MDA Mutation Analysis Precision Panel Liquid Biopsy

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MDA Mutation Analysis Precision Panel Liquid Biopsy (MDA MAPP LB)

Indication:

Tumor biomarkers are profiled to identify somatic drivers for predictive, diagnostic, prognostic and therapeutic indicators for patients with solid tumors. Specific clinical indications include LB genotyping when no tumor tissue is available, estimating treatment response using a baseline sample (single use), estimating treatment response in a follow-up sample (single use), or clinical suspicion of treatment resistance. Utilizing cfDNA from blood avoids the cost and invasive nature of tumor biopsies when accurate information regarding the variety of genetic abnormalities harbored in the tumor is very valuable, not only for clinical and prognostic classification but also to decide the most suitable treatment options for the patient. Detailed profiling of the mutations existing in the tumor is warranted to understand the genetic basis of cancer and improve overall patient diagnosis and treatment. In the recent years the push towards implementing “Personalized Cancer Therapy” has resulted in keen interest to obtain mutational profile of the tumor not only to predict the response to therapy but also to design the most appropriate therapy, which would minimize the risk of side-effects and maximize the efficacy of therapy. To this end, greater information regarding the mutational status of a tumor would ensure better clinical classification of the patient and improve selection of treatment strategies.

Methodology:

MDA MAPP LB assay uses the NovaSeq 6000 next generation sequencing platform to sequence and identify nucleic acid variants located in coding regions of 701 genes, including 1 promoter region (TERT), 1 non-coding RNA (TERC) gene, and selected intronic regions from 34 genes for rearrangements in cfDNA extracted from patient’s plasma specimens. Reported somatic events are identified by comparison to the human genome reference sequence GRCh37/hg19 and reviewed in OncoSeek against a process-matched normal control. Data analysis is performed in house by the MDA MAPP LB Bioinformatics pipeline (BIP) which relies on the dual-duplex molecular barcoding to reduce sequencing artifacts and achieve a lower limit of detection of 0.5% (one mutant allele in the background of one hundred and ninety-nine wild type alleles) with increased overall panel analytical sensitivity for SNVs 100%, indels 100%, CNVs 96.4% and fusions 98.3%.

Test Parameters:

Clinical specimens were reviewed for the markers listed in the following tables.

