PlainSEEK Panel Print

WSLH Department: Cytogenetics
WSLH Test Code: 895M47
Availability: Monday-Friday 7:45 AM - 4:30 PM, Saturday 7:45 AM - 12:00 PM
Turn-around Time: Approximately 28 days
Recommended Uses: This assay was developed for the Plain (Amish and Mennonite) populations of Wisconsin and surrounding states.
Additional Tests Performed:
Patient Preparations:
Specimen Requirements: Peripheral Blood: 3 ml - 5 ml peripheral blood in EDTA

Dried Blood Spots: Two completely filled spots collected on FTA cards

DNA: 500 ng - 1000 ng of purified DNA from a CLIA-certified laboratory
Specimen Handling & Transport: Store and transport specimens at room temperature (may transport with coolant during hot, >85 degrees Fahrenheit weather). DO NOT FREEZE blood. It is recommended that the laboratory receive the specimen within 48 hours of collection.
Collection Kit/Container:
Collection Instructions:
Unacceptable Conditions: Blood that is clotted or hemolyzed is not acceptable. Blood must not be frozen. Plasma and serum are not acceptable.
Requisition Form: Cytogenetics Lab Genetic Diagnosis Form #131
Required Information: Laboratory regulations require the following minimum information to be provided on the requisition form for a specimen to be accepted for testing: Patient name or unique identifier; date and time of collection, patient date of birth and sex, specimen type/site of collection, test request(s), reason for referral, clinician name and UPIN/NPI, and address for reporting results. Please be certain that name/identifier on the form matches that on the specimen label.
Results Include:
Limitations: This assay is designed to detect specified variants in select genes only, and is not intended to discover additional disease-associated variants within these genes. Variants may be present below the limit of detection. Copy number variants and low-level mosaic variants may not be detected. Rare diagnostic errors may occur due to primer site mutations.
Additional Tests Recommended:
Additional Comments:
Methodology: Next-Generation Sequencing (NGS), with additional Sanger sequencing as necessary, is performed on isolated genomic DNA extracted from patient specimens. For NGS, custom polymerase chain reaction (PCR) primers (PlexSeq Diagnostics, Cleveland, OH) amplify target genomic regions of interest. Amplified PCR products are sequenced on the MiSeq System (Illumina, San Diego, CA) using 1x100 bp single-end sequencing. A custom bioinformatics analysis pipeline is used to compare sequence changes (variants) to the reference sequence. For Sanger sequencing, custom PCR primers amplify target regions and cycle sequencing is carried out using the Big Dye Terminator v.3.1 kit (Applied Biosystems, Bedford, MA). PCR products are resolved by electrophoresis on the 3500xl Genetic Analyzer (Applied Biosystems, Bedford, MA). DNA sequences are aligned and compared to reference gene sequences based on human genome build GRCh37/hg19.

NGS variant annotation and sorting is performed using NxClinical software (BioDiscovery, El Segundo, CA). Sanger sequences are analyzed using Mutation Surveyor software (Soft Genetics, State College, PA). Nomenclature for sequence variants comes from the HUGO Gene Nomenclature Society (HGNC; and the Human Genome Variation Society (HGVS; Each variant has been evaluated for pathogenicity according to the American College of Medical Genetics and Genomics (ACMG) guidelines for the interpretation of sequence variants (PMID: 25741868).
Includes: The PlainSEEK Panel (v1.0) provides sequencing coverage of 157 specified variants in 124 genes. A comprehensive variant list can be found on our laboratory's website
CPT Code: 81479
Price: For pricing information, please call 608-262-0402.
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