Additional file 5: of Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

Additional file 5: of Fn14 overcomes cisplatin resistance of high-grade serous ovarian cancer by promoting Mdm2-mediated p53-R248Q ubiquitination and degradation

An-Yue Wu (6636974)
Li-Ying Gu (6636977)
Wei Cang (6636980)
Meng-Xing Cheng (6636983)
Wen-Jing Wang (769627)
Wen Di (384960)
Lei Huang (35191)
Li-Hua Qiu (6636986)

April 2019

Figure S5. Fn14 could reduce the formation of Mdm2-p53-R248Q-Hsp90. (A)-(B) Statistical data of West...

Additional file 5: of Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

S. Yang (2246380)
Stephanie Lheureux (5919803)
Katherine Karakasis (5919806)
Julia Burnier (1864015)
Jeffery Bruce (5919809)
Derek Clouthier (5919812)
Arnavaz Danesh (5919815)
Rene Quevedo (5919818)
Mark Dowar (5919821)
Youstina Hanna (5919824)
Tiantian Li (53740)
Lin Lu (5759)
Wei Xu (28953)
Blaise Clarke (2202952)
Pamela Ohashi (5919827)
Patricia Shaw (359876)
Trevor Pugh (41426)
Amit Oza (3421889)

November 2018

All Strelka indels. All Indels called by Strelka and annotated by Oncotator. (TXT 3458 kb

Additional file 5: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Xu Liang (433535)
Sophie Vacher (233965)
Anais Boulai (5612039)
Virginie Bernard (2226220)
Sylvain Baulande (5113562)
Mylene Bohec (5612042)
Ivan BiĂ¨che (5506235)
Florence Lerebours (303656)
CĂŠline Callens (5612045)

August 2018

Figure S3. DNA copy number alterations in the IBC cohort. The genes with DNA copy number alterations...

Additional file 6: of Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

Alexandre Costa (204738)
Luisa Canto (6670367)
Simon Larsen (6408551)
Adriana Ribeiro (6670373)
Carlos Stecca (6670382)
Annabeth Petersen (6670385)
Mads Aagaard (6670391)
Louise Brot (6291917)
Jan Baumbach (14867)
Glauco Baiocchi (6291902)
Maria Achatz (6116561)
Silvia Rogatto (3994691)

May 2019

Overall survival according to the genomic imbalances. A. Telomeric allelic imbalance (TAI); B. Loss ...

Additional file 3: of Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

Alexandre Costa (204738)
Luisa Canto (6670367)
Simon Larsen (6408551)
Adriana Ribeiro (6670373)
Carlos Stecca (6670382)
Annabeth Petersen (6670385)
Mads Aagaard (6670391)
Louise Brot (6291917)
Jan Baumbach (14867)
Glauco Baiocchi (6291902)
Maria Achatz (6116561)
Silvia Rogatto (3994691)

May 2019

Spearman correlation of four different homologous recombination deficiency scores. TAI, Telomeric al...

Additional file 4: of Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

Alexandre Costa (204738)
Luisa Canto (6670367)
Simon Larsen (6408551)
Adriana Ribeiro (6670373)
Carlos Stecca (6670382)
Annabeth Petersen (6670385)
Mads Aagaard (6670391)
Louise Brot (6291917)
Jan Baumbach (14867)
Glauco Baiocchi (6291902)
Maria Achatz (6116561)
Silvia Rogatto (3994691)

May 2019

BRCA1 and BRCA2 variants categorized according to ACMG (American College of Medical Genetics and Gen...

Additional file 1: of Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

Alexandre Costa (204738)
Luisa Canto (6670367)
Simon Larsen (6408551)
Adriana Ribeiro (6670373)
Carlos Stecca (6670382)
Annabeth Petersen (6670385)
Mads Aagaard (6670391)
Louise Brot (6291917)
Jan Baumbach (14867)
Glauco Baiocchi (6291902)
Maria Achatz (6116561)
Silvia Rogatto (3994691)

May 2019

Flowchart representative of the inclusion criteria adopted in the study. (JPG 245 kb

