Functional genomics across scale : from cell free nucleic acids to single chromosomes and single cell genomics
Abstract/Contents
- Abstract
- Incorporation of sequencing techniques into molecular biology studies has led to the scaling up of experimental approaches and the generation of "-omics" data types. These studies are driving the discovery of novel diagnostics and biomarkers that has the potential to deliver both preventive and therapeutic value. In this thesis, we explore the impact that the scale of starting material, spanning from nucleic acids in plasma to chromosomes and genome of single cells, has on functional genomics. We will also address the multidisciplinary approaches that integrate microfluidics, bioinformatics, and statistical models that are required to assess effectively the data generated from these ranges of starting material. The thesis will begin with a transcriptome-wide characterization of circulating cell free RNA in plasma. The presence of circulating nucleic acids from fetal sources being detectable in the plasma of pregnant woman has the obvious benefit of being a non-invasive diagnostic tool for fetal health. We used the high-throughput methods of microarrays and next-generation sequencing to characterize the global landscape of circulating RNA in cohorts of human subjects. Using bioinformatics approaches to focus on genes whose expression is highly specific to certain tissues, we were able to infer the relative contributions of these tissues towards circulating RNA and monitor changes in tissue development and health. The second part of the thesis will address the analytical framework of using sequenced reads from single chromosomes isolated using microfluidics to scaffold genomes during de novo assembly. Genomes assembled de novo from short reads are typically highly fragmented and lack chromosome scale contiguity. Here, we used microfluidics techniques to trap single chromosomes for sequencing, and used the sequenced reads from these chromosome preparations as a source of long range information in grouping scaffolds together as chromosomes. The concluding part of the thesis will be on the application of single cell genomics to dissect tumor heterogeneity. Substantial genomic heterogeneity occurs within a given tumor, and to fully understand that diversity requires the ability to perform genomics at single cell resolution. We performed targeted sequencing of a panel of single nucleotide variants (SNVs) and deletions in acute lymphoblastic leukemia (ALL) patients. By accurately segregating groups of co-occurring mutations into distinct clonal populations, we inferred the clonal architecture in these patients.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2015 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Koh, Lian Chye Winston |
|---|---|
| Associated with | Stanford University, Department of Bioengineering. |
| Primary advisor | Quake, Stephen Ronald |
| Thesis advisor | Quake, Stephen Ronald |
| Thesis advisor | Altman, Russ |
| Thesis advisor | Bejerano, Gill, 1970- |
| Thesis advisor | Covert, Markus |
| Advisor | