{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,22]],"date-time":"2025-08-22T05:16:35Z","timestamp":1755839795202,"version":"3.41.2"},"reference-count":28,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2024,12,27]],"date-time":"2024-12-27T00:00:00Z","timestamp":1735257600000},"content-version":"vor","delay-in-days":361,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"AWS Cloud Credit for Research program"},{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005385","name":"Israeli Council for Higher Education","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100005385","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001738","name":"Ministry of Science, Technology and Space","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001738","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Morris Kahn Foundation"},{"name":"AWS Cloud Credit for Research program"},{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005385","name":"Israeli Council for Higher Education","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100005385","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001738","name":"Ministry of Science, Technology and Space","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001738","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Morris Kahn Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Originally developed to meet the challenges of genomic data deluge, GeniePool emerged as a pioneering platform, enabling efficient storage, accessibility, and analysis of vast genomic datasets, enabled due to its data lake architecture. Building on this foundation, GeniePool 2.0 advances genomic analysis through the integration of cutting-edge variant databases, such as CHM13-T2T, AlphaMissense, and gnomAD V4, coupled with the capability for variant co-occurrence queries. This evolution offers an unprecedented level of granularity and scope in genomic analyses, from enhancing our understanding of variant pathogenicity and phenotypic associations to facilitating research collaborations. The introduction of CHM13-T2T provides a more accurate reference for human genetic variation, AlphaMissense enriches the platform with protein-level impact predictions of missense mutations, and gnomAD V4 offers a comprehensive view of human genetic diversity. Additionally, the innovative feature for variant co-occurrence analysis is pivotal for exploring the combined effects of genetic variations, advancing our comprehension of compound heterozygosity, epistasis, and polygenic risk factors in disease pathogenesis. GeniePool 2.0 is a comprehensive and scalable platform, which aims to enhance genomic data analysis and contribute to genomic research, potentially supporting new discoveries and clinical innovations.<\/jats:p>\n               <jats:p>Database URL: https:\/\/GeniePool.link<\/jats:p>","DOI":"10.1093\/database\/baae130","type":"journal-article","created":{"date-parts":[[2024,12,27]],"date-time":"2024-12-27T14:25:56Z","timestamp":1735309556000},"source":"Crossref","is-referenced-by-count":1,"title":["GeniePool 2.0: advancing variant analysis through CHM13-T2T, AlphaMissense, gnomAD V4 integration, and variant co-occurrence queries"],"prefix":"10.1093","volume":"2024","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4823-4757","authenticated-orcid":false,"given":"Grisha","family":"Weintraub","sequence":"first","affiliation":[{"name":"Department of Computer Science, Faculty of Natural Sciences , Ben Gurion University of the Negev, Beer Sheva 84105,","place":["Israel"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2483-2090","authenticated-orcid":false,"given":"Noam","family":"Hadar","sequence":"additional","affiliation":[{"name":"The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev , Beer Sheva 84105,","place":["Israel"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4805-0651","authenticated-orcid":false,"given":"Ehud","family":"Gudes","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Faculty of Natural Sciences , Ben Gurion University of the Negev, Beer Sheva 84105,","place":["Israel"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5418-6670","authenticated-orcid":false,"given":"Shlomi","family":"Dolev","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Faculty of Natural Sciences , Ben Gurion University of the Negev, Beer Sheva 84105,","place":["Israel"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1430-1296","authenticated-orcid":false,"given":"Ohad S","family":"Birk","sequence":"additional","affiliation":[{"name":"The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev , Beer Sheva 84105,","place":["Israel"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,12,27]]},"reference":[{"key":"2025030818071365500_R1","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baad043","article-title":"GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture","volume":"2023","author":"Hadar","year":"2023","journal-title":"Database"},{"key":"2025030818071365500_R2","doi-asserted-by":"crossref","DOI":"10.1145\/3579370.3594750","article-title":"Analyzing large-scale genomic data with cloud data lakes","author":"Weintraub","year":"2023"},{"article-title":"Needle in a haystack queries in cloud data lakes","year":"2021","author":"Weintraub","key":"2025030818071365500_R3"},{"key":"2025030818071365500_R4","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq1019","article-title":"The sequence read archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2025030818071365500_R5","doi-asserted-by":"publisher","first-page":"D57","DOI":"10.1093\/nar\/gkr1163","article-title":"BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata","volume":"40","author":"Barrett","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2025030818071365500_R6","first-page":"44","article-title":"The complete sequence of a human genome","volume":"376","author":"Nurk","year":"2022","journal-title":"Science(1979)"},{"key":"2025030818071365500_R7","article-title":"Accurate proteome-wide missense variant effect prediction with AlphaMissense","volume":"381","author":"Cheng","year":"2023","journal-title":"Science(1979)"},{"key":"2025030818071365500_R8","doi-asserted-by":"publisher","first-page":"434","DOI":"10.1038\/s41586-020-2308-7","article-title":"The mutational constraint spectrum quantified from variation in 141,456 humans","volume":"581","author":"Karczewski","year":"2020","journal-title":"Nature"},{"key":"2025030818071365500_R9","doi-asserted-by":"publisher","first-page":"796","DOI":"10.1101\/gr.278378.123","article-title":"A harmonized public resource of deeply sequenced diverse human genomes","volume":"2024","author":"Koenig","year":"2024","journal-title":"Genome Res."