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.

Toby Bloom

Deputy Scientific Director, Informatics

Michael Zody

Research Director, Computational Biology

Dayna Oschwald

Senior Director, Informatics Program Management

Nicolas Robine

Assistant Director, Computational Biology

Avinash Abhyankar

Manager, Clinical Informatics

Uday Evani

Senior Software Engineer

Kazimierz Wrzeszczynski

Bioinformatics Scientist

Giuseppe Narzisi

Senior Bioinformatics Scientist

Marta Byrska-Bishop

Bioinformatics Scientist

Will Liao

Senior Bioinformatics Scientist

Phaedra Agius

Senior Bioinformatics Scientist

Andre Corvelo

Senior Bioinformatics Scientist

Kanika Arora

Senior Bioinformatics Analyst

Minita Shah

Senior Bioinformatics Analyst

Caitlin McHugh

Senior Bioinformatics Analyst, Statistical Genetics

Wayne Clarke

Senior Bioinformatics Analyst

Dillon Maloney

Bioinformatics Analyst

Rajeeva Musunuri

Bioinformatics Programmer

Molly Johnson

Bioinformatics Analyst

Heather Geiger

Bioinformatics Analyst

Jennifer Shelton

Bioinformatics programmer

Alice Fang

Biocurator

Amrita Kar

Bioinformatics Analyst, Metagenomics

Sadia Rahman

Biocurator, Molecular Diagnostics

Disease variants in genomes of 44 centenarians

To identify previously reported disease mutations that are compatible with extraordinary longevity, we screened the coding regions of the genomes of 44 Ashkenazi Jewish centenarians. Individual genome sequences were generated with 30× coverage on the Illumina HiSeq 2000 and single-nucleotide...

Authors:  Avinash Abhyankar  

Deficiency of UBE2T, the E2 Ubiquitin Ligase Necessary for FANCD2 and FANCI Ubiquitination, Causes FA-T Subtype of Fanconi Anemia

Fanconi anemia (FA) is a rare bone marrow failure and cancer predisposition syndrome resulting from pathogenic mutations in genes encoding proteins participating in the repair of DNA interstrand crosslinks (ICLs). Mutations in 17 genes (FANCA-FANCS) have been identified in FA...

Authors:  Avinash Abhyankar  

A novel mutation in the POLE2 gene causing combined immunodeficiency

Early lymphocyte development requires the orchestrated interplay of pathways to maintain genomic integrity and accurate DNA repair during the proliferative bursts associated with antigen receptor rearrangement (1). Inborn errors in replication control or DNA repair can lead to primary immunodeficiency...

Authors:  Avinash Abhyankar  

Massively Parallel Processing of Whole Genome Sequence Data: An In-Depth Performance Study

This paper presents a joint effort between a group of computer scientists and bioinformaticians to take an important step towards a general big data platform for genome analysis pipelines. The key goals of this study are to develop a thorough...

Authors:  Toby Bloom   Avinash Abhyankar   Uday Evani  

The cellular and molecular origin of tumor-associated macrophages

Long recognized as an evolutionarily ancient cell type involved in tissue homeostasis and immune defense against pathogens, macrophages are being rediscovered as regulators of several diseases, including cancer. Here we show that in mice, mammary tumor growth induces the accumulation...

Authors:  Will Liao  

Genome wide mapping of Foxo1 binding-sites in murine T lymphocytes

The Forkhead box O (Foxo) family of transcription factors has a critical role in controlling the development, differentiation, and function of T cells. However, the direct target genes of Foxo transcription factors in T cells have not been well characterized....

Authors:  Will Liao  

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