Organic Acidemia/Aciduria & Cobalamin Deficiency Panel

Updated
Summary
  • Is a 54 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion of cobalamin deficiency, homocystinuria, maple syrup urine disease, methylmalonic acidemia, organic acidemia/aciduria or propionic acidemia. The genes on this panel are included in the Comprehensive Metabolism Panel.

Analysis methods
  • PLUS
Availability

4 weeks

Number of genes

54

Test code

ME0901

Panel size

Large

CPT codes
81479

Summary

The Blueprint Genetics Organic Acidemia/Aciduria & Cobalamin Deficiency Panel (test code ME0901):

ICD codes

Commonly used ICD-10 code(s) when ordering the Organic Acidemia/Aciduria & Cobalamin Deficiency Panel

ICD-10 Disease
E71.0 Maple syrup urine disease
E71.121 Propionic acidemia
E72.10 Methylmalonic acidemia
E72.10 Cobalamin deficiency
E72.10 Homocystinuria
E71.110 Isovaleric acidemia
E71.311 Multiple acyl-CoA dehydrogenase deficiency

Sample Requirements

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)

Label the sample tube with your patient's name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. Read more about our sample requirements here.

Organic acidemia and aciduria refer to many disorders, where non-amino organic acids are excreted in urine. This is usually a result of deficient enzyme activity in amino acid catabolism. The clinical presentation of organic acidemia in young children includes neurologic symptoms, poor feeding and lethargy progressing to coma. Older persons with this disorder often also have neurological signs, recurrent ketoacidosis and loss of intellectual function. The symptoms result from the damaging accumulation of precursors of the defective pathway. The combined prevalence of organic acidurias is estimated at 1:1,000 newborns. Cobalamin, also known as vitamin B12, has cobalt in its structure. Humans are not able to synthesize B12. It must therefore be obtained from a food of animal origin (the only natural source of cobalamin in the human diet). Intracellular cobalamin deficiencies can be subgrouped based on the cellular complementation groups and defective genes. Mutations in genes MMAA, MMAB and MMADHC cause deficient synthesis of the coenzyme adenosylcobalamin (AdoCbl), while mutations in genes MMADHC, MTRR and MTR cause defective methylcobalamin (MeCbl) synthesis. Mutation in genes MMACHC, MMADHC, LMBRD1 and ABCD4 result in combined AdoCbl and MeCbl deficiency. Mutations in MMACHC explain approximately 80% of the cases with intracellular cobalamin deficiency, followed by MMADHC (<5%), TRR (<5%), LMBRD1 (<5%), MTR (<5%) and ABCD4 (<1%). The presentation of cobalamin deficiency can be perinatal in onset or during childhood or adulthood. The symptoms are wide ranging based on the complementation group and gene affected. Perinatal onset is characterized by growth restriction, microcephaly, heart disease and dysmorphic features. This presentation is often severe and may be lethal. Babies with cobalamin deficiency often have poor feeding, hypotonia, seizures and multiorgan involvement. Cobalamin deficiency in adulthood often presents with neurological and neuropsychiatric problems. Some specific types of cobalamin deficiencies are extremely rare with only dozens of patients described. The combined prevalence is estimated at >1:100,000.

