We present NeurASP, a simple extension of answer set programs by embracing neural networks. By treating the neural network output as the probability distribution over atomic facts in answer set programs, NeurASP provides a simple and effective way to integrate sub-symbolic and symbolic computation. We demonstrate how NeurASP can make use of a pre-trained neural network in symbolic computation and how it can improve the neural network's perception result by applying symbolic reasoning in answer set programming. Also, NeurASP can make use of ASP rules to train a neural network better so that a neural network not only learns from implicit correlations from the data but also from the explicit complex semantic constraints expressed by the rules. <<<

The fine-scale cell-free DNA fragmentation patterns in early-stage cancers are poorly understood. We developed a de novo approach to characterize the cell-free DNA fragmentation hotspots from plasma whole-genome sequencing. Hotspots are enriched in open chromatin regions, and, interestingly, 3'end of transposons. Hotspots showed global hypo-fragmentation in early-stage liver cancers and are associated with genes involved in the initiation of hepatocellular carcinoma and associated with cancer stem cells. The hotspots varied across multiple early-stage cancers and demonstrated high performance for the diagnosis and identification of tissue-of-origin in early-stage cancers. We further validated the performance with a small number of independent case-control-matched early-stage cancer samples. <<<

Daniel B Rosen, Elisabeth A Murphy, Ron S Gejman, Allyson Capili, Rachel L Friedlander, Sophie Rand, Kristen A Cagino, Shannon M Glynn, Kathy C Matthews, Jeff M Kubiak, Jim Yee, Malavika Prabhu, Laura E Riley, Yawei J Yang <<<

OBJECTIVE: To study how severity and progression of coronavirus disease (COVID-19) affect cytokine profiles in pregnant women.MATERIALS AND METHODS: 69 third-trimester, pregnant women were tested for COVID-19 infection and SARS-CoV-2 specific IgM and IgG antibodies. Patients were stratified according to SARS-CoV-2 Reverse Transcriptase-PCR (RT-PCR) status and serology (IgM and IgG) status. Cytokines G-CSF, HGF, IL-18, IL-1Ra, IL-2Ra, IL-8, and IP-10 were measured via ELISA. Retrospective chart review for COVID-19 symptoms and patient vitals was conducted, and cytokine levels were compared between SARS-CoV-2 positive and negative cohorts, by seronegative and seropositive infection, by time course since onset of infection, and according to NIH defined clinical severity.RESULTS: IL-18, IL-1Ra, and IP-10 increased in the 44 RT-PCR positive pregnant women compared to the 25 RT-PCR negative pregnant controls. Elevated cytokine levels were found in early infections, defined by positive RT-PCR and seronegative status, and higher cytokine levels were also associated with more severe disease. By IgM seroconversion, IL-8 and IP-10 returned to levels seen in uninfected patients, while IL-18 levels remained significantly elevated.CONCLUSION: Cytokine profiles of third-trimester pregnant women vary with the time course of infection and are correlated with clinical severity. <<<

Keyur Talsania , Tsai-wei Shen , Xiongfong Chen , Erich Jaeger , Zhipan Li , Zhong Chen , Wanqiu Chen , Bao Tran , Rebecca Kusko , Limin Wang , Andy Wing Chun Pang , Zhaowei Yang , Sulbha Choudhari , Michael Colgan , Li Tai Fang , Andrew Carroll , Jyoti Shetty , Yuliya Kriga , Oksana German , Tatyana Smirnova , Tiantain Liu , Jing Li , Ben Kellman , Karl Hong , Alex R. Hastie , Aparna Natarajan , Ali Moshrefi , Anastasiya Granat , Tiffany Truong , Robin Bombardi , Veronnica Mankinen , Daoud Meerzaman , Christopher E. Mason , Jack Collins , Eric Stahlberg , Chunlin Xiao , Charles Wang , Wenming Xiao , Yongmei Zhao <<<

Abstract Background The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples. Results We systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy. Conclusions A high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods. <<<

