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.