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| 2. |
- Fang, Li Tai, et al.
(författare)
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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1151-1160
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Tidskriftsartikel (refereegranskat)abstract
- Tumor-normal paired DNA samples from a breast cancer cell line and a matched lymphoblastoid cell line enable calibration of clinical sequencing pipelines and benchmarking 'tumor-only' or 'matched tumor-normal' analyses. The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
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| 3. |
- Ren, Luyao, et al.
(författare)
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
- 2023
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome.RESULTS: We established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data.CONCLUSIONS: The Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.
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| 4. |
- Wei, Xiaodan, et al.
(författare)
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The Number of Stenotic Intracranial Arteries Is Independently Associated with Ischemic Stroke Severity
- 2016
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:9
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Tidskriftsartikel (refereegranskat)abstract
- Background The severity of ischemic stroke symptoms varies among patients and is a critical determinant of patient outcome. To date, the association between the number of stenotic intracranial arteries and stroke severity remains unclear. Aims We aimed to investigate the association between the number of stenotic major intracranial arteries (NSMIA) and ischemic stroke severity, as well as the degree of stenosis and common stroke risk factors. Methods We performed a retrospective analysis of patients with digital subtraction angiography (DSA)-confirmed ischemic stroke. Clinical stroke severity was measured using the National Institutes of Health Stroke Scale (NIHSS). The number of stenotic vessels was counted from the internal carotid arteries and vertebral arteries, bilaterally. Results Eighty three patients were recruited from a single center and included in the study. NSMIA was significantly correlated with stroke severity (Pearson Correlation Coefficient = 0.485, P < 0.001), but not with the degree of stenosis (Pearson Correlation Coefficient = 0.01, P = 0.90). Multivariate regression analysis revealed that NSMIA was significantly associated with the NIHSS score after adjusting for stroke risk factors. The adjusted odds ratio (per lateral) was 2.092 (95% CI, 0.865 to 3.308, P = 0.001). The degree of stenosis was also significantly associated with the NIHSS score after adjusting for common risk factors. The odds ratio (per 10%) was 0.712 (95% CI, 0.202 to 1.223, P = 0.007). Conclusions The number of stenotic intracranial major arteries is associated with the severity of ischemic stroke independent of the degree of stenosis and other stroke risk factors. To the best of our knowledge, this has not been previosuly studied in great detail using DSA. Our data highlight the importance of examining all major arteries in stroke patients.
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| 5. |
- Xiao, Wenming, et al.
(författare)
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1141-1150
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Tidskriftsartikel (refereegranskat)abstract
- Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing. Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
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| 6. |
- Chen, Jie, et al.
(författare)
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Risk of incident cardiovascular disease among patients with gastrointestinal disorder : a prospective cohort study of 330,751 individuals.
- 2023
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Ingår i: European Heart Journal - Quality of Care and Clinical Outcomes. - 2058-5225 .- 2058-1742.
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND AND AIMS: The associations between gastrointestinal diseases (GIs) and cardiovascular disease (CVD) were unclear. We conducted a prospective cohort study to explore their associations.METHODS: This study included 330 751 individuals without baseline CVD from the UK Biobank cohort. Individuals with and without GIs were followed up until the ascertainment of incident CVDs, including coronary heart disease (CHD), cerebrovascular disease (CeVD), heart failure (HF) and peripheral artery disease (PAD). The diagnosis of diseases was confirmed with combination of the nationwide inpatient data, primary care data, and cancer registries. A multivariable Cox proportional hazard regression model was used to estimate the associations between GIs and the risk of incident CVD.RESULTS: During a median follow-up of 11.8 years, 31 605 incident CVD cases were diagnosed. Individuals with GIs had an elevated risk of CVD (hazard ratio 1.37; 95% confidence interval 1.34-1.41, P < 0.001). Eleven out of fifteen GIs were associated with an increased risk of CVD after Bonferroni-correction, including cirrhosis, non-alcoholic fatty liver disease, gastritis and duodenitis, irritable bowel syndrome, Barrett's esophagus, gastroesophageal reflux disease, peptic ulcer, celiac disease, diverticulum, appendicitis, and biliary disease. The associations were stronger among women, individuals aged ≤ 60 years, and those with body mass index ≥ 25 kg/m2.CONCLUSIONS: This large-scale prospective cohort study revealed the associations of GIs with an increased risk of incident CVD, in particular CHD and PAD. These findings support the reinforced secondary CVD prevention among patients with gastrointestinal disorders.
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| 7. |
- Yan, Jingjie, et al.
