Additional file 1: of Circulating tumour DNA for monitoring colorectal cancerâa prospective cohort study to assess relationship to tissue methylation, cancer characteristics and surgical resection

Erin Symonds (3426014)
Susanne Pedersen (3426032)
David Murray (34352)
Maher Jedi (5212688)
Susan Byrne (464523)
Philippa Rabbitt (5229419)
Rohan Baker (3426029)
Dawn Bastin (5229422)
Graeme Young (3416597)

Publication date

May 2018

DOI

10.6084/m9.figshare.6279944.v1

Abstract

Table S1. Characteristics of patients included in analyses. Table S2. Concordance between detection of methylated BCAT1 and IKZF1 in tissues and blood. Figure S1. ctDNA status before and after surgical resection for 93 cases. (DOCX 36Â kb

Extracted data

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Data Protection

Additional file 1: of Circulating tumour DNA for monitoring colorectal cancerâa prospective cohort study to assess relationship to tissue methylation, cancer characteristics and surgical resection

Erin Symonds (3426014)
Susanne Pedersen (3426032)
David Murray (34352)
Maher Jedi (5212688)
Susan Byrne (464523)
Philippa Rabbitt (5229419)
Rohan Baker (3426029)
Dawn Bastin (5229422)
Graeme Young (3416597)

Open link

Publication date

May 2018

DOI

10.6084/m9.figshare.6279944.v1

Abstract

Extracted data

Simeng Gu (6438257)
Shujuan Lin (6169328)
Ding Ye (405963)
Sangni Qian (6438266)
Danjie Jiang (395701)
Xiaocong Zhang (6438269)
Qilong Li (5477081)
Jinhua Yang (2019088)
Xiaojiang Ying (538813)
Zhenjun Li (275953)
Mengling Tang (644955)
Jianbing Wang (5118731)
Mingjuan Jin (186609)
Kun Chen (131048)

March 2019

Table S3. Results of ROC curve analysis between CRC tissues and adjacent normal tissues. (DOCX 12 kb

Additional file 1: of Blood DNA methylation and breast cancer risk: a meta-analysis of four prospective cohort studies

Clara Bodelon (106771)
Srikant Ambatipudi (228815)
Pierre-Antoine DuguĂŠ (4745514)
Annelie Johansson (6652820)
Joshua Sampson (3466985)
Belynda Hicks (3385295)
Eric Karlins (395884)
Amy Hutchinson (106802)
Cyrille Cuenin (487673)
Veronique ChajĂ¨s (6652832)
Melissa Southey (81752)
Isabelle Romieu (115136)
Graham Giles (521929)
Dallas English (3421334)
Silvia Polidoro (151290)
Manuela Assumma (6712148)
Laura Baglietto (89917)
Paolo Vineis (115119)
Gianluca Severi (89918)
Zdenko Herceg (251863)
James Flanagan (13713)
Roger Milne (260033)
Montserrat Garcia-Closas (89866)

May 2019

Description of the four prospective studies. Also, a figure with the results of the association betw...

Additional file 2: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S2. A. Number of CDGs mutated in at least 5 samples with methylation data in one tumor type; B...

Additional file 1 of Circulating cell-free DNA methylation patterns as non-invasive biomarkers to monitor colorectal cancer treatment efficacy without referencing primary site mutation profiles

Kazuya Yasui (10874552)
Toshiaki Toshima (10874555)
Ryo Inada (13980987)
Yuzo Umeda (762721)
Shuya Yano (157763)
Hiroaki Tanioka (7491530)
Akihiro Nyuya (4764216)
Toshiyoshi Fujiwara (157767)
Takeshi Yamada (160800)
Yoshio Naomoto (360090)
Ajay Goel (130080)
Takeshi Nagasaka (8474)

January 2024

Additional file 1: Fig. S1. Study Flow Charts. Fig. S2. Representative Hi-SA results for ccfDNA. Fig...

Additional file 1: Table S1. of Assessment of DNA methylation profiling and copy number variation as indications of clonal relationship in ipsilateral and contralateral breast cancers to distinguish recurrent breast cancer from a second primary tumour

Katie Huang (3420263)
Thomas Mikeska (274849)
Jason Li (23213)
Elena Takano (3420257)
Ewan Millar (3420266)
Peter Graham (831821)
Samantha Boyle (562679)
Ian Campbell (205212)
Terence Speed (3420260)
Alexander Dobrovic (8304)
Stephen Fox (152886)

October 2015

Comparison of DNA methylation frequency of genes screened in breast carcinomas with the methylation ...

