Targeted Re-Sequencing Identified rs3106189 at the 5′ UTR of TAPBP and rs1052918 at the 3′ UTR of TCF3 to Be Associated with the Overall Survival of Colorectal Cancer Patients
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{"title"=>"Targeted Re-Sequencing Identified rs3106189 at the 5′ UTR of TAPBP and rs1052918 at the 3′ UTR of TCF3 to Be Associated with the Overall Survival of Colorectal Cancer Patients", "type"=>"journal", "authors"=>[{"first_name"=>"Jiaofang", "last_name"=>"Shao", "scopus_author_id"=>"36187399800"}, {"first_name"=>"Xiaoyan", "last_name"=>"Lou", "scopus_author_id"=>"54788020100"}, {"first_name"=>"Jun", "last_name"=>"Wang", "scopus_author_id"=>"35188136400"}, {"first_name"=>"Jing", "last_name"=>"Zhang", "scopus_author_id"=>"55720152300"}, {"first_name"=>"Chen", "last_name"=>"Chen", "scopus_author_id"=>"55664378400"}, {"first_name"=>"Dasong", "last_name"=>"Hua", "scopus_author_id"=>"36801633700"}, {"first_name"=>"Fan", "last_name"=>"Mo", "scopus_author_id"=>"54916875000"}, {"first_name"=>"Xu", "last_name"=>"Han", "scopus_author_id"=>"55267755700"}, {"first_name"=>"Shu", "last_name"=>"Zheng", "scopus_author_id"=>"7403146372"}, {"first_name"=>"Biaoyang", "last_name"=>"Lin", "scopus_author_id"=>"35199806000"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84881148108", "scopus"=>"2-s2.0-84881148108", "doi"=>"10.1371/journal.pone.0070307", "pui"=>"369507259", "issn"=>"19326203", "pmid"=>"23940558"}, "id"=>"df87bb07-d619-3cf5-80fd-1bf6995069e6", "abstract"=>"Recent studies have demonstrated the power of deep re-sequencing of the whole genome or exome in understanding cancer genomes. However, targeted capture of selected genomic whole gene-body regions, rather than the whole exome, have several advantages: 1) the genes can be selected based on biology or a hypothesis; 2) mutations in promoter and intronic regions, which have important regulatory roles, can be investigated; and 3) less expensive than whole genome or whole exome sequencing. Therefore, we designed custom high-density oligonucleotide microarrays (NimbleGen Inc.) to capture approximately 1.7 Mb target regions comprising the genomic regions of 28 genes related to colorectal cancer including genes belonging to the WNT signaling pathway, as well as important transcription factors or colon-specific genes that are over expressed in colorectal cancer (CRC). The 1.7 Mb targeted regions were sequenced with a coverage ranged from 32× to 45× for the 28 genes. We identified a total of 2342 sequence variations in the CRC and corresponding adjacent normal tissues. Among them, 738 were novel sequence variations based on comparisons with the SNP database (dbSNP135). We validated 56 of 66 SNPs in a separate cohort of 30 CRC tissues using Sequenom MassARRAY iPLEX Platform, suggesting a validation rate of at least 85% (56/66). We found 15 missense mutations among the exonic variations, 21 synonymous SNPs that were predicted to change the exonic splicing motifs, 31 UTR SNPs that were predicted to occur at the transcription factor binding sites, 20 intronic SNPs located near the splicing sites, 43 SNPs in conserved transcription factor binding sites and 32 in CpG islands. Finally, we determined that rs3106189, localized to the 5' UTR of antigen presenting tapasin binding protein (TAPBP), and rs1052918, localized to the 3' UTR of transcription factor 3 (TCF3), were associated with overall survival of CRC patients.", "link"=>"http://www.mendeley.com/research/targeted-resequencing-identified-rs3106189-5-utr-tapbp-rs1052918-3-utr-tcf3-associated-overall-survi", "reader_count"=>13, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Librarian"=>1, "Student > Doctoral Student"=>2, "Researcher"=>1, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>1, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Librarian"=>1, "Student > Doctoral Student"=>2, "Researcher"=>1, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>1, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>5, "Medicine and Dentistry"=>1, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>3}}, "reader_count_by_country"=>{"Denmark"=>1, "United Kingdom"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143056/Figure_1.tif"], "description"=>"<p>(A) The GC content and coverage in CRC (colorectal cancer) tissue. (B) The GC content and coverage in CRN (colorectal normal tissue) tissue. (C) The relationship between sequence coverage and SNP detection. Red line shows the sequence coverage and percentage of SNPs detected at that coverage in CRC pool, and green line in CRN pool (D) Venn diagram of SNPs for CRC and CRN samples. (E) An overview of SNPs identified in cancer and adjacent normal tissue.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "mutagenesis", "population genetics", "Genetic polymorphism", "Cancer genetics", "genomics", "Functional genomics", "Genome sequencing", "Population biology", "Clinical genetics", "Clinical research design", "epidemiology", "Genetic epidemiology", "Gastroenterology and hepatology", "Gastrointestinal cancers", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "snp"], "article_id"=>764602, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Jiaofang Shao", "Xiaoyan Lou", "Jun Wang", "Jing Zhang", "Chen Chen", "Dasong Hua", "Fan Mo", "Xu Han", "Shu Zheng", "Biaoyang Lin"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0070307.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_GC_content_coverage_and_SNP_count_/764602", "title"=>"GC content, coverage and SNP count.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-05 04:30:46"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143058/Figure_2.tif"], "description"=>"<p>(A) Kaplan-Meier plot for rs3106189 localized to the 5′ UTR of TAPBP. (B) Kaplan-Meier plot for rs1052918 localized to the 3′ UTR of the TCF3. Y-axis, CRC survival probability; X-axis, months from surgery. Blue lines are homozygous wildtype (wild), green are homozygous variant (var), red are heterozygous variant (het).</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "mutagenesis", "population genetics", "Genetic polymorphism", "Cancer genetics", "genomics", "Functional genomics", "Genome sequencing", "Population biology", "Clinical genetics", "Clinical research design", "epidemiology", "Genetic epidemiology", "Gastroenterology and hepatology", "Gastrointestinal cancers", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "cancer"], "article_id"=>764603, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Jiaofang Shao", "Xiaoyan Lou", "Jun Wang", "Jing Zhang", "Chen Chen", "Dasong Hua", "Fan Mo", "Xu Han", "Shu Zheng", "Biaoyang Lin"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0070307.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Colorectal_cancer_overall_survival_in_relationship_to_SNPs_/764603", "title"=>"Colorectal cancer overall survival in relationship to SNPs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-05 04:30:46"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143059/Table_5.xls"], "description"=>"a<p>Tissue samples with SNP detected by NGS. CRC is the colorectal cancer tissue, and CRN is the colorectal cancer adjacent normal tissue.</p>b<p>“+” indicates “validated” and “−” indicated “not tested” by Sequenom.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "mutagenesis", "population genetics", "Genetic polymorphism", "Cancer genetics", "genomics", "Functional genomics", "Genome sequencing", "Population biology", "Clinical genetics", "Clinical research design", "epidemiology", "Genetic epidemiology", "Gastroenterology and hepatology", "Gastrointestinal cancers", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "snps", "splice", "sites"], "article_id"=>764604, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Jiaofang Shao", "Xiaoyan Lou", "Jun Wang", "Jing Zhang", "Chen Chen", "Dasong Hua", "Fan Mo", "Xu Han", "Shu Zheng", "Biaoyang Lin"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0070307.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Intronic_SNPs_near_splice_sites_lt_30_nt_/764604", "title"=>"Intronic SNPs near splice sites (<30 nt).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-05 04:30:46"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143060/Table_4.xls"], "description"=>"a<p>Tissue samples with SNP detected by NGS. CRC is the colorectal cancer tissue, and CRN is the colorectal cancer adjacent normal tissue.</p>b<p>“+” indicates “validated” and “−” indicated “not tested” by Sequenom.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "mutagenesis", "population genetics", "Genetic polymorphism", "Cancer genetics", "genomics", "Functional genomics", "Genome sequencing", "Population biology", "Clinical genetics", "Clinical research design", "epidemiology", "Genetic epidemiology", "Gastroenterology and hepatology", "Gastrointestinal cancers", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "utr", "snps", "transcription", "binding", "sites", "changed"], "article_id"=>764605, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Jiaofang Shao", "Xiaoyan Lou", "Jun Wang", "Jing Zhang", "Chen Chen", "Dasong Hua", "Fan Mo", "Xu Han", "Shu Zheng", "Biaoyang Lin"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0070307.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_List_of_UTR_SNPs_with_transcription_factor_binding_sites_changed_using_TFSEARCH_/764605", "title"=>"List of UTR SNPs with transcription factor binding sites changed using TFSEARCH.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-05 04:30:46"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143061/Table_7.xls"], "description"=>"<p>Note: The significant P values (≤0.05) are in bold.</p><p>WW, homozygous wild-type genotype; WV heterozygous genotype; VV, homozygous variant genotype.</p><p>Abbreviations: CI, confidence interval; HR, hazard ratio; omit, no results due to missing information on the death status.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "mutagenesis", "population genetics", "Genetic polymorphism", "Cancer genetics", "genomics", "Functional genomics", "Genome sequencing", "Population biology", "Clinical genetics", "Clinical research design", "epidemiology", "Genetic epidemiology", "Gastroenterology and hepatology", "Gastrointestinal cancers", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "snp", "crc"], "article_id"=>764606, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Jiaofang Shao", "Xiaoyan Lou", "Jun Wang", "Jing Zhang", "Chen Chen", "Dasong Hua", "Fan Mo", "Xu Han", "Shu Zheng", "Biaoyang Lin"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0070307.t007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_The_association_of_single_SNP_with_CRC_patient_survival_/764606", "title"=>"The association of single SNP with CRC patient survival.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-05 04:30:46"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143062/Table_6.xls"], "description"=>"<p>Overview of RegulomeDB annotation.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "mutagenesis", "population genetics", "Genetic polymorphism", "Cancer genetics", "genomics", "Functional genomics", "Genome sequencing", "Population biology", "Clinical genetics", "Clinical research design", "epidemiology", "Genetic epidemiology", "Gastroenterology and hepatology", "Gastrointestinal cancers", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "regulomedb"], "article_id"=>764607, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Jiaofang Shao", "Xiaoyan Lou", "Jun Wang", "Jing Zhang", "Chen Chen", "Dasong Hua", "Fan Mo", "Xu Han", "Shu Zheng", "Biaoyang Lin"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0070307.t006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Overview_of_RegulomeDB_annotation_/764607", "title"=>"Overview of RegulomeDB annotation.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-05 04:30:46"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143063/Table_1.xls"], "description"=>"a.<p>NG coverage (%): the percentage of regions covered by final reads out of the whole NimbleGen captured regions for each gene, including 10-kb upstream and 5-kb downstream.</p>b.<p>total coverage (%): the percentage of regions covered by final reads out of the whole designed regions for each gene.</p>c.<p>folds coverage (x): the average read depth.</p>d.<p>no. SNPs: the total SNPs identified for the gene.</p>e.<p>SNP rate (‰): the average count of SNP in a 1k-bp window.</p>f.<p>The chromosome names and locations of the genomic regions that were captured for each gene.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "mutagenesis", "population genetics", "Genetic polymorphism", "Cancer genetics", "genomics", "Functional genomics", "Genome sequencing", "Population biology", "Clinical genetics", "Clinical research design", "epidemiology", "Genetic epidemiology", "Gastroenterology and hepatology", "Gastrointestinal cancers", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "28", "genes", "snps", "crc", "crn"], "article_id"=>764608, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Jiaofang Shao", "Xiaoyan Lou", "Jun Wang", "Jing Zhang", "Chen Chen", "Dasong Hua", "Fan Mo", "Xu Han", "Shu Zheng", "Biaoyang Lin"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0070307.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_The_sequence_coverage_of_28_selected_genes_and_number_of_SNPs_in_CRC_and_CRN_identified_by_NGS_/764608", "title"=>"The sequence coverage of 28 selected genes and number of SNPs in CRC and CRN identified by NGS.