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Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies
Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies
Cold Spring Harbor Laboratory
2019
Abstract
We characterized two reference samples for NGS technologies: a human triple-negative breast cancer cell line and a matched normal cell line. Leveraging several whole-genome sequencing (WGS) platforms, multiple sequencing replicates, and orthogonal mutation detection bioinformatics pipelines, we minimized the potential biases from sequencing technologies, assays, and informatics. Thus, our “truth sets” were defined using evidence from 21 repeats of WGS runs with coverages ranging from 50X to 100X (a total of 140 billion reads). These “truth sets” present many relevant variants/mutations including 193 COSMIC mutations and 9,016 germline variants from the ClinVar database, nonsense mutations in BRCA1/2 and missense mutations in TP53 and FGFR1. Independent validation in three orthogonal experiments demonstrated a successful stress test of the truth set. We expect these reference materials and “truth sets” to facilitate assay development, qualification, validation, and proficiency testing. In addition, our methods can be extended to establish new fully characterized reference samples for the community.
Details
- Title
- Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies
- Authors/Creators
- L.T. Fang (Author/Creator) - RocheB. Zhu (Author/Creator) - National Institutes of HealthY. Zhao (Author/Creator)W. Chen (Author/Creator) - Loma Linda UniversityZ. Yang (Author/Creator) - Loma Linda UniversityL. Kerrigan (Author/Creator) - American Type Culture CollectionK. Langenbach (Author/Creator) - American Type Culture CollectionM. de Mars (Author/Creator) - American Type Culture CollectionC. Lu (Author/Creator)K. Idler (Author/Creator)H. Jacob (Author/Creator)Y. Yu (Author/Creator) - Fudan UniversityL. Ren (Author/Creator) - Fudan UniversityY. Zheng (Author/Creator) - Fudan UniversityE. Jaeger (Author/Creator) - IlluminaG. Schroth (Author/Creator) - IlluminaO.D. Abaan (Author/Creator) - IlluminaJ. Lack (Author/Creator)T-W Shen (Author/Creator)K. Talsania (Author/Creator)Z. Chen (Author/Creator) - Loma Linda UniversityS. Stanbouly (Author/Creator) - Loma Linda UniversityJ. Shetty (Author/Creator)B. Tran (Author/Creator)D. Meerzaman (Author/Creator)C. Nguyen (Author/Creator)V. Petitjean (Author/Creator) - NovartisM. Sultan (Author/Creator) - NovartisM. Cam (Author/Creator) - Office of ScienceT. Hung (Author/Creator)E. Peters (Author/Creator)R. Kalamegham (Author/Creator)S.M. Ebrahim Sahraeian (Author/Creator)M. Mohiyuddin (Author/Creator) - RocheY. Guo (Author/Creator) - RocheL. Yao (Author/Creator) - RocheL. Song (Author/Creator) - National Institutes of HealthH.Y.K. Lam (Author/Creator) - RocheJ. Drabek (Author/Creator) - Palacký University OlomoucR. Maestro (Author/Creator)D. Gasparotto (Author/Creator)S. Kõks (Author/Creator) - Murdoch UniversityE. Reimann (Author/Creator) - Murdoch UniversityA. Scherer (Author/Creator) - University of HelsinkiJ. Nordlund (Author/Creator) - Science for Life LaboratoryU. Liljedahl (Author/Creator) - Science for Life LaboratoryR.V. Jensen (Author/Creator) - Virginia TechM. Pirooznia (Author/Creator) - National Institutes of HealthZ. Li (Author/Creator)C. Xiao (Author/Creator) - National Institutes of HealthS. Sherry (Author/Creator) - National Institutes of HealthR. Kusko (Author/Creator)M. Moos (Author/Creator) - Center for Biologics Evaluation and ResearchE. Donaldson (Author/Creator) - Center for Drug Evaluation and ResearchZ. Tezak (Author/Creator) - Center for Devices and Radiological HealthB. Ning (Author/Creator) - National Center for Toxicological ResearchJ. Li (Author/Creator) - Guangzhou Medical UniversityP. Duerken-Hughes (Author/Creator) - Loma Linda UniversityH. Hong (Author/Creator) - National Center for Toxicological ResearchL. Shi (Author/Creator) - Fudan UniversityC. Wang (Author/Creator) - Loma Linda UniversityW. Xiao (Author/Creator) - National Center for Toxicological Research
- Publication Details
- Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies
- Publisher
- Cold Spring Harbor Laboratory
- Identifiers
- 991005541159807891
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Other
- Resource Sub-type
- Nonrefereed Article
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