Table 2.

Several genomic imbalances identified in the three tumor samples and their clinical association described in the literature

					Present Study
Chr.	Genes	Type of alteration	Clinical association	References	Primary Tumor	Recurrence	SPT
3p21.31	SEMA3F	Loss	High metastasis and poor survival	[14]	No	Yes	Yes
3p22.2	MLH1	Loss	Early stages of disease	[15]	Yes	Yes	Yes
3p14.2	FHIT	Loss	Early Event	[16]	No	Yes	No
3q26.32	PIK3CA	Gain	Poor prognosis	[17, 18]	No	No	Yes
3q26.33	SOX2	Gain	Metastasis,worse outcome, resistance to cisplatin	[19]	No	Yes	No
4q32.3	PALLD	LOH	Poor survival	[20]	No	Yes	No
4q32.3	DDX60L	LOH	Poor survival	[20]	No	Yes	No
4q35.2	ING2	LOH	Advanced stage	[21]	Yes	Yes	No
4q35.2	FAT1	LOH	Advanced tumour stage	[22]	No	Yes	No
7p11.2	EGFR	Gain	Poor prognostic	[23]	No	Yes	Yes
9p21.3	CDKN2A	Loss	High frequency of recurrences; early event in HNSCC progression	[24]	No	Yes	Gain
9p21.3	CDKN2B	Loss	Early event in HNSCC progression	[25]	No	Yes	Gain
11q13.3	FADD	Gain	Worse disease-specific survival	[26]	No	Yes	Yes
11q13.3	ANO1	Gain	Poor overall survival, metastases	[27, 28]	No	Yes	Yes
11q13.3	CTTN	Gain	Lymph node metastasis	[29]	No	Yes	Yes
11q13.3	CCND1	Gain	Presence of occult lymph node metastases, advanced clinical stage and shorter survival	[30, 31]	No	Yes	Yes
11q21	MRE11A	Loss	Reduced sensitivity to ionizing radiation in HNSCC	[32]	No	No	Yes
11q22.3	ATM	Loss	Reduced sensitivity to ionizing radiation in HNSCC	[32]	Yes	Yes	Yes
11q23.3	H2AFX	Loss	Reduced sensitivity to ionizing radiation in HNSCC	[32]	Yes	Yes	Yes
13q13.1	BRCA2	LOH	Poor patient outcome	[33]	Yes	Yes	Yes
13q14.2	RB1	LOH	Poor patient outcome	[33]	Yes	Yes	Yes
17p13.1	TP53	Loss	Nonresponse to neoadjuvant chemotherapy	[34]	Yes	Yes	Yes
18q21.2	SMAD4	Loss	Advanced stage and poor prognosis	[35]	No	Yes	No
18q23	GALR1	Methylation	Advanced stage and poor prognosis	[36, 37]	No	Loss	No
22q13.2	CYB5R3	Loss	Worse prognosis, decreased survival	[38]	Yes	No	No