Additional file 3: of Droplet digital PCR for the quantification of Alu methylation status in hematological malignancies

DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia

Figueroa, Maria E.
Lugthart, Sanne
Li, Yushan
Erpelinck-Verschueren, Claudia
Deng, Xutao
Christos, Paul J.
Schifano, Elizabeth
Booth, James
van Putten, Wim
Skrabanek, Lucy
Campagne, Fabien
Mazumdar, Madhu
Greally, John M.
Valk, Peter J.M.
Löwenberg, Bob
Delwel, Ruud
Melnick, Ari

January 2010

SummaryWe hypothesized that DNA methylation distributes into specific patterns in cancer cells, whic...

Additional file 1: of Sex-related DNA methylation differences in B cell chronic lymphocytic leukemia

Shuchun Lin (6182390)
Yun Liu (84346)
Lynn Goldin (73680)
Chen Lyu (6182393)
Xiangyin Kong (48989)
Yan Zhang (8098)
Neil Caporaso (186673)
Song Xiang (2510860)
Ying Gao (145030)

January 2019

Table S1. Samples for RNA-Seq analysis and replication of DNA methylation. Table S2. CLL subgroups o...

Additional file 4: of Impact of chemotherapy for breast cancer on leukocyte DNA methylation landscape and cognitive function: a prospective study

Song Yao (202481)
Qiang Hu (122686)
Sarah Kerns (6456668)
Li Yan (107001)
Adedayo Onitilo (6456671)
Jamal Misleh (6456674)
Kelley Young (6456677)
Lianlian Lei (3739801)
Javier Bautista (6456680)
Mostafa Mohamed (6456683)
Supriya Mohile (6456686)
Christine Ambrosone (334756)
Song Liu (9858)
Michelle Janelsins (6456692)

March 2019

Table S1. Descriptive characteristics of breast cancer cases and non-cancer controls. (DOCX 17 kb

Additional file 1: of Droplet digital PCR for the quantification of Alu methylation status in hematological malignancies

Paola Orsini (3564068)
Luciana Impera (3564071)
Elisa Parciante (6114650)
Cosimo Cumbo (3564065)
Crescenzio Minervini (3564089)
Angela Minervini (3564092)
Antonella Zagaria (3564074)
Luisa Anelli (3564086)
Nicoletta Coccaro (3564083)
Paola Casieri (3564095)
Giuseppina Tota (3564080)
Claudia Brunetti (203426)
Alessandra Ricco (6114659)
Paola Carluccio (6114662)
Giorgina Specchia (453927)
Francesco Albano (833659)

December 2018

Table S1. Clinical characteristics of the CLL patients included in the study. (DOCX 13 kb

Additional file 2: of Droplet digital PCR for the quantification of Alu methylation status in hematological malignancies

Paola Orsini (3564068)
Luciana Impera (3564071)
Elisa Parciante (6114650)
Cosimo Cumbo (3564065)
Crescenzio Minervini (3564089)
Angela Minervini (3564092)
Antonella Zagaria (3564074)
Luisa Anelli (3564086)
Nicoletta Coccaro (3564083)
Paola Casieri (3564095)
Giuseppina Tota (3564080)
Claudia Brunetti (203426)
Alessandra Ricco (6114659)
Paola Carluccio (6114662)
Giorgina Specchia (453927)
Francesco Albano (833659)

December 2018

Table S2. Clinical characteristics of the MDS patients retrospectively analyzed in this study. The n...

Additional file 4: of Droplet digital PCR for the quantification of Alu methylation status in hematological malignancies

Paola Orsini (3564068)
Luciana Impera (3564071)
Elisa Parciante (6114650)
Cosimo Cumbo (3564065)
Crescenzio Minervini (3564089)
Angela Minervini (3564092)
Antonella Zagaria (3564074)
Luisa Anelli (3564086)
Nicoletta Coccaro (3564083)
Paola Casieri (3564095)
Giuseppina Tota (3564080)
Claudia Brunetti (203426)
Alessandra Ricco (6114659)
Paola Carluccio (6114662)
Giorgina Specchia (453927)
Francesco Albano (833659)

December 2018

Table S4. Genomic distribution of Alu consensus sequences, considering a Transcription starting site...

Droplet digital PCR for the quantification of Alu methylation status in hematological malignancies

Paola Orsini
Luciana Impera
Elisa Parciante
Cosimo Cumbo
Crescenzio F. Minervini
Angela Minervini
Antonella Zagaria
Luisa Anelli
Nicoletta Coccaro
Paola Casieri
Giuseppina Tota
Claudia Brunetti
Alessandra Ricco
Paola Carluccio
Giorgina Specchia
Francesco Albano

December 2018

Abstract Background Alu repeats, belonging to the Short Interspersed Repetitive Elements (SINEs) cla...

Additional file 1: of DNA-methylation in C1R is a prognostic biomarker for acute myeloid leukemia

Tanja Božić (3509498)
Qiong Lin (205415)
Joana Frobel (3509495)
Stefan Wilop (3482498)
Melanie Hoffmann (3509501)
Carsten Müller-Tidow (105305)
Tim Brümmendorf (3446933)
Edgar Jost (223396)
Wolfgang Wagner (47115)

November 2015

PDF with all supplemental data. This file contains additional details on methods, Tables S1–S7, and ...

Additional file 1: of DNA methylation holds prognostic information in relapsed precursor B-cell acute lymphoblastic leukemia

Magnus Borssén (419233)
Jessica Nordlund (172693)
Zahra Haider (4913311)
Mattias Landfors (195135)
Pär Larsson (171191)
Jukka Kanerva (4913308)
Kjeld Schmiegelow (3633592)
Trond Flaegstad (4721907)
Ólafur Jónsson (4913305)
Britt-Marie Frost (4913299)
Josefine Palle (4913302)
Erik Forestier (419238)
Mats Heyman (4354924)
Magnus Hultdin (245971)
Gudmar Lönnerholm (172700)
Sofie Degerman (419239)

March 2018

Methods description, figures, and tables can be found at the Clinical Epigenetics webpage. (DOCX 282...

Additional file 1: of Increased methylation upstream of the MEG3 promotor is observed in acute myeloid leukemia patients with better overall survival

Zachariah Sellers (3767671)
Lukasz Bolkun (6472304)
Janusz Kloczko (2278879)
Marzena Wojtaszewska (6472307)
Krzysztof Lewandowski (804436)
Marcin Moniuszko (805899)
Mariusz Ratajczak (3556316)
Gabriela Schneider (2414419)

March 2019

Scheme of densitometry analysis. a Equal amounts of PCR product (treated and untreated with restrict...

MOESM3 of Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia

Sara Wernig-Zorc (6182348)
Mukesh Yadav (4223692)
Pradeep Kopparapu (6182351)
Mats Bemark (6182354)
Hallgerdur Kristjansdottir (6182357)
Per-Ola Andersson (3479795)
Chandrasekhar Kanduri (378764)
Meena Kanduri (2592481)

January 2019

Additional file 3. List of common, hyper and hypo DhMRS between CLL samples and normal controls comp...

MOESM2 of Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia

Sara Wernig-Zorc (6182348)
Mukesh Yadav (4223692)
Pradeep Kopparapu (6182351)
Mats Bemark (6182354)
Hallgerdur Kristjansdottir (6182357)
Per-Ola Andersson (3479795)
Chandrasekhar Kanduri (378764)
Meena Kanduri (2592481)

January 2019

Additional file 2. Clinical and molecular data of patient samples and summary of obtained reads from...

DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia

Figueroa, Maria Eugenia
Lugthart, Sanne
Li, Yushan
Erpelinck, Claudia
Deng, Xutao
Christos, Paul
Schifano, Elizabeth
Booth, James
Putten, Wim
Skrabanek, Lucy
Campagne, Fabien
Mazumdar, Madhu
Greally, John
Valk, Peter
Löwenberg, Bob
Delwel, Ruud
Melnick, Ari

January 2010

Abstract: We hypothesized that DNA methylation distributes into specific patterns in cancer cells, ...

