Leadership Message

We are delighted that Tom Maniatis, one of the original founders of the NYGC, has accepted the Board’s offer to become the NYGC’s full-time Scientific Director and CEO. Tom’s outstanding reputation as a pioneer scientist in breakthrough molecular research and innovation precedes him, and I am excited that he is joining our team to bring scientific vision to the Center. With the continued support of the Board, and in partnership with our founding academic and medical institutions, Tom and I are looking forward to continuing our work together to define the next phase of the NYGC’s strategy, and to realize the full potential of the NYGC through technology innovation, advances in personalized medicine and community-driven research.

As you will see in the highlights from our team’s achievements below, we continue to make important strides in innovation, scientific discovery and collaborative genomic research. We appreciate your continued support and look forward to sharing more with you.

 
Cheryl A. Moore
President and Chief Operating Officer

 

In the News

NYGC Awarded Chan Zuckerberg Initiative Grant to Develop CITE-seq for the Human Cell Atlas Project

Rahul Satija, PhD, and Peter Smibert, PhD, are principal investigators on the project focused on the benchmarking and optimization of CITE-seq for the Human Cell Atlas project, the international collaborative effort to create a comprehensive reference map of all human cells as a resource for studies of health and disease. CITE-seq is a powerful new technology developed by the NYGC Technology Innovation Lab, in a team led by Marlon Stoeckius, PhD, Senior Research Scientist, in close collaboration with the Satija Lab.  READ MORE

Neville Sanjana, PhD, Granted NIH “New Innovator” Award For Genome Editing

The award will support the Sanjana Lab’s work in deciphering the logic of gene regulation through the development of new tools for targeted, precise modifications to the genome. READ MORE

 

 

Bioinformatics

Designing Analytical Tools for NYCKidSeq, "Natural Product" Discovery and More

The Bioinformatics team is involved in an array of ongoing activities and collaborative projects tapping into its expertise in assessing and presenting complex genomics data.

Toby Bloom, PhD, is leading the Bioinformatics team developing a web-based tool that will give physicians easy-to-understand access to the genomic data that will be within the electronic medical records of children who participate in NYCKidSeq, a major new study being led by the Icahn School of Medicine at Mount Sinai, in partnership with the Albert Einstein College of Medicine, the Children’s Hospital at Montefiore and the NYGC.

In August, Mount Sinai was awarded $13 million from the National Institutes of Health for this four-year research project, which will offer genome sequencing to 1,100 underserved children from the Bronx and Harlem suspected of having a genetic disease and evaluate whether genome sequencing leads to better health outcomes and how it impacts patients, families, medical professionals and health systems. Special areas of focus for the study include three areas of childhood disease: inherited neurologic disorders, primary immunodeficiencies and cardiovascular disorders.

Dr. Bloom’s team will work closely with Dr. John Greally, a clinical geneticist at Montefiore and professor of genetics, medicine and pediatrics at Einstein, to develop the new tool, which will be an intuitive, interactive, web-based interface that will give users the ability to drill down into the sequencing data and explore sections of the genome for research and clinical purposes.

Funding for NYCKidSeq is part of Phase II of a federally funded program called CSER2 (Clinical Sequencing Evidence-Generating Research) — a national multisite research program that evaluates the integration of genome sequencing into clinical care. For more information on NYCKidSeq, visit the recently launched NYCKidseq website and follow the project on Twitter at @NYCKidSeq.

On August 15, Senior Bioinformatics Scientist Phaedra Agius, PhD (pictured at left), presented a prototype of CRYNCLET, a computational tool to rank gene clusters for their potential to form natural products, at The Rockefeller University to the NIH and other researchers involved in the project.

Dr. Agius is co-principal investigator on the project with Dr. Sean Brady at Rockefeller, who leads the Bacteria Working Group within the Genomes to Natural Products Network (GNPN) consortium, a group of cross-disciplinary research teams selected by the NIH and its National Institute of General Medical Sciences to support discovery and development of natural products (NPs). NPs are chemical compounds produced by living organisms that have proven to be effective pharmaceutical agents, with roughly 75 percent of antibacterial and anticancer drugs either NPs or inspired by NPs. Genome sequencing has revealed an enormous diversity of gene clusters in fungi, plant and bacteria, and the advent of synthetic biology now makes it possible to engineer these clusters to develop NP organisms in laboratories.

To develop the tool, Dr. Agius and NYGC Bioinformatics Analyst Amrita Kar, PhD, have been charting NP building blocks and using that knowledge to tailor algorithms for predicting new NP candidates. They have observed co-evolutionary trends amongst building block genes, suggesting that NP genes evolve in concert across species. Once completed, CRYNCLET will serve as an interactive visual and relational database that will scan all gene clusters in fully annotated bacterial genomes, score their co-evolutionary trends and assign them an inherent ranking by order of their NP likelihood. The development of CRYNCLET, being funded as part of a five-year NIH/GNPN grant awarded to Rockefeller, is expected to be completed next year.

