Clinical evaluation of panel testing by next-generation sequencing (NGS) for gene mutations in myeloid neoplasms

Au, Chun Hang; Wa, Anna; Ho, Dona N.; Chan, Tsun Leung; Ma, Edmond S. K.

doi:10.1186/s13000-016-0456-8

Diagnostic Pathology

Table 1 Summary of 50 patients in this study.

From: Clinical evaluation of panel testing by next-generation sequencing (NGS) for gene mutations in myeloid neoplasms

No.	Sex/Age	Diagnosis	Cytogenetics	Conventional molecular testing	NGS myeloid panel	Clinical outcome
1	M/56	AML-NOS^*	Not done	FLT3-	KIT p.D816V	Alive on treatment
2	F/37	M1	Near-tetraploid and complex	NPM-, FLT3-	TP53 p.E62^*	Treated in Mainland China
3	M/60	High grade MDS	Normal	FLT3-ITD (189 bp), del(5q) FISH-	FLT3 ITD (189 bp)	Alive in CR after BMT
4	F/83	M6	No growth	FLT3-ITD-TKD+	FLT3 p.D835Y	Died
5	M/58	High grade MDS	Complex > 3 abnormality	NPM1-, FLT3-	Negative	Died after BMT
6	M/57	AML-TMDS	Normal	NPM1-, FLT3-	DNMT3A p.E423^*	Died of relapse after BMT
					IDH2 p.R140Q
					STAG2 p.R259^*
7	F/66	AML-TMDS	Normal	NPM1+, FLT3-ITD-TKD+	FLT3 p.D835Y	Died of CNS disease
7	F/66	AML-TMDS	Normal	NPM1+, FLT3-ITD-TKD+	NPM1 p.W288Cfs*12	Died of CNS disease
8	F/49	Refractory AML	Not done	FLT3-	SF3B1 p.K666E	Died
9	F/35	M2	inv(16)	KIT+	KIT p.D816V	Alive in CR after BMT
10	F/44	M4	Normal	NPM+, FLT3-	NPM1 p.W288Cfs*12	Alive in CR
11	F/82	M5a	No growth	FLT3-	Negative	Died
12	F/25	M2	No growth	AML1-ETO-, NPM1-, FLT3-, KIT-	Negative	Alive in CR
13	F/76	AML transformed from MDS	No growth	FLT3-, del(5q) FISH-, BCR-ABL1-	Negative	Died
14	F/52	M1	+14	NPM1-, FLT3-	CSF3R p.T816I	Lost to follow up
					IKZF1 p.R111^*
					IDH2 p.R140Q
					STAG2 p.R1012^*
15	M/82	M1	add(3q), add(7q), +8,	FLT3-, BCR-ABL-	Negative	Died
16	F/59	M6	Poor growth	NPM1+, FLT3-	NPM1 p.W288Cfs*12	Died
					ETV6 p.Y346^*
					IDH2 p.R140W
17	F/78	M2	+10	NPM1-, FLT3-, AML1-ETO-, PML-RARA-	IDH1 p.R132C	In CR with vidaza and died of second cancer
18	M/61	AML transformed from CMML	Poor growth	FLT3-, del(5q) FISH-, PDGFRB FISH-, BCR-ABL-	CSF3R p.T618I	Died
18	M/61	AML transformed from CMML	Poor growth	FLT3-, del(5q) FISH-, PDGFRB FISH-, BCR-ABL-	CEBPA p.Y67^*	Died
19	F/64	AML-NOS^b	Normal	NPM1+, FLT3 ITD-TKD+	NPM1 p.W288Cfs*12	Died
					FLT3 p.D835Y
					DNMT3A p.W313^*
					SMC3 c.3105 + 2 T > C
					RAD21 p.Q132^*
20	M/54	M1	Normal	NPM1+, FLT3-	NPM1 p.W288Cfs*12	Alive in CR
					IDH1 p.R132H
					FLT3 ITD (25 bp)
					FLT3 ITD (119 bp)
21	M/44	M1	Constitutional inv(9)	FLT3-, BCR-ABL-	Negative	Died. History of HD treated by BEACOPP
22	F/44	M2	Not done	FLT3 ITD + TKD-	NPM1 p.W288Cfs*12	Died
					RAD21 c.1161 + 2 T > A
					FLT3 ITD (72 bp)
23	F/33	M2 therapy-related	Poor growth	NPM1-, FLT3-	Negative	Died. History of treated breast cancer
24	F/26	M3	No growth	PML-RARA(s)+, FLT3 ITD + TKD-	FLT3 ITD (33 bp)	Alive in CR
25	M/65	M5a	+8	NPM1-, FLT3 ITD + TKD-	FLT3 ITD (54 bp)	Died
26	F/74	M0	+22	CBFB-MYH11- NPM1- FLT3- BCR-ABL1-	Negative	Alive in CR and maintained on monthly vidaza
27	F/77	AML-TMDS	+8	Not done	Negative	Lost to follow up. History of lung cancer
28	M/18	M2	t(8;21),-Y	AML1-ETO+, KIT-, NPM1-, FLT3-	Negative	Alive in CR
29	F/61	AML-NOS^a	Poor growth	NPM1-, FLT3 ITD-TKD+, BCR-ABL-, AML1-ETO-	FLT3 p.D835Y	Alive in CR
30	F/39	M2	+8	AML1-ETO-, NPM+, FLT3-	NPM1 p.W288Cfs*12	Alive in CR
