NGS (Tissue)
Suitable for broad-based genomic profiling
that includes targets in addition to FGFR3
Full coverage of FGFR3 gene is preferred over hotspot sequencing
PCR-based
Will detect selected mutations
NGS (cfDNA)
Useful when tissue biopsy sample is limited/
unavailable
Higher false negative rate than tissue-based
NGS testing
Point mutations*
FGFR3 R248C, FGFR3 S249C
FGFR3 G370C, FGFR3 Y373C
*Point mutations occur at higher frequency (15%-20%)9,10 than fusions (2%-3%).10,11
†List not exhaustive of all activating alterations.
NGS (Tissue)
Suitable for broad-based genomic profiling
that includes targets in addition to FGFR3
Full coverage of FGFR3 gene is preferred over hotspot sequencing
Assay should minimally cover exons 17 and
18 to ensure detection of most common
fusions
RNA-based NGS is most suitable for fusions
NGS (cfDNA)
Useful when tissue biopsy sample is limited/
unavailable
Higher false negative rate than tissue-based
NGS testing
PCR-based
Will detect known fusions but may miss novel FGFR3 rearrangements
Gene fusions*
FGFR3-TACC3
*Point mutations occur at higher frequency (15%-20%)9,10 than fusions (2%-3%).10,11
†List not exhaustive of all activating alterations.
NGS (Tissue)
Detects amplification of FGFR3 gene (DNA-based) or overexpression of FGFR3 mRNA (RNA-based)
Suitable for broad-based genomic profiling that includes FGFR3 point mutations, fusions, and other targets
PCR-based
Detects FGFR3 mRNA overexpression
Sensitive
Does not provide spatial information
IHC
Directly measures FGFR3 protein expression
Provides spatial information
Short TAT
Requires pathologist training or central testing
RNA-ISH
Detects FGFR3 mRNA overexpression
Short TAT
Requires pathologist training or central testing
Amplification/Overexpression
FGFR3 gene, FGFR3 mRNA,
FGFR3 protein or its ligands
NGS (Tissue)
Suitable for broad-based genomic profiling that includes targets in addition to IDH1/IDH2
Able to detect all possible IDH1/IDH2 mutations
Detection may require higher tumor content than PCR-based assays
NGS (cfDNA)
Useful when tissue biopsy sample is limited/
unavailable
Higher false negative rate than tissue-based
NGS testing
PCR-based
Will detect selected mutations but may miss novel IDH1/IDH2 alterations
Sanger Sequencing
Able to detect all possible IDH1/IDH2
mutations within an exon
Detection may require higher tumor content
than PCR-based assays
Point mutations
IDH1 R132C/L/G/S/H
IDH2 R172K/M/G/W
*IDH1 mutations more common than IDH2 mutations in CCA9,10
NGS (Blood/Marrow)
Suitable for broad-based genomic profiling
that includes targets in addition to IDH1/IDH2
PCR-based
Will detect selected mutations but may miss
novel IDH1/IDH2 alterations
Sanger Sequencing
Detection may require higher tumor content
than PCR-based assays
Able to detect all possible IDH mutations
within an exon
Point mutations
IDH1 and IDH2 mutations present in roughly equal proportion of AML cases:
IDH1 R132H/C/S/G
IDH2 R140Q/K
*IDH1 and IDH2 mutations present in roughly equal proportion of AML cases10
NGS (Tissue)9
Suitable for broad-based genomic profiling
that includes targets in addition to KRAS
NGS (cfDNA)9
Useful when tissue biopsy sample is limited/
unavailable
Higher false negative rate than tissue-based
NGS testing
PCR-based9
Will detect selected mutations but may miss novel KRAS alterations
Selected assay should have full coverage of
exon 2
Point mutations
KRAS G12C, KRAS G12D
NGS (Tissue)
Should have full coverage of Exon 20
NGS (cfDNA)
Useful when tissue biopsy sample is limited/
unavailable
Higher false negative rate than tissue-based
NGS testing
Sanger Sequencing
Can detect all possible PIK3CA mutations
within an exon
Detection may require higher tumor content than PCR-based assays
PCR-based
Will detect selected mutations but may miss
novel PIK3CA alterations
Single base extension/MassArray
Will detect selected mutations but may miss
novel PIK3CA alterations
Point mutations
PIK3CA H1047R
NGS (Tissue)
Suitable for broad-based genomic profiling
that includes targets in addition to RET
NGS (cfDNA)
Useful when tissue biopsy sample is limited/
unavailable
Higher false negative rate than tissue-based
NGS testing
PCR-based
Selected assay should have full coverage of
exons 8, 10, 11, and 13-16
Sanger Sequencing
Lower sensitivity than NGS for somatic
alterations, thus more suitable for germline
testing in MTC
Detection may require higher tumor content
than PCR-based assays
Point mutations*
RET M918T
*Point mutations occur in MTC, and gene fusions occur in PTC and NSCLC.
†List is not exhaustive of all activating alterations.
NGS (Tissue)
Suitable for broad-based genomic profiling
that includes targets in addition to RET
RNA-based NGS is most suitable for fusions
NGS (cfDNA)
Useful when tissue biopsy sample is limited/
unavailable
Higher false negative rate than tissue-based
NGS testing
FISH
Lack of standard cutoffs to define positivity
Close proximity of common fusion partners
can complicate analysis
Cannot determine if fusion results in
functional protein, leading to false positives
PCR-based
Will detect known fusions but may miss novel
RET rearrangements
Selected assay should have full coverage of
exons 8, 10, 11, and 13-16
Sanger Sequencing
Lower sensitivity than NGS for somatic
alterations, thus more suitable for germline
testing in MTC
Detection may require higher tumor content
than PCR-based assays
Gene fusions*
KIF5B-RET, CCDC6-RET, NCOA4-RET
*Gene fusions occur in PTC and NSCLC, point mutations occur in MTC.
†List is not exhaustive of all activating alterations.
NGS (Tissue)
Suitable for broad-based genomic profiling that includes targets in addition to SMARCA2 and SMARCA4
Full coverage of SMARCA4 gene is preferred over hotspot sequencing
NGS (cfDNA)
Useful when tissue biopsy sample is limited/
unavailable
Higher false negative rate than tissue-based
NGS testing
PCR-based
Will only detect selected mutations
Dependent on coverage by primers
Point mutations
Deletions
Rearrangements
Any putative truncating alteration (nonsense mutations, frameshift mutations, indels, splice-site mutations, etc.)
IHC
Directly measures nuclear expression of SMARCA4
Provides spatial information
Short TAT
Requires pathologist training or reference lab testing*
Protein Expression
Decreased or absent BRG1 protein
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