Other recent studies with NYGC Bioinformatics contributors include:

  • The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain, published by Nature Genetics in July. A Mount Sinai-led study of DNA folding & neurological disorders, the paper includes Senior Bioinformatics Scientist Will Liao, PhD, as co-author.
  • ATRX is a regulator of therapy induced senescence in human cells, a paper published by Nature Communications in August. Led by researchers at Memorial Sloan Kettering Cancer Center, this study demonstrates that the chromatin remodeling enzyme ATRX is a critical regulator of therapy-induced senescence, or using cytostatic chemotherapy to arrest tumor cells. NYGC’s Will Liao, PhD, Senior Bioinformatics Scientist; Nicolas Robine, PhD, Assistant Director, Computational Biology, and Heather Geiger, Senior Bioinformatics Analyst, are co-authors.
  • An NF-kB Transcription-Factor-Dependent Lineage Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function, a paper published by Cell Press’s Immunity in September. One of two related studies led by Columbia University Medical Center researchers, this paper explores how the type of T cell known as regulatory T cells, or Tregs, may suppress the immune system’s attack on cancer. NYGC’s Will Liao, PhD, Senior Bioinformatics Scientist, and Dillon Maloney, Bioinformatics Analyst, are co-authors.
  • Detection of long repeat expansions from PCR-free whole-genome sequence data, published by Genome Research in September. The study provides the latest testing results in the development of ExpansionHunter, a tool for estimating genotype repeats in whole genome sequencing (WGS). Researchers applied their algorithm to WGS data from 3,001 ALS patients who have been tested for the presence of the C9orf72 repeat expansion. The study, a collaboration with Illumina’s Population and Medical Genomics group, includes NYGC’s Giuseppe Narzisi, PhD, Senior Bioinformatics Scientist; Catherine Reeves, Scientific Collaboration Manager; and Lara Winterkorn, Associate Scientific Project Manager, as co-authors.

 

Clinical Lab

NYGC Clinical Lab Licensed to Perform Clinical Testing Throughout the U.S.

Vaidehi Jobanputra, PhD, FACMG (third from right, middle row in photo at top) leads a lab team whose responsibilities including physician relations, sequencing, bioinformatics and quality assurance.

As of this past summer, the NYGC’s Clinical Laboratory, led by Vaidehi Jobanputra, PhD, FACMG, Director, Molecular Diagnostics, has successfully completed its state-by-state application processes and is now licensed to perform clinical testing in all 50 states as well as the federal district of D.C. The lab can now conduct its New York State-approved Constitutional Whole Genome (WGS) and Whole Exome (WES) assays, Targeted Variant (Sanger) testing, KRAS testing and Reference Sequencing services to any patient throughout the U.S. when ordered by their physicians.

The lab is currently awaiting approval from New York State for its Oncology Whole Genome and Transcriptome Sequencing (WGTS) test. During this waiting period, physicians and patients can request a waiver from the State to order this test from the lab, with waivers granted on a case-by-case basis.

Once the lab’s Oncology WGTS test is formally approved by NYS, the lab will be able to complete its application for accreditation by the College of American Pathologists (CAP). CAP, one of the world’s leading organizations in clinical laboratory quality assurance, is affiliated with the American Medical Association and authorized by the Centers for Medicare and Medicaid Services to accredit laboratories. The lab is already certified by the Clinical Laboratory Evaluation Program (CLEP), New York State’s quality assurance accreditation program, and the Clinical Laboratory Improvement Amendments (CLIA), which regulate laboratory testing and require clinical laboratories to be certificated by their state as well as the Center for Medicare and Medicaid Services (CMS) before they can accept human samples for diagnostic testing.

The lab is also working on the Dominant Inherited ALS Network project, in conjunction with the NYGC’s Center for Genomics of Neurodegenerative Disease, Massachusetts General Hospital and Washington University School of Medicine. For this project, the lab will perform its WGS testing for asymptomatic first-degree adult relatives of people with familial ALS, which runs in families. The other type of ALS that doesn’t run in families, sporadic ALS, is much more common. Familial ALS is very rare; only about 10 percent of all ALS cases are familial.

Technology Innovation Lab

CITE-seq and miniDrops Attract Scientific Community Interest, NIH Grant

It has been a productive and exciting few months for the Technology Innovation Lab.

In May, Single-Cell RNA-Seq Of Rheumatoid Arthritis Synovial Tissue Using Low Cost Microfluidic Instrumentation, one of the lab’s ongoing research collaborations with the Satija Lab – this one in conjunction with the Hospital for Special Surgery (HSS) – was posted on bioRxiv. This work used miniDrops, a portable, low-cost droplet microfluidic control instrument developed by Will Stephenson, PhD, a Senior Research Engineer in the Technology Innovation Lab, to profile the cellular response to rheumatoid arthritis. The portability of the device enabled the researchers to perform cell isolation and library prep on a HHS patient within hours of surgery.

The proof-of-concept study of genomics tool CITE-seq, Simultaneous epitope and transcriptome measurement in single cells, originally posted on bioRxiv this past spring, has now been formally reviewed, with an expanded study published online in Nature Methods in July. The paper also appears in the September issue of the magazine, together with a profile piece on Marlon Stoeckius, PhD, Senior Research Scientist in the Technology Innovation Lab and the study’s lead author. CITE-seq has garnered significant attention, with numerous protocol requests and interest from companies, with Dr. Stoeckius and Technology Innovation Manager Peter Smibert, PhD, presenting the tool at Regeneron, the Broad Institute and an upstate New York Illumina user group meeting. Dr. Stoeckius also conducted a webinar on CITE-seq as part of a webinar series jointly run by GenomeWeb and the Association of Biomolecular Resource Facilities (ABRF) on September 26. The CITE-seq publication also generated wide media coverage, including an article in GenomeWeb. Access the NYGC press release and media coverage highlights on CITE-seq study here.

Also this past summer, the Technology Innovation Lab was awarded a National Institutes of Health grant worth $380,000 over three years to improve the CITE-seq method and refine and make open-source the miniDrops device, with a goal of increasing access to these droplet-based single-cell RNA sequencing approaches.

Faculty Updates

Neville Sanjana, PhD, Collaborates with NCI on Innovative CRISPR-Focused Cancer Immunotherapy Research

It is, quite literally, “knockout” research: On August 7, Nature published Identification of essential genes for cancer immunotherapy, a study from the New York Genome Center, New York University and the National Cancer Institute (NCI) that uncovered dozens of new genes that create T cell-resistant cancer through the use of large-scale gene editing.

NYGC Core Faculty Member Neville Sanjana, PhD, co-first author of the study, worked with NCI investigators to develop and deploy an innovative version of the gene-editing technique CRISPR, specifically a “two-cell type” CRISPR screen that examined how genetic mutations in one cell can affect the interaction between two different cell types.

The 2CT CRISPR screen consisted of human T cells, often referred to as “the executioners” because of the key role they play in attacking cancer, as effectors and human melanoma tumor cells as targets. The melanoma cells were modified by CRISPR and then tested for resistance by applying T cells. The researchers “knocked out” – one by one – each of the approximately 19,000 genes in the tumor cell’s genome, and then tested whether tumor cells with specific gene knock-outs were now resistant to the T cells. This was done in a pooled manner, enabling a single investigator to simultaneously visualize more than 123,000 distinct cuts or edits to the tumor’s genome. This approach led them to discover which genes – when knocked out in cancer cells – create T cell-resistant cancer cells.

Researchers were able to identify which loss-of-function mutations in melanoma reduced the effectiveness of the T cells and led to immunotherapy-resistant tumors. Many new genes never suspected to be involved in preventing the immune system from killing cancer cells were uncovered.

The team correlated the genes uncovered by the 2CT CRISPR screen with a large dataset from The Cancer Genome Atlas (TCGA), containing more than 11,000 tumors from 36 cancer types. Analysis of the TCGA data suggested that across cancer types there is a core set of genes important for effective immune response to cancer and this same core set was found in the 2CT CRISPR screen.

Of particular interest was a gene called APLNR. While it has been implicated as contributing to some cancers, this was the first evidence that it played a role in disarming T cells.

As Dr. Sanjana noted to an Oncology Network reporter, the “take-home message” of the study is that “each tumor can carry unique mutations that can drastically change how a patient responds to immunotherapy. If we can figure out which mutations are present in the patient’s tumor, it will soon be possible to predict how well or how poorly that patient will respond to immunotherapies and whether we should treat with other drugs in combination with immunotherapies.”

The study received significant media attention, with coverage including consumer media outlets such as United Press International and an interview on nationally syndicated NBC News Radio. See the NYGC press release and media coverage highlights on this study here.

In its September print issue, Nature Methods published GUIDES: sgRNA design for loss-of-function screens, co-authored by Dr. Sanjana. The correspondence details GUIDES (Graphical User Interface for DNA Editing Screens), a web application that designs CRISPR knockout libraries to target custom subsets of genes in the human or mouse genome. The application is available at http://guides.sanjanalab.org/ and https://github.com/sanjanalab/GUIDES.

