Exome sequencing in children with cerebral palsy:a comparison of capture performance between TruSeq and NimbleGen kits
10.3969/j.issn.1672-8467.2025.06.012
- VernacularTitle:基于脑瘫患儿的外显子组测序:TruSeq与NimbleGen试剂盒的捕获性能比较
- Author:
Yan-gong WANG
1
;
Ye CHENG
;
Yang LIU
;
Yi-ran XU
;
Qing-he XING
Author Information
1. 复旦大学生物医学研究院 上海 200032
- Publication Type:Journal Article
- Keywords:
whole exome sequencing(WES);
capture;
kit;
cerebral palsy
- From:
Fudan University Journal of Medical Sciences
2025;52(6):868-876
- CountryChina
- Language:Chinese
-
Abstract:
Objective To compare the capture performance differences between TruSeq? Exome and NimbleGen SeqCap EZ Human Exome kits in children with cerebral palsy(CP),and to provide a technical selection basis for clinical genetic research and diagnosis.Methods Peripheral blood samples from 48 sporadic CP patients were included.Exome libraries were constructed using TruSeq(DNA probes)and NimbleGen(RNA probes),followed by sequencing on the Illumina HiSeq 2000 platform.Bioinformatics analysis was applied to evaluate mapping rate,target region coverage,variant concordance,and clinical relevance based on a CP-related gene set(2 293 genes).The statistical analysis was performed using a paired t-test with a significance threshold of α=0.05.Results The results showed no significant differences between NimbleGen and TruSeq exome capture kits in basic data quality(alignment rate,insert size)and GC content.However,they exhibited complementary characteristics in key performance metrics:NimbleGen demonstrated superior performance in specific depth coverage(1×coverage rate,P=1.84×10-5;20×coverage rate,P=1.49×10-20).TruSeq,on the other hand,showed higher sensitivity in Indel detection(TruSeq vs.NimbleGen:11 371±1 689 vs.11 274±1 670,P=3.24×10-7)and rare variant capture(TruSeq vs.NimbleGen:3 164±766 vs.3 072±774,P=1.20×10-4),successfully identifying all 11 pathogenic variants(including 2 missed by NimbleGen).Conclusion TruSeq,with its superior variant detection rate,is more suitable for clinical diagnostic applications,while NimbleGen's coverage stability may be advantageous for research-oriented projects.
