{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T01:30:56Z","timestamp":1772155856423,"version":"3.50.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T00:00:00Z","timestamp":1548115200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1RM1HG009491"],"award-info":[{"award-number":["1RM1HG009491"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HG008135"],"award-info":[{"award-number":["HG008135"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["EY025090"],"award-info":[{"award-number":["EY025090"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["CA217642"],"award-info":[{"award-number":["CA217642"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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 \u2018synthetic haplotypes\u2019 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 \u2018assemblon\u2019 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.<\/jats:p>","DOI":"10.1093\/pcmedi\/pby019","type":"journal-article","created":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T02:05:17Z","timestamp":1548122717000},"page":"1-7","source":"Crossref","is-referenced-by-count":9,"title":["Big DNA as a tool to dissect an age-related macular degeneration-associated haplotype"],"prefix":"10.1093","volume":"2","author":[{"given":"Jon M","family":"Laurent","sequence":"first","affiliation":[{"name":"Institute for Systems Genetics"},{"name":"Department of Biochemistry and Molecular Pathology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Fu","sequence":"additional","affiliation":[{"name":"Shiley Eye Institute, UCSD School of Medicine"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sergei","family":"German","sequence":"additional","affiliation":[{"name":"Institute for Systems Genetics"},{"name":"Department of Biochemistry and Molecular Pathology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew T","family":"Maurano","sequence":"additional","affiliation":[{"name":"Institute for Systems Genetics"},{"name":"Department of Pathology, NYU Langone Health"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shiley Eye Institute, UCSD School of Medicine"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jef D","family":"Boeke","sequence":"additional","affiliation":[{"name":"Institute for Systems Genetics"},{"name":"Department of Biochemistry and Molecular Pathology"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,1,22]]},"reference":[{"key":"2022032115004812000_pby019C1","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1001\/archopht.122.4.564","article-title":"Prevalence of age-related macular degeneration in the United States","volume":"122","author":"Friedman","year":"2004","journal-title":"Arch Ophthalmol"},{"key":"2022032115004812000_pby019C2","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1016\/S0161-6420(92)31871-8","article-title":"Prevalence of age-related maculopathy. The Beaver Dam Eye Study","volume":"99","author":"Klein","year":"1992","journal-title":"Ophthalmology"},{"key":"2022032115004812000_pby019C3","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/S0161-6420(95)31034-2","article-title":"The prevalence of age-related maculopathy in the Rotterdam Study","volume":"102","author":"Vingerling","year":"1995","journal-title":"Ophthalmology"},{"key":"2022032115004812000_pby019C4","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/nrn2007","article-title":"Macular degeneration: recent advances and therapeutic opportunities","volume":"7","author":"Rattner","year":"2006","journal-title":"Nat Rev Neurosci"},{"key":"2022032115004812000_pby019C5","first-page":"142","article-title":"Early detection and treatment of neovascular age-related macular degeneration","volume":"15","author":"Bressler","year":"2002","journal-title":"J Am Board Fam Pract"},{"key":"2022032115004812000_pby019C6","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/j.ophtha.2004.10.047","article-title":"Risk factors for the incidence of Advanced Age-Related Macular Degeneration in the Age-Related Eye Disease Study (AREDS) AREDS report no. 19","volume":"112","author":"Clemons","year":"2005","journal-title":"Ophthalmology"},{"key":"2022032115004812000_pby019C7","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1056\/NEJMoa062655","article-title":"Ranibizumab versus verteporfin for neovascular age-related macular degeneration","volume":"355","author":"Brown","year":"2006","journal-title":"N Engl J Med"},{"key":"2022032115004812000_pby019C8","doi-asserted-by":"crossref","first-page":"1419","DOI":"10.1056\/NEJMoa054481","article-title":"Ranibizumab for