Diagnostic Overview – Centro Hospitalar do Sao Joao, E.P.E
Centro Hospitalar do Sao Joao, E.P.E. – Genetic and Basic Metabolite & Enzyme testing
Genetic and Basic Metabolic & Enzyme testing
This HCP participates in the ERNDIM Quality Assessment scheme (2019)
1. Genetic testing overview
| Department of Genetics Faculty of Medicine, Universidade do Porto | Alameda Prof Hernani Monteiro, 4200-319 Porto- Portugal
https://sigarra.up.pt/fmup/en/uni_geral.unidade_view?pv_unidade=165 |
| Contact Person Miguel Leão | mjleao2357@gmail.com |
Available molecular techniques:
- Sanger sequencing,
- Multiplex ligation-dependent probe (MLPA),
- aCGH
- The genetic laboratory/geneticist collaborates with other professionals on complementing the genetic findings with the clinical and biochemical phenotype (multidisciplinary approach)
- The overall metabolic panel is a real panel (i.e a fixed number of genes that are physically isolated and sequenced)
- the genetic laboratory offers an Overall metabolic gene panel that contains 172 genes
| Tests that are being offered in this lab | |||
| Amino and organic acids disorders (AOA) | |||
| Aminoacidopaties | Sanger sequencing available | Turnaround time 2-4 weeks | |
| Urea cycle disorders | Sanger sequencing available | Turnaround time 2-4 weeks | |
| Organic acidurias | Sanger sequencing available | Turnaround time 2-4 weeks | |
| Fatty Acid Oxidation (FAO Disorders) | |||
| FAO disorders | Sanger sequencing available | Turnaround time 2-4 weeks | |
| Glycogen storage diseases (GSD) | Sanger sequencing available | Turnaround time 2-4 weeks | |
| Carbohydrate disorders other than GSD
|
Sanger sequencing available | Turnaround time 2-4 weeks | |
| Ketogenesis diorders
|
Sanger sequencing available | Turnaround time 2-4 weeks | |
| Ketolysis disorders | Sanger sequencing available | Turnaround time 2-4 weeks | |
| Lysosomal Storage Disorders (LSD) | |||
| Sphingolipidoses | Sanger sequencing available | Turnaround time 4-8 weeks | |
| Gangliosidoses | Sanger sequencing available | Turnaround time 4-8 weeks | |
| Sphingolipid synthesis | Sanger sequencing available | Turnaround time 4-8 weeks | |
| Mucopolysaccharidoses | Sanger sequencing available | Turnaround time 4-8 weeks | |
| Oligosaccharidoses | Turnaround time 4-8 weeks | ||
| Peroxisomal Disorders (PD) | |||
| Single peroxisomal enzyme deficiencies | Sanger sequencing available | Turnaround time 4-8 weeks | |
| Peroxisome biogenesis | Sanger sequencing available | Turnaround time 4-8 weeks | |
| Disorders of Cholesterol Synthesis | Sanger sequencing available | Information not provided | |
| Phospholipid and Glycosphingolipid Synthesis | Sanger sequencing available | Turnaround time 4-8 weeks | |
| N-glycosylation deficiencies | Sanger sequencing available | Information not provided | |
| Neurotransmitter disorders | Sanger sequencing available | Information not provided | |
| Disorders of Pyruvate Metabolism, Krebs cycle defects, mitochondrial oxidative phosphorylation disorders, disorders of thiamine transport and metabolism (PM-MD) | |||
| Nuclear mitochondrial genes Contained in real panel
|
Contained in real panel | Turnaround time 4-8 weeks | |
| mtDNA genes | Contained in real panel | Turnaround time 4-8 weeks | |
| Databases used to link variants with clinical phenotype:
Clinvar, HGMD (Human Gene Mutation Database), VARSOME |
|||
Basic metabolite and enzyme testing
| INSA- Newborn Screening Metabolism and Genetics Unit
External metabolic laboratory |
Rua Alexandre Herculano, 321, Porto Portugal |
| Contact person Laura Vilarinho | laura.vilarinho@insa.min-saude.pt |
2. Metabolite Tests |
|
| Type of Test | Name of |
| Amino and organic acids disorders (AOA) | |
| Urine | Amino acids qualitative |
| Carnitine Total, Free | |
| Formiminoglutamic acid (FIGLU) | |
| Glycerate, | |
| Glycolic Acid | |
| Homocitrulline (special assay) | |
| Organic acids qualitative | |
| Organic acids quantitative | |
| Orotic acid | |
| Oxalate | |
| Succinylacetone | |
