Optimizing identification of consensus molecular subtypes in muscle-invasive bladder cancer: a comparison of two sequencing methods and gene sets using FFPE specimens

Table 2 Molecular subtype, histological subtype and immunohistochemical expression of CK5/6 and GATA3 for each patient

ID	MACE consensus	HTP consensus	MACE TCGA	HTP TCGA	CK5/6 IHC	GATA3 IHC	Histological subtype
41	Ba/Sq	Ba/Sq	Basal squamous	Basal squamous	pos	pos	Squamous
21	LumU	LumU	Luminal	Luminal papillary	neg	pos	NOS
7	LumP	LumP	Luminal papillary	Luminal papillary	neg	pos	NOS
32	Ba/Sq	Ba/Sq	Luminal infiltrated	Basal squamous	pos	pos	Squamous
26	NE-like	NE-like	Neuronal	Neuronal	neg	neg	Neuroendocrine
49	Ba/Sq	Stroma-rich	Basal squamous	Basal squamous	neg	neg	NOS
48	Stroma-rich	Ba/Sq	Luminal infiltrated	Basal squamous	neg	pos	NOS
45	Ba/Sq	Ba/Sq	Basal squamous	Basal squamous	pos	pos	Squamous
44	Ba/Sq	Ba/Sq	Basal squamous	Basal squamous	neg	neg	Lymphoepithelial
8	Ba/Sq	Ba/Sq	Basal squamous	Basal squamous	neg	pos	NOS
42	LumP	LumP	Luminal papillary	Luminal papillary	neg	pos	NOS
17	Ba/Sq	N/A	Basal squamous	N/A	pos	pos	NOS
9	Ba/Sq	Ba/Sq	Basal squamous	Basal squamous	pos	N/A	Squamous
46	Stroma-rich	LumNS	Luminal infiltrated	Luminal	neg	pos	NOS
20	LumNS	Stroma-rich	Luminal infiltrated	Lumina infiltrated	neg	pos	NOS

IHC Immunohistochemistry, pos positive (at least 10% of tumor cells show clear protein expression), neg negative, NOS not otherwise specified, N/A not available for evaluation

ISSN: 1471-2407