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.
Our diverse team of bioinformatics scientists has expertise in:
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.
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.
Intracranial metastases in prostate cancer are uncommon but clinically aggressive. A detailed molecular characterization of prostate cancer intracranial metastases would improve our understanding of their pathogenesis and the search for new treatment strategies. We evaluated the clinical and molecular characteristics...
Authors: Nicolas Robine Will Hooper Tim Chu
New Jersey was among the first states impacted by the COVID-19 pandemic, with one of the highest overall death rates in the nation. Nevertheless, relatively few reports have been published focusing specifically on New Jersey. Here we report on molecular,...
Authors: Michael Zody Andre Corvelo
Neuroblastoma is a lethal childhood solid tumor of developing peripheral nerves. Two percent of children with neuroblastoma develop opsoclonus myoclonus ataxia syndrome (OMAS), a paraneoplastic disease characterized by cerebellar and brainstem-directed autoimmunity but typically with outstanding cancer-related outcomes. We compared...
Authors: Zalman Vaksman
Modeling with longitudinal electronic health record (EHR) data proves challenging given the high dimensionality, redundancy, and noise captured in EHR. In order to improve precision medicine strategies and identify predictors of disease risk in advance, evaluating meaningful patient disease trajectories...
Authors: Marta Byrska-Bishop
CAG repeat expansions in exon 1 of the AR gene on the X chromosome cause spinal and bulbar muscular atrophy, a male-specific progressive neuromuscular disorder associated with a variety of extra-neurological symptoms. The disease has a reported male prevalence of...
Authors: Giuseppe Narzisi
Several studies have identified rare and common genetic variants associated with severe COVID-19, but no study has reported genetic determinants as predisposition factors for neurological complications. In this report, we identified rare/unique structural variants (SVs) implicated in neurological functions in...
Authors: Michael Zody
Lancet is a somatic variant caller (SNVs and indels) for short read data. Lancet uses a localized micro-assembly strategy to detect somatic mutation with high sensitivity and accuracy on a tumor/normal pair. Lancet is based on the colored de Bruijn...
Contributors: Michael Zody Nicolas Robine Giuseppe Narzisi Andre Corvelo Rajeeva Musunuri
nygc-short-alignment-marking is a tool to mark short alignments in a bam file. It parses the bam and marks as unmapped a read with alignment length below a user-defined threshold. Reads are not filtered from the bam file but kept as...
Contributors: Andre Corvelo
Conpair is a fast and robust method dedicated for human tumor-normal studies to perform concordance verification (i.e. samples coming from the same individual), as well as cross-individual contamination level estimation in whole-genome and whole-exome sequencing experiments. Importantly, our method of...
Contributors: Michael Zody
taxMaps is an ultra-efficient, customizable and fully scalable taxonomic classification tool for short-read data designed to deal with large DNA/RNA metagenomics samples. Its performance and comprehensiveness makes it highly suitable for unbiased contamination detection in large-scale sequencing operations, microbiome studies...
Contributors: Michael Zody Nicolas Robine Andre Corvelo Wayne Clarke
SCANVIS is a set of tools for SCoring, ANnotating and VISualizing splice junctions using gencode annotation. It scores splice junctions by using a Relative Read Support (RRS) measure that relates the reads supporting a query junction to reads supporting nearby annotated splice junctions....
Contributors: Nicolas Robine Heather Geiger
NYGC's cancer pipeline identifies somatic and germline variants from whole genome sequencing (WGS), whole exome sequencing (WES) or targeted panel tumor and normal data. The pipeline can be run on sequencing data from human, mouse and patient-derived xenograft (PDX) models. Additionally,...
Contributors: Nicolas Robine Tim Chu Jennifer Shelton
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