neovascular age-related macular degeneration","volume":"355","author":"Rosenfeld","year":"2006","journal-title":"N Engl J Med"},{"key":"2022032115004812000_pby019C9","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1016\/S0161-6420(00)00580-7","article-title":"Risk factors for age-related macular degeneration: Pooled findings from three continents","volume":"108","author":"Smith","year":"2001","journal-title":"Ophthalmology"},{"key":"2022032115004812000_pby019C10","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1126\/science.1110189","article-title":"Complement factor H polymorphism and age-related macular degeneration","volume":"308","author":"Edwards","year":"2005","journal-title":"Science"},{"key":"2022032115004812000_pby019C11","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1126\/science.1110359","article-title":"Complement factor H variant increases the risk of age-related macular degeneration","volume":"308","author":"Haines","year":"2005","journal-title":"Science"},{"key":"2022032115004812000_pby019C12","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1038\/ejhg.2008.140","article-title":"Variation near complement factor I is associated with risk of advanced AMD","volume":"17","author":"Fagerness","year":"2009","journal-title":"Eur J Hum Genet"},{"key":"2022032115004812000_pby019C13","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1038\/ng1750","article-title":"Variation in factor B (BF) and complement component 2 (C2) genes is associated with age-related macular degeneration","volume":"38","author":"Gold","year":"2006","journal-title":"Nat Genet"},{"key":"2022032115004812000_pby019C14","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1038\/ng2131","article-title":"Variation in complement factor 3 is associated with risk of age-related macular degeneration","volume":"39","author":"Maller","year":"2007","journal-title":"Nat Genet"},{"key":"2022032115004812000_pby019C15","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1086\/422476","article-title":"Age-related maculopathy: a genomewide scan with continued evidence of susceptibility loci within the 1q31, 10q26, and 17q25 regions","volume":"75","author":"Weeks","year":"2004","journal-title":"Am J Hum Genet"},{"key":"2022032115004812000_pby019C16","doi-asserted-by":"crossref","first-page":"3227","DOI":"10.1093\/hmg\/ddi353","article-title":"Hypothetical LOC387715 is a second major susceptibility gene for age-related macular degeneration, contributing independently of complement factor H to disease risk","volume":"14","author":"Rivera","year":"2005","journal-title":"Hum Mol Genet"},{"key":"2022032115004812000_pby019C17","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1126\/science.1133811","article-title":"A variant of the HTRA1 gene increases susceptibility to age-related macular degeneration","volume":"314","author":"Yang","year":"2006","journal-title":"Science"},{"key":"2022032115004812000_pby019C18","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1126\/science.1133807","article-title":"HTRA1 promoter polymorphism in wet age-related macular degeneration","volume":"314","author":"Dewan","year":"2006","journal-title":"Science"},{"key":"2022032115004812000_pby019C19","doi-asserted-by":"crossref","first-page":"e1000836","DOI":"10.1371\/journal.pgen.1000836","article-title":"Genetic and functional dissection of HTRA1 and LOC387715 in age-related macular degeneration","volume":"6","author":"Yang","year":"2010","journal-title":"PLoS Genet"},{"key":"2022032115004812000_pby019C20","doi-asserted-by":"crossref","first-page":"16227","DOI":"10.1073\/pnas.0703933104","article-title":"A variant of mitochondrial protein LOC387715\/ARMS2, not HTRA1, is strongly associated with age-related macular degeneration","volume":"104","author":"Kanda","year":"2007","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022032115004812000_pby019C21","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1038\/ng.170","article-title":"Age-related macular degeneration is associated with an unstable ARMS2 (LOC387715) mRNA","volume":"40","author":"Fritsche","year":"2008","journal-title":"Nat Genet"},{"key":"2022032115004812000_pby019C22","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1038\/nature10403","article-title":"Synthetic chromosome arms function in yeast and generate phenotypic diversity by design","volume":"477","author":"Dymond","year":"2011","journal-title":"Nature"},{"key":"2022032115004812000_pby019C23","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1126\/science.1249252","article-title":"Total