Lappalainen Lab Explores Role of Genetic Variants in Human Immune System

Lab postdoc Sarah Kim-Hellmuth, PhD, (left) was lead author of the study; Tuuli Lappalainen, PhD (right), was co-senior author.

A study conducted by the Lappalainen Lab, working in collaboration with an international team of researchers, reveals the intricate interplay of genetics and environment in disease risk.

The team’s findings, published in the article Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations in Nature Communications in August, offer novel insights into the genetic contribution to varying immune responses among individuals and its consequences on immune-mediated diseases.

The lab and partners performed what is known as eQTL analysis, which aims to find an association between genotypes of genetic variants and gene expression levels in a population sample. Expression quantitative trait loci, or eQTLs, are regions of the genome containing DNA sequence variants that influence the expression level of one or more genes.

The researchers collected blood from 134 volunteers and treated monocytes – a type of white blood cells – in the laboratory with three components that mimic infection with bacteria or a virus. They then analyzed how cells from different individuals respond to infection by measuring gene expression both during the early and late immune response. Integrating the gene expression profiles with genome-wide genetic data of each individual, they were able to map how genetic variants affect gene expression, and how this genetic effect changes with immune stimulus.

Genetic variants whose effects on gene regulation was different depending on the different infectious state of the cells included four associations to diseases such as cholesterol level and celiac disease. Furthermore, the researchers discovered a trend of genetic risk for autoimmune diseases such as lupus and celiac disease to be enriched for gene regulatory effects modified by the immune state. “This supports a paradigm where genetic disease risk is sometimes driven not by genetic variants causing constant cellular dysregulation, but by causing a failure to respond properly to environmental conditions such as infection,” noted Lappalainen Lab postdoc and Marie Curie Fellow Sarah Kim-Hellmuth, PhD, lead author of the study.

NYGC Core Faculty Member Tuuli Lappalainen, PhD, the study’s co-senior author, hopes the team’s eQTL methodology sparks further explorations. “We are still in early stages of understanding the interplay of genetics and environment, but our results indicate that this is a key component of human biology and disease,” she said. “The molecular approach that we took in our study can be a particularly powerful way for researchers to delve deeper into this question.”

See the NYGC press release and highlights of media coverage on the study here.

Modified penetrance of coding variants by cis-regulatory variation shapes human traits, a new preprint from the lab with postdoctoral researcher Stephane Castel, PhD, as first author, was published on bioRxiv in September. The preprint shares findings from the lab’s NIH-funded research exploring the phenomenon known as variable penetrance, where the severity of the effect of disease-causing variants differs among individuals who carry them. In this study, the lab conducted analyses of large-scale data sets from the Genotype-Tissue Expression (GTEx) project and The Cancer Genome Atlas (TCGA) as well as deployed CRISPR-Cas9 gene editing to demonstrate how genetic variants that regulate gene expression of nearby genes modify the penetrance of coding variants in their target gene.

Imielinski Lab Contributes to Pancancer Analysis of Whole Genomes Initiative

“Implications for early cancer intervention?” That question was posed on Twitter upon the release of The evolutionary history of 2,658 cancers, with NYGC Core Faculty Member Marcin Imielinski, MD, PhD, among its nearly 50 authors.

This preprint, posted on bioRxiv, offers early findings from the Pancancer Analysis of Whole Genomes (PCAWG) study, an international collaboration to identify common patterns of mutation in the large cohort of cancer whole genomes from the International Cancer Genome Consortium.

Dr. Imielinski is a member of PCAWG’s Evolution and Heterogeneity Working Group, with his lab significantly involved in the initiative. The relationship is a natural fit given a key goal of the Imielinski Lab is to understand how complex somatic DNA rearrangements shape the tumor epigenome and drive cancer progression.

As the preprint paper outlines, deep sequencing of bulk tumor samples makes it possible to examine the evolutionary history of individual tumors, based on the catalogue of somatic mutations accumulated. Using the PCAWG dataset, the researchers reconstructed the evolutionary history of tumor samples from 2,658 donors spanning 39 cancer types, then created “typical timelines” of tumor evolution.

The findings provide a new roadmap of insights for researchers and clinicians. As the authors noted, study results “suggest that driver mutations often precede diagnosis by many years, and in some cases decades. Taken together, this data reveals common and divergent trajectories of cancer evolution, pivotal for understanding tumor biology and guiding early cancer detection.”

The preprint was the start of a large number of publications expected to come from PCAWG, with Imielinski Lab contributions, in the fall and then throughout the next two years.

First Wave of Satija Lab Projects Come to Fruition

NYGC Core Faculty Member Rahul Satija, PhD (pictured at podium above) presented a study of Seurat 2.0 at BioC 2017, an annual conference hosted by Bioconductor, a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.

