Organic Acidemia/Aciduria & Cobalamin Deficiency Panel

Last modified: Jun 12, 2018

Summary

  • Is a 53 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
  • SEQ
  • DEL/DUP

Availability

3-4 weeks

Number of genes

53

Test code

ME0901

CPT codes

SEQ 81404
SEQ 81405
SEQ 81406
DEL/DUP 81479

Summary

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

  • Is a 53 gene panel that includes assessment of selected non-coding disease-causing variants
  • Is available as PLUS analysis (sequencing analysis and deletion/duplication analysis), sequencing analysis only or deletion/duplication analysis only

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

Sample Requirements

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • Saliva (Oragene DNA OG-500 kit)

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.

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 5 7
ACADSB 2-methylbutyryl-CoA dehydrogenase deficiency AR 7 12
ACAT1 Alpha-methylacetoacetic aciduria AR 30 91
ACSF3 Combined malonic and methylmalonic aciduria AR 19 19
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 26 33
BCKDHA Maple syrup urine disease AR 46 91
BCKDHB Maple syrup urine disease AR 69 94
BCS1L Bjornstad syndrome, GRACILE syndrome, Leigh syndrome, Mitochondrial complex III deficiency, nuclear type 1 AR 33 37
CBS Homocystinuria due to cystathionine beta-synthase deficiency AR 72 187
CD320 Methylmalonic aciduria due to transcobalamin receptor defect AR 1
CLPB 3-methylglutaconic aciduria with cataracts, neurologic involvement, and neutropenia (MEGCANN) AR 25 25
CTH Cystathioninuria AR 5 9
CUBN* Megaloblastic anemia-1, Finnish AR 37 52
D2HGDH D-2-hydroxyglutaric aciduria 1 AR 10 32
DBT Maple syrup urine disease AR 32 72
DLD Dihydrolipoyl dehydrogenase deficiency AR 24 21
ETFA Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 9 29
ETFB Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 6 14
ETFDH Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 41 173
FLAD1 Lipid storage myopathy due to FLAD1 deficiency (LSMFLAD) AR 9 10
GCDH Glutaric aciduria AR 70 208
GIF Intrinsic factor deficiency AR 7 20
GNMT Glycine N-methyltransferase deficiency AR 3 5
HCFC1 Combined methylmalonic acidemia and hyperhomocysteinemia XL 9 16
HIBCH 3-hydroxyisobutryl-CoA hydrolase deficiency AR 19 13
HMGCL 3-hydroxy-3-methylglutaryl-CoA lyase deficiency AR 13 60
IDH2 D-2-hydroxyglutaric aciduria 2 AD 10 3
IVD Isovaleric acidemia AR 39 87
L2HGDH L-2-hydroxyglutaric aciduria AR 13 76
LMBRD1 Methylmalonic aciduria and homocystinuria AR 4 9
MCCC1 3-Methylcrotonyl-CoA carboxylase 1 deficiency AR 34 103
MCCC2 3-Methylcrotonyl-CoA carboxylase 2 deficiency AR 22 113
MCEE Methylmalonyl-CoA epimerase deficiency AR 1 4
MLYCD Malonyl-CoA decarboxylase deficiency AR 13 38
MMAA Methylmalonic acidemia AR 46 74
MMAB Methylmalonic acidemia AR 23 39
MMACHC Methylmalonic aciduria and homocystinuria AR 30 93
MMADHC Methylmalonic aciduria and homocystinuria AR 16 13
MTHFR Homocystinuria due to MTHFR deficiency AR 63 120
MTR Methylmalonic acidemia AR 13 40
MTRR Homocystinuria-megaloblastic anemia, cobalamin E AR 9 30
MUT Methylmalonic acidemia due to methylmalonyl-CoA mutase deficiency AR 114 359
PCCA Propionic acidemia AR 48 123
PCCB Propionic acidemia AR 41 114
PEPD Prolidase deficiency AR 12 30
SERAC1 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome AR 23 48
SLC25A1 Combined D-2- and L-2-hydroxyglutaric aciduria AR 8 16
SUCLG1 Mitochondrial DNA depletion syndrome AR 11 28
SUGCT Glutaric aciduria III AR 6 5
TCN2 Transcobalamin II deficiency AR 9 33
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 the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
BCKDHA Chr19:41930736 c.*223T>A NM_000709.3 rs373164531
BCS1L Chr2:219524871 c.-147A>G NM_004328.4
D2HGDH Chr2:242680425 c.293-23A>G NM_152783.3
DBT Chr1:100661453 c.*358A>C NM_001918.3
DBT Chr1:100672742 c.1018-550A>G NM_001918.3 rs796052135
ETFDH Chr4:159593534 c.-75A>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
MCEE Chr2:71337896 c.379-644A>G NM_032601.3
MLYCD Chr16:83948547 c.949-14A>G NM_012213.2 rs761146008
MTHFR Chr1:11863212 c.-13-28_-13-27delCT NM_005957.4 rs786204005
MTHFR Chr1:11850973 c.1753-18G>A NM_005957.4 rs777661576
MTR Chr1:237057461 c.3205-196A>G NM_000254.2 rs544410324
MTR Chr1:236971838 c.340-166A>G NM_000254.2
MTR Chr1:236977232 c.609+1088G>A NM_000254.2 rs752526782
MTRR Chr5:7883859 c.984+469T>C NM_024010.2
MUT Chr6:49427219 c.-39-1G>A NM_000255.3
MUT Chr6:49404228 c.1957-892C>A NM_000255.3
MUT Chr6:49404235 c.1957-899A>G NM_000255.3
PCCA Chr13:100958030 c.1285-1416A>G NM_000282.3
PCCB Chr3:136003251 c.714+462A>G NM_001178014.1
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
ACADSB
ADK
AHCY
AMN
BCS1L
CLPB
CTH
CUBN
D2HGDH
FLAD1
GNMT
HIBCH
IDH2
L2HGDH
MLYCD
PEPD
SERAC1
SLC25A1
SUCLG1
SUGCT
UMPS

Test strength

The strengths of this test include:
  • CAP and ISO-15189 accreditations covering all operations at Blueprint Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • 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 publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in Blueprint WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG 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

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. 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
  • 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 Whole Exome Sequencing (WES) assay. All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%

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 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 such as, 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, the customer has an access to details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with inadequate coverage if present. This reflects our mission to build fully transparent diagnostics where customers have easy access to 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 of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant at least three times at Blueprint Genetics. Reported variants of uncertain significance are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size <10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen 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 used, congress abstracts and mutation databases to help our customers 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 within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counseling. For eligible cases, Blueprint Genetics offers a no charge service to investigate the role of reported VUS (VUS Clarification Service).

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. 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.