Additional file 2 of Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers

Fusion Genes in Prostate Cancer: A Comparison in Men of African and European Descent

Rebecca Morgan
Dulcie Keeley
E. Starr Hazard
Emma H. Allott
Bethany Wolf
Stephen J. Savage
Chanita Hughes Halbert
Sebastiano Gattoni-Celli
Gary Hardiman

April 2022

Prostate cancer is one of the most prevalent cancers worldwide, particularly affecting men living a ...

Additional file 2: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

Kasey Jividen (5846180)
Katarzyna Kedzierska (5846183)
Chun-Song Yang (5846186)
Karol Szlachta (5511017)
Aakrosh Ratan (279792)
Bryce Paschal (5846189)

October 2018

Table S2. Potential deleterious alterations of DNA damage response genes in prostate cancer cell lin...

Additional file 8: of Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Jennifer Myers (4241683)
Karin Vallega (4241680)
Jason White (146854)
Kaixian Yu (2836718)
Clayton Yates (572584)
Qing-Xiang Sang (3461384)

July 2017

Additional Analysis on Reproducibility of Protein Fold Changes between Paired Malignant and Non-Mali...

Additional file 1 of Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers

Tingting Gong (540807)
Weerachai Jaratlerdsiri (519605)
Jue Jiang (6565325)
Cali Willet (3456962)
Tracy Chew (8901187)
Sean M. Patrick (13559456)
Ruth J. Lyons (13559459)
Anne-Maree Haynes (5706494)
Gabriela Pasqualim (688774)
Ilma Simoni Brum (5540651)
Phillip D. Stricker (5706485)
Shingai B. A. Mutambirwa (13559462)
Rosemarie Sadsad (495058)
Anthony T. Papenfuss (9450362)
Riana M. S. Bornman (13559465)
Eva K. F. Chan (9311796)
Vanessa M. Hayes (13559468)

August 2022

Additional file 1: Figure S1. Concordant SV call generation from Manta and GRIDSS. Figure S2. Summar...

Additional file 1: of Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer

Tarun Mamidi (6468017)
Jiande Wu (6468020)
Chindo Hicks (5003561)

March 2019

Table S1. Comprehensive list of single nucleotide polymorphisms (herein called genetic variants) and...

Additional file 5: of Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer

Tarun Mamidi (6468017)
Jiande Wu (6468020)
Chindo Hicks (5003561)

March 2019

Table S5. Comprehensive list of genes containing both germline and somatic mutation, chromosome posi...

Additional file 2: of Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer

Tarun Mamidi (6468017)
Jiande Wu (6468020)
Chindo Hicks (5003561)

March 2019

Table S2. Comprehensive list of somatic mutations, gene symbols, Ensemble gene IDs, chromosome numbe...

Additional file 4: of Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer

Tarun Mamidi (6468017)
Jiande Wu (6468020)
Chindo Hicks (5003561)

March 2019

r Table S4. Significantly differentially expressed genes without somatic mutations. (XLSX 272 kb

Additional file 1: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

Kasey Jividen (5846180)
Katarzyna Kedzierska (5846183)
Chun-Song Yang (5846186)
Karol Szlachta (5511017)
Aakrosh Ratan (279792)
Bryce Paschal (5846189)

October 2018

Table S1. DNA damage response gene variants in prostate cancer cell lines. (XLSX 16 kb

Additional file 2: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer (5997515)
Bram De Laere (5997518)
Tom Whitington (5997521)
Peter Van Oyen (5997524)
Christophe Ghysel (5997527)
Jozef Ampe (5997530)
Piet Ost (837668)
Wim Demey (5997533)
Lucien Hoekx (5997536)
Dirk Schrijvers (5997539)
Barbara Brouwers (647613)
Willem Lybaert (5997542)
Els Everaert (5997545)
Daan De Maeseneer (4216804)
Michiel Strijbos (5997548)
Alain Bols (5997551)
Karen Fransis (5997554)
Steffi Oeyen (5997557)
Pieter-Jan van Dam (5997560)
Gert Van den Eynden (526153)
Annemie Rutten (5997563)
Markus Aly (523056)
Tobias NordstrĂśm (5997575)
Steven Van Laere (161546)
Mattias Rantalainen (166786)
Prabhakar Rajan (192485)
Lars Egevad (124325)
Anders UllĂŠn (5997578)
Jeffrey Yachnin (3396692)
Luc Dirix (61984)
Henrik GrĂśnberg (3458312)
Johan Lindberg (18863)

