Low-Pass Whole Genome Sequencing of Cell-Free DNA from Cerebrospinal Fluid: A Focus on Pediatric Central Nervous System Tumors.

IF 7.1 2区 医学 Q1 MEDICAL LABORATORY TECHNOLOGY
Katrina O'Halloran, Eirini Christodoulou, Vera A Paulson, Bonnie L Cole, Ashley S Margol, Jaclyn A Biegel, Sarah E S Leary, Christina M Lockwood, Erin E Crotty
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Abstract

Background: Cell-free DNA (cfDNA) technology has allowed for cerebrospinal fluid (CSF), a previously underutilized biofluid, to be analyzed in new ways. The interrogation of CSF-derived cfDNA is giving rise to novel molecular insights, particularly in pediatric central nervous system (CNS) tumors, where invasive tumor tissue acquisition may be challenging. Contemporary disease monitoring is currently restricted to radiographic surveillance by magnetic resonance imaging and CSF cytology to directly detect abnormal cells and cell clusters. Alternatively, cfDNA is often present in the CSF from pediatric patients with both malignant and nonmalignant CNS tumors and can be accessed by minimally invasive lumbar puncture and other CSF-liberating procedures, offering a promising alternative for longitudinal molecular disease analysis and surveillance.

Content: This review explores the use of low-pass whole genome sequencing (LP-WGS) to analyze cfDNA from the CSF of pediatric patients with CNS tumors. This platform is uniquely poised for the detection of tumors harboring copy number variants, which are prevalent in this population. The utility and sensitivity of LP-WGS as a clinical tool is explored and discussed in the context of alternative CSF liquid biopsy interrogation modalities, including nanopore sequencing and methylation array.

Summary: Analysis of CSF-derived cfDNA by LP-WGS has broad diagnostic, prognostic, and clinical implications for pediatric patients with CNS tumors. Careful interpretation of LP-WGS results may aid in therapeutic targeting of pediatric CNS tumors and may provide insight into tumor heterogeneity and evolution over time, without the need for invasive and potentially risky tissue sampling.

脑脊液无细胞DNA的低通全基因组测序:儿童中枢神经系统肿瘤的焦点。
背景:无细胞DNA (cfDNA)技术允许以新的方式分析脑脊液(CSF),这是一种以前未充分利用的生物流体。对csf衍生的cfDNA的研究正在产生新的分子见解,特别是在儿童中枢神经系统(CNS)肿瘤中,在这些肿瘤组织的侵入性获取可能具有挑战性。当代疾病监测目前仅限于通过磁共振成像和脑脊液细胞学进行放射学监测,直接检测异常细胞和细胞簇。另外,cfDNA通常存在于患有恶性和非恶性中枢神经系统肿瘤的儿童患者的脑脊液中,可以通过微创腰椎穿刺和其他释放脑脊液的手术获得,为纵向分子疾病分析和监测提供了一个有希望的替代方案。内容:本文探讨了利用低通全基因组测序(LP-WGS)分析小儿中枢神经系统肿瘤患者脑脊液cfDNA的方法。这个平台是唯一的准备为检测肿瘤窝藏拷贝数变异,这是普遍存在于这一人群。LP-WGS作为临床工具的实用性和敏感性在替代脑脊液活检询问方式的背景下进行了探索和讨论,包括纳米孔测序和甲基化阵列。摘要:通过LP-WGS分析csf来源的cfDNA对小儿中枢神经系统肿瘤患者具有广泛的诊断、预后和临床意义。仔细解释LP-WGS结果可能有助于儿科中枢神经系统肿瘤的治疗靶向,并可能提供肿瘤异质性和随时间演变的见解,而无需侵入性和潜在风险的组织采样。
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来源期刊
Clinical chemistry
Clinical chemistry 医学-医学实验技术
CiteScore
11.30
自引率
4.30%
发文量
212
审稿时长
1.7 months
期刊介绍: Clinical Chemistry is a peer-reviewed scientific journal that is the premier publication for the science and practice of clinical laboratory medicine. It was established in 1955 and is associated with the Association for Diagnostics & Laboratory Medicine (ADLM). The journal focuses on laboratory diagnosis and management of patients, and has expanded to include other clinical laboratory disciplines such as genomics, hematology, microbiology, and toxicology. It also publishes articles relevant to clinical specialties including cardiology, endocrinology, gastroenterology, genetics, immunology, infectious diseases, maternal-fetal medicine, neurology, nutrition, oncology, and pediatrics. In addition to original research, editorials, and reviews, Clinical Chemistry features recurring sections such as clinical case studies, perspectives, podcasts, and Q&A articles. It has the highest impact factor among journals of clinical chemistry, laboratory medicine, pathology, analytical chemistry, transfusion medicine, and clinical microbiology. The journal is indexed in databases such as MEDLINE and Web of Science.
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