Table 2 Summary of molecular genetic findings in 20 cases of lipofibromatosis

From: Aberrant receptor tyrosine kinase signaling in lipofibromatosis: a clinicopathological and molecular genetic study of 20 cases

Case

Dv200a

RNA-seqb

RT-PCR/sequencing

Fusion breakpointsc

FISHd

Combined result

1

37

HBEGF-RBM27*

Confirmed

ex3-ex2

FN1-neg

HBEGF-RBM27

2

31

Not done

Not done

 

FN1-neg*

No fusion

3

44

EGR1-GRIA1*

Confirmed

ex1-ex3

FN1-neg

EGR1-GRIA1

4

37

Negative*

Not done

 

FN1-neg

No fusion

5

40

Negative*

Not done

Unknown

FN1-EGF

FN1-EGF

6

44

Negative*

Not done

Unknown

FN1-EGF

FN1-EGF

7

68

TPR-ROS1

Confirmed

ex31-ex36

ROS1-pos, FN1-neg

TPR-ROS1

8

29

Negative

Not done

 

FN1-neg

No fusion

9

37

Negative*

Not done

 

Not done

No fusion

10

31

SPARC-PDGFRB*

Confirmed

ex9-ex11

PDGFRB-pos

SPARC-PDGFRB

11

28

Negative

Not done

 

FN1-neg

No fusion

12

<25

Not done

Not done

 

FN1-neg*

No fusion

13

67

FN1-TGFA

Confirmed

ex20-ex3

FN1-TGFA

FN1-TGFA

14e

<25

Not done

Not done

Unknown

FN1-EGF

FN1-EGF

15

<25

Not done

Not done

 

FN1-neg*

No fusion

16

<25

Not done

Not done

 

FN1-neg

No fusion

17

40

FN1-EGF

Not done

ex36-ex16

Not done

FN1-EGF

18a

54

VCL-RET

Not done

ex18-ex12

Not done

VCL-RET

18b

38

VCL-RET

Not done

ex18-ex12

Not done

VCL-RET

19

33

EGFR-BRAF f

Not done

ex27-ex10

Not done

EGFR-BRAF

20

42

Negative

Not done

 

Not done

No fusion

  1. aDv200 = fraction (%) of RNA fragments > 200 nt
  2. bCases sequenced twice, using the same mRNA but with separate library preparations, are indicated with an asterisk
  3. cSequence variants for breakpoint assignment were: EGF (NM_001963), EGR1 (NM_001964), FN1 (NM_212482), GRIA1 (NM_001258020), HBEGF (NM_001945), PDGFRB (NM_002609), RBM27 (NM_018989), RET (NM_020975), ROS1 (NM_002944), SPARC (NM_003118), TGFA (NM_001308158), TPR (NM_003292), VCL (NM_014000)
  4. dFISH = fluorescence in situ hybridization. Cases were scored as FN1-negative if <35% of the nuclei showed split signals with a break-apart probe (BAP) for FN1 or <30% fusion signals with probes for FN1 and EGF. Cases analyzed only with the FN1 BAP are indicated with an asterisk
  5. eIndex case
  6. fThe EGFR-BRAF fusion transcript was detected by only one of the two algorithms used to detect fusion transcripts
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