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Additional file 2: of Lost in translation: returning germline genetic results in genome-scale cancer research

Amber Johns (3988427)
Skye McKay (3988442)
Jeremy Humphris (3988421)
Mark Pinese (52475)
Lorraine Chantrill (3988445)
R. Mead (3988433)
Katherine Tucker (55580)
Lesley Andrews (55577)
Annabel Goodwin (3988436)
Conrad Leonard (132638)
Hilda High (3988430)
Katia Nones (132620)
Ann-Marie Patch (481815)
Neil Merrett (3988439)
Nick Pavlakis (783392)
Karin Kassahn (3988424)
Jaswinder Samra (3161070)
David Miller (62440)
David Chang (217413)
Marina Pajic (132629)
John Pearson (629146)
Sean Grimmond (47488)
Nicola Waddell (481824)
Nikolajs Zeps (347380)
Anthony Gill (603787)
Andrew Biankin (3703264)

Publication date

April 2017

DOI

10.6084/m9.figshare.c.3767627_d2.v1

Abstract

Gene List, which includes the list of candidate genes selected for the RoR process. (XLSX 60 kb

Extracted data

Related items

Additional file 2: Table S2. of Identification of mRNA isoform switching in breast cancer

Wei Zhao (14321)
Katherine Hoadley (3530135)
Joel Parker (17174)
Charles Perou (3530138)

March 2016

43 genes with more than 10 expressed and detected transcripts per gene. (XLSX 10 kb

Additional file 1: of Diagnostic yield and clinical utility of a comprehensive gene panel for hereditary tumor syndromes

Jonas Henn (6258308)
Isabel Spier (4632118)
Ronja S. Adam (6258311)
Stefanie Holzapfel (6258314)
Siegfried Uhlhaas (6258317)
Katrin Kayser (6258320)
Guido Plotz (22851)
Sophia Peters (4632115)
Stefan Aretz (4632109)

January 2019

Table S1. List of all 64 patients with known germline mutationsâ=âgroup K. With the exception of...

Additional file 2: of ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

Serghei Mangul (4973068)
Harry Yang (4376224)
Nicolas Strauli (3551255)
Franziska Gruhl (220206)
Hagit Porath (4485907)
Kevin Hsieh (4973062)
Linus Chen (4973059)
Timothy Daley (3312627)
Stephanie Christenson (4973065)
Agata Wesolowska-Andersen (3683038)
Roberto Spreafico (4246897)
Cydney Rios (3683041)
Celeste Eng (179050)
Andrew Smith (11197)
Ryan Hernandez (218444)
Roel Ophoff (573364)
Jose Santana (421066)
Erez Levanon (3408371)
Prescott Woodruff (4055044)
Esteban Burchard (1262)
Max Seibold (3683044)
Sagiv Shifman (86805)
Eleazar Eskin (108069)
Noah Zaitlen (120787)

February 2018

Table S1. The effect of altering order of ROP step on the classification accuracy. Table S2. Concord...

Additional file 2: of The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens

Dimitra Repana (6173975)
Joel Nulsen (6173978)
Lisa Dressler (6173981)
Michele Bortolomeazzi (6173984)
Santhilata Venkata (6173987)
Aikaterini Tourna (6173990)
Anna Yakovleva (778118)
Tommaso Palmieri (6173993)
Francesca Ciccarelli (6173996)

January 2019

Table S1. Systems-level properties of cancer genes. Table S2 List of 273 publications describing can...

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 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: Table S2. of A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients

Lőrinc Pongor (3574811)
Máté Kormos (3574814)
Christos Hatzis (565382)
Lajos Pusztai (78763)
András Szabó (3034779)
Balázs Győrffy (110652)

October 2015

The complete set of all genes included in the metagenes for each of the putative driver genes listed...

Additional file 2: of Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication

Fantao Zhang (844781)
Tao Xu (3537)
Linyong Mao (184164)
Shuangyong Yan (3464606)
Xiwen Chen (323415)
Zhenfeng Wu (735649)
Rui Chen (95310)
Xiangdong Luo (461876)
Jiankun Xie (844782)
Shan Gao (46743)

April 2016

This file reports mapping the 1568 deletions to rice genes in the reference genome. This file is in ...

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 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 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 Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

Tianyu Wang (397547)
Boyang Li (4268965)
Craig Nelson (3498350)
Sheida Nabavi (3493139)

January 2019

Results of the Gene Ontology Process enrichment analysis of the 300 top-ranked DE genes and the list...

