Big DNA as a tool to dissect an age-related macular degeneration-associated haplotype

Jon M. Laurent, Xin Fu, Sergei German, Matthew T. Maurano, Kang Zhang, Jef Boeke

Research output: Contribution to journalArticlepeer-review

Abstract

Age-related Macular Degeneration (AMD) is a leading cause of blindness in the developed world, especially in aging populations, and is therefore an important target for new therapeutic development. Recently, there have been several studies demonstrating strong associations between AMD and sites of heritable genetic variation at multiple loci, including a highly significant association at 10q26. The 10q26 risk region contains two genes, HTRA1 and ARMS2, both of which have been separately implicated as causative for the disease, as well as dozens of sites of non-coding variation. To date, no studies have successfully pinpointed which of these variant sites are functional in AMD, nor definitively identified which genes in the region are targets of such regulatory variation. In order to efficiently decipher which sites are functional in AMD phenotypes, we describe a general framework for combinatorial assembly of large ‘synthetic haplotypes’ along with delivery to relevant disease cell types for downstream functional analysis. We demonstrate the successful and highly efficient assembly of a first-draft 119kb wild-type ‘assemblon’ covering the HTRA1/ARMS2 risk region. We further propose the parallelized assembly of a library of combinatorial variant synthetic haplotypes covering the region, delivery and analysis of which will identify functional sites and their effects, leading to an improved understanding of AMD development. We anticipate that the methodology proposed here is highly generalizable towards the difficult problem of identifying truly functional variants from those discovered via GWAS or other genetic association studies.
Original languageEnglish (US)
Number of pages7
JournalPrecision Clinical Medicine
Volume2
Issue number1
DOIs
StatePublished - 2019

Fingerprint

Dive into the research topics of 'Big DNA as a tool to dissect an age-related macular degeneration-associated haplotype'. Together they form a unique fingerprint.

Cite this