Additional file 6: of Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

Additional file 1: Table S1. of Mutational landscape of mucinous ovarian carcinoma and its neoplastic precursors

Georgina Ryland (3556145)
Sally Hunter (3556154)
Maria Doyle (3556148)
Franco Caramia (583700)
Jason Li (23213)
Simone Rowley (3540932)
Michael Christie (3556142)
Prue Allan (3556151)
Andrew Stephens (184557)
David Bowtell (17430)
Ian Campbell (205212)
Kylie Gorringe (3540923)

August 2015

Clinicopathological data for MOTs. Table S2. Summary of whole exome sequencing statistics. Table S3....

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 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 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 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...

Additional file 7 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 1. SNV mutations called by Mutect and annotated by Oncotator for samples LTS-00...

Additional file 11: 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 5. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

Additional file 12 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 6. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

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 14: 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 8. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

Additional file 13: 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 7. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

Additional file 10: 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 4. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

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 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 6: of Classifying cancer genome aberrations by their mutually exclusive effects on transcription

Jonathan Dayton (4777662)
Stephen Piccolo (3566870)

December 2017

Correlation coefficients and measures of significance for each gene pair in our analysis of ovarian ...

Additional file 1: Table S1. of Mutational landscape of mucinous ovarian carcinoma and its neoplastic precursors

Georgina Ryland (3556145)
Sally Hunter (3556154)
Maria Doyle (3556148)
Franco Caramia (583700)
Jason Li (23213)
Simone Rowley (3540932)
Michael Christie (3556142)
Prue Allan (3556151)
Andrew Stephens (184557)
David Bowtell (17430)
Ian Campbell (205212)
Kylie Gorringe (3540923)

August 2015

Clinicopathological data for MOTs. Table S2. Summary of whole exome sequencing statistics. Table S3....

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 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 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 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...

Additional file 7 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 1. SNV mutations called by Mutect and annotated by Oncotator for samples LTS-00...

Additional file 11: 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 5. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

Additional file 12 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 6. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

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 14: 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 8. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

Additional file 13: 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 7. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

Additional file 10: 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 4. All SNV mutations called by Mutect and annotated by Oncotator for samples LT...

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 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 6: of Classifying cancer genome aberrations by their mutually exclusive effects on transcription

Jonathan Dayton (4777662)
Stephen Piccolo (3566870)

December 2017

Correlation coefficients and measures of significance for each gene pair in our analysis of ovarian ...

Additional file 1: Table S1. of Mutational landscape of mucinous ovarian carcinoma and its neoplastic precursors

Georgina Ryland (3556145)
Sally Hunter (3556154)
Maria Doyle (3556148)
Franco Caramia (583700)
Jason Li (23213)
Simone Rowley (3540932)
Michael Christie (3556142)
Prue Allan (3556151)
Andrew Stephens (184557)
David Bowtell (17430)
Ian Campbell (205212)
Kylie Gorringe (3540923)

August 2015

Clinicopathological data for MOTs. Table S2. Summary of whole exome sequencing statistics. Table S3....

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

Abstract

Extracted data

Additional file 6: of Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

Abstract

Extracted data

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