Table 3 Representative studies showing evidence for relevant genomic alterations in MDS and AML

AML with complex karyotype

60

2.8K BAC/PAC aCGH

100%

Frequent losses of 5q(77%), 17p(55%), 7q(45%), 16q, 18q, 17q, 3p, 12q, 20q, 12p, 18p, 13q, 11q; gains/amplifications of 11q(40%), 8q(38%), 21q, 1p, 9p, 22q, 13q, 6p, 19p

II

8

de novo AML

100

44K oligo-aCGH (Agilent)

74%

Five smallest overlapping regions of imblances: 5q31.3, 16q23.1, 16q24.2, 17q11.2(NF1), 18p11.2

I

9

AML with normal karyotype

26

44K oligo-aCGH (Agilent)

15%

Cryptic losses of 8q24.11, 12p12.3, 1q41, 18q21,32, 12p13.2(ETV6), gain 3p21.3, dmin 8q24.13-q24.21(MYC)

II

10

MDS/AML with normal karyotype

38

SNP-chip (Affymetrix)

49%

CNN-LOH of 1p, 6p, 8q, 13q, 19p, 5q, 12q, 21q, 9p; losses of 17q11.2(NF1), 12p13.31p13.2(ETV6), 2q36.2, 4q24, 9p21.3p21.2(CDKN2A), 3p26.3, 14q21.2, 21q21.2, 8p23.2, 2p23.1; gains of 1q43, 18q21.2, 8q24.13q24.21(MYC)

II

11

Low risk MDS (CD34+ cells)

44

32K BAC tiling array

82%

Recurring common regions: losses of 2p23.1, 2q33.1-q33.2, 4p14, 5q13.1q13.2, 5q14.3q33, 5q33.3, 6p23, 10q21.3, 14q12, 19p12p13.2, 20q11.21q13.13, 22q13.1q13.2; gains of 7q34, 11q12.2, 11q24.2qter, 17q11.2, 17q12

II

12

Adult de novo AML

86

SNP 6.0 genechip (Affymetrix)

40%

12 recurring alterations found from 201 CNAs: losses of 3p14.1(FHIT), 5q31.1(CTNNA1), 7q31.31, 12p12.3(ETV6), 16q22.1(CEFB), 17p13.1(TP53), 17q11.2(NF1), 18p11.31; amplifications of 8q23.2(MYC), 11q23.3(MLL), 19q13.43, 21q22.2(ETS2)

I

13

Pediatric de novo AML

111

SNP-chips (Affymetrix)

Low#

Signficant losses of 5p15.33, 7p21.3, 7q36.1, 8q21.3 (RUNX1T1), 9p21.3 (CDKN2A), 9p21.2(TUSC1), 9p22.33(XPA), 11p14.1, 11q23.3(MLL), 12p13.31, 16p13.11(MYH11), 16q22.1(CBFB), 18p11.21; amplifications of 8q24.21(CCDC26), 13q32.1(ABCC4), 19p13.2), 21q22.2(ERG, TMPRSS2), 22q12.3.

I

14

MDS/MPN/AML with abnormal karyotype

30

SignatureChipWGBAC (v1.01)

80%

Cryptic RUNX1 deletions, hidden deletions of 3q26.2(EVI1), 5q22(APC),5q32(TCERG1), 12p13.1(EMP1), 12q21.3(KITLG), 17q11.2(NF1), gains of 12p13.32(CCND2)

II

15

MDS/AML with abnormal karyotype

30

44K oligo-aCGH (Agilent)

93%

Recurring alterations: losses of 5q(RPS14), 12p12.3(ETV6), 17p13(TP53), 17q11.2(NF1), 20q; gains of 8q24(MYC),11q23.2(MLL).

II

this report