Additional file 1: of Evaluation of an assay for methylated BCAT1 and IKZF1 in plasma for detection of colorectal neoplasia

Susanne Pedersen (3426032)
Erin Symonds (3426014)
Rohan Baker (3426029)
David Murray (34352)
Aidan McEvoy (187194)
Sascha Van Doorn (3426011)
Marco Mundt (3426026)
Stephen Cole (155332)
Geetha Gopalsamy (3416618)
Dileep Mangira (3426023)
Lawrence LaPointe (3426017)
Evelien Dekker (3426020)
Graeme Young (3416597)

October 2015

Detailed assay protocol. Table S1. DNA sequences for the oligonucleotides used in the 2-marker blood...

Additional file 2 of Potential value of ctDNA monitoring in metastatic HR + /HER2 − breast cancer: longitudinal ctDNA analysis in the phase Ib MONALEESASIA trial

Joanne Chiu (10818178)
Fei Su (106529)
Mukta Joshi (16829977)
Norikazu Masuda (3511787)
Takashi Ishikawa (206896)
Tomoyuki Aruga (5122379)
Juan Pablo Zarate (5991164)
Naveen Babbar (9244692)
O. Alejandro Balbin (16829980)
Yoon-Sim Yap (12253401)

August 2023

Additional file 2: Supplementary Table 1. cfDNA Samples Included in 23This Analysisa. Abbreviations:...

Additional file 2: Figure S1. of Migration of mitochondrial DNA in the nuclear genome of colorectal adenocarcinoma

Vinodh Srinivasainagendra (3877369)
Michael Sandel (3877375)
Bhupendra Singh (343330)
Aishwarya Sundaresan (3877372)
Ved Mooga (3877378)
Prachi Bajpai (813828)
Hemant Tiwari (29034)
Keshav Singh (334761)

March 2017

NUMT density in tumor and normal genomes (sorted by disease (T2) and fold change in NUMT abundance (...

Additional file 1: of Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer

Yimin Zhu (101874)
Hanlin Lu (2925378)
Dandan Zhang (228849)
Meiyan Li (441468)
Xiaohui Sun (520181)
Ledong Wan (1947580)
Dan Yu (214174)
Yiping Tian (4908259)
Hongchuan Jin (194460)
Aifen Lin (3504350)
Fei Gao (29262)
Maode Lai (15338)

March 2018

Table S1. The basic characteristics of six patients of colorectal cancer. Table S2. Summary of MeDIP...

Additional file 1: of Comparison of quantification algorithms for circulating cell-free DNA methylation biomarkers in blood plasma from cancer patients

Luka de Vos (4635880)
Heidrun Gevensleben (3308331)
Andreas Schröck (395005)
Alina Franzen (395009)
Glen Kristiansen (76479)
Friedrich Bootz (395015)
Dimo Dietrich (22859)

December 2017

Baseline characteristics and clinicopathological variables. Table with characteristics of HNSCC and ...

Additional file 1: Table S1. of Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages

Meng Yang (162251)
Umit Topaloglu (626154)
W. Petty (4004927)
Matthew Pagni (4004912)
Kristie Foley (4004936)
Stefan Grant (4004939)
Mac Robinson (4004903)
Rhonda Bitting (4004951)
Alexandra Thomas (4004906)
Angela Alistar (3216504)
Rodwige Desnoyers (4004924)
Michael Goodman (37506)
Carol Albright (4004930)
Mercedes Porosnicu (4004921)
Mihaela Vatca (4004933)
Shadi Qasem (4004945)
Barry DeYoung (4004918)
Ville Kytola (4004942)
Matti Nykter (21557)
Kexin Chen (181385)
Edward Levine (4004909)
Edgar Staren (4004915)
Ralph DâAgostino (4004897)
Robin Petro (4004948)
William Blackstock (289137)
Bayard Powell (4004954)
Edward Abraham (322531)
Boris Pasche (4004900)
Wei Zhang (405)

May 2017

Clinical and treatment characteristics of the 18 cases with no ctDNA alterations detected. Table S2....

Additional file 4: Table S2. of Prognostic and predictive significance of long interspersed nucleotide element-1 methylation in advanced-stage colorectal cancer

Mami Kaneko (3453911)
Masanori Kotake (3453902)
Hiroyuki Bando (3453908)
Tetsuji Yamada (3453914)
Hirofumi Takemura (3453905)
Toshinari Minamoto (280844)

December 2016

Comparison of the levels of tumor LINE-1 methylation with the clinical and histopathological charact...

Additional file 2: of Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer

Simeng Gu (6438257)
Shujuan Lin (6169328)
Ding Ye (405963)
Sangni Qian (6438266)
Danjie Jiang (395701)
Xiaocong Zhang (6438269)
Qilong Li (5477081)
Jinhua Yang (2019088)
Xiaojiang Ying (538813)
Zhenjun Li (275953)
Mengling Tang (644955)
Jianbing Wang (5118731)
Mingjuan Jin (186609)
Kun Chen (131048)

March 2019

Table S2. A list of differentially hypermethylated and expressed genes identified by both EPIC array...

Additional file 3 of Individualized dynamic methylation-based analysis of cell-free DNA in postoperative monitoring of lung cancer

Kezhong Chen (10659830)
Guannan Kang (15014708)
Zhihong Zhang (2027)
Analyn Lizaso (7331654)
Stephan Beck (5246)
Iben Lyskjær (13541927)
Olga Chervova (16550007)
Bingsi Li (10094899)
Haifeng Shen (10659833)
Chenyang Wang (170127)
Bing Li (43671)
Heng Zhao (333503)
Xi Li (19208)
Fan Yang (1413)
Nnennaya Kanu (3426848)
Jun Wang (5906)

July 2023

Additional file 3: Table S1. Baseline clinicopathologic characteristics of the 36 patients in the DY...

Additional file 4: of Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer

Simeng Gu (6438257)
Shujuan Lin (6169328)
Ding Ye (405963)
Sangni Qian (6438266)
Danjie Jiang (395701)
Xiaocong Zhang (6438269)
Qilong Li (5477081)
Jinhua Yang (2019088)
Xiaojiang Ying (538813)
Zhenjun Li (275953)
Mengling Tang (644955)
Jianbing Wang (5118731)
Mingjuan Jin (186609)
Kun Chen (131048)

March 2019

Table S3. Results of ROC curve analysis between CRC tissues and adjacent normal tissues. (DOCX 12 kb

Additional file 1: of Blood DNA methylation and breast cancer risk: a meta-analysis of four prospective cohort studies

Clara Bodelon (106771)
Srikant Ambatipudi (228815)
Pierre-Antoine DuguĂŠ (4745514)
Annelie Johansson (6652820)
Joshua Sampson (3466985)
Belynda Hicks (3385295)
Eric Karlins (395884)
Amy Hutchinson (106802)
Cyrille Cuenin (487673)
Veronique ChajĂ¨s (6652832)
Melissa Southey (81752)
Isabelle Romieu (115136)
Graham Giles (521929)
Dallas English (3421334)
Silvia Polidoro (151290)
Manuela Assumma (6712148)
Laura Baglietto (89917)
Paolo Vineis (115119)
Gianluca Severi (89918)
Zdenko Herceg (251863)
James Flanagan (13713)
Roger Milne (260033)
Montserrat Garcia-Closas (89866)

May 2019

Description of the four prospective studies. Also, a figure with the results of the association betw...

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S2. A. Number of CDGs mutated in at least 5 samples with methylation data in one tumor type; B...

Additional file 1 of Circulating cell-free DNA methylation patterns as non-invasive biomarkers to monitor colorectal cancer treatment efficacy without referencing primary site mutation profiles

Kazuya Yasui (10874552)
Toshiaki Toshima (10874555)
Ryo Inada (13980987)
Yuzo Umeda (762721)
Shuya Yano (157763)
Hiroaki Tanioka (7491530)
Akihiro Nyuya (4764216)
Toshiyoshi Fujiwara (157767)
Takeshi Yamada (160800)
Yoshio Naomoto (360090)
Ajay Goel (130080)
Takeshi Nagasaka (8474)

January 2024

Additional file 1: Fig. S1. Study Flow Charts. Fig. S2. Representative Hi-SA results for ccfDNA. Fig...

Katie Huang (3420263)
Thomas Mikeska (274849)
Jason Li (23213)
Elena Takano (3420257)
Ewan Millar (3420266)
Peter Graham (831821)
Samantha Boyle (562679)
Ian Campbell (205212)
Terence Speed (3420260)
Alexander Dobrovic (8304)
Stephen Fox (152886)

October 2015

Comparison of DNA methylation frequency of genes screened in breast carcinomas with the methylation ...

