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Genomic
Technology

We develop and apply cutting edge: 1) molecular profiling technologies for comprehensive high resolution molecular measurements of disease, which enable improved computational predictions of novel therapies; 2) functional genomics technologies for testing predicted therapies in model systems recapitulating key aspects of disease.

Molecular Profiling
Functional Genomics

Sequencing Technologies

Single cell characterization of tumor heterogeneity helps identify rare cellular populations that are thought to drive metastasis.

The rapid pace of technological advancement in genome sequencing has created ample opportunity for novel discoveries across basic and translational sciences. To pioneer this data transformation, the Icahn Institute for Data Science and Genomic Technology has built a multifaceted technology toolbox with unprecedented access and application of novel methods and existing expertise in a multitude of genomics technologies.  These capabilities span bulk and single cell genomic sequencing methods, all of which are leveraged to generate complimentary cross-platform, orthogonally validated datasets to foster novel discovery and advance clinical applicability using model and primary sample cohorts. Technologies include novel molecular methods for extremely low input library preparation methods, targeting genes of interest in both DNA and RNA profiling applications, including non-amplificaiton based Cas9-based enrichment strategies; as well as a wide breadth of sequencing platforms, including the current and future state of the art for short read, high throughput, single molecule and nanopore sequencing methods. Complimentary purposing of these integrated technologies to critical open research questions creates the opportunity to accelerate discovery and characterization of previously unknown genetic structure, variation, and function across collaborative research at Sinai and well beyond.

Immune Profiling

The immune system is an incredibly complicated network of billions of highly specialized cells distributed throughout the body. In addition to its essential role in protecting us from viruses, bacteria, and other pathogens, it is becoming increasingly clear that the immune system is involved in almost all diseases, in either a causative, reactive, or correlative fashion. Profiling the immune system to identify immune biomarkers that correlate with or predict a clinical outcome has the potential to better define biological mechanisms underlying disease progression or treatment response. This in turn can help to predict treatment responses and stratify patient cohorts to tailored therapies and to better refine therapeutic strategies.

Given the tremendous complexity of the immune system, generating informative and meaningful immune profiling data requires powerful technology platforms. High dimensional single cell profiling technologies, such as mass cytometry and single cell sequencing, are valuable tools that help to elucidate the complex phenotypic and functional characteristics of heterogenous immune populations. Combing these powerful technology platforms with rigorous protocols to minimize and monitor experimental and technical variation and applying them to a wide range of well-defined patient cohorts can offer valuable insights into disease mechanisms in the context of many clinical conditions.

Featured Scientist: Adeeb Rahman

Peripheral blood samples were analyzed by CyTOF to identify immune populations responsive to IFNγ. (A) A comprehensive panel of antibodies against cell surface markers allows identification of all major immune subsets. (B) Antibodies against dynamic phosphorus-STAT epitopes allow functional characterization of single cell signaling responses across defined cell types in response to stimuli

Epigenomic Technology

Researchers at the Icahn Institute are working to develop cutting-edge genomic technologies that can enable more precise profiling and characterization of the epigenomes of pathogens and human and translate the advancement in basic science to actionable strategies for disease diagnosis and treatment. By combining expertise in epigenetics and third-generation sequencing technology, we have pioneered the field of bacterial epigenomes. We aim to fundamentally advance the understanding of bacterial DNA methylation: epigenetic heterogeneity of pathogenic bacteria and its regulatory roles in bacterial gene expression, virulence, and antibiotic resistance. Recently, we discovered that microbial DNA methylations can be exploited for high-resolution metagenomic analysis. Beyond bacteria, we study novel forms of DNA modification in eukaryotic genomes.

Featured Scientist: Gang Fang

Innovative technology for high-resolution metagenomic analysis based on long reads and microbial methylation

Human Microbiome Science

Human microbiome science explores how the microbial communities living in our body surfaces, including the skin, oral cavity, vagina, or gut, impact host health and disease.

