Additional file 1: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

Duarte Mendes Oliveira (849198)
Katia Grillone (5113460)
Chiara Mignogna (849203)
Valentina De Falco (141865)
Carmelo Laudanna (213505)
Flavia Biamonte (713540)
Rosa Locane (5113457)
Francesco Corcione (5113454)
Massimiliano Fabozzi (5113451)
Rosario Sacco (575749)
Giuseppe Viglietto (184159)
Donatella Malanga (184157)
Antonia Rizzuto (849202)

Open link

Publication date

April 2018

DOI

10.6084/m9.figshare.6152966.v1

Abstract

Table S1. Clinical-pathological characteristics of the 37 colon cancer patients included in the study. (XLSX 12Â kb

Extracted data

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Data Protection

Additional file 1: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

Duarte Mendes Oliveira (849198)
Katia Grillone (5113460)
Chiara Mignogna (849203)
Valentina De Falco (141865)
Carmelo Laudanna (213505)
Flavia Biamonte (713540)
Rosa Locane (5113457)
Francesco Corcione (5113454)
Massimiliano Fabozzi (5113451)
Rosario Sacco (575749)
Giuseppe Viglietto (184159)
Donatella Malanga (184157)
Antonia Rizzuto (849202)

Open link

Publication date

April 2018

DOI

10.6084/m9.figshare.6152966.v1

Abstract

Table S1. Clinical-pathological characteristics of the 37 colon cancer patients included in the study. (XLSX 12Â kb

Extracted data

Neda Stjepanovic (5618591)
Tracy Stockley (3421913)
Philippe Bedard (362729)
Jeanna McCuaig (5618594)
Melyssa Aronson (5618597)
Spring Holter (5618600)
Kara Semotiuk (5618603)
Natasha Leighl (703141)
Raymond Jang (5618606)
Monika Krzyzanowska (3421910)
Amit Oza (3421889)
Abha Gupta (3902173)
Christine Elser (5618618)
Lailah Ahmed (5618627)
Lisa Wang (3046971)
Suzanne Kamel-Reid (3421898)
Lillian Siu (3421904)
Raymond Kim (3421883)

August 2018

Table S1. 48 genes included in the TruSeq Amplicon Cancer Panel (TSACP, Illumina), which includes 21...

Additional file 1: Table S1. of ENVE: a novel computational framework characterizes copy-number mutational landscapes in colorectal cancers from African American patients

Vinay Varadan (16064)
Salendra Singh (3588476)
Arman Nosrati (3588479)
Lakshmeswari Ravi (3588482)
James Lutterbaugh (517259)
Jill Barnholtz-Sloan (125096)
Sanford Markowitz (3588473)
Joseph Willis (459937)
Kishore Guda (169995)

July 2015

Cohorts, ethnicity, and tumor stage of samples used for WES, SNP array, and qPCR. Table S2. Regions ...

Additional file 1: of Characteristic profiles of DNA epigenetic modifications in colon cancer and its predisposing conditionsâbenign adenomas and inflammatory bowel disease

Tomasz Dziaman (677130)
Daniel Gackowski (433277)
Jolanta Guz (433276)
Kinga Linowiecka (5319692)
Magdalena Bodnar (507883)
Marta Starczak (837314)
Ewelina Zarakowska (433280)
Martyna Modrzejewska (837315)
Anna Szpila (433282)
Justyna Szpotan (5319680)
Maciej Gawronski (5319686)
Anna Labejszo (4633510)
Ariel Liebert (5319683)
Zbigniew Banaszkiewicz (677133)
Maria Klopocka (5319689)
Marek Foksinski (433278)
Andrzej Marszalek (507884)
Ryszard Olinski (433285)

May 2018

Table S1. Characteristics of antibodies used in immunohistochemical staining. (PDF 499Â kb