In the summer of 2017, the Satija Lab released collaborative manuscripts reporting the discovery of a new subset of human dendritic cells (Villani*, Satija* et al, Science), the identification of the transcription factor Daschund as an essential factor for second heart field development (Wang*, Niu*, et al., bioRxiv), and the multimodal characterization of immune cell subsets using CITE-seq (Stoeckius et al., Nature Methods), with the Technology Innovation Lab.

Andrew Butler, a second-year PhD student in the lab, led the development of a new computational method to integrate single cell RNA-seq datasets, when they are produced across different conditions, technologies, or species (Butler and Satija, bioRxiv). Mr. Butler demonstrated how methods traditionally used to ‘align’ high-dimensional imaging datasets could be applied to sequencing data as well, and jointly led the open-source release of this method as part of the Seurat 2.0 package with Bioinformatics Analyst Paul Hoffman. These methods open exciting future directions for the lab, and have the potential to help us understand how distinct cell states respond to perturbation, disease and evolution.

Highlighting the summer was a discovery jointly led by postdocs Christian Mayer, PhD, and Christoph Hafemeister, PhD, and MD/PhD student Rachel Bandler (Mayer*, Hafemeister*, Bandler*, bioRxiv). The team, representing a wonderful collaboration with Gord Fishell’s lab, sequenced more than 60,000 mouse single cells across a time course of mouse interneuron development, starting from the embryo and ending with the adult cortex. Integrating these datasets, they discovered that progenitors in the embryo fell into four “cardinal classes,” expressing distinct genes that could predict their future fates. One of these genes, Mef2c, has been implicated in autism and other neuropsychiatric disorders, and the team demonstrated that it plays an essential role in the developments of parvalbumin interneurons.

NYGC's Center for Genomics of Neurodegenerative Disease Continues to Expand ALS Partnerships 

This past summer, The ALS Association announced what it termed an “extraordinary collaboration” – bringing together researchers at Project MinE USA, Answer ALS and the ALS Consortium at the Center for Genomics of Neurodegenerative Disease (CGND) at the NYGC. Led by Hemali Phatnani, PhD, Director, the group will work toward their shared mission for new treatments and effective therapies for ALS. All of these global collaborative projects are supported by The ALS Association through The ALS Ice Bucket Challenge donations and are sharing genome sequencing information and research expertise to move efforts forward more rapidly and efficiently.

Through the new collaboration announced by The ALS Association, Answer ALS is now partnering with Project MinE USA and the CGND’s ALS Consortium to share its well-characterized cohort of whole genomic sequencing data to further Project MinE USA’s international efforts in genetics. In return, Project MinE USA will contribute results from its global genetic studies to further Answer ALS’s objectives, in addition to lending its technical expertise in analyzing sequence data. All of this engagement adds to the sequencing expertise being provided by the NYGC, which is performing the whole genome sequencing analysis of Answer ALS participants.

The CGND’s ALS Consortium, a global collaboration between clinicians, scientists, geneticists and computational biologists, establishes a framework to apply state-of-the-art clinical and functional genomics together with bioinformatics to the study of ALS disease mechanisms. In partnership with the Genomic Translation for ALS Care (GTAC) Consortium, the Consortium is in the process of sequencing and analyzing the genomes of 3,200 clinically well-annotated ALS samples. Nine member institutions – Brigham and Women’s Hospital; Cold Spring Harbor Laboratory; Icahn School of Medicine at Mount Sinai; National Institutes of Health’s National Institute of Neurological Disorders and Stroke; Stony Brook University; Temple University; University of Edinburgh; Washington University, St. Louis; and the Weizmann Institute of Science – have recently joined the Consortium. The ALS Consortium now consists of 27 member organizations: Academic Medical Center, Amsterdam; Brigham and Women’s Hospital; Cedars-Sinai Medical Center; Cold Spring Harbor Laboratory; Columbia University; Gladstone Institute; Henry Ford Health System; Icahn School of Medicine at Mount Sinai; The Jackson Lab; Johns Hopkins University; Massachusetts General Hospital; Massachusetts Institute of Technology; the National Institutes of Health’s National Institute of Neurological Disorders and Stroke; New York Genome Center; The Pennsylvania State University; Queen Mary University of London; Stony Brook University; Temple University; University of California at Irvine; University of California at San Francisco; University College London; University of Edinburgh; University of Maryland, Baltimore; University of Pennsylvania; University of Thessaly, Washington University in St. Louis; and the Weizmann Institute of Science.

Dan Landau, MD, PhD, Discusses Potential of Liquid Biopsy Technologies at Scientific Workshop, NYGC General Public Event

“Algorithmically-driven quantitative combination cancer therapy will be applicable across cancer with emerging liquid biopsy technology.”

