Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Limited DNA Sequencing Based on Tube and Droplet
Whole genome amplification (WGA) is crucial for whole genome sequencing to investigate complex genomic alteration at the single-cell or even single-molecule level. Multiple displacement amplification (MDA) and multiple annealing and looping based amplification cycles (MALBAC) are two most widely app...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-06-01
|
| Series: | Micromachines |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2072-666X/11/7/645 |
| _version_ | 1827713966497857536 |
|---|---|
| author | Xiaoxiang Zhou Ying Xu Libo Zhu Zhen Su Xiaoming Han Zhen Zhang Yan Huang Quanjun Liu |
| author_facet | Xiaoxiang Zhou Ying Xu Libo Zhu Zhen Su Xiaoming Han Zhen Zhang Yan Huang Quanjun Liu |
| author_sort | Xiaoxiang Zhou |
| collection | DOAJ |
| description | Whole genome amplification (WGA) is crucial for whole genome sequencing to investigate complex genomic alteration at the single-cell or even single-molecule level. Multiple displacement amplification (MDA) and multiple annealing and looping based amplification cycles (MALBAC) are two most widely applied WGA methods, which have different advantages and disadvantages, dependent on research objectives. Herein, we compared the MDA and MALBAC to provide more information on their performance in droplets and tubes. We observed that the droplet method could dramatically reduce the amplification bias and retain the high accuracy of replication than the conventional tube method. Furthermore, the droplet method exhibited higher efficiency and sensitivity for both homozygous and heterozygous single nucleotide variants (SNVs) at the low sequencing depth. In addition, we also found that MALBAC offered a greater uniformity and reproducibility and MDA showed a better efficiency of genomic coverage and SNV detection. Our results provided insights that will allow future decision making. |
| first_indexed | 2024-03-10T18:48:14Z |
| format | Article |
| id | doaj.art-3a9555fdcbdf4020a0e6cbafe9bef79c |
| institution | Directory Open Access Journal |
| issn | 2072-666X |
| language | English |
| last_indexed | 2024-03-10T18:48:14Z |
| publishDate | 2020-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Micromachines |
| spelling | doaj.art-3a9555fdcbdf4020a0e6cbafe9bef79c2023-11-20T05:20:30ZengMDPI AGMicromachines2072-666X2020-06-0111764510.3390/mi11070645Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Limited DNA Sequencing Based on Tube and DropletXiaoxiang Zhou0Ying Xu1Libo Zhu2Zhen Su3Xiaoming Han4Zhen Zhang5Yan Huang6Quanjun Liu7State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, ChinaState Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, ChinaState Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, ChinaState Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, ChinaState Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, ChinaState Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, ChinaState Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, ChinaState Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, ChinaWhole genome amplification (WGA) is crucial for whole genome sequencing to investigate complex genomic alteration at the single-cell or even single-molecule level. Multiple displacement amplification (MDA) and multiple annealing and looping based amplification cycles (MALBAC) are two most widely applied WGA methods, which have different advantages and disadvantages, dependent on research objectives. Herein, we compared the MDA and MALBAC to provide more information on their performance in droplets and tubes. We observed that the droplet method could dramatically reduce the amplification bias and retain the high accuracy of replication than the conventional tube method. Furthermore, the droplet method exhibited higher efficiency and sensitivity for both homozygous and heterozygous single nucleotide variants (SNVs) at the low sequencing depth. In addition, we also found that MALBAC offered a greater uniformity and reproducibility and MDA showed a better efficiency of genomic coverage and SNV detection. Our results provided insights that will allow future decision making.https://www.mdpi.com/2072-666X/11/7/645whole genome amplificationdropletsmultiple displacement amplificationmultiple annealing and looping based amplification cycles |
| spellingShingle | Xiaoxiang Zhou Ying Xu Libo Zhu Zhen Su Xiaoming Han Zhen Zhang Yan Huang Quanjun Liu Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Limited DNA Sequencing Based on Tube and Droplet Micromachines whole genome amplification droplets multiple displacement amplification multiple annealing and looping based amplification cycles |
| title | Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Limited DNA Sequencing Based on Tube and Droplet |
| title_full | Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Limited DNA Sequencing Based on Tube and Droplet |
| title_fullStr | Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Limited DNA Sequencing Based on Tube and Droplet |
| title_full_unstemmed | Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Limited DNA Sequencing Based on Tube and Droplet |
| title_short | Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Limited DNA Sequencing Based on Tube and Droplet |
| title_sort | comparison of multiple displacement amplification mda and multiple annealing and looping based amplification cycles malbac in limited dna sequencing based on tube and droplet |
| topic | whole genome amplification droplets multiple displacement amplification multiple annealing and looping based amplification cycles |
| url | https://www.mdpi.com/2072-666X/11/7/645 |
| work_keys_str_mv | AT xiaoxiangzhou comparisonofmultipledisplacementamplificationmdaandmultipleannealingandloopingbasedamplificationcyclesmalbacinlimiteddnasequencingbasedontubeanddroplet AT yingxu comparisonofmultipledisplacementamplificationmdaandmultipleannealingandloopingbasedamplificationcyclesmalbacinlimiteddnasequencingbasedontubeanddroplet AT libozhu comparisonofmultipledisplacementamplificationmdaandmultipleannealingandloopingbasedamplificationcyclesmalbacinlimiteddnasequencingbasedontubeanddroplet AT zhensu comparisonofmultipledisplacementamplificationmdaandmultipleannealingandloopingbasedamplificationcyclesmalbacinlimiteddnasequencingbasedontubeanddroplet AT xiaominghan comparisonofmultipledisplacementamplificationmdaandmultipleannealingandloopingbasedamplificationcyclesmalbacinlimiteddnasequencingbasedontubeanddroplet AT zhenzhang comparisonofmultipledisplacementamplificationmdaandmultipleannealingandloopingbasedamplificationcyclesmalbacinlimiteddnasequencingbasedontubeanddroplet AT yanhuang comparisonofmultipledisplacementamplificationmdaandmultipleannealingandloopingbasedamplificationcyclesmalbacinlimiteddnasequencingbasedontubeanddroplet AT quanjunliu comparisonofmultipledisplacementamplificationmdaandmultipleannealingandloopingbasedamplificationcyclesmalbacinlimiteddnasequencingbasedontubeanddroplet |