Additional file 3: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

Duarte Mendes Oliveira (849198)
Katia Grillone (5113460)
Chiara Mignogna (849203)
Valentina De Falco (141865)
Carmelo Laudanna (213505)
Flavia Biamonte (713540)
Rosa Locane (5113457)
Francesco Corcione (5113454)
Massimiliano Fabozzi (5113451)
Rosario Sacco (575749)
Giuseppe Viglietto (184159)
Donatella Malanga (184157)
Antonia Rizzuto (849202)

April 2018

Table S3. List of mutated RTKs in each patient included in the study. (XLSX 11Â kb

Additional file 5: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

Duarte Mendes Oliveira (849198)
Katia Grillone (5113460)
Chiara Mignogna (849203)
Valentina De Falco (141865)
Carmelo Laudanna (213505)
Flavia Biamonte (713540)
Rosa Locane (5113457)
Francesco Corcione (5113454)
Massimiliano Fabozzi (5113451)
Rosario Sacco (575749)
Giuseppe Viglietto (184159)
Donatella Malanga (184157)
Antonia Rizzuto (849202)

April 2018

Table S5. List of mutations identified in CC20 after the next generation sequencing analysis pipelin...

Additional file 1: of Association of pathway mutation with survival after recurrence in colorectal cancer patients treated with adjuvant fluoropyrimidine and oxaliplatin chemotherapy

Dae-Won Lee (706990)
Sae-Won Han (177138)
Yongjun Cha (313463)
Jeong Bae (3584285)
Hwang-Phill Kim (177130)
Jaemyun Lyu (6670232)
Hyojun Han (6670235)
Hyoki Kim (715590)
Hoon Jang (760001)
Duhee Bang (736906)
Jae-Kyung Won (304024)
Seung-Yong Jeong (414029)
Kyu Park (5944334)
Gyeong Kang (3440075)
Tae-You Kim (73316)

May 2019

Table S1. Mutation rate of 40 genes included in the study. Table S2. Mutation rate of critical pathw...

Additional file 5: of Comparative sequence analysis of patient-matched primary colorectal cancer, metastatic, and recurrent metastatic tumors after adjuvant FOLFOX chemotherapy

Kazuaki Harada (6496544)
Wataru Okamoto (6496550)
Sachiyo Mimaki (457666)
Yasuyuki Kawamoto (6496553)
Hideaki Bando (6286331)
Riu Yamashita (1612)
Satoshi Yuki (3572459)
Takayuki Yoshino (616028)
Yoshito Komatsu (3572462)
Atsushi Ohtsu (223901)
Naoya Sakamoto (205073)
Katsuya Tsuchihara (392821)

March 2019

Table S3. Detailed information for all detected gene mutations. List of all gene mutations detected ...

Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: Identification of gain-of-function mutations in the RET proto-oncogene

Mendes Oliveira, Duarte
Grillone, Katia
Mignogna, Chiara
De Falco, Valentina
Laudanna, Carmelo
Biamonte, Flavia
Locane, Rosa
Corcione, Francesco
Fabozzi, Massimiliano
Sacco, Rosario
Viglietto, Giuseppe
Malanga, Donatella
Rizzuto, Antonia

January 2018

BACKGROUND: Improvement in genetic characterization of Colon Cancer (CC) patients is required to pr...

Additional file 1: of Next-generation sequencing-based genomic profiling analysis reveals novel mutations for clinical diagnosis in Chinese primary epithelial ovarian cancer patients

Lei Zhang (38117)
Min Luo (258201)
Hongying Yang (131218)
Shaoyan Zhu (6385814)
Xianliang Cheng (6385817)
Chen Qing (164164)

February 2019

Figure S1. Result of sanger sequencing. (A) Eleven mutations which were sanger sequenced. (B) - (H) ...

Additional file 1: Table S1. of A transcriptome-based protein network that identifies new therapeutic targets in colorectal cancer

Stéphanie Durand (149800)
Killian Trillet (4480687)
Arnaud Uguen (587564)
Aude Saint-Pierre (4480696)
Catherine Le Jossic-Corcos (4480693)
Laurent Corcos (176717)

September 2017

List of genes from the five different RT² Profiler™ PCR Array Human Systems used in this study, clas...

