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Test Code ALPSG Autoimmune Lymphoproliferative Syndrome (ALPS) Gene Panel, Varies


Ordering Guidance


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.



Shipping Instructions


Specimen preferred to arrive within 96 hours of collection.



Specimen Required


Patient Preparation: A previous bone marrow transplant from an allogenic donor will interfere with testing. Call 800-533-1710 for instructions for testing patients who have received a bone marrow transplant.

 

Submit only 1 of the following specimens:

 

Specimen Type: Whole blood

Container/Tube:

Preferred: Lavender top (EDTA) or yellow top (ACD)

Acceptable: Any anticoagulant

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send whole blood specimen in original tube. Do not aliquot.

Specimen Stability Information: Ambient (preferred)/Refrigerated

 

Specimen Type: Skin biopsy

Supplies: Fibroblast Biopsy Transport Media (T115)

Container/Tube: Sterile container with any standard cell culture media (eg, minimal essential media, RPMI 1640). The solution should be supplemented with 1% penicillin and streptomycin.

Specimen Volume: 4-mm punch

Specimen Stability Information: Refrigerated (preferred)/Ambient

Additional Information: A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing. An additional 3 to 4 weeks is required to culture fibroblasts before genetic testing can occur.

 

Specimen Type: Cultured fibroblasts

Container/Tube: T-25 flask

Specimen Volume: 2 Flasks

Collection Instructions: Submit confluent cultured fibroblast cells from a skin biopsy from another laboratory. Cultured cells from a prenatal specimen will not be accepted.

Specimen Stability Information: Ambient (preferred)/Refrigerated (<24 hours)

Additional Information: A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing. An additional 3 to 4 weeks is required to culture fibroblasts before genetic testing can occur.


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)

2. Molecular Genetics: Congenital Inherited Diseases Patient Information (T521)

3. Inborn Errors of Immunity, Autoimmunity, and Autoinflammatory Disease Patient Information

Useful For

Providing a comprehensive genetic evaluation for patients with a personal or family history suggestive of autoimmune lymphoproliferative syndrome (ALPS) or related disorders

 

Establishing a diagnosis of ALPS or a related disorder, allowing for appropriate management and surveillance for disease features based on the gene or variant involved

 

Identifying variants within genes known to be associated with ALPS or a related disorder, allowing for predictive testing of at-risk family members

Genetics Test Information

This test utilizes next-generation sequencing to detect single nucleotide and copy number variants in 26 genes associated with autoimmune lymphoproliferative syndrome (ALPS) and ALPS-like disorders: ADA2, CARD11, CASP10, CASP8, CTLA4, DEF6, FADD, FAS, FASLG, IL2RA, IL2RB, ITK, LRBA, MAGT1, PIK3CD, PIK3R1, PRKCD, RASGRP1, SH2D1A, STAT3, STK4, TET2, TNFAIP3, TNFRSF9, TPP2, and XIAP. See Targeted Genes and Methodology Details for Autoimmune Lymphoproliferative Syndrome (ALPS) Gene Panel and Method Description for additional details.

 

Identification of a disease-causing variant may assist with diagnosis, prognosis, clinical management, recurrence risk assessment, familial screening, and genetic counseling for ALPS or an ALPS-like disorder.

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
CULFB Fibroblast Culture for Genetic Test Yes No

Testing Algorithm

For skin biopsy or cultured fibroblast specimens, fibroblast culture will be performed at an additional charge. If viable cells are not obtained, the client will be notified.

Method Name

Sequence Capture and Targeted Next-Generation Sequencing (NGS)

Reporting Name

ALPS Gene Panel

Specimen Type

Varies

Specimen Minimum Volume

Blood: 1 mL; Skin biopsy or cultured fibroblasts: See Specimen Required

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Varies

Reject Due To

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

Clinical Information

Autoimmune lymphoproliferative syndrome (ALPS) is a complex clinical disorder of dysregulated lymphocyte homeostasis characterized by chronic nonmalignant lymphoproliferative disease, splenomegaly, lymphadenopathy, and autoimmunity (mainly autoimmune cytopenias), with an increased susceptibility to lymphomas. Typically, ALPS is diagnosed by childhood or young adulthood. Lymphoproliferation and autoimmunity are usually the first presentations. Lymphomas (Hodgkin and non-Hodgkin) can occur at any age but are usually late complications. ALPS is reported worldwide in various racial and ethnic backgrounds but affects more men than women (approximately 2.2 affected men per 1.6 affected women).

