
  • Watkins D. and Rosenblatt D.S. 2014. Inherited Disorders of Folate and Cobalamin Transport and Metabolism. In: Valle D, Beaudet A.L., Vogelstein B, et al., editors. New York, NY: McGraw-Hill. OMMBID.
  • Watkins D. et al. 2002. American Journal of Human Genetics. 71: 143-53. PubMed ID: 12068375
  • Wilson A. et al. 1999. Human Molecular Genetics. 8: 2009-16. PubMed ID: 10484769
  • Zavadáková P. et al. 2005. Human Mutation. 25: 239-47. PubMed ID: 15714522
Order Kits
TEST METHODS

NextGen Sequencing using PG-Designed 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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