Signal peptidases are vital enzymes in the protein secretion pathway. In Archaea, type I signal peptidase, responsible for the cleavage of secretory signal peptides from the majority of secreted proteins, and prepilin peptidase-like signal peptidase, responsible for processing signal peptides from prepilin-like proteins like the preflagellins and various sugar-binding proteins, have been identified. In addition, the archaeal signal peptide peptidase, responsible for degradation of signal peptides after their removal from precursor proteins, has been characterized. These enzymes seem to have a mosaic of eukaryal and bacterial characteristics, and also possess unique archaeal traits. In this review, the most current knowledge with regard to these enzymes is summarized, including their cellular function, catalytic mechanism and distribution and conservation among archaeal species. Comparisons are drawn of these enzymes to their bacterial and eukaryal counterparts, and unique archaeal features highlighted. <<<

Bingfei Yu, Quanming Shi, Julia A Belk, Kathryn E Yost, Kevin R Parker, Rui Li, Betty B Liu, Huang Huang, Daniel Lingwood, William J Greenleaf, Mark M Davis, Ansuman T Satpathy, Howard Y Chang <<<

Cells communicate with each other via receptor-ligand interactions. Here, we describe lentiviral-mediated cell entry by engineered receptor-ligand interaction (ENTER) to display ligand proteins, deliver payloads, and record receptor specificity. We optimize ENTER to decode interactions between T cell receptor (TCR)-MHC peptides, antibody-antigen, and other receptor-ligand pairs. A viral presentation strategy allows ENTER to capture interactions between B cell receptor and any antigen. We engineer ENTER to deliver genetic payloads to antigen-specific T or B cells to selectively modulate cellular behavior in mixed populations. Single-cell readout of ENTER by RNA sequencing (ENTER-seq) enables multiplexed enumeration of antigen specificities, TCR clonality, cell type, and states of individual T cells. ENTER-seq of CMV-seropositive patient blood samples reveals the viral epitopes that drive effector memory T cell differentiation and inter-clonal vs. intra-clonal phenotypic diversity targeting the same epitope. ENTER technology enables systematic discovery of receptor specificity, linkage to cell fates, and antigen-specific cargo delivery. <<<

Enormous waves of technological innovations over the past several years, marked by the advances in AI technologies, are profoundly reshaping the industry and the society. However, down the road, a key challenge awaits us, that is, our capability of meeting rapidly-growing scenario-specific demands is severely limited by the cost of acquiring a commensurate amount of training data. This difficult situation is in essence due to limitations of the mainstream learning paradigm: we need to train a new model for each new scenario, based on a large quantity of well-annotated data and commonly from scratch. In tackling this fundamental problem, we move beyond and develop a new learning paradigm named INTERN. By learning with supervisory signals from multiple sources in multiple stages, the model being trained will develop strong generalizability. We evaluate our model on 26 well-known datasets that cover four categories of tasks in computer vision. In most cases, our models, adapted with only 10% of the training data in the target domain, outperform the counterparts trained with the full set of data, often by a significant margin. This is an important step towards a promising prospect where such a model with general vision capability can dramatically reduce our reliance on data, thus expediting the adoption of AI technologies. Furthermore, revolving around our new paradigm, we also introduce a new data system, a new architecture, and a new benchmark, which, together, form a general vision ecosystem to support its future development in an open and inclusive manner. See project website at this https URL . <<<

