Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches

Arran K Turnbull; Cigdem Selli Karakaya; Carlos Martinez-Perez; Anu  Fernando; Lorna Renshaw; Jane Keys; Jonine Figueroa; Xiaping He; Maki Tanioka; Alison Munro; Lee Murphy; Angie  Fawkes; Richard Clark; Audrey Coutts; Charles M. Perou; Lisa A. Carey; Michael Dixon; Andrew Sims

doi:10.1186/s12859-020-3365-5

Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches

Arran K Turnbull, Cigdem Selli Karakaya, Carlos Martinez-Perez, Anu Fernando, Lorna Renshaw, Jane Keys, Jonine Figueroa, Xiaping He, Maki Tanioka, Alison Munro, Lee Murphy, Angie Fawkes, Richard Clark, Audrey Coutts, Charles M. Perou, Lisa A. Carey, Michael Dixon, Andrew Sims

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

Abstract

High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it challenging to directly evaluate performance and whether data from different platforms can be reliably compared or integrated.

Original language	English
Journal	BMC Bioinformatics
Early online date	28 Jan 2020
DOIs	https://doi.org/10.1186/s12859-020-3365-5
Publication status	E-pub ahead of print - 28 Jan 2020

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Unlocking the transcriptomic potential of formalin-fixed paraffin ...Final published version, 1.92 MB

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Turnbull, A. K., Selli Karakaya, C., Martinez-Perez, C., Fernando, A., Renshaw, L., Keys, J., Figueroa, J., He, X., Tanioka, M., Munro, A., Murphy, L., Fawkes, A., Clark, R., Coutts, A., M. Perou, C., A. Carey, L., Dixon, M., & Sims, A. (2020). Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches. BMC Bioinformatics. https://doi.org/10.1186/s12859-020-3365-5

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abstract = "High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it challenging to directly evaluate performance and whether data from different platforms can be reliably compared or integrated.",

author = "Turnbull, {Arran K} and {Selli Karakaya}, Cigdem and Carlos Martinez-Perez and Anu Fernando and Lorna Renshaw and Jane Keys and Jonine Figueroa and Xiaping He and Maki Tanioka and Alison Munro and Lee Murphy and Angie Fawkes and Richard Clark and Audrey Coutts and {M. Perou}, Charles and {A. Carey}, Lisa and Michael Dixon and Andrew Sims",

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Turnbull, AK, Selli Karakaya, C , Martinez-Perez, C, Fernando, A, Renshaw, L, Keys, J, Figueroa, J, He, X, Tanioka, M, Munro, A, Murphy, L, Fawkes, A, Clark, R, Coutts, A, M. Perou, C, A. Carey, L, Dixon, M & Sims, A 2020, 'Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches', BMC Bioinformatics. https://doi.org/10.1186/s12859-020-3365-5

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T1 - Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches

AU - Turnbull, Arran K

AU - Selli Karakaya, Cigdem

AU - Martinez-Perez, Carlos

AU - Fernando, Anu

AU - Renshaw, Lorna

AU - Keys, Jane

AU - Figueroa, Jonine

AU - He, Xiaping

AU - Tanioka, Maki

AU - Munro, Alison

AU - Murphy, Lee

AU - Fawkes, Angie

AU - Clark, Richard

AU - Coutts, Audrey

AU - M. Perou, Charles

AU - A. Carey, Lisa

AU - Dixon, Michael

AU - Sims, Andrew

PY - 2020/1/28

Y1 - 2020/1/28

N2 - High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it challenging to directly evaluate performance and whether data from different platforms can be reliably compared or integrated.

AB - High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it challenging to directly evaluate performance and whether data from different platforms can be reliably compared or integrated.

U2 - 10.1186/s12859-020-3365-5

DO - 10.1186/s12859-020-3365-5

M3 - Article

JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

ER -

Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches

Abstract

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