Additional file 2: of Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

Alexandre Costa (204738)
Luisa Canto (6670367)
Simon Larsen (6408551)
Adriana Ribeiro (6670373)
Carlos Stecca (6670382)
Annabeth Petersen (6670385)
Mads Aagaard (6670391)
Louise Brot (6291917)
Jan Baumbach (14867)
Glauco Baiocchi (6291902)
Maria Achatz (6116561)
Silvia Rogatto (3994691)

May 2019

Summary of the bioinformatic pipeline used to classify the variants detected by tNGS. (JPG 509 kb

Additional file 1: of Deregulation of the spindle assembly checkpoint is associated with paclitaxel resistance in ovarian cancer

Taryne Chong (5060453)
Amila Sarac (5060456)
Cindy Yao (3440612)
Linda Liao (3440618)
Nicola Lyttle (3440624)
Paul Boutros (196570)
John Bartlett (602286)
Melanie Spears (3440621)

April 2018

Table S1. List of significant genes illustrating enrichment and depletion of genes across 3 ovarian ...

Additional file 3: of Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

S. Yang (2246380)
Stephanie Lheureux (5919803)
Katherine Karakasis (5919806)
Julia Burnier (1864015)
Jeffery Bruce (5919809)
Derek Clouthier (5919812)
Arnavaz Danesh (5919815)
Rene Quevedo (5919818)
Mark Dowar (5919821)
Youstina Hanna (5919824)
Tiantian Li (53740)
Lin Lu (5759)
Wei Xu (28953)
Blaise Clarke (2202952)
Pamela Ohashi (5919827)
Patricia Shaw (359876)
Trevor Pugh (41426)
Amit Oza (3421889)

November 2018

CNV segment size as distribution per sample. Distribution of CNV segment size as percentage of chrom...

Additional file 9: of Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

S. Yang (2246380)
Stephanie Lheureux (5919803)
Katherine Karakasis (5919806)
Julia Burnier (1864015)
Jeffery Bruce (5919809)
Derek Clouthier (5919812)
Arnavaz Danesh (5919815)
Rene Quevedo (5919818)
Mark Dowar (5919821)
Youstina Hanna (5919824)
Tiantian Li (53740)
Lin Lu (5759)
Wei Xu (28953)
Blaise Clarke (2202952)
Pamela Ohashi (5919827)
Patricia Shaw (359876)
Trevor Pugh (41426)
Amit Oza (3421889)

November 2018

All Mutect mutations 3. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

Homologous Recombination DNA Repair Pathway Disruption and Retinoblastoma Protein Loss Are Associated with Exceptional Survival in High-Grade Serous Ovarian Cancer.

Garsed, Dale W
Alsop, Kathryn
Fereday, Sian
Emmanuel, Catherine
Kennedy, Catherine J
Etemadmoghadam, Dariush
Gao, Bo
Gebski, Val
Garès, Valérie
Christie, Elizabeth L
Wouters, Maartje C A
Milne, Katy
George, Joshy
Patch, Ann-Marie
Li, Jason
Arnau, Gisela Mir
Semple, Timothy
Gadipally, Sreeja R
Chiew, Yoke-Eng
Hendley, Joy
Mikeska, Thomas
Zapparoli, Giada V
Amarasinghe, Kaushalya
Grimmond, Sean M
Pearson, John V
Waddell, Nicola
Hung, Jillian
Stewart, Colin J R
Sharma, Raghwa
Allan, Prue E
Rambau, Peter F
McNally, Orla
Mileshkin, Linda
Hamilton, Anne
Ananda, Sumitra
Grossi, Marisa
Cohen, Paul A
Leung, Yee C
Rome, Robert M
Beale, Philip
Blomfield, Penny
Friedlander, Michael
Brand, Alison
Dobrovic, Alexander
Köbel, Martin
Harnett, Paul
Nelson, Brad H
Bowtell, David D L
deFazio, Anna

February 2018

Purpose: Women with epithelial ovarian cancer generally have a poor prognosis; however, a subset of ...

Additional file 1: of BRCA1 and BRCA2 mutations and clinical interpretation in 398 ovarian cancer patients: comparison with breast cancer variants in a similar population

Florencia Cardoso (5626418)
Susana Goncalves (5626421)
Pablo Mele (5626424)
Natalia Liria (5626427)
Leonardo Sganga (2164849)
Ignacio Diaz Perez (5626430)
Ernesto Podesta (5626433)
Angela Solano (5626436)

November 2018

Pathogenic mutations in BRCA1 (NM_007294.3) and BRCA2 (NM_000059.3) genes (n = 96) detected in 398 p...

