Massively parallel reporter assays and variant scoring identified functional variants and target genes for melanoma loci and highlighted cell-type specificity

Includes a Live Web Event on 02/08/2023 at 12:00 PM (EST)

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Erping Long will discuss their study using massively parallel reporter assays and variant scoring to identify functional variants from 78% of known melanoma GWAS loci, including those specific to cell of origin versus cancer contexts. Linking prioritized functional variants to eQTLs identified target genes as validated by CRISPRi.

 

Overview of Presentation

  • Massively parallel reporter assays identified 285 functional variants from 78% of the known melanoma risk loci. 
  • A scoring system integrated multi-layer functional datasets and prioritized a single variant for 43% of these loci. 
  • CRISPRi of top-scoring variants validated their cis-regulatory effect on the eQTL target genes, MAFF (22q13.1) and GPRC5A (12p13.1). 
  • Cell-type specificity were observed for variants in the context of malignant melanoma and normal melanocyte cells. 

Erping Long, MD, PhD

Postdoctoral Fellow at Laboratory of Translational Genomics

National Institutes of Health

Dr. Erping Long is the postdoctoral fellow in the Laboratory of Translational Genomics (LTG). Dr. Long completed his M.D., Ph.D.in Clinical Medicine (Ophthalmology) from Zhongshan Ophthalmic Center, Sun Yat-sen University, China in 2020. An independent part of his doctoral research was conducted at the University of Michigan, Ann Arbor, where he worked on how evolutionary force shapes the genetic risk of human senescence and disease. In LTG, Dr. Long conducts research that leverages computational approaches and large-scale functional genomics resources to understand genetic susceptibility to lung cancer and melanoma, under the mentorship of Dr. Choi, and Mitchell Machiela, Sc.D., M.P.H., Earl Stadtman Investigator, Integrative Tumor Epidemiology Branch. He was one of 10 recipients awarded the Ray Wu Prize in 2020, the highest honor for Chinese Ph.D. students in Life Science. 

Jiyeon Choi, PhD

Stadtman Investigator at Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute

National Institutes of Health

Dr. Jiyeon Choi is an Earl Stadtman Investigator at the Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, in National Cancer Institute (NCI). Dr. Choi received her B.S. from Ewha Womans University and her M.S. from Korea University in Seoul, Korea, and her Ph.D. in cell and developmental biology from Rutgers University in New Jersey. Dr. Choi joined NCI for her postdoctoral training and was promoted to an Investigator in 2019. Dr. Choi’s research focuses on understanding genetic susceptibility to lung cancer and melanoma. Dr. Choi has received numerous awards for her work, including the NCI Director’s Intramural Innovation Award, the DCEG Outstanding Research Paper by a Fellow, and the NCI Outstanding Mentor Award. Dr. Choi was selected for the NIH Distinguished Scholars Program in 2019.

Kylee Spencer, PhD (Moderator)

Assistant Editor

American Journal of Human Genetics

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February Journal Club
02/08/2023 at 12:00 PM (EST)  |  30 minutes
02/08/2023 at 12:00 PM (EST)  |  30 minutes February Journal Club - AJHG