Additional file 2: of Combining genomic analyses with tumour-derived slice cultures for the characterization of an EGFR-activating kinase mutation in a case of glioblastoma

Lea Loriguet (5844800)
Mony Morisse (5844803)
Julie Dremaux (5844806)
Louison Collet (5844809)
Christophe Attencourt (5844812)
Alexandre Coutte (5844815)
Mathieu Boone (5844818)
Henri Sevestre (49129)
Antoine Galmiche (252260)
Brigitte Gubler (394579)
Bruno Chauffert (2144650)
Stephanie Trudel (5844821)

October 2018

Table S2. The number of reads per amplicon obtained with panel-based, next-generation sequencing. Th...

Additional file 2: Table S1. of Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response

Esther Lips (3581426)
Magali Michaut (76734)
Marlous Hoogstraat (630624)
Lennart Mulder (3581420)
Nicolle Besselink (630626)
Marco Koudijs (3581423)
Edwin Cuppen (9902)
Emile Voest (3581435)
Rene Bernards (3581432)
Petra Nederlof (3581429)
Jelle Wesseling (248405)
Sjoerd Rodenhuis (523940)
Lodewyk Wessels (66823)

October 2015

1977 Cancer Gene Panel. This file lists all 1,977 genes in the Cancer Gene Panel, used in this study...

Additional file 3: of The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens

Dimitra Repana (6173975)
Joel Nulsen (6173978)
Lisa Dressler (6173981)
Michele Bortolomeazzi (6173984)
Santhilata Venkata (6173987)
Aikaterini Tourna (6173990)
Anna Yakovleva (778118)
Tommaso Palmieri (6173993)
Francesca Ciccarelli (6173996)

January 2019

Lists of all cancer genes, known cancer genes, and candidate cancer genes. (XLSX 840 kb

Additional file 2: Table S2. of Identification of mRNA isoform switching in breast cancer

Wei Zhao (14321)
Katherine Hoadley (3530135)
Joel Parker (17174)
Charles Perou (3530138)

March 2016

43 genes with more than 10 expressed and detected transcripts per gene. (XLSX 10 kb

Additional file 1: of Diagnostic yield and clinical utility of a comprehensive gene panel for hereditary tumor syndromes

Jonas Henn (6258308)
Isabel Spier (4632118)
Ronja S. Adam (6258311)
Stefanie Holzapfel (6258314)
Siegfried Uhlhaas (6258317)
Katrin Kayser (6258320)
Guido Plotz (22851)
Sophia Peters (4632115)
Stefan Aretz (4632109)

January 2019

Table S1. List of all 64 patients with known germline mutationsâ=âgroup K. With the exception of...

Additional file 2: of ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

Serghei Mangul (4973068)
Harry Yang (4376224)
Nicolas Strauli (3551255)
Franziska Gruhl (220206)
Hagit Porath (4485907)
Kevin Hsieh (4973062)
Linus Chen (4973059)
Timothy Daley (3312627)
Stephanie Christenson (4973065)
Agata Wesolowska-Andersen (3683038)
Roberto Spreafico (4246897)
Cydney Rios (3683041)
Celeste Eng (179050)
Andrew Smith (11197)
Ryan Hernandez (218444)
Roel Ophoff (573364)
Jose Santana (421066)
Erez Levanon (3408371)
Prescott Woodruff (4055044)
Esteban Burchard (1262)
Max Seibold (3683044)
Sagiv Shifman (86805)
Eleazar Eskin (108069)
Noah Zaitlen (120787)

February 2018

Table S1. The effect of altering order of ROP step on the classification accuracy. Table S2. Concord...

Additional file 2: of The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens

Dimitra Repana (6173975)
Joel Nulsen (6173978)
Lisa Dressler (6173981)
Michele Bortolomeazzi (6173984)
Santhilata Venkata (6173987)
Aikaterini Tourna (6173990)
Anna Yakovleva (778118)
Tommaso Palmieri (6173993)
Francesca Ciccarelli (6173996)

January 2019

Table S1. Systems-level properties of cancer genes. Table S2 List of 273 publications describing can...

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 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: Table S2. of A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients

Lőrinc Pongor (3574811)
Máté Kormos (3574814)
Christos Hatzis (565382)
Lajos Pusztai (78763)
András Szabó (3034779)
Balázs Győrffy (110652)

October 2015

The complete set of all genes included in the metagenes for each of the putative driver genes listed...