Additional file 8: of Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

S. Yang (2246380)
Stephanie Lheureux (5919803)
Katherine Karakasis (5919806)
Julia Burnier (1864015)
Jeffery Bruce (5919809)
Derek Clouthier (5919812)
Arnavaz Danesh (5919815)
Rene Quevedo (5919818)
Mark Dowar (5919821)
Youstina Hanna (5919824)
Tiantian Li (53740)
Lin Lu (5759)
Wei Xu (28953)
Blaise Clarke (2202952)
Pamela Ohashi (5919827)
Patricia Shaw (359876)
Trevor Pugh (41426)
Amit Oza (3421889)

November 2018

All Mutect mutations 2. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

Additional file 1: Table S1. of Identification of recurrent focal copy number variations and their putative targeted driver genes in ovarian cancer

Liangcai Zhang (156659)
Ying Yuan (133529)
Karen Lu (202927)
Li Zhang (8200)

May 2016

Sample information of 587 ovarian patients and normal tissue samples with Copy number variation and ...

Additional file 5: of Fn14 overcomes cisplatin resistance of high-grade serous ovarian cancer by promoting Mdm2-mediated p53-R248Q ubiquitination and degradation

An-Yue Wu (6636974)
Li-Ying Gu (6636977)
Wei Cang (6636980)
Meng-Xing Cheng (6636983)
Wen-Jing Wang (769627)
Wen Di (384960)
Lei Huang (35191)
Li-Hua Qiu (6636986)

April 2019

Figure S5. Fn14 could reduce the formation of Mdm2-p53-R248Q-Hsp90. (A)-(B) Statistical data of West...

Additional file 5: of Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

S. Yang (2246380)
Stephanie Lheureux (5919803)
Katherine Karakasis (5919806)
Julia Burnier (1864015)
Jeffery Bruce (5919809)
Derek Clouthier (5919812)
Arnavaz Danesh (5919815)
Rene Quevedo (5919818)
Mark Dowar (5919821)
Youstina Hanna (5919824)
Tiantian Li (53740)
Lin Lu (5759)
Wei Xu (28953)
Blaise Clarke (2202952)
Pamela Ohashi (5919827)
Patricia Shaw (359876)
Trevor Pugh (41426)
Amit Oza (3421889)

November 2018

All Strelka indels. All Indels called by Strelka and annotated by Oncotator. (TXT 3458 kb

Additional file 5: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Xu Liang (433535)
Sophie Vacher (233965)
Anais Boulai (5612039)
Virginie Bernard (2226220)
Sylvain Baulande (5113562)
Mylene Bohec (5612042)
Ivan BiĂ¨che (5506235)
Florence Lerebours (303656)
CĂŠline Callens (5612045)

August 2018

Figure S3. DNA copy number alterations in the IBC cohort. The genes with DNA copy number alterations...

Additional file 6: of Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

Alexandre Costa (204738)
Luisa Canto (6670367)
Simon Larsen (6408551)
Adriana Ribeiro (6670373)
Carlos Stecca (6670382)
Annabeth Petersen (6670385)
Mads Aagaard (6670391)
Louise Brot (6291917)
Jan Baumbach (14867)
Glauco Baiocchi (6291902)
Maria Achatz (6116561)
Silvia Rogatto (3994691)

May 2019

Overall survival according to the genomic imbalances. A. Telomeric allelic imbalance (TAI); B. Loss ...

Additional file 3: of Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

Alexandre Costa (204738)
Luisa Canto (6670367)
Simon Larsen (6408551)
Adriana Ribeiro (6670373)
Carlos Stecca (6670382)
Annabeth Petersen (6670385)
Mads Aagaard (6670391)
Louise Brot (6291917)
Jan Baumbach (14867)
Glauco Baiocchi (6291902)
Maria Achatz (6116561)
Silvia Rogatto (3994691)

May 2019

Spearman correlation of four different homologous recombination deficiency scores. TAI, Telomeric al...

