As a complementary subtype assignment, a classification method to nearest centroids (ClaNC), classified the 28 cell lines into the four SqCC subtypes, with seven basal, seven classical, five primitive and nine secretory cell lines (first subtype of ClaNC in Table 2).
This patient was diagnosed with undifferentiated pleomorphic sarcoma (giant cell subtype).
Sequence analysis of the core region confirmed the subtype assignment performed within the NS5b region in 63 isolates.
In order to support the genotype assignment based on the NS5B region, sequence analysis was performed on the core region for selected isolates, confirming the subtype assignment performed within the NS5B region in 63 of them (Figure 3).
The reliability of clustering was evaluated using bootstrap analysis with 1,000 replicates [40], where bootstrap values above 70 were considered significant for subtype assignment.
A 100% concordance was found between the subtype assignment in the NS5B and core region, implying no evidence of recombination in the samples analyzed in these regions.
Molecular subtype assignment according to the subtype clustering method [ 17].
Immunophenotyping and subtype assignment was carried out as previously described.
This procedure improved the subtype assignment for several cancer samples.
