Tumour DNA was isolated using the QIAmp DNA Mini kit (Qiagen, Venlo, The Netherlands). Single-nucleotide polymorphism (SNP) analysis was performed using an Affymetrix 250K_NSP or Affymetrix SNP 6.0 array to detect chromosome 3 loss. Additional copies of chromosome 8q were detected by Affymetrix SNP 6.0 array and analyzed using the GISTIC 2.0 algorithm [20 (link),21 (link)].
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