Test Catalog

Test Id : BAKDM

BCR/ABL1, Tyrosine Kinase Inhibitor Resistance, Kinase Domain Mutation Screen, Sanger Sequencing, Varies

Useful For
Suggests clinical disorders or settings where the test may be helpful

Evaluating patients with chronic myelogenous leukemia and Philadelphia chromosome positive B-cell acute lymphoblastic leukemia receiving tyrosine kinase inhibitor (TKI) therapy, who are apparently failing treatment

 

Preferred initial test to identify the presence of acquired BCR-ABL1 mutations associated with TKI-resistance

Reflex Tests
Lists tests that may or may not be performed, at an additional charge, depending on the result and interpretation of the initial tests.

Test Id Reporting Name Available Separately Always Performed
BADX BCR/ABL1, RNA-Qual, Diagnostic Yes No

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

If BCR/ABL1 fusion type (p210, p190, p205 or p230) is not provided, BADX / BCR/ABL1, Qualitative, Diagnostic Assay, Varies will be performed at an additional charge.

 

In the event that no fusion form (p190, p205, p210, p230) is identified by qualitative testing, this test will be canceled.

 

For more information see BCR/ABL1 Ordering Guide for Blood and Bone Marrow.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Name
A short description of the method used to perform the test

Reverse Transcription-Polymerase Chain Reaction (RT-PCR) with Sanger Sequencing

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

BCR/ABL1 Mutation, Sequencing

Aliases
Lists additional common names for a test, as an aid in searching

E255K

E355G

F317L

F369V

G250E

H396R

M244V

M351T

Q252H

T315I

Y253F

Y253H

T315A

V299L

Tyrosine kinase inhibitor (TKI)

Kinase domain mutation, ABL

Imatinib resistance

Chronic myeloid leukemia

Chronic myelogenous leukemia (CML)

BCR-ABL1

BCR/ABL

BCR ABL

Acute lymphoblastic leukemia (ALL)

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

If BCR/ABL1 fusion type (p210, p190, p205 or p230) is not provided, BADX / BCR/ABL1, Qualitative, Diagnostic Assay, Varies will be performed at an additional charge.

 

In the event that no fusion form (p190, p205, p210, p230) is identified by qualitative testing, this test will be canceled.

 

For more information see BCR/ABL1 Ordering Guide for Blood and Bone Marrow.

Specimen Type
Describes the specimen type validated for testing

Varies

Ordering Guidance

This is the preferred initial test to identify the presence of acquired BCR/ABL1 mutations associated with tyrosine kinase inhibitor (TKI)-resistance.

Shipping Instructions

1. Refrigerated specimens must arrive within 5 days of collection, and ambient specimens must arrive within 3 days (72 hours) of collection.

2. Draw and package specimen as close to shipping time as possible.

Necessary Information

The following information is required:

1. Patient's fusion type (p210, p190, p205 or p230)

2. Pertinent clinical history

3. Clinical or morphologic suspicion

4. Date of collection

5. Specimen source (blood or bone marrow)

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

Submit only 1 of the following specimens:

 

Preferred:

Specimen Type: Whole blood

Container/Tube: Lavender top (EDTA)

Specimen Volume: 10 mL

Collection Instructions:

1. Invert several times to mix blood.

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

3. Label specimen as blood.

 

Acceptable:

Specimen Type: Bone marrow

Container/Tube: Lavender top (EDTA)

Specimen Volume: 4 mL

Collection Instructions:

1. Invert several times to mix bone marrow.

2. Send bone marrow specimen in original tube. Do not aliquot.

3. Label specimen as bone marrow.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Forms

1. Hematopathology Patient Information (T676)

2. If not ordering electronically, complete, print, and send a Hematopathology/Cytogenetics Test Request (T726) with the specimen.

