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Test Code MTRTI MatePair, Targeted Rearrangements, Oncology

Secondary ID

64936

Useful For

Second-tier testing in oncologic specimens when previous cytogenetic testing has detected an acquired chromosome abnormality of unknown significance

 

Determining the size, precise breakpoints, gene content, and any unappreciated complexity of abnormalities detected by other methods such as conventional chromosome and FISH studies

 

Providing important diagnostic, prognostic, and therapeutic information critical to proper patient management

Method Name

Mate-Pair Whole Genome Sequencing

Reporting Name

MatePair, Targeted, Oncology

Specimen Type

Tissue


Shipping Instructions


Advise Express Mail or equivalent if not on courier service.



Necessary Information


1. Previous cytogenetic or FISH testing is required in order to perform this test. If previous testing was performed at another institution, supply a copy of those results. If sufficient information regarding the patient's known chromosome abnormality is not made available, this testing will be cancelled.

2. Provide a reason for referral with each specimen. The laboratory will not reject testing if this information is not provided, but appropriate testing and interpretation may be compromised or delayed.

3. Specimens that are submitted as cultured cells or cryo-frozen samples will need confirmation of abnormal karyotype with the specimen submitted to ensure that the abnormality is present before proceeding.



Specimen Required


Submit only 1 of the following specimens:

 

Supplies: Hank's Solution (T132)

Specimen Type: Tumor biopsy

Container/Tube: Sterile container with sterile Hank's balanced salt solution (T132), Ringer's solution, or normal saline

Specimen Volume: 0.5-3 cm(3) or larger

 

Supplies: Hank's Solution (T132)

Specimen Type: Lymph node

Container/Tube: Sterile container with sterile Hank's balanced salt solution (T132), Ringer's solution, or normal saline.

Specimen Volume: 1 cm(3)

 

Supplies: Hank's Solution (T132)

Specimen Type: Skin biopsy

Container/Tube: Sterile container with sterile Hank's balanced salt solution (T132), Ringer's solution, or normal saline.

Specimen Volume: 4-mm diameter

Collection Instructions:

1. Wash biopsy site with an antiseptic soap.

2. Thoroughly rinse area with sterile water.

3. Do not use alcohol or iodine preparations.

4. A local anesthetic may be used.

5. Biopsy specimens are best taken by punch biopsy to include full thickness of dermis.

 

Specimen Type: Snap Frozen tissue

Container/Tube: Polycon flat

Specimen Volume: 3 cm(3)/Lymph Node: 1 cm(3)/Skin Biopsy: 4 mm diameter

 

Specimen Type: Cultured tumor cells

Container/Tube: T-25 flask filled with transport media

Specimen Volume: T-25 flask

 

Specimen Type: Cryo-frozen cultured tumor cells

Container/Tube: Sterile container in media with DMSO or other safe cryopreservation solution

Specimen Volume: 5 million cells

 

Specimen Type: Cryo-Frozen tissue

Container/Tube: Polycon flat

Specimen Volume: 3 cm(3)/Lymph Node: 1 cm(3)/Skin Biopsy: 4-mm diameter


Specimen Minimum Volume

Tumor Biopsy: 3 cm(3); Lymph Node: 1 cm(3); Skin Biopsy: 4-mm diameter; Cultured tumor cells: T-25 flask; Cryo-frozen cultured tumor cells: 5 million cells

Specimen Stability Information

Specimen Type Temperature Time
Tissue Varies

Reject Due To

No specimen should be rejected.

Clinical Information

While many tumors have a subset of common or well-characterized acquired chromosome abnormalities, some tumors may be found to have acquired chromosome abnormalities of uncertain significance. Further characterization of these abnormalities may lead to a better understanding of their pathogenicity and potentially lead to prognostic information or guide treatment/management of the patient.

 

Mate-pair sequencing is a next-generation sequencing technology that can aid in the further characterization of chromosome abnormalities by sequencing the entire genome and bioinformatically mapping short fragments of the genome to create a structural map of the genome. This technique enables the mapping of chromosome rearrangements to a resolution of approximately 2 kilobases or less, which allows for determination of genes at/near the breakpoints.

Reference Values

An interpretive report will be provided.

Interpretation

The interpretation describes the further characterization of the previously identified acquired abnormality. When possible, the interpretation will state how this finding might be associated with the neoplastic process and any potential information on diagnosis, prognosis, and/or treatment options given the finding.

 

The continual discovery of novel structural rearrangements and published clinical reports means that the interpretation of any finding may evolve with increased scientific understanding.

 

Although the presence of a clonal abnormality usually indicates a neoplasia, in some situations it may reflect a benign or constitutional genetic change. If a genetic change is identified that is likely constitutional and clearly pathogenic, follow-up with a medical genetics consultation may be suggested.

 

The absence of an abnormal clone may be the result of specimen collection from a site that is not involved in the neoplasm, or may indicate that the genetic abnormality is not detectable by this assay.

Clinical Reference

1. Vergult S, Van Binsbergen E, Sante T, et al: Mate pari sequencing for the detection of chromosomal aberrations in patients with intellectual disability and congenital malformations. Eur J Hum Genet. 2014 May;22(5):652-659

2. Fonseca A, Bonaldi A, Fonseca S, et al: The segregation of different submicroscopic imbalances underlying the clinical variability associates with familial karyotypically balanced translocation. Mol Cytogenet. 2015 Dec 30;8:106

Day(s) and Time(s) Performed

Samples processed Monday through Friday. Results reported Monday through Friday, 8 a.m.-5 p.m.

Analytic Time

14 days

Performing Laboratory

Mayo Medical Laboratories in Rochester

Test Classification

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

CPT Code Information

0013U

 

LOINC Code Information

Test ID Test Order Name Order LOINC Value
MTRTI MatePair, Targeted, Oncology In Process

 

Result ID Test Result Name Result LOINC Value
48023 Result Summary 50397-9
48326 Result In Process
48024 Nomenclature In Process
48025 Interpretation In Process
CG988 Reason for Referral 42349-1
CG986 Specimen 31208-2
48028 Source 31208-2
48029 Method 49549-9
48030 Additional Information 48767-8
48032 Released By In Process

Forms

1. New York Clients-Informed consent is required. Please document on the request form or electronic order that a copy is on file. An Informed Consent for Genetic Testing (T576) is available in Special Instructions.

2. If not ordering electronically, complete, print, and send an Oncology Test Request Form (T729) with the specimen (http://www.mayomedicallaboratories.com/it-mmfiles/oncology-request-form.pdf)