DeepOM: single-molecule optical genome mapping via deep learning.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 03 2023
01 03 2023
Historique:
received:
08
11
2022
revised:
22
02
2023
accepted:
13
03
2023
medline:
30
3
2023
pubmed:
18
3
2023
entrez:
17
3
2023
Statut:
ppublish
Résumé
Efficient tapping into genomic information from a single microscopic image of an intact DNA molecule is an outstanding challenge and its solution will open new frontiers in molecular diagnostics. Here, a new computational method for optical genome mapping utilizing deep learning is presented, termed DeepOM. Utilization of a convolutional neural network, trained on simulated images of labeled DNA molecules, improves the success rate in the alignment of DNA images to genomic references. The method is evaluated on acquired images of human DNA molecules stretched in nano-channels. The accuracy of the method is benchmarked against state-of-the-art commercial software Bionano Solve. The results show a significant advantage in alignment success rate for molecules shorter than 50 kb. DeepOM improves the yield, sensitivity, and throughput of optical genome mapping experiments in applications of human genomics and microbiology. The source code for the presented method is publicly available at https://github.com/yevgenin/DeepOM.
Identifiants
pubmed: 36929928
pii: 7079794
doi: 10.1093/bioinformatics/btad137
pmc: PMC10049785
pii:
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press.
Références
Genome Res. 2019 Apr;29(4):646-656
pubmed: 30846530
Science. 2022 Apr;376(6588):44-53
pubmed: 35357919
Bioinformatics. 2021 Jul 12;37(Suppl_1):i327-i333
pubmed: 34252972
ACS Infect Dis. 2020 May 8;6(5):1076-1084
pubmed: 32294378
ACS Nano. 2018 Jul 24;12(7):7148-7158
pubmed: 29924591
Nucleic Acids Res. 2022 Sep 9;50(16):e92
pubmed: 35657088
Nat Rev Methods Primers. 2021;1:
pubmed: 35663461
Nat Methods. 2021 Sep;18(9):1082-1090
pubmed: 34480155
Deep Learn Med Image Anal Multimodal Learn Clin Decis Support (2017). 2017;2017:240-248
pubmed: 34104926
J Comput Biol. 2006 Mar;13(2):442-62
pubmed: 16597251
Essays Biochem. 2021 Apr 16;65(1):51-66
pubmed: 33739394
Chem Commun (Camb). 2019 Sep 19;55(76):11414-11417
pubmed: 31482872
Nat Methods. 2020 Jul;17(7):734-740
pubmed: 32541853
Nucleic Acids Res. 2015 Oct 15;43(18):e117
pubmed: 26019180
Science. 2021 Apr 2;372(6537):
pubmed: 33632895
Curr Opin Biotechnol. 2013 Aug;24(4):690-8
pubmed: 23428595
Bioinformatics. 2018 Jan 1;34(1):134-136
pubmed: 29036307
Nucleic Acids Res. 2019 Jul 9;47(12):e68
pubmed: 30918971
Lab Chip. 2017 Feb 14;17(4):579-590
pubmed: 28098301
NAR Genom Bioinform. 2019 Oct 05;2(1):lqz007
pubmed: 33575560