Identification of major factors associated with failed clinical molecular oncology testing performed by next generation sequencing (NGS)
Identification of major factors associated with failed clinical molecular oncology testing performed by next generation sequencing (NGS)
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DOI：
10.1016/j.molonc.2015.05.004
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发表时间：
2015-11-01
影响因子：
6.6
通讯作者：
Pfeifer, John D.
中科院分区：
文献类型：
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作者：
Al-Kateb, Hussam;Nguyen, TuDung T.;Pfeifer, John D.
目的：NGS DNA分析已成为指导癌症患者临床护理的重要手段。然而，NGS并不是在所有病例中都能成功，导致测试失败的因素也没有得到系统的评估。材料和方法：2012-2014年间，由NGS综合癌症小组对1528例实体和血淋巴肿瘤标本进行了检测。利用Illumina HiSeq和MiSeq平台提取DNA，对肿瘤相关基因进行2x101bp的双端序列读取。结果：343例(22.5%)标本检测不成功。失败原因为组织(Inst)不足223/343(65%)，DNA(Ins-DNA)不足99/343(28.9%)，文库(FL)失败21/343(6.1%)。87/99(88%)的INS-DNA病例可供检测的DNA低于10 ng。与INST和INS-DNA失败相关的因素是活检部位(SOB)和活检类型(TOB)(P<；0.0001)，以及活检的临床环境(CSB，初诊或复发)(P<；0.0001)。INST和FL的共同因素是标本的年龄(p
Purpose: DNA analysis by NGS has become important to direct the clinical care of cancer patients. However, NGS is not successful in all cases, and the factors responsible for test failures have not been systematically evaluated.Materials and methods: A series of 1528 solid and hematolymphoid tumor specimens was tested by an NGS comprehensive cancer panel during 2012-2014. DNA was extracted and 2x101 bp paired-end sequence reads were generated on cancer-related genes utilizing Illumina HiSeq and MiSeq platforms.Results: Testing was unsuccessful in 343 (22.5%) specimens. The failure was due to insufficient tissue (INST) in 223/343 (65%) cases, insufficient DNA (INS-DNA) in 99/343 (28.9%) cases, and failed library (FL) in 21/343 (6.1%) cases. 87/99 (88%) of the INS-DNA cases had below 10 ng DNA available for testing. Factors associated with INST and INS-DNA failures were site of biopsy (SOB) and type of biopsy (TOB) (both p < 0.0001), and clinical setting of biopsy (CSB, initial diagnosis or recurrence) (p < 0.0001). Factors common to INST and FL were age of specimen (p