Prognostic impact of gene mutations in

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primer digestion with the FuPa reagent (Thermo Fisher). Pooled amplicons were then ligated with universal adapters and different barcodes (Ion Xpress ...
Martín et al. 2017

Supplement – Gene mutations in MDS-RS

Prognostic impact of gene mutations in myelodysplastic syndromes with ring sideroblasts.

Supplementary methods, tables and figures in order of appearance.

Supplementary methods. Primers design. Primers were designed with Ion AmpliSeq™ technology (Thermo Fisher) to generate amplicons with an average length of 200 bp, providing a minimum coverage of 90% of the coding sequence. These primers were synthesized and pooled into 2 multiplex reactions based on PCR compatibility, minimizing the likelihood of primer-primer interactions. Sequencing protocol. For libraries preparation, 10 nanograms of each DNA sample was amplified using the gene panel Primer Pools and AmpliSeq HiFi mix (Thermo Fisher) in a Veriti® Thermal Cycler with 17 amplification cycles. PCR pools for each sample were subjected to primer digestion with the FuPa reagent (Thermo Fisher). Pooled amplicons were then ligated with universal adapters and different barcodes (Ion Xpress Barcodes™) for each sample. After a first purification with Agencourt® AMPure® XP Kit (Beckman Coulter), libraries were amplified with Platinum® PCR SuperMix High Fidelity and Library Amplification Primer Mix (Thermo Fisher). After a second purification, libraries were quantified using a Qubit® 2.0 Fluorometer with the Qubit® dsDNA HS Assay Kit and then they were normalized to 100 pmol/L. The normalized libraries were pooled in equal ratios for emulsion PCR (ePCR) on an Ion OneTouch System. Then, the templated Ion Sphere particles were enriched using the Ion OneTouch ES. The template-positive Ion PI Ion Sphere particles were loaded in an Ion PI chip V3 and sequenced on the Ion Proton instrument. Analyses were run on Torrent Suite and Ion Reporter Software providing sequence reads and variants in an exportable BAM, VCF and Excel file format.

1

Martín et al. 2017

Supplement – Gene mutations in MDS-RS

Molecular analysis. All listed variants were visually revised with the Integrative Genomics Viewer (IGV) software.1 The literature and the Catalogue Of Somatic Mutations In Cancer database (COSMIC) were employed to explore the impact of somatic mutations found. The potential severity of de novo mutations was evaluated using the SIFT, Polyphen2 and Mutation Taster algorithms.2 For variants located in splicing sites the Human Splicing Finder, NNSplice and NetGene2 algorithms were used to predict their pathogenicity.3 Finally, the “cBioPortal Tools” were applied to construct the DNMT3A mutations map and the DNMT3A protein 3D structure.4,5 Statistical analysis. Numerical variables were summarized by median and range and categorical variables described with count and relative frequency (percentage) of subjects in each category. Comparison of numerical variables between groups was performed using a nonparametric approach (Mann-Whitney test). Comparison of the distribution of categorical variables in different groups was performed with the X² test and Fisher’s exact test where appropriate. Overall survival was measured from the time of diagnosis to the last follow-up or death from any cause. Time to AML progression was measured from the date of MDS diagnosis to the time of AML diagnosis. Survival curves were generated using the Kaplan-Meier method and differences were assessed by log-rank test. For multivariable analysis, a Cox proportional hazard model was constructed. Statistical analyses were generated using the SPSS software and PG c.3516_3523del c.3818G>T c.2218A>T c.2225G>A c.2204A>G c.2098A>G c.2225G>A c.284C>G c.4280A>T c.3299A>G c.2098A>G c.2098A>G c.1986C>A c.1849G>T c.1759C>T c.2098A>G c.2098A>G c.1997A>C c.1849G>T c.2098A>G c.2645G>A c.2098A>G c.3852_3854del c.2098A>G c.1866G>C c.626G>A c.2098A>G c.737_737del c.2127_2128ins c.1643T>C c.2098A>G c.1984C>T c.5170_5171ins c.2018A>T c.2644C>T c.1986C>G c.1849G>T c.1759C>G c.2098A>G c.3862G>A