Scientists in the Icahn Institute for Data Science and Genomic Technology study human microbiomes from birth through adulthood. We are developing novel algorithms to characterize microbial communities, from tracking individual strains transmitted from donors to patients in fecal microbiota transplantation to understanding temporal changes in the microbiome during early life. We have generated state-of-the-art methods to identify bacteria with high accuracy, to estimate their density, their viability, or to characterize the methylation patterns of whole communities. These methods are being applied to various human diseases in which the microbiome plays a critical role including inflammatory bowel disease, cancer, allergies, and even neurological disorders.

These computational and genomic tools to characterize the microbiome are coupled with our unique resources. The Icahn Institute for Data Science and Genomic Technology has a cutting-edge germ-free mouse facility where mice raised without any microbes can be colonized with specific strains or communities to understand their impact on host health. We also have one of the world’s most advanced high-throughput anaerobic culturing facilities to isolate bacterial strains from different humans, which can then be tested to identify their beneficial or deleterious properties. Our expertise in computational and genomic methods, together with the Institute’s facilities and Mount Sinai’s clinical expertise puts us in a unique position to unravel how the microbiome is associated with disease and to understand how we can manipulate it for therapeutic purposes.

Featured Scientist: Jeremiah Faith

Microbiome resources and discoveries in the Icahn School of Medicine at Mount Sinai include identification of the dietary combinations on intestinal inflammation, methods to measure the density of the microbiota, high throughput culturing facilities, and host/microbe imaging.

Equipment

The Technology Development Lab at the Icahn Institute for Data Science and Genomic Technology

We run a state of the art technology development lab that houses major equipment and infrastructure for application and development of advanced genomic technologies. Current equipment in the lab includes:

Major Next Generation Sequencing Equipment and Infrastructure:

  • Three IIlumina HiSeq 2500: Mainstay second-generation sequencer with capacity of ~200M single end read sequencing up to 100nt in length. Sequencing can be carried out either in single end or paired end format in convectional 8-lane flow cell as well as rapid run mode to sequence one human genome is ~30 hours
  • One Illumina NovaSeq – The highest throughout sequencer available from ILMN and most flexible for arranging modular sequencing pipelines for generating extremely large data sets
  • One Illumina NextSeq 550 – Similar to ILMN 2500 but with rapid data generation capability and extremely useful for single cell sequencing purposes
  • Two Illumina MiSeq: A primary instrument for targeted panel sequencing and sequencing of small genomes using Illumina chemistry
  • Three Pacific Biosystems RSII – Continuous long read single molecule sequencer with wide range of read lengths from 250 bp up to 80 kb. It is the first instrument of its kind that monitors in vitro biochemical synthesis of a double stranded DNA library
  • Three Pacific Biosciences Sequel systems – Continuous long read sequencing at ~7X the capacity of standard RSII systems
  • Three Ion S5XL instruments: Second generation high through put rapid run sequencers from Torrent, particularly suited for targeted diagnostic sequencing assays
  • Two PGMs: Low throughput rapid run sequencers from Life Technologies, particularly useful for low gene number or hotspot targeted sequencing purposes
  • Three Ion Chefs: Used for automation of library enrichment and sequencing chip preparation for the Torrent Proton and PGM systems
  • Two 10X Genomics Chromium system for constructed linked long reads using UMI and droplet technology toward structural variation discovery in WES and WGS data
  • One BioNano Genomics Irys system for generating 500kb+ genome maps for scaffolding in high quality platinum genome assemblies
  • One Illumina HiScan: Provides best possible gridding and scanning of new generation Illumina Bead Arrays used for Genome Wide Association Studies (GWAS), Pharmacogenomics, Methylation, gene expression, Goldengate, and custom genotyping analyses
  • One Illumina Bead Express System: For veracode genotyping assays
  • One Applied Biosystems 3730xl – 96 capillary dye-terminator sequencer for Sanger Sequencing
  • One Applied Biosystems 7900HT – Real-Time thermocycler with robotic loader for quantitative PCR and end-point allele discrimination
  • MinIon Oxford Nanopore Sequencing capability
  • Advanced Analytical FEMTO Pulse Automated Pulsed-Field CE instrument – Allows for the rapid automated detection, quantification and quality assessment of low concentration DNA and RNA samples (down to 5 fg/uL) and very large fragments (up to 200 kb)