MOESM6 of Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia

Sara Wernig-Zorc (6182348)
Mukesh Yadav (4223692)
Pradeep Kopparapu (6182351)
Mats Bemark (6182354)
Hallgerdur Kristjansdottir (6182357)
Per-Ola Andersson (3479795)
Chandrasekhar Kanduri (378764)
Meena Kanduri (2592481)

January 2019

Additional file 6. List of REACTOME and GO Biological pathways from DhMRs obtained between CLL sampl...

Distinction of acute lymphoblastic leukemia from acute myeloid leukemia through microarray-based DNA methylation analysis

Scholz, C.
Nimmrich, I.
Burger, M.
Becker, E.
Doerken, B.
Ludwig, W.D.
Maier, S.

January 2005

Patterns of DNA methylation are substantially altered in malignancies compared to normal tissue, wit...

DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia

Figueroa, Maria E.
Lugthart, Sanne
Li, Yushan
Erpelinck-Verschueren, Claudia
Deng, Xutao
Christos, Paul J.
Schifano, Elizabeth
Booth, James
van Putten, Wim
Skrabanek, Lucy
Campagne, Fabien
Mazumdar, Madhu
Greally, John M.
Valk, Peter J.M.
Löwenberg, Bob
Delwel, Ruud
Melnick, Ari

January 2010

SummaryWe hypothesized that DNA methylation distributes into specific patterns in cancer cells, whic...

Additional file 1: of Sex-related DNA methylation differences in B cell chronic lymphocytic leukemia

Shuchun Lin (6182390)
Yun Liu (84346)
Lynn Goldin (73680)
Chen Lyu (6182393)
Xiangyin Kong (48989)
Yan Zhang (8098)
Neil Caporaso (186673)
Song Xiang (2510860)
Ying Gao (145030)

January 2019

Table S1. Samples for RNA-Seq analysis and replication of DNA methylation. Table S2. CLL subgroups o...

Additional file 4: of Impact of chemotherapy for breast cancer on leukocyte DNA methylation landscape and cognitive function: a prospective study

Song Yao (202481)
Qiang Hu (122686)
Sarah Kerns (6456668)
Li Yan (107001)
Adedayo Onitilo (6456671)
Jamal Misleh (6456674)
Kelley Young (6456677)
Lianlian Lei (3739801)
Javier Bautista (6456680)
Mostafa Mohamed (6456683)
Supriya Mohile (6456686)
Christine Ambrosone (334756)
Song Liu (9858)
Michelle Janelsins (6456692)

March 2019

Table S1. Descriptive characteristics of breast cancer cases and non-cancer controls. (DOCX 17 kb

Additional file 1: of Droplet digital PCR for the quantification of Alu methylation status in hematological malignancies

Paola Orsini (3564068)
Luciana Impera (3564071)
Elisa Parciante (6114650)
Cosimo Cumbo (3564065)
Crescenzio Minervini (3564089)
Angela Minervini (3564092)
Antonella Zagaria (3564074)
Luisa Anelli (3564086)
Nicoletta Coccaro (3564083)
Paola Casieri (3564095)
Giuseppina Tota (3564080)
Claudia Brunetti (203426)
Alessandra Ricco (6114659)
Paola Carluccio (6114662)
Giorgina Specchia (453927)
Francesco Albano (833659)

December 2018

Table S1. Clinical characteristics of the CLL patients included in the study. (DOCX 13 kb

Additional file 2: of Droplet digital PCR for the quantification of Alu methylation status in hematological malignancies

Paola Orsini (3564068)
Luciana Impera (3564071)
Elisa Parciante (6114650)
Cosimo Cumbo (3564065)
Crescenzio Minervini (3564089)
Angela Minervini (3564092)
Antonella Zagaria (3564074)
Luisa Anelli (3564086)
Nicoletta Coccaro (3564083)
Paola Casieri (3564095)
Giuseppina Tota (3564080)
Claudia Brunetti (203426)
Alessandra Ricco (6114659)
Paola Carluccio (6114662)
Giorgina Specchia (453927)
Francesco Albano (833659)

December 2018

Table S2. Clinical characteristics of the MDS patients retrospectively analyzed in this study. The n...

