1. NGS panel - Genetic testing for pancreatitis

Pancreatitis

April 12, 2017

Clinical features

Pancreatitis is a common inflammatory disorder of the pancreas. There are a variety of disorders of the pancreas including acute pancreatitis, chronic pancreatitis, hereditary pancreatitis, and pancreatic cancer.

Signs and symptoms of pancreatitis may vary, depending on the disease1, 2.

Acute pancreatitis clinical symptoms include the following:

  • Upper abdominal pain
  • Abdominal pain that feels worse after eating and radiates to the back
  • Tenderness when touching the abdomen
  • Nausea, vomiting
  • Fever
  • Rapid pulse

Chronic pancreatitis symptoms include:

  • Upper abdominal pain
  • Oily, smelly stools (steatorrhea)
  • Losing weight without trying

Pancreatic diseases have a strong genetic component. Hereditary pancreatitis is a disease of recurrent injury to the pancreas, and it is most often caused by genetically caused abnormal regulation of trypsin, the master regulator of pancreatic digestive enzyme activation. Genes associated with hereditary pancreatitis include the following: CFTR, CPA1, CTRC, PRSS1, SPINK11,2. All of these genes are included in CENTOGENE´s pancreatitis panel, designed for fast and reliable molecular diagnostics of this hereditary and severe disease.

A heterozygous pathogenic mutation in PRSS1 gene, which results in autosomal dominant inherited hereditary pancreatitis, is found in 60-100% of affected families2. PRSS1 encodes trypsin-1, a major pancreatic digestive enzyme which also catalyzes activation of other pancreatic zymogens to active enzymes, a process that normally occurs in the intestine. HP-causing PRSS1 pathogenic variants typically result in a trypsin protein that is either prematurely activated or resistant to degradation.

Pathogenic mutations in SPINK1, encoding serine protease inhibitor, can lead to autosomal dominant hereditary pancreatitis and autosomal recessive pancreatitis. In the United States, Europe, and India a high-risk haplotype containing SPINK1 p.Asn34Ser (NM_003122.3:c.101A>G) is common, with a minor allele frequency as high as 3%3. In China, Japan, and Korea the SPINK1 splice variant (c.194+2T>C, also known as IVS3+2T>C) is common3.

Pathogenic variants in CFTR, encoding the cystic fibrosis transmembrane conductance protein, are associated with recurrent acute and chronic pancreatitis. CFTR is the most important molecule for the function of the pancreatic duct cells. These cells secrete a bicarbonate-rich fluid that flushes the zymogens into the duodenum. Dysfunction of CFTR results in retention of zymogens in the duct where they can become active and start digesting the surrounding tissue of the pancreas, leading to acute pancreatitis. The functional effect of CFTR variants is determined by the less severe pathogenic variant. Recent data suggest that CFTR pathogenic variants that affect bicarbonate conductance while maintaining chloride conductance (for example: p.Arg75Gln; NM_000492.3:c.224G>A) have major effects on the pancreas but minimal effects on the lungs because the pancreas uses CFTR as a bicarbonate channel4, 5.

Treatment of acute pancreatitis usually focuses on pain management and to decrease the likelihood of complications, including pancreatic cancer. Treatment of chronic pancreatitis focuses on improving quality of life by managing pancreatic pain, maldigestion, and diabetes mellitus. Total pancreatectomy with islet autotransplantation should be used only as a last resort to manage those patients with severe manifestations of pancreatitis1.

CENTOGENE´s pancreatitis panel includes the genes: CFTR, CPA1, CTRC, PRSS1, SPINK1 and we offer full gene sequencing, deletion/duplication analysis of selected genes (SPINK1, CFTR, PRSS1).


Differential diagnosis

The differential diagnosis of pancreatitis disorders – depending on the major symptoms in the initial case – includes the following diseases1:

Acute pancreatitis:

  • Acute peritonitis
  • Macroamylasemia
  • Macrolipasemia
  • Malabsorption syndromes/processes
  • Perforated viscus

Chronic pancreatitis:

  • Ampullary carcinoma
  • Cholangitis
  • Cholecystitis
  • Chronic gastritis
  • Community-acquired pneumonia (CAP)
  • Crohn disease
  • Intestinal perforation
  • Mesenteric artery ischemia

Testing strategy

CENTOGENE offers advanced, fast and cost-effective strategy to test large NGS panels and diagnose complex phenotypes based on the PCR-free whole genome sequencing and NGS technology. This approach offers an unparalleled advantage by reducing amplification/capture biases and provides sequencing of entire gene at a more uniform coverage.