synthesis of a functional designer eukaryotic chromosome","volume":"344","author":"Annaluru","year":"2014","journal-title":"Science"},{"key":"2022032115004812000_pby019C24","doi-asserted-by":"crossref","first-page":"eaaf4831","DOI":"10.1126\/science.aaf4831","article-title":"Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond","volume":"355","author":"Mitchell","year":"2017","journal-title":"Science"},{"key":"2022032115004812000_pby019C25","doi-asserted-by":"crossref","first-page":"1040","DOI":"10.1126\/science.aaf4557","article-title":"Design of a synthetic yeast genome","volume":"355","author":"Richardson","year":"2017","journal-title":"Science"},{"key":"2022032115004812000_pby019C26","doi-asserted-by":"crossref","first-page":"eaaf4791","DOI":"10.1126\/science.aaf4791","article-title":"Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome","volume":"355","author":"Shen","year":"2017","journal-title":"Science"},{"key":"2022032115004812000_pby019C27","doi-asserted-by":"crossref","first-page":"eaaf4706","DOI":"10.1126\/science.aaf4706","article-title":"Bug mapping and fitness testing of chemically synthesized chromosome X","volume":"355","author":"Wu","year":"2017","journal-title":"Science"},{"key":"2022032115004812000_pby019C28","doi-asserted-by":"crossref","first-page":"eaaf4704","DOI":"10.1126\/science.aaf4704","article-title":"\u2018Perfect\u2019 designer chromosome V and behavior of a ring derivative","volume":"355","author":"Xie","year":"2017","journal-title":"Science"},{"key":"2022032115004812000_pby019C29","doi-asserted-by":"crossref","first-page":"eaaf3981","DOI":"10.1126\/science.aaf3981","article-title":"Engineering the ribosomal DNA in a megabase synthetic chromosome","volume":"355","author":"Zhang","year":"2017","journal-title":"Science"},{"key":"2022032115004812000_pby019C30","author":"Mitchell","year":"2018"},{"key":"2022032115004812000_pby019C31","doi-asserted-by":"crossref","first-page":"1387","DOI":"10.1093\/hmg\/ddr020","article-title":"Risk- and non-risk-associated variants at the 10q26 AMD locus influence ARMS2 mRNA expression but exclude pathogenic effects due to protein deficiency","volume":"20","author":"Friedrich","year":"2011","journal-title":"Hum Mol Genet"},{"key":"2022032115004812000_pby019C32","doi-asserted-by":"crossref","first-page":"14578","DOI":"10.1073\/pnas.1102853108","article-title":"Increased expression of multifunctional serine protease, HTRA1, in retinal pigment epithelium induces polypoidal choroidal vasculopathy in mice","volume":"108","author":"Jones","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022032115004812000_pby019C33","doi-asserted-by":"crossref","first-page":"D896","DOI":"10.1093\/nar\/gkw1133","article-title":"The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)","volume":"45","author":"MacArthur","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2022032115004812000_pby019C34","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1126\/science.1222794","article-title":"Systematic localization of common disease-associated variation in regulatory DNA","volume":"337","author":"Maurano","year":"2012","journal-title":"Science"},{"key":"2022032115004812000_pby019C35","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/j.cell.2006.11.044","article-title":"Manipulating the mouse genome to engineer precise functional syntenic replacements with human sequence","volume":"128","author":"Wallace","year":"2007","journal-title":"Cell"},{"key":"2022032115004812000_pby019C36","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1126\/science.1160930","article-title":"Species-specific transcription in mice carrying human chromosome 21","volume":"322","author":"Wilson","year":"2008","journal-title":"Science"}],"container-title":["Precision Clinical Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/pcm\/article-pdf\/2\/1\/1\/42965303\/pby019.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/pcm\/article-pdf\/2\/1\/1\/42965303\/pby019.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,21]],"date-time":"2022-03-21T11:05:40Z","timestamp":1647860740000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/pcm\/article\/2\/1\/1\/5298619"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1,22]]},"references-count":36,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/pcmedi\/pby019","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/461251","asserted-by":"object"}]},"ISSN":["2516-1571"],"issn-type":[{"value":"2516-1571","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,3]]},"published":{"date-parts":[[2019,1,22]]}}}