In neuroimaging, cortical surface atlases play a fundamental role for spatial normalization, analysis, visualization, and comparison of results across individuals and different studies. However, existing cortical surface atlases created for adults are not suitable for infant brains during the first two postnatal years, which is the most dynamic period of postnatal structural and functional development of the highly-folded cerebral cortex. Therefore, spatiotemporal cortical surface atlases for infant brains are highly desired yet still lacking for accurate mapping of early dynamic brain development. To bridge this significant gap, leveraging our infant-dedicated computational pipeline for cortical surface-based analysis and the unique longitudinal infant MRI dataset acquired in our research center, in this paper, we construct the first spatiotemporal (4D) high-definition cortical surface atlases for the dynamic developing infant cortical structures at seven time points, including 1, 3, 6, 9, 12, 18, and 24 months of age, based on 202 serial MRI scans from 35 healthy infants. For this purpose, we develop a novel method to ensure the longitudinal consistency and unbiasedness to any specific subject and age in our 4D infant cortical surface atlases. Specifically, we first compute the within-subject mean cortical folding by unbiased groupwise registration of longitudinal cortical surfaces of each infant. Then we establish longitudinally-consistent and unbiased inter-subject cortical correspondences by groupwise registration of the geometric features of within-subject mean cortical folding across all infants. Our 4D surface atlases capture both longitudinally-consistent dynamic mean shape changes and the individual variability of cortical folding during early brain development. Experimental results on two independent infant MRI datasets show that using our 4D infant cortical surface atlases as templates leads to significantly improved accuracy for spatial normalization of cortical surfaces across infant individuals, in comparison to the infant surface atlases constructed without longitudinal consistency and also the FreeSurfer adult surface atlas. Moreover, based on our 4D infant surface atlases, for the first time, we reveal the spatially-detailed, region-specific correlation patterns of the dynamic cortical developmental trajectories between different cortical regions during early brain development. <<<

Motivation: Molecular subtypes of cancers and autoimmune disease, defined by transcriptomic profiling, have provided insight into disease pathogenesis, molecular heterogeneity and therapeutic responses. However, technical biases inherent to different gene expression profiling platforms present a unique problem when analyzing data generated from different studies. Currently, there is a lack of effective methods designed to eliminate platform-based bias. We present a method to normalize and classify RNA-seq data using machine learning classifiers trained on DNA microarray data and molecular subtypes in two datasets: breast invasive carcinoma (BRCA) and colorectal cancer (CRC).Results: Multiple analyses show that feature specific quantile normalization (FSQN) successfully removes platform-based bias from RNA-seq data, regardless of feature scaling or machine learning algorithm. We achieve up to 98% accuracy for BRCA data and 97% accuracy for CRC data in assigning molecular subtypes to RNA-seq data normalized using FSQN and a support vector machine trained exclusively on DNA microarray data. We find that maximum accuracy was achieved when normalizing RNA-seq datasets that contain at least 25 samples. FSQN allows comparison of RNA-seq data to existing DNA microarray datasets. Using these techniques, we can successfully leverage information from existing gene expression data in new analyses despite different platforms used for gene expression profiling.Availability and implementation: FSQN has been submitted as an R package to CRAN. All code used for this study is available on Github (https://github.com/jenniferfranks/FSQN).Contact: michael.l.whitfield@dartmouth.edu.Supplementary information: Supplementary data are available at Bioinformatics online. <<<

Linn Sofie Sæther, Thor Ueland, Beathe Haatveit, Luigi Angelo Maglanoc, Attila Szabo, Srdjan Djurovic, Pål Aukrust, Daniel Roelfs, Christine Mohn, Monica Bettina Elkjaer Greenwood Ormerod, Trine Vik Lagerberg, Nils Eiel Steen, Ingrid Melle, Ole Andreas Andreassen, Torill Ueland <<<

A potential relationship between dysregulation of immune/inflammatory pathways and cognitive impairment has been suggested in severe mental illnesses (SMI), such as schizophrenia (SZ) and bipolar (BD) spectrum disorders. However, multivariate relationships between peripheral inflammatory/immune-related markers and cognitive domains are unclear, and many studies do not account for inter-individual variance in both cognitive functioning and inflammatory/immune status. This study aimed to investigate covariance patterns between inflammatory/immune-related markers and cognitive domains and further elucidate heterogeneity in a large SMI and healthy control (HC) cohort (SZ = 343, BD = 289, HC = 770). We applied canonical correlation analysis (CCA) to identify modes of maximum covariation between a comprehensive selection of cognitive domains and inflammatory/immune markers. We found that poor verbal learning and psychomotor processing speed was associated with higher levels of interleukin-18 system cytokines and beta defensin 2, reflecting enhanced activation of innate immunity, a pattern augmented in SMI compared to HC. Applying hierarchical clustering on covariance patterns identified by the CCA revealed a high cognition-low immune dysregulation subgroup with predominantly HC (24% SZ, 45% BD, 74% HC) and a low cognition-high immune dysregulation subgroup predominantly consisting of SMI patients (76% SZ, 55% BD, 26% HC). These subgroups differed in IQ, years of education, age, CRP, BMI (all groups), level of functioning, symptoms and defined daily dose (DDD) of antipsychotics (SMI cohort). Our findings suggest a link between cognitive impairment and innate immune dysregulation in a subset of individuals with severe mental illness. <<<

