Clinical diagnostics for Ph-like ALL
| Category . | Laboratory test . | Clinical utility . | Advantages . | Disadvantages . |
|---|---|---|---|---|
| Flow cytometry | ||||
| Surface TSLPR immunophenotyping | Identification of increased TSLPR protein expression that usually correlates with CRLF2 rearrangements | Widely available testing platform Rapid turnaround time Cost-effective | Only specific for CRLF2-overexpressing B-ALL Does not distinguish between CRLF2-overexpressing Ph-like ALL vs non–Ph-like ALL | |
| FISH | ||||
| ABL1, ABL2, CSF1R/PDGFRB, PDGFRA, CRLF2, EPOR, JAK2, NTRK3 break-apart probes | Identification of known 3′ kinase genetic rearrangements in Ph-like ALL | Widely available testing platform Rapid turnaround time Cost-effective | Requires further molecular confirmation to identify specific 5′ fusion partner genes | |
| Gene expression profiling | ||||
| LDA | Detection of the kinase-activated Ph-like gene signature | Rapid turnaround time Cost-effective Capable of direct detection of P2RY8-CRLF2 fusions | Requires downstream molecular testing to identify specific kinase fusions Testing available through few reference laboratories | |
| Next-generation sequencing | ||||
| Anchored multiplex PCR-based RNA sequencing | Detection of specific gene fusions that can guide potential targeted therapy approaches | Single assay capable of identifying canonical Ph-like ALL kinase fusions Often can identify novel/previously unknown 5′ fusion partners Moderately cost-effective given comprehensive analysis (may be combined with DNA-based NGS in a single assay) | Slower time to results May miss detection of fusions involving immunoglobulin or T-cell receptor genes May not detect point mutations or insertions/deletions outside of customized gene panels | |
| Comparative genomic hybridization microarray | Genome-wide identification of copy number changes in genes relevant to hematologic malignancies | Can detect Ph-like gene fusions resulting from interstitial deletions (eg, P2RY8-CRLF2, EBF1-PDGFRB) Can detect IKZF1 and other transcription factor deletions enriched in Ph-like ALL Rapid turnaround time | Cannot detect gene fusions resulting from chromosomal translocations Relatively higher cost given limited scope of results | |
| DNA amplicon-based NGS panels | Identification of single-nucleotide variants, indels, internal tandem duplications, and copy number variations recurrently mutated in hematologic malignancies | Rapid turnaround time Can detect IKZF1 and other transcription factor deletions enriched in Ph-like ALL Can detect sequence mutations in JAK-STAT and RAS pathway genes occurring in Ph-like ALL | Does not detect gene fusions Expensive | |
| Whole transcriptome sequencing (RNA sequencing) | Comprehensive genome-wide and unbiased RNA-based analysis of gene expression, fusion transcripts, and mutations | Single assay to identify the specific gene signature, fusions and mutations of Ph-like ALL Can identify novel/previously unknown kinase alterations | Limited clinical testing availability, mostly performed in a research setting at the present time Very expensive Long time to results | |
| Category . | Laboratory test . | Clinical utility . | Advantages . | Disadvantages . |
|---|---|---|---|---|
| Flow cytometry | ||||
| Surface TSLPR immunophenotyping | Identification of increased TSLPR protein expression that usually correlates with CRLF2 rearrangements | Widely available testing platform Rapid turnaround time Cost-effective | Only specific for CRLF2-overexpressing B-ALL Does not distinguish between CRLF2-overexpressing Ph-like ALL vs non–Ph-like ALL | |
| FISH | ||||
| ABL1, ABL2, CSF1R/PDGFRB, PDGFRA, CRLF2, EPOR, JAK2, NTRK3 break-apart probes | Identification of known 3′ kinase genetic rearrangements in Ph-like ALL | Widely available testing platform Rapid turnaround time Cost-effective | Requires further molecular confirmation to identify specific 5′ fusion partner genes | |
| Gene expression profiling | ||||
| LDA | Detection of the kinase-activated Ph-like gene signature | Rapid turnaround time Cost-effective Capable of direct detection of P2RY8-CRLF2 fusions | Requires downstream molecular testing to identify specific kinase fusions Testing available through few reference laboratories | |
| Next-generation sequencing | ||||
| Anchored multiplex PCR-based RNA sequencing | Detection of specific gene fusions that can guide potential targeted therapy approaches | Single assay capable of identifying canonical Ph-like ALL kinase fusions Often can identify novel/previously unknown 5′ fusion partners Moderately cost-effective given comprehensive analysis (may be combined with DNA-based NGS in a single assay) | Slower time to results May miss detection of fusions involving immunoglobulin or T-cell receptor genes May not detect point mutations or insertions/deletions outside of customized gene panels | |
| Comparative genomic hybridization microarray | Genome-wide identification of copy number changes in genes relevant to hematologic malignancies | Can detect Ph-like gene fusions resulting from interstitial deletions (eg, P2RY8-CRLF2, EBF1-PDGFRB) Can detect IKZF1 and other transcription factor deletions enriched in Ph-like ALL Rapid turnaround time | Cannot detect gene fusions resulting from chromosomal translocations Relatively higher cost given limited scope of results | |
| DNA amplicon-based NGS panels | Identification of single-nucleotide variants, indels, internal tandem duplications, and copy number variations recurrently mutated in hematologic malignancies | Rapid turnaround time Can detect IKZF1 and other transcription factor deletions enriched in Ph-like ALL Can detect sequence mutations in JAK-STAT and RAS pathway genes occurring in Ph-like ALL | Does not detect gene fusions Expensive | |
| Whole transcriptome sequencing (RNA sequencing) | Comprehensive genome-wide and unbiased RNA-based analysis of gene expression, fusion transcripts, and mutations | Single assay to identify the specific gene signature, fusions and mutations of Ph-like ALL Can identify novel/previously unknown kinase alterations | Limited clinical testing availability, mostly performed in a research setting at the present time Very expensive Long time to results | |
TSLPR, thymic stromal lymphopoietin receptor.