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-05 04:30:46"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143064/Table_3.xls"], "description"=>"a<p>Tissue samples with SNP detected by NGS. CRC is the colorectal cancer tissue, and CRN is the colorectal cancer adjacent normal tissue.</p>b<p>“+”indicates “validated” and “−” indicated “not tested” by Sequenom.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "mutagenesis", "population genetics", "Genetic polymorphism", "Cancer genetics", "genomics", "Functional genomics", "Genome sequencing", "Population biology", "Clinical genetics", "Clinical research design", "epidemiology", "Genetic epidemiology", "Gastroenterology and hepatology", "Gastrointestinal cancers", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "synonymous", "snps", "motifs"], "article_id"=>764609, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Jiaofang Shao", "Xiaoyan Lou", "Jun Wang", "Jing Zhang", "Chen Chen", "Dasong Hua", "Fan Mo", "Xu Han", "Shu Zheng", "Biaoyang Lin"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0070307.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_List_of_synonymous_SNPs_with_ESE_ESS_motifs_changed_/764609", "title"=>"List of synonymous SNPs with ESE/ESS motifs changed.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-05 04:30:46"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143065/Table_2.xls"], "description"=>"a<p>Tissue samples with SNP detected by NGS. CRC is the colorectal cancer tissue pool, and CRN is the colorectal cancer adjacent normal tissue pool.</p>b<p>“+”indicates “validated” and “−” indicated “not tested” by Sequenom.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "mutagenesis", "population genetics", "Genetic polymorphism", "Cancer genetics", "genomics", "Functional genomics", "Genome sequencing", "Population biology", "Clinical genetics", "Clinical research design", "epidemiology", "Genetic epidemiology", "Gastroenterology and hepatology", "Gastrointestinal cancers", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "sift", "provean", "non-synonymous", "variations"], "article_id"=>764610, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Jiaofang Shao", "Xiaoyan Lou", "Jun Wang", "Jing Zhang", "Chen Chen", "Dasong Hua", "Fan Mo", "Xu Han", "Shu Zheng", "Biaoyang Lin"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0070307.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_PolyPhen_SIFT_and_PROVEAN_prediction_results_for_non_synonymous_variations_identified_/764610", "title"=>"PolyPhen, SIFT and PROVEAN prediction results for non-synonymous variations identified.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-05 04:30:46"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143066/Table_9.xls"], "description"=>"<p>The Hardy-Weinberg equilibrium of the SNPs.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "mutagenesis", "population genetics", "Genetic polymorphism", "Cancer genetics", "genomics", "Functional genomics", "Genome sequencing", "Population biology", "Clinical genetics", "Clinical research design", "epidemiology", "Genetic epidemiology", "Gastroenterology and hepatology", "Gastrointestinal cancers", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "hardy-weinberg", "equilibrium"], "article_id"=>764611, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Jiaofang Shao", "Xiaoyan Lou", "Jun Wang", "Jing Zhang", "Chen Chen", "Dasong Hua", "Fan Mo", "Xu Han", "Shu Zheng", "Biaoyang Lin"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0070307.t009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_The_Hardy_Weinberg_equilibrium_of_the_SNPs_/764611", "title"=>"The Hardy-Weinberg equilibrium of the SNPs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-05 04:30:46"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143067/Table_8.xls"], "description"=>"<p>The clinicopathological characteristics of 117 Chinese CRC patients.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "mutagenesis", "population genetics", "Genetic polymorphism", "Cancer genetics", "genomics", "Functional genomics", "Genome sequencing", "Population biology", "Clinical genetics", "Clinical research design", "epidemiology", "Genetic epidemiology", "Gastroenterology and hepatology", "Gastrointestinal cancers", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "clinicopathological", "117", "chinese", "crc"], "article_id"=>764612, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Jiaofang Shao", "Xiaoyan Lou", "Jun Wang", "Jing Zhang", "Chen Chen", "Dasong Hua", "Fan Mo", "Xu Han", "Shu Zheng", "Biaoyang Lin"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0070307.t008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_The_clinicopathological_characteristics_of_117_Chinese_CRC_patients_/764612", "title"=>"The clinicopathological characteristics of 117 Chinese CRC patients.