Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.
Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.
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DOI：
10.18632/oncotarget.4671
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发表时间：
2015-09-22
期刊：
影响因子：
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通讯作者：
Chien J
中科院分区：
文献类型：
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作者：
Munchel S;Hoang Y;Zhao Y;Cottrell J;Klotzle B;Godwin AK;Koestler D;Beyerlein P;Fan JB;Bibikova M;Chien J
目前的基因组研究受到新鲜冷冻组织样本的限制。尽管福尔马林固定的诊断样本数量丰富，但由于担心福尔马林固定伪影，它们很少用于当前的基因组研究。这些伪影的更好表征将允许在转化和临床研究中使用存档的临床标本。为了对Illumina测序中的福尔马林固定伪影进行系统分析，我们从13对匹配的福尔马林固定石蜡包埋（FFPE）和新鲜冷冻（FF）组织样本中生成了26个DNA测序数据集。结果表明，在三种常用的测序方法（全基因组、全外显子组和靶向外显子测序）中，在参考位置和变体位置处匹配的FF/FFPE对之间的一致性调用率很高。匹配的FF/FFPE样本之间的总体错配率和C·G > T·A置换相当，所有样本的不一致率均较低（<0.26%）。最后，低通全基因组测序在FF/FFPE对之间产生类似的拷贝数改变模式。我们的研究结果表明，诊断FFPE样品在癌症基因组研究中的潜在用途是表征和编目癌症基因组中的变异。
Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole genome, whole exome, and targeted exon sequencing). Global mismatch rates and C·G > T·A substitutions were comparable between matched FF/FFPE samples, and discordant rates were low (<0.26%) in all samples. Finally, low-pass whole genome sequencing produces similar pattern of copy number alterations between FF/FFPE pairs. The results from our studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes.