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Publications

Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer

Pancreatic cancer is the most lethal common solid malignancy. Systemic therapies are often ineffective, and predictive biomarkers to guide treatment are urgently needed. We generated a pancreatic cancer patient-derived organoid (PDO) library that recapitulates the mutational spectrum and transcriptional subtypes...

Authors:  Rasheh Sanghvi   Nicolas Robine   Kanika Arora   Minita Shah   Molly Johnson  

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

Hundreds of thousands of human whole genome sequencing (WGS) datasets will be generated over the next few years. These data are more valuable in aggregate: joint analysis of genomes from many sources increases sample size and statistical power. A central...

Authors:  Michael Zody  

Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient Derived Tumors Clinical Application of Whole-Genome Sequencing for Reporting Targetable Variants in Cancer

We have developed and validated a clinical whole-genome and transcriptome sequencing (WGTS) assay which provides a comprehensive genomic profile of a patient's tumor. The ability to fully capture the mappable genome with sufficient sequencing coverage to precisely call DNA somatic...

Authors:  Nicolas Robine   Avinash Abhyankar   Kazimierz Wrzeszczynski   Kanika Arora   Minita Shah   Heather Geiger   Alice Fang  

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  

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