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Here we combine CRISPR\/Cas9 gene editing with an innovative high-throughput genotyping pipeline utilizing KASP (<jats:bold>K<\/jats:bold>ompetitive <jats:bold>A<\/jats:bold>llele-<jats:bold>S<\/jats:bold>pecific <jats:bold>P<\/jats:bold>CR) genotyping technology to create scarless isogenic cell models of cancer variants in ~1 month. We successfully modeled two novel variants previously identified by our lab in the <jats:italic>PALB2<\/jats:italic> gene in HEK239 cells, resulting in isogenic cells representing all three genotypes for both variants. We also modeled a known functional risk SNP of colorectal cancer, rs6983267, in HCT-116 cells. Cells with extremely low levels of gene editing could still be identified and isolated using this approach. We also introduce a novel molecular assay, ChIPnQASO (<jats:bold>Ch<\/jats:bold>romatin <jats:bold>I<\/jats:bold>mmuno<jats:bold>p<\/jats:bold>recipitation a<jats:bold>n<\/jats:bold>d <jats:bold>Q<\/jats:bold>uantitative <jats:bold>A<\/jats:bold>llele-<jats:bold>S<\/jats:bold>pecific <jats:bold>O<\/jats:bold>ccupation), which uses the same technology to reveal allele-specific function of these variants at the DNA-protein interaction level. We demonstrated preferential binding of the transcription factor TCF7L2 to the rs6983267 risk allele over the non-risk. Our pipeline provides a platform for functional variant discovery and validation that is accessible and broadly applicable for the progression of efforts towards precision medicine.<\/jats:p>","DOI":"10.1038\/s41598-017-15407-4","type":"journal-article","created":{"date-parts":[[2017,11,2]],"date-time":"2017-11-02T19:32:29Z","timestamp":1509651149000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Methods for Scarless, Selection-Free Generation of Human Cells and Allele-Specific Functional Analysis of Disease-Associated SNPs and Variants of Uncertain Significance"],"prefix":"10.1038","volume":"7","author":[{"given":"Nicole B.","family":"Coggins","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacob","family":"Stultz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henriette","family":"O\u2019Geen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7129-2918","authenticated-orcid":false,"given":"Luis G.","family":"Carvajal-Carmona","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8962-3105","authenticated-orcid":false,"given":"David J.","family":"Segal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,11,8]]},"reference":[{"key":"15407_CR1","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1038\/ng.840","volume":"43","author":"ML Freedman","year":"2011","unstructured":"Freedman, M. 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The error has not been fixed in the paper.","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"15044"}}