| Trimetylamine | |
| Sulfite test | |
| S-Sulfocysteine | |
| Plasma
|
Amino acids quantitative |
| Acylcarnitines | |
| Carnitine, free and total | |
| Methylmalonic acid (MMA) | |
| Organic acids profile, | |
| Oxalic acid | |
| Succinylacetone | |
| Total homocysteine | |
| Dry blood spots | Amino acids |
| Acylcarnitines | |
| Total homocysteine | |
| Methylmalonic acid | |
| CSF | Aminoacids |
| Fatty Acid Oxidation (C-FAO Disorders) | |
| Urine | Reducing substances |
| Sugars qualitative | |
| Fructose quantitative | |
| Plasma: | Galactose |
| Dry blood spots: | Gal and Gal-1P semiquantitative |
| Lysosomal Storage Disorders (LSD) | |
| Urine
|
Glycosaminoglycans qualitative (screening tests) |
| Glycosaminoglycans quantitative | |
| L-Cystine, | |
| Mucopolysaccharide electrophoresis/TLC | |
| Sterol biosynthesis intermediates | |
| Sialic acid | |
| Neuraminic acid | |
| Oligosaccharides TLC | |
| Sialyloligosaccharides TLC | |
| Sulfatides | |
| Plasma/EDTA | Glycosylsphingosine |
| Lyso-Gb3 | |
| CCL18 | |
| Glucosylceramide | |
| Hexosylsphingosine (LysoGL1) | |
| Sialic acid | |
| White blood cells | Cystine |
| CSF | Sialic acid |
| Peroxisomal Disorders (PD) | |
| Urine | Sterol biosynthesis intermediates |
|
Plasma
|
7-Dehydrocholesterol |
| 7-Ketocholesterol | |
| Cholestane-3?,5?,6?-triol | |
| Cholestanol | |
| Cholesterol | |
| Phytanic acid | |
| Plasmalogens | |
| Pristanic acid | |
| Sterol biosynthesis intermediates | |
| Very long chain fatty acids- VLCFA | |
| Erythrocytes | Plasmalogens |
| Congenital Disorders of glycosylation and Disorders of intracellular trafficking (CDG) | |
| Plasma | N-Glycosylation: Isoelectric focusing |
| Disorders of Neuromodulators and other small Molecules (NOMS) | |
| Urine
|
L-Pipecolic acid |
| Neurotransmitters | |
| Pterines | |
| Purines and pyrimidines | |
| Plasma | Porphyrins |
| CSF | 5-methyltetrahydrofolate |
| N-acetylaspartylglutamic acid (NAAG) | |
| Neurotransmitters | |
| Pipecolic acid | |
| Pterins | |
| Faeces
|
Porphyrins |
| Erythrocytes | Protoporphyrin |
| Disorders of Pyruvate Metabolism, Krebs cycle defects, mitochondrial oxidative phosphorylation disorders, disorders of thiamine transport and metabolism (PM-MD) | |
| Urine | Creatine, creatinine,guanidinoacetate |
| Plasma | Creatine, guanidinoacetate |
| CSF | Pyruvate/lactate |
Enzyme Tests |
||
| Type of Disease | Yes or No | |
| Amino and organic acids disorders (AOA) | ||
| Aminoacidopathies | Yes | |
| Organic Acidurias | No | |
| Urea cycle disorders | No | |
| Fatty Acid Oxidation (C-FAO Disorders) | ||
| Glycogen storage diseases
|
Yea | |
| Carbohydrate diseases other than Glycogen storage diseases
|
No | |
| Fatty acid oxidation and carnitine transport disorders
|
No | |
| Disorders of Ketogenesis and Ketolysis | No | |
| Lysosomal Storage Disorders (LSD) | ||
| Mucopolysaccharidoses
|
Yes | |
| Sphingolipidoses | Yes | |
| Oligosaccharidosis | Yes | |
| Mucolipidoses | Yes | |
| Lysosomal glycogen storage disease (Pompe disease) | Yes | |
| Peroxisomal Disorders (PD) | ||
| Peroxisome biogenesis | No | |
| Single peroxisomal enzyme deficiencies | No | |
| Disorders of Cholesterol synthesis | No | |
| Bile Acid Synthesis | No | |
| Phospholipid and Glycosphingolipid Synthesis | Yes | |
| Congenital Disorders of glycosylation and Disorders of intracellular trafficking (CDG) | ||
| N-glycosylation disorders | No | |
| O-glycosylation disorders | No | |
| Disorders of Neuromodulators and other small Molecules (NOMS) | ||
| Neurotransmitter disorders | No | |
| Porphyrias | No | |
| Disorders of Purine and pyrimidine metabolism | No | |
| Disorders of Pyruvate Metabolism, Krebs cycle defects, mitochondrial oxidative phosphorylation disorders, disorders of thiamine transport and metabolism (PM-MD) | ||
| Creatine metabolism | Yes | |
| Pyruvate dehydrogenase | No | |
| TCA-cycle enzymes | Yes | |
| Respiratory chain disorders | Yes | |
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