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Proposed Analysis: AML subtyping #55

Closed kgaonkar6 closed 2 years ago

kgaonkar6 commented 3 years ago

What are the scientific goals of the analysis?

From email discussion with Dr. Sarah Tasian, we have the following information that we should use to subtype AML.

I have included our pediatric AML risk classification from our current COG phase 3 clinical trial (AAML1831) and how we are stratifying patients by underlying genetic alterations in case helpful. An earlier version of this clinical protocol table is included in a review paper attached if you need a reference. Please note that ‘RAM phenotype’ is a flow cytometry designation (CD56++ and dim for CD45/CD38/HLA-DR) and usually aligns with the CBFA2T3-GLIS2 fusion in AMKL. ‘Low risk’ AML: RUNX1-RUNXT1 from t(8;21), CBFB-MYH11 from inv(16), CEBPA point mutations, NPM1 point mutations ‘High risk’ AML: classically monosomy 7, monosomy 5/5q-, and FLT3-ITD, but now with many others Lesions that are not clearly prognostic fall into an intermediate category, and we use end-induction measurable residual disease (MRD) to refine risk stratification and allocate to transplant in first remission or not.

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What methods do you plan to use to accomplish the scientific goals?

🚨 This is a draft @jharenza will update/add information We will use fusion calls to subtype the samples the subtypes for now

What input data are required for this analysis?

fusion-putative-oncogenic.tsv

How long do you expect is needed to complete the analysis? Will it be a multi-step analysis?

2-3 days

Who will complete the analysis (please add a GitHub handle here if relevant)?

@kgaonkar6

What relevant scientific literature relates to this analysis?

jharenza commented 3 years ago

Adding to this data dictionary prepared by Sam V and discussed with Sarah T to the ticket. I also sent an email to Sarah today asking if she would like us to use the below designations or the high/med/low risk designations as above. If using above, they won't match NCIT IDs, so we will have to figure out how to best do that part.

inv(16)(p13q22) NCIT:C36373
t(16;16)(p13.1;q22) NCIT:C27759
t(15;17)(q24;q21) NCIT:C27758
t(9;11)(p22;q23) / MLL-MLLT3(AF9) NCIT:C36370
t(10;11)(p12;q23) / MLL-MLLT10(AF10) NCIT:C132102
t(10;11)(p11.2;q23) NCIT:C168758
t(1;11)(q21;q23) / MLL-MLLT11(AF1Q) NCIT:C168759
t(4;11)(q21;q23) / MLL-MLLT2(AF4) NCIT:C36365
t(6;11)(q27;q23) / MLL-MLLT4(AF6) NCIT:C36610
t(6;9)(p23;q34) DEK/NUP214 NCIT:C36532
t(11;19)(q23;p13) / (MLL-ENL)/(MLL-ELL) NCIT:C168764
t(11;19)(q23;p13.1) / (MLL-ELL) NCIT:C36371
t(11;19)(q23;p13.3) / (MLL-ENL) NCIT:C36372
MLL Other Partner NCIT:C36517
t(11;17)(AF17) NCIT:C168760
t(8;16)MOZ/CBP NCIT:C167194
Monosomy 7 NCIT:C36411
Monosomy 5 NCIT:C36523
Trisomy 8 NCIT:C36396
der.12p NCIT:C173542
t(2;12) NCIT:C173543
t(5;11)(q35;p15) / NSD1/NUP98 NCIT:C131503
t(7;12)(q36;p13) / HLXB9(MNX1)/ETV6(TEL) NCIT:C122689
t(9;22)(q34;q11.2) / ABL/BCR NCIT:C13271
inv(3)(q21.3;q26.2) NCIT:C36407
t(3;3)(q21;q26.2) NCIT:C36406
t(3;12)(q23;p12.3) / ETV6/EVI1 NCIT:C168766
del(5q)(5q31-q32) NCIT:C168769
t(1;22)(RBM15-MKL1) NCIT:C36417
del(13q)(13q14-21) NCIT:C168770
del(17p) NCIT:C36499
MLL Rearrangement NCIT:C122623
Non-KMT2A MLLT10 NCIT:C168771
inv(16)(p13.3q24.3) / CBFA2T3-GLIS2 NCIT:C167195
t(11;15)(p15;q35) / NUP98/JARID1A NCITC131505
t(16;21)(q24;q22) / RUNX1-CBFA2T3 NCIT:C168773
t(3;5)(q25;q34) / NPM1/MLF1 NCIT:C36415
t(16;21)(p11;q22) / FUS/ERG NCIT:C36616
NPM1 Mutation NCIT:C82429
Monoallelic CEBPA Gene Mutation NCIT:C168774
Biallelic CEBPA Gene Mutation NCIT:C157569
CEBPA Gene Mutation NCIT:C38372
FLT3 Internal Tandem Duplication NCIT:C67494
FLT3 Tyrosine Kinase Domain Point Mutation NCIT:C67495
WT1 Mutation NCIT:C146726
CKIT Mutation - Ex17 NCIT:C116396
CKIT Mutation - Ex8 NCIT:C128660
CKIT Mutation - Unspecified NCIT:C39712
GATA1 Mutation NCIT:C82340
RUNX1 Mutation NCIT:C38362
PTPN11 Mutation NCIT:C82612
N-RAS Mutation NCIT:C41381
K-RAS Mutation NCIT:C41361
Other NCIT:C17649
Unknown NCIT:C17998
Not Reported NCIT:C43234
kgaonkar6 commented 3 years ago

Just wanted to verify the nomenclature, since I don't think we have use cytogenetic terms before for subtyping.

del(5q)(5q31-q32) http://atlasgeneticsoncology.org/Anomalies/del5qID1092.html deletion anywhere in chr5 q or chr 5q31-32

inv(16)(p13q22) http://atlasgeneticsoncology.org/Anomalies/inv16ID1036.html which I believe denotes a inversion chr16 in p13 and q22

t(9;22)(q34;q11.2) / ABL/BCR http://atlasgeneticsoncology.org/Anomalies/t0922ALLID1024.html, denotes a translocation and chr 9 q34 and chr22q11.2 AND OR a fusion of ABL-BCR

der.12p ?

jharenza commented 3 years ago

Oh yes - I have a new email from Sarah and still have to compile this - we will not search fro these, but rather include in the subtype itself. Have to think about how we want to do this.