},{"key":"2025030818071365500_R10","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1038\/s41588-023-01608-3","article-title":"Inferring compound heterozygosity from large-scale exome sequencing data","volume":"56","author":"Guo","year":"2023","journal-title":"Nat Genet"},{"article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","year":"2013","author":"Li","key":"2025030818071365500_R11"},{"key":"2025030818071365500_R12","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res"},{"key":"2025030818071365500_R13","doi-asserted-by":"publisher","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"2025030818071365500_R14","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1038\/s41586-023-06045-0","article-title":"A genomic mutational constraint map using variation in 76,156 human genomes","volume":"625","author":"Chen","year":"2023","journal-title":"Nature"},{"key":"2025030818071365500_R15","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1016\/j.biochi.2019.07.019","article-title":"Matrix metalloproteinase-2: Not (just) a \u2018hero\u2019 of the past","volume":"166","author":"Henriet","year":"2019","journal-title":"Biochimie"},{"key":"2025030818071365500_R16","doi-asserted-by":"publisher","first-page":"879","DOI":"10.2353\/ajpath.2008.080128","article-title":"Thrombospondin-2 modulates extracellular matrix remodeling during physiological angiogenesis","volume":"173","author":"Krady","year":"2008","journal-title":"Am J Pathol"},{"key":"2025030818071365500_R17","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1083\/jcb.140.2.419","article-title":"Mice that lack thrombospondin 2 display connective tissue abnormalities that are associated with disordered collagen fibrillogenesis, an increased vascular density, and a bleeding diathesis","volume":"140","author":"Kyriakides","year":"1998","journal-title":"J Cell Biol"},{"key":"2025030818071365500_R18","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1038\/S41431-024-01559-1","article-title":"Heterozygous THBS2 pathogenic variant causes Ehlers-Danlos syndrome with prominent vascular features in humans and mice","volume":"32","author":"Hadar","year":"2024","journal-title":"Eur J Hum Genet"},{"key":"2025030818071365500_R19","doi-asserted-by":"publisher","first-page":"1101","DOI":"10.1038\/s41431-022-01278-5","article-title":"X-linked C1GALT1C1 mutation causes atypical hemolytic uremic syndrome","volume":"31","author":"Hadar","year":"2023","journal-title":"Eur J Hum Genet"},{"key":"2025030818071365500_R20","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2211087120","article-title":"Germline C1GALT1C1 mutation causes a multisystem chaperonopathy","volume":"120","author":"Erger","year":"2023","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025030818071365500_R21","doi-asserted-by":"publisher","first-page":"5049","DOI":"10.1158\/1078-0432.CCR-18-3571","article-title":"Inferring the evolution and progression of small-cell lung cancer by single-cell sequencing of circulating tumor cells","volume":"25","author":"Su","year":"2019","journal-title":"Clin Cancer Res"},{"key":"2025030818071365500_R22","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1016\/j.canlet.2006.08.010","article-title":"Biological significance of cancer-associated sialyl-Tn antigen: modulation of malignant phenotype in gastric carcinoma cells","volume":"249","author":"Pinho","year":"2007","journal-title":"Cancer Lett"},{"key":"2025030818071365500_R23","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3892\/ol.2022.13217","article-title":"Update on the role of C1GALT1 in cancer (Review)","volume":"23","author":"Xia","year":"2022","journal-title":"Oncol Lett"},{"key":"2025030818071365500_R24","doi-asserted-by":"publisher","DOI":"10.1177\/1176935117747259","article-title":"Longitudinal transcriptional response of glycosylation-related genes, regulators, and targets in cancer cell lines treated with 11 antitumor agents","volume":"16","author":"Krushkal","year":"2017","journal-title":"Cancer Inform"},{"key":"2025030818071365500_R25","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1007\/s00439-024-02671-4","article-title":"VARista: a free web platform for streamlined whole-genome variant analysis across T2T, hg38, and hg19","volume":"143","author":"Hadar","year":"2024","journal-title":"Hum Genet"},{"article-title":"GPT-4 Technical Report","year":"2023","author":"OpenAI","key":"2025030818071365500_R26"},{"key":"2025030818071365500_R27","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pdig.0000417","article-title":"Peer review of GPT-4 technical report and systems card","volume":"3","author":"Gallifant","year":"2024","journal-title":"PLOS Digital Health"},{"article-title":"Llama 2: open foundation and fine-tuned chat models","year":"2023","author":"Touvron","key":"2025030818071365500_R28"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baae130\/61286522\/baae130.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baae130\/61286522\/baae130.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,8]],"date-time":"2025-03-08T18:07:42Z","timestamp":1741457262000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baae130\/7933718"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024]]},"references-count":28,"URL":"https:\/\/doi.org\/10.1093\/database\/baae130","relation":{},"ISSN":["1758-0463"],"issn-type":[{"type":"electronic","value":"1758-0463"}],"subject":[],"published-other":{"date-parts":[[2024]]},"published":{"date-parts":[[2024]]},"article-number":"baae130"}}