Single Cell Equipment

  • One Fluidigm C1: For isolation of up to 96 single cells to then use for single cell sequencing purposes in combination with various molecular pipelines for the amplification of single cell RNA and DNA
  • One Berkeley Lights Beacon: For isolation of up to 1000 single cells (or batches of cells) for single cell or low input real-time cellular biology and isolation purposes in combination with various molecular pipelines for the amplification of selected single cells
  • Two 10X Genomics Chromium system for high throughput 3’ RNA Sequencing of thousands to tens of thousands of single cells for subclonal identification and expression analyses
  • One BioRad / Illumina ddSeq instrument for low to medium throughput single cell sequencing input
  • One Mission Bio Tapestri single cell targeted DNA sequencing platform
  • One CellSee single cell tissue / blood cellular retrieval and analysis platform (Q4 2019)

Sample Preparation and Storage Equipment

  • One Agilent Bravo – Automated robotic system for library creation for next generation sequencing
  • Two Tecan Evos – automated robotics systems for sample preparation for Illumina HiScan
  • One Covaris E210 – Focused Acoustic Disrupter/Sonicator for automated high yield preparation of multiple genomic/mRNA libraries
  • One Tape Station and three Agilent BioAnalyzer 2100s – microfluidics-based platform for sizing, quantification and quality control of DNA and RNA; crucial in preparation of libraries for sequencing
  • One Sage Blue Pippin Size-selection purification instrument for generating long fragment libraries for SMRT sequencing and genome finishing purposes
  • One Sage Blue Pippin HT size selection instrument that has ~3X the capacity of a Blue Pippin instrument
  • One Sage Pippin ELF, which allows for high throughput size selection of multiple bands within a single sample, as opposed to a single targeted band as utilized in the Blue Pippin series
  • One Beckman Biomek FX – Automated robotics system for accurate liquid handling tasks, including real time PCR set up in 384 wells as well as automated sequencing reaction cleanup and normalization of DNA amount for high throughput genotyping on microarray
  • 12+ Thermocyclers
  • Various sample storage formats at -80C, -20C, and 4C

Stem Cell Functional Models

We are each unique, comprised of distinct genetic, epigenetic and environmental risk factors that predispose us to some diseases and confer resilience to others. As expanding genetic studies increasingly demonstrate that both rare variants of large effect and common variants of small effect contribute to a variety of neuropsychiatric disorders, it becomes increasingly critical that we unravel how these risk factors interact within and between the diverse cell types populating the brain. While mouse models are uniquely suited for demonstrating how the aberrant function of single gene products contributes to aberrant circuit function and behavior, genetic studies of penetrance and complex gene interactions are nearly impossible to address using inbred mouse lines. Similarly, the lack of human post-mortem tissue, coupled with the inability to conduct functional validations on human cells, has to date left us with a very limited understanding of how rare and common variants impact gene expression or cellular function. By developing a human induced pluripotent stem cell (hiPSC)-based model for the study of predisposition to neuropsychiatric disease, we have established a new mechanism by which to systematically test the impact of causal variants in human cells. The future of psychiatry must be towards a model of precision medicine, whereby how the patient’s genetic variants, and the many interactions between them, impact disease course and treatment response is carefully considered before the prescription of any pills.

