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Publications

Whole-genome bisulfite sequencing with improved accuracy and cost

DNA methylation patterns in the genome both reflect and help to mediate transcriptional regulatory processes. The digital nature of DNA methylation, present or absent on each allele, makes this assay capable of quantifying events in subpopulations of cells, whereas genome-wide...

Authors:  Toby Bloom   Michael Zody   Will Liao  

Unexpected similarities between C9ORF72 and sporadic forms of ALS/FTD suggest a common disease mechanism

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) represent two ends of a disease spectrum with shared clinical, genetic and pathological features. These include near ubiquitous pathological inclusions of the RNA binding protein (RBP) TDP-43, and often the presence of...

Authors:  Phaedra Agius  

YES1 amplification is a mechanism of acquired resistance to EGFR inhibitors identified by transposon mutagenesis and clinical genomics.

In ∼30% of patients with EGFR-mutant lung adenocarcinomas whose disease progresses on EGFR inhibitors, the basis for acquired resistance remains unclear. We have integrated transposon mutagenesis screening in an EGFR-mutant cell line and clinical genomic sequencing in cases of acquired...

Authors:  Nicolas Robine   Giuseppe Narzisi  

Genomic and Geographic Context for the Evolution of High-Risk Carbapenem-Resistant Enterobacter cloacae Complex Clones ST171 and ST78.

Recent reports have established the escalating threat of carbapenem-resistant Enterobacter cloacae complex (CREC). Here, we demonstrate that CREC has evolved as a highly antibiotic-resistant rather than highly virulent nosocomial pathogen. Applying genomics and Bayesian phylogenetic analyses to a 7-year collection of CREC...

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taxMaps: Comprehensive and highly accurate taxonomic classification of short-read data in reasonable time.

High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive and fully scalable...

Authors:  Michael Zody   Nicolas Robine   Andre Corvelo   Wayne Clarke  

Genome-wide somatic variant calling using localized colored de Bruijn graphs

Reliable detection of somatic variations is of critical importance in cancer research. Here we present Lancet, an accurate and sensitive somatic variant caller, which detects SNVs and indels by jointly analyzing reads from tumor and matched normal samples using colored...

Authors:  Michael Zody   Nicolas Robine   Giuseppe Narzisi   Andre Corvelo   Kanika Arora   Minita Shah   Rajeeva Musunuri  

Whole Genome Sequencing-Based Discovery of Structural Variants in Glioblastoma.

Next-generation DNA sequencing (NGS) technologies are currently being applied in both research and clinical settings for the understanding and management of disease. The goal is to use high-throughput sequencing to identify specific variants that drive tumorigenesis within each individual's tumor...

Authors:  Kazimierz Wrzeszczynski   Minita Shah  

Identification of Three Rheumatoid Arthritis Disease Subtypes by Machine Learning Integration of Synovial Histologic Features and RNA Sequencing Data

We sought to refine histologic scoring of rheumatoid arthritis synovial tissue by training with gene expression data and machine learning. METHODS: Twenty histologic features were assessed on 129 synovial tissue samples. Consensus clustering was performed on gene expression data from a subset...

Authors:  Nicolas Robine   Phaedra Agius   Heather Geiger  

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