Diagnostic Overview – San Paolo Hospital, ASST Santi Paolo e Carlo
San Paolo Hospital, ASST Santi Paolo e Carlo
Genetic and Basic Metabolic & Enzyme testing
This HCP participates in the ERNDIM Quality Assessment scheme (2019)
1. Genetic testing overview
| SC Anatomia Patologica e Genetica Medica
An in-house genetic laboratory only |
Via A. di Rudinì, 8, Milan- Italy
rosa.alfano@asst-santipaolocarlo.it https://www.asst-santipaolocarlo.it/anatomia-patologica-san-paolo |
| Contact Person Gaetano Bulfamante | gaetano.bulfamante@unimi.it |
Available molecular techniques:
- Sanger sequencing,
- Multiplex ligation-dependent probe (MLPA)
- Clinical exome sequencing
- the genetic laboratory offers an overall metabolic gene panel that contains more than 100 genes
- The overall metabolic panel is a virtual panel (i.e the gene-panel is generated bioinformatically and is more flexible as it allows further analysis of other genes).
| Tests that are being offered in this lab | |||
| Amino and organic acids disorders (AOA) | |||
| Aminoacidopaties | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Urea cycle disorders | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Organic acidurias | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Fatty Acid Oxidation (FAO Disorders) | |||
| FAO disorders | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Glycogen storage diseases (GSD) | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Carbohydrate disorders other than GSD
|
Contained in virtual panel | Turnaround time 8-12 weeks | |
| Ketogenesis diorders
|
Contained in virtual panel | Turnaround time 8-12 weeks | |
| Ketolysis disorders | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Lysosomal Storage Disorders (LSD) | |||
| Sphingolipidoses | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Gangliosidoses | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Sphingolipid synthesis | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Mucopolysaccharidoses | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Oligosaccharidoses | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Peroxisomal Disorders (PD) | |||
| Single peroxisomal enzyme deficiencies | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Peroxisome biogenesis | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Disorders of Cholesterol Synthesis | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Bile Acid Synthesis | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Phospholipid and Glycosphingolipid Synthesis | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Congenital Disorders of glycosylation and Disorders of intracellular trafficking (CDG) | |||
| N-glycosylation deficiencies
|
Contained in virtual panel | Turnaround time 8-12 weeks | |
| O-glycosylation deficiencies
|
Contained in virtual panel | Turnaround time 8-12 weeks | |
| Disorders of Neuromodulators and other small Molecules (NOMS) | |||
| Neurotransmitter disorders | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Porphyrias | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Purine and Pyrimidine metabolism | Contained in virtual panel | Turnaround time 8-12 weeks | |
| PM-MD SUBNETWORK | |||
| Nuclear mitochondrial genes | Contained in virtual panel | Turnaround time 8-12 weeks | |
| Variants found in virtual NGS panel are all confirmed with Sanger sequencing
Databases used to link variants with clinical phenotype: Clinvar, HGMD (Human Gene Mutation Database), Locus specific Databases (LSDBs), GnomAD |
|||
2. Basic metabolite and enzyme testing
| Laboratorio di Riferimewnto Regionale per lo Screenin Neonatale
External laboratory |
Via Castelvetro, 32, Milan – Italy |
| Contact person Carlo Corbetta | carlo.corbetta@asst-fbf-sacco.it |
| Metabolite Tests | |
| Type of Test | Name of |
| Amino and organic acids disorders (AOA) | |
| Urine | Amino acids qualitative |
| Amino acids quantitative | |
| Homocitrulline (special assay) | |
| Organic acids qualitative | |
| Organic acids quantitative | |
| Orotic acid | |
| Oxalate | |
| Succinylacetone | |
| Sulfite test | |
| Plasma
|
Amino acids quantitative |
| Acylcarnitines | |
| Carnitine,free and total | |
| Methylmalonic acid (MMA) | |
| Organic acids profile | |
| Oxalic acid | |
| Succinylacetone | |
| Total homocysteine | |
| S-adenosylhomocysteine | |
| S-adenosylmethionine | |
| Dry blood spots | Amino acids |
| Acylcarnitines | |
| Total homocysteine | |
| Methylmalonic acid | |
| CSF | Aminoacids |
| S-adenosylhomocysteine | |
| S-adenosylmethionine | |
| Fatty Acid Oxidation (C-FAO Disorders) | |
| Urine | Sugars qualitative |
| Fructose quantitative | |
| Plasma: | 3-OH-butyrate and acetoacetate |
| Free fatty acids | |
| 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 | |
| Sulfatides | |
| Peroxisomal Disorders (PD) | |
| Plasma | Very long chain fatty acids- VLCFA |
| Congenital Disorders of glycosylation and Disorders of intracellular trafficking (CDG) | |
| Plasma | N-Glycosylation: Isoelectric focusing |
| Disorders of Neuromodulators and other small Molecules (NOMS) | |
| Urine
|
Neurotransmitters |
| Pterines | |
| Purines and pyrimidines | |
| U-Copper (24h) | |
| Plasma | Purines/pyrimidines, |
| p-Copper | |
| p-Ceruloplasmin | |
| CSF | 5-methyltetrahydrofolate |
| N-acetylaspartylglutamic acid (NAAG) | |
| Neurotransmitters | |
| Pterins | |
| 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 | No | |
| Organic Acidurias | No | |
| Urea cycle disorders | No | |
| Fatty Acid Oxidation (C-FAO Disorders) | ||
| Glycogen storage diseases |
No | |
| 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 | Yes | |
| Single peroxisomal enzyme deficiencies | Yes | |
| Disorders of Cholesterol synthesis | Yes | |
| Bile Acid Synthesis | Yes | |
| 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 | Yes | |
| Porphyrias | No | |
| Disorders of Purine and pyrimidine metabolism | Yes | |
| Disorders of Pyruvate Metabolism, Krebs cycle defects, mitochondrial oxidative phosphorylation disorders, disorders of thiamine transport and metabolism (PM-MD) | ||
| Creatine metabolism | Yes | |
| Pyruvate dehydrogenase | Yes | |
| TCA-cycle enzymes | / | |
| Respiratory chain disorders | Yes | |
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