Organic Acidemia/Aciduria & Cobalamin Deficiency Panel

SEQmethod-seq-icon Our Sequence Analysis is based on a proprietary targeted sequencing method OS-Seq™ and offers panels targeted for genes associated with certain phenotypes. A standard way to analyze NGS data for finding the genetic cause for Mendelian disorders. Results in 21 days. DEL/DUPmethod-dup-icon Targeted Del/Dup (CNV) analysis is used to detect bigger disease causing deletions or duplications from the disease-associated genes. Results in 21 days. PLUSmethod-plus-icon Plus Analysis combines Sequence + Del/Dup (CNV) Analysis providing increased diagnostic yield in certain clinical conditions, where the underlying genetic defect may be detectable by either of the analysis methods. Results in 21 days.

Test code: ME0901

The Blueprint Genetics Organic Acidemia/Aciduria & Cobalamin Deficiency Panel is a 32 gene test for genetic diagnostics of patients with clinical suspicion of cobalamin deficiency, homocystinuria, maple syrup urine disease, methylmalonic acidemia, organic acidemia/aciduria or propionic acidemia.

All disorders of organic acidemia/aciduria and cobalamin metabolism are inherited in an autosomal recessive manner. This Panel is included in the Comprehensive Metabolism Panel.

About Organic Acidemia/Aciduria & Cobalamin Deficiency

Organic acidemia and aciduria refer to many disorders, where non-amino organic acids are excreated in urine. Usually this is a result of a deficient enzyme activity in amino acid catabolism. The clinical presentation of organic acidemia in young child 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 often result from the accumulation of precursors of the defective pathway. The combined prevalence of organic acidurias is estimated at 1:1000 newborns. Cobalamin is vitamin B12. This vitamin has cobalt in its structure. Humans are not able to synthesize B12 vitamin but it needs to be obtained from a food of animal origin that is the only natural source of cobalamin in 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 mutation 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 alone circa 80% of the cases with intracellular cobalamin deficiency, followed by MMADHC (<5%), MTRR (<5%), LMBRD1 (<5%), MTR (<5%) and ABCD4 (<1%). Clinical manifestation of cobalamin deficiency can have an onset already in perinatal period or later during childhood or adulthood. Symptoms seen also have a wide range, based on the complementation group and defective gene. Perinatal manifestations often include growth retardation, microcephaly, heart diseases and dysmorhic features. Infantile 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 predisposes often to neurological and neuropsychiatric problems. Some specific types of cobalamin deficiencies are extreme rare with only dozens of patients described. The combined prevalence is estimated at >1:100 000.

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Results in 3-4 weeks.

Genes in the Organic Acidemia/Aciduria & Cobalamin Deficiency Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
ABCD4Methylmalonic aciduria and homocystinuriaAR55
ACAT1Alpha-methylacetoacetic aciduriaAR2868
ACSF3Combined malonic and methylmalonic aciduriaAR1518
BCKDHAMaple syrup urine diseaseAR3891
BCKDHBMaple syrup urine diseaseAR4892
CBSHomocystinuria due to cystathionine beta-synthase deficiencyAR51192
CD320Methylmalonic aciduria due to transcobalamin receptor defectAR12
DBTMaple syrup urine diseaseAR2971
DLDDihydrolipoyl dehydrogenase deficiencyAR1621
ETFAGlutaric aciduria, Multiple acyl-CoA dehydrogenase deficiencyAR728
ETFBGlutaric aciduria, Multiple acyl-CoA dehydrogenase deficiencyAR713
ETFDHGlutaric aciduria, Multiple acyl-CoA dehydrogenase deficiencyAR36168
GCDHGlutaric aciduriaAR36198
GIFIntrinsic factor deficiencyAR619
HCFC1Combined methylmalonic acidemia and hyperhomocysteinemiaXL715
HMGCL3-hydroxy-3-methylglutaryl-CoA lyase deficiencyAR851
IVDIsovaleric acidemiaAR2671
LMBRD1Methylmalonic aciduria and homocystinuriaAR39
MCCC13-Methylcrotonyl-CoA carboxylase 1 deficiencyAR25103
MCCC23-Methylcrotonyl-CoA carboxylase 2 deficiencyAR21113
MCEEMethylmalonyl-CoA epimerase deficiencyAR34
MMAAMethylmalonic acidemiaAR2249
MMABMethylmalonic acidemiaAR2340
MMACHCMethylmalonic aciduria and homocystinuriaAR2785
MMADHCMethylmalonic aciduria and homocystinuriaAR1613
MTHFRHomocystinuria due to MTHFR deficiencyAR51127
MTRMethylmalonic acidemiaAR1139
MTRRHomocystinuria-megaloblastic anemia, cobalamin EAR735
MUTMethylmalonic acidemia due to methylmalonyl-CoA mutase deficiencyAR98341
PCCAPropionic acidemiaAR43118
PCCBPropionic acidemiaAR44109
TCN2Transcobalamin II deficiencyAR429

Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/); HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/). The list of associated (gene specific) phenotypes are generated from CDG (http://research.nhgri.nih.gov/CGD/) or Orphanet (http://www.orpha.net/) databases.

Blueprint Genetics offers a comprehensive organic acidemia/Aciduria & cobalamin deficiency panel that covers classical genes associated with cobalamin deficiency, DLD deficiency, homocystinuria, isovaleric acidemia, maple syrup urine disease, methylmalonic acidemia, multiple acyl-CoA dehydrogenase deficiency, organic acidemia/aciduria, propionic acidemia and transcobalamin receptor defect. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.

Please see our latest validation report showing sensitivity and specificity for SNPs and indels, sequencing depth, % of the nucleotides reached at least 15x coverage etc. If the Panel is not present in the report, data will be published when the Panel becomes available for ordering. Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. All the Panels available for ordering have sensitivity and specificity higher than > 0.99 to detect single nucleotide polymorphisms and a high sensitivity for indels ranging 1-19 bp. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile. Detection limit for Del/Dup analysis varies through the genome from one to six exon Del/Dups depending on exon size, sequencing coverage and sequence content.

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. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (http://www.1000genomes.org), the NHLBI GO Exome Sequencing Project (ESP; http://evs.gs.washington.edu/EVS), the Exome Aggregation Consortium (ExAC; http://exac.broadinstitute.org), ClinVar database of genotype-phenotype associations (http://www.ncbi.nlm.nih.gov/clinvar) and the Human Gene Mutation Database (http://www.hgmd.cf.ac.uk). The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (http://sift.jcvi.org), Polyphen (http://genetics.bwh.harvard.edu/pph2/), and Mutation Taster (http://www.mutationtaster.org).

Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.

In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.

Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.

A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.

We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.

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ICD & CPT codes

CPT codes

SEQ81479
DEL/DUP81479


ICD codes

Commonly used ICD-10 codes when ordering the Organic Acidemia/Aciduria & Cobalamin Deficiency Panel

ICD-10Disease
E71.0Maple syrup urine disease
E71.1Propionic acidemia
E72.1Methylmalonic acidemia
E72.1Cobalamin deficiency
E72.1Homocystinuria

Accepted sample types

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 5μg
  • 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.