Panel for Liver Diseases

Analysis of all known genes associated with genetic liver diseases.

Panel diagnostics: The panel for genetic liver diseases covers 47 genes. All these genes are sequenced simultaneously, as part of the CeGaT ExomeXtra®. We interpret all genes associated with the patient’s phenotype, referred to as a gene set. Additionally, mtDNA is part of the enrichment.

Maximize diagnostic options: Each gene set can be requested individually or in combination with other gene sets. It’s also possible to select a custom combination of genes (Custom Panel). Click here to view our gene sets.

Extensive medical reporting: The interpretation includes single nucleotide variants (SNVs), small insertions and deletions (INDELs), and copy number variants (CNVs) of single and/or multiple exons. For every gene depicted in the gene sets, we analyse all coding regions. For mtDNA, phenotype associated hotspots are part of the analysis. Full analysis of mtDNA available upon request.

This diagnostic panel has a sensitivity of >99.9% for the heterozygous variant; the average coverage is >130x.

General Information

It is possible to select one or multiple predefined gene sets.
In addition to the comprehensive analysis of the genes of the requested gene set, we can extend the analysis to all genes of the diagnostic panel on request. We report pathogenic and probably pathogenic variants (ACMG classes 4 and 5), which may be associated with the indication of the person seeking advice.
This panel is based on the CeGaT Exome Xtra enrichment. It is possible to expand the analysis to phenotypically relevant gene sets from other CeGaT Panels or individual genes, without additional sequencing. If you are looking for a custom panel, please contact us. We support you with the ordering process.
In addition to the primary diagnostic order, assessing the ACMG genes and creating a pharmacogenetic profile can also be ordered.

Material, Turnaround Time and Costs

1-2 ml EDTA blood or 1-2 µg genomic DNA
Order form with declaration of consent according to German Genetic Diagnosis Act (GenDG)
Turnaround time: less than 4 weeks

The prices for our human genetic diagnostics depend on the size of the selected Diagnostic Panel and the selected gene sets. All prices include sequencing, bioinformatic analysis, and issuing of a medical report by our team of experts in human genetic diagnostics.

Method

The enrichment of the coding regions and the adjacent intronic regions is performed using a in-solution hybridization technology. The selection of the targeted regions and the design of the enrichment baits is performed in-house.

High throughput sequencing is performed on Illumina platforms.
Bioinformatic processing of the data is achieved using an in-house computer cluster.

Following data processing, our team of scientists and specialists in human genetics analyze the data and issue a medical report.

Gene sets – Liver Diseases

Gene set (10 genes, LIV01)

Progressive Familial Intrahepatic Cholestasis

ABCB11, ABCB4, ATP8B1, KIF12, NR1H4, MYO5B, TJP2, USP53, VPS33B, ZFYVE19

Order Form (pdf)

Gene set (5 genes, LIV06)

Lysosomal Storage Disorders with Liver Involvement

GBA, LIPA, NPC1, NPC2, SMPD1

Order Form (pdf)

Gene set (42 genes, LIV10)

Cholestasis

ABCB11, ABCB4, ABCC2, ACOX2, ADK, AKR1D1, AMACR, ATP7B, ATP8B1, BAAT, CCDC115, CFTR, CLDN1, CYP27A1, CYP7B1, DCDC2, DGUOK, FAH, FOCAD, GALE, GALT, GIMAP5, HSD3B7, JAG1, KIF12, MPV17, MYO5B, NBAS, NOTCH2, NR1H4, PKHD1, POLG, RINT1, SLC25A13, TJP2, TRMU, TULP3, USP53, VIPAS39, VPS33B, VPS50, ZFYVE19

Order Form (pdf)

Hemochromatosis

HFE (p.Cys282Tyr)

Order Form (pdf)

Alpha-1-antitrypsin Deficiency

SERPINA1 (common pathogenic alleles)

Order Form (pdf)

Gene Directory

Gene Directory (47 Genes)

Liver Panel:

