scholarly journals Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

2013 ◽  
Vol 31 (11) ◽  
pp. 1023-1031 ◽  
Author(s):  
Garrett M Frampton ◽  
Alex Fichtenholtz ◽  
Geoff A Otto ◽  
Kai Wang ◽  
Sean R Downing ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Massively Parallel ◽  
Genomic Profiling ◽  
Clinical Cancer ◽  
Massively Parallel Dna Sequencing ◽  
Development And Validation

Validation of a comprehensive cancer genomic profiling assay based on massively parallel DNA sequencing.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e13138-e13138
Author(s):  
Yuanyuan Hong ◽  
Weizhi Chen ◽  
Huiting Yan ◽  
Linlin Yan ◽  
Xuexia Zeng ◽  
...  
Keyword(s):  
Capillary Electrophoresis ◽  
Dna Sequencing ◽  
Tumor Tissue ◽  
Hot Spot ◽  
Massively Parallel ◽  
Clinical Validation ◽  
Genomic Profiling ◽  
Tissue Samples ◽  
Fluorescent Pcr ◽  
Massively Parallel Dna Sequencing

e13138 Background: Validation is very important for diagnostic assays, here we describe a validation process of a comprehensive cancer genomic profiling assay based on massively parallel DNA sequencing. This assay can detect base substitutions, short insertions and deletions, copy number alterations, tumor mutation burden (TMB) and microsatellite instability (MSI) across 543 cancer-related genes from tumor specimens or plasma. Methods: Analytical validation was conducted with 20 cell line pools whose mutation were verified by digital droplet PCR (ddPCR). Clinical validation was conducted with Proficiency Test samples and clinical samples whose mutation were verified by ddPCR. Sensitivity, positive predictive value (PPV) and precision of tumor specimens and plasma were assessed across the reportable range of the assay. For measurement of TMB， NGS libraries of a cohort of tumor samples were tested by whole exosome panel (WES) and this assay respectively. And clinical tumor tissue samples whose MSI status were identified by fluorescent PCR-capillary electrophoresis were also tested by this assay. Results: The SNV/Indel LOD95 was 0.6% for hot-spot variants, and 1.3% for panel-wised variants of tumor tissue samples with high specificity (PPV >99%). The SNV/Indel LOD95 was 0.4% for hot-spot variants, and 1.1% for panel-wised variants of plasma samples (cfDNA≥15ng), with PPV >99%. LOD95 of CNV was 2.2-2.3, with PPV>99%. Precision of CNV was higher than 95%, precision of SNV/Indel was higher than 97%. Concordance between TMB results tested by WES and this assay was 0.94. MSI results identified by this assay was the same as fluorescent PCR-capillary electrophoresis method. Conclusions: In summary, we present the analytical and clinical validation of a comprehensive NGS-based diagnostic assay for comprehensive tumor genomic profiling.

Novel OTOF gene mutations identified using a massively parallel DNA sequencing technique in DFNB9 deafness

2018 ◽  
Vol 138 (10) ◽  
pp. 865-870 ◽  
Author(s):  
Yanfei Wang ◽  
Yu Lu ◽  
Jing Cheng ◽  
Lei Zhang ◽  
Dongyi Han ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Gene Mutations ◽  
Massively Parallel ◽  
Sequencing Technique ◽  
Massively Parallel Dna Sequencing

scholarly journals Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia

Blood ◽  
2014 ◽  
Vol 124 (3) ◽  
pp. 453-462 ◽  
Author(s):  
Mohini Rajasagi ◽  
Sachet A. Shukla ◽  
Edward F. Fritsch ◽  
Derin B. Keskin ◽  
David DeLuca ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Dna Sequencing ◽  
Lymphocytic Leukemia ◽  
Class I ◽  
Massively Parallel ◽  
Central Tolerance ◽  
Key Points ◽  
Tumor Specificity ◽  
Massively Parallel Dna Sequencing ◽  
Systematic Identification

Key Points Tumor neoantigens are a promising class of immunogens based on exquisite tumor specificity and the lack of central tolerance against them. Massively parallel DNA sequencing with class I prediction enables systematic identification of tumor neoepitopes (including from CLL).

scholarly journals Novel ACTG1 mutations in patients identified by massively parallel DNA sequencing cause progressive hearing loss

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hiroki Miyajima ◽  
Hideaki Moteki ◽  
Timothy Day ◽  
Shin-ya Nishio ◽  
Takaaki Murata ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Dna Sequencing ◽  
Massively Parallel ◽  
Progressive Hearing Loss ◽  
Massively Parallel Dna Sequencing

scholarly journals The complete genome of an individual by massively parallel DNA sequencing

Nature ◽  
2008 ◽  
Vol 452 (7189) ◽  
pp. 872-876 ◽  
Author(s):  
David A. Wheeler ◽  
Maithreyan Srinivasan ◽  
Michael Egholm ◽  
Yufeng Shen ◽  
Lei Chen ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Complete Genome ◽  
Massively Parallel ◽  
Massively Parallel Dna Sequencing
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