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-05 04:30:46"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143069/Figure_S1.tif", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143070/Table_S1.xlsx", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143072/Table_S2.xlsx", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143073/Table_S3.xlsx", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143074/Table_S4.xlsx", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143075/Table_S5.xlsx", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143076/Table_S6.xlsx", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1143077/Table_S7.xlsx"], "description"=>"<div><p>Recent studies have demonstrated the power of deep re-sequencing of the whole genome or exome in understanding cancer genomes. However, targeted capture of selected genomic whole gene-body regions, rather than the whole exome, have several advantages: 1) the genes can be selected based on biology or a hypothesis; 2) mutations in promoter and intronic regions, which have important regulatory roles, can be investigated; and 3) less expensive than whole genome or whole exome sequencing. Therefore, we designed custom high-density oligonucleotide microarrays (NimbleGen Inc.) to capture approximately 1.7 Mb target regions comprising the genomic regions of 28 genes related to colorectal cancer including genes belonging to the WNT signaling pathway, as well as important transcription factors or colon-specific genes that are over expressed in colorectal cancer (CRC). The 1.7 Mb targeted regions were sequenced with a coverage ranged from 32× to 45× for the 28 genes. We identified a total of 2342 sequence variations in the CRC and corresponding adjacent normal tissues. Among them, 738 were novel sequence variations based on comparisons with the SNP database (dbSNP135). We validated 56 of 66 SNPs in a separate cohort of 30 CRC tissues using Sequenom MassARRAY iPLEX Platform, suggesting a validation rate of at least 85% (56/66). We found 15 missense mutations among the exonic variations, 21 synonymous SNPs that were predicted to change the exonic splicing motifs, 31 UTR SNPs that were predicted to occur at the transcription factor binding sites, 20 intronic SNPs located near the splicing sites, 43 SNPs in conserved transcription factor binding sites and 32 in CpG islands. Finally, we determined that rs3106189, localized to the 5′ UTR of antigen presenting tapasin binding protein (TAPBP), and rs1052918, localized to the 3′ UTR of transcription factor 3 (TCF3), were associated with overall survival of CRC patients.</p></div>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "mutagenesis", "population genetics", "Genetic polymorphism", "Cancer genetics", "genomics", "Functional genomics", "Genome sequencing", "Population biology", "Clinical genetics", "Clinical research design", "epidemiology", "Genetic epidemiology", "Gastroenterology and hepatology", "Gastrointestinal cancers", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "re-sequencing", "rs3106189", "utr", "tapbp", "rs1052918", "tcf3", "colorectal", "cancer"], "article_id"=>764614, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Jiaofang Shao", "Xiaoyan Lou", "Jun Wang", "Jing Zhang", "Chen Chen", "Dasong Hua", "Fan Mo", "Xu Han", "Shu Zheng", "Biaoyang Lin"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0070307"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Targeted_Re_Sequencing_Identified_rs3106189_at_the_5_8242_UTR_of_TAPBP_and_rs1052918_at_the_3_8242_UTR_of_TCF3_to_Be_Associated_with_the_Overall_Survival_of_Colorectal_Cancer_Patients_/764614", "title"=>"Targeted Re-Sequencing Identified rs3106189 at the 5′ UTR of TAPBP and rs1052918 at the 3′ UTR of TCF3 to Be Associated with the Overall Survival of Colorectal Cancer Patients", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-08-05 04:30:46"}

PMC Usage Stats | Further Information

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Relative Metric

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