Table 1 Summary of fusion detection results.

From: Multiplexed transcriptome analysis to detect ALK, ROS1 and RET rearrangements in lung cancer

Sample Number (SN)

FISH

Nanostring

Agena LungFUSION panel

ThermoFisher NGS

Comment

ALK

RET

ROS1

ALK

RET

ROS1

ALK

RET

ROS1

ALK

RET

ROS1

01

P

nk

nk

P

N

N

P

N

N

P

N

N

 

02

N

N

N

N

N

N

N

N

N

N

N

N

 

03

N

N

N

N

N

N

N

N

N

N

N

N

 

04

P

nk

nk

P

N

N

P

N

N

P

N

N

 

05

P

nk

nk

P

N

N

P

N

N

P

N

N

 

06

P

nk

nk

P

N

N

P

N

N

P

N

N

 

07

P

nk

nk

P

N

N

P

N

N

P

N

N

 

08

P

nk

nk

P

N

N

P

N

N

P

N

N

 

09

nk

P

nk

F

F

F

N

P

N

N

N

N

Low RET Agena

10

P

N

N

N

N

N

N

N

N

N

N

N

FISH +ve cells 1–50, −ve cells 51–100, IHC −ve, some narrow breaks, non-specific staining

11

N

N

N

N

N

N

F

F

F

N

N

N

Normal in Agena but below threshold

13

P

nk

nk

P

N

N

P

N

N

P

N

N

 

14

N

N

N

N

N

N

N

N

N

N

N

N

 

15

N

N

N

N

N

N

N

N

N

N

N

N

 

16

N

N

N

N

N

N

N

N

N

N

N

N

 

17

N

N

N

N

N

N

N

N

N

N

N

N

 

18

P

nk

nk

P

N

N

P

N

N

P

N

N

 

19

N

N

N

N

N

N

N

N

N

N

N

N

 

20

N

N

N

N

N

N

N

N

N

N

N

N

 

21

N

N

N

N

N

N

N

N

N

N

N

N

 

22

N

N

N

N

N

N

N

N

N

N

N

N

 

23

N

N

N

N

N

N

N

N

N

N

N

N

 

24

P

nk

nk

P

N

N

P

N

N

P

N

N

 

25

N

N

N

N

N

N

N

N

N

N

N

N

 

26

P

nk

nk

P

N

N

P

N

N

P

N

N

 

27

nk

N*

N*

N

N

N

N

N

N

N

N

N

FISH atypical for RET and ROS1

29

P

nk

nk

F

F

F

P

N

N

P

N

N

Failed Nanostring normalization, although ALK fusion was observed

30

N

N

N

N

N

N

N

N

N

N

N

P

 

32

nk

nk

P

F

F

F

N

N

P

N

N

P

 

33

P

N

N

P

N

N

P

N

N

P

N

N

Low ROS1 Agena detected in variant specific

34

N

N

N

N

N

N

N

N

N

N

N

N

 

35

N

N

N

N

N

N

N

N

N

N

N

N

 

36

N

N

N

N

N

N

N

N

N

N

N

N

 

37

N

N

N

P

N

N

P

N

N

P

N

N

 

38

nk

nk

P

N

N

P

N

N

P

N

N

P

 

39

N

N

N

N

N

N

N

N

P

N

N

N

Low ROS1 Agena detected in variant specific

40

N

N

N

N

N

N

N

N

N

N

N

N

 

41

N

N

N

N

N

N

N

N

N

N

N

N

 

42

P

nk

nk

P

N

N

P

N

N

P

N

N

 

43

P

nk

nk

P

N

N

P

N

N

P

N

N

 

44

N

N

N

N

N

N

N

N

N

N

N

N

 

45

P

nk

nk

P

N

N

P

N

N

P

N

N

 

46

nk

nk

N*

N

N

N

N

N

N

N

N

N

FISH atypical for ROS1

47

N

N

N

N

N

N

N

N

N

N

N

N

 

48

P

nk

nk

P

N

N

P

N

N

P

N

N

Agena–High ALK + Low ROS1 detected, ROS1 not confirmed by variant analysis–reportable sample result = ALK Fusion Positive

49

N

N

N

N

N

N

N

N

N

N

N

N

 

50

N

N

N

N

N

N

N

N

N

P

N

N

 

51

N

N

N

N

N

N

N

N

N

P

N

N

 

52

N

N

N

N

N

N

F

F

F

N

N

N

Normal in Agena but below threshold

53

N

N

N

N

N

N

N

N

N

N

N

N

 

55

N

N

N

N

N

N

N

N

N

P

N

N

 
  1. N = Negative, P = Positive, nk = not done or not known, F = Failed test result, Atypical by FISH *, Discordant cases compared to FISH are highlighted in bold font.
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