一种快速浅层整个基因组测序工作流程，适用于极少量的细胞外自由DNA。
A Rapid, Shallow Whole Genome Sequencing Workflow Applicable to Limiting Amounts of Cell-Free DNA.
发表日期：2023 Feb 07
作者：
Rebecca C Allsopp, Karen Page, Bana Ambasager, Marc K Wadsley, Emmanuel Acheampong, Tumisang P Ntereke, Qi Guo, Gurdeep Matharu Lall, Kelly L T Gleason, Evie Wren, Georgios Nteliopoulos, Amelia J Rushton, R Charles Coombes, Jacqueline A Shaw
来源：
CLINICAL CHEMISTRY
摘要：
体细胞拷贝数改变（sCNAs）在乳腺癌演变过程中的获取提供了有价值的预后和治疗信息。在这里，我们提出了一种使用皮克克量的无细胞DNA（cfDNA）和单个循环肿瘤细胞（CTCs）筛选sCNAs的工作流程。我们重新利用Ion ReproSeq PGS™着床前遗传测试套件，对10名转移性乳腺癌（MBC）患者的178个cfDNA样本（300pg）和单个CTCs进行浅的全基因组测序。使用经过定制的ichorCNA工作流程分析结果。39％的MBC患者（41/105）和13％的随访原发性乳腺癌（PBC FU）（3/23）cfDNA中检测到sCNAs，所有这些患者随后都复发了。在10例MBC中，8例单个CTCs的拷贝数计数高于配对的cfDNA。ichorCNA检测到的中位肿瘤分数为0.34（范围为0.17-0.58）和0.36（范围为0.31-0.37）的PBC FU和MBC。检测到肿瘤分数（≥0.1）和TFx和OncomineTM变体的患者具有显著较低的总生存率（log-rank检验P值分别为0.002和P <0.0001）。
ReproSeq PGS检测速度快，每个样本约为120美元，提供sCNA概要和肿瘤DNA分数估计，限制cfDNA模板（300pg）和单个CTCs。此方法可用于随时间检查拷贝数景观，以指导治疗决策，支持未来的试验设计，并可应用于低体积血斑样本，实现远程监测。©美国临床化学协会2023。
Somatic copy number alterations (sCNAs) acquired during the evolution of breast cancer provide valuable prognostic and therapeutic information. Here we present a workflow for screening sCNAs using picogram amounts of cell-free DNA (cfDNA) and single circulating tumor cells (CTCs).We repurposed the Ion ReproSeq PGS™ preimplantation genetic testing kit to perform shallow whole genome sequencing on 178 cfDNA samples (300 pg) and individual CTCs from 10 MBC patients with metastatic breast cancer (MBC) recovered by CellSearch®/DEPArray™. Results were analyzed using a tailored ichorCNA workflow.sCNAs were detected in cfDNA of 41/105 (39%) patients with MBC and 3/23 (13%) primary breast cancers on follow-up (PBC FU), all of whom subsequently relapsed. In 8 of 10 MBCs, individual CTCs had a higher copy number count than matched cfDNA. The median tumor fraction detected by ichorCNA was 0.34 (range 0.17-0.58) for MBC and 0.36 (range 0.31-0.37) for PBC FU. Patients with detectable tumor fraction (≥ 0.1) and TFx and OncomineTM variants had significantly lower overall survival rates (P values P = 0.002 and P < 0.0001 for the log-rank test, respectively).The ReproSeq PGS assay is rapid, at approximately $120 per sample, providing both a sCNA profile and estimation of the tumor DNA fraction from limiting cfDNA template (300pg) and individual CTCs. The approach could be used to examine the copy number landscape over time to guide treatment decisions, support future trial designs, and be applied to low volume blood spot samples enabling remote monitoring.© American Association for Clinical Chemistry 2023.