Genes in the Organic Acidemia/Aciduria & Cobalamin Deficiency Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ABCD4 Methylmalonic aciduria and homocystinuria AR 6 7
ACADSB 2-methylbutyryl-CoA dehydrogenase deficiency AR 8 12
ACAT1 Alpha-methylacetoacetic aciduria AR 31 95
ACSF3 Combined malonic and methylmalonic aciduria AR 18 22
ADK Hypermethioninemia due to adenosine kinase deficiency AD 6 14
AHCY Hypermethioninemia with S-adenosylhomocysteine hydrolase deficiency AR 3 9
AMN Megaloblastic anemia-1, Norwegian AR 29 34
BCKDHA Maple syrup urine disease AR 57 98
BCKDHB Maple syrup urine disease AR 87 103
BCS1L Bjornstad syndrome, GRACILE syndrome, Leigh syndrome, Mitochondrial complex III deficiency, nuclear type 1 AR 42 37
CBS Homocystinuria due to cystathionine beta-synthase deficiency AR 88 205
CD320 Methylmalonic aciduria due to transcobalamin receptor defect AR 2
CLPB 3-methylglutaconic aciduria with cataracts, neurologic involvement, and neutropenia (MEGCANN) AR 26 25
CTH Cystathioninuria AR 5 9
CUBN* Megaloblastic anemia-1, Finnish AR 42 53
D2HGDH D-2-hydroxyglutaric aciduria 1 AR 13 33
DBT Maple syrup urine disease AR 39 75
DLD Dihydrolipoyl dehydrogenase deficiency AR 36 21
ETFA Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 8 29
ETFB Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 6 15
ETFDH Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 43 190
FLAD1 Lipid storage myopathy due to FLAD1 deficiency (LSMFLAD) AR 9 10
GCDH Glutaric aciduria AR 90 241
GIF Intrinsic factor deficiency AR 7 22
GNMT Glycine N-methyltransferase deficiency AR 3 5
HCFC1 Combined methylmalonic acidemia and hyperhomocysteinemia XL 9 17
HIBCH 3-hydroxyisobutryl-CoA hydrolase deficiency AR 18 16
HMGCL 3-hydroxy-3-methylglutaryl-CoA lyase deficiency AR 24 60
IDH2 D-2-hydroxyglutaric aciduria 2 AD 10 4
IVD Isovaleric acidemia AR 51 90
L2HGDH L-2-hydroxyglutaric aciduria AR 15 79
LMBRD1 Methylmalonic aciduria and homocystinuria AR 4 9
MCCC1 3-Methylcrotonyl-CoA carboxylase 1 deficiency AR 40 105
MCCC2 3-Methylcrotonyl-CoA carboxylase 2 deficiency AR 24 114
MCEE Methylmalonyl-CoA epimerase deficiency AR 1 4
MLYCD Malonyl-CoA decarboxylase deficiency AR 14 38
MMAA Methylmalonic acidemia AR 61 75
MMAB Methylmalonic acidemia AR 31 40
MMACHC Methylmalonic aciduria and homocystinuria AR 59 93
MMADHC Methylmalonic aciduria and homocystinuria AR 16 13
MTHFR Homocystinuria due to MTHFR deficiency AR 65 122
MTR Methylmalonic acidemia AR 13 43
MTRR Homocystinuria-megaloblastic anemia, cobalamin E AR 10 31
MUT Methylmalonic acidemia due to methylmalonyl-CoA mutase deficiency AR 159 366
PCCA Propionic acidemia AR 66 125
PCCB# Propionic acidemia AR 68 115
PEPD Prolidase deficiency AR 12 31
SERAC1 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome AR 22 52
SLC25A1 Combined D-2- and L-2-hydroxyglutaric aciduria AR 8 24
SUCLA2 Mitochondrial DNA depletion syndrome AR 9 29
SUCLG1 Mitochondrial DNA depletion syndrome AR 12 28
SUGCT Glutaric aciduria III AR 6 7
TCN2 Transcobalamin II deficiency AR 9 35
UMPS Orotic aciduria AR 3 12

* Some, or all, of the gene is duplicated in the genome. Read more.

# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads).

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.

