Alberta Precision Laboratories

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Organization:

Alberta Precision Laboratories

Message Alert:

PLEASE NOTE: This Test Directory is in an interim state and due to changes pertaining to the DynaLIFE transition, performing site for routing has not been updated. Please refer to Laboratory Information System for appropriate routing.

Test Name/Synonym:

Lynch Syndrome Cancer Panel (Synonyms: LYNCH, MLH1, MSH2, MSH6, PMS2, EPCAM, Inherited Cancer and Endocrine Gene Panel, Constitutional Mismatch Repair)

Test Includes:

Genes: MLH1, MSH2, MSH6, PMS2, EPCAM

Ordering Alert:

Ordering is Restricted to:

Confirmation of Diagnosis¹

Clinical Genetics and
Oncology clinicians who have had mainstreaming orientation from Hereditary Cancer Clinic Hub

Presymptomatic Testing² Clinical Genetics

¹patient has signs or symptoms of the disease/disorder
²patient does not presently have symptoms, positive family history of the condition

Collection Alert:

Unopened dedicated tubes (do not share) are required for Molecular Genetics testing.

LABID (Connect Care):

LAB2599

Test Code:

CALGARY ZONE	MDLBL; IN MDL TEST NAME PROMPT ENTER HERED CANCER
CENTRAL ZONE	HCA
EDMONTON ZONE	HCA
NORTH ZONE	DNAM
OTHER ZONES	NOT SPECIFIED

Specimen Type:

Blood, Swab, Urine, Tissue, DNA, Amniotic Fluid, Other

Specimen Source:

Indicate a specimen source.

Primary Container:

Lavender top EDTA

Alternate Containers:

Microcollection EDTA
Sterile polypropylene centrifuge tube
DNA tube
Sterile container
Sterile urine container

Minimum Collection Volume:

See Specimen Collection Requirements

Specimen Collection Requirements:

For Blood Specimen (peripheral or cord blood)
EDTA tubes should be completely full, 2/3 full at minimum, testing may be affected by partial draw

For Patients over 20 kg: 2 EDTA tubes each containing 3.0 mL of blood
For Patients up to 20 kg: 2 EDTA tubes each containing 2.0 mL of blood
For Neonates: 1 EDTA containing a minimum of 0.5 mL of blood

For Postnatal (cord blood)

A maternal blood sample must be collected for maternal cell contamination studies.

For Prenatal Specimens (chorionic villi or amniotic fluid)

For Chorionic Villi specimens: 15 mg
For Amniotic Fluid specimens: 25 mL
Submit in a sterile polypropylene centrifuge tube or in a plain sterile tube with screw cap.
A maternal blood sample must be collected for maternal cell contamination studies.

For Other Tissue Specimens

For Fresh or Frozen Tissue specimens: Submit a minimum of 20 mg in a sterile container with NO fixative.
For Cultured Cells (for Molecular Genetics South only): Confluent (overgrown) T25 flask (or equivalent) placed in transport media.

For Extracted DNA

Submit 10ug @ >100ng/uL.

For Buccal Swab Specimens

Collect 4 buccal brushes.

For Pleural Fluid Specimen

Will attempt DNA extraction on any amount received
Submit in a sterile container with screw cap.

For Urine Specimens

Collect first morning urine (NOT mid stream).
Submit 50 to 100 mL in a sterile urine container.
Note: Can submit from multiple collections throughout the day if patient catheterized or unable to provide in a single collection.

Test Resources:

Pre-test Counselling Information-Genetic and GenomicTesting

Lynch Syndrome NGS Panel Information Sheet

Submit requests using requisition or Connect Care online order entry:

Molecular Genetics Cancer and Endocrine Next Generation Sequencing Requisition

Please ensure all required information, including patient's clinical history/indication, is provided on the requisition.

Stability and Storage:

Room temperature: For all specimen types (except frozen tissue) if being shipped on same day of collection (preferred).
Refrigerated: If shipping is delayed.
Frozen: Frozen tissue specimens at -20^oC to -80^oC.

Processing:

Do not centrifuge or aliquot specimens.

Transportation:

Transport all specimen types (except frozen tissue) at room temperature.
Specimens must not freeze in transit.

Transport frozen tissue specimens with adequate amounts of dry ice to keep specimen frozen.
Specimens must not thaw in transport.

Specimens, should be received by the Molecular Genetics Laboratory:

Within 5 days of date of collection for Blood and Extracted DNA specimens.
Within 24 hours of date of collection for Amniotic Fluid, Chorionic Villi and Tissue specimen types.
And must include the original paper requisition and accompanying documentation

Submitting to Molecular Genetics North
Transport specimens (except extracted DNA) to Molecular Genetics Laboratory via UAH Specimen Control WMC 4B2.10.
For Extracted DNA samples only, transport specimens to Molecular Genetics Laboratory via UAH Shipping Receiving, UNIVERSITY OF ALBERTA HOSPITAL, 8440 112 STREET, Room: 8-26 MSB, EDMONTON, T6G 2B7

Blood, Amniotic Fluid, Tissue, Buccal Swab, Pleural fluid, Urine and Extracted DNA specimens

Are received Mon – Fri: 07:30 to 15:00.
If received after 15:00, will be processed on the next working day.

Chorionic Villi specimens

Are received Mon – Thurs: 07:30 to 15:00.
Cannot be received on Fridays.

If Amnio and CVS specimens are sent from outside of Edmonton for testing in Molecular Genetics North, please call the laboratory at 780-407-1542 or fax shipping information to 780-407-3059 to inform the lab of expected arrival times and mode of transport.
If Tissue specimens are sent from outside of Edmonton for testing in Molecular Genetics North, please call the laboratory at 780-407-1434 or fax shipping information to 780-407-1761 to inform the lab of expected arrival times and mode of transport.

Submitting to Molecular Genetics South
Transport specimens to Molecular Genetics Laboratory at Alberta Children’s Hospital Room B0-020.

Method:

Next Generation Sequencing
For PMS2 - MLPA (if clinically indicated)

Method and Interpretation of Results:

Genomic DNA is analyzed using next generation sequencing technology (NGS). NGS detects nucleotide substitutions, small insertions and deletions, and copy number variants. If a variant is clinically relevant or of uncertain significance and does not meet our validated analytic requirements it is confirmed by an appropriate molecular method. Sanger sequencing is used to analyze regions which do not meet requirements for depth of sequence coverage.

MLH1, MSH2, MSH6, PMS2 (exons 1-10 only) by NGS: Genomic DNA is sequenced on a NGS instrument. Sanger sequencing is used to confirm all variants with clinical or uncertain significance and to analyze regions with <90% technical sensitivity by NGS.

EPCAM ( exon copy number only)

PMS2 by MLPA: Detects deletions and duplications. Copy number analysis by MLPA is completed on exons 11-15 only if clinically indicated. i.e. IHC results.

Routine Turn Around Time:

Routine: up to 16 weeks, Stat: 4 weeks

Reference Interval:

Interpretation provided on report.

Testing Area:

Molecular Genetics

Performing Site:

University of Alberta Hospital or Alberta Children’s Hospital

Additional Test Information:

To obtain buccal swab collection kits, contact:

Molecular Genetics North	Molecular Genetics South
780-407-1434	403-955-3097

Contact Comments:

For additional information refer to Genetics and Genomics webpage or contact:

Molecular Genetics North	Molecular Genetics South
780-407-1434 (phone) 780-407-1761 (fax)	403-955-3097 (phone) 403-955-7624 (fax)

Last Updated On:

Monday, August 29, 2022

Date of Last Review:

Aug 1 2022 12:00AM