November 2018

Table S1. Detailed overview of the capture designs and targeted regions. (XLSX 974 kb

Additional file 9: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer (5997515)
Bram De Laere (5997518)
Tom Whitington (5997521)
Peter Van Oyen (5997524)
Christophe Ghysel (5997527)
Jozef Ampe (5997530)
Piet Ost (837668)
Wim Demey (5997533)
Lucien Hoekx (5997536)
Dirk Schrijvers (5997539)
Barbara Brouwers (647613)
Willem Lybaert (5997542)
Els Everaert (5997545)
Daan De Maeseneer (4216804)
Michiel Strijbos (5997548)
Alain Bols (5997551)
Karen Fransis (5997554)
Steffi Oeyen (5997557)
Pieter-Jan van Dam (5997560)
Gert Van den Eynden (526153)
Annemie Rutten (5997563)
Markus Aly (523056)
Tobias NordstrĂśm (5997575)
Steven Van Laere (161546)
Mattias Rantalainen (166786)
Prabhakar Rajan (192485)
Lars Egevad (124325)
Anders UllĂŠn (5997578)
Jeffrey Yachnin (3396692)
Luc Dirix (61984)
Henrik GrĂśnberg (3458312)
Johan Lindberg (18863)

November 2018

Table S7. Table comparing relevant germline alterations, presented here, with other publications. (X...

Additional file 4: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer (5997515)
Bram De Laere (5997518)
Tom Whitington (5997521)
Peter Van Oyen (5997524)
Christophe Ghysel (5997527)
Jozef Ampe (5997530)
Piet Ost (837668)
Wim Demey (5997533)
Lucien Hoekx (5997536)
Dirk Schrijvers (5997539)
Barbara Brouwers (647613)
Willem Lybaert (5997542)
Els Everaert (5997545)
Daan De Maeseneer (4216804)
Michiel Strijbos (5997548)
Alain Bols (5997551)
Karen Fransis (5997554)
Steffi Oeyen (5997557)
Pieter-Jan van Dam (5997560)
Gert Van den Eynden (526153)
Annemie Rutten (5997563)
Markus Aly (523056)
Tobias NordstrĂśm (5997575)
Steven Van Laere (161546)
Mattias Rantalainen (166786)
Prabhakar Rajan (192485)
Lars Egevad (124325)
Anders UllĂŠn (5997578)
Jeffrey Yachnin (3396692)
Luc Dirix (61984)
Henrik GrĂśnberg (3458312)
Johan Lindberg (18863)

November 2018

Table S3. Overview of which samples that were sequenced with which capture design. (XLSX 123 kb

Additional file 3: of Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer

Tarun Mamidi (6468017)
Jiande Wu (6468020)
Chindo Hicks (5003561)

March 2019

Table S3. Comprehensive list of somatically mutated and significantly differentially expressed genes...

Additional file 2: of Microsatellite instability in prostate cancer by PCR or next-generation sequencing

Jennifer Hempelmann (843937)
Christina Lockwood (5113295)
Eric Konnick (5113292)
Michael Schweizer (5113283)
Emmanuel Antonarakis (5113298)
Tamara Lotan (4589959)
Bruce Montgomery (5113289)
Peter Nelson (414128)
Nola Klemfuss (5113301)
Stephen Salipante (5113286)
Colin Pritchard (2612)

April 2018

Table S1. Large-Panel NGS Microsatellite Loci. Table S2. Detail on Samples, Targeted Sequencing, Mic...

Additional file 10: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

Kasey Jividen (5846180)
Katarzyna Kedzierska (5846183)
Chun-Song Yang (5846186)
Karol Szlachta (5511017)
Aakrosh Ratan (279792)
Bryce Paschal (5846189)

October 2018

Table S8. DNA damage response genes in prostate cancer xenografts and patient metastases. (XLSX 10 k...

Fusion Genes in Prostate Cancer: A Comparison in Men of African and European Descent

Rebecca Morgan
Dulcie Keeley
E. Starr Hazard
Emma H. Allott
Bethany Wolf
Stephen J. Savage
Chanita Hughes Halbert
Sebastiano Gattoni-Celli
Gary Hardiman

April 2022

Prostate cancer is one of the most prevalent cancers worldwide, particularly affecting men living a ...

