Acute Myeloid Leukemia / LAML (TCGA)

Overview

LAML is the TCGA cohort identifier for acute myeloid leukemia. It corresponds to OncoTree AML (Acute Myeloid Leukemia). LAML is used specifically in the TCGA PanCancer Atlas context. The liquid-tumor nature of AML creates unique challenges for matched-normal somatic variant calling, as skin biopsies used as “normals” are often contaminated with circulating tumor cells.

Cohorts in the corpus

  • TCGA LAML cohort: included as one of 33 cancer types in the MC3 pan-cancer mutation-calling project and the TCGA fusion landscape study; subset of the PanCancer Atlas (laml_tcga_pan_can_atlas_2018).

Recurrent alterations

  • MC3 pan-cancer mutation-calling project recovered only 44% of the LAML AWG calls because tumor-in-normal contamination (LAML skin “normals” enriched with tumor cells) causes conservative MC3 filtering to misclassify somatic calls as germline; the legacy LAML AWG MAF relied on Sanger-based manual recovery not in the exome data PMID:29596782.
  • Pan-cancer fusion study (9,624 TCGA samples) found 14.0% of LAML tumors had fusions but no driver-gene mutations; recovered fusions include CBFB–MYH11 (n=3), BCR–ABL1 (n=2), PML–RARA (n=2), and NUP98–NSD1 (n=2); PML–RARA fusions annotated as druggable (16 samples); mutual exclusivity between CBFB fusions and CBFB point mutations observed PMID:29617662.

Subtypes

  • LAML (TCGA) encompasses multiple AML cytogenetic/molecular subtypes including CBF-AML (CBFB–MYH11, RUNX1–RUNX1T1), APL (PML–RARA), and FLT3-ITD driven cases.

Therapeutic landscape

  • PML–RARA fusions are actionable with all-trans retinoic acid (ATRA) and arsenic trioxide; 16 LAML samples with PML–RARA fusions were annotated druggable in the pan-cancer fusion analysis PMID:29617662.

Sources

  • PMID:29596782 — MC3 multi-center mutation calling (Ellrott et al., 2018)
  • PMID:29617662 — Pan-cancer fusion landscape (Gao et al., 2018)

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