The proliferation of telco networks and mobile terminals brings the accumulation of tremendous amounts of measure report(MR) data at a rapid pace. The MR data is generated by mobile objects while connecting to data services and is stored in backend data centers. To geo-tag or localize such MR data is believed to have a profound effect on the analytics and optimizations of telco and traffic networks. However, MR records are of noisy and partial observations regarding to mobile objects' geo-locations and hence pose challenges to accurate telco data localization. There have been quite a few attempts. Single-point localization methods map a MR record to a location, but come out with limited accuracies due to the ignorance of spatiotemporal coherence of successive MR records. Recent efforts on sequential localization techniques alleviate this by mapping a sequence of MR records to a trajectory. However, existing solutions are often with assumptions on specific models, e.g., mobility and signal strength distributions, or priori knowledge on topology space, e.g., road networks, limiting the deployment in practice. To this end, we propose a data-driven framework to tackle the challenges in sequential telco localization. We solely use raw MR records and a public third-party GPS dataset for the learning of the correlations between mobile objects' locations and MR records, requiring no model assumptions and priori knowledge. To handle the data-intensive workloads during the learning process, we use materialized views for efficient online localization and light-weighted indexing techniques for periodical parameters tuning, in order to improve the efficiency and scalability. Results on real data show that our solution achieves 58.8 percent improvement in median localization errors compared with state-of-art sequential localization techniques that require hypothesis models and priori knowledge, making our solution superior in terms of effectiveness, efficiency, and employability. <<<

Most genetic variations associated with human complex traits are located in non-coding genomic regions. Therefore, understanding the genotype-to-phenotype axis requires a comprehensive catalog of functional non-coding genomic elements, most of which are involved in epigenetic regulation of gene expression. Genome-wide maps of open chromatin regions can facilitate functional analysis of cis- and trans-regulatory elements via their connections with trait-associated sequence variants. Currently, Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) is considered the most accessible and cost-effective strategy for genome-wide profiling of chromatin accessibility. Single-cell ATAC-seq (scATAC-seq) technology has also been developed to study cell type-specific chromatin accessibility in tissue samples containing a heterogeneous cellular population. However, due to the intrinsic nature of scATAC-seq data, which are highly noisy and sparse, accurate extraction of biological signals and devising effective biological hypothesis are difficult. To overcome such limitations in scATAC-seq data analysis, new methods and software tools have been developed over the past few years. Nevertheless, there is no consensus for the best practice of scATAC-seq data analysis yet. In this review, we discuss scATAC-seq technology and data analysis methods, ranging from preprocessing to downstream analysis, along with an up-to-date list of published studies that involved the application of this method. We expect this review will provide a guideline for successful data generation and analysis methods using appropriate software tools and databases for the study of chromatin accessibility at single-cell resolution. <<<

Zachariah H Foda, Akshaya V Annapragada, Kavya Boyapati, Daniel C Bruhm, Nicholas A Vulpescu, Jamie E Medina, Dimitrios Mathios, Stephen Cristiano, Noushin Niknafs, Harry T Luu, Michael G Goggins, Robert A Anders, Jing Sun, Shruti H Meta, David L Thomas, Gregory D Kirk, Vilmos Adleff, Jillian Phallen, Robert B Scharpf, Amy K Kim, Victor E Velculescu <<<

