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Clinical utility of custom-designed NGS panel testing in pediatric tumors.
Genome Medicine ( IF 10.4 ) Pub Date : 2019-05-28 , DOI: 10.1186/s13073-019-0644-8
Lea F Surrey 1, 2 , Suzanne P MacFarland 3 , Fengqi Chang 2 , Kajia Cao 2 , Komal S Rathi 4, 5, 6 , Gozde T Akgumus 2 , Daniel Gallo 2 , Fumin Lin 2 , Adam Gleason 2 , Pichai Raman 4, 5, 6 , Richard Aplenc 3, 5, 7 , Rochelle Bagatell 3, 5, 7 , Jane Minturn 3, 5, 7 , Yael Mosse 3, 5, 7 , Mariarita Santi 1 , Sarah K Tasian 3, 5, 7 , Angela J Waanders 3, 4, 5, 7 , Mahdi Sarmady 1, 2 , John M Maris 3, 5, 7 , Stephen P Hunger 3, 5, 7 , Marilyn M Li 1, 2, 7, 8
Affiliation  

BACKGROUND Somatic genetic testing is rapidly becoming the standard of care in many adult and pediatric cancers. Previously, the standard approach was single-gene or focused multigene testing, but many centers have moved towards broad-based next-generation sequencing (NGS) panels. Here, we report the laboratory validation and clinical utility of a large cohort of clinical NGS somatic sequencing results in diagnosis, prognosis, and treatment of a wide range of pediatric cancers. METHODS Subjects were accrued retrospectively at a single pediatric quaternary-care hospital. Sequence analyses were performed on 367 pediatric cancer samples using custom-designed NGS panels over a 15-month period. Cases were profiled for mutations, copy number variations, and fusions identified through sequencing, and their clinical impact on diagnosis, prognosis, and therapy was assessed. RESULTS NGS panel testing was incorporated meaningfully into clinical care in 88.7% of leukemia/lymphomas, 90.6% of central nervous system (CNS) tumors, and 62.6% of non-CNS solid tumors included in this cohort. A change in diagnosis as a result of testing occurred in 3.3% of cases. Additionally, 19.4% of all patients had variants requiring further evaluation for potential germline alteration. CONCLUSIONS Use of somatic NGS panel testing resulted in a significant impact on clinical care, including diagnosis, prognosis, and treatment planning in 78.7% of pediatric patients tested in our institution. Somatic NGS tumor testing should be implemented as part of the routine diagnostic workup of newly diagnosed and relapsed pediatric cancer patients.

中文翻译:

定制设计的NGS面板测试在小儿肿瘤中的临床实用性。

背景技术体细胞基因检测正迅速成为许多成年和小儿癌症中的护理标准。以前,标准方法是单基因或集中多基因测试,但是许多中心已转向基础广泛的下一代测序(NGS)面板。在这里,我们报告了一大批临床NGS体细胞测序结果在许多儿科癌症的诊断,预后和治疗中的实验室验证和临床实用性。方法回顾性收集在一家儿科四级护理医院中的受试者。在15个月内使用定制设计的NGS面板对367个儿科癌症样品进行了序列分析。分析病例的突变,拷贝数变异和通过测序确定的融合物,以及它们对诊断,预后,并评估了治疗方法。结果该研究组将88.7%的白血病/淋巴瘤,90.6%的中枢神经系统(CNS)肿瘤和62.6%的非CNS实体瘤有效地纳入了NGS面板测试。3.3%的病例由于测试而导致诊断改变。此外,所有患者中有19.4%的变体需要进一步评估潜在的种系改变。结论体细胞NGS面板检测的使用对我们机构中78.7%的儿科患者的临床护理(包括诊断,预后和治疗计划)产生了重大影响。NGS肿瘤测试应作为新诊断和复发的小儿癌症患者常规诊断检查的一部分进行。结果该研究组将88.7%的白血病/淋巴瘤,90.6%的中枢神经系统(CNS)肿瘤和62.6%的非CNS实体瘤有效地纳入了NGS面板测试。3.3%的病例由于测试而导致诊断改变。此外,所有患者中有19.4%的变体需要进一步评估潜在的种系改变。结论体细胞NGS面板检测的使用对我们机构中78.7%的儿科患者的临床护理(包括诊断,预后和治疗计划)产生了重大影响。NGS肿瘤测试应作为新诊断和复发的小儿癌症患者常规诊断检查的一部分进行。结果该研究组将88.7%的白血病/淋巴瘤,90.6%的中枢神经系统(CNS)肿瘤和62.6%的非CNS实体瘤有效地纳入了NGS面板测试。3.3%的病例由于测试而导致诊断改变。此外,所有患者中有19.4%的变体需要进一步评估潜在的种系改变。结论体细胞NGS面板检测的使用对我们机构中78.7%的儿科患者的临床护理(包括诊断,预后和治疗计划)产生了重大影响。NGS肿瘤测试应作为新诊断和复发的小儿癌症患者常规诊断检查的一部分进行。该队列中有6%的非CNS实体瘤。3.3%的病例由于测试而导致诊断改变。此外,所有患者中有19.4%的变体需要进一步评估潜在的种系改变。结论体细胞NGS面板检测的使用对我们机构中78.7%的儿科患者的临床护理(包括诊断,预后和治疗计划)产生了重大影响。NGS肿瘤测试应作为新诊断和复发的小儿癌症患者常规诊断检查的一部分进行。该队列中有6%的非CNS实体瘤。3.3%的病例由于测试而导致诊断改变。此外,所有患者中有19.4%的变体需要进一步评估潜在的种系改变。结论体细胞NGS面板检测的使用对我们机构中78.7%的儿科患者的临床护理(包括诊断,预后和治疗计划)产生了重大影响。NGS肿瘤测试应作为新诊断和复发的小儿癌症患者常规诊断检查的一部分进行。结论体细胞NGS面板检测的使用对我们机构中78.7%的儿科患者的临床护理(包括诊断,预后和治疗计划)产生了重大影响。NGS肿瘤测试应作为新诊断和复发的小儿癌症患者常规诊断检查的一部分进行。结论体细胞NGS面板检测的使用对我们机构中78.7%的儿科患者的临床护理(包括诊断,预后和治疗计划)产生了重大影响。NGS肿瘤测试应作为新诊断和复发的小儿癌症患者常规诊断检查的一部分进行。
更新日期:2019-05-28
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