(författare)
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FENP : A Database of Neonatal Facial Expression for Pain Analysis
- 2023
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Ingår i: IEEE Transactions on Affective Computing. - : Institute of Electrical and Electronics Engineers (IEEE). - 1949-3045. ; 14:1, s. 245-254
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Tidskriftsartikel (refereegranskat)abstract
- In this article, we introduce a new neonatal facial expression database for pain analysis. This database, called facial expression of neonatal pain (FENP), contains 11,000 neonatal facial expression images associated with 106 Chinese neonates from two children's hospitals, i.e., the Children's Hospital Affiliated to Nanjing Medical University and Second Affiliated Hospital Affiliated to Nanjing Medical University in China. The facial expression images cover four categories of facial expressions, i.e., severe pain expression, mild pain expression, crying expression and calmness expression, where each category contains 2750 neonatal facial expression images. Based on this database, we also investigate the pain facial expression recognition problem using several state-of-the-art facial expression features and expression recognition methods, such as Gabor+SVM, LBP+SVM, HOG+SVM, LBP+HOG+SVM, and several Convolutional Neural Network (CNN) methods (including AlexNet, VGGNet, GoogLeNet, ResNet and DenseNet). The experimental results indicate that the proposed neonatal pain facial expression database is very suitable for the study of both neonatal pain and facial expression recognition. Moreover, the FENP database is publicly available after signing a license agreement (the users can contact Jingjie Yan (yanjingjie@njupt.edu.cn), Guanming Lu (lugm@njupt.edu.cn)) or Xiaonan Li (xnli@njmu.edu.cn).
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| 8. |
- Zhang, Bin, et al.
(författare)
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Perylene Diimide-Based Low-Cost and Thickness-Tolerant Electron Transport Layer Enables Polymer Solar Cells Approaching 19% Efficiency
- 2024
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Ingår i: Advanced Functional Materials. - 1616-3028 .- 1616-301X. ; In Press
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Tidskriftsartikel (refereegranskat)abstract
- The materials for electron transport layers (ETLs) play a significant role in the performance of polymer solar cells (PSCs) but face challenges, such as low electron transport mobility and conductivity, low solution processibility, and extreme thickness sensitivity, which will undermine the photovoltaic performance and hinder compatibility of large-scale fabrication technique. To address these challenges, a new n-type perylene diimide-based molecule (PDINB) with two special amine-anchored long-side chains is designed and synthesized feasibly. PDINB shows very high solubility in common organic solvents, such as dichloromethane (>75 mg ml−1) and methanol with acetic acid as an additive (>37 mg ml−1), which leads to excellent film formability when deposited on active layers. With PDINB as ETLs, the photovoltaic performance of the PSCs is boosted comprehensively, leading to power conversion efficiency (PCE) up to 18.81%. Thanks to the strong self-doping effect and high conductivity of PDINB, it displays an appreciable thickness-tolerant property as ETLs, where the devices remain consistently high PCE values with the thickness varying from 5 to 30 nm. Interestingly, PDINB can be used as a generic ETL in different types of PSCs including non-fullerene PSCs and all-polymer PSCs. Therefore, PDINB can be a potentially competitive candidate as an efficient ETL for PSCs.
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| 9. |
- Foox, Jonathan, et al.
(författare)
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The SEQC2 epigenomics quality control (EpiQC) study
- 2021
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundCytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA’s Epigenomics Quality Control Group.ResultsEach sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms.ConclusionsThe data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.
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| 10. |
- Guo, Xueying, et al.
(författare)
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Location Privacy-Preserving Method Based on Historical Proximity Location
- 2020
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Ingår i: Wireless Communications & Mobile Computing. - : Hindawi Publishing Corporation. - 1530-8669 .- 1530-8677. ; 2020
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Tidskriftsartikel (refereegranskat)abstract
- With the rapid development of Internet services, mobile communications, and IoT applications, Location-Based Service (LBS) has become an indispensable part in our daily life in recent years. However, when users benefit from LBSs, the collection and analysis of users' location data and trajectory information may jeopardize their privacy. To address this problem, a new privacy-preserving method based on historical proximity locations is proposed. The main idea of this approach is to substitute one existing historical adjacent location around the user for his/her current location and then submit the selected location to the LBS server. This method ensures that the user can obtain location-based services without submitting the real location information to the untrusted LBS server, which can improve the privacy-preserving level while reducing the calculation and communication overhead on the server side. Furthermore, our scheme can not only provide privacy preservation in snapshot queries but also protect trajectory privacy in continuous LBSs. Compared with other location privacy-preserving methods such ask-anonymity and dummy location, our scheme improves the quality of LBS and query efficiency while keeping a satisfactory privacy level.
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