Additional file 2: of Comparative proteogenomic analysis of right-sided colon cancer, left-sided colon cancer and rectal cancer reveals distinct mutational profiles

Robin Imperial (6113699)
Zaheer Ahmed (2471398)
Omer Toor (6113702)
Cihat ErdoÄan (6113705)
Ateeq Khaliq (6113708)
Paul Case (6113711)
James Case (6113714)
Kevin Kennedy (40172)
Lee Cummings (6113717)
Niklas Melton (6113720)
Shahzad Raza (6113723)
Banu Diri (4598581)
Ramzi Mohammad (3520061)
Bassel El-Rayes (4006997)
Timothy Pluard (6113726)
Arif Hussain (226527)
Janakiraman Subramanian (5150669)
Ashiq Masood (6113729)

December 2018

Inclusion and exclusion criteria for somatic mutation analysis. MSI-H, POLE mutation samples, rectos...

Additional file 4: of Comparative proteogenomic analysis of right-sided colon cancer, left-sided colon cancer and rectal cancer reveals distinct mutational profiles

Robin Imperial (6113699)
Zaheer Ahmed (2471398)
Omer Toor (6113702)
Cihat ErdoÄan (6113705)
Ateeq Khaliq (6113708)
Paul Case (6113711)
James Case (6113714)
Kevin Kennedy (40172)
Lee Cummings (6113717)
Niklas Melton (6113720)
Shahzad Raza (6113723)
Banu Diri (4598581)
Ramzi Mohammad (3520061)
Bassel El-Rayes (4006997)
Timothy Pluard (6113726)
Arif Hussain (226527)
Janakiraman Subramanian (5150669)
Ashiq Masood (6113729)

December 2018

Tables S1-S3.Â PicNiC statistics (bic and aic) for RCC, LCC and rectal cancers. (XLSX 43 kb

Additional file 1: of Alteration of tumor suppressor BMP5 in sporadic colorectal cancer: a genomic and transcriptomic profiling based study

Erfei Chen (6109421)
Fangfang Yang (115725)
Hongjuan He (445849)
Qiqi Li (1365630)
Wei Zhang (405)
Jinliang Xing (125690)
Ziqing Zhu (6109427)
Jingjing Jiang (128923)
Hua Wang (13530)
Xiaojuan Zhao (328276)
Ruitao Liu (6109430)
Lei Lei (85503)
Jing Dong (102657)
Yuchen Pei (1499557)
Ying Yang (24175)
Junqiang Pan (6109433)
Pan Zhang (206408)
Shuzhen Liu (2344411)
Le Du (693720)
Yuan Zeng (332785)
Jin Yang (86490)

December 2018

Table S1. Sample details. Table S2. BMP5 primer sequences. Table S3. qPCR Primers used in this study...

Additional file 1: of Genomic alterations accompanying tumour evolution in colorectal cancer: tracking the differences between primary tumours and synchronous liver metastases by whole-exome sequencing

M. Mogensen (5542115)
M. Rossing (5542109)
O. Ăstrup (5542196)
P. Larsen (5542124)
P. Heiberg Engel (5542136)
L. JĂ¸rgensen (5542193)
E. Hogdall (5542145)
J. Eriksen (5542142)
P. Ibsen (5542133)
P. Jess (5542112)
M. Grauslund (5542148)
H. Nielsen (5542127)
F. Nielsen (5542121)
B. Vainer (5542151)
K. Osterlind (5542130)

July 2018

Table S1. Private mutations. Abbreviations: SIFT (sort intolerant from tolerant), PP (mutation priva...

Additional file 1: of Additional germline findings from a tumor profiling program

Neda Stjepanovic (5618591)
Tracy Stockley (3421913)
Philippe Bedard (362729)
Jeanna McCuaig (5618594)
Melyssa Aronson (5618597)
Spring Holter (5618600)
Kara Semotiuk (5618603)
Natasha Leighl (703141)
Raymond Jang (5618606)
Monika Krzyzanowska (3421910)
Amit Oza (3421889)
Abha Gupta (3902173)
Christine Elser (5618618)
Lailah Ahmed (5618627)
Lisa Wang (3046971)
Suzanne Kamel-Reid (3421898)
Lillian Siu (3421904)
Raymond Kim (3421883)

August 2018

Table S1. 48 genes included in the TruSeq Amplicon Cancer Panel (TSACP, Illumina), which includes 21...

Additional file 1: Table S1. of ENVE: a novel computational framework characterizes copy-number mutational landscapes in colorectal cancers from African American patients

Vinay Varadan (16064)
Salendra Singh (3588476)
Arman Nosrati (3588479)
Lakshmeswari Ravi (3588482)
James Lutterbaugh (517259)
Jill Barnholtz-Sloan (125096)
Sanford Markowitz (3588473)
Joseph Willis (459937)
Kishore Guda (169995)

July 2015

Cohorts, ethnicity, and tumor stage of samples used for WES, SNP array, and qPCR. Table S2. Regions ...

Additional file 1: of Characteristic profiles of DNA epigenetic modifications in colon cancer and its predisposing conditionsâbenign adenomas and inflammatory bowel disease

Tomasz Dziaman (677130)
Daniel Gackowski (433277)
Jolanta Guz (433276)
Kinga Linowiecka (5319692)
Magdalena Bodnar (507883)
Marta Starczak (837314)
Ewelina Zarakowska (433280)
Martyna Modrzejewska (837315)
Anna Szpila (433282)
Justyna Szpotan (5319680)
Maciej Gawronski (5319686)
Anna Labejszo (4633510)
Ariel Liebert (5319683)
Zbigniew Banaszkiewicz (677133)
Maria Klopocka (5319689)
Marek Foksinski (433278)
Andrzej Marszalek (507884)
Ryszard Olinski (433285)

May 2018

Table S1. Characteristics of antibodies used in immunohistochemical staining. (PDF 499Â kb

Duarte Mendes Oliveira (849198)
Katia Grillone (5113460)
Chiara Mignogna (849203)
Valentina De Falco (141865)
Carmelo Laudanna (213505)
Flavia Biamonte (713540)
Rosa Locane (5113457)
Francesco Corcione (5113454)
Massimiliano Fabozzi (5113451)
Rosario Sacco (575749)
Giuseppe Viglietto (184159)
Donatella Malanga (184157)
Antonia Rizzuto (849202)

April 2018

Table S3. List of mutated RTKs in each patient included in the study. (XLSX 11Â kb

Duarte Mendes Oliveira (849198)
Katia Grillone (5113460)
Chiara Mignogna (849203)
Valentina De Falco (141865)
Carmelo Laudanna (213505)
Flavia Biamonte (713540)
Rosa Locane (5113457)
Francesco Corcione (5113454)
Massimiliano Fabozzi (5113451)
Rosario Sacco (575749)
Giuseppe Viglietto (184159)
Donatella Malanga (184157)
Antonia Rizzuto (849202)

April 2018

Table S5. List of mutations identified in CC20 after the next generation sequencing analysis pipelin...

Additional file 1: of Association of pathway mutation with survival after recurrence in colorectal cancer patients treated with adjuvant fluoropyrimidine and oxaliplatin chemotherapy

Dae-Won Lee (706990)
Sae-Won Han (177138)
Yongjun Cha (313463)
Jeong Bae (3584285)
Hwang-Phill Kim (177130)
Jaemyun Lyu (6670232)
Hyojun Han (6670235)
Hyoki Kim (715590)
Hoon Jang (760001)
Duhee Bang (736906)
Jae-Kyung Won (304024)
Seung-Yong Jeong (414029)
Kyu Park (5944334)
Gyeong Kang (3440075)
Tae-You Kim (73316)

May 2019

Table S1. Mutation rate of 40 genes included in the study. Table S2. Mutation rate of critical pathw...