Additional file 1: of Evaluation of an assay for methylated BCAT1 and IKZF1 in plasma for detection of colorectal neoplasia

Susanne Pedersen (3426032)
Erin Symonds (3426014)
Rohan Baker (3426029)
David Murray (34352)
Aidan McEvoy (187194)
Sascha Van Doorn (3426011)
Marco Mundt (3426026)
Stephen Cole (155332)
Geetha Gopalsamy (3416618)
Dileep Mangira (3426023)
Lawrence LaPointe (3426017)
Evelien Dekker (3426020)
Graeme Young (3416597)

October 2015

Detailed assay protocol. Table S1. DNA sequences for the oligonucleotides used in the 2-marker blood...

Additional file 2 of Potential value of ctDNA monitoring in metastatic HR + /HER2 − breast cancer: longitudinal ctDNA analysis in the phase Ib MONALEESASIA trial

Joanne Chiu (10818178)
Fei Su (106529)
Mukta Joshi (16829977)
Norikazu Masuda (3511787)
Takashi Ishikawa (206896)
Tomoyuki Aruga (5122379)
Juan Pablo Zarate (5991164)
Naveen Babbar (9244692)
O. Alejandro Balbin (16829980)
Yoon-Sim Yap (12253401)

August 2023

Additional file 2: Supplementary Table 1. cfDNA Samples Included in 23This Analysisa. Abbreviations:...

Additional file 2: Figure S1. of Migration of mitochondrial DNA in the nuclear genome of colorectal adenocarcinoma

Vinodh Srinivasainagendra (3877369)
Michael Sandel (3877375)
Bhupendra Singh (343330)
Aishwarya Sundaresan (3877372)
Ved Mooga (3877378)
Prachi Bajpai (813828)
Hemant Tiwari (29034)
Keshav Singh (334761)

March 2017

NUMT density in tumor and normal genomes (sorted by disease (T2) and fold change in NUMT abundance (...

Additional file 1: of Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer

Yimin Zhu (101874)
Hanlin Lu (2925378)
Dandan Zhang (228849)
Meiyan Li (441468)
Xiaohui Sun (520181)
Ledong Wan (1947580)
Dan Yu (214174)
Yiping Tian (4908259)
Hongchuan Jin (194460)
Aifen Lin (3504350)
Fei Gao (29262)
Maode Lai (15338)

March 2018

Table S1. The basic characteristics of six patients of colorectal cancer. Table S2. Summary of MeDIP...

Additional file 1: of Comparison of quantification algorithms for circulating cell-free DNA methylation biomarkers in blood plasma from cancer patients

Luka de Vos (4635880)
Heidrun Gevensleben (3308331)
Andreas Schröck (395005)
Alina Franzen (395009)
Glen Kristiansen (76479)
Friedrich Bootz (395015)
Dimo Dietrich (22859)

December 2017

Baseline characteristics and clinicopathological variables. Table with characteristics of HNSCC and ...

Additional file 1: Table S1. of Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages

Meng Yang (162251)
Umit Topaloglu (626154)
W. Petty (4004927)
Matthew Pagni (4004912)
Kristie Foley (4004936)
Stefan Grant (4004939)
Mac Robinson (4004903)
Rhonda Bitting (4004951)
Alexandra Thomas (4004906)
Angela Alistar (3216504)
Rodwige Desnoyers (4004924)
Michael Goodman (37506)
Carol Albright (4004930)
Mercedes Porosnicu (4004921)
Mihaela Vatca (4004933)
Shadi Qasem (4004945)
Barry DeYoung (4004918)
Ville Kytola (4004942)
Matti Nykter (21557)
Kexin Chen (181385)
Edward Levine (4004909)
Edgar Staren (4004915)
Ralph DâAgostino (4004897)
Robin Petro (4004948)
William Blackstock (289137)
Bayard Powell (4004954)
Edward Abraham (322531)
Boris Pasche (4004900)
Wei Zhang (405)

May 2017

Clinical and treatment characteristics of the 18 cases with no ctDNA alterations detected. Table S2....

Additional file 4: Table S2. of Prognostic and predictive significance of long interspersed nucleotide element-1 methylation in advanced-stage colorectal cancer

Mami Kaneko (3453911)
Masanori Kotake (3453902)
Hiroyuki Bando (3453908)
Tetsuji Yamada (3453914)
Hirofumi Takemura (3453905)
Toshinari Minamoto (280844)

December 2016

Comparison of the levels of tumor LINE-1 methylation with the clinical and histopathological charact...

