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Test Code PCMSP Postmortem Inherited Congenital Myasthenia Syndrome Gene Panel, Tissue


Ordering Guidance


This test is intended for use when whole blood is not available, and formalin-fixed, paraffin-embedded (FFPE) tissue is the only available specimen. If whole blood is available, consider CMSP / Inherited Congenital Myasthenic Syndrome Gene Panel, Varies.

 

Targeted testing for familial variants (also called site-specific or known variants testing) is available for the genes on this panel. See FMTT / Familial Variant, Targeted Testing, Varies. To obtain more information about this testing option, call 800-533-1710.



Specimen Required


Specimen Type: Tissue block

Collection Instructions: Submit a formalin-fixed, paraffin-embedded tissue block

Additional Information: Testing will be attempted on blocks of any age but may be canceled if adequate DNA concentration cannot be obtained.


Forms

1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file. The following documents are available:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing (Spanish) (T826)

-Informed Consent for Genetic Testing for Deceased Individuals (T782)

2. Molecular Genetics: Neurology Patient Information

Secondary ID

620638

Useful For

Identifying variants within genes known to be associated with congenital myasthenic syndrome, allowing for predictive testing of at-risk family members

 

Providing a comprehensive postmortem genetic evaluation in the setting of a congenital myasthenic syndrome

 

Identifying a disease-causing variant in the decedent, which may assist with risk assessment and predictive testing of at-risk family members

Method Name

Sequence Capture and Targeted Next-Generation Sequencing (NGS)

Specimen Type

Varies

Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)
  Refrigerated 

Reject Due To

All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.

Reference Values

An interpretive report will be provided.

Interpretation

All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(3) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Method Description

Next-generation sequencing (NGS) is performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known disease-causing variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least 99% of the bases are covered at a read depth over 20X. Sensitivity is estimated at above 99% for single nucleotide variants and above 94% for deletions-insertions (delins) less than 40 base pairs.

 

There may be regions of genes that cannot be effectively evaluated by sequencing as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. Confirmation of NGS results by Sanger sequencing is typically not performed for this test.(Unpublished Mayo method)

 

Genes analyzed: AGRN, ALG14, ALG2, CHAT, CHRNA1, CHRNB1, CHRND, CHRNE, COL13A1, COLQ, DNM2, DOK7, DPAGT1, GAA, GFPT1, GMPPB, LAMB2, LRP4, MUSK, PLEC, PREPL, RAPSN, SCN4A, SLC18A3, SLC25A1, SLC5A7, SYT2, and VAMP1

Day(s) Performed

Varies

Report Available

28 to 42 days

Specimen Retention Time

FFPE tissue block: Client provided paraffin blocks (FFPE) will be returned to client after testing is complete; Extracted DNA: 3 months

Performing Laboratory

Mayo Clinic Laboratories in Rochester

CPT Code Information

81443

LOINC Code Information

Test ID Test Order Name Order LOINC Value
PCMSP Postmortem Myasthenia Panel In Process

 

Result ID Test Result Name Result LOINC Value
620639 Test Description 62364-5
620640 Specimen 31208-2
620641 Source 31208-2
620642 Result Summary 50397-9
620643 Result 82939-0
620644 Interpretation 69047-9
620645 Additional Results 82939-0
620646 Resources 99622-3
620647 Additional Information 48767-8
620648 Method 85069-3
620649 Genes Analyzed 82939-0
620650 Disclaimer 62364-5
620651 Released By 18771-6