ABCB11, ABCB4, ABCC2, ACOX2, ADK, AKR1D1, AMACR, ATP7B, ATP8B1, BAAT, CCDC115, CFTR, CLDN1, CYP27A1, CYP7B1, DCDC2, DGUOK, FAH, FOCAD, GALE, GALT, GBA1, GIMAP5, HSD3B7, JAG1, KIF12, LIPA, MPV17, MYO5B, NBAS, NOTCH2, NPC1, NPC2, NR1H4, PKHD1, POLG, RINT1, SLC25A13, SMPD1, TJP2, TRMU, TULP3, USP53, VIPAS39, VPS33B, VPS50, ZFYVE19

ACMG Genes

Genetic variation may sometimes be identified, which does not fit within the scope of the requested genetic analysis (so-called secondary findings). The reporting of these variants is limited to pathogenic alterations (ACMG classes 4 and 5) within selected genes, for which a treatment or course of action exists for you or your family (according to the current guidelines of the American College of Medical Genetics and Genomics; details on genes and associated diseases can be found here.

Pharmacogenetics

Pharmacogenetic analysis detects genetic changes that affect the effectiveness of drugs. Genetic variants that affect proteins responsible for the metabolism of substances can significantly change their tolerance and efficacy. These drugs include, among others, antidepressants, pain relievers, neuroleptics, chemotherapeutics, AIDS drugs, thrombosis drugs, anesthetics, beta-blockers, or statins.

The reduced activity of a specific enzyme can lead to an increased drug level in the standard dosage, which is often associated with undesirable side effects. With drugs that are only activated by metabolism, the therapeutic effect can be completely absent. Likewise, due to the resulting increased rate of degradation of the medicinal substance, an increased enzyme activity leads to inadequate effectiveness of the therapy.

The pharmacogenetics option analyzes known variants in 22 genes involved in the metabolism of drugs. If specific gene variants occur, the treating doctor can adapt the therapy individually. The pharmacogenetic analysis can minimize serious side effects and helps to avoid failure of the treatment.

Several differential diagnoses to primary liver disease, especially metabolic disorders, might be of interest. Here are some selected gene sets from different panels, which may be added to the analysis:

Mitochondriopathies, nuclear-encoded (MIT-02)
Panel: Metabolic Diseases

Glycogen Storage Disease (MET-14)
Panel: Metabolic Diseases

Peroxisomal Disorders (MET-03 / MET-19)
Panel: Metabolic Diseases

Joubert Syndrome (BRN-07)
Panel: Epilepsy & Brain Development Disorders

Nephronophthisis (KID-01)
Panel: Kidney Diseases

Information

The liver is the central organ for metabolism in the body and has many functions reaching from protein production and depletion to blood clotting as well as the metabolism of cholesterol, glucose and iron. Thus, injuries and diseases of the liver have serious consequences for health. Usual symptoms are amongst others jaundice, cholestasis, liver enlargement, ascites, hepatic encephalopathy and at last liver failure.

The reasons of liver diseases are often virus infections, alcohol, liver cancer or obesity. But there could also be genetic causes. Here, frequent inherited liver disorders are for example hereditary hemochromatosis (gene: HFE), α1-antitrypsin deficiency (gene: SERPINA1) or Wilson disease (gene: ATP7B). Beside the transport and metabolic disturbances underlying these disorders, a malformation of the biliary tracts and other biliary tract diseases or structural impairments during organomorphogenesis can also lead to disturbance of liver function. Thus, a therapy of liver diseases, which often respond well to a treatment, is highly specific according to the underlying cause. Therefore, the diagnosis of the exact cause of the respective disease is indispensable.

Within the scope of genetic diagnosis we offer a large gene panel, which comprises the actual known disease-causing genes for inherited liver disorders. It comprises both disorders with a main affection of the liver (e.g. familial cholestasis, hypercholanemia and defects of bile acid synthesis, impairments of transport in hepatocytes and cholangiocytes) and with a liver involvement beside other clinical symptoms (e.g. lysosomal storage disorders, hepatic mitochondriopathies).