Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1038/s41375-020-0817-x | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Precise identification of somatic and germline variants in the absence of matched normal samples.
Brief Bioinform
November 2024
The Department of Medical Oncology, Jilin Cancer Hospital, No. 1066, Jinhu Road, Changchun, 130012, China.
Somatic variants play a crucial role in the occurrence and progression of cancer. However, in the absence of matched normal controls, distinguishing between germline and somatic variants becomes challenging in tumor samples. The existing tumor-only genomic analysis methods either suffer from limited performance or insufficient interpretability due to an excess of features.
View Article and Find Full Text PDFA robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.
bioRxiv
December 2024
Material Measurement Laboratory, National Institute of Standards and Technology (NIST), 100 Bureau Dr, MS8312, Gaithersburg, MD 20899, USA.
Somatic mosaicism is an important cause of disease, but mosaic and somatic variants are often challenging to detect because they exist in only a fraction of cells. To address the need for benchmarking subclonal variants in normal cell populations, we developed a benchmark containing mosaic variants in the Genome in a Bottle Consortium (GIAB) HG002 reference material DNA from a large batch of a normal lymphoblastoid cell line. First, we used a somatic variant caller with high coverage (300x) Illumina whole genome sequencing data from the Ashkenazi Jewish trio to detect variants in HG002 not detected in at least 5% of cells from the combined parental data.
View Article and Find Full Text PDF[Clinicopathological and molecular genetic features of POLE-mutated endometrioid carcinoma].
Zhonghua Bing Li Xue Za Zhi
December 2024
Department of Pathology, the Seventh Medical Center of Peoples's Liberation Army General Hospital, Beijing100700, China.
To investigate the clinicopathological and molecular genetic features of POLE mutant endometrioid carcinoma. Genetic test data of 230 cases of endometrial carcinoma that underwent surgical resection and molecular typing by next generation sequencing in the First Medical Center of Chinese PLA General Hospital from January 2021 to June 2023 were retrospectively analyzed. Seventeen cases of endometrioid carcinoma with POLE mutation were selected.
View Article and Find Full Text PDFscMSI: Accurately inferring the sub-clonal Micro-Satellite status by an integrated deconvolution model on length spectrum.
PLoS Comput Biol
December 2024
School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China.
Microsatellite instability (MSI) is an important genomic biomarker for cancer diagnosis and treatment, and sequencing-based approaches are often applied to identify MSI because of its fastness and efficiency. These approaches, however, may fail to identify MSI on one or more sub-clones for certain cancers with a high degree of heterogeneity, leading to erroneous diagnoses and unsuitable treatments. Besides, the computational cost of identifying sub-clonal MSI can be exponentially increased when multiple sub-clones with different length distributions share MSI status.
View Article and Find Full Text PDFElucidating acquired PARP inhibitor resistance in advanced prostate cancer.
Cancer Cell
December 2024
The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK. Electronic address:
Article Synopsis
- - PARP inhibitors show promise in treating castration-resistant prostate cancer (CRPC) with homologous recombination repair (HRR) defects, but the reasons behind resistance are not completely understood.
- - A study from the TOPARP-B trial found that 79% of BRCA2/PALB2-mutated tumors exhibited reversion mutations at the end of treatment, with many related to POLQ-mediated DNA repair mechanisms.
- - In cases of BRCA2 homozygous deletions, rare subclones lacking the BRCA2 deletion are selected for after PARP inhibitor treatment, indicating the necessity for restored HRR function in developing resistance.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!