Peutz-Jeghers Syndrome via the STK11 Gene
- Summary and Pricing
- Clinical Features and Genetics
|Test Code||Test||Individual Gene Price||CPT Code Copy CPT Codes|
For ordering targeted known variants, please proceed to our Targeted Variants landing page.
The great majority of tests are completed within 18 days.
|Test Code||Test||Individual Gene Price||CPT Code Copy CPT Codes|
The great majority of tests are completed within 20 days.
Indications for Test
|Official Gene Symbol||OMIM ID|
- Genetic Counselor Team - firstname.lastname@example.org
- Jerry Machado, PhD, DABMG, FCCMG - email@example.com
- Amos et al. GeneReviews. 2011
- Hearle, N., et.al. (2006). "Frequency and spectrum of cancers in the Peutz-Jeghers syndrome." Clin Cancer Res 12(10): 3209-3215. PubMed ID: 16707622
- Human Gene Mutation Database.
- Lim W, Hearle N, Shah B, Murday V, Hodgson SV, Lucassen A, Eccles D, Talbot I, Neale K, Lim AG, O’Donohue J, Donaldson A, et al. 2003. Further observations on LKB1/STK11 status and cancer risk in Peutz–Jeghers syndrome. British Journal of Cancer 89: 308–313. PubMed ID: 12865922
- Tiainen M, Ylikorkala A, Mäkelä TP. 1999. Growth suppression by Lkb1 is mediated by a G1 cell cycle arrest. Proceedings of the National Academy of Sciences 96: 9248–9251. PubMed ID: 10430928
Bi-Directional Sanger Sequencing
Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org). As required, DNA is extracted from the patient specimen. PCR is used to amplify the indicated exons plus additional flanking non-coding sequence. After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit. Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer. In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions. In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.
As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.
Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).
In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.
Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.
In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.
In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.
Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.
Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.
Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.
Multiplex Ligation-Dependent Probe Amplification Assay
As required, genomic DNA (gDNA) is extracted from the patient specimen. gDNA extracted from blood samples/submitted DNA from the patient is denatured and hybridized to MLPA probes specific to exonic or intronic regions of a particular gene(s). Each probe consists of two adjacent sequences that once hybridized to patient/reference DNA are ligated into a single probe. Fluorescently labeled PCR is then used to amplify each ligated probe using a common PCR primer set. The amplicon is then visualized during fragment separation using a capillary electrophoresis instrument. The relative peak height of each amplified probe from the patient’s sample is compared to four internal negative control results to determine relative copy number. For each patient sample the data for only the gene(s) of interest is analyzed and reported.
MLPA enables the detection of relatively small deletion and amplification mutations within a single exon of a given gene or deletion and amplification mutations encompassing the entire gene. PreventionGenetics has established and verified this test’s accuracy and precision.
Interpretation of the test results is limited by the information that is currently available. Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.
Only the indicated gene or genes were analyzed. Test reports contain no information about other regions of the genome, including genes that are not requested, and genes that are not targeted. This test does not provide any information about deletions or duplications within repetitive elements.
Balanced translocations or inversions within a targeted gene, or large unbalanced translocations or inversions that extend beyond the genomic location of a targeted gene are not detected.
We cannot determine if the duplicated segment is inserted in tandem within the gene or inserted elsewhere in the genome. Similarly, we cannot determine the orientation of the duplicated segment (direct or inverted), and whether it will disrupt the open reading frame of the given gene.
For a single probe deletion or duplication we will compare MLPA results to sequencing results to ensure that no single nucleotide polymorphisms are underlying the specific probe, which may affect probe hybridization.
Any partial exonic deletions and duplications outside the probe binding sequence cannot be detected.
Impurities in the test and reference DNA samples can increase the chance of false positive or negative results. Where possible similar DNA extraction methods between test and reference samples are ideal for relative copy number analysis.
Our ability to detect minor copy number change, due for example to somatic mosaicism may be limited.
Unless otherwise indicated, MLPA results are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about copy number changes in other tissues.
We cannot be certain that the reference sequence(s) are correct. Exons, for example, may be misidentified.
We have confidence in our ability to track a specimen once it has been received by PreventionGenetics. However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.
Normal findings within a targeted gene do not rule out the clinical diagnosis of a genetic disease.
Genetic counseling to help explain test results to the patients and to discuss reproductive or medical options is recommended.
myPrevent - Online Ordering
- The test can be added to your online orders in the Summary and Pricing section.
- Once the test has been added log in to myPrevent to fill out an online requisition form.
- The first four pages of the requisition form must accompany all specimens.
- Billing information is on the third and fourth pages.
- Specimen and shipping instructions are listed on the fifth and sixth pages.
- All testing must be ordered by a qualified healthcare provider.
(Delivery accepted Monday - Saturday)
- Collect 3-5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10-20 ml of whole blood.
- For small babies, we require a minimum of 1 ml of blood.
- Only one blood tube is required for multiple tests.
- Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
- During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
- In cold weather, include an unfrozen ice pack in the shipping container as insulation.
- At room temperature, blood specimen is good for up to 48 hours.
- If refrigerated, blood specimen is good for up to one week.
- Label the tube with the patient name, date of birth and/or ID number.
(Delivery accepted Monday - Saturday)
- NextGen Sequencing Tests: Send in screw cap tube at least 10 µg of purified DNA at a concentration of at least 50 µg/ml
- Sanger Sequencing Tests: Send in a screw cap tube at least 15 µg of purified DNA at a concentration of at least 20 µg/ml. For tests involving the sequencing of more than three genes, send an additional 5 µg DNA per gene. DNA may be shipped at room temperature.
- Deletion/Duplication via aCGH: Send in screw cap tube at least 1 µg of purified DNA at a concentration of at least 100 µg/ml.
- Whole-Genome Chromosomal Microarray: Collect at least 5 µg of DNA in TE (10 mM Tris-cl pH 8.0, 1mM EDTA), dissolved in 200 µl at a concentration of at least 100 ng/ul (indicate concentration on tube label). DNA extracted using a column-based method (Qiagen) or bead-based technology is preferred.
(Delivery accepted Monday - Thursday)
- PreventionGenetics should be notified in advance of arrival of a cell culture.
- Ship at least two T25 flasks of confluent cells.
- Label the flasks with the patient name, date of birth, and/or ID number.
- We do not culture cells.