Covid 19 Host Genome Structural Variation Consortium

A Global Open Host Genome Structural Variation Consortium for the COVID-19 Response

The COVID-19 (SARS-CoV2) pandemic has been declared a global emergency by the WHO. This disease is affecting not only the elderly and high-risk individuals with pre-existing conditions, but also affecting young adults severely and causing mortality in both young and elderly patients. This variation in manifestation of the disease leads to the notion that the host genome’s immune response will play a role in SARS-CoV2 disease susceptibility or resistance.

Goals of the COVID-19 Host genome SV consortium:

This COVID-19 host genome structural variation consortium is formed to build a group of researchers studying the role of structural variation in contributing to the host genome’s immune and overall response to the infection. The efforts of this consortium will shed light on genomic research to search for informative structural variants including common polymorphisms, protective genome variation, and other genomic factors that contribute to SARS-CoV-2 infection, progression, or recovery. With the rise of the number of individuals being tested globally, researchers have access to groups of individuals with SARS-CoV-2-infection that express the clinical symptoms ranging from asymptomatic individuals, mild flu-like symptoms, or severe disease progression leading to death. Host genome structural variation using newer genomic technologies could lead to the identification of key genetic variation that could explain the variability in host response. This information on structural variants could help us to generate hypotheses for drug repurposing, identify individuals at unusually high or low risk, and contribute to global knowledge of the biology of SARS-CoV-2 infection, COVID-19 disease, and host response.

Objectives of the COVID-19 Host genome SV consortium:

  1. Create a global network of laboratories using novel long read molecule technologies for assessing structural variation in the host genome that could be contributing to COVID-19 susceptibility or progression.
  2. Create a global network of laboratories geared towards global data generation and data sharing of the host genome SV genomic data.
  3. Create a global forum to share host genome SV data generated from different genomic methods, different bioinformatics tools, and different methods of interpretation of host genome SV data.
  4. Create this consortium to develop global guidance on data and knowledge sharing of host genome SV data.