Additional file 4: of Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

Alexandre Costa (204738)
Luisa Canto (6670367)
Simon Larsen (6408551)
Adriana Ribeiro (6670373)
Carlos Stecca (6670382)
Annabeth Petersen (6670385)
Mads Aagaard (6670391)
Louise Brot (6291917)
Jan Baumbach (14867)
Glauco Baiocchi (6291902)
Maria Achatz (6116561)
Silvia Rogatto (3994691)

May 2019

BRCA1 and BRCA2 variants categorized according to ACMG (American College of Medical Genetics and Gen...

Additional file 1: of Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

Alexandre Costa (204738)
Luisa Canto (6670367)
Simon Larsen (6408551)
Adriana Ribeiro (6670373)
Carlos Stecca (6670382)
Annabeth Petersen (6670385)
Mads Aagaard (6670391)
Louise Brot (6291917)
Jan Baumbach (14867)
Glauco Baiocchi (6291902)
Maria Achatz (6116561)
Silvia Rogatto (3994691)

May 2019

Flowchart representative of the inclusion criteria adopted in the study. (JPG 245 kb

Additional file 2: of Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

Alexandre Costa (204738)
Luisa Canto (6670367)
Simon Larsen (6408551)
Adriana Ribeiro (6670373)
Carlos Stecca (6670382)
Annabeth Petersen (6670385)
Mads Aagaard (6670391)
Louise Brot (6291917)
Jan Baumbach (14867)
Glauco Baiocchi (6291902)
Maria Achatz (6116561)
Silvia Rogatto (3994691)

May 2019

Summary of the bioinformatic pipeline used to classify the variants detected by tNGS. (JPG 509 kb

Additional file 1: of Deregulation of the spindle assembly checkpoint is associated with paclitaxel resistance in ovarian cancer

Taryne Chong (5060453)
Amila Sarac (5060456)
Cindy Yao (3440612)
Linda Liao (3440618)
Nicola Lyttle (3440624)
Paul Boutros (196570)
John Bartlett (602286)
Melanie Spears (3440621)

April 2018

Table S1. List of significant genes illustrating enrichment and depletion of genes across 3 ovarian ...

Additional file 3: of Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

S. Yang (2246380)
Stephanie Lheureux (5919803)
Katherine Karakasis (5919806)
Julia Burnier (1864015)
Jeffery Bruce (5919809)
Derek Clouthier (5919812)
Arnavaz Danesh (5919815)
Rene Quevedo (5919818)
Mark Dowar (5919821)
Youstina Hanna (5919824)
Tiantian Li (53740)
Lin Lu (5759)
Wei Xu (28953)
Blaise Clarke (2202952)
Pamela Ohashi (5919827)
Patricia Shaw (359876)
Trevor Pugh (41426)
Amit Oza (3421889)

November 2018

CNV segment size as distribution per sample. Distribution of CNV segment size as percentage of chrom...

Additional file 9: of Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

S. Yang (2246380)
Stephanie Lheureux (5919803)
Katherine Karakasis (5919806)
Julia Burnier (1864015)
Jeffery Bruce (5919809)
Derek Clouthier (5919812)
Arnavaz Danesh (5919815)
Rene Quevedo (5919818)
Mark Dowar (5919821)
Youstina Hanna (5919824)
Tiantian Li (53740)
Lin Lu (5759)
Wei Xu (28953)
Blaise Clarke (2202952)
Pamela Ohashi (5919827)
Patricia Shaw (359876)
Trevor Pugh (41426)
Amit Oza (3421889)

November 2018

All Mutect mutations 3. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

Homologous Recombination DNA Repair Pathway Disruption and Retinoblastoma Protein Loss Are Associated with Exceptional Survival in High-Grade Serous Ovarian Cancer.

Garsed, Dale W
Alsop, Kathryn
Fereday, Sian
Emmanuel, Catherine
Kennedy, Catherine J
Etemadmoghadam, Dariush
Gao, Bo
Gebski, Val
Garès, Valérie
Christie, Elizabeth L
Wouters, Maartje C A
Milne, Katy
George, Joshy
Patch, Ann-Marie
Li, Jason
Arnau, Gisela Mir
Semple, Timothy
Gadipally, Sreeja R
Chiew, Yoke-Eng
Hendley, Joy
Mikeska, Thomas
Zapparoli, Giada V
Amarasinghe, Kaushalya
Grimmond, Sean M
Pearson, John V
Waddell, Nicola
Hung, Jillian
Stewart, Colin J R
Sharma, Raghwa
Allan, Prue E
Rambau, Peter F
McNally, Orla
Mileshkin, Linda
Hamilton, Anne
Ananda, Sumitra
Grossi, Marisa
Cohen, Paul A
Leung, Yee C
Rome, Robert M
Beale, Philip
Blomfield, Penny
Friedlander, Michael
Brand, Alison
Dobrovic, Alexander
Köbel, Martin
Harnett, Paul
Nelson, Brad H
Bowtell, David D L
deFazio, Anna