Additional file 4: of Droplet digital PCR for the quantification of Alu methylation status in hematological malignancies

Paola Orsini (3564068)
Luciana Impera (3564071)
Elisa Parciante (6114650)
Cosimo Cumbo (3564065)
Crescenzio Minervini (3564089)
Angela Minervini (3564092)
Antonella Zagaria (3564074)
Luisa Anelli (3564086)
Nicoletta Coccaro (3564083)
Paola Casieri (3564095)
Giuseppina Tota (3564080)
Claudia Brunetti (203426)
Alessandra Ricco (6114659)
Paola Carluccio (6114662)
Giorgina Specchia (453927)
Francesco Albano (833659)

December 2018

Table S4. Genomic distribution of Alu consensus sequences, considering a Transcription starting site...

Droplet digital PCR for the quantification of Alu methylation status in hematological malignancies

Paola Orsini
Luciana Impera
Elisa Parciante
Cosimo Cumbo
Crescenzio F. Minervini
Angela Minervini
Antonella Zagaria
Luisa Anelli
Nicoletta Coccaro
Paola Casieri
Giuseppina Tota
Claudia Brunetti
Alessandra Ricco
Paola Carluccio
Giorgina Specchia
Francesco Albano

December 2018

Abstract Background Alu repeats, belonging to the Short Interspersed Repetitive Elements (SINEs) cla...

Additional file 1: of DNA-methylation in C1R is a prognostic biomarker for acute myeloid leukemia

Tanja Božić (3509498)
Qiong Lin (205415)
Joana Frobel (3509495)
Stefan Wilop (3482498)
Melanie Hoffmann (3509501)
Carsten Müller-Tidow (105305)
Tim Brümmendorf (3446933)
Edgar Jost (223396)
Wolfgang Wagner (47115)

November 2015

PDF with all supplemental data. This file contains additional details on methods, Tables S1–S7, and ...

Additional file 1: of DNA methylation holds prognostic information in relapsed precursor B-cell acute lymphoblastic leukemia

Magnus Borssén (419233)
Jessica Nordlund (172693)
Zahra Haider (4913311)
Mattias Landfors (195135)
Pär Larsson (171191)
Jukka Kanerva (4913308)
Kjeld Schmiegelow (3633592)
Trond Flaegstad (4721907)
Ólafur Jónsson (4913305)
Britt-Marie Frost (4913299)
Josefine Palle (4913302)
Erik Forestier (419238)
Mats Heyman (4354924)
Magnus Hultdin (245971)
Gudmar Lönnerholm (172700)
Sofie Degerman (419239)

March 2018

Methods description, figures, and tables can be found at the Clinical Epigenetics webpage. (DOCX 282...

Additional file 1: of Increased methylation upstream of the MEG3 promotor is observed in acute myeloid leukemia patients with better overall survival

Zachariah Sellers (3767671)
Lukasz Bolkun (6472304)
Janusz Kloczko (2278879)
Marzena Wojtaszewska (6472307)
Krzysztof Lewandowski (804436)
Marcin Moniuszko (805899)
Mariusz Ratajczak (3556316)
Gabriela Schneider (2414419)

March 2019

Scheme of densitometry analysis. a Equal amounts of PCR product (treated and untreated with restrict...

MOESM3 of Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia

Sara Wernig-Zorc (6182348)
Mukesh Yadav (4223692)
Pradeep Kopparapu (6182351)
Mats Bemark (6182354)
Hallgerdur Kristjansdottir (6182357)
Per-Ola Andersson (3479795)
Chandrasekhar Kanduri (378764)
Meena Kanduri (2592481)

January 2019

Additional file 3. List of common, hyper and hypo DhMRS between CLL samples and normal controls comp...

