List of diseases covered by Polyposis Syndromes NGS panel

Published 12/07/2018

List of diseases covered by
Polyposis Syndromes NGS panel

Gene Condition
APC Adenomatous polyposis coli; Colorectal cancer, somatic;
Desmoid disease, hereditary; Gardner syndrome;
Gastric cancer, somatic; Hepatoblastoma, somatic
BMPR1A Juvenile polyposis syndrome, infantile form;
Polyposis syndrome, hereditary mixed, 2
MUTYH Adenomas, multiple colorectal;
Colorectal adenomatous polyposis, autosomal recessive,
with pilomatricomas; Gastric cancer, somatic
PTEN Glioma susceptibility 2, Meningioma, Macrocephaly/autism syndrome;
Endometrial carcinoma, somatic; Malignant melanoma, somatic;
Squamous cell carcinoma, head and neck, somatic; Prostate cancer, somatic;
VATER association with macrocephaly and ventriculomegaly;
Bannayan-Riley-Ruvalcaba syndrome; Cowden syndrome 1
SMAD4 Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome;
Myhre syndrome; Pancreatic cancer, somatic; Polyposis, juvenile intestinal
STK11 Pancreatic cancer; Peutz-Jeghers syndrome;
Testicular tumor, somatic

Polyposis Syndromes

Published 05/04/2013

Polyposis Syndromes
NGS panel

Genes
(full coding
region):		 APC, BMPR1A, GREM1, MSH3, MUTYH, PTEN, RNF43, SMAD4, STK11

List of diseases covered by the panel
Lab method: NGS panel with CNV analysis
TAT: 6-9 weeks
Specimen requirements: 2-4 ml of blood with anticoagulant EDTA

1 µg DNA in TE, AE or pure sterile water at 100-250 ng/µl
The A260/A280 ratio should be 1.8-2.0. DNA sample should be run on an agarose gel as a single band, showing no degradation, alongside with a quantitative DNA marker.
Ordering information: Go to online ordering or download sample submission form

Del/dup analysis

Genes: BMPR1A, PTEN, SMAD4, STK11
Lab method: MLPA
TAT: 4-6 weeks
Specimen requirements: 2-4 ml of blood with anticoagulant EDTA

2 µg DNA in TE, AE or pure sterile water at 100-250 ng/µl
The A260/A280 ratio should be 1.8-2.0. DNA sample should be run on an agarose gel as a single band, showing no degradation, alongside with a quantitative DNA marker.
Ordering information: Go to online ordering or download sample submission form

Indications for genetic testing:

    1. Confirmation of clinical diagnosis
    2. Testing of individuals with family history of polyposis syndromes
    3. Differentiation of FAP from MUTYH-associated polyposis
    4. Differentiation of juvenile polyposis from other hamartomatous polyposis syndromes
    5. Genetic counseling

Numerous polyposis syndromes may present with gastrointestinal (GI) polyps. Hereditary types include familial adenomatous polyposis and hamartomatous polyposis, and other rare polyposis syndromes. Molecular genetic testing enables differential diagnosis of GI polyposis syndromes often defined with overlapping and indistinguishable phenotypes.

Familial adenomatous polyposis (FAP), MUTYH-associated polyposis, BMPR1A-related juvenile polyposis, SMAD4-related juvenile polyposis, PTEN hamartoma tumor syndrome, and Peutz-Jeghers syndrome are included in the testing.

 

References:

Bronner MP. Gastrointestinal Inherited Polyposis Syndromes. Mod Pathol 2003;16(4):359–365
Jasperson KW, Burt RW. APC-Associated Polyposis Conditions. GeneReviews® 1998 December 18 (Updated 2014 March 27).

MUTYH-associated polyposis genetic testing

Published 24/04/2012

MUTYH-associated Polyposis
Sequencing of the MUTYH gene

Genes
(full coding
region):		 MUTYH
Lab method: Sanger sequencing
TAT: 2-4 weeks
Specimen requirements: 2-4 ml of blood with anticoagulant EDTA

1 µg DNA in TE, AE or pure sterile water at 100-250 ng/µl
The A260/A280 ratio should be 1.8-2.0. DNA sample should be run on an agarose gel as a single band, showing no degradation, alongside with a quantitative DNA marker.
Ordering information: Go to online ordering or download sample submission form

Targeted mutation analysis

Genes: MUTYH
No of
detectable
markers:		 2 (c.536A>G (p.Tyr179Cys); c.1187G>A (p.Gly396Asp))
Lab method: RFLP
TAT: 2-4 weeks
Specimen requirements: 2-4 ml of blood with anticoagulant EDTA

200 ng DNA in TE, AE or pure sterile water at 100-250 ng/µl
The A260/A280 ratio should be 1.8-2.0. DNA sample should be run on an agarose gel as a single band, showing no degradation, alongside with a quantitative DNA marker.
Ordering information: Go to online ordering or download sample submission form

Del/dup analysis

Genes: GREM1, MUTYH, SCG5
Lab method: MLPA
TAT: 4-6 weeks
Specimen requirements: 2-4 ml of blood with anticoagulant EDTA

1 µg DNA in TE, AE or pure sterile water at 100-250 ng/µl
The A260/A280 ratio should be 1.8-2.0. DNA sample should be run on an agarose gel as a single band, showing no degradation, alongside with a quantitative DNA marker.
Ordering information: Go to online ordering or download sample submission form

Indications for genetic testing:

    1. Testing of individuals with clinical symptoms similar to FAP or AFAP but in whom no APC gene mutation has been identified
    2. Testing of first degree relatives of the affected individuals
    3. Genetic counseling

MUTYH-associated polyposis (MAP) is an autosomal recessive disorder characterized by a variable number of colorectal adenomas with a high risk of developing colorectal cancer. MAP is caused by biallelic germline mutations in MUTYH gene, but there is also evidence that monoallelic mutation carriers have an increased risk for developing colorectal cancer. The clinical symptoms of MAP are often undistinguishable from that of familial adenomatous polyposis (FAP) or attenuated FAP (AFAP) caused by mutations in adenomatous polyposis coli (APC) gene, but the age of onset is usually later compared to FAP patients. The two most common mutations in Caucasians, accounting for about 80% of mutant MUTYH alleles, are p.Y179C and p.G396D (also known as Y165C and G382D).