CpG island methylator phenotype in adenocarcinomas from the digestive tract: Methods, conclusions, and controversies

doi:10.4251/wjgo.v9.i3.105

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World Journal of Gastrointestinal Oncology

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

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World J Gastrointest Oncol. Mar 15, 2017; 9(3): 105-120
Published online Mar 15, 2017. doi: 10.4251/wjgo.v9.i3.105

Table 4 Somatic mutations found in the tumor suppressor gene MLH1 in gastrointestinal adenocarcinoma samples

Sample	Cancer type	CIMP class	Mutation	Mutation type	AA pos.	Aff. AAs	VEST score¹
TCGA-A6-6780-01	COAD	CIMP+	chr3:37038192.G>A	Missense substitution	67	1	0.994
TCGA-CA-6719-01	COAD	CIMP+	chr3:37067243.G>A	Missense substitution	385	1	0.701
TCGA-CM-6171-01	COAD	CIMP+	chr3:37070349.C>-	Frameshift deletion	495	262	-
TCGA-EI-6917-01	READ	CIMP+	chr3:37058999.C>T	Missense substitution	265	1	0.981
TCGA-BR-6452-01	STAD	CIMP+	chr3:37107356.A>G	3' UTR	-	-	-
TCGA-FP-A4BE-01	STAD	CIMP+	chr3:37090086.C>T	Nonsense substitution	659	98	-
TCGA-A6-6138-01	COAD	CIMPi	chr3:37035084.G>A	Missense substitution	16	1	0.901
TCGA-AD-6889-01	COAD	CIMPi	chr3:37053348.->A	Frameshift insertion	195	562	-
TCGA-AZ-6601-01	COAD	CIMPi	chr3:37067242.C>T	Missense substitution	385	1	0.952
TCGA-CM-4746-01	COAD	CIMPi	chr3:37059062.A>-	Frameshift deletion	286	471	-
TCGA-EI-6884-01	READ	CIMPi	chr3:37058995.A>G	Acceptor splice site	264	493	-
TCGA-BR-6802-01	STAD	CIMPi	chr3:37053348.A>-	Frameshift deletion	195	562	-
TCGA-F1-6874-01	STAD	CIMPi	chr3:37050312.ACCTTTTTTACAACATAGCC>-	Frameshift deletion	154	603	-
TCGA-A6-6781-01	COAD	CIMP-	chr3:37053348.A>-	Frameshift deletion	195	562	-
TCGA-CM-6674-01	COAD	CIMP-	chr3:37058999.C>-	Frameshift deletion	265	492	-
TCGA-F4-6856-01	COAD	CIMP-	chr3:37089123.GAA>-	In-frame deletion	615	1	-
TCGA-R6-A6KZ-01	EAC	CIMP-	chr3:37034874.T>C	5’ UTR	-	-	-
TCGA-CG-5723-01	STAD	CIMP-	chr3:37053550.G>-	Frameshift deletion	213	544	-

¹Computed using the VEST tool[100], which evaluates only the effect of missense substitutions. AA pos.: Amino acid position; Aff. AAs: Number of affected amino acids (the MLH1 protein contains 756 residues); CIMP: CpG island methylator phenotype; CIMPi: CIMP intermediate; COAD: Colon adenocarcinoma; EAC: Esophageal adenocarcinoma; READ: Rectal adenocarcinoma; STAD: Stomach adenocarcinoma; VEST: Variant effect scoring tool.

Citation: Sánchez-Vega F, Gotea V, Chen YC, Elnitski L. CpG island methylator phenotype in adenocarcinomas from the digestive tract: Methods, conclusions, and controversies. World J Gastrointest Oncol 2017; 9(3): 105-120
URL: https://www.wjgnet.com/1948-5204/full/v9/i3/105.htm
DOI: https://dx.doi.org/10.4251/wjgo.v9.i3.105