Additional file 5: of Comparative sequence analysis of patient-matched primary colorectal cancer, metastatic, and recurrent metastatic tumors after adjuvant FOLFOX chemotherapy

Kazuaki Harada (6496544)
Wataru Okamoto (6496550)
Sachiyo Mimaki (457666)
Yasuyuki Kawamoto (6496553)
Hideaki Bando (6286331)
Riu Yamashita (1612)
Satoshi Yuki (3572459)
Takayuki Yoshino (616028)
Yoshito Komatsu (3572462)
Atsushi Ohtsu (223901)
Naoya Sakamoto (205073)
Katsuya Tsuchihara (392821)

March 2019

Table S3. Detailed information for all detected gene mutations. List of all gene mutations detected ...

Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: Identification of gain-of-function mutations in the RET proto-oncogene

Mendes Oliveira, Duarte
Grillone, Katia
Mignogna, Chiara
De Falco, Valentina
Laudanna, Carmelo
Biamonte, Flavia
Locane, Rosa
Corcione, Francesco
Fabozzi, Massimiliano
Sacco, Rosario
Viglietto, Giuseppe
Malanga, Donatella
Rizzuto, Antonia

January 2018

BACKGROUND: Improvement in genetic characterization of Colon Cancer (CC) patients is required to pr...

Additional file 1: of Next-generation sequencing-based genomic profiling analysis reveals novel mutations for clinical diagnosis in Chinese primary epithelial ovarian cancer patients

Lei Zhang (38117)
Min Luo (258201)
Hongying Yang (131218)
Shaoyan Zhu (6385814)
Xianliang Cheng (6385817)
Chen Qing (164164)

February 2019

Figure S1. Result of sanger sequencing. (A) Eleven mutations which were sanger sequenced. (B) - (H) ...

Additional file 1: Table S1. of A transcriptome-based protein network that identifies new therapeutic targets in colorectal cancer

Stéphanie Durand (149800)
Killian Trillet (4480687)
Arnaud Uguen (587564)
Aude Saint-Pierre (4480696)
Catherine Le Jossic-Corcos (4480693)
Laurent Corcos (176717)

September 2017

List of genes from the five different RT² Profiler™ PCR Array Human Systems used in this study, clas...

Additional file 2: of Comparative proteogenomic analysis of right-sided colon cancer, left-sided colon cancer and rectal cancer reveals distinct mutational profiles

Robin Imperial (6113699)
Zaheer Ahmed (2471398)
Omer Toor (6113702)
Cihat ErdoÄan (6113705)
Ateeq Khaliq (6113708)
Paul Case (6113711)
James Case (6113714)
Kevin Kennedy (40172)
Lee Cummings (6113717)
Niklas Melton (6113720)
Shahzad Raza (6113723)
Banu Diri (4598581)
Ramzi Mohammad (3520061)
Bassel El-Rayes (4006997)
Timothy Pluard (6113726)
Arif Hussain (226527)
Janakiraman Subramanian (5150669)
Ashiq Masood (6113729)

December 2018

Inclusion and exclusion criteria for somatic mutation analysis. MSI-H, POLE mutation samples, rectos...

Additional file 4: of Comparative proteogenomic analysis of right-sided colon cancer, left-sided colon cancer and rectal cancer reveals distinct mutational profiles

Robin Imperial (6113699)
Zaheer Ahmed (2471398)
Omer Toor (6113702)
Cihat ErdoÄan (6113705)
Ateeq Khaliq (6113708)
Paul Case (6113711)
James Case (6113714)
Kevin Kennedy (40172)
Lee Cummings (6113717)
Niklas Melton (6113720)
Shahzad Raza (6113723)
Banu Diri (4598581)
Ramzi Mohammad (3520061)
Bassel El-Rayes (4006997)
Timothy Pluard (6113726)
Arif Hussain (226527)
Janakiraman Subramanian (5150669)
Ashiq Masood (6113729)

December 2018

Tables S1-S3.Â PicNiC statistics (bic and aic) for RCC, LCC and rectal cancers. (XLSX 43 kb