 

Laboratory investigations showed that ALPS patients have an increase in a normally rare population of T cells (typically <1%) that are alpha beta T-cell receptor-positive, as well as negative for both CD4 and CD8 coreceptors (double-negative T cells). In addition, there are elevated peripheral blood interleukin (IL)-10, IL-18, vitamin B12, and soluble FAS ligand (FASL) levels. Defective FAS-mediated apoptosis on in vitro assays is another main characteristic of ALPS.

 

Genetic defects in the apoptosis (programmed cell death) pathway have been determined for most cases of ALPS. Apoptosis plays a role in normal immune homeostasis by limiting lymphocyte accumulation and autoimmune reactivity. The interaction of the surface receptor CD95 (FAS) and its ligand (FASL or CD95L) triggers the apoptotic pathway in lymphocytes. Germline variants in CD95 (FAS) are the most common cause (60%-75%) of ALPS (ALPS-FAS), followed by somatic mutations in CD95 (ALPS-sFAS). Variants in CD95L (ALPS-FASL), CASP10 (ALPS-CAS10), and others are rare causes. Currently, up to 20% of patients do not have an identifiable genetic variant (ALPS-U).

 

All these forms present with the main clinical features of ALPS, but there are differences in the results of laboratory tests used to evaluate ALPS patients. Genotype-phenotype correlations are noted in ALPS-FAS, which is the only form common enough for these studies. Both mono- and bi-allelic variants in FAS can cause disease. Dominant negative, haploinsufficient mechanisms are invoked to explain the disease mechanism. It appears that biallelic disease-causing FAS variants cause a more severe clinical phenotype than the monoallelic forms. Lymphomas are mostly associated with disease-causing variants in the intracellular domain of FAS. Penetrance of the clinical phenotype is reduced and varies based on the location and type of causative variant (30%-90%).

 

The latest diagnostic criteria for ALPS were published in 2010.(1) A definitive diagnosis is based on the presence of both required criteria and one primary accessory criterion. A probable diagnosis is based on the presence of both required criteria plus one secondary accessory criterion.

 

Several other diseases can present with an ALPS-like phenotype, including other inborn errors of immunity, like CTLA4 deficiency (also known as CTLA4 haploinsufficiency or CTLA4 haploinsufficiency with autoimmune infiltration [CHAI]) and LRBA (lipopolysaccharide-responsive and beige-like anchor protein) deficiency, gain-of-function variants in STAT3 and CARD11 genes, as well as conditions like Evans syndrome (a combination of autoimmune hemolytic anemia and autoimmune thrombocytopenic purpura) and malignant conditions like Hodgkin disease and large granular lymphocyte leukemias. Genes associated with several ALPS-like disorders are also included on this panel.

Reference Values

An interpretive report will be provided.

Interpretation

All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(2) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Day(s) Performed

Varies

Report Available

28 to 42 days

Specimen Retention Time

Whole blood: 2 weeks (if available); Extracted DNA: 3 months; Cultured fibroblasts, skin biopsy: 1 month

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information

81443

88233-Tissue culture, skin, solid tissue biopsy (if appropriate)

88240-Cryopreservation (if appropriate)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
ALPSG ALPS Gene Panel 103743-1

 

Result ID Test Result Name Result LOINC Value
619747 Test Description 62364-5
619748 Specimen 31208-2
619749 Source 31208-2
619750 Result Summary 50397-9
619751 Result 82939-0
619752 Interpretation 69047-9
619753 Additional Results 82939-0
619754 Resources 99622-3
619755 Additional Information 48767-8
619756 Method 85069-3
619757 Genes Analyzed 82939-0
619758 Disclaimer 62364-5
619759 Released By 18771-6