Role of chromosome 1q copy number variation in hepatocellular carcinoma

Table 1 Amplified genes within/near 1q21-23 that have been associated with hepatocellular carcinoma

Gene1	Location2	Description of protein product	Ref.
JTB	1q21.3	Promotes cell resistance to apoptosis	Wong et al[11] and Kanome et al[12]
SHC1	1q21.3	Downstream signaling from receptor tyrosine kinases	Wong et al[11], Midorikawa et al[8], Pelicci et al[13], Kavanaugh and Williams[14], and van der Geer et al[15]
CCT3	1q22	Associated with cell cycle regulation	Wong et al[11], Midorikawa et al[8], Won et al[16]
COPA	1q23.2	Assists in retrograde vesicular transport from Golgi to endoplasmic reticulum	Wong et al[11] and Vece et al[17]
CKS1B	1q21.2	Associated with cell cycle regulation	Midorikawa et al[8] and Ganoth et al[19]
HAX-1 (HAX1)	1q21.3	Plays a role in the activation of receptor tyrosine kinases	Midorikawa et al[8] and Suzuki et al[18]
CREB3L4	1q21.3	Associated with androgen receptor signaling	Inagaki et al[21] and Qi et al[22]
INTS3	1q21.3	Associated with RNA polymerase II	Inagaki et al[21] and Baillat et al[24]
SNAPAP (SNAPIN)	1q21.3	Part of SNARE complex (docking and fusion of synaptic vesicles)	Inagaki et al[21] and Ilardi et al[25]
ALC1 (CHD1L)	1q21.1	Facilitates DNA synthesis and cell cycle when over expressed	Ma et al[26]
ASH1L	1q22	Histone methyltransferase involved in gene expression	Elsemman et al[27] and An et al[29]
METTL13 (EEF1AKNMT)	1q24.3	Regulates protein synthesis in cancer cells; promotes tumor growth and metastasis	Elsemman et al[27]; Liu et al[30], and Li et al[31]
TARBP1	1q42.2	Double-stranded RNA binding protein; promotes HIV-1 and -2 and HCV replication	Elsemman et al[27], Zhang et al[50], and Christensen et al[32]
SMYD2	1q32.2	Part of the protein lysine methyltransferase family of enzymes	Elsemman et al[27] and Leinhart and Brown[34]
SMYD3	1q44	Part of the protein lysine methyltransferase family of enzymes	Elsemman et al[27] and Leinhart and Brown[34]

¹Alternative gene designation provided in parentheses (see text).

²Chromosome locations are as found on the Genome Browser at http://genome.ucsc.edu[65]. HIV: Human immunodeficiency virus; HCV: Hepatitis C virus.

Table 2 Correlation between TPM3 and NUF2 alterations and prognosis

Gene	n (affected)	Overall1	Disease-specific1	Progression free1	Disease free1
TPM3 (all)	92	1.283e-3	1.263e-3	0.108	0.0242
NUF2 (all)	87	4.931e-3	2.357e-4	6.231e-4	4.931e-3
TPM3 (mRNA)	78	4.046e-5	4.046e-5	1.231e-3	2.238e-3
NUF2 (mRNA)	65	3.898e-4	1.441e-5	3.374e-4	1.520e-3

¹All Logrank test survival P and q values were generated using the Comparison/Survival tool at cBioPortal to compare survival rates between groups of patients. Various types of survival values were calculated for individuals with any type of alteration (all) or only those with altered mRNA levels (mRNA). The q-values shown were derived from the initially P values using the Benjamini-Hochberg False Discovery Rate correction procedure.