Featured Scientist: Kristen Brennand

The Icahn Institute integrates stem cell approaches and CRISPR-based genomic and epigenomic editing to functionally resolve how genetic variants, as well as the interactions between variants and cell types, impact cellular function and underlie risk to neuropsychiatric disease.

Single Cell Functional Genomics

(A) Our microfluidic system allows optical sorting of single cells or groups of cells into individual “pens” based on morphologic or fluorescence measurements. (B) Individual cells remain viable within the pen and can be grown to form organoid like structures amenable to functional testing or molecular profiling. (C) Fluorescence markers are used to label CA125 (green) and HE4 (red) and individual cells are sorted into pens based on these fluorescence markers.

Icahn Institute researchers have developed methods for the integration of sequencing information with multilayered real-time phenotypic characterization at the single cell level using novel high-throughput single cell fluidics systems to monitor morphologic, expression, and growth kinetics alongside our extensive genomics capabilities. Application of these approaches reveals a complex but recently inaccessible picture of cellular heterogeneity, which is illuminating across many different disease states and biologic systems, enabling a deeper understanding of not only tissue but the role of each cell within complex networks. We are also focusing on technologic advancements to facilitate rapid end-to-end phenotypic and genotypic characterization for better understanding perturbations in therapy, microenvironment, immune regulation, infection and fundamental developmental biology in resected primary cells alongside various model systems. Together with basic bulk and cellular biologic resources, these single cell capabilities will allow us to redefine the landscape of the functional genomics field toward better translational science and medicine.

CRISPR Single Cell Genomics

Annotating the genome and discovering new drug targets via ProCode-enhanced CRISPR Genomics

Researchers at the Icahn Institute have developed a novel technology to enhance functional genomic efforts. This new technology synergizes with CRISPR genome editing to enable genetic screens with high dimensional phenotyping at single cell resolution. The technology is comprised of linear epitopes which are arranged in a combinatorial manner to form a higher order set of protein barcodes (Pro-Codes). By pairing Pro-Codes with CRISPR/Cas9 technology, we are able to simultaneously analyze multiple phenotypic markers, including phospho-signaling, on dozens of knockouts with single cell resolution. This can be used to help determine the functions of 100s of genes in normal and disease processes, and even decipher gene cooperation. Our researchers are using the Pro-Codes to identify the genes used by tumor cells to evade the immune system with the goal of developing drugs to target these genes, and unleash the immune system against cancer.

CRISPR Screens

The figure illustrates an example of integrative studies to design a personalized therapy for a breast cancer patient. After clinical diagnosis, the tumor mass of the patient is analyzed in depth to catalog all the genetic and epigenetic alteration of malignant cells (Genomics). Then, functional genetic screens (gain and loss-of function, GOF/LOF) pinpoint which of the myriad of alterations that cancer cells accumulate is critical for the tumor (Genetics). Finally, computational studies integrate all this information to design a personalized therapeutic strategy, specially tailored for each patient.

We are in the post-genomic era. Great technological advances allow us to sequence the entire genome of a patient to catalog the genetic and epigenetic alterations associated with his/her disease. Additionally, novel computational approaches have been developed to integrate this massive amount of information. While these methods are critical for identifying molecular alterations and generating mechanistic hypotheses, they are association studies that lack the ability to prove causal links between individual alterations and a specific disease.

Fortunately, during the past years, the development of genetic tools (e.g. cDNA, RNAi and CRISPR libraries) to experimentally modify the expression of a gene at will have brought unlimited opportunities to investigate gene function. Icahn Institute scientists have developed, validated, and constructed libraries of genetic tools to study the function of every single gene in the genome. Furthermore, our research groups have pioneered the development of experimental and analytical approaches allowing for the investigation of gene function at a genome-wide level.

By combining these state-of-the-art genomics, computational, and genetics technologies, investigators at the Icahn Institute are developing an ambitious plan to catalog and functionally test all the alterations present in each patient. These studies will allow us to design personalized therapies for each individual patient with an unprecedented level of precision.