0 0 0

1 1 1

0

1

0.08 0 0 0.08 0.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0

0.966 1 1 0.966 0.134 1 0.998 1 1 1 0.996 1 1 1 1 0.996 1 1 1

0 0 0 0

1 1 0.998 1

0 0 0

1 1 1

0 0 0 0 0.57 0 0

DNMT3A SF3B1 TET2 SF3B1 SF3B1 SF3B1 TET2

p.Arg771Ter p.His662Gln p.Arg1202Ile p.Lys700Glu p.Arg625Gly p.Lys700Glu p.Tyr867His

c.2311C>T c.1986C>A c.3605G>T c.2098A>G c.1873C>G c.2098A>G c.2599T>C

0 0 0 0 0 0

MUTATION TASTER

COSMIC

ANNOTATION

84677 131553 131555

1 1 1 0.996 0.064 1 1

damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage

Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Possible oncogenic Oncogenic Oncogenic

1 1 1 1 1 0.999

damage damage damage damage damage damage damage

231563 130416

87135 145923 133126 84677 145923 211661

84677 84677 130416 12600 84677 84677 131556 12600 84677 52944 84677 211724 84677 132938 84677

84677 131560

53042 130416 12600 84677 110780

MDS-RS_22 MDS-RS_23 MDS-RS_24 MDS-RS_25 MDS-RS_26 MDS-RS_27

6

84677 1169490 84677 327337

Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic

Martín et al. 2017

MDS-RS_28 MDS-RS_29 MDS-RS_30 MDS-RS_31 MDS-RS_32 MDS-RS_33

MDS-RS_34

MDS-RS_35

MDS-RS_36

MDS-RS_37 MDS-RS_38 MDS-RS_39 MDS-RS_40 MDS-RS_41 MDS-RS_42 MDS-RS_43 MDS-RS_44 MDS-RS_45 MDS-RS_46 MDS-RS_47 MDS-RS_48 MDS-RS_49 MDS-RS_50

MDS-RS_51

MDS-RS_52

MDS-RS_53

MDS-RS_54

Supplement – Gene mutations in MDS-RS

SF3B1 EZH2 PTPN11 SF3B1 SF3B1 DNMT3A SF3B1 ASXL1 SF3B1 SF3B1 LUC7L2 TET2 DNMT3A SF3B1 SF3B1 ZRSR2 ZRSR2 DNMT3A SF3B1 SF3B1 TET2 TET2 SRSF2 SETBP1 GNAS

p.Glu622Asp p.Tyr133Asp p.Gly503Ala p.Lys700Glu p.Lys666Gln p.Trp327fs p.Lys700Glu p.Gln283His p.Glu622Asp p.Lys700Glu p.Glu111Asp p.Gln1541Ter p.Gly10fs p.Lys700Glu p.Lys700Glu p.Gln32Ter p.Cys312Tyr p.Arg736His p.Lys700Glu p.His662Asp p.Gln80Ter p.Gln969Ter p.Pro95His p.Asp868Asn p.Arg844Cys

c.1866G>T c.397T>G c.1508G>C c.2098A>G c.1996A>C c.979_979del c.2098A>G c.849G>C c.1866G>T c.2098A>G c.333G>C c.4621C>T c.27_28ins c.2098A>G c.2098A>G c.94C>T c.935G>A c.2207G>A c.2098A>G c.1984C>G c.238C>T c.2905C>T c.284C>A c.2602G>A c.2530C>T

SF3B1 SF3B1 SF3B1 SF3B1 SF3B1 JAK2 SF3B1 SF3B1 SRSF2 SF3B1 SF3B1 SF3B1 SF3B1 CBL DNMT3A SF3B1 DNMT3A SF3B1 SF3B1 TET2 DNMT3A DNMT3A SF3B1 TET2 JAK2 DNMT3A SF3B1 DNMT3A SF3B1 TET2 BCOR

p.Lys700Glu p.Lys700Glu p.Gly742Asp p.Arg625Gly p.His662Gln p.Val617Phe p.Lys700Glu p.Lys666Asn p.Pro95His p.Lys700Glu p.Lys700Glu p.Lys700Glu p.Lys700Glu p.Arg462Ter p.Arg882Cys p.Lys700Glu p.Arg882His p.Lys700Glu p.Lys700Glu p.His1219Tyr p.Arg882Cys p.Gly685Arg p.Lys700Glu p.Leu699Ter p.Val617Phe p.Asn403fs p.Arg625Leu p.Ile369fs p.Glu622Asp p.Thr1884Ala p.Ala970Glu

c.2098A>G c.2098A>G c.2225G>A c.1873C>G c.1986C>A c.1849G>T c.2098A>G c.1998G>C c.284C>A c.2098A>G c.2098A>G c.2098A>G c.2098A>G c.1384C>T c.2644C>T c.2098A>G c.2645G>A c.2098A>G c.2098A>G c.3655C>T c.2644C>T c.2053G>A c.2098A>G c.2096T>A c.1849G>T c.1208_1208del c.1874G>T c.1105_1117del c.1866G>T c.5650A>G c.2909C>A

