Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity.
Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity.
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DOI：
10.1186/1755-8794-4-68
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发表时间：
2011-09-29
影响因子：
2.7
通讯作者：
Schweiger MR
中科院分区：
文献类型：
--
作者：
Kerick M;Isau M;Timmermann B;Sültmann H;Herwig R;Krobitsch S;Schaefer G;Verdorfer I;Bartsch G;Klocker H;Lehrach H;Schweiger MR
大规模并行测序技术极大地提高了测序通量。然而，这些技术在可重复性和对临床样本和环境的适用性方面需要进一步改进。以前列腺癌遗传变异的鉴定为例，我们解决了靶向重测序领域的三个关键挑战：福尔马林固定石蜡包埋（FFPE）组织材料样品中的小核苷酸变异（SNV）检测，最小输入样本量和考虑组织异质性的采样。研究表明，FFPE组织材料可以作为新鲜冷冻组织的补充，用于snv的检测，并且基于溶液的富集实验可以用少量DNA完成，对富集均匀性和数据方差的影响很小。最后，我们讨论了肿瘤的异质性是否通过不同的遗传改变来反映的问题，例如，肿瘤的不同病灶显示不同的基因组模式。我们发现肿瘤的异质性对拷贝数变异的检测起着重要的作用。高通量测序技术在癌症基因组学中的应用，为疾病机制的识别开辟了一个新的维度。特别是能够使用从外科肿瘤切除和组织病理学检查中获得的少量FFPE样本，有助于收集宝贵的组织材料。然而，需要注意活检的位置，这可能对拷贝数变化的预测产生影响。牢记这些技术挑战将大大改善许多大规模测序研究，并将-从长远来看-导致更可靠的个体癌症治疗预测。
Massively parallel sequencing technologies have brought an enormous increase in sequencing throughput. However, these technologies need to be further improved with regard to reproducibility and applicability to clinical samples and settings. Using identification of genetic variations in prostate cancer as an example we address three crucial challenges in the field of targeted re-sequencing: Small nucleotide variation (SNV) detection in samples of formalin-fixed paraffin embedded (FFPE) tissue material, minimal amount of input sample and sampling in view of tissue heterogeneity. We show that FFPE tissue material can supplement for fresh frozen tissues for the detection of SNVs and that solution-based enrichment experiments can be accomplished with small amounts of DNA with only minimal effects on enrichment uniformity and data variance. Finally, we address the question whether the heterogeneity of a tumor is reflected by different genetic alterations, e.g. different foci of a tumor display different genomic patterns. We show that the tumor heterogeneity plays an important role for the detection of copy number variations. The application of high throughput sequencing technologies in cancer genomics opens up a new dimension for the identification of disease mechanisms. In particular the ability to use small amounts of FFPE samples available from surgical tumor resections and histopathological examinations facilitates the collection of precious tissue materials. However, care needs to be taken in regard to the locations of the biopsies, which can have an influence on the prediction of copy number variations. Bearing these technological challenges in mind will significantly improve many large-scale sequencing studies and will - in the long term - result in a more reliable prediction of individual cancer therapies.
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影响因子：
64.8
作者：
通讯作者：
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影响因子：
64.8
作者：
通讯作者：
--
影响因子：
11.2
作者：
Mehra, Rohit;Tomlins, Scott A.;Chinnaiyan, Arul M.
通讯作者：
Chinnaiyan, Arul M.
影响因子：
7
作者：
Navin, Nicholas;Krasnitz, Alexander;Wigler, Michael
通讯作者：
Wigler, Michael
DOI：
10.1126/science.1164382
发表时间：
2008-09-26
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Parsons DW;Jones S;Zhang X;Lin JC;Leary RJ;Angenendt P;Mankoo P;Carter H;Siu IM;Gallia GL;Olivi A;McLendon R;Rasheed BA;Keir S;Nikolskaya T;Nikolsky Y;Busam DA;Tekleab H;Diaz LA Jr;Hartigan J;Smith DR;Strausberg RL;Marie SK;Shinjo SM;Yan H;Riggins GJ;Bigner DD;Karchin R;Papadopoulos N;Parmigiani G;Vogelstein B;Velculescu VE;Kinzler KW
通讯作者：
Kinzler KW