TY - JOUR
T1 - Detection and Correction of Sample Misidentifications in a Biobank Using the MassARRAY System and Genomic Information
AU - Kudo, Hisaaki
AU - Ishida, Noriko
AU - Nobukuni, Takahiro
AU - Aoki, Yuichi
AU - Saito, Sakae
AU - Nishijima, Ichiko
AU - Terakawa, Takahiro
AU - Yamamoto, Masayuki
AU - Minegishi, Naoko
AU - Yamashita, Riu
AU - Kumada, Kazuki
N1 - Publisher Copyright:
© Mary Ann Liebert, Inc.
PY - 2024/8/1
Y1 - 2024/8/1
N2 - With the number of samples increasing in many biobanks, one of the most pressing tasks is recording the correct relationships between information and the specimens. Genomic information is useful in determining the identity of these specimens. The Tohoku Medical Megabank Organization is running one of the largest biobanks in Japan. Here, we introduce a management system, which includes the development of a new probe set for the MassARRAY system for use during the production of proliferating T cells (T cells) and lymphoblastoid cell lines (LCLs). We selected single nucleotide variants that could be detected by next-generation sequencing and showed high resolution with *0.5 minor allele frequencies. After checking the set of probes against 96 samples from 48 people, we obtained no contradictory results in comparison with our genome sequence information. When we applied the set to our 3035 LCLs and 2256 T cells, the result showed 98.93% consistency with the corresponding genomic information. We surveyed the handling records of the 1.07% of samples that showed inconsistencies, and found that most had resulted from human errors (ID swapping between samples) during manual operations. After improving a few error-prone protocols, the error rate dropped to 0.47% for LCLs and 0% for T cells. Overall, the system that we developed shows high accuracy with easy and fast operability, and provides a good opportunity to improve the validation procedure to facilitate high-quality banking, especially in cases involving genomic information.
AB - With the number of samples increasing in many biobanks, one of the most pressing tasks is recording the correct relationships between information and the specimens. Genomic information is useful in determining the identity of these specimens. The Tohoku Medical Megabank Organization is running one of the largest biobanks in Japan. Here, we introduce a management system, which includes the development of a new probe set for the MassARRAY system for use during the production of proliferating T cells (T cells) and lymphoblastoid cell lines (LCLs). We selected single nucleotide variants that could be detected by next-generation sequencing and showed high resolution with *0.5 minor allele frequencies. After checking the set of probes against 96 samples from 48 people, we obtained no contradictory results in comparison with our genome sequence information. When we applied the set to our 3035 LCLs and 2256 T cells, the result showed 98.93% consistency with the corresponding genomic information. We surveyed the handling records of the 1.07% of samples that showed inconsistencies, and found that most had resulted from human errors (ID swapping between samples) during manual operations. After improving a few error-prone protocols, the error rate dropped to 0.47% for LCLs and 0% for T cells. Overall, the system that we developed shows high accuracy with easy and fast operability, and provides a good opportunity to improve the validation procedure to facilitate high-quality banking, especially in cases involving genomic information.
KW - LCLs
KW - MassARRAY
KW - T cells
KW - TMM
KW - biobanking
UR - http://www.scopus.com/inward/record.url?scp=85180322474&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85180322474&partnerID=8YFLogxK
U2 - 10.1089/bio.2022.0211
DO - 10.1089/bio.2022.0211
M3 - Article
C2 - 38079195
AN - SCOPUS:85180322474
SN - 1947-5535
VL - 22
SP - 373
EP - 382
JO - Biopreservation and Biobanking
JF - Biopreservation and Biobanking
IS - 4
ER -