7

0 0 0 0 0

1 0.068 0.998 1 1

0 0.02 0 0 0.03

1 1 1 1 0.565

0 0

1 1

0 0.39 0 0

1 0.997 1 1

0 0 0

1 1 1

0 0 0 0 0 0 0 0 0 0 0 0 0

1 1 1 1 1 0.996 1 1 0.065 1 1 1 1

0 0 0 0 0 0 0 0.01 0

1 1 1 1 1 1 1 1 1

0

0.996

0

1

0 0 0

1 1 1

damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage

132938 144172 13027 84677 132950 84677 132938 84677

84677 84677

133737 84677 131560 43428 211504 1318400 1566192 84677 84677 145923 1169490 130416 12600 84677 131557 211504 84677 84677 84677 84677 34079 53042 84677 452944 84677 84677 53042 1235163 84677 12600 110695 144493 132938

Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Possible oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic

Martín et al. 2017

MDS-RS_55

Supplement – Gene mutations in MDS-RS

DNMT3A DNMT3A SF3B1

p.Asp702fs p.Gly10fs p.Lys666Thr

c.2104_2104del c.27_28ins c.1997A>C

SF3B1 TET2 TET2 SF3B1 TET2 TET2 TET2 ZRSR2 DNMT3A SF3B1 BCOR SF3B1

p.Lys666Gln p.Glu28fs p.Cys677fs p.His662Gln p.Gln1030Ter p.His1219Asn p.Arg1891Gly p.Trp111Ter p.Arg882Cys p.Lys700Glu p.Val598fs p.Lys666Arg

c.1996A>C c.81_82del c.2027_2030del c.1986C>A c.3088C>T c.3655C>A c.5671A>G c.333G>A c.2644C>T c.2098A>G c.1791_1792ins c.1997A>G

RUNX1

p.Arg169fs

c.506_507ins

SF3B1 CALR SF3B1 SPARC ETV6 STAG2 SF3B1 SF3B1 SF3B1 TET2 SF3B1 TET2

p.Lys700Glu p.Glu380Gly p.Lys700Glu p.Arg268His p.Met389Val p.Arg1012Gln p.Lys666Arg p.Glu622Asp p.His662Gln p.Gly1152Glu p.Asn626Asp p.Gln866fs

c.2098A>G c.1139A>G c.2098A>G c.803G>A c.1165A>G c.3035G>A c.1997A>G c.1866G>C c.1986C>G c.3455G>A c.1876A>G c.2593_2597del

DNMT3A

p.Arg320Ter

c.958C>T

SF3B1 TET2 SF3B1 TET2 JAK2 SF3B1 SF3B1 TET2 SETBP1 SETBP1 SF3B1 TET2 TET2 SF3B1 TET2 ETV6 SRSF2 SETBP1 SETBP1 SF3B1 ETV6 TET2 DNMT3A SF3B1 TET2 TET2 ETV6

p.Lys700Glu p.Phe1309Leu p.Lys700Glu p.Pro1419Arg p.Val617Phe p.Lys700Glu p.Lys700Glu p.Gln1034Ter p.Asp868Asn p.Gly870Ser p.Arg625Leu p.Gln591Ter p.His1416Asp p.Lys700Glu p.Leu1212fs p.Tyr346Cys p.Pro95_Arg102del p.Asp868Asn p.Asp874Asn p.Lys700Glu p.Leu201Pro p.Glu783Ter p.Gln692Ter p.Thr663Ile p.Gln1084Pro p.Glu783Ter p.Leu201Pro

c.2098A>G c.3927T>A c.2098A>G c.4256C>G c.1849G>T c.2098A>G c.2098A>G c.3100C>T c.2602G>A c.2608G>A c.1874G>T c.1771C>T c.4246C>G c.2098A>G c.3633_3633del c.1037A>G c.284_307del c.2602G>A c.2620G>A c.2098A>G c.602T>C c.2347G>T c.2074C>T c.1988C>T c.3251A>C c.2347G>T c.602T>C