Additional file 1: of Alteration of tumor suppressor BMP5 in sporadic colorectal cancer: a genomic and transcriptomic profiling based study

Erfei Chen (6109421)
Fangfang Yang (115725)
Hongjuan He (445849)
Qiqi Li (1365630)
Wei Zhang (405)
Jinliang Xing (125690)
Ziqing Zhu (6109427)
Jingjing Jiang (128923)
Hua Wang (13530)
Xiaojuan Zhao (328276)
Ruitao Liu (6109430)
Lei Lei (85503)
Jing Dong (102657)
Yuchen Pei (1499557)
Ying Yang (24175)
Junqiang Pan (6109433)
Pan Zhang (206408)
Shuzhen Liu (2344411)
Le Du (693720)
Yuan Zeng (332785)
Jin Yang (86490)

December 2018

Table S1. Sample details. Table S2. BMP5 primer sequences. Table S3. qPCR Primers used in this study...

M. Mogensen (5542115)
M. Rossing (5542109)
O. Ăstrup (5542196)
P. Larsen (5542124)
P. Heiberg Engel (5542136)
L. JĂ¸rgensen (5542193)
E. Hogdall (5542145)
J. Eriksen (5542142)
P. Ibsen (5542133)
P. Jess (5542112)
M. Grauslund (5542148)
H. Nielsen (5542127)
F. Nielsen (5542121)
B. Vainer (5542151)
K. Osterlind (5542130)

July 2018

Table S1. Private mutations. Abbreviations: SIFT (sort intolerant from tolerant), PP (mutation priva...

Additional file 1: of Additional germline findings from a tumor profiling program

Neda Stjepanovic (5618591)
Tracy Stockley (3421913)
Philippe Bedard (362729)
Jeanna McCuaig (5618594)
Melyssa Aronson (5618597)
Spring Holter (5618600)
Kara Semotiuk (5618603)
Natasha Leighl (703141)
Raymond Jang (5618606)
Monika Krzyzanowska (3421910)
Amit Oza (3421889)
Abha Gupta (3902173)
Christine Elser (5618618)
Lailah Ahmed (5618627)
Lisa Wang (3046971)
Suzanne Kamel-Reid (3421898)
Lillian Siu (3421904)
Raymond Kim (3421883)

August 2018

Table S1. 48 genes included in the TruSeq Amplicon Cancer Panel (TSACP, Illumina), which includes 21...

Additional file 1: Table S1. of ENVE: a novel computational framework characterizes copy-number mutational landscapes in colorectal cancers from African American patients

Vinay Varadan (16064)
Salendra Singh (3588476)
Arman Nosrati (3588479)
Lakshmeswari Ravi (3588482)
James Lutterbaugh (517259)
Jill Barnholtz-Sloan (125096)
Sanford Markowitz (3588473)
Joseph Willis (459937)
Kishore Guda (169995)

July 2015

Cohorts, ethnicity, and tumor stage of samples used for WES, SNP array, and qPCR. Table S2. Regions ...

Additional file 1: of Characteristic profiles of DNA epigenetic modifications in colon cancer and its predisposing conditionsâbenign adenomas and inflammatory bowel disease

Tomasz Dziaman (677130)
Daniel Gackowski (433277)
Jolanta Guz (433276)
Kinga Linowiecka (5319692)
Magdalena Bodnar (507883)
Marta Starczak (837314)
Ewelina Zarakowska (433280)
Martyna Modrzejewska (837315)
Anna Szpila (433282)
Justyna Szpotan (5319680)
Maciej Gawronski (5319686)
Anna Labejszo (4633510)
Ariel Liebert (5319683)
Zbigniew Banaszkiewicz (677133)
Maria Klopocka (5319689)
Marek Foksinski (433278)
Andrzej Marszalek (507884)
Ryszard Olinski (433285)

May 2018

Table S1. Characteristics of antibodies used in immunohistochemical staining. (PDF 499Â kb

Additional file 1: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

Abstract

Extracted data

Additional file 1: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

Abstract

Extracted data

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