Additional file 2: of Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer

Simeng Gu (6438257)
Shujuan Lin (6169328)
Ding Ye (405963)
Sangni Qian (6438266)
Danjie Jiang (395701)
Xiaocong Zhang (6438269)
Qilong Li (5477081)
Jinhua Yang (2019088)
Xiaojiang Ying (538813)
Zhenjun Li (275953)
Mengling Tang (644955)
Jianbing Wang (5118731)
Mingjuan Jin (186609)
Kun Chen (131048)

March 2019

Table S2. A list of differentially hypermethylated and expressed genes identified by both EPIC array...

Additional file 3 of Individualized dynamic methylation-based analysis of cell-free DNA in postoperative monitoring of lung cancer

Kezhong Chen (10659830)
Guannan Kang (15014708)
Zhihong Zhang (2027)
Analyn Lizaso (7331654)
Stephan Beck (5246)
Iben Lyskjær (13541927)
Olga Chervova (16550007)
Bingsi Li (10094899)
Haifeng Shen (10659833)
Chenyang Wang (170127)
Bing Li (43671)
Heng Zhao (333503)
Xi Li (19208)
Fan Yang (1413)
Nnennaya Kanu (3426848)
Jun Wang (5906)

July 2023

Additional file 3: Table S1. Baseline clinicopathologic characteristics of the 36 patients in the DY...

Additional file 4: of Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer

Simeng Gu (6438257)
Shujuan Lin (6169328)
Ding Ye (405963)
Sangni Qian (6438266)
Danjie Jiang (395701)
Xiaocong Zhang (6438269)
Qilong Li (5477081)
Jinhua Yang (2019088)
Xiaojiang Ying (538813)
Zhenjun Li (275953)
Mengling Tang (644955)
Jianbing Wang (5118731)
Mingjuan Jin (186609)
Kun Chen (131048)

March 2019

Table S3. Results of ROC curve analysis between CRC tissues and adjacent normal tissues. (DOCX 12 kb

Additional file 1: of Blood DNA methylation and breast cancer risk: a meta-analysis of four prospective cohort studies

Clara Bodelon (106771)
Srikant Ambatipudi (228815)
Pierre-Antoine DuguĂŠ (4745514)
Annelie Johansson (6652820)
Joshua Sampson (3466985)
Belynda Hicks (3385295)
Eric Karlins (395884)
Amy Hutchinson (106802)
Cyrille Cuenin (487673)
Veronique ChajĂ¨s (6652832)
Melissa Southey (81752)
Isabelle Romieu (115136)
Graham Giles (521929)
Dallas English (3421334)
Silvia Polidoro (151290)
Manuela Assumma (6712148)
Laura Baglietto (89917)
Paolo Vineis (115119)
Gianluca Severi (89918)
Zdenko Herceg (251863)
James Flanagan (13713)
Roger Milne (260033)
Montserrat Garcia-Closas (89866)

May 2019

Description of the four prospective studies. Also, a figure with the results of the association betw...

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S2. A. Number of CDGs mutated in at least 5 samples with methylation data in one tumor type; B...

Additional file 1: of Circulating tumour DNA for monitoring colorectal cancerâa prospective cohort study to assess relationship to tissue methylation, cancer characteristics and surgical resection

Abstract

Extracted data

Additional file 1: of Circulating tumour DNA for monitoring colorectal cancerâa prospective cohort study to assess relationship to tissue methylation, cancer characteristics and surgical resection

Abstract

Extracted data

Related items

Related items

Additional file 1: of Circulating tumour DNA for monitoring colorectal cancerâa prospective cohort study to assess relationship to tissue methylation, cancer characteristics and surgical resection

Abstract

Extracted data

Additional file 1: of Circulating tumour DNA for monitoring colorectal cancerâa prospective cohort study to assess relationship to tissue methylation, cancer characteristics and surgical resection

Abstract

Extracted data

Related items

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Additional file 1: of Circulating tumour DNA for monitoring colorectal cancerâa prospective cohort study to assess relationship to tissue methylation, cancer characteristics and surgical resection

Additional file 1: of Circulating tumour DNA for monitoring colorectal cancerâa prospective cohort study to assess relationship to tissue methylation, cancer characteristics and surgical resection