This predictive statement on the broad implications of liquid biopsies was offered by NYGC Core Faculty Dan Landau, MD, PhD, during his talk “On the Origins of CLL Evolution” at the Workshop on Mathematical Methods in Cancer Evolution and Heterogeneity held at The Simons Center for Systems Biology at the Institute for Advanced Study in Princeton, NJ this past June.

The presentation showcased Dr. Landau’s innovative research studying the dynamics of cancer at the cellular level, specifically the body’s monoclonal cells that are produced from a single ancestral cell by repeated cellular replication. The lab team develops computational and experimental tools to study cancer evolution, using both patient-derived samples and experimental models. The overall goal is to apply this knowledge to designing the next generation of precision medicine tools to overcome cancer evolution, which is a central challenge in the treatment of cancer. To view a video of the Workshop presentation, click here.

Cancer geneticists’ work in this “game of clones,” as Dr. Landau has dubbed his research, has led to the creation of liquid biopsy technologies that are allowing clinicians to trace and monitor the presence of cancer genes via blood samples. These liquid biopsies are transforming cancer care and represent an exciting new tool in precision medicine to supplement, or in some cases even replace, the traditional tumor tissue biopsy.

Dr. Landau also discussed the potential of liquid biopsies as a panelist at NYGC’s Evening Talks event “Breast Cancer & Genomics: BRCA & Beyond” in May. Watch a video of that event here.

In July, Columbia University’s Physical Sciences in Oncology Center, established in May by the National Cancer Institute, awarded a pilot grant to the Landau Lab in collaboration with Columbia University’s Rabadan Lab to study novel multi-omics single cell technology development.

Other lab activities include publication of Chromosomal Instability as a Driver of Tumor Heterogeneity and Evolution, a study that Dr. Landau co-authored with Weill Cornell Medicine colleague Samuel F. Bakhoum MD, PhD, which appeared in Cold Spring Harbor Perspectives in Medicine in June.

Publications & Preprints

NYGC faculty and staff continue to contribute to advancements in genomic science, publishing their findings in high-impact scientific journals. For an up-to-date listing of the NYGC publications and preprints by NYGC faculty and staff, visit the Publications section of the NYGC website.

Education & Outreach

Faculty-Led "Genomic Innovation" Course and Genomics Hackathon Launched at the NYGC

As part of our educational mission, the NYGC continues to host many scientific meetings, workshops, conferences and lectures. We’ve also recently launched two more exciting initiatives in this arena – a new graduate-level course taught by our faculty, the first ever to be held on NYGC premises, and an inaugural Genomics Hackathon collaboration with the National Center for Biotechnology Information (NCBI).

See below for more on all these events:

Faculty-Led “Genomic Innovation” Course Launches at the NYGC

“We are all part of something new and exciting – this should be fun!”

NYGC Scientific Director and Chief Executive Officer Tom Maniatis, PhD (at left in left photo) speaks to the students at the first session of the Genomic Innovation course launched by NYGC Core Faculty Members Neville Sanjana, PhD (at right in left photo; at bottom in right photo) and Tuuli Lappalainen, PhD (top in right photo).

That description by NYGC Core Faculty Member Neville Sanjana, PhD, set the upbeat tone at the September 7 launch of “Genomic Innovation,” a 14-week project-focused course developed with fellow Core Faculty Member Tuuli Lappalainen, PhD. Drs. Sanjana and Lappalainen are jointly leading the four-credit graduate-level course this fall semester, the first-ever graduate course to be hosted by the NYGC.

The course introduces students to cutting-edge technologies and applications in genetics and genomics and their responsible use in science and society. Over the course of the semester, the students form small teams to develop a new venture to address an unmet need in genomics. Each week, students will also learn about new topics in genomics and entrepreneurship from world-expert scientists, clinicians, nonprofit leaders, entrepreneurs and legal scholars. This year’s speakers include thought leaders from Novartis, Flagship Ventures, Pfizer Ventures, The ALS Association, Good Start Genetics, AbVitro, Gencove, Regeneron, ELab NYC, NY Law School, the NYGC, NYU, NYU Med, Columbia Med and Weill Cornell Medicine (WCM). See the 2017 speaker list here.

Graduate students from Cold Spring Harbor Laboratory, Columbia University, Albert Einstein College of Medicine, Mount Sinai, Memorial Sloan Kettering (MSK), NYU, The Rockefeller University, Stony Brook University and WCM can receive credit for the class through their registrar’s office and the course is officially listed in the course catalogs of Columbia, NYU, and Albert Einstein College of Medicine. This fall 2017 class includes students from NYU, Columbia, Einstein, WCM and MSK.