Non-coding variants covered by Organic Acidemia/Aciduria & Cobalamin Deficiency Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ACAT1 Chr11:108004534 c.121-13T>A NM_000019.3
BCKDHA Chr19:41930736 c.*223T>A NM_000709.3 rs373164531
BCS1L Chr2:219524871 c.-147A>G NM_004328.4
CBS Chr21:44496326 c.-86_-85+8delAGGTAGAAGA NM_001178008.1
D2HGDH Chr2:242680425 c.293-23A>G NM_152783.3
DBT Chr1:100672742 c.1018-550A>G NM_001918.3 rs796052135
ETFDH Chr4:159593534 c.-75A>G NM_004453.2
ETFDH Chr4:159602711 c.176-636C>G NM_004453.2
GCDH Chr19:13010271 c.1244-11A>G NM_000159.3
HCFC1 ChrX:153237261 c.-970T>C NM_005334.2 rs398122908
L2HGDH Chr14:50735527 c.906+354G>A NM_024884.2
MCCC2 Chr5:70898313 c.384-20A>G NM_022132.4 rs770917710
MCCC2 Chr5:70939634 c.1073-12C>G NM_022132.4 rs1280511914
MCEE Chr2:71337896 c.379-644A>G NM_032601.3
MLYCD Chr16:83948547 c.949-14A>G NM_012213.2 rs761146008
MTHFR Chr1:11850973 c.1753-18G>A NM_005957.4 rs777661576
MTHFR Chr1:11863212 c.-13-28_-13-27delCT NM_005957.4 rs786204005
MTR Chr1:236971838 c.340-166A>G NM_000254.2
MTR Chr1:236977232 c.609+1088G>A NM_000254.2 rs752526782
MTR Chr1:237057461 c.3205-196A>G NM_000254.2 rs544410324
MTRR Chr5:7883859 c.984+469T>C NM_024010.2
MUT Chr6:49427219 c.-39-1G>A NM_000255.3
PCCA Chr13:100958030 c.1285-1416A>G NM_000282.3
PCCB Chr3:136003251 c.714+462A>G NM_001178014.1
SERAC1 Chr6:158576548 c.92-165C>T NM_032861.3
SERAC1 Chr6:158576622 c.92-239G>C NM_032861.3
TCN2 Chr22:31011112 c.581-176A>G NM_000355.3 rs372866837
TCN2 Chr22:31011112 c.581-176A>T NM_000355.3

Added and removed genes from the panel

Genes added Genes removed
SUCLA2

Test Strengths

The strengths of this test include:
  • CAP and ISO-15189 accredited laboratory
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publicly available analytic validation demonstrating complete details of test performance
  • ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test Limitations

The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: PCCB (NM_001178014:4). Genes with suboptimal coverage in our assay are marked with number sign (#) and genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. Gene is considered to have suboptimal coverage when >90% of the gene's target nucleotides are not covered at >20x with mapping quality score (MQ>20) reads. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).
This test may not reliably detect the following:
  • Low level mosaicism (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

The Blueprint Genetics organic acidemia/Aciduria & cobalamin deficiency panel covers classical genes associated with organic acidemia/aciduria, maple syrup urine disease, propionic acidemia, methylmalonic acidemia, cobalamin deficiency, homocystinuria, isovaleric acidemia, transcobalamin receptor defect, DLD deficiency and multiple acyl-CoA dehydrogenase deficiency. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics' Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient's phenotype is suggestive of a specific mutation type.

Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.89% (99,153/99,266) >99.9999
Insertions, deletions and indels by sequence analysis
1-10 bps 96.9% (7,563/7,806) >99.9999
11-50 bps 99.13% (2,524/2,546) >99.9999
Copy number variants (exon level dels/dups)
1 exon level deletion (heterozygous) 100% (20/20) NA
1 exon level deletion (homozygous) 100% (5/5) NA
1 exon level deletion (het or homo) 100% (25/25) NA
2-7 exon level deletion (het or homo) 100% (44/44) NA
1-9 exon level duplication (het or homo) 75% (6/8) NA
Simulated CNV detection
5 exons level deletion/duplication 98.7% 100.00%
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 143X
Nucleotides with >20x sequencing coverage (%) 99.86%

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding and regulatory variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases including, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as  SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with <20X sequencing depth if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis is orthogonal confirmation. Sequence variants classified as pathogenic, likely pathogenic and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing when they do not meet our stringent NGS quality metrics for a true positive call.
Reported heterozygous and homo/hemizygous copy number variations with a size <10 and <3 target exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen and confirmed less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references, abstracts and variant databases used to help ordering providers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification. We do not recommend using variants of uncertain significance (VUS) for family member risk stratification or patient management. Genetic counseling is recommended.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Our internal database and our understanding of variants and related phenotypes increases with every case analyzed. Our laboratory is therefore well-positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.

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