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      Non-invasive early detection of cancer four years before conventional diagnosis using a blood test

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          Abstract

          Early detection has the potential to reduce cancer mortality, but an effective screening test must demonstrate asymptomatic cancer detection years before conventional diagnosis in a longitudinal study. In the Taizhou Longitudinal Study (TZL), 123,115 healthy subjects provided plasma samples for long-term storage and were then monitored for cancer occurrence. Here we report the preliminary results of PanSeer, a noninvasive blood test based on circulating tumor DNA methylation, on TZL plasma samples from 605 asymptomatic individuals, 191 of whom were later diagnosed with stomach, esophageal, colorectal, lung or liver cancer within four years of blood draw. We also assay plasma samples from an additional 223 cancer patients, plus 200 primary tumor and normal tissues. We show that PanSeer detects five common types of cancer in 88% (95% CI: 80–93%) of post-diagnosis patients with a specificity of 96% (95% CI: 93–98%), We also demonstrate that PanSeer detects cancer in 95% (95% CI: 89–98%) of asymptomatic individuals who were later diagnosed, though future longitudinal studies are required to confirm this result. These results demonstrate that cancer can be non-invasively detected up to four years before current standard of care.

          Abstract

          Patients whose disease is diagnosed in its early stages have better outcomes. In this study, the authors develop a non invasive blood test based on circulating tumor DNA methylation that can potentially detect cancer occurrence even in asymptomatic patients.

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          Most cited references39

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          We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.
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            Anchored multiplex PCR for targeted next-generation sequencing.

            We describe a rapid target enrichment method for next-generation sequencing, termed anchored multiplex PCR (AMP), that is compatible with low nucleic acid input from formalin-fixed paraffin-embedded (FFPE) specimens. AMP is effective in detecting gene rearrangements (without prior knowledge of the fusion partners), single nucleotide variants, insertions, deletions and copy number changes. Validation of a gene rearrangement panel using 319 FFPE samples showed 100% sensitivity (95% confidence limit: 96.5-100%) and 100% specificity (95% confidence limit: 99.3-100%) compared with reference assays. On the basis of our experience with performing AMP on 986 clinical FFPE samples, we show its potential as both a robust clinical assay and a powerful discovery tool, which we used to identify new therapeutically important gene fusions: ARHGEF2-NTRK1 and CHTOP-NTRK1 in glioblastoma, MSN-ROS1, TRIM4-BRAF, VAMP2-NRG1, TPM3-NTRK1 and RUFY2-RET in lung cancer, FGFR2-CREB5 in cholangiocarcinoma and PPL-NTRK1 in thyroid carcinoma. AMP is a scalable and efficient next-generation sequencing target enrichment method for research and clinical applications.
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              Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA.

              This protocol describes a method for converting short single-stranded and double-stranded DNA into libraries compatible with high-throughput sequencing using Illumina technology. This method has primarily been developed to improve sequence retrieval from ancient DNA, but it is also applicable to the sequencing of short or degraded DNA from other sources, and it can also be used for sequencing oligonucleotides. Single-stranded library preparation is performed by ligating a biotinylated adapter oligonucleotide to the 3' ends of heat-denatured DNA. The resulting strands are then immobilized on streptavidin-coated beads and copied with a polymerase. A second adapter is attached by blunt-end ligation, and library preparation is completed by PCR amplification. We estimate that intact DNA strands are recovered in the library with ∼50% efficiency. Libraries can be generated from up to 12 DNA or oligonucleotide samples in parallel within 2 d.

                Author and article information

                Contributors
                weimin.ye@ki.se
                gary.gao@singleragenomics.com
                kzhang@bioeng.ucsd.edu
                rliu@singleragenomics.com
                lijin@fudan.edu.cn
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                21 July 2020
                21 July 2020
                2020
                : 11
                : 3475
                Affiliations
                [1 ]ISNI 0000 0001 0125 2443, GRID grid.8547.e, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, , Fudan University, ; 200438 Shanghai, China
                [2 ]ISNI 0000 0001 0125 2443, GRID grid.8547.e, Taizhou Institute of Health Sciences, , Fudan University, ; 225300 Taizhou, Jiangsu China
                [3 ]ISNI 0000 0001 0125 2443, GRID grid.8547.e, Human Phenome Institute, , Fudan University, ; 201203 Shanghai, China
                [4 ]Singlera Genomics Inc., La Jolla, CA 92037 USA
                [5 ]Singlera Genomics (Shanghai) Ltd., 201203 Shanghai, China
                [6 ]GRID grid.452402.5, Clinical Epidemiology Unit, , Qilu Hospital of Shandong University, ; 250012 Jinan, Shandong China
                [7 ]ISNI 0000 0001 0125 2443, GRID grid.8547.e, Department of Epidemiology, School of Public Health, , Fudan University, ; 200032 Shanghai, China
                [8 ]Taizhou Disease Control and Prevention Center, 225300 Taizhou, Jiangsu China
                [9 ]Taixing Disease Control and Prevention Center, 225400 Taizhou, Jiangsu China
                [10 ]ISNI 0000 0004 1937 0626, GRID grid.4714.6, Department of Medical Epidemiology and Biostatistics, , Karolinska Institutet, ; 17177 Stockholm, Sweden
                [11 ]ISNI 0000 0001 2107 4242, GRID grid.266100.3, Department of Bioengineering, , University of California at San Diego, ; La Jolla, CA 92093 USA
                Author information
                http://orcid.org/0000-0002-7596-5224
                Article
                17316
                10.1038/s41467-020-17316-z
                7374162
                32694610
                9f2c4d19-f2ef-4da3-8d38-031d93615932
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 11 March 2020
                : 24 June 2020
                Categories
                Article
                Custom metadata
                © The Author(s) 2020

                Uncategorized
                next-generation sequencing,tumour biomarkers,epigenomics
                Uncategorized
                next-generation sequencing, tumour biomarkers, epigenomics

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