Performance characterization of PCR-free whole genome sequencing for clinical diagnosis
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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Performance characterization of PCR-free whole genome sequencing for clinical diagnosis. / Zhou, Guiju; Zhou, Meizhen; Zeng, Fanwei; Zhang, Ningzhi; Sun, Yan; Qiao, Zhihong; Guo, Xueqin; Zhou, Shihao; Yun, Guojun; Xie, Jiansheng; Wang, Xiaodan; Liu, Fengxia; Fan, Chunna; Wang, Yaoshen; Fang, Zhonghai; Tian, Zhongming; Dai, Wentao; Sun, Jun; Peng, Zhiyu; Song, Lijie.
I: Medicine, Bind 101, Nr. 10, e28972, 2022.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - Performance characterization of PCR-free whole genome sequencing for clinical diagnosis
AU - Zhou, Guiju
AU - Zhou, Meizhen
AU - Zeng, Fanwei
AU - Zhang, Ningzhi
AU - Sun, Yan
AU - Qiao, Zhihong
AU - Guo, Xueqin
AU - Zhou, Shihao
AU - Yun, Guojun
AU - Xie, Jiansheng
AU - Wang, Xiaodan
AU - Liu, Fengxia
AU - Fan, Chunna
AU - Wang, Yaoshen
AU - Fang, Zhonghai
AU - Tian, Zhongming
AU - Dai, Wentao
AU - Sun, Jun
AU - Peng, Zhiyu
AU - Song, Lijie
N1 - Publisher Copyright: © 2022 Lippincott Williams and Wilkins. All rights reserved.
PY - 2022
Y1 - 2022
N2 - To evaluate the performance of polymerase chain reaction (PCR)-free whole genome sequencing (WGS) for clinical diagnosis, and thereby revealing how experimental parameters affect variant detection.Five NA12878 samples were sequenced using MGISEQ-2000. NA12878 samples underwent WGS with differing deoxyribonucleic acid (DNA) input and library preparation protocol (PCR-based vs PCR-free protocols for library preparation). The depth of coverage and genotype quality of each sample were compared. The performance of each sample was measured for sensitivity, coverage of depth and breadth of coverage of disease-related genes, and copy number variants. We also developed a systematic WGS pipeline (PCR-free) for the analysis of 11 clinical cases.In general, NA12878-2 (PCR-free WGS) showed better depth of coverage and genotype quality distribution than NA12878-1 (PCR-based WGS). With a mean depth of ∼40×, the sensitivity of homozygous and heterozygous single nucleotide polymorphisms (SNPs) of NA12878-2 showed higher sensitivity (>99.77% and >99.82%) than NA12878-1, and positive predictive value exceeded 99.98% and 99.07%. The sensitivity and positive predictive value of homozygous and heterozygous indels for NA12878-2 (PCR-free WGS) showed great improvement than NA128878-1. The breadths of coverage for disease-related genes and copy number variants are slightly better for samples with PCR-free library preparation protocol than the sample with PCR-based library preparation protocol. DNA input also influences the performance of variant detection in samples with PCR-free WGS. All the 19 previously confirmed variants in 11 clinical cases were successfully detected by our WGS pipeline (PCR free).Different experimental parameters may affect variant detection for clinical WGS. Clinical scientists should know the range of sensitivity of variants for different methods of WGS, which would be useful when interpreting and delivering clinical reports.
AB - To evaluate the performance of polymerase chain reaction (PCR)-free whole genome sequencing (WGS) for clinical diagnosis, and thereby revealing how experimental parameters affect variant detection.Five NA12878 samples were sequenced using MGISEQ-2000. NA12878 samples underwent WGS with differing deoxyribonucleic acid (DNA) input and library preparation protocol (PCR-based vs PCR-free protocols for library preparation). The depth of coverage and genotype quality of each sample were compared. The performance of each sample was measured for sensitivity, coverage of depth and breadth of coverage of disease-related genes, and copy number variants. We also developed a systematic WGS pipeline (PCR-free) for the analysis of 11 clinical cases.In general, NA12878-2 (PCR-free WGS) showed better depth of coverage and genotype quality distribution than NA12878-1 (PCR-based WGS). With a mean depth of ∼40×, the sensitivity of homozygous and heterozygous single nucleotide polymorphisms (SNPs) of NA12878-2 showed higher sensitivity (>99.77% and >99.82%) than NA12878-1, and positive predictive value exceeded 99.98% and 99.07%. The sensitivity and positive predictive value of homozygous and heterozygous indels for NA12878-2 (PCR-free WGS) showed great improvement than NA128878-1. The breadths of coverage for disease-related genes and copy number variants are slightly better for samples with PCR-free library preparation protocol than the sample with PCR-based library preparation protocol. DNA input also influences the performance of variant detection in samples with PCR-free WGS. All the 19 previously confirmed variants in 11 clinical cases were successfully detected by our WGS pipeline (PCR free).Different experimental parameters may affect variant detection for clinical WGS. Clinical scientists should know the range of sensitivity of variants for different methods of WGS, which would be useful when interpreting and delivering clinical reports.
KW - clinical diagnosis
KW - deoxyribonucleic acid input
KW - polymerase chain reaction-free
KW - sequencing depth and coverage
KW - whole genome sequencing
U2 - 10.1097/MD.0000000000028972
DO - 10.1097/MD.0000000000028972
M3 - Journal article
C2 - 35451387
AN - SCOPUS:85128678073
VL - 101
JO - Medicine (Baltimore)
JF - Medicine (Baltimore)
SN - 0025-7974
IS - 10
M1 - e28972
ER -
ID: 308120037