30	F/39	M2	+8	AML1-ETO-, NPM+, FLT3-	NRAS p.G12D	Alive in CR
31	M/70	M1	Normal	NPM-, FLT3-, PDGFRB FISH-, FIP1L1-PDGFRA-, BCR-ABL-,	TET2 p.S1848^*	NR to vidaza. Further treatment in Mainland China
				NPM-, FLT3-, PDGFRB FISH-, FIP1L1-PDGFRA-, BCR-ABL-,	TET2 p.G1152E
				JAK2 V617F weak+	JAK2 p.V617F (VAF 4.1 %, below original reportable threshold)
32	F/80	M2	del(5q), +8	Not done	IDH1 p.R132C	Alive and on vidaza
					TET2 p.K693Nfs*18
					TP53 p.R249S
					ASXL1 p.W960^*
33	F/68	M4	Normal	FLT3-	NPM1 p.W288Cfs*12	Difficult CR and on vidaza
33	F/68	M4	Normal	FLT3-	TET2 p.L346Rfs*2	Difficult CR and on vidaza
34	F/24	M2	t(8;21)	AML1-ETO+, BCR-ABL-, PML-RARA-, NPM1-, FLT3-	Negative	Alive in CR
35	M/60	M5a	+8	Not done	NPM1 p.W288Cfs*12	Alive on treatment
					PTPN11 p.G503A
					ASXL1 p.G646Wfs*12
36	F/62	M1	Normal	AML1-ETO-, BCR-ABL1-, PML-RARA-, NPM1+, FLT3 ITD+ in cis with 3 bp deletion (c.1739_1741delAGG)	NPM1 p.W288Cfs*12	CR for 1 year. Relapsed on treatment
					FLT3 p.Q580_V581delinsL (c.1739_1741delAGG)
					FLT3 ITD (54 bp)
					FLT3 ITD (63 bp)
					IDH2 p.R140Q
37	F/46	M4	Near-tetraploid	AML-ETO-, BCR-ABL1-,	FLT3 p.D835Y	Responded to sorafenib and HHT. Received BMT from sibling donor and on treatment
37	F/46	M4	Near-tetraploid	FLT3 ITD+ (30 bp), FLT3 TKD+	FLT3 ITD (30 bp)
38	M/66	AML-TMDS	Complex > 3 abnormalities	FLT3-, BCR-ABL1-, JAK2 V617F-	DNMT3A p.M801Nfs*11	Alive on vidaza. History of lung cancer
38	M/66	AML-TMDS	Complex > 3 abnormalities		TP53 p.R175H	Alive on vidaza. History of lung cancer
39	F/62	AML-M5 post-BMT relapse	Complex > 3 abnormalities	Not done	TP53 p.Y220C	Died
40	M/62	M5a transformed from MDS	Normal	NPM1+, FLT3-, MLL FISH-	NPM1 p.W288Cfs*12	Died
40	M/62	M5a transformed from MDS	Normal	NPM1+, FLT3-, MLL FISH-	CBL c.1096-1G > T	Died
41	F/78	AML-TMDS	add(21q)	FLT3 ITD + TKD-	FLT3 ITD (30 bp)	Died
42	M/88	AML-NOS^*	Not done	Not done	IDH2 p.R140Q	Alive on palliative care
43	M/63	M2	Normal	Not done	IDH2 p.R172K	Alive on vidaza
44	F/60	M2 and bone marrow fibrosis	Normal	5/7/del(20q) FISH-, BCR-ABL-, FLT3-, JAK2 V617F/CALR/MPL-	DNMT3A c.855 + 1G > T	Alive on treatment
					NPM1 p.W288Cfs*12
					IDH2 p.R140Q
45	F/28	M4Eo	inv(16)	CBFB FISH+, CBFB-MYH11 PCR+	Negative	Alive in CR
46	F/84	M4Eo	Not done	CBFB-MYH11 PCR+, FLT3-, NPM1-, KIT-	Negative	Died
47	M/51	Atypical CML	Normal	CSF3R-, BCR-ABL-, JAK2 V617F-, PDGFRB FISH-, PDGFRA FISH-	EZH2 c.1852-2A > G	Died
					SETBP1 p.D868N
					ASXL1 p.G646Wfs*12
					ZRSR2 p.Q103*
48	F/53	M2	t(8;21)	KIT-	SMC3 p.S674_R675insL	Alive in CR
49	M/65	High-grade MDS	Normal	Not done	ASXL1 p.G646Wfs*12	Alive on vidaza + eltrombopag trial
50	M/51	M2	Normal	NPM1-, FLT3-, AML1-ETO-	CEBPA p.R343Afs*79	Alive on treatment
50	M/51	M2	Normal	NPM1-, FLT3-, AML1-ETO-	CEBPA p.K313dup	Alive on treatment

CR complete remission, NR non-remission, FISH fluorescence in-situ hybridization, vidaza 5-azacytadine, HHT homoharringtonine, HD Hodgkin lymphoma, PML-RARA(s) short isoform of fusion transcript from PML bcr3 breakpoint, VAF variant allele frequency, FLT3 testing included detection of both ITD and TKD
^*Diagnosis on PB only
^aAparticulate aspirate and diagnosis by immunophenotyping only
^bDiagnosis in another hospital

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ISSN: 1746-1596

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