0

1

0

1

0

1

0 0

1 1

0 0

1 1

0

1

0 0.4 0 0.06 0 0.15 0 0 0 0 0

1 0 1 1 1 0.971 1 1 1 1 1

0 0 0 0 0 0 0

1 0.999 1 1 0.996 1 1

0 0 0

1 1 1

0 0

1 1

0

1

0 0 0 0.01

1 1 1 0.641

0 0

1 0.325

0.01

0.641

damage damage damage

131556

Oncogenic Oncogenic Oncogenic

MDS-RS_56 MDS-RS_57

MDS-RS_58

MDS-RS_59

MDS-RS_60 MDS-RS_61

MDS-RS_62

MDS-RS_63 MDS-RS_64 MDS-RS_65 MDS-RS_66

MDS-RS_67

MDS-RS_68 MDS-RS_69 MDS-RS_70 MDS-RS_71 MDS-RS_72 MDS-RS_73 MDS-RS_74

MDS-RS_75

MDS-RS_76

MDS-RS_77

MDS-RS_78

8

damage damage damage damage damage damage damage damage damage damage damage damage

132950 1426202 43519 130416 96929

131553

Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic

damage

1318812

Oncogenic

damage damage damage damage damage damage damage damage damage damage damage damage

84677

Oncogenic Possible oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic

53042 84677

84677

1465378 131553 132938 130416 53268 131555

damage

133721

Oncogenic

damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage

84677

Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic

84677 100055 12600 84677 84677 1318400 1234973 110695

84677 87124 146289 1318400 1717365 84677 546746

145921

546746

Martín et al. 2017

MDS-RS_79 MDS-RS_80 MDS-RS_81 MDS-RS_82 MDS-RS_83 MDS-RS_84 MDS-RS_85 MDS-RS_86 MDS-RS_87

MDS-RS_88

MDS-RS_89 MDS-RS_90 MDS-RS_91

MDS-RS_92

MDS-RS_93 MDS-RS_94 MDS-RS_95 MDS-RS_96 MDS-RS_97 MDS-RS_98 MDS-RS_99

MDS-RS_100 MDS-RS_101 MDS-RS_102 MDS-RS_103 MDS-RS_104

MDS-RS_105 MDS-RS_106 MDS-RS_107 MDS-RS_108 MDS-RS_109 MDS-RS_110

SF3B1 TET2 SF3B1 TET2 SRSF2 STAG2 SF3B1 SF3B1 SF3B1 SF3B1 TET2 TP53 ZRSR2 SF3B1 SF3B1 TET2 NF1 SETBP1 SF3B1 IDH2 SF3B1 SF3B1 ETV6 ZRSR2 SF3B1 TET2 SMC3 IDH1 SF3B1 SF3B1 SF3B1 SETBP1 GNAS SF3B1 SF3B1 SF3B1 DNMT3A SF3B1 TET2 SF3B1 JAK2 SF3B1 SF3B1 SF3B1 SF3B1 TET2 TET2 TET2 EZH2 IDH2 SRSF2 SF3B1 SF3B1 TET2 SF3B1 TET2 CBL

Supplement – Gene mutations in MDS-RS

p.Lys700Glu p.Cys1289Tyr p.Lys700Glu p.Gln769fs p.Pro95_Arg102del p.Glu1023Val p.Lys700Glu p.Lys700Glu p.Lys700Glu p.Lys700Glu p.Gln876Ter p.Cys176Trp p.Tyr292Asn p.Lys666Arg p.Lys700Glu p.Asn1805fs p.Thr1730Ser p.Arg1321His p.Glu622Asp p.Arg140Gln p.His662Gln p.His662Asp p.Leu201Pro p.Lys90Met p.Lys666Thr p.Leu878fs p.Tyr1140Asn p.Phe32Val p.Lys700Glu p.Lys700Glu p.Lys700Glu p.Arg627Cys p.Arg844His p.Arg625Cys p.Lys700Glu p.Lys700Glu p.Cys559Tyr p.Lys700Glu p.Gln341Ter p.Lys700Glu p.Pro708Ser p.Lys700Glu p.Lys666Arg p.Lys700Glu p.Lys700Glu p.Trp564Ter p.Ser714Ter p.Leu500fs p.Asp657Tyr p.Arg140Gln p.Pro95Arg p.Lys666Asn p.Lys700Glu p.Gln684fs p.Trp658Arg p.Arg1404Ter p.Arg420Gln

c.2098A>G c.3866G>A c.2098A>G c.2305_2305del c.284_307del c.3068A>T c.2098A>G c.2098A>G c.2098A>G c.2098A>G c.2626C>T c.528C>G c.874T>A c.1997A>G c.2098A>G c.5413_5413del c.5189C>G c.3962G>A c.1866G>T c.419G>A c.1986C>G c.1984C>G c.602T>C c.269A>T c.1997A>C c.2632_2632del c.3418T>A c.94T>G c.2098A>G c.2098A>G c.2098A>G c.1879C>T c.2531G>A c.1873C>T c.2098A>G c.2098A>G c.1676G>A c.2098A>G c.1021C>T c.2098A>G c.2122C>T c.2098A>G c.1997A>G c.2098A>G c.2098A>G c.1691G>A c.2141C>G c.1494_1495ins c.1969G>T c.419G>A c.284C>G c.1998G>T c.2098A>G c.2046_2046del c.1972T>A c.4210C>T c.1259G>A