MOESM2 of Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia

Sara Wernig-Zorc (6182348)
Mukesh Yadav (4223692)
Pradeep Kopparapu (6182351)
Mats Bemark (6182354)
Hallgerdur Kristjansdottir (6182357)
Per-Ola Andersson (3479795)
Chandrasekhar Kanduri (378764)
Meena Kanduri (2592481)

January 2019

Additional file 2. Clinical and molecular data of patient samples and summary of obtained reads from...

DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia

Figueroa, Maria Eugenia
Lugthart, Sanne
Li, Yushan
Erpelinck, Claudia
Deng, Xutao
Christos, Paul
Schifano, Elizabeth
Booth, James
Putten, Wim
Skrabanek, Lucy
Campagne, Fabien
Mazumdar, Madhu
Greally, John
Valk, Peter
Löwenberg, Bob
Delwel, Ruud
Melnick, Ari

January 2010

Abstract: We hypothesized that DNA methylation distributes into specific patterns in cancer cells, ...

MOESM6 of Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia

Sara Wernig-Zorc (6182348)
Mukesh Yadav (4223692)
Pradeep Kopparapu (6182351)
Mats Bemark (6182354)
Hallgerdur Kristjansdottir (6182357)
Per-Ola Andersson (3479795)
Chandrasekhar Kanduri (378764)
Meena Kanduri (2592481)

January 2019

Additional file 6. List of REACTOME and GO Biological pathways from DhMRs obtained between CLL sampl...

Distinction of acute lymphoblastic leukemia from acute myeloid leukemia through microarray-based DNA methylation analysis

Scholz, C.
Nimmrich, I.
Burger, M.
Becker, E.
Doerken, B.
Ludwig, W.D.
Maier, S.

January 2005

Patterns of DNA methylation are substantially altered in malignancies compared to normal tissue, wit...

DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia

Figueroa, Maria E.
Lugthart, Sanne
Li, Yushan
Erpelinck-Verschueren, Claudia
Deng, Xutao
Christos, Paul J.
Schifano, Elizabeth
Booth, James
van Putten, Wim
Skrabanek, Lucy
Campagne, Fabien
Mazumdar, Madhu
Greally, John M.
Valk, Peter J.M.
Löwenberg, Bob
Delwel, Ruud
Melnick, Ari

January 2010

SummaryWe hypothesized that DNA methylation distributes into specific patterns in cancer cells, whic...

Additional file 1: of Sex-related DNA methylation differences in B cell chronic lymphocytic leukemia

Shuchun Lin (6182390)
Yun Liu (84346)
Lynn Goldin (73680)
Chen Lyu (6182393)
Xiangyin Kong (48989)
Yan Zhang (8098)
Neil Caporaso (186673)
Song Xiang (2510860)
Ying Gao (145030)

January 2019

Table S1. Samples for RNA-Seq analysis and replication of DNA methylation. Table S2. CLL subgroups o...

Additional file 4: of Impact of chemotherapy for breast cancer on leukocyte DNA methylation landscape and cognitive function: a prospective study

Song Yao (202481)
Qiang Hu (122686)
Sarah Kerns (6456668)
Li Yan (107001)
Adedayo Onitilo (6456671)
Jamal Misleh (6456674)
Kelley Young (6456677)
Lianlian Lei (3739801)
Javier Bautista (6456680)
Mostafa Mohamed (6456683)
Supriya Mohile (6456686)
Christine Ambrosone (334756)
Song Liu (9858)
Michelle Janelsins (6456692)

March 2019

Table S1. Descriptive characteristics of breast cancer cases and non-cancer controls. (DOCX 17 kb

Additional file 3: of Droplet digital PCR for the quantification of Alu methylation status in hematological malignancies

Abstract

Extracted data

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