bioinformatics_introbl2

Bioinformatics

Bioinformatics @ NYGC

Our team of bioinformaticians aims to develop, maintain and improve our analysis pipelines by leveraging the large amounts of sequencing data we produce. We work on estimating the sources of errors and variability in the data, defining methods to correct them, both computationally and on the lab side. We are also continually evaluating and benchmarking available tools, refining best practices to analyze and combine results, and are developing novel tools and methods.

We are also supporting our CLEP lab by providing the expertise in clinical interpretation of constitutional and cancer genomics.

Expertise

processOur diverse team of bioinformatics scientists has expertise in:

  • Statistical and population genetics
  • Cancer genomics
  • Expression analysis
  • Epigenomics and functional genomics
  • de novo genome assembly
  • Metagenomics
  • Clinical interpretation

Process

A typical project is initiated with one of the sequencing project managers. Our bioinformatics scientists are consulted to further refine the experimental design, analytic plan, and project deliverables.

The bioinformatics team performs standard and project-specific quality control, and analysis of sequencing data (e.g., differential expression and functional enrichment for RNA-Seq, variant annotation and interpretation for genome and exome sequencing, and somatic variant—both SNV and structural variant—for cancer). Results are delivered via our web interface or APIs and are stored and accessible for a period of time as part of NYGC’s Integrated Genomics.

Clinical Interpretation

As exome and genome sequencing data are processed and genomic variation between the sample and a reference are defined, annotated, and compared to existing databases, our bioinformatics scientists contribute to the last step of the analysis: clinical interpretation.

This usually requires ranking and filtering of putative candidates, manual curation, and functional validation (when possible) of our findings. NYGC’s analysis alleviates the need for the investigator to perform the standard computationally intensive analysis steps, thus freeing up time to focus on the biology.

Rasheh Sanghvi

Bioinformatics Analyst

Toby Bloom

Senior Director, Strategic Genomic Analytics

Michael Zody

Senior Director, Computational Biology

Nicolas Robine

Assistant Director, Computational Biology

Avinash Abhyankar

Manager, Clinical Informatics

Uday Evani

Senior Software Engineer

Kazimierz Wrzeszczynski

Assistant Director, Clinical Oncology Informatics

Giuseppe Narzisi

Lead Bioinformatics Scientist

Marta Byrska-Bishop

Bioinformatics Scientist

Will Liao

Senior Bioinformatics Scientist

Phaedra Agius

Senior Bioinformatics Scientist

Andre Corvelo

Senior Bioinformatics Scientist

Kanika Arora

Bioinformatics Scientist

Minita Shah

Bioinformatics Scientist

Wayne Clarke

Bioinformatics Scientist

Dillon Maloney

Bioinformatics Analyst

Rajeeva Musunuri

Bioinformatics Programmer

Molly Johnson

Bioinformatics Analyst

Heather Geiger

Senior Bioinformatics Analyst

Jennifer Shelton

Bioinformatics programmer

Alice Fang

Biocurator

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  

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