Table 1 Structural variations identified from WGS analysis

From: Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas

Samples

Structural variationa

Description

WES SCNA

Coverageb

(Tumor/Blood)

Sex

Grade

Histology

Locationc

Events with a breakpoint between IHH and ABCB6

MN-60370

2:217,875,406-220,056,209

Tandem duplication

Focal gain at 2q35

43.7/18.9

Female

I

Transitional

SB

MN-61891

2:218,024,502-220,058,113

Tandem duplication

Focal gain at 2q35

80/35.5

Female

I

Transitional

SB

MN-61983

2:218,258,592-220,067,681

Tandem duplication

Focal gain at 2q35

15.9/.

Male

I

Meningothelial

SB

MN-52323

2:218,152,515-220,060,111

Tandem duplication

Focal gain at 2q35

80.8/48

Male

I

Meningothelial

SB

MN-52420

2:161,061,851-219,931,428 (DUP),

2:220,090,023-242,064,976 (INV)

Tandem duplication and inversion,

a part of 2q chromothripsis

2q chromothripsis

79.8/31.5

Male

I

Meningothelial

NSB

MN-51500

2:218,324,785-220,073,582

Inversion between

DIRC3 and ZFAND2B

2q35 complex

rearrangement

12.9/.

Male

I

–

NSB

MN-52288

2:pter-220,029,008||10:77,508,708-qter,

10:pter-77,508,707||2:220,029,009-qter

Reciprocal inter-chromosomal

translocation (SLC23A3-LRMDA fusion)

None

79.5/30.7

Female

I

Meningothelial

SB

MN-63401

2:pter-220,034,453||1:218,632,910-qter,

15:pter-66,094,810||2:220,034,456-qter

Inter-chromosomal translocation

(SLC23A3-1q41/15q22.31)

No WES

67.8/.

Female

I

Meningothelial

SB

Events with a breakpoint between SHH and LMBR1

MN-52454

7:106,249,821-156,213,808

Tandem duplication,

a part of 7q chromothripsis

7q complex gains

61.1/26.2

Female

I

-

NSB

MN-61063

7:103,724,817-155,637,947 (DEL),

7:134,233,909-155,637,315 (DUP)

Deletion and tandem duplication,

a part of 7q chromothripsis

7q chromothripsis

70.5/37.5

Male

I

Meningothelial

SB

MN-52406

7:15,845,930-156,073,765

Inversion

None

67.9/37.6

Female

I

Meningothelial

SB

MN-63565

7:pter-156,288,487||8:69,296,588-qter,

8:pter-69,296,287||7:156,288,488-qter

Reciprocal inter-chromosomal

translocation (7q36.3-C8orf34)

None

56.2/19

Male

I

Meningothelial

SB

MN-61486d

7:pter-155,619,365||18:39,033,373-qter

Inter-chromosomal translocation

(7q36.3-18q12.3)

None

13.1/.

Male

I

Meningothelial

SB

Other events

MN-50008

2:219,483,604-219,925,168

Inversion between IHH and PLCD4

(IHH is disrupted)e

None

61.4/37.5

Male

I

Meningothelial

SB

MN-52396

12:51,635,001-63,918,911

Tandem duplication,

a part of 12q chromothripsis

No WES

67/36.7

Female

II

Atypical

NSB

MN-52391

1:pter-156,104,233||19:45,974,291-qter,

19:pter-45,974,314||1:156,104,245-qter

Reciprocal inter-chromosomal

translocation (FOSB-LMNA fusion)

None

61.8/35.4

Female

I

Transitional

NSB

MN-62105

22:pter-29,683,454||2:208,438,909-qter,

2:pter-208,439,319||22:29,683,029-qter

Reciprocal inter-chromosomal

translocation (EWSR1-CREB1 fusion)

None

56.9/17.8

Female

I

Meningothelial

SB

  1. All the events identified by MANTA from our samples (n = 24) can be found in Supplementary Data 11. Among the 24 samples, 19 acquired at least one structural variation (SV). Two of the 19 samples (MN-60690 and MN-61306) not listed here were subjected to tumor-only low-coverage WGS and their targeted SVs (tandem duplication at 2q35 implicated from WES and an event near IHH implicated from RNA-Seq) were not detected.
  2. aStructural variations were described using a (chromosome):(start)-(end) format for duplication and inversion while a (the first chromosomal segment)||(the second chromosomal segment) format for inter-chromosomal translocations.
  3. bThe mean coverages of tumor and blood samples. The missing value was indicated by a dot.
  4. cSB, skull base. NSB, non-skull base.
  5. dThis sample was sequenced to follow-up the finding of the ectopic expression of SHH.
  6. eThis event is unlikely to be a driver alteration (see the main text).
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