Table 1 Summary of tumor cohort and analyses performed

From: MDM2 amplification in rod-shaped chromosomes provides clues to early stages of circularized gene amplification in liposarcoma

Case No.

Diagnosisa

Ploidyb

G-bandc

SNP arrayd

WGSe

RNA-seqf

scWGSg

Chr12h

CN MDM2i

CN chr12j

CN chr1k

Group A: Tumors with gain of MDM2 in rod-shaped chromosomes

 1

WDLS

Dip

Yes

Yes

shortWGS

Yes

67

1

3/4 (WGS)

3–5/3–7 (WGS)

No

 2

WDLS

Dip

Yes

ND

shortWGS

Yes

ND

1

3 (WGS,VI)

3 (WGS, VI)

No

 3

Lipoma

Dip

Yes

Yes

ND

Yes

ND

2

3

3

No

 4

WDLS

Dip

Yes

ND

ND

Yes

ND

1

5 (FISH)

Unknown

Unknown

 5

WDLS

Dip

Yes

ND

shortWGS, longWGS

Yes

46

2

6 (WGS)/7 (FISH)

3–6 (WGS)

3–8 (WGS)

 6

Lipoma

Dip

Yes

Yes

ND

Yes

ND

1

3/4 (FISH)

3

No

 7

WDLS

Dip

Yes

Yes

shortWGS

Yes

ND

1

3/3 (WGS;FISH)

3/3 (WGS)

No

Group B1: Tumors with gain of MDM2 in ring chromosomes and with large contigues of 12q gain > 10 Mb

 8

WDLS

Dip

ND (FISH)

Yes

ND

Yes

30

2 (FISH)

4

3–8

3–7

 9

WDLSl

Dip

ND (FISH)

Yes

ND

Yes

18

2 (FISH)

6

3–15

3–10

 10a

WDLS

Dip

Yes

Yes

ND

ND

ND

2

8

3–12

No

 10b

WDLS

Dip/Tet

Yes

Yes

ND

ND

ND

2/4

8

3–11

No

 10c

WDLS

Dip

Yes

Yes

ND

ND

ND

2

8–10

3–14

No

 10d

WDLS

Dip

ND

Yes

ND

Yes

ND

ND

6

3–9

No

 11

WDLS

Dip

Yes

Yes

ND

Yes

ND

2

8

5–9

No

 12

Lipoma

Dip

Yes

Yes

ND

Yes

ND

2

7

3–7

3–8

 13a

WDLS

Dip

Yes

Yes

ND

Yes

ND

2

9

3–11

No

 13b

WLDS

Dip

ND

Yes

ND

ND

ND

ND

9

3–16

No

 14

WLDS

Dip

ND (FISH)

Yes

ND

Yes

ND

2

8

3–11

3–9

 15

WDLS

Dip/Tet

Yes

Yes

ND

ND

ND

2/4

10

3–16

3–13

 16a

WDLS

Dip/Tet

Yes

Yes

ND

ND

ND

2/4

12

3–14

3

 16b

WDLS

Dip/Tet

ND

ND

shortWGS

Yes

ND

ND

60 (WGS)

4–97 (WGS)

4–13 (WGS)

 17

WDLS

Dip

Yes

Yes

ND

Yes

ND

2

10

3–14

3–8

 18

WDLS

Dip

ND (FISH)

Yes

ND

Yes

ND

2

19

5–20

1–20

 19

WLDS

Dip/Tet

Yes

Yes

ND

Yes

ND

2/4

9

3–11

3–9

Group B2: Tumors with gain of MDM2 in ring chromosomes and with shorter contigues of 12q gain < 6 Mb

 20a

WDLS

Dip

Yes

Yes

ND

ND

ND

2

11

3–13

No

 20b

WDLS

Dip

Yes

Yes

ND

Yes

8

2

13

3–14

No

 20c

DDLS

Dip

Yes

Yes

shortWGS

ND

37

2

2–16/36 (WGS)

3–16/3–52 (WGS)

No

 21

WDLS

Dip

Yes

Yes

longWGS

Yes

ND

2

8

3–8

3–7

  1. aWDLS atypical lipoma/well-differentiated liposarcoma, DDLS dedifferentiated liposarcoma.
  2. bDip diploid, Tet tetraploid.
  3. cKaryotype from G-banding analysis available; ND not done, (FISH) ring chromosome confirmed by metaphase FISH.
  4. dSNP array single nucleotide polymorphism array; ND not done.
  5. eWGS whole genome sequencing, ND not done, shortWGS short read WGS with x90 coverage, longWGS long read WGS.
  6. fRNA-seq mRNA sequencing, ND not done.
  7. gscWGS single cell whole genome sequencing, No. of cells analyzed shown; ND not done.
  8. hChr12 number of intact chromosomes 12, ND not done.
  9. iMDM2 number of MDM2 copies, as estimated with SNP array and/or other method (other method shown in parentheses), VI visual inspection.
  10. jCN Chr12 Copy number levels in gained segments on chromosome 12, as estimated with SNP array and/or other method (other method shown in parentheses), VI visual inspection.
  11. kCN Chr1 Copy number levels in gained segments on chromosome 1, as estimated with SNP array and/or other method (other method shown in parentheses).
  12. lWDLS with minimal atypia (Supplementary Fig. 4).
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