The DNA integrity number and concentration are useful parameters for successful comprehensive genomic profiling test for cancer using formalin‐fixed paraffin embedded tissue
The DNA integrity number and concentration are useful parameters for successful comprehensive genomic profiling test for cancer using formalin‐fixed paraffin embedded tissue
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DNA 完整性数和浓度是使用福尔马林固定石蜡包埋组织成功进行癌症综合基因组分析测试的有用参数
DOI：
10.1111/pin.13318
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发表时间：
2023
影响因子：
2.2
通讯作者：
Nishihara Hiroshi
中科院分区：
文献类型：
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作者：
Yanagita Emmy;Yamada Hiroshi;Kobayashi Tetsuro;Aimono Eriko;Nakamura Kohei;Hirasawa Akira;Nishihara Hiroshi
获取高质量的生物标本并适当处理这些材料对于成功的临床测序是必不可少的。我们开发了一种针对160个癌症基因的癌症临床测序系统：PleSSision‐Rapid。通过PleSSision-Rapid系统，我们分析了1329份福尔马林固定石蜡包埋（FFPE）样本的DNA质量，其中包括477份前瞻性采集的基因组检测（P）组织和852份常规病理诊断后的存档样本（A1/A2）。结果显示，前瞻性采集样品（P）中超过DIN 2.1的样品占92.0%（439/477），而两类档案样品（A1/A2）中超过DIN 2.1的样品分别为85.6%（332/388）和76.7%（356/464）。我们使用DIN 2.1以上且DNA浓度>10 ng/μL的样本进行了PleSSision‐Rapid测序，我们能够构建DNA文库，在所有类型的样本处理过程中，测序成功的概率几乎相等，在（P）中为90.7%（398/439），A1组为92.5%（307/332），A2组为90.2%（321/356）。我们的结果表明，为无可争议的临床序列准备前瞻性FFPE材料集具有临床益处，DIN ≥ 2.1将是全面基因组分析测试样品制备的可靠参数。
The acquisition of high‐quality biospecimens and the appropriate handling of these materials are indispensable for successful clinical sequencing. We developed a cancer clinical sequencing system targeting 160 cancer genes: PleSSision‐Rapid. Through the PleSSision‐Rapid system, we have analyzed DNA quality evaluated by DIN (DNA integrity number) with 1329 formalin‐fixed paraffin embedded (FFPE) samples including 477 prospectively collected tissues for genomic test (P) and 852 archival samples after routine pathological diagnosis (A1/A2). As a result, the samples with more than DIN 2.1 was 92.0% (439/477) in prospectively collected sample (P), while it was 85.6% (332/388) and 76.7% (356/464) in two types of archival samples (A1/A2). We performed the PleSSision‐Rapid sequence using the samples with over DIN 2.1 and DNA concentration >10 ng/μL with which we were able to construct a DNA library, and the probability of sequence success was almost equivalent during all types of specimen processing, at 90.7% (398/439) in (P), 92.5% (307/332) in (A1) and 90.2% (321/356) in (A2), respectively. Our result indicated the clinical benefit to prepare the prospective collection of FFPE materials for indisputable clinical sequence, and that DIN ≥ 2.1 would be a solid parameter for sample preparation of comprehensive genomic profiling tests.