mRNA status was obtained from fresh frozen tumor tissue. RNA for gene expression profiling was isolated with the RNeasy mini kit (Qiagen). HLA Class I expression was measured on an Illumina HT-12v4 chip (Illumina) following the manufacturer’s guidelines. The probes seen in Table 5 were used for this analysis. They had previously been compared with immunohistochemical data [24 (link),28 (link)].
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