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Best practices for variant calling in clinical sequencing
DC Koboldt - Genome medicine, 2020 - Springer
Next-generation sequencing technologies have enabled a dramatic expansion of clinical
genetic testing both for inherited conditions and diseases such as cancer. Accurate variant …
genetic testing both for inherited conditions and diseases such as cancer. Accurate variant …
Patient-derived explants (PDEs) as a powerful preclinical platform for anti-cancer drug and biomarker discovery
IR Powley, M Patel, G Miles, H Pringle… - British journal of …, 2020 - nature.com
Preclinical models that can accurately predict outcomes in the clinic are much sought after in
the field of cancer drug discovery and development. Existing models such as organoids and …
the field of cancer drug discovery and development. Existing models such as organoids and …
A deep-learning model for transforming the style of tissue images from cryosectioned to formalin-fixed and paraffin-embedded
Histological artefacts in cryosectioned tissue can hinder rapid diagnostic assessments
during surgery. Formalin-fixed and paraffin-embedded (FFPE) tissue provides higher quality …
during surgery. Formalin-fixed and paraffin-embedded (FFPE) tissue provides higher quality …
Tumor mutation burden as a biomarker in resected non–small-cell lung cancer
Purpose The survival benefit with adjuvant chemotherapy for patients with resected stage II-
III non–small-cell lung cancer (NSCLC) is modest. Efforts to develop prognostic or predictive …
III non–small-cell lung cancer (NSCLC) is modest. Efforts to develop prognostic or predictive …
A critical spotlight on the paradigms of FFPE-DNA sequencing
TA Steiert, G Parra, M Gut, N Arnold… - Nucleic Acids …, 2023 - academic.oup.com
In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was
developed as a fixation and conservation method and is still used to this day in routine …
developed as a fixation and conservation method and is still used to this day in routine …
ERIC recommendations for TP53 mutation analysis in chronic lymphocytic leukemia—update on methodological approaches and results interpretation
In chronic lymphocytic leukemia (CLL), TP53 gene defects, due to deletion of the 17p13
locus and/or mutation (s) within the TP53 gene, are associated with resistance to …
locus and/or mutation (s) within the TP53 gene, are associated with resistance to …
Best practices for bioinformatic characterization of neoantigens for clinical utility
Neoantigens are newly formed peptides created from somatic mutations that are capable of
inducing tumor-specific T cell recognition. Recently, researchers and clinicians have …
inducing tumor-specific T cell recognition. Recently, researchers and clinicians have …
Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project
Purpose Fresh-frozen (FF) tissue is the optimal source of DNA for whole-genome
sequencing (WGS) of cancer patients. However, it is not always available, limiting the …
sequencing (WGS) of cancer patients. However, it is not always available, limiting the …
Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients
A growing number of druggable targets and national initiatives for precision oncology
necessitate broad genomic profiling for many cancer patients. Whole exome sequencing …
necessitate broad genomic profiling for many cancer patients. Whole exome sequencing …
[HTML][HTML] Next-generation sequencing in high-sensitive detection of mutations in tumors: challenges, advances, and applications
RR Singh - The Journal of Molecular Diagnostics, 2020 - Elsevier
Next-generation sequencing (NGS) technologies have come of age as preferred
technologies for screening of genomic variants of pathologic and therapeutic potential …
technologies for screening of genomic variants of pathologic and therapeutic potential …