Genes of Interest for SNVs and INDELs

ABL1	CCND2	EED	FUBP1	INPP4A	MTAP	PIK3R3	RIF1	STAT4
ABL2	CCND3	EGFL7	FYN	INPP4B	MTOR	PIM1	RIPK1	STAT5A
ABRAXAS1	CCNE1	EGFR	FZR1	INSR	MUSK	PLCG1	RIT1	STAT5B
ACVR1	CCNE2	EGR1	GABRA6	IRAK1	MUTYH	PLCG2	RMI1	STAT6
ACVR1B	CCR4	EGR2	GADD45A	IRF2	MXD4	PLEKHG5	RMI2	STK11
ACVR2A	CCR7	EIF1AX	GATA1	IRF4	MYB	PLK2	RNF43	STK19
ADGRA2	CD274	EIF4A2	GATA2	IRF8	MYBL1	PMAIP1	ROR1	STK40
AJUBA	CD276	EIF4E	GATA3	IRS1	MYC	PML	ROS1	SUFU
AKT1	CD28	ELF3	GATA4	IRS2	MYCL	PMS1	RPA1	SUZ12
AKT2	CD58	ELF4	GATA6	ITPKB	MYCN	PMS2	RPA2	SYK
AKT3	CD74	ELOC	GEN1	JAK1	MYD88	PNKP	RPA3	TBC1D4
AKTIP	CD79A	EMSY	GID4	JAK2	MYOD1	PNRC1	RPA4	TBL1XR1
ALK	CD79B	ENO1	GLI1	JAK3	NBN	POLA1	RPS15	TBX3
ALOX12B	CD8A	EP300	GNA11	JUN	NCOA3	POLD1	RPS6KA4	TCF3
AMER1	CDC20	EPCAM	GNA13	KAT6A	NCOR1	POLE	RPS6KB1	TCF7L2
ANKRD11	CDC27	EPHA2	GNAQ	KDM3B	NEGR1	POLQ	RPS6KB2	TEK
APC	CDC42	EPHA3	GNAS	KDM5A	NF1	POT1	RPTOR	TENT5C
AR	CDC6	EPHA5	GPR183	KDM5C	NF2	PPARG	RRAGC	TERC
ARAF	CDC73	EPHA7	GPS2	KDM6A	NFE2L2	PPM1D	RRAS	TERT
ARFRP1	CDH1	EPHB1	GREM1	KDR	NFKB2	PPP1R3A	RSPO1	TET1
ARID1A	CDK12	EPHB4	GRIN2A	KEAP1	NFKBIA	PPP2R1A	RSPO2	TET2
ARID1B	CDK2	ERBB2	GRM3	KEL	NFKBIE	PPP2R2A	RUNX1	TFE3
ARID2	CDK4	ERBB3	GSK3B	KIT	NGFR	PPP4R4	RUNX1T1	TFEB
ARID5B	CDK6	ERBB4	H1-2	KLF2	NHEJ1	PPP6C	RYBP	TGFB1
ASCC3	CDK8	ERCC1	H1-4	KLF4	NKX2-1	PRAME	RYK	TGFBR1
ASPM	CDKN1A	ERCC2	H2AX	KLHL6	NKX3-1	PRC1	S1PR1	TGFBR2
ASXL1	CDKN1B	ERCC3	H2BC5	KMT2A	NOTCH1	PRDM1	S1PR2	TMEM127
ASXL2	CDKN2A	ERCC4	H3-3A	KMT2B	NOTCH2	PREX2	SAMHD1	TMEM30A
ATM	CDKN2B	ERCC5	H3-3B	KMT2C	NOTCH3	PRG4	SDHA	TMPRSS2
ATR	CDKN2C	ERCC6	H3-4	KMT2D	NOTCH4	PRKAR1A	SDHAF2	TNF
ATRIP	CEBPA	ERG	H3-5	KNSTRN	NPM1	PRKCI	SDHB	TNFAIP3
ATRX	CENPA	ERRFI1	H3C1	KRAS	NRAS	PRKD1	SDHC	TNFRSF14
AURKA	CENPE	ESR1	H3C10	LATS1	NSD1	PRKDC	SDHD	TOP1
AURKB	CHAF1A	ETV1	H3C11	LATS2	NSD2	PRKN	SESN1	TOP2A
AURKC	CHD2	ETV4	H3C12	LCK	NSD3	PTCH1	SETBP1	TOP3A
AXIN1	CHEK1	ETV5	H3C13	LIG4	NT5C2	PTEN	SETD2	TOPBP1
AXIN2	CHEK2	ETV6	H3C2	LMO1	NTHL1	PTK2	SETDB1	TP53
AXL	CHTF8	EWSR1	H3C3	LRP1B	NTRK1	PTPN1	SF3B1	TP53BP1
B2M	CIC	EXO1	H3C4	LTB	NTRK2	PTPN11	SGK1	TP53I3
BAP1	CIITA	EZH2	H3C6	LTK	NTRK3	PTPRB	SH2B3	TP63
BARD1	CNOT3	FADD	H3C7	LYN	NUP93	PTPRD	SH2D1A	TRAF2
BAZ2A	COL2A1	FAM50A	H3C8	MAD2L2	NUTM1	PTPRS	SHLD1	TRAF3
BBC3	COP1	FANCA	HDAC2	MAGOH	NXF1	PTPRT	SHLD2	TRAF6
BCL10	CREBBP	FANCC	HDAC9	MALT1	P2RY8	QKI	SHLD3	TRAF7
BCL11A	CRKL	FANCD2	HELQ	MAP2K1	PAK1	RAB35	SHPRH	TRAPPC13
BCL2	CRLF2	FANCE	HERC2	MAP2K2	PAK3	RAC1	SHQ1	TRIM28
BCL2L1	CSF1R	FANCF	HFM1	MAP2K4	PAK5	RAD17	SLC34A2	TRIM37
BCL2L11	CSF3R	FANCG	HGF	MAP2K7	PALB2	RAD21	SLIT2	TSC1
BCL2L2	CTCF	FANCI	HLA-A	MAP3K1	PARP1	RAD50	SLX4	TSC2
BCL6	CTLA4	FANCL	HLA-B	MAP3K13	PARP2	RAD51	SMAD2	TSHR
BCL7A	CTNNA1	FANCM	HLA-C	MAP3K14	PARP3	RAD51AP1	SMAD3	TSPAN31
BCOR	CTNNB1	FAS	HMGA2	MAP3K4	PARP4	RAD51B	SMAD4	TTK
BCORL1	CUL3	FAT1	HNF1A	MAPK1	PARPBP	RAD51C	SMARCA2	TYRO3
BCR	CUL4A	FBXW7	HOXB13	MAPK3	PAX5	RAD51D	SMARCA4	U2AF1
BIRC2	CUL4B	FGF10	HRAS	MAPK8	PAXX	RAD52	SMARCAD1	UBR5
BIRC3	CUX1	FGF14	HSD3B1	MAX	PBRM1	RAD54L	SMARCB1	VAV1
BLM	CXCR4	FGF19	HSP90AA1	MCL1	PCBP1	RAF1	SMARCD1	VEGFA
BLNK	CYLD	FGF23	HSP90AB1	MDC1	PCNA	RARA	SMC1A	VHL
BMPR1A	CYP2C19	FGF3	HUWE1	MDM2	PDCD1	RASA1	SMC3	VTCN1
BRAF	DAXX	FGF4	HVCN1	MDM4	PDCD1LG2	RASSF1	SMC5	WRN
BRCA1	DCLRE1C	FGF5	ICOSLG	MED12	PDGFB	RB1	SMC6	WT1
BRCA2	DCUN1D1	FGF6	ID3	MEF2B	PDGFRA	RBM10	SMO	XIAP
BRCC3	DDB1	FGF9	IDH1	MEN1	PDGFRB	RBMX	SNCAIP	XPO1
BRD4	DDR1	FGFR1	IDH2	MERTK	PDK1	RECQL4	SOCS1	XPO5
BRIP1	DDR2	FGFR2	IFNGR1	MET	PER1	REL	SOS1	XRCC2
BTG1	DDX3X	FGFR3	IGF1	MFHAS1	PGD	RELN	SOX10	XRCC3
BTG2	DICER1	FGFR4	IGF1R	MGA	PGR	REST	SOX11	XRCC4
BTK	DIS3	FH	IGF2	MGMT	PHF6	RET	SOX17	XRCC5
BUB1	DIS3L2	FLCN	IGLL5	MITF	PHOX2B	REV3L	SOX2	XRCC6
CALR	DLL3	FLT1	IKBKE	MLH1	PIK3C2B	RFC1	SOX9	YAP1
CARD11	DNA2	FLT3	IKZF1	MLH3	PIK3C2G	RFC2	SP140	YES1
CASP8	DNAJB1	FLT4	IKZF3	MPL	PIK3C3	RFC3	SPEN	ZFAT
CBFB	DNMT1	FOXA1	IL10	MRE11	PIK3CA	RFC4	SPOP	ZFHX3
CBL	DNMT3A	FOXL2	IL2RG	MSH2	PIK3CB	RFC5	SRC	ZMYM3
CCKAR	DNMT3B	FOXO1	IL7R	MSH3	PIK3CD	RFTN1	SRSF2	ZNF217
CCN6	DOT1L	FOXP1	INHA	MSH6	PIK3CG	RHEB	SSBP1	ZNF703
CCNA2	DUSP2	FRS2	INHBA	MST1	PIK3R1	RHOA	STAG2	ZRSR2
CCND1	E2F3	FTO	INO80	MST1R	PIK3R2	RICTOR	STAT3

