DC Field | Value | Language |
---|---|---|
dc.contributor.author | Sohn, Jang-il | ko |
dc.contributor.author | Choi, Min-Hak | ko |
dc.contributor.author | Yi, Dohun | ko |
dc.contributor.author | Menon, Vipin A. A. | ko |
dc.contributor.author | Kim, Yeon Jeong | ko |
dc.contributor.author | Lee, Junehawk | ko |
dc.contributor.author | Park, Jung Woo | ko |
dc.contributor.author | Kyung, Sungkyu | ko |
dc.contributor.author | Shin, Seung-Ho | ko |
dc.contributor.author | Na, Byunggook | ko |
dc.contributor.author | Joung, Je-Gun | ko |
dc.contributor.author | Ju, Young Seok | ko |
dc.contributor.author | Yeom, Min Sun | ko |
dc.contributor.author | Koh, Youngil | ko |
dc.contributor.author | Yoon, Sung-Soo | ko |
dc.contributor.author | Baek, Daehyun | ko |
dc.contributor.author | Kim, Tae-Min | ko |
dc.contributor.author | Nam, Jin-Wu | ko |
dc.date.accessioned | 2023-07-30T00:00:28Z | - |
dc.date.available | 2023-07-30T00:00:28Z | - |
dc.date.created | 2023-01-16 | - |
dc.date.created | 2023-01-16 | - |
dc.date.issued | 2023-07 | - |
dc.identifier.citation | NATURE BIOMEDICAL ENGINEERING, v.7, no.7, pp.853 - 866 | - |
dc.identifier.issn | 2157-846X | - |
dc.identifier.uri | http://hdl.handle.net/10203/310952 | - |
dc.description.abstract | Variant callers typically produce massive numbers of false positives for structural variations, such as cancer-relevant copy-number alterations and fusion genes resulting from genome rearrangements. Here we describe an ultrafast and accurate detector of somatic structural variations that reduces read-mapping costs by filtering out reads matched to pan-genome k-mer sets. The detector, which we named ETCHING (for efficient detection of chromosomal rearrangements and fusion genes), reduces the number of false positives by leveraging machine-learning classifiers trained with six breakend-related features (clipped-read count, split-reads count, supporting paired-end read count, average mapping quality, depth difference and total length of clipped bases). When benchmarked against six callers on reference cell-free DNA, validated biomarkers of structural variants, matched tumour and normal whole genomes, and tumour-only targeted sequencing datasets, ETCHING was 11-fold faster than the second-fastest structural-variant caller at comparable performance and memory use. The speed and accuracy of ETCHING may aid large-scale genome projects and facilitate practical implementations in precision medicine. | - |
dc.language | English | - |
dc.publisher | NATURE PORTFOLIO | - |
dc.title | Ultrafast prediction of somatic structural variations by filtering out reads matched to pan-genome k-mer sets | - |
dc.type | Article | - |
dc.identifier.wosid | 000900853800002 | - |
dc.identifier.scopusid | 2-s2.0-85144184220 | - |
dc.type.rims | ART | - |
dc.citation.volume | 7 | - |
dc.citation.issue | 7 | - |
dc.citation.beginningpage | 853 | - |
dc.citation.endingpage | 866 | - |
dc.citation.publicationname | NATURE BIOMEDICAL ENGINEERING | - |
dc.identifier.doi | 10.1038/s41551-022-00980-5 | - |
dc.contributor.localauthor | Ju, Young Seok | - |
dc.contributor.nonIdAuthor | Sohn, Jang-il | - |
dc.contributor.nonIdAuthor | Choi, Min-Hak | - |
dc.contributor.nonIdAuthor | Yi, Dohun | - |
dc.contributor.nonIdAuthor | Menon, Vipin A. A. | - |
dc.contributor.nonIdAuthor | Kim, Yeon Jeong | - |
dc.contributor.nonIdAuthor | Lee, Junehawk | - |
dc.contributor.nonIdAuthor | Park, Jung Woo | - |
dc.contributor.nonIdAuthor | Kyung, Sungkyu | - |
dc.contributor.nonIdAuthor | Shin, Seung-Ho | - |
dc.contributor.nonIdAuthor | Na, Byunggook | - |
dc.contributor.nonIdAuthor | Joung, Je-Gun | - |
dc.contributor.nonIdAuthor | Yeom, Min Sun | - |
dc.contributor.nonIdAuthor | Koh, Youngil | - |
dc.contributor.nonIdAuthor | Yoon, Sung-Soo | - |
dc.contributor.nonIdAuthor | Baek, Daehyun | - |
dc.contributor.nonIdAuthor | Kim, Tae-Min | - |
dc.contributor.nonIdAuthor | Nam, Jin-Wu | - |
dc.description.isOpenAccess | N | - |
dc.type.journalArticle | Article | - |
dc.subject.keywordPlus | GENE FUSIONS | - |
dc.subject.keywordPlus | PAIRED-END | - |
dc.subject.keywordPlus | CANCER | - |
dc.subject.keywordPlus | ONCOGENE | - |
dc.subject.keywordPlus | TRANSLOCATIONS | - |
dc.subject.keywordPlus | IDENTIFICATION | - |
dc.subject.keywordPlus | REARRANGEMENTS | - |
dc.subject.keywordPlus | DISCOVERY | - |
dc.subject.keywordPlus | VARIANTS | - |
dc.subject.keywordPlus | IMPACT | - |
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