Additional file 2: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

Kasey Jividen (5846180)
Katarzyna Kedzierska (5846183)
Chun-Song Yang (5846186)
Karol Szlachta (5511017)
Aakrosh Ratan (279792)
Bryce Paschal (5846189)

October 2018

Table S2. Potential deleterious alterations of DNA damage response genes in prostate cancer cell lin...

Additional file 8: of Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Jennifer Myers (4241683)
Karin Vallega (4241680)
Jason White (146854)
Kaixian Yu (2836718)
Clayton Yates (572584)
Qing-Xiang Sang (3461384)

July 2017

Additional Analysis on Reproducibility of Protein Fold Changes between Paired Malignant and Non-Mali...

Additional file 1 of Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers

Tingting Gong (540807)
Weerachai Jaratlerdsiri (519605)
Jue Jiang (6565325)
Cali Willet (3456962)
Tracy Chew (8901187)
Sean M. Patrick (13559456)
Ruth J. Lyons (13559459)
Anne-Maree Haynes (5706494)
Gabriela Pasqualim (688774)
Ilma Simoni Brum (5540651)
Phillip D. Stricker (5706485)
Shingai B. A. Mutambirwa (13559462)
Rosemarie Sadsad (495058)
Anthony T. Papenfuss (9450362)
Riana M. S. Bornman (13559465)
Eva K. F. Chan (9311796)
Vanessa M. Hayes (13559468)

August 2022

Additional file 1: Figure S1. Concordant SV call generation from Manta and GRIDSS. Figure S2. Summar...

Additional file 1: of Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer

Tarun Mamidi (6468017)
Jiande Wu (6468020)
Chindo Hicks (5003561)

March 2019

Table S1. Comprehensive list of single nucleotide polymorphisms (herein called genetic variants) and...

Additional file 5: of Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer

Tarun Mamidi (6468017)
Jiande Wu (6468020)
Chindo Hicks (5003561)

March 2019

Table S5. Comprehensive list of genes containing both germline and somatic mutation, chromosome posi...

Additional file 2: of Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer

Tarun Mamidi (6468017)
Jiande Wu (6468020)
Chindo Hicks (5003561)

March 2019

Table S2. Comprehensive list of somatic mutations, gene symbols, Ensemble gene IDs, chromosome numbe...

Additional file 4: of Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer

Tarun Mamidi (6468017)
Jiande Wu (6468020)
Chindo Hicks (5003561)

March 2019

r Table S4. Significantly differentially expressed genes without somatic mutations. (XLSX 272 kb

Additional file 1: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

Kasey Jividen (5846180)
Katarzyna Kedzierska (5846183)
Chun-Song Yang (5846186)
Karol Szlachta (5511017)
Aakrosh Ratan (279792)
Bryce Paschal (5846189)

October 2018

Table S1. DNA damage response gene variants in prostate cancer cell lines. (XLSX 16 kb

Additional file 2: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer (5997515)
Bram De Laere (5997518)
Tom Whitington (5997521)
Peter Van Oyen (5997524)
Christophe Ghysel (5997527)
Jozef Ampe (5997530)
Piet Ost (837668)
Wim Demey (5997533)
Lucien Hoekx (5997536)
Dirk Schrijvers (5997539)
Barbara Brouwers (647613)
Willem Lybaert (5997542)
Els Everaert (5997545)
Daan De Maeseneer (4216804)
Michiel Strijbos (5997548)
Alain Bols (5997551)
Karen Fransis (5997554)
Steffi Oeyen (5997557)
Pieter-Jan van Dam (5997560)
Gert Van den Eynden (526153)
Annemie Rutten (5997563)
Markus Aly (523056)
Tobias NordstrĂśm (5997575)
Steven Van Laere (161546)
Mattias Rantalainen (166786)
Prabhakar Rajan (192485)
Lars Egevad (124325)
Anders UllĂŠn (5997578)
Jeffrey Yachnin (3396692)
Luc Dirix (61984)
Henrik GrĂśnberg (3458312)
Johan Lindberg (18863)

November 2018

Table S1. Detailed overview of the capture designs and targeted regions. (XLSX 974 kb