A key objective of the course is for students to “analyze an opportunity in genomics” (as the syllabus puts it) and work in teams to develop final projects which could be a research spinoff idea for a product or service or become the foundation of a startup company, a new nonprofit organization or a research project to pursue in an academic or corporate environment. As Dr. Lappalainen noted to students at the course launch, “This course will cover biological and technical details, but we encourage you to ask questions, bigger questions, about the recent revolutions in genomics, about the new frontiers of biological and technology understanding that are developing.”

L-r: NYGC President and Chief Operating Officer Cheryl Moore, NYGC Core Faculty Member Tulli Lappalainen, PhD, and NYGC Scientific Director and Chief Executive Officer Tom Maniatis, PhD

The first questions that students asked turned out to be to each other. Paired up to interview a classmate, students then shared that information back to the group. Through this process, the range of students taking this inaugural course was revealed: the group includes biology graduate students, those attaining MBA or medical degrees and those already working in some capacity in biotech or business, all interested in how their worlds intersect with genomics.

At the class launch, Tom Maniatis, PhD, NYGC Scientific Director and Chief Executive Officer, and Cheryl Moore, NYGC President and Chief Operating Officer, welcomed the students to show their support for NYGC faculty and their new course. “We’re excited by what our faculty has organized and hope it is a beginning of a long tradition at the New York Genome Center,” said Dr. Maniatis. “We are very pleased to have you here, there is a lot of enthusiasm for this program.” Ms. Moore promised the students that “there are outstanding guest speakers coming up, and you’re going to enjoy them and learn a lot. You are in great hands and are getting an incredible education you won’t get anywhere else.”

Inaugural Genomics Hackathon Yields Prototypes, Another Planned for Next Year

Over a three-day period in June, the NYGC hosted its first Genomics Hackathon in collaboration with the National Center for Biotechnology Information (NCBI). Researchers from New York City-area institutions and beyond gathered at the NYGC to take part in a “sprint-like” collaborative workshop whereby participants intensively worked together on computational projects related to genomics and clinical research.

Over a dozen teams assembled to brainstorm creation of bioinformatic software, tools for the study of proteins and cancer genomics, and pipelines to analyze large-scale genomic datasets. Data science-oriented projects to address biological questions in the field were also developed.

Over the course of the Hackathon, the majority of the teams crafted working prototypes of their ideas for the use of fellow researchers. Development highlights from the NYGC Hackathon included an interactive app for bioinformaticians to process, visualize and statistically explore protein correlation profiling data and a user-friendly tool to query genomes of the bacteria responsible for staph infection, with the latter software having the potential to impact clinical diagnosis. Other tools can be primarily used for research in the genomics community by other bioinformaticians, such as simulation software and packages to more efficiently sort data. All software from the Hackathon is hosted under an open-source license on GitHub. Manuscripts based on projects developed at the event are currently being prepared.

Most of the projects initiated at the NYGC Hackathon have been completed or are in the final stages. “Naturally, some projects do tend to take a bit longer than expected,” said Evan Biederstedt, a student in the Imielinski Lab at the NYGC and Weill Cornell Medicine, who assisted the NCBI in organizing the event. “These projects are often continued after the Hackathon, with participants contributing as time allows. More often than not, a useful tool for the field does emerge.”

Several NYGC researchers took part in the event, both coordinating projects and participating as team members. Biocurator Alice Fang, PhD, and Bioinformatics Analyst David Lin, who both focused on developing a pipeline to evaluate tumor tissue clonality, expressed positive feedback about the workshop. “This was my first Hackathon experience, and it was a most useful experience, especially as it encourages collaborations on future projects and allows us to become acquainted with how others in the field are tackling similar problems,” noted Dr. Fang. “I’m glad that I was able to work on a great team and learn from my team members.” “I thought it was a great opportunity to work with people coming from different backgrounds and expertise,” Mr. Lin agreed.

Indeed, a key goal of NCBI’s Hackathons is to provide a forum for investigators from different backgrounds to interact with each other, share their expertise with fellow participants and learn new skills. “I had the opportunity to meet the Hackathon participants while they were actively working on their projects,” said NYGC Senior Bioinformatics Scientist Giuseppe Narzisi, PhD. “I was impressed by the diversity of the backgrounds and skill sets of the people that joined this workshop. Projects were highly creative and visionary without lacking the practical component, which is necessary to serve the bioinformatic community. New York City has a large genomics community, and the NYGC is the perfect hub for tapping into this expertise and hosting this event again in the future.”

Another NYGC/NCBI Genomics Hackathon in 2018 is in the planning stages.

