Faculty Opinions recommendation of Single-molecule sequencing of an individual human genome.

2009 ◽  
Author(s):  
Charles Auffray
Keyword(s):  
Human Genome ◽  
Single Molecule ◽  
Single Molecule Sequencing ◽  
Individual Human

scholarly journals Single-molecule sequencing of an individual human genome

2009 ◽  
Vol 27 (9) ◽  
pp. 847-850 ◽  
Author(s):  
Dmitry Pushkarev ◽  
Norma F Neff ◽  
Stephen R Quake
Keyword(s):  
Human Genome ◽  
Single Molecule ◽  
Single Molecule Sequencing ◽  
Individual Human

2. How to read the book of life

2018 ◽  
pp. 12-27
Author(s):  
John Archibald
Keyword(s):  
Dna Sequencing ◽  
Human Genome ◽  
Single Molecule ◽  
Human Genome Project ◽  
Genome Project ◽  
Chain Termination ◽  
Single Molecule Sequencing ◽  
Semiconductor Sequencing ◽  
The Cost ◽  
The Human Genome Project

For all its biological importance, DNA is a fragile molecule so extracting it is a difficult process. ‘How to read the book of life’ explains the techniques required to sequence DNA. It begins by explaining the techniques developed for protein and RNA sequencing by Frederick Sanger, Robert Holley, and Carl Woese that were then developed further for DNA sequencing. Following the success of the Human Genome Project, the next generation of DNA sequencing was developed in the mid-2000s. Pyrosequencing was capable of generating orders of magnitude more data at a fraction of the cost, but was superceded within a decade by semiconductor sequencing, reversible chain-termination sequencing, and single-molecule sequencing.

scholarly journals Resolving the complexity of the human genome using single-molecule sequencing

Nature ◽  
2014 ◽  
Vol 517 (7536) ◽  
pp. 608-611 ◽  
Author(s):  
Mark J. P. Chaisson ◽  
John Huddleston ◽  
Megan Y. Dennis ◽  
Peter H. Sudmant ◽  
Maika Malig ◽  
...  
Keyword(s):  
Human Genome ◽  
Single Molecule ◽  
Single Molecule Sequencing

scholarly journals HySA: A Hybrid Structural variant Assembly approach using next generation and single-molecule sequencing technologies

2016 ◽  
Author(s):  
Xian Fan ◽  
Mark Chaisson ◽  
Luay Nakhleh ◽  
Ken Chen
Keyword(s):  
Human Genome ◽  
Single Molecule ◽  
Clustering Algorithm ◽  
Hydatidiform Mole ◽  
Cost Effective ◽  
Next Generation ◽  
Structural Variations ◽  
Single Molecule Sequencing ◽  
Structural Variant ◽  
Sequencing Technologies

AbstractAchieving complete, accurate and cost-effective assembly of human genome is of great importance for realizing the promises of precision medicine. The abundance of repeats and genetic variations in human genome and the limitations of existing sequencing technologies call for the development of novel assembly methods that could leverage the complementary strengths of multiple technologies.We propose a Hybrid Structural variant Assembly (HySA) approach that integrates sequencing reads from next generation sequencing (NGS) and single-molecule sequencing (SMS) technologies to accurately assemble and detect structural variations (SV) in human genome. By identifying homologous SV-containing reads from different technologies through a bipartite-graph-based clustering algorithm, our approach turns a whole genome assembly problem into a set of independent SV assembly problems, each of which can be effectively solved to enhance assembly of structurally altered regions in human genome.In testing our approach using data generated from a haploid hydatidiform mole genome (CHM1) and a diploid human genome (NA12878), we found that our approach substantially improved the detection of many types of SVs, particularly novel large insertions, small INDELs (10-50bp) and short tandem repeat expansions and contractions over existing approaches with a low false discovery rate. Our work highlights the strengths and limitations of current approaches and provides an effective solution for extending the power of existing sequencing technologies for SV discovery.

scholarly journals Assembly and diploid architecture of an individual human genome via single-molecule technologies

2015 ◽  
Vol 12 (8) ◽  
pp. 780-786 ◽  
Author(s):  
Matthew Pendleton ◽  
Robert Sebra ◽  
Andy Wing Chun Pang ◽  
Ajay Ummat ◽  
Oscar Franzen ◽  
...  
Keyword(s):  
Human Genome ◽  
Single Molecule ◽  
Individual Human

scholarly journals Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

2021 ◽  
Author(s):  
Fei Ge ◽  
Jingtao Qu ◽  
Peng Liu ◽  
Lang Pan ◽  
Chaoying Zou ◽  
...  
Keyword(s):  
Single Molecule ◽  
Inbred Line ◽  
Genome Mapping ◽  
Maize Inbred Line ◽  
Sequencing Data ◽  
Structural Variations ◽  
Single Molecule Sequencing ◽  
Maize Genetic ◽  
Induction Ratio ◽  
Phenotypic Variations

Heretofore, little is known about the mechanism underlying the genotype-dependence of embryonic callus (EC) induction, which has severely inhibited the development of maize genetic engineering. Here, we report the genome sequence and annotation of a maize inbred line with high EC induction ratio, A188, which is assembled from single-molecule sequencing and optical genome mapping. We assembled a 2,210 Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to those of 9.73 Mb for B73 and 10.2 Mb for Mo17. Comparative analysis revealed that ~30% of the predicted A188 genes had large structural variations to B73, Mo17 and W22 genomes, which caused considerable protein divergence and might lead to phenotypic variations between the four inbred lines. Combining our new A188 genome, previously reported QTLs and RNA sequencing data, we reveal 8 large structural variation genes and 4 differentially expressed genes playing potential roles in EC induction.

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