Detection of iAMP21 leukemia by sequencing leukemia cells, fluorescence in situ hybridization analysis, and sequencing cell-free DNA. (A) Estimated DNA copy number via targeted capture sequencing of ∼400 known cancer genes from the patient’s bone marrow, showing amplification (∼6-7 copies) of 3 genes located on 21q22 (RUNX1, ERG, TMPRSS2) as well as copy number gain of Xp, including CRLF2, FANCB, ZRSR2, and NR0B1. (B) Bone marrow metaphase fluorescence in situ hybridization demonstrating multiple signals from a RUNX1 probe (21q22, red) on the marker chromosome and 2 normal (green) signals for ETV6 (12p13). (C) Normalized DNA copy number estimations on chromosome 21 from cfDNA derived from maternal plasma demonstrating an amplification spanning ∼12 Mb of chr21q22 containing RUNX1, DYRK1A, ERG, and HMGN1.