Ongoing Education & Outreach Events

There have also been several well-attended events at the NYGC in September to kick off the fall season:

Cancer Genomics Research Network Meetings

To advance collaborative efforts on cancer genomics, the NYGC hosts Cancer Genomics Research Network Meetings on the first Tuesday of every month to bring together leading cancer researchers, clinicians and postdocs from the NYGC’s Institutional Founding Members and other key academic institutions. The organizers include Drs. Harold Varmus (Weill Cornell Medicine and NYGC), Marcin Imielinski (Weill Cornell Medicine and NYGC), Ross Levine (Memorial Sloan Kettering Cancer Center) and Sohail Tavazoie (The Rockefeller University).

Speakers for the September 5th fall season kickoff meeting included:

  • Yibin Kang, PhD, Warner-Lambert/Parke-Davis Professor of Molecular Biology at Princeton University, presenting on “Mammary Gland Cell Fate Determinants as Regulators of Breast Cancer.”
  • Alex Kentsis, MD, PhD Cancer Biologist & Pediatric Oncologist at Memorial Sloan Kettering Cancer Center, presenting on “On the Causes of Childhood Cancer: Mechanisms and Therapy of Site-Specific Oncogenic Mutations by the Human DNA Transposase PGBD5.”
  • David Tuveson, MD, PhD, Professor & Director of the Cold Spring Harbor Laboratory Cancer Center at Cold Spring Harbor Laboratory, presenting on “Pancreatic Cancer Biology and Medicine.”

Speakers for the October 3 meeting included:

  • Ekta Khurana, PhD, Assistant Professor of Computational Genomics,  Meyer Cancer Center at Weill Cornell Medicine, presenting on “Integration of genetic and epigenetic alterations with tissue-specific network reveals novel regulatory drivers
    of prostate cancer.”
  • Laura Landweber, PhD, Professor, Biological Sciences, Columbia University, presenting on “RNA-programmed genome rearrangement in the ciliate Oxytricha.”
  • Ben Neel, MD, PhD, Director, Laura and Isaac Perlmutter Cancer Center & Professor, Department of Medicine, NYU Langone Health, presenting on “Pik3c3 is a haploinsufficient lung cancer tumor suppressor gene.”

Evening Talks

The NYGC’s Evening Talks events are intended to showcase and explain high science to the non-scientific community.

On September 13, the NYGC hosted an Evening Talks event entitled “High Tech, Low Cost: Next-Generation Genomic Testing,” featuring Joseph Pickrell, PhD, NYGC Core Faculty Member currently on leave to serve as CEO of Gencove, a NYGC spinout company; Sophie Zaaijer, PhD; former Erlich Lab team member at the NYGC and now CEO and Co-Founder of PlayDNA and Runway Fellow at Cornell Tech, and Christopher Mason, PhD, Associate Professor, Department of Physiology and Biophysics, Weill Cornell Medicine. These panelists engaged the audience on what a “spit kit” of saliva can reveal about a person’s ancestry and potential health conditions; how to get connected to mobile apps that let you “bring your own genome” and help advance genomic science; and how geneticists, working with NASA, are tracking twin astronauts to prepare us for long-term human space travel and how they now routinely sequence DNA in space. Evening Talks, a lecture series on advances in genomic science for the general public, is sponsored by the New York Community Trust–Pyewacket Fund.

Sequencing Informatics Workshop

On September 25-29, NYGC hosted its third Sequencing Informatics Workshop organized by Michael Zody, PhD, Senior Director, Computational Biology. Participants learn the basics of sequence data alignment, data analysis and identifying somatic variation in cancer samples; how to read and understand common file formats; and how to analyze RNA-seq data for expression and differential expression. This weeklong workshop is designed for colleagues at our Institutional Founding Members and others who are graduate students, postdocs, faculty and core and research lab staff with a background and interest in next-generation sequencing and computational training. The workshop received very positive feedback from the attendees and will be offered again in the spring of 2018.

Five Points Lecture Series

NYGC’s faculty members and scientists also continue to serve as moderators/hosts for the NYGC’s Five Points Lecture Series, which feature presentations from leading researchers from around the country. On September 26, Mike Zody, PhD, Senior Director, Computational Biology, hosted a presentation by Ben Voight, PhD, Associate Professor for Systems Pharmacology and Translational Therapeutics and of Genetics at the University of Pennsylvania, who discussed “Computational Approaches to Identify Meaningful Complex Disease Loci in the Human Genome.” On October 11, NYGC Core Faculty Member Tulli Lappalainen, PhD, and Nicolas Robine, Assistant Director, Computational Biology, NYGC hosted  Jeff Leek, PhD, Associate Professor of Biostatistics, Johns Hopkins Bloomberg School of Public Health, who discussed “Building a Comprehensive Resource for the Study of Human Gene Expression with Machine Learning and Data Science.”

Upcoming Events

Visit the Events section of the NYGC website.

Communications Update

For the latest NYGC news (press releases, media highlights) and info on upcoming events, visit the News and Events sections of the NYGC website.

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