Formalin-fixed paraffin-embedded sample conditions for deep next generation sequencing.
Formalin-fixed paraffin-embedded sample conditions for deep next generation sequencing.
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DOI：
10.1016/j.jss.2017.06.077
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发表时间：
2017-12
期刊：
影响因子：
--
通讯作者：
Wakai T
中科院分区：
文献类型：
--
作者：
Nagahashi M;Shimada Y;Ichikawa H;Nakagawa S;Sato N;Kaneko K;Homma K;Kawasaki T;Kodama K;Lyle S;Takabe K;Wakai T
只有当片段 DNA 中的靶向基因（例如来自福尔马林固定石蜡包埋 (FFPE) 样本的 DNA）可以使用下一代测序 (NGS) 进行测序时，精准医疗才可能在肿瘤学实践中实现。本研究的目的是检查来自手术切除和活检标本的 FFPE 癌组织样本中 DNA 的质量和数量。 DNA 是从手术切除的乳腺癌、结直肠癌和胃癌标本以及乳腺癌活检标本制备的未染色 FFPE 组织切片中提取的。样品中 DNA 总量≥60 ng 被认为足以进行 NGS。 DNA 质量通过 Q 比进行评估，Q 比 >0.1 被认为足以进行 NGS。使用中性缓冲福尔马林处理的 FFPE 组织的 DNA 的 Q 比明显优于使用未缓冲福尔马林处理的 DNA。乳腺癌、结直肠癌和胃癌样本 DNA 的所有 Q 比均表明 DNA 水平足以进行 NGS。从过去七年内制备的胃癌 FFPE 样本中提取的 DNA 适合进行 NGS 分析，而超过七年的样本可能不适合进行 NGS 分析。我们的数据表明，可以从 FFPE 样本中提取足够量的 DNA，不仅可以从手术切除的组织中提取，还可以从活检标本中提取。用于固定的福尔马林类型以及 FFPE 样品制备后的时间会影响 DNA 质量。可以从手术切除和活检组织的 FFPE 样本中提取足够量的 DNA，从而扩大 NGS 在临床环境中的潜在诊断用途。
Precision medicine is only possible in oncology practice if targetable genes in fragmented DNA, such as DNA from formalin-fixed paraffin-embedded (FFPE) samples, can be sequenced using next generation sequencing (NGS). The aim of this study is to examine the quality and quantity of DNA from FFPE cancerous tissue samples from surgically resected and biopsy specimens. DNA was extracted from unstained FFPE tissue sections prepared from surgically resected specimens of breast, colorectal and gastric cancer, and biopsy specimens of breast cancer. A total quantity of DNA ≥60 ng from a sample was considered adequate for NGS. The DNA quality was assessed by Q-ratios, with a Q-ratio >0.1 considered sufficient for NGS. The Q-ratio for DNA from FFPE tissue processed with neutral-buffered formalin was significantly better than that processed with unbuffered formalin. All Q-ratios for DNA from breast, colorectal and gastric cancer samples indicated DNA levels sufficient for NGS. DNA extracted from gastric cancer FFPE samples prepared within the last seven years is suitable for NGS analysis, whereas those older than seven years may not be suitable. Our data suggested that adequate amounts of DNA can be extracted from FFPE samples, not only of surgically resected tissue but also of biopsy specimens. The type of formalin used for fixation and the time since FFPE sample preparation affect DNA quality. Sufficient amounts of DNA can be extracted from FFPE samples of both surgically resected and biopsy tissue, thus expanding the potential diagnostic uses of NGS in a clinical setting.
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影响因子：
3.7
作者：
Kari L;Hill KA;Sayem AS;Karamichalis R;Bryans N;Davis K;Dattani NS
通讯作者：
Dattani NS
DOI：
10.1016/j.atg.2016.06.001
发表时间：
2016-09
期刊：
Applied & translational genomics
影响因子：
--
作者：
Endrullat, Christoph;Glokler, Jorn;Franke, Philipp;Frohme, Marcus
通讯作者：
Frohme, Marcus
影响因子：
4.1
作者：
Spencer, David H.;Sehn, Jennifer K.;Duncavage, Eric J.
通讯作者：
Duncavage, Eric J.
影响因子：
3.7
作者：
Carrick DM;Mehaffey MG;Sachs MC;Altekruse S;Camalier C;Chuaqui R;Cozen W;Das B;Hernandez BY;Lih CJ;Lynch CF;Makhlouf H;McGregor P;McShane LM;Phillips Rohan J;Walsh WD;Williams PM;Gillanders EM;Mechanic LE;Schully SD
通讯作者：
Schully SD
影响因子：
3
作者：
Karamichalis R;Kari L;Konstantinidis S;Kopecki S;Solis-Reyes S
通讯作者：
Solis-Reyes S