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Inferring Transmission Fitness Advantage of SARS-CoV-2 Variants of Concern in Wastewater Using Digital PCR
(2021)medRxivThroughout the global COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterized by increased transmissibility, increased virulence, or reduced neutralization by antibodies obtained from prior infection or vaccination. Tracking the introduction and transmission of VOCs relies on sequencing, typically whole-genome sequencing of clinical samples. Wastewater surveillance ...Working Paper -
The Tumor Profiler Study: Integrated, multi-omic, functional tumor profiling for clinical decision support
(2020)medRxivRecent technological advances allow profiling of tumor samples to an unparalleled level with respect to molecular and spatial composition as well as treatment response. We describe a prospective, observational clinical study performed within the Tumor Profiler (TuPro) Consortium that aims to show the extent to which such comprehensive information leads to advanced mechanistic insights of a patient’s tumor, enables prognostic and predictive ...Working Paper -
Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data
(2020)medRxivPathogen genomes provide insights into their evolution and epidemic spread. We sequenced 1,439 SARS-CoV-2 genomes from Switzerland, representing 3-7% of all confirmed cases per week. Using these data, we demonstrate that no one lineage became dominant, pointing against evolution towards general lower virulence. On an epidemiological level, we report no evidence of cryptic transmission before the first confirmed case. We find many early ...Working Paper -
Detection and surveillance of SARS-CoV-2 genomic variants in wastewater
(2021)medRxivThe emergence of SARS-CoV-2 mutants with altered transmissibility, virulence, or immunogenicity emphasizes the need for early detection and epidemiological surveillance of genomic variants. Wastewater samples provide an opportunity to assess circulating viral lineages in the community. We performed genomic sequencing of 122 wastewater samples from three locations in Switzerland to analyze the B.1.1.7, B.1.351, and P.1 variants of SARS-CoV-2 ...Working Paper -
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data
(2020)bioRxivHigh-throughput sequencing technologies are used increasingly, not only in viral genomics research but also in clinical surveillance and diagnostics. These technologies facilitate the assessment of the genetic diversity in intra-host virus populations, which affects transmission, virulence, and pathogenesis of viral infections. However, there are two major challenges in analysing viral diversity. First, amplification and sequencing errors ...Working Paper -
Single-cell copy number calling and event history reconstruction
(2020)bioRxivCopy number alterations are driving forces of tumour development and the emergence of intra-tumour heterogeneity. A comprehensive picture of these genomic aberrations is therefore essential for the development of personalised and precise cancer diagnostics and therapies. Single-cell sequencing offers the highest resolution for copy number profiling down to the level of individual cells. Recent high-throughput protocols allow for the ...Working Paper -
Within-patient genetic diversity of SARS-CoV-2
(2020)bioRxivSARS-CoV-2, the virus responsible for the current COVID-19 pandemic, is evolving into different genetic variants by accumulating mutations as it spreads globally. In addition to this diversity of consensus genomes across patients, RNA viruses can also display genetic diversity within individual hosts, and co-existing viral variants may affect disease progression and the success of medical interventions. To systematically examine the ...Working Paper -
GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers
(2020)bioRxivSynthetic lethal interactions, where the simultaneous but not individual inactivation of two genes is lethal to the cell, have been successfully exploited to treat cancer. GATA3 is frequently mutated in estrogen receptor (ER)-positive breast cancers and its deficiency defines a subset of patients with poor response to hormonal therapy and poor prognosis. However, GATA3 is not targetable. Here we show that GATA3 and MDM2 are synthetically ...Working Paper -
SCIM: Universal Single-Cell Matching with Unpaired Feature Sets
(2020)bioRxivMotivation Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences ...Working Paper -
scAmpi - A versatile pipeline for single-cell RNA-seq analysis from basics to clinics
(2021)bioRxivSingle-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique to decipher tissue composition at the single-cell level and to inform on disease mechanisms, tumor heterogeneity, and the state of the immune microenvironment. Although multiple methods for the computational analysis of scRNA-seq data exist, their application in a clinical setting demands standardized and reproducible workflows, targeted to extract, condense, and ...Working Paper