{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:53Z","timestamp":1772138033579,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,4,28]],"date-time":"2025-04-28T00:00:00Z","timestamp":1745798400000},"content-version":"vor","delay-in-days":123,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AI171984"],"award-info":[{"award-number":["R01 AI171984"]}],"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":["R03 CA290259"],"award-info":[{"award-number":["R03 CA290259"]}],"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":["R01 CA230551"],"award-info":[{"award-number":["R01 CA230551"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["F99 1F99CA294248"],"award-info":[{"award-number":["F99 1F99CA294248"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The National Cancer Institute Genomic Data Commons (GDC) provides controlled access to sequencing data from thousands of subjects, enabling large-scale study of impactful genetic alterations such as simple and complex germline and structural variants. However, efficient analysis requires significant computational resources and expertise, especially when calling variants from raw sequence reads. To solve these problems, we developed bamSliceR, a R\/bioconductor package that builds upon the GenomicDataCommons package to extract aligned sequence reads from cross-GDC meta-cohorts, followed by targeted analysis of variants and effects (including transcript-aware variant annotation from transcriptome-aligned GDC RNA data).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we demonstrate population-scale genomic and transcriptomic analyses with minimal compute burden using bamSliceR, identifying recurrent, clinically relevant sequence, and structural variants in the TARGET acute myeloid leukemia (AML) and BEAT-AML cohorts. We then validate results in the (non-GDC) Leucegene cohort, demonstrating how the bamSliceR pipeline can be seamlessly applied to replicate findings in non-GDC cohorts. These variants directly yield clinically impactful and biologically testable hypotheses for mechanistic investigation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>bamSliceR has been submitted to the Bioconductor project, where it is presently under review, and is available on GitHub at https:\/\/github.com\/trichelab\/bamSliceR<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioadv\/vbaf098","type":"journal-article","created":{"date-parts":[[2025,4,25]],"date-time":"2025-04-25T07:57:25Z","timestamp":1745567845000},"source":"Crossref","is-referenced-by-count":1,"title":["<i>bamSliceR<\/i>\n                    : a Bioconductor package for rapid, cross-cohort variant and allelic bias analysis"],"prefix":"10.1093","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-5689-0193","authenticated-orcid":false,"given":"Yizhou 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