diff --git a/tests/cassettes/test_hard_reconciles.yaml b/tests/cassettes/test_hard_reconciles.yaml new file mode 100644 index 00000000..2ec90f5f --- /dev/null +++ b/tests/cassettes/test_hard_reconciles.yaml @@ -0,0 +1,195 @@ +interactions: + - request: + body: null + headers: {} + method: GET + uri: https://api.crossref.org/works?mailto=example@papercrow.ai&query.title=High-throughput+screening+of+human+genetic+variants+by+pooled+prime+editing.&rows=1 + response: + body: + string: + '{"status":"ok","message-type":"work-list","message-version":"1.0.0","message":{"facets":{},"total-results":5224658,"items":[{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2024,4,5]],"date-time":"2024-04-05T00:42:23Z","timestamp":1712277743507},"posted":{"date-parts":[[2024,4,1]]},"group-title":"Genomics","reference-count":50,"publisher":"Cold + Spring Harbor Laboratory","content-domain":{"domain":[],"crossmark-restriction":false},"accepted":{"date-parts":[[2024,4,1]]},"abstract":"ABSTRACT<\/jats:title>Understanding + the effects of rare genetic variants remains challenging, both in coding and + non-coding regions. While multiplexed assays of variant effect (MAVEs) have + enabled scalable functional assessment of variants, established MAVEs are + limited by either exogenous expression of variants or constraints of genome + editing. Here, we introduce a pooled prime editing (PE) platform in haploid + human cells to scalably assay variants in their endogenous context. We first + optimized delivery of variants to HAP1 cells, defining optimal pegRNA designs + and establishing a co-selection strategy for improved efficiency. We characterize + our platform in the context of negative selection by testing over 7,500 pegRNAs + targetingSMARCB1<\/jats:italic>for editing activity and observing + depletion of highly active pegRNAs installing loss-of-function variants. We + next assess variants inMLH1<\/jats:italic>via 6-thioguanine selection, + assaying 65.3% of all possible SNVs in a 200-bp region spanning exon 10 and + distinguishing LoF variants with high accuracy. Lastly, we assay 362 non-codingMLH1<\/jats:italic>variants + across a 60 kb region in a single experiment, identifying pathogenic variants + acting via multiple mechanisms with high specificity. Our analyses detail + how filtering for highly active pegRNAs can facilitate both positive and negative + selection screens. Accordingly, our platform promises to enable highly scalable + functional assessment of human variants.<\/jats:p>","DOI":"10.1101\/2024.04.01.587366","type":"posted-content","created":{"date-parts":[[2024,4,2]],"date-time":"2024-04-02T02:05:17Z","timestamp":1712023517000},"source":"Crossref","is-referenced-by-count":0,"title":["High-throughput + screening of human genetic variants by pooled prime editing"],"prefix":"10.1101","author":[{"given":"Michael","family":"Herger","sequence":"first","affiliation":[]},{"given":"Christina + M.","family":"Kajba","sequence":"additional","affiliation":[]},{"given":"Megan","family":"Buckley","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Cunha","sequence":"additional","affiliation":[]},{"given":"Molly","family":"Strom","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-7767-8608","authenticated-orcid":false,"given":"Gregory + M.","family":"Findlay","sequence":"additional","affiliation":[]}],"member":"246","reference":[{"key":"2024040415500652000_2024.04.01.587366v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/gim.2015.30"},{"key":"2024040415500652000_2024.04.01.587366v1.2","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/j.cels.2017.11.003","article-title":"Quantitative + Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data","volume":"6","year":"2018","journal-title":"Cell + Syst"},{"key":"2024040415500652000_2024.04.01.587366v1.3","doi-asserted-by":"publisher","DOI":"10.1126\/science.abi8207"},{"key":"2024040415500652000_2024.04.01.587366v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELL.2018.12.015"},{"key":"2024040415500652000_2024.04.01.587366v1.5","doi-asserted-by":"crossref","first-page":"eabn8153","DOI":"10.1126\/science.abn8197","article-title":"The + landscape of tolerated genetic variation in humans and primates","volume":"380","year":"2023","journal-title":"Science"},{"key":"2024040415500652000_2024.04.01.587366v1.6","doi-asserted-by":"crossref","first-page":"eadg7492","DOI":"10.1126\/science.adg7492","article-title":"Accurate + proteome-wide missense variant effect prediction with AlphaMissense","volume":"381","year":"2023","journal-title":"Science"},{"key":"2024040415500652000_2024.04.01.587366v1.7","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1222"},{"key":"2024040415500652000_2024.04.01.587366v1.8","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1038\/s41436-021-01172-3","article-title":"ACMG + SF v3.0 list for reporting of secondary findings in clinical exome and genome + sequencing: a policy statement of the American College of Medical Genetics + and Genomics (ACMG)","volume":"23","year":"2021","journal-title":"Genet. 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