Søren Germer

Songbird is a single cell whole genome sequencing copy number caller that detects whole genome duplication and outperforms existing tools in breakpoints identification and true copy number detection.

This study benchmarks six duplex sequencing technologies to evaluate their performance in detecting somatic mutations across different genomic contexts and tissue types.

The paper uses single-cell DNA sequencing to analyze somatic mosaicism in postmortem lung and colon tissues, revealing mutation heterogeneity, chromosomal abnormalities, and cellular ancestry.

The paper benchmarks somatic variant and indel detection at low allele fractions using short- and long-read data, finding sensitivity and precision around 80% at 300x coverage.

This paper introduces ppmSeq, a sequencing technology that improves accuracy and efficiency in detecting SNVs by sequencing both DNA strands, showing superior performance in clinical applications like ctDNA detection.

The paper identifies 83 rare lncRNA variant sets associated with blood lipid levels using WGS data from the TOPMed program and validates some in UK Biobank data.

This study shows that common splice-regulatory variants can reduce the pathogenicity of rare exonic variants by modulating mRNA splicing.

The paper presents a comprehensive catalog of structural variants across 138,134 individuals, identifying novel variants and their associations with cardio-metabolic and hematologic traits.

This study applies low-cost whole genome sequencing to detect circulating tumor DNA at high sensitivity in plasma samples, achieving error rates as low as 10^-7 and enabling cancer monitoring without matched tumor sequencing.

The paper performs whole genome sequence analysis of plasma lipid levels in 66,329 individuals, identifying new lipid-associated alleles, including rare non-coding variants.

The paper presents a high coverage whole genome sequencing resource of 3,202 samples, including 602 trios, generated from the expanded 1000 Genomes Project.

This study identifies 35 genes associated with circulating lipid levels using rare coding variants from 170,000 exomes across multiple ancestries.

Over 400 million variants, 97% below 1% frequency, emerge from deep whole-genome sequencing of 53,831 diverse TOPMed participants; TOPMed haplotypes enable imputation down to ~0.01% frequency.

The paper identifies eQTLs for ACE2 and TMPRSS2 in children's airway transcriptomes and links their expression to T2 inflammation and interferon responses, influencing SARS-CoV-2 infectivity.

The paper benchmarks a new sequencing platform and develops a somatic calling pipeline using deep sequencing of cancer cell lines on two platforms.

The paper optimizes library preparation and sequencing for whole genome bisulphite sequencing on the Illumina HiSeq X system, eliminating an artefact affecting several percent of reads.

This study identifies pharmacogenetic variants associated with albuterol bronchodilator response in minority children with asthma using whole genome sequencing.