TY  - GEN
N2  - Cancers are among the most deadly and intractable of human diseases, for which the standard of care may involve aggressive yet only partially effective therapies. Immunotherapy, which harnesses the body's immune system to target cancer cells and can lead to long-term remission in some of the most advanced treatment-refractory cases, and liquid biopsy assays, which can potentially detect cancer at an earlier and more easily treatable stage, require the identification of cancer-specific genetic variants. Overall in this work, I show the potential scale of sample counts and types required for a comprehensive normal background of splicing against which truly cancer-specific RNA splicing can be identified; the instability of such identifications and their sensitivity to specific methods and filtering parameter values used; and the poor reliability of intron retention detection from short-read RNA-seq data.
DO  - 10.6083/4j03d0427
DO  - DOI
AB  - Cancers are among the most deadly and intractable of human diseases, for which the standard of care may involve aggressive yet only partially effective therapies. Immunotherapy, which harnesses the body's immune system to target cancer cells and can lead to long-term remission in some of the most advanced treatment-refractory cases, and liquid biopsy assays, which can potentially detect cancer at an earlier and more easily treatable stage, require the identification of cancer-specific genetic variants. Overall in this work, I show the potential scale of sample counts and types required for a comprehensive normal background of splicing against which truly cancer-specific RNA splicing can be identified; the instability of such identifications and their sensitivity to specific methods and filtering parameter values used; and the poor reliability of intron retention detection from short-read RNA-seq data.
T1  - Detection and validation of aberrant splicing in cancer
DA  - 2022
AU  - David, Julianne K.
L1  - https://digitalcollections.ohsu.edu/record/9646/files/David.Julianne.2022.pdf
PB  - Oregon Health and Science University
PY  - 2022
ID  - 9646
L4  - https://digitalcollections.ohsu.edu/record/9646/files/David.Julianne.2022.pdf
KW  - Immunotherapy
KW  - RNA Splicing
KW  - Standard of Care
KW  - Liquid Biopsy
KW  - Alternative Splicing
KW  - neoplasm rna
TI  - Detection and validation of aberrant splicing in cancer
Y1  - 2022
L2  - https://digitalcollections.ohsu.edu/record/9646/files/David.Julianne.2022.pdf
LK  - https://digitalcollections.ohsu.edu/record/9646/files/David.Julianne.2022.pdf
UR  - https://digitalcollections.ohsu.edu/record/9646/files/David.Julianne.2022.pdf
ER  -