Research Sequencing

NYGC offers short-read whole genome sequencing(WGS) for a broad range of sample types, with specialized workflows available for challenging samples, including FFPE tissue, circulating cell-free DNA (cfDNA), and circulating tumor DNA (ctDNA). Standard data analysis workflows are included for a variety of applications, including germline variant analysis and somatic detection of single nucleotide variants, insertions, deletions, copy number variants, and structural variants. Our integrated sequencing and bioinformatics expertise supports researchers from sample preparation through high-quality genomic data delivery.

NYGC provides comprehensive bulk RNA sequencing services to support a wide range of transcriptomic research applications. Our bulk RNA sequencing offerings include poly(A)-selected mRNA sequencing, total RNA sequencing, and specialized workflows for FFPE-derived samples. Standard data analysis workflows are included for a variety of applications, including germline variant analysis, somatic variant detection, transcript abundance, alternative splicing, and differential expression. Our integrated sequencing and bioinformatics expertise supports researchers from sample preparation through high-quality genomic data delivery.

NYGC offers comprehensive long read sequencing services using the Oxford Nanopore Technologies PromethION 24 and PacBio Revio platforms. Our long-read capabilities support a wide range of research applications, including whole-genome sequencing, transcriptome profiling, and specialized sequencing workflows designed to address complex genomic and biological questions. Long-read whole genome sequencing provides improved resolution of complex genomic regions, enabling more comprehensive detection of structural variants, repeat expansions, haplotypes, and other genomic features that may be difficult to characterize using short-read approaches. Long-read RNA sequencing provides enhanced resolution of transcript structure, enabling detailed characterization of full-length isoforms, alternative splicing events, and complex RNA biology that may be challenging to resolve with short-read technologies. NYGC provides standard bioinformatics workflows for applications including structural variant detection, genome characterization, and methylation analysis. Our Project Management and Computational Biology teams work closely with researchers during project planning to recommend appropriate experimental designs, sequencing strategies, and analysis approaches to meet specific research objectives. 

High molecular weight (HMW) extraction workflows are standardly included.

NYGC supports sequencing of client-prepared libraries generated in your own laboratory. Pooled libraries can be submitted for sequencing across our available sequencing platforms, with data delivered in standard formats such as FASTQ or CRAM files, depending on the sequencing workflow and project requirements.

Our team works closely with researchers to review library specifications, submission requirements, and sequencing objectives prior to submission. This collaborative planning process helps ensure library compatibility, appropriate sequencing configuration, and successful generation of high-quality research data.

NYGC offers a broad range of single cell sequencing, single nuclei sequencing, and spatial transcriptomics technologies to support diverse research applications, including 10x Genomics Gene Expression, 10x Multiome, ASAP-seq, DOGMA-seq, 10x Visium, 10x Xenium, and additional emerging technologies.

These advanced assays require careful experimental planning to ensure the appropriate technology, sample preparation strategy, and sequencing approach are aligned with your research objectives. Our Technology Development team works closely with researchers to design workflows tailored to project goals and sample characteristics.

PerturbSeq is an advanced single-cell genomics technology that enables high-throughput investigation of gene function by combining CRISPR-based perturbations with single-cell RNA sequencing. By selectively altering gene activity and measuring the resulting cellular responses, Perturb-seq allows researchers to explore gene regulation, biological pathways, and cellular phenotypes at unprecedented scale.

NYGC specializes in VIPerturb-seq, an optimized approach that leverages the scalable 10x Genomics Flex Apex platform to enable genome-scale and genome-wide single-cell perturbation studies with increased throughput and cost efficiency. Our team works with researchers during project planning to design and execute Perturb-seq experiments tailored to their biological questions and study goals.

NYGC supports flexible data and analysis solutions, including processing of compatible external sequencing data through our established bioinformatics pipelines. Our team can work with researchers to evaluate data compatibility and determine the appropriate analysis approach for their project needs.

In addition to standard analysis workflows, NYGC’s bioinformatics experts may provide consulting services to address specific research questions, develop customized analytical strategies, and generate publication-ready visualizations and reports. For projects requiring deeper scientific collaboration, custom method development, or ongoing analytical partnerships, NYGC can establish collaborative engagements tailored to the goals of the research program.

NYGC may offer nucleic acid extraction services on a project-by-project basis, depending on laboratory capacity, sample requirements, and project timelines. When available, extraction services are used to support downstream sequencing and genomic applications across a variety of biological sample types.

Available extraction options may include DNA and RNA isolation from whole blood, peripheral blood mononuclear cells (PBMCs), bone marrow, plasma, fresh frozen tissue, OCT-embedded tissue, FFPE tissue, buccal swabs, saliva, and other cell types. 

For applications requiring long DNA molecules, high molecular weight (HMW) extraction workflows are standardly included.

NYGC offers DNA methylation profiling using the Illumina Infinium Human Methylation EPIC v2.0 array, enabling comprehensive analysis of genome-wide DNA methylation patterns for a wide range of research applications, including epigenomics studies, biomarker discovery, and disease research.

Additional Illumina array-based profiling options may also be available on a project-specific basis, depending on sample requirements, platform availability, and research objectives. Our team can work with you to identify the most appropriate approach for your study.

Turnaround Times: Estimated turnaround times are provided based on projects that meet standard sample submission requirements, expected submission volumes, and include standard service deliverables. Actual timelines may vary depending on sample quality, project scope, requested services, and other project-specific factors. Your NYGC Project Manager will work with you during project planning to provide a realistic timeline and communicate any updates throughout the project.