The In Vitro Stability of Circulating Tumour DNA.
The In Vitro Stability of Circulating Tumour DNA.
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循环肿瘤DNA的体外稳定性。
DOI：
10.1371/journal.pone.0168153
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Lindberg J
中科院分区：
文献类型：
--
作者：
Henao Diaz E;Yachnin J;Grönberg H;Lindberg J
存在于循环中的来自凋亡癌细胞的DNA具有促进基因组分析和疾病监测的潜力。然而，只有低部分的总细胞游离DNA来源于癌细胞，限制了循环肿瘤DNA（ctDNA）的适用性。因此，最佳的样品处理至关重要。因此，我们评估了ctDNA的体外稳定性。将血液收集在10 ml EDTA或Streck管中。研究了三种条件（室温下的EDTA和Streck管，五度下的EDTA管）和四个时间点（在长达24 h的时间序列中从每个10 ml管的血液等分试样中收获的血浆）。在5名转移性前列腺癌患者中评估了每种情况。随后，采集了另外3例患者，以研究EDTA试管中长达48 h的体外稳定性。ctDNA的体外稳定性通过低通全基因组测序来询问，其允许鉴定体细胞拷贝数改变（CNA）。计算机模拟表明，非参数检测可检测到1%的白色血细胞DNA污染。通过靶向的基于溶液中的杂交捕获和随后的测序进行突变谱分析。使用单个突变的等位基因分数作为体外稳定性的估计值。所有患者均检出体细胞CNA。令人惊讶的是，在任何研究条件下，0小时的ctDNA水平与24或48小时的体外孵育没有显著差异。随后，突变分析证实了CNA分析的结论。ctDNA的稳定性简化了物流，而不需要立即处理或应用固定剂来防止白色血细胞裂解。
DNA from apoptotic cancer cells, present in the circulation, has the potential to facilitate genomic profiling and disease monitoring. However, only low fractions of total cell-free DNA originates from cancer cells, limiting the applicability of circulating tumour DNA (ctDNA). Optimal sample processing is consequently of uttermost importance. Therefore, we evaluated the in vitro stability of ctDNA. Blood was collected in 10 ml EDTA or Streck tubes. Three conditions (EDTA and Streck tubes in room temperature, EDTA tubes at five degrees) and four time points (plasma harvested from blood aliquots of each 10 ml tube in a time series up to 24 h) were investigated. Each condition was evaluated in five metastatic prostate cancer patients. Subsequently, three additional patients were collected enabling investigation of the in vitro stability in EDTA tubes up to 48 h. The in vitro stability of ctDNA was interrogated by low-pass whole genome sequencing which allows for the identification of somatic copy-number alterations (CNAs). In silico simulations demonstrated that non-parametric testing could detect a 1% contamination by white blood cell DNA. Mutational profiling was performed by targeted, in-solution based hybridization capture and subsequent sequencing. The allelic fraction of individual mutations was used as an estimate of the in vitro stability. Somatic CNAs were detected in all patients. Surprisingly, the ctDNA levels at zero hours were not significantly different to 24 or 48 hour in vitro incubation in any investigated condition. Subsequently, mutational profiling corroborated the conclusions from the CNA analysis. The stability of ctDNA simplifies logistics without the requirement of immediate processing or applying fixatives to prevent white blood cell lysis.
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影响因子：
50.3
作者：
Taylor BS;Schultz N;Hieronymus H;Gopalan A;Xiao Y;Carver BS;Arora VK;Kaushik P;Cerami E;Reva B;Antipin Y;Mitsiades N;Landers T;Dolgalev I;Major JE;Wilson M;Socci ND;Lash AE;Heguy A;Eastham JA;Scher HI;Reuter VE;Scardino PT;Sander C;Sawyers CL;Gerald WL
通讯作者：
Gerald WL
影响因子：
17.1
作者：
Leary RJ;Kinde I;Diehl F;Schmidt K;Clouser C;Duncan C;Antipova A;Lee C;McKernan K;De La Vega FM;Kinzler KW;Vogelstein B;Diaz LA Jr;Velculescu VE
通讯作者：
Velculescu VE
影响因子：
2.8
作者：
Buysse, Karen;Beulen, Lean;Faas, Brigitte H. W.
通讯作者：
Faas, Brigitte H. W.
DOI：
10.1073/pnas.0507904102
发表时间：
2005-11-08
影响因子：
11.1
作者：
Diehl, F;Li, M;Vogelstein, B
通讯作者：
Vogelstein, B
使用癌症特异性基因组重排来量化实体瘤患者血浆中的疾病负担。
影响因子：
3.7
作者：
McBride, David J.;Orpana, Arto K.;Sotiriou, Christos;Joensuu, Heikki;Stephens, Philip J.;Mudie, Laura J.;Hamalainen, Eija;Stebbings, Lucy A.;Andersson, Leif C.;Flanagan, Adrienne M.;Durbecq, Virginie;Ignatiadis, Michail;Kallioniemi, Olli;Heckman, Caroline A.;Alitalo, Kari;Edgren, Henrik;Futreal, P. Andrew;Stratton, Michael R.;Campbell, Peter J.
通讯作者：
Campbell, Peter J.