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

Blood: 8 mL

Bone Marrow: 2 mL

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

Gross hemolysis Reject
Other Moderately to severely clotted

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

Specimen Type Temperature Time Special Container
Varies Refrigerated (preferred) 5 days PURPLE OR PINK TOP/EDTA
Ambient 72 hours PURPLE OR PINK TOP/EDTA

Useful For
Suggests clinical disorders or settings where the test may be helpful

Evaluating patients with chronic myelogenous leukemia and Philadelphia chromosome positive B-cell acute lymphoblastic leukemia receiving tyrosine kinase inhibitor (TKI) therapy, who are apparently failing treatment

 

Preferred initial test to identify the presence of acquired BCR-ABL1 mutations associated with TKI-resistance

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

If BCR/ABL1 fusion type (p210, p190, p205 or p230) is not provided, BADX / BCR/ABL1, Qualitative, Diagnostic Assay, Varies will be performed at an additional charge.

 

In the event that no fusion form (p190, p205, p210, p230) is identified by qualitative testing, this test will be canceled.

 

For more information see BCR/ABL1 Ordering Guide for Blood and Bone Marrow.

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Chronic myeloid leukemia (CML) is characterized by the presence of the t(9:22) BCR/ABL1 abnormality, resulting in formation of a fusion BCR/ABL1 messenger RNA (mRNA) and protein. The ABL1 component of this oncoprotein contains tyrosine kinase activity and is thought to play a central role in the proliferative phenotype of this leukemia.

 

Recent advances have resulted in a number of therapeutic drugs that inhibit the ABL1 tyrosine kinase, as well as other protein tyrosine kinases. Imatinib mesylate (Gleevec, Novartis) is the prototype of these tyrosine kinase inhibitors (TKI), which are capable of inducing durable hematologic and (in most patients) cytogenetic remissions. Unfortunately, a significant subset of patients can develop functional resistance to TKI, due in a large number of cases (approximately 50%) to the acquisition of point mutations in the kinase domain (KD) of the chimeric ABL1 gene. To date, over 50 distinct mutations have been described, although a smaller subset of these (<20) account for the majority of patients with clinical resistance to TKI, or have well documented in vitro data in the published literature.

 

Recognition of TKI resistance is important in CML, as the effect of some mutations can be overcome by increasing imatinib dosage, whereas others require switching to either a different (second-generation) TKI, or alternative therapy. The common T315I KD mutation is particularly important, given that this alteration confers pan-resistance to all currently employed TKI except ponatinib. Typically, TKI resistance is suspected in a CML patient who shows loss of initial therapeutic response (eg, cytogenetic relapse), or a significant and sustained increase in molecular BCR/ABL1 quantitative levels. Similar considerations are also present in patients with Philadelphia chromosome positive B-cell acute lymphoblastic leukemia, who can also be treated using TKI therapy.

 

Point mutations in the oncogenic BCR/ABL1 are typically detected by direct sequencing of polymerase chain reaction (PCR) products, following reverse transcription PCR (RT-PCR) amplification of the BCR/ABL mRNA transcript from a peripheral blood specimen. This approach ensures comprehensive screening of the clinically relevant KD region. Because this technique requires inclusion of a longer region of ABL1 in the BCR/ABL1 RT-PCR product, low levels of the BCR/ABL1 mRNA transcript (below 0.01% normalized BCR/ABL1 on the International Scale: IS) may not be efficiently amplified (in contrast to similar amplicons generated by quantitative RT-PCR for diagnosis or monitoring).

Reference Values
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretive report will be provided.

Interpretation
Provides information to assist in interpretation of the test results

The presence of one or more point mutations in the translocated portion of the ABL1 region of the BCR/ABL1 fusion messenger RNA is considered a positive result, indicating tyrosine kinase inhibitor (TKI) resistance. The specific type of mutation may influence the sensitivity to a specific TKI and could be useful in guiding therapeutic options for an individual patient.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

This assay is comprehensive for detecting BCR/ABL1 kinase domain (KD) mutations but does not detect all possible mutations in ABL1; therefore, a negative result by this assay does not exclude the presence of a rare, less-well characterized, or unknown mutation that could be associated with some degree of tyrosine kinase inhibitor resistance. The clinical significance of such rarely occurring mutations is, however, uncertain.