Genes of Interest for CNVs

AR	BRAF	CCND1	CCND2	CCNE1	CDK4	CDK6	EGFR	ERBB2
FGFR2	FGFR3	KIT	KRAS	MET	MYC	PDGFRA	PIK3CA	RAF1
FGFR1

Genes of Interest for Fusions

ALK	BCR	BRAF	BRCA1	BRCA2	CD74	EGFR	EML4	ETV4
ETV5	ETV6	EWSR1	EZR	FGFR1	FGFR2	FGFR3	KIT	KMT2A
MSH2	MYB	MYC	NOTCH2	NTRK1	NTRK2	NUTM1	PDGFRA	RAF1
RARA	RET	ROS1	RSPO2	SDC4	SLC34A2	TMPRSS2

Turnaround Time:

10 days

Sample Requirements:

30 ml peripheral blood (PB) in Cell-Free DNA BCT® Streck Tube, sent on room temperature.

CPT Codes:

81479(x17), 81201, 81163, 81165, 81216, 81235(x2), 81401, 81403, 81404, 81210, 81272, 81275, 81311, 81276, 81191, 81309, 81351

The CPT codes provided are based on AMA guidelines and are for informational purposes only. CPT coding is the sole responsibility of the billing party. Please direct any questions regarding coding to the payer being billed.