Copy number alterations (CNAs)
Germline chromosome microarray analysis was performed for Patients 1 and 2 using a 180K platform (Agilent Technologies), as previously reported38. Somatic CNA events in the tumor from Patient 1 were derived from exome data obtained from the FFPE sample using the software Nexus Copy Number 9 (Biodiscovery), with the SNP-FASST2 segmentation algorithm (threshold log2 Cy3/Cy5 ratio of |0.2| for gains and losses; |1.2| for high copy number gains and homozygous losses; minimum LOH length of 10 Mb). Common CNVs (Database of Genomic Variants, http://dgv.tcag.ca/dgv/app/home) were disregarded.