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for Pancreatitis using NGS Panel Genomic targeted towards this specific phenotype:

Step 1: Whole genome sequencing from a single filter card. The sequencing covers the entire genic region (coding region, exon/intron boundaries, intronic and promoter) for all the genes included in the Pancreatitis panel. Copy Number Variants analysis derived from NGS data is also included.

Step 2: If no mutation is identified after analysis of the Pancreatitis panel, based on the approval and consent, we further recommend to continue the bioinformatics analysis of the data obtained by whole genome sequencing to cover genes that are either implicated in an overlapping phenotype or could be involved in a similar pathway but not strongly clinically implicated based on the current information in literature.


Referral reasons

The following individuals are candidates for this particular gene testing

  • Individuals with a family history of disease and presentation of the most common symptoms
  • Individuals without a positive family history, but with symptoms resembling this disease
  • Individuals with a negative but suspected family history, in order to perform proper genetic counseling (prenatal analyses are recommended in families with affected individuals).

Test utility

Sequencing, deletion/duplication of this gene and related genes should be performed in all individuals suspected for this particular phenotype. In parallel, other genes reported to be related with this clinical phenotype should also be analyzed for the presence of mutations, due to the overlap in many clinical features caused by those particular genes.

Confirmation of a clinical diagnosis through genetic testing can allow for genetic counseling and may direct medical management.

Genetic counseling can provide a patient and/or family with the natural history of the condition, identify at-risk family members, provide reproductive risks as well as preconception/prenatal options, and allow for appropriate referral for patient support and/or resources.



Overview of the genes in CENTOGENE´s pancreatitis panel

Gene (OMIM) Pancreatitis type (Locus) Inheritance Protein % of individuals with pancreatitis
CFTR
(602421)
Idiopathic pancreatitis, Cystic fibrosis
7q31.2
AD, AR Cystic fibrosis transmembrane conductance regulator 11.2% in Australiana, 12,2% in Italian cohortb
CPA1
(114850)
Early onset chronic pancreatitis
7q32.2
unknown Carboxypeptidase A, pancreatic exopeptidase 29/944 (3.1%) German cases and 5/3,938 (0.1%) controlsc
CTRC
(601405)
Chronic hereditary pancreatitis
1p36.21
AD Chymotrypsin C R254W mutation found in 0.9% of patients with alcoholic pancreatitis d
PRSS1
(276000)
Hereditary pancreatitis, Trypsinogen deficiency
7q34
AD, AR Protease serine 1; Trypsinogen 1 60%-100% in hereditary pancreatitise 90% of PRSS1 pathogenic variants include p.Asn29Ile and p.Arg122Hise
SPINK1
(167790)
Hereditary pancreatitis, Tropical calcific pancreatitis, susceptibility to Fibrocalculous pancreatic diabetes
5q32
AD, AR Serine protease inhibitor, Kazel-type 1 p.Asn34Ser in 3% of affected in US and Europef
c.194+2T>C common in China, Japan, and Koreaf

a) Zoller et al. CFTR gene mutations in pancreatitis: Frequency and clinical manifestations in an Austrian patient cohort. Wien Klin Wochenschr. 2007;119(17-18):527-33.
b) Pezzilli et al. Mutations of the CFTR gene in pancreatic disease. Pancreas. 2003 Nov;27(4):332-6.
c) Witt et al. Variants in CPA1 are strongly associated with early onset chronic pancreatitis. Nat Genet. 2013 Oct;45(10):1216-20.
d) da Costa et al. Frequency of Tabagism and N34S and P55S Mutations of Serine Peptidase Inhibitor, Kazal Type 1 (SPINK1) and R254W Mutation of Chymotrypsin C (CTRC) in Patients With Chronic Pancreatitis and Controls. Pancreas. 2016 Oct;45(9):1330-1335.
e) Rebours et al. The natural history of hereditary pancreatitis: a national series. Gut. 2009;58:97–103.
f) LaRusch et al. Pancreatitis Overview. GeneReviews®. Pagon RA, Adam MP, Ardinger HH, et al., editors. Seattle (WA): University of Washington, Seattle; 1993-2017.


More information on CENTOGENE´s pancreatitis panel can be found in our genetic test catalogue.