Liver cancer is a major cause of cancer mortality worldwide. Screening individuals at high risk, including those with cirrhosis and viral hepatitis, provides an avenue for improved survival, but current screening methods are inadequate. In this study, we used whole-genome cell-free DNA (cfDNA) fragmentome analyses to evaluate 724 individuals from the United States, the European Union, or Hong Kong with hepatocellular carcinoma (HCC) or who were at average or high-risk for HCC. Using a machine learning model that incorporated multifeature fragmentome data, the sensitivity for detecting cancer was 88% in an average-risk population at 98% specificity and 85% among high-risk individuals at 80% specificity. We validated these results in an independent population. cfDNA fragmentation changes reflected genomic and chromatin changes in liver cancer, including from transcription factor binding sites. These findings provide a biological basis for changes in cfDNA fragmentation in patients with liver cancer and provide an accessible approach for noninvasive cancer detection. <<<

Manuela Costa, Diego Lozano-Soldevilla, Antonio Gil-Nagel, Rafael Toledano, Carina R Oehrn, Lukas Kunz, Mar Yebra, Costantino Mendez-Bertolo, Lennart Stieglitz, Johannes Sarnthein, Nikolai Axmacher, Stephan Moratti, Bryan A Strange <<<

Memory for aversive events is central to survival but can become maladaptive in psychiatric disorders. Memory enhancement for emotional events is thought to depend on amygdala modulation of hippocampal activity. However, the neural dynamics of amygdala-hippocampal communication during emotional memory encoding remain unknown. Using simultaneous intracranial recordings from both structures in human patients, here we show that successful emotional memory encoding depends on the amygdala theta phase to which hippocampal gamma activity and neuronal firing couple. The phase difference between subsequently remembered vs. not-remembered emotional stimuli translates to a time period that enables lagged coherence between amygdala and downstream hippocampal gamma. These results reveal a mechanism whereby amygdala theta phase coordinates transient amygdala -hippocampal gamma coherence to facilitate aversive memory encoding. Pacing of lagged gamma coherence via amygdala theta phase may represent a general mechanism through which the amygdala relays emotional content to distant brain regions to modulate other aspects of cognition, such as attention and decision-making. <<<

We present a novel framework for multivariate time series representation learning based on the transformer encoder architecture. The framework includes an unsupervised pre-training scheme, which can offer substantial performance benefits over fully supervised learning on downstream tasks, both with but even without leveraging additional unlabeled data, i.e., by reusing the existing data samples. Evaluating our framework on several public multivariate time series datasets from various domains and with diverse characteristics, we demonstrate that it performs significantly better than the best currently available methods for regression and classification, even for datasets which consist of only a few hundred training samples. Given the pronounced interest in unsupervised learning for nearly all domains in the sciences and in industry, these findings represent an important landmark, presenting the first unsupervised method shown to push the limits of state-of-the-art performance for multivariate time series regression and classification. <<<

Artists rarely paint in a single style throughout their career. More often they change styles or develop variations of it. In addition, artworks in different styles and even within one style depict real content differently: while Picasso's Blue Period displays a vase in a blueish tone but as a whole, his Cubist works deconstruct the object. To produce artistically convincing stylizations, style transfer models must be able to reflect these changes and variations. Recently many works have aimed to improve the style transfer task, but neglected to address the described observations. We present a novel approach which captures particularities of style and the variations within and separates style and content. This is achieved by introducing two novel losses: a fixpoint triplet style loss to learn subtle variations within one style or between different styles and a disentanglement loss to ensure that the stylization is not conditioned on the real input photo. In addition the paper proposes various evaluation methods to measure the importance of both losses on the validity, quality and variability of final stylizations. We provide qualitative results to demonstrate the performance of our approach. <<<

Genomic microarrays used to assess DNA copy number are now recommended as first-tier tests for the postnatal evaluation of individuals with intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies. Application of this technology has resulted in the discovery of widespread copy number variation in the human genome, both polymorphic variation in healthy individuals and novel pathogenic copy number imbalances. To assist clinical laboratories in the evaluation of copy number variants and to promote consistency in interpretation and reporting of genomic microarray results, the American College of Medical Genetics has developed the following professional guidelines for the interpretation and reporting of copy number variation. These guidelines apply primarily to evaluation of constitutional copy number variants detected in the postnatal setting. <<<

AbstractRecent human electrophysiology work has uncovered the presence of high frequency oscillatory events, termed ripples, during awake behavior. This prior work focuses on ripples in the medial temporal lobe (MTL) during memory retrieval. Few studies, however, investigate ripples during item encoding. Many studies have found neural activity during encoding that predicts later recall, termed subsequent memory effects (SMEs), but it is unclear if ripples during encoding also predict subsequent recall. Detecting ripples in 124 neurosurgical participants performing an episodic memory task, we find insignificant ripple SMEs in any MTL region, even as these regions exhibit robust high frequency activity (HFA) SMEs. Instead, hippocampal ripples increase during encoding of items leading to recall of temporally or semantically associated items, a phenomenon known as clustering. This subsequent clustering effect (SCE) arises specifically when hippocampal ripples occur during both encoding and retrieval, suggesting that ripples mediate the encoding and future reinstatement of episodic memories. <<<

Development of ketosis in high-producing dairy cows contributes to several animal health issues and highlights the need for a better understanding of the genetic basis of metabolic diseases. To evaluate the pattern of differential gene expression in the liver of cows under negative energy balance (NEB), and under subclinical and clinical ketosis, a meta-analysis of gene expression and genome-wide association studies results was performed. An initial systematic review identified 118 articles based on the key words "cow," "liver," "negative energy balance," "ketosis," "expression," "qPCR," "microarray," "proteomic," "RNA-Seq," and "GWAS." After further screening for only peer-reviewed and pertinent articles for gene expression during NEB and clinical and subclinical ketosis (considering plasma levels of β-hydroxybutyrate), 20 articles were included in the analysis. From the systematic review, 430 significant SNPs identified by genome-wide association studies (GWAS) were assigned to genes reported in gene expression studies by considering chromosome and base pair positions in the ARS-UCD 1.2 bovine assembly. Venn diagrams were created to integrate the data obtained in the systematic review, and Gene Ontology enrichment analysis was carried out using official gene names. A QTL enrichment analysis was also performed to identify potential positional candidate loci. Twenty-four significant SNPs were located within the coordinates of differentially expressed genes located on chromosomes 2, 3, 6, 9, 11, 14, 27, and 29. Three significant metabolic pathways were associated with NEB and subclinical and clinical ketosis. In addition, 2 important genes, PPARA (peroxisome proliferator activated receptor alpha) and ACACA (acetyl-coenzyme A carboxylase α), were identified, which were differentially expressed in the 3 metabolic conditions. The PPARA gene is involved in the regulation of lipid metabolism and fatty liver disease and the ACACA gene encodes an enzyme that catalyzes the carboxylation of acetyl-coenzyme A to malonyl-coenzyme A, which is a rate-limiting step in fatty acid synthesis. Gene network analysis revealed co-expression interactions among 34 genes associated with functions involving fatty acid transport and fatty acid metabolism. For the annotated QTL, 9 QTL were identified for ketosis. The genes FN1 (fibronectin 1) and PTK2 (protein tyrosine kinase 2), which are mainly involved in cell adhesion and formation of extracellular matrix constituents, were enriched for QTL previously associated with the trait "ketosis" on chromosome 2 and for the trait "milk iron content" on chromosome 14, respectively. This integration of gene expression and GWAS data provides an additional understanding of the genetic background of NEB and subclinical and clinical ketosis in dairy cattle. Thus, it is a useful approach to identify biological mechanisms underlying these metabolic conditions in dairy cattle. <<<

S M Ashiqul Islam, Marcos Díaz-Gay, Yang Wu, Mark Barnes, Raviteja Vangara, Erik N Bergstrom, Yudou He, Mike Vella, Jingwei Wang, Jon W Teague, Peter Clapham, Sarah Moody, Sergey Senkin, Yun Rose Li, Laura Riva, Tongwu Zhang, Andreas J Gruber, Christopher D Steele, Burçak Otlu, Azhar Khandekar, Ammal Abbasi, Laura Humphreys, Natalia Syulyukina, Samuel W Brady, Boian S Alexandrov, Nischalan Pillay, Jinghui Zhang, David J Adams, Iñigo Martincorena, David C Wedge, Maria Teresa Landi, Paul Brennan, Michael R Stratton, Steven G Rozen, Ludmil B Alexandrov <<<

Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues. <<<