February 2018

Purpose: Women with epithelial ovarian cancer generally have a poor prognosis; however, a subset of ...

Additional file 1: of BRCA1 and BRCA2 mutations and clinical interpretation in 398 ovarian cancer patients: comparison with breast cancer variants in a similar population

Florencia Cardoso (5626418)
Susana Goncalves (5626421)
Pablo Mele (5626424)
Natalia Liria (5626427)
Leonardo Sganga (2164849)
Ignacio Diaz Perez (5626430)
Ernesto Podesta (5626433)
Angela Solano (5626436)

November 2018

Pathogenic mutations in BRCA1 (NM_007294.3) and BRCA2 (NM_000059.3) genes (n = 96) detected in 398 p...

Additional file 8: of Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

S. Yang (2246380)
Stephanie Lheureux (5919803)
Katherine Karakasis (5919806)
Julia Burnier (1864015)
Jeffery Bruce (5919809)
Derek Clouthier (5919812)
Arnavaz Danesh (5919815)
Rene Quevedo (5919818)
Mark Dowar (5919821)
Youstina Hanna (5919824)
Tiantian Li (53740)
Lin Lu (5759)
Wei Xu (28953)
Blaise Clarke (2202952)
Pamela Ohashi (5919827)
Patricia Shaw (359876)
Trevor Pugh (41426)
Amit Oza (3421889)

November 2018

All Mutect mutations 2. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

Additional file 1: Table S1. of Identification of recurrent focal copy number variations and their putative targeted driver genes in ovarian cancer

Liangcai Zhang (156659)
Ying Yuan (133529)
Karen Lu (202927)
Li Zhang (8200)

May 2016

Sample information of 587 ovarian patients and normal tissue samples with Copy number variation and ...

Additional file 5: of Fn14 overcomes cisplatin resistance of high-grade serous ovarian cancer by promoting Mdm2-mediated p53-R248Q ubiquitination and degradation

An-Yue Wu (6636974)
Li-Ying Gu (6636977)
Wei Cang (6636980)
Meng-Xing Cheng (6636983)
Wen-Jing Wang (769627)
Wen Di (384960)
Lei Huang (35191)
Li-Hua Qiu (6636986)

April 2019

Figure S5. Fn14 could reduce the formation of Mdm2-p53-R248Q-Hsp90. (A)-(B) Statistical data of West...

Additional file 5: of Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

S. Yang (2246380)
Stephanie Lheureux (5919803)
Katherine Karakasis (5919806)
Julia Burnier (1864015)
Jeffery Bruce (5919809)
Derek Clouthier (5919812)
Arnavaz Danesh (5919815)
Rene Quevedo (5919818)
Mark Dowar (5919821)
Youstina Hanna (5919824)
Tiantian Li (53740)
Lin Lu (5759)
Wei Xu (28953)
Blaise Clarke (2202952)
Pamela Ohashi (5919827)
Patricia Shaw (359876)
Trevor Pugh (41426)
Amit Oza (3421889)

November 2018

All Strelka indels. All Indels called by Strelka and annotated by Oncotator. (TXT 3458 kb

Additional file 5: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Xu Liang (433535)
Sophie Vacher (233965)
Anais Boulai (5612039)
Virginie Bernard (2226220)
Sylvain Baulande (5113562)
Mylene Bohec (5612042)
Ivan BiĂ¨che (5506235)
Florence Lerebours (303656)
CĂŠline Callens (5612045)

August 2018

Figure S3. DNA copy number alterations in the IBC cohort. The genes with DNA copy number alterations...

Additional file 5: of Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

Abstract

Extracted data

Additional file 5: of Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

Abstract

Extracted data

Related items

Related items