Additional file 2: of Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication

Fantao Zhang (844781)
Tao Xu (3537)
Linyong Mao (184164)
Shuangyong Yan (3464606)
Xiwen Chen (323415)
Zhenfeng Wu (735649)
Rui Chen (95310)
Xiangdong Luo (461876)
Jiankun Xie (844782)
Shan Gao (46743)

April 2016

This file reports mapping the 1568 deletions to rice genes in the reference genome. This file is in ...

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 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 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 Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

Tianyu Wang (397547)
Boyang Li (4268965)
Craig Nelson (3498350)
Sheida Nabavi (3493139)

January 2019

Results of the Gene Ontology Process enrichment analysis of the 300 top-ranked DE genes and the list...

Additional file 2: of Combining genomic analyses with tumour-derived slice cultures for the characterization of an EGFR-activating kinase mutation in a case of glioblastoma

Lea Loriguet (5844800)
Mony Morisse (5844803)
Julie Dremaux (5844806)
Louison Collet (5844809)
Christophe Attencourt (5844812)
Alexandre Coutte (5844815)
Mathieu Boone (5844818)
Henri Sevestre (49129)
Antoine Galmiche (252260)
Brigitte Gubler (394579)
Bruno Chauffert (2144650)
Stephanie Trudel (5844821)

October 2018

Table S2. The number of reads per amplicon obtained with panel-based, next-generation sequencing. Th...

Additional file 2: Table S1. of Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response

Esther Lips (3581426)
Magali Michaut (76734)
Marlous Hoogstraat (630624)
Lennart Mulder (3581420)
Nicolle Besselink (630626)
Marco Koudijs (3581423)
Edwin Cuppen (9902)
Emile Voest (3581435)
Rene Bernards (3581432)
Petra Nederlof (3581429)
Jelle Wesseling (248405)
Sjoerd Rodenhuis (523940)
Lodewyk Wessels (66823)

October 2015

1977 Cancer Gene Panel. This file lists all 1,977 genes in the Cancer Gene Panel, used in this study...

Additional file 3: of The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens

Dimitra Repana (6173975)
Joel Nulsen (6173978)
Lisa Dressler (6173981)
Michele Bortolomeazzi (6173984)
Santhilata Venkata (6173987)
Aikaterini Tourna (6173990)
Anna Yakovleva (778118)
Tommaso Palmieri (6173993)
Francesca Ciccarelli (6173996)

January 2019

Lists of all cancer genes, known cancer genes, and candidate cancer genes. (XLSX 840 kb

Additional file 2: Table S2. of Identification of mRNA isoform switching in breast cancer

Wei Zhao (14321)
Katherine Hoadley (3530135)
Joel Parker (17174)
Charles Perou (3530138)

March 2016

43 genes with more than 10 expressed and detected transcripts per gene. (XLSX 10 kb

Additional file 1: of Diagnostic yield and clinical utility of a comprehensive gene panel for hereditary tumor syndromes

Jonas Henn (6258308)
Isabel Spier (4632118)
Ronja S. Adam (6258311)
Stefanie Holzapfel (6258314)
Siegfried Uhlhaas (6258317)
Katrin Kayser (6258320)
Guido Plotz (22851)
Sophia Peters (4632115)
Stefan Aretz (4632109)

January 2019

Table S1. List of all 64 patients with known germline mutationsâ=âgroup K. With the exception of...

Additional file 2: of ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

Serghei Mangul (4973068)
Harry Yang (4376224)
Nicolas Strauli (3551255)
Franziska Gruhl (220206)
Hagit Porath (4485907)
Kevin Hsieh (4973062)
Linus Chen (4973059)
Timothy Daley (3312627)
Stephanie Christenson (4973065)
Agata Wesolowska-Andersen (3683038)
Roberto Spreafico (4246897)
Cydney Rios (3683041)
Celeste Eng (179050)
Andrew Smith (11197)
Ryan Hernandez (218444)
Roel Ophoff (573364)
Jose Santana (421066)
Erez Levanon (3408371)
Prescott Woodruff (4055044)
Esteban Burchard (1262)
Max Seibold (3683044)
Sagiv Shifman (86805)
Eleazar Eskin (108069)
Noah Zaitlen (120787)

February 2018

Table S1. The effect of altering order of ROP step on the classification accuracy. Table S2. Concord...