 

The quantitative level of BCR/ABL1 transcript is critical for a successful assay mutation analysis because the amplification efficiency for a longer messenger RNA (mRNA) template is decreased with a low abundance of target. If the BCR/ABL1 quantitative polymerase chain reaction (PCR) level is too low, reverse transcription-PCR amplification of BCR/ABL1 may be unsuccessful to yield product for sequencing. Although laboratory standards are yet to be developed, a BCR-ABL1/ABL1 quantitative level above 0.1% is generally considered to be required to detect KD mutations by this assay.

 

Subclonal mutations may be difficult to identify by Sanger sequencing method, even if the BCR/ABL1 mRNA amplification was successful. This is due to the inherit sensitivity level limit of sequencing, which is typically around 15% to 20% mutant allele in a wild-type background.

 

EDTA blood specimens are preferred for testing. Bone marrow specimens are acceptable; there occasionally are specimen failures from bone marrow RNA, for reasons that are not completely understood. Heparin anticoagulant cannot be used due to PCR inhibition.

 

Assay precision does not appear to be significantly affected by specimen transport or moderate delays in processing. However, in specimens with lower levels of BCR/ABL, these conditions may cause sufficient RNA degradation to produce false-negative results. Thus, specimens should be shipped as quickly as possible. Ambient specimens over 3 days old and refrigerate specimens over 5 days old at the time of receipt are unacceptable.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

1. Hughes T, Deininger M, Hochhaus A, et al: Monitoring CML patients responding to treatment with tyrosine kinase inhibitors: review and recommendations for harmonizing current methodology for detecting BCR-ABL transcripts and kinase domain mutations and for expressing results. Blood. 2006 Jul 1;108(1):28-37. doi: 10.1182/blood-2006-01-0092

2. Press RD, Kamel-Reid S, Ang D: BCR-ABL1 RT-qPCR for Monitoring the Molecular Response to Tyrosine Kinase Inhibitors in Chronic Myeloid Leukemia. J Mol Diagn. 2013 Sep;15(5):565-576. doi: 10.1016/j.jmoldx.2013.04.007

3. Baccarani M, Deininger MW, Rosti G, et al: European LeukemiaNet recommendations for the management of chronic myeloid leukemia: 2013. Blood. 2013 Aug 8;122(6):872-884. doi: 10.1182/blood-2013-05-501569

4. Jones D, Kamel-Reid S, Bahler D, et al: Laboratory practice guidelines for detecting and reporting BCR-ABL drug resistance mutations in chronic myelogenous leukemia and acute lymphoblastic leukemia: a report of the Association for Molecular Pathology. J Mol Diagn. 2009 Jan;11(1):4-11. doi: 10.2353/jmoldx.2009.080095

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Description
Describes how the test is performed and provides a method-specific reference

Total RNA is extracted from the sample using an extraction kit. Complementary DNA is transcribed, and polymerase chain reaction (PCR) performed using primers directed against BCR and ABL1 regions to generate a long PCR product representing the translocated allele only (p210, p190, p205, or p230 transcript types) and encompassing the ABL1 region through exon 7. Second (nested) PCR amplifications are next performed to amplify the ABL1 kinase domain region using template from the first-round PCR product. Aliquots of the nested ABL1 PCR products are analyzed by Sanger sequencing and post-sequence software interpretation.(Unpublished Mayo method)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Monday through Friday

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

5 to 7 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

Blood/bone marrow: 2 weeks; Extracted RNA: 3 months

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their Regional Manager. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

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 US Food and Drug Administration.

CPT Code Information
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

81170-ABL1 (ABL proto-ongogene 1, non-receptor tyrosine kinase)(eg, acquired imatinib tyrosine kinase inhibitor resistance), gene analysis, variants in the kinase domain

LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.

Test Id Test Order Name Order LOINC Value
BAKDM BCR/ABL1 Mutation, Sequencing 55135-8
Result Id Test Result Name Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
MP004 Specimen Type 31208-2
MOFF BCRABL Fusion (210, 190, 205, 230) 55135-8
19824 Final Diagnosis: 34574-4

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Create a PDF

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports