TY - JOUR
T1 - CDNA hybrid capture improves transcriptome analysis on low-input and archived samples
AU - Cabanski, Christopher R.
AU - Magrini, Vincent
AU - Griffith, Malachi
AU - Griffith, Obi L.
AU - McGrath, Sean
AU - Zhang, Jin
AU - Walker, Jason
AU - Ly, Amy
AU - Demeter, Ryan
AU - Fulton, Robert S.
AU - Pong, Winnie W.
AU - Gutmann, David H.
AU - Govindan, Ramaswamy
AU - Mardis, Elaine R.
AU - Maher, Christopher A.
PY - 2014/7
Y1 - 2014/7
N2 - The use of massively parallel sequencing for studying RNA expression has greatly enhanced our understanding of the transcriptome through the myriad ways these data can be characterized. In particular, clinical samples provide important insights about RNA expression in health and disease, yet these studies can be complicated by RNA degradation that results from the use of formalin as a clinical preservative and by the limited amounts of RNA often available from these precious samples. In this study we describe the combined use of RNA sequencing with an exome capture selection step to enhance the yield of on-exon sequencing read data when compared with RNA sequencing alone. In particular, the exome capture step preserves the dynamic range of expression, permitting differential comparisons and validation of expressed mutations from limited and FFPE preserved samples, while reducing the data generation requirement. We conclude that cDNA hybrid capture has the potential to significantly improve transcriptome analysis from low-yield FFPE material.
AB - The use of massively parallel sequencing for studying RNA expression has greatly enhanced our understanding of the transcriptome through the myriad ways these data can be characterized. In particular, clinical samples provide important insights about RNA expression in health and disease, yet these studies can be complicated by RNA degradation that results from the use of formalin as a clinical preservative and by the limited amounts of RNA often available from these precious samples. In this study we describe the combined use of RNA sequencing with an exome capture selection step to enhance the yield of on-exon sequencing read data when compared with RNA sequencing alone. In particular, the exome capture step preserves the dynamic range of expression, permitting differential comparisons and validation of expressed mutations from limited and FFPE preserved samples, while reducing the data generation requirement. We conclude that cDNA hybrid capture has the potential to significantly improve transcriptome analysis from low-yield FFPE material.
UR - http://www.scopus.com/inward/record.url?scp=84902967827&partnerID=8YFLogxK
U2 - 10.1016/j.jmoldx.2014.03.004
DO - 10.1016/j.jmoldx.2014.03.004
M3 - Article
C2 - 24814956
AN - SCOPUS:84902967827
SN - 1525-1578
VL - 16
SP - 440
EP - 451
JO - Journal of Molecular Diagnostics
JF - Journal of Molecular Diagnostics
IS - 4
ER -