Consortium Members

  • Clemente Adebamowo, Professor - University of Maryland SOM - Baltimore, MD - Bio
  • Ali Andalibi, Dean - College of Science George Mason University - Fairfax, VA - Bio
  • Silviu-Alin Bacanu, Professor - Virginia Commonwealth University - Richmond, VA - Bio
  • Vineet Bafna, Professor - UC San Diego - San Diego, CA - Bio
  • Justin Bahl, Associate Professor - University of Georgia - Athens, GA - Bio
  • Hayk Barseghyan, Researcher - Children's National Medical Center - Washington, DC - Bio
  • Alan Beggs, Director, The Manton Center - Boston's Childrens Hospital - Boston, MA - Bio
  • Catherine Brownstein, Assistant Professor - Boston's Childrens Hospital - Boston, MA - Bio
  • Lauri Burdett, Senior Scientist - NCI/Leidos - Gaithersburg, MD - Bio
  • Manish Butte, Chief, Division of Allergy, Immunology, and Rheumatology - UC Los Angeles, Los Angeles, CA - Bio
  • Alka Chaubey, Head of Cyto/Lab Director - Augusta University/PerkinElmer - Augusta, GA - Bio
  • Stephen Chanock, Director, Division of Cancer Epidemiology - National Cancer Institute - Rockville, MD - Bio
  • Janet Chou, Assistant Professor of Pediatrics - Boston's Childrens Hospital - Boston, MA - Bio
  • Keith Crandall, Professor - George Washington University - Washington, D.C. - Bio
  • Megan Dennis, Assistant Professor - UC Davis - Davis, CA - Bio
  • Gang Fang, Associate Professor - Icahn School of Medicine - New York, NY - Bio
  • Olivier Fedrigo, Lab Director - Rockefeller University - New York, NY - Bio
  • Darrin "Ben" Finlay, Director of Tumor Analysis - Sanford Burnham Prebys - San Diego, CA - Bio
  • Carla Gamis, Grad Student - UP Diliman - Quezon City, NCR - Bio
  • Michael Goldman, Professor - San Francisco State - San Francisco, CA - Bio
  • Umamaheswaran Gurusami, Professor - UC San Francisco - San Francisco, CA - Bio
  • Glenn Hickey, Research Consultant - UCSC - Santa Cruz, CA - Bio
  • Alexander Ioannidis, Professor - Stanford - Palo Alto, CA - Bio
  • Erich Jarvis, Professor - Rockefeller University - New York, NY - Bio
  • Rashmi Kanagal-Shamanna, Associate Professor - MD Anderson - Houston, TX - Bio
  • Ravindra Kohle, Vice-Chair of Pathology/Section Chief of Molecular and Genetic Pathology - Augusta University - Augusta, GA - Bio
  • Naoru Koizumi, Director of Research - George Mason University - Fairfax, VA - Bio
  • Meriem Laamarti, Biotechnology - Medbiotech Laboratory - Rabat, Rabat - Bio
  • Celia LaBranche, Associate Professor - Duke University - Durham, NC - Bio
  • Sandra Liebel, Assistant Professor, Pediatrics - UC San Diego - San Diego, CA - Bio
  • Brynn Levy, Professor - Columbia University - New York, NY - Bio
  • Matthew Loose, Professor - University of Nottingham - Nottingham, UK - Bio
  • Claudio Mello, Professor - Oregon Health and Science University - Portland, OR - Bio
  • Jamal Nassir, Genetics Lecturer - University of Northampton, UK - Bio
  • Thuy Phung, Associate Professor - University of South Alabama - Mobile, AL - Bio
  • Nikhil, Sahajpal, Post-Doctoral Fellow, Augusta University, Augusta, GA
  • Maximilian Schieck, Dept Human Genetics - Hannover, Lower Saxony - Bio
  • Daniela Soto, Phd Student - UC Davis - Davis, CA - Bio
  • Adrienne Randolph, Professor of Anaesthesia - Boston's Childrens Hospital - Boston, MA - Bio
  • Siavash Reisi, Grad Student - UC San Diego - San Diego, CA
  • Amir Trabelsi, CEO at Genoox - Palo Alto, CA - Bio
  • Chetham Venkatasubba Rao, Section Head, Vascular Neurology and Neurocritical Care - Baylor St. Luke's Medical Center - Houston, TX - Bio
  • Tedd Ross, Professor - University of Georgia - Athens, GA - Bio
  • Sion Williams, Director, Onco-Genomics - University of Miami - Miami, FL - Bio
  • Victoria Wright, Professor - University of Nottingham - Nottingham, UK - Bio
  • Hua Zhao, Professor - Virginia Commonwealth University - Richmond, VA - Bio
  • Michael Zody, Scientific Director - New York Genome Center - New York, NY - Bio

Consortium Leadership

Dr. Ravindra Kolhe the Vice-Chair of Pathology and Section Chief of Molecular and Genetic Pathology at Augusta University, is the lead investigator of the COVID-19 Host Genome Structural Variation Consortium. He is also one of the co-investigators in the State of Georgia Public Health Department Ongoing Task Force for viral RNA testing and serology surveillance program for the public. Dr. Kolhe intends to build a global network of researchers who can contribute to our collective knowledge on host genome response to the SARS-CoV-2 infection and COVID-19 disease.

The Medical College of Georgia at Augusta University is an academic health center located in Augusta Georgia. It’s 478 bed multispeciality medical institute is a part of a health care network that offers primary, specialty, and sub-specialty care. Augusta is a medium-sized city with a large African American population (65%) that serves people in eastern Georgia and western South Carolina with a metropolitan population of ~750,000 people.

 


 

Alka Chaubey, Ph.D., FACMG is the Chief Medical Officer for Bionano Genomics. Additionally, she is a Scientific Director for the Georgia Esoteric & Molecular Lab at Augusta University. Dr. Chaubey is an ABMGG-board certified diplomat in clinical cytogenetics/genomics and clinical molecular genetics/genomics. She is also a fellow of the American College of Medical Genetics and Genomics (FACMG). Previously, Dr. Chaubey was the Director of the Cytogenomics Laboratory at Greenwood Genetic Center. She received her Doctorate degree (PhD) from Guru Nanak Dev University, Amritsar, India and completed her post-doctoral studies at Center for Cellular and Molecular Biology (CCMB), Hyderabad, India and University of Illinois at Chicago (UIC).