Development and validation of a targeted gene sequencing panel for application to disparate cancers

Mark J. McCabe; Marie-Emilie A. Gauthier; Chia-Ling Chan; Tanya J. Thompson; Sunita M. C. De Sousa; Clare Puttick; John P. Grady; Velimir Gayevskiy; Jiang Tao; Kevin Ying; Arcadi Cipponi; Niantao Deng; Alex Swarbrick; Melissa L. Thomas; Morteza Aghmesheh; David Amor; Lesley Andrews; Yoland Antill; Shane Armitage; Leanne Arnold; Rosemary Balleine; Patti Bastik; Jonathan Beesley; John Beilby; Ian Bennett; Anneke Blackburn; Michael Bogwitz; Leon Botes; Meagan Brennan; Melissa Brown; Michael Buckley; Matthew J. Burgess; Jo Burke; Phyllis Butow; Liz Caldon; David Callen; Ian Campbell; Deepa Chauhan; Manisha Chauhan; Georgia Chenevix-Trench; Alice Christian; Christine Clarke; Paul Cohen; Alison Colley; Ashley Crook; James Cui; Bronwyn Culling; Margaret Cummings; Sarah-Jane Dawson; Anna deFazio; Martin Delatycki; Rebecca Dickson; Joanne Dixon; Alexander Dobrovic; Tracy Dudding; Ted Edkins; Stacey Edwards; Maurice Eisenbruch; Gelareh Farshid; Andrew Fellows; Georgina Fenton; Michael Field; James Flanagan; Peter Fong; Laura Forrest; Stephen Fox; Juliet French; Michael Friedlander; Clara Gaff; David Gallego; Mike Gatta; Peter George; Graham Giles; Grantley Gill; Sian Greening; Eric Haan; Marion Harris; Stewart Hart; Nick Hayward; Louise Heiniger; John Hopper; Clare Hunt; Paul James; Mark Jenkins; Rick Kefford; Alexa Kidd; Judy Kirk; Jessica Koehler; James Kollias; Sunil Lakhini; Geoff Lindeman; Lara Lipton; Liz Lobb; Graham Mann; Deborah Marsh; Sue Ann McLachaln; Bettina Meiser; Roger Milne; Sophie Nightingale; Shona O'Connell; Sarah O'Sullivan; Nick Pachter; Briony Patterson; Kelly Phillips; Ellen Pieper; Edwina Rickard; Bridget Robinson; Mona Saleh; Elizabeth Salisbury; Joe Sambrook; Christobel Saunders; Jodi Saunus; Elizabeth Salisbury; Clare L. Scott; Rodney Scott; Adrienne Sexton; Andrew Shelling; Peter Simpson; Melissa Southey; Amanda Spurdle; Jessica Taylor; Heather Thorne; Alison Trainer; Kathy Tucker; Jane Visvader; Logan Walker; Rachael Williams; Ingrid Winship; Mary-Anne Young; Reginald V. Lord; Amber L. Johns; Maija Kohonen-Corish; Sandra A. O'Toole; et al

doi:10.1038/s41598-019-52000-3

Development and validation of a targeted gene sequencing panel for application to disparate cancers

Mark J. McCabe
, Marie-Emilie A. Gauthier
, Chia-Ling Chan
, Tanya J. Thompson
, Sunita M. C. De Sousa
, Clare Puttick
, John P. Grady
, Velimir Gayevskiy
, Jiang Tao
, Kevin Ying
, Arcadi Cipponi
, Niantao Deng
, Alex Swarbrick
, Melissa L. Thomas
, Morteza Aghmesheh
, David Amor
, Lesley Andrews
, Yoland Antill
, Shane Armitage
, Leanne Arnold

Rosemary Balleine, Patti Bastik, Jonathan Beesley, John Beilby, Ian Bennett, Anneke Blackburn, Michael Bogwitz, Leon Botes, Meagan Brennan, Melissa Brown, Michael Buckley, Matthew J. Burgess, Jo Burke, Phyllis Butow, Liz Caldon, David Callen, Ian Campbell, Deepa Chauhan, Manisha Chauhan, Georgia Chenevix-Trench, Alice Christian, Christine Clarke, Paul Cohen, Alison Colley, Ashley Crook, James Cui, Bronwyn Culling, Margaret Cummings, Sarah-Jane Dawson, Anna deFazio, Martin Delatycki, Rebecca Dickson, Joanne Dixon, Alexander Dobrovic, Tracy Dudding, Ted Edkins, Stacey Edwards, Maurice Eisenbruch, Gelareh Farshid, Andrew Fellows, Georgina Fenton, Michael Field, James Flanagan, Peter Fong, Laura Forrest, Stephen Fox, Juliet French, Michael Friedlander, Clara Gaff, David Gallego, Mike Gatta, Peter George, Graham Giles, Grantley Gill, Sian Greening, Eric Haan, Marion Harris, Stewart Hart, Nick Hayward, Louise Heiniger, John Hopper, Clare Hunt, Paul James, Mark Jenkins, Rick Kefford, Alexa Kidd, Judy Kirk, Jessica Koehler, James Kollias, Sunil Lakhini, Geoff Lindeman, Lara Lipton, Liz Lobb, Graham Mann, Deborah Marsh, Sue Ann McLachaln, Bettina Meiser, Roger Milne, Sophie Nightingale, Shona O'Connell, Sarah O'Sullivan, Nick Pachter, Briony Patterson, Kelly Phillips, Ellen Pieper, Edwina Rickard, Bridget Robinson, Mona Saleh, Elizabeth Salisbury, Joe Sambrook, Christobel Saunders, Jodi Saunus, Elizabeth Salisbury, Clare L. Scott, Rodney Scott, Adrienne Sexton, Andrew Shelling, Peter Simpson, Melissa Southey, Amanda Spurdle, Jessica Taylor, Heather Thorne, Alison Trainer, Kathy Tucker, Jane Visvader, Logan Walker, Rachael Williams, Ingrid Winship, Mary-Anne Young, Reginald V. Lord, Amber L. Johns, Maija Kohonen-Corish, Sandra A. O'Toole, et al

Research output: Contribution to journal › Article › peer-review

25 Citations (Scopus)

Abstract

Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour's molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy.

Original language	English
Article number	17052
Number of pages	16
Journal	Scientific Reports
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41598-019-52000-3
Publication status	Published - 2019

Open Access - Access Right Statement

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UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

cancer
exomes
genes
genomes

Access to Document

10.1038/s41598-019-52000-3

Cite this

McCabe, M. J., Gauthier, M.-E. A., Chan, C.-L., Thompson, T. J., De Sousa, S. M. C., Puttick, C., Grady, J. P., Gayevskiy, V., Tao, J., Ying, K., Cipponi, A., Deng, N., Swarbrick, A., Thomas, M. L., Aghmesheh, M., Amor, D., Andrews, L., Antill, Y., Armitage, S., ... et al (2019). Development and validation of a targeted gene sequencing panel for application to disparate cancers. Scientific Reports, 9(1), Article 17052. https://doi.org/10.1038/s41598-019-52000-3

@article{86c6c19c4bc54a5698ff9ad78c592245,

title = "Development and validation of a targeted gene sequencing panel for application to disparate cancers",

abstract = "Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour's molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99\% and precision of >97\%. Liquid biopsy revealed detection to 1.25\% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy.",

keywords = "cancer, exomes, genes, genomes",

author = "McCabe, \{Mark J.\} and Gauthier, \{Marie-Emilie A.\} and Chia-Ling Chan and Thompson, \{Tanya J.\} and \{De Sousa\}, \{Sunita M. C.\} and Clare Puttick and Grady, \{John P.\} and Velimir Gayevskiy and Jiang Tao and Kevin Ying and Arcadi Cipponi and Niantao Deng and Alex Swarbrick and Thomas, \{Melissa L.\} and Morteza Aghmesheh and David Amor and Lesley Andrews and Yoland Antill and Shane Armitage and Leanne Arnold and Rosemary Balleine and Patti Bastik and Jonathan Beesley and John Beilby and Ian Bennett and Anneke Blackburn and Michael Bogwitz and Leon Botes and Meagan Brennan and Melissa Brown and Michael Buckley and Burgess, \{Matthew J.\} and Jo Burke and Phyllis Butow and Liz Caldon and David Callen and Ian Campbell and Deepa Chauhan and Manisha Chauhan and Georgia Chenevix-Trench and Alice Christian and Christine Clarke and Paul Cohen and Alison Colley and Ashley Crook and James Cui and Bronwyn Culling and Margaret Cummings and Sarah-Jane Dawson and Anna deFazio and Martin Delatycki and Rebecca Dickson and Joanne Dixon and Alexander Dobrovic and Tracy Dudding and Ted Edkins and Stacey Edwards and Maurice Eisenbruch and Gelareh Farshid and Andrew Fellows and Georgina Fenton and Michael Field and James Flanagan and Peter Fong and Laura Forrest and Stephen Fox and Juliet French and Michael Friedlander and Clara Gaff and David Gallego and Mike Gatta and Peter George and Graham Giles and Grantley Gill and Sian Greening and Eric Haan and Marion Harris and Stewart Hart and Nick Hayward and Louise Heiniger and John Hopper and Clare Hunt and Paul James and Mark Jenkins and Rick Kefford and Alexa Kidd and Judy Kirk and Jessica Koehler and James Kollias and Sunil Lakhini and Geoff Lindeman and Lara Lipton and Liz Lobb and Graham Mann and Deborah Marsh and McLachaln, \{Sue Ann\} and Bettina Meiser and Roger Milne and Sophie Nightingale and Shona O'Connell and Sarah O'Sullivan and Nick Pachter and Briony Patterson and Kelly Phillips and Ellen Pieper and Edwina Rickard and Bridget Robinson and Mona Saleh and Elizabeth Salisbury and Joe Sambrook and Christobel Saunders and Jodi Saunus and Elizabeth Salisbury and Scott, \{Clare L.\} and Rodney Scott and Adrienne Sexton and Andrew Shelling and Peter Simpson and Melissa Southey and Amanda Spurdle and Jessica Taylor and Heather Thorne and Alison Trainer and Kathy Tucker and Jane Visvader and Logan Walker and Rachael Williams and Ingrid Winship and Mary-Anne Young and Lord, \{Reginald V.\} and Johns, \{Amber L.\} and Maija Kohonen-Corish and O'Toole, \{Sandra A.\} and \{et al\}",

year = "2019",

doi = "10.1038/s41598-019-52000-3",

language = "English",

volume = "9",

journal = "Scientific Reports",

issn = "2045-2322",

publisher = "Nature Research",

number = "1",

}

McCabe, MJ, Gauthier, M-EA, Chan, C-L, Thompson, TJ, De Sousa, SMC, Puttick, C, Grady, JP, Gayevskiy, V, Tao, J, Ying, K, Cipponi, A, Deng, N, Swarbrick, A, Thomas, ML, Aghmesheh, M, Amor, D, Andrews, L, Antill, Y, Armitage, S, Arnold, L, Balleine, R, Bastik, P, Beesley, J, Beilby, J, Bennett, I, Blackburn, A, Bogwitz, M, Botes, L, Brennan, M, Brown, M, Buckley, M, Burgess, MJ, Burke, J, Butow, P, Caldon, L, Callen, D, Campbell, I, Chauhan, D, Chauhan, M, Chenevix-Trench, G, Christian, A, Clarke, C, Cohen, P, Colley, A, Crook, A, Cui, J, Culling, B, Cummings, M, Dawson, S-J, deFazio, A, Delatycki, M, Dickson, R, Dixon, J, Dobrovic, A, Dudding, T, Edkins, T, Edwards, S, Eisenbruch, M, Farshid, G, Fellows, A, Fenton, G, Field, M, Flanagan, J, Fong, P, Forrest, L, Fox, S, French, J, Friedlander, M, Gaff, C, Gallego, D, Gatta, M, George, P, Giles, G, Gill, G, Greening, S, Haan, E, Harris, M, Hart, S, Hayward, N, Heiniger, L, Hopper, J, Hunt, C, James, P, Jenkins, M, Kefford, R, Kidd, A, Kirk, J, Koehler, J, Kollias, J, Lakhini, S, Lindeman, G, Lipton, L, Lobb, L, Mann, G, Marsh, D, McLachaln, SA, Meiser, B, Milne, R, Nightingale, S, O'Connell, S, O'Sullivan, S, Pachter, N, Patterson, B, Phillips, K, Pieper, E, Rickard, E, Robinson, B, Saleh, M, Salisbury, E, Sambrook, J, Saunders, C, Saunus, J, Salisbury, E, Scott, CL, Scott, R, Sexton, A, Shelling, A, Simpson, P, Southey, M, Spurdle, A, Taylor, J, Thorne, H, Trainer, A, Tucker, K, Visvader, J, Walker, L, Williams, R, Winship, I, Young, M-A, Lord, RV, Johns, AL, Kohonen-Corish, M, O'Toole, SA & et al 2019, 'Development and validation of a targeted gene sequencing panel for application to disparate cancers', Scientific Reports, vol. 9, no. 1, 17052. https://doi.org/10.1038/s41598-019-52000-3

TY - JOUR

T1 - Development and validation of a targeted gene sequencing panel for application to disparate cancers

AU - McCabe, Mark J.

AU - Gauthier, Marie-Emilie A.

AU - Chan, Chia-Ling

AU - Thompson, Tanya J.

AU - De Sousa, Sunita M. C.

AU - Puttick, Clare

AU - Grady, John P.

AU - Gayevskiy, Velimir

AU - Tao, Jiang

AU - Ying, Kevin

AU - Cipponi, Arcadi

AU - Deng, Niantao

AU - Swarbrick, Alex

AU - Thomas, Melissa L.

AU - Aghmesheh, Morteza

AU - Amor, David

AU - Andrews, Lesley

AU - Antill, Yoland

AU - Armitage, Shane

AU - Arnold, Leanne

AU - Balleine, Rosemary

AU - Bastik, Patti

AU - Beesley, Jonathan

AU - Beilby, John

AU - Bennett, Ian

AU - Blackburn, Anneke

AU - Bogwitz, Michael

AU - Botes, Leon

AU - Brennan, Meagan

AU - Brown, Melissa

AU - Buckley, Michael

AU - Burgess, Matthew J.

AU - Burke, Jo

AU - Butow, Phyllis

AU - Caldon, Liz

AU - Callen, David

AU - Campbell, Ian

AU - Chauhan, Deepa

AU - Chauhan, Manisha

AU - Chenevix-Trench, Georgia

AU - Christian, Alice

AU - Clarke, Christine

AU - Cohen, Paul

AU - Colley, Alison

AU - Crook, Ashley

AU - Cui, James

AU - Culling, Bronwyn

AU - Cummings, Margaret

AU - Dawson, Sarah-Jane

AU - deFazio, Anna

AU - Delatycki, Martin

AU - Dickson, Rebecca

AU - Dixon, Joanne

AU - Dobrovic, Alexander

AU - Dudding, Tracy

AU - Edkins, Ted

AU - Edwards, Stacey

AU - Eisenbruch, Maurice

AU - Farshid, Gelareh

AU - Fellows, Andrew

AU - Fenton, Georgina

AU - Field, Michael

AU - Flanagan, James

AU - Fong, Peter

AU - Forrest, Laura

AU - Fox, Stephen

AU - French, Juliet

AU - Friedlander, Michael

AU - Gaff, Clara

AU - Gallego, David

AU - Gatta, Mike

AU - George, Peter

AU - Giles, Graham

AU - Gill, Grantley

AU - Greening, Sian

AU - Haan, Eric

AU - Harris, Marion

AU - Hart, Stewart

AU - Hayward, Nick

AU - Heiniger, Louise

AU - Hopper, John

AU - Hunt, Clare

AU - James, Paul

AU - Jenkins, Mark

AU - Kefford, Rick

AU - Kidd, Alexa

AU - Kirk, Judy

AU - Koehler, Jessica

AU - Kollias, James

AU - Lakhini, Sunil

AU - Lindeman, Geoff

AU - Lipton, Lara

AU - Lobb, Liz

AU - Mann, Graham

AU - Marsh, Deborah

AU - McLachaln, Sue Ann

AU - Meiser, Bettina

AU - Milne, Roger

AU - Nightingale, Sophie

AU - O'Connell, Shona

AU - O'Sullivan, Sarah

AU - Pachter, Nick

AU - Patterson, Briony

AU - Phillips, Kelly

AU - Pieper, Ellen

AU - Rickard, Edwina

AU - Robinson, Bridget

AU - Saleh, Mona

AU - Salisbury, Elizabeth

AU - Sambrook, Joe

AU - Saunders, Christobel

AU - Saunus, Jodi

AU - Salisbury, Elizabeth

AU - Scott, Clare L.

AU - Scott, Rodney

AU - Sexton, Adrienne

AU - Shelling, Andrew

AU - Simpson, Peter

AU - Southey, Melissa

AU - Spurdle, Amanda

AU - Taylor, Jessica

AU - Thorne, Heather

AU - Trainer, Alison

AU - Tucker, Kathy

AU - Visvader, Jane

AU - Walker, Logan

AU - Williams, Rachael

AU - Winship, Ingrid

AU - Young, Mary-Anne

AU - Lord, Reginald V.

AU - Johns, Amber L.

AU - Kohonen-Corish, Maija

AU - O'Toole, Sandra A.

AU - et al, null

PY - 2019

Y1 - 2019

N2 - Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour's molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy.

AB - Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour's molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy.

KW - cancer

KW - exomes

KW - genes

KW - genomes

UR - http://hdl.handle.net/1959.7/uws:55537

U2 - 10.1038/s41598-019-52000-3

DO - 10.1038/s41598-019-52000-3

M3 - Article

SN - 2045-2322

VL - 9

JO - Scientific Reports

JF - Scientific Reports

IS - 1

M1 - 17052

ER -

Development and validation of a targeted gene sequencing panel for application to disparate cancers

Abstract

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Keywords

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