ORCID Profile
0000-0002-6336-3007
Current Organisations
Zhejiang University
,
Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare
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Publisher: Sociedade Entomologica do Brasil
Date: 08-12-2019
DOI: 10.37486/2675-1305.EC01006
Abstract: The parasitoid wasp family Ichneumonidae is arguably one of the groups for which current knowledge lags most strongly behind their enormous ersity. In a five-day meeting in Basel (Switzerland) in June 2019, 22 researchers from 14 countries met to discuss the most important issues in ichneumonid research, including increasing the speed of species discovery, resolving higher-level relationships, and studying the radiation of these parasitoids onto various host groups through time. All agreed that it is time to advertise ichneumonid research more broadly in the scientific community and thereby attract young talents to this group for which specialists are sorely lacking. In order to popularize the group, we here suggest a new name for the family, “Darwin wasps”, to reflect the pivotal role they played in convincing Charles Darwin that not all of creation could have been created by a benevolent god. We hope that the name catches on, and that Darwin wasps start buzzing more loudly across all disciplines of biology.
Publisher: Elsevier BV
Date: 08-2022
Publisher: Ivyspring International Publisher
Date: 2022
DOI: 10.7150/THNO.71038
Publisher: Springer Science and Business Media LLC
Date: 03-01-2022
DOI: 10.1186/S13059-021-02569-8
Abstract: Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically assessing reproducibility of inherited variants with WGS and impact of each step in the process is needed for understanding and improving quality of inherited variants from WGS. To dissect the impact of factors involved in detection of inherited variants with WGS, we sequence triplicates of eight DNA s les representing two populations on three short-read sequencing platforms using three library kits in six labs and call variants with 56 combinations of aligners and callers. We find that bioinformatics pipelines (callers and aligners) have a larger impact on variant reproducibility than WGS platform or library preparation. Single-nucleotide variants (SNVs), particularly outside difficult-to-map regions, are more reproducible than small insertions and deletions (indels), which are least reproducible when 5 bp. Increasing sequencing coverage improves indel reproducibility but has limited impact on SNVs above 30×. Our findings highlight sources of variability in variant detection and the need for improvement of bioinformatics pipelines in the era of precision medicine with WGS.
Publisher: Elsevier BV
Date: 06-2021
Publisher: Springer Science and Business Media LLC
Date: 30-07-2022
DOI: 10.1038/S41467-022-32111-8
Abstract: Spatially resolved transcriptomics provides genetic information in space toward elucidation of the spatial architecture in intact organs and the spatially resolved cell-cell communications mediating tissue homeostasis, development, and disease. To facilitate inference of spatially resolved cell-cell communications, we here present SpaTalk, which relies on a graph network and knowledge graph to model and score the ligand-receptor-target signaling network between spatially proximal cells by dissecting cell-type composition through a non-negative linear model and spatial mapping between single-cell transcriptomic and spatially resolved transcriptomic data. The benchmarked performance of SpaTalk on public single-cell spatial transcriptomic datasets is superior to that of existing inference methods. Then we apply SpaTalk to STARmap, Slide-seq, and 10X Visium data, revealing the in-depth communicative mechanisms underlying normal and disease tissues with spatial structure. SpaTalk can uncover spatially resolved cell-cell communications for single-cell and spot-based spatially resolved transcriptomic data universally, providing valuable insights into spatial inter-cellular tissue dynamics.
Publisher: Springer Science and Business Media LLC
Date: 11-2021
Publisher: Springer Science and Business Media LLC
Date: 16-04-2021
DOI: 10.1186/S13059-021-02315-0
Abstract: Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing. All panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5–20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden. This comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.
Location: China
No related grants have been discovered for Xiaohui Fan.