Additional file 9: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer (5997515)
Bram De Laere (5997518)
Tom Whitington (5997521)
Peter Van Oyen (5997524)
Christophe Ghysel (5997527)
Jozef Ampe (5997530)
Piet Ost (837668)
Wim Demey (5997533)
Lucien Hoekx (5997536)
Dirk Schrijvers (5997539)
Barbara Brouwers (647613)
Willem Lybaert (5997542)
Els Everaert (5997545)
Daan De Maeseneer (4216804)
Michiel Strijbos (5997548)
Alain Bols (5997551)
Karen Fransis (5997554)
Steffi Oeyen (5997557)
Pieter-Jan van Dam (5997560)
Gert Van den Eynden (526153)
Annemie Rutten (5997563)
Markus Aly (523056)
Tobias NordstrĂśm (5997575)
Steven Van Laere (161546)
Mattias Rantalainen (166786)
Prabhakar Rajan (192485)
Lars Egevad (124325)
Anders UllĂŠn (5997578)
Jeffrey Yachnin (3396692)
Luc Dirix (61984)
Henrik GrĂśnberg (3458312)
Johan Lindberg (18863)

November 2018

Table S7. Table comparing relevant germline alterations, presented here, with other publications. (X...

Additional file 4: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer (5997515)
Bram De Laere (5997518)
Tom Whitington (5997521)
Peter Van Oyen (5997524)
Christophe Ghysel (5997527)
Jozef Ampe (5997530)
Piet Ost (837668)
Wim Demey (5997533)
Lucien Hoekx (5997536)
Dirk Schrijvers (5997539)
Barbara Brouwers (647613)
Willem Lybaert (5997542)
Els Everaert (5997545)
Daan De Maeseneer (4216804)
Michiel Strijbos (5997548)
Alain Bols (5997551)
Karen Fransis (5997554)
Steffi Oeyen (5997557)
Pieter-Jan van Dam (5997560)
Gert Van den Eynden (526153)
Annemie Rutten (5997563)
Markus Aly (523056)
Tobias NordstrĂśm (5997575)
Steven Van Laere (161546)
Mattias Rantalainen (166786)
Prabhakar Rajan (192485)
Lars Egevad (124325)
Anders UllĂŠn (5997578)
Jeffrey Yachnin (3396692)
Luc Dirix (61984)
Henrik GrĂśnberg (3458312)
Johan Lindberg (18863)

November 2018

Table S3. Overview of which samples that were sequenced with which capture design. (XLSX 123 kb

Additional file 3: of Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer

Tarun Mamidi (6468017)
Jiande Wu (6468020)
Chindo Hicks (5003561)

March 2019

Table S3. Comprehensive list of somatically mutated and significantly differentially expressed genes...

Additional file 2: of Microsatellite instability in prostate cancer by PCR or next-generation sequencing

Jennifer Hempelmann (843937)
Christina Lockwood (5113295)
Eric Konnick (5113292)
Michael Schweizer (5113283)
Emmanuel Antonarakis (5113298)
Tamara Lotan (4589959)
Bruce Montgomery (5113289)
Peter Nelson (414128)
Nola Klemfuss (5113301)
Stephen Salipante (5113286)
Colin Pritchard (2612)

April 2018

Table S1. Large-Panel NGS Microsatellite Loci. Table S2. Detail on Samples, Targeted Sequencing, Mic...

Additional file 10: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

Kasey Jividen (5846180)
Katarzyna Kedzierska (5846183)
Chun-Song Yang (5846186)
Karol Szlachta (5511017)
Aakrosh Ratan (279792)
Bryce Paschal (5846189)

October 2018

Table S8. DNA damage response genes in prostate cancer xenografts and patient metastases. (XLSX 10 k...

Fusion Genes in Prostate Cancer: A Comparison in Men of African and European Descent

Rebecca Morgan
Dulcie Keeley
E. Starr Hazard
Emma H. Allott
Bethany Wolf
Stephen J. Savage
Chanita Hughes Halbert
Sebastiano Gattoni-Celli
Gary Hardiman

April 2022

Prostate cancer is one of the most prevalent cancers worldwide, particularly affecting men living a ...

Additional file 2: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

Kasey Jividen (5846180)
Katarzyna Kedzierska (5846183)
Chun-Song Yang (5846186)
Karol Szlachta (5511017)
Aakrosh Ratan (279792)
Bryce Paschal (5846189)

October 2018

Table S2. Potential deleterious alterations of DNA damage response genes in prostate cancer cell lin...

Additional file 8: of Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Jennifer Myers (4241683)
Karin Vallega (4241680)
Jason White (146854)
Kaixian Yu (2836718)
Clayton Yates (572584)
Qing-Xiang Sang (3461384)

July 2017

Additional Analysis on Reproducibility of Protein Fold Changes between Paired Malignant and Non-Mali...

Additional file 2 of Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers

Abstract

Extracted data

Additional file 2 of Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers

Abstract

Extracted data

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