9

0 0 0

1 1 1

0 0 0 0 0

0.974 1 1 1 1

0 0 0 0

1 1 1 1

0.01 0 0 0 0 0 0.01 0 0

1 1 1 1 1 1 0.641 0.998 1

0 0.02 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0

1 0.303 1 1 1 1 1 1 1 1 1 1 1 1 0.999 1 1 1 1

0 0 0.05 0 0

1 1 0.134 1 1

0

1

0

1

damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage

84677 87136 84677 87100 146289 84677 84677 84677 84677 211613 1268357 131553 84677

132938 41590 130416 131560 546746 131556

1581043 84677 84677 84677 1236142 94388 110696 84677 84677 84677 84677 84677 131553 84677 84677 1716596 211641 1000720 41590 211661 131557 84677 211686

34077

Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic

Martín et al. 2017

Supplement – Gene mutations in MDS-RS

MDS-RS_120 MDS-RS_121

SF3B1 TET2 SF3B1 TET2 TET2 SF3B1 IDH2 RUNX1 SF3B1 TET2 SF3B1 SF3B1 DNMT3A SF3B1 SF3B1 SF3B1 JAK2 SF3B1 DNMT3A

p.Lys700Glu p.Lys1339fs p.Lys700Glu p.Ser657Ter p.Gln1084Pro p.Asp584Glu p.Arg140Gln p.Asn96Ser p.Lys700Glu p.Cys1271fs p.Lys700Glu p.Glu622Asp p.Trp327Ter p.Lys700Glu p.Lys700Glu p.His662Gln p.Val617Phe p.Lys700Glu p.Tyr436Ter

c.2098A>G c.4011_4012ins c.2098A>G c.1970C>G c.3251A>C c.1752T>A c.419G>A c.287A>G c.2098A>G c.3811_3812ins c.2098A>G c.1866G>C c.981G>A c.2098A>G c.2098A>G c.1986C>A c.1849G>T c.2098A>G c.1308C>A

MDS-RS_122

SF3B1

p.Glu622Asp

c.1866G>T

MDS-RS_111

MDS-RS_112

MDS-RS_113

MDS-RS_114 MDS-RS_115 MDS-RS_116 MDS-RS_117 MDS-RS_118 MDS-RS_119

0

1

0

1

0 0.03 0 0.08 0

0.325 1 1 0.988 1

0 0

1 1

0 0 0 0 0

1 1 1 0.996 1

0

1

damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage damage

84677 87145 84677

41590 84677 87134 84677 132938 84677 84677 130416 12600 84677 132938

Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic Oncogenic

Supplementary Table 5. Splicing mutations in study.

SAMPLE ID.

LOCUS

REF/CHANGE

GENE

LOCATION

NNSPLICE

HSF

NETGENE2

MUTATION TASTER

ANNOTATION

MDS-RS_55 MDS-RS_79 MDS-RS_81 MDS-RS_95

chr2:25458695 chrX:15836766 chr21:36259138 chr10:112342401

C/T G/A A/G G/A

DNMT3A ZRSR2 RUNX1 SMC3

splicesite_5 splicesite_3 splicesite_3 splicesite_3

damage damage damage damage

damage damage damage neutral

neutral damage damage damage

damage damage damage damage

Possible oncogenic Possible oncogenic Possible oncogenic Possible oncogenic

MDS-RS_110

chr7:148543690

T/TT

EZH2

splicesite_5

neutral

damage

neutral

damage

Possible oncogenic

10

Martín et al. 2017

Supplement – Gene mutations in MDS-RS

Supplementary Table 6. Multivariable analyses for overall survival and risk of AML progression.

Variable

Overall survival

Risk of AML progression

HR

95% CI

P value

HR

95% CI

P value

Intermediate-1 vs. Low

2.28

1.01 to 5.17

0.048

0.00

Age ≥75 vs. ˂75 years

4.47

2.13 to 9.39