Juvenile polyposis syndrome

Juvenile polyposis syndrome is associated with the development of hamartomatous juvenile polyps in the gastrointestinal tract. Common symptoms include gastrointestinal bleeding, anemia, diarrhea, and abdominal pain. 

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Test Code: 1686 Test Name: SMAD4 specific site analysis TAT 7-14 days Gene: 1
Test Code: 2822 Test Name: BMPR1A specific site analysis TAT 7-14 days Gene: 1
Test Code: 8604 Test Name: BMPR1A & SMAD4 seq and del/dup TAT 14-21 days Genes: 2

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Test Description

BMPR1A and SMAD4 coding exons 1-11 and well into the 5’ and 3’ ends of all the introns and untranslated regions are analyzed by sequencing. Gross deletion/duplication analysis determines gene copy number for coding exons 1-11.Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Genomic deoxyribonucleic acid (gDNA) is isolated from the patient’s specimen using standardized methodology and quantified. Sequence enrichment of the targeted coding exons and adjacent intronic nucleotides is carried out by a bait-capture methodology, using long biotinylated oligonucleotide probes followed by polymerase chain reaction (PCR) and next generation sequencing (NGS). Sanger sequencing is performed for any regions missing or with insufficient read depth coverage for reliable heterozygous variant detection. Reportable small insertions and deletions, potentially homozygous variants, variants in regions complicated by pseudogene interference, and single nucleotide variant calls not satisfying 100x depth of coverage and 40% het ratio thresholds are verified by Sanger sequencing. Gross deletion/duplication analysis of BMPR1A and SMAD4 using read-depth from NGS data is also performed. Any copy number changes detected by NGS are confirmed by multiplex ligation-dependent probe amplification (MLPA) and/or targeted chromosomal microarray.

 

1. Mu W, et al. Sanger confirmation is required to achieve optimal sensitivity and specificity in next-generation sequencing panel testing. J Mol Diagn. 2016. 18(6):923-932.

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