Clinical and Research Genomics (Spring 2016)


Professor: Christopher E. Mason, Ph.D.

Teaching Assistants: Priyanka Vijay, Ebrahim Afshinnekoo

Office: 1305 York Ave., Y13-04

Email: chm2042 [at] med . cornell .edu

Lectures: Thursdays 12:30 - 2:00 PM

Location: 1305 York Ave., 13th Fl Conference Room

Office Hours: By appointment

Other: Please see below


The rapid advancement of Next-Generation Sequencing (NGS) has opened a wealth of opportunities for research in many fields: cancer biology, epigenetics, tumor evolution, microbiome and infectious disease dynamics, neuro-degeneration, personalized medicine, and improved diagnosis and risk assessment for patients. Moreover, there are emerging, faster NGS technologies that promise comprehensive molecular portraits of disease and actionable clinical results for doctors within a single day. Scientists and physicians will be better equipped to design studies and help patients if they possess an intricate knowledge of these molecular-profiling methods, their biological context, and their applicability to specific cases and diseases. Finally, a rich understanding of the complexity of the human genome is essential for the proper annotation of characterization of any new mutations/modifications found, since large-scale efforts at tumor and normal genome sequencing have dramatically altered our view of the “normal” genome and epigenome.

Thus, in this course, students will build a strong foundation of knowledge of high-throughput and NGS technologies (both existing and emerging), learn the applications of these technologies for basic and clinical research, and finally learn the essential tools for the analysis, integration, and application of these data relative to other public databases and phenotype repositories. Students will learn, first-hand, how to analyze and integrate data from: whole genome sequencing, RNA-sequencing, epigenome data (RRBS/ATAC-seq), proteomics data (LC-MS), microbiome, metagenomic, and cancer data, and then compare them to public repositories.

We have a broad range of expertise being contributed from many leaders in the field, including:

Constantin Aliferis, M.D., Ph.D., New York University School of Medicine

Doron Betel, Ph.D., Weill Cornell Medicine

Joel Dudley, Ph.D., Mount Sinai School of Medicine

Olivier Elemento, Ph.D., Weill Cornell Medicine

Sheng Li, Ph.D., Weill Cornell Medicine

Steven Gross, Ph.D., Weill Cornell Medicine

Ekta Khurana, Ph.D., Weill Cornell Medicine

Ross Levine, M.D., Ph.D., Memorial Sloan-Kettering Cancer Center

Gholson Lyon, M.D., Ph.D., Cold Spring Harbor Laboratory

Christopher Mason, Ph.D., Weill Cornell Medicine

Ari Melnick, M.D., Weill Cornell Medicine

Andrea Sboner, Ph.D., Weill Cornell Medicine

Shijia Zhu, Ph.D., Mount Sinai School of Medicine

Marcin Imielinski, M.D., Ph.D., Weill Cornell Medicine

Deborah Estrin, Ph.D., Cornell Tech

Prerequisites: N/A

Textbook: N/A


[05.05.2016]  HW5 is posted.

[04.29.2016]  HW4 and slides from last class are posted.

[04.02.2016]  HW1 and slides and readings from class 1 are posted.

[03.31.2016]  Welcome to the Class!