TY - JOUR
T1 - Impact of DNA integrity on the success rate of tissue-based next-generation sequencing
T2 - Lessons from nationwide cancer genome screening project SCRUM-Japan GI-SCREEN
AU - SCRUM-Japan GI-SCREEN Pathology Group
AU - Kuwata, Takeshi
AU - Wakabayashi, Masashi
AU - Hatanaka, Yutaka
AU - Morii, Eiichi
AU - Oda, Yoshinao
AU - Taguchi, Kenichi
AU - Noguchi, Masayuki
AU - Ishikawa, Yuichi
AU - Nakajima, Takashi
AU - Sekine, Shigeki
AU - Nomura, Shogo
AU - Okamoto, Wataru
AU - Fujii, Satoshi
AU - Yoshino, Takayuki
N1 - Funding Information:
The authors thank all pathologists and medical technologists at the participating institutions for helping to prepare the samples. The authors also thank the members of SCRUM-Japan data center, especially Mr. Tomohisa Sudo, Ms. Izumi Miki and Mr. Yasutoshi Sakamoto, for data management; Mr. Makio Tokiwa and IDC Inc. for help with the statistical analyses; and Ms. Suzanne Salazer at ThermoFisher Scientific for reviewing the manuscript and providing QC-metric information. This work was supported in part by Health, Labor, and Welfare Sciences Research Grants (H26-Policy for Cancer General-005), AMED under Grant No. JP18ck0106233h0003, and The National Cancer Research and Development Fund (grant No. 28-A-5 and 31-A-2).
Funding Information:
The authors thank all pathologists and medical technologists at the participating institutions for helping to prepare the samples. The authors also thank the members of SCRUM‐Japan data center, especially Mr. Tomohisa Sudo, Ms. Izumi Miki and Mr. Yasutoshi Sakamoto, for data management; Mr. Makio Tokiwa and IDC Inc. for help with the statistical analyses; and Ms. Suzanne Salazer at ThermoFisher Scientific for reviewing the manuscript and providing QC‐metric information. This work was supported in part by Health, Labor, and Welfare Sciences Research Grants (H26‐Policy for Cancer General‐005), AMED under Grant No. JP18ck0106233h0003, and The National Cancer Research and Development Fund (grant No. 28‐A‐5 and 31‐A‐2).
Publisher Copyright:
© 2020 The Authors. Pathology International published by Japanese Society of Pathology and John Wiley & Sons Australia, Ltd
PY - 2020/12
Y1 - 2020/12
N2 - In the nationwide cancer genome screening project SCRUM-Japan GI-SCREEN, 2590 archival formalin-fixed paraffin-embedded (FFPE) tumor tissues from 19 institutions were analyzed with two tissue-based next-generation sequencing (NGS) panels at the Clinical Laboratory Improvement Amendments (CLIA)-certified College of American Pathologists (CAP)-accredited central laboratory. The Oncomine Cancer Research Panel (OCP; 143 genes) succeeded in producing validated results for only 68.3% of the samples (%OCP-success). CE-IVD (25 genes) succeeded in 45.9% of the OCP-failed samples, leading to an overall NGS success (%combined-success) rate as high as 82.9%. Among 2573 samples, the DNA-integrity (ΔCt)-high (ΔCt < 4.4, n = 1253) samples showed significantly higher %OCP- and %combined-success rates (90.2% and 97.4%, respectively) than the DNA-integrity-intermediate (4.4 < ΔCt < 6.3, n = 911; 68.9% and 88.7%) and DNA-integrity-low ones (ΔCt > 6.3 or polymerase chain reaction-failed, n = 409; 5.6% and 24.7%). Other factors associated with NGS success included the FFPE-sample storage period (<4 years), the specimen type (surgical) and the primary tumor site (colorectal). Multivariable analysis revealed DNA integrity as the factor with the strongest independent association with NGS success, although it was suggested that other institution-specific factors contribute to the discordance of inter-institutional NGS success rates. Our results emphasize the importance of DNA quality in FFPE samples for NGS tests and the impact of DNA integrity on quality monitoring of pathology specimens for achieving successful NGS.
AB - In the nationwide cancer genome screening project SCRUM-Japan GI-SCREEN, 2590 archival formalin-fixed paraffin-embedded (FFPE) tumor tissues from 19 institutions were analyzed with two tissue-based next-generation sequencing (NGS) panels at the Clinical Laboratory Improvement Amendments (CLIA)-certified College of American Pathologists (CAP)-accredited central laboratory. The Oncomine Cancer Research Panel (OCP; 143 genes) succeeded in producing validated results for only 68.3% of the samples (%OCP-success). CE-IVD (25 genes) succeeded in 45.9% of the OCP-failed samples, leading to an overall NGS success (%combined-success) rate as high as 82.9%. Among 2573 samples, the DNA-integrity (ΔCt)-high (ΔCt < 4.4, n = 1253) samples showed significantly higher %OCP- and %combined-success rates (90.2% and 97.4%, respectively) than the DNA-integrity-intermediate (4.4 < ΔCt < 6.3, n = 911; 68.9% and 88.7%) and DNA-integrity-low ones (ΔCt > 6.3 or polymerase chain reaction-failed, n = 409; 5.6% and 24.7%). Other factors associated with NGS success included the FFPE-sample storage period (<4 years), the specimen type (surgical) and the primary tumor site (colorectal). Multivariable analysis revealed DNA integrity as the factor with the strongest independent association with NGS success, although it was suggested that other institution-specific factors contribute to the discordance of inter-institutional NGS success rates. Our results emphasize the importance of DNA quality in FFPE samples for NGS tests and the impact of DNA integrity on quality monitoring of pathology specimens for achieving successful NGS.
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U2 - 10.1111/pin.13029
DO - 10.1111/pin.13029
M3 - Article
C2 - 33030786
AN - SCOPUS:85092253184
VL - 70
SP - 932
EP - 942
JO - Acta Pathologica Japonica
JF - Acta Pathologica Japonica
SN - 1320-5463
IS - 12
ER -
