Haplotype-resolved assembly of diploid and polyploid genomes using quantum computing
Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved..
Precision medicine's emphasis on individual genetic variants highlights the importance of haplotype-resolved assembly, a computational challenge in bioinformatics given its combinatorial nature. While classical algorithms have made strides in addressing this issue, the potential of quantum computing remains largely untapped. Here, we present the vehicle routing problem (VRP) assembler: an approach that transforms this task into a vehicle routing problem, an optimization formulation solvable on a quantum computer. We demonstrate its potential and feasibility through a proof of concept on short synthetic diploid and triploid genomes using a D-Wave quantum annealer. To tackle larger-scale assembly problems, we integrate the VRP assembler with Google's OR-Tools, achieving a haplotype-resolved local assembly across the human major histocompatibility complex (MHC) region. Our results show encouraging performance compared to Hifiasm with phasing accuracy approaching the theoretical limit, underscoring the promising future of quantum computing in bioinformatics.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
Zur Gesamtaufnahme - year:2024 |
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| Enthalten in: |
Cell reports methods - (2024) vom: 04. Apr., Seite 100754 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Chen, Yibo [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Revised 13.04.2024 published: Print-Electronic Citation Status Publisher |
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| doi: |
10.1016/j.crmeth.2024.100754 |
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| Förderinstitution / Projekttitel: |
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| 520 | |a Precision medicine's emphasis on individual genetic variants highlights the importance of haplotype-resolved assembly, a computational challenge in bioinformatics given its combinatorial nature. While classical algorithms have made strides in addressing this issue, the potential of quantum computing remains largely untapped. Here, we present the vehicle routing problem (VRP) assembler: an approach that transforms this task into a vehicle routing problem, an optimization formulation solvable on a quantum computer. We demonstrate its potential and feasibility through a proof of concept on short synthetic diploid and triploid genomes using a D-Wave quantum annealer. To tackle larger-scale assembly problems, we integrate the VRP assembler with Google's OR-Tools, achieving a haplotype-resolved local assembly across the human major histocompatibility complex (MHC) region. Our results show encouraging performance compared to Hifiasm with phasing accuracy approaching the theoretical limit, underscoring the promising future of quantum computing in bioinformatics | ||
| 650 | 4 | |a Journal Article | |
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| 650 | 4 | |a polyploid genome assembly | |
| 650 | 4 | |a quantum annealing | |
| 650 | 4 | |a quantum computing application | |
| 650 | 4 | |a quantum life sciences | |
| 650 | 4 | |a quantum optimization | |
| 650 | 4 | |a vehicle routing problem | |
| 700 | 1 | |a Huang, Jun-Han |e verfasserin |4 aut | |
| 700 | 1 | |a Sun, Yuhui |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Yong |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Yuxiang |e verfasserin |4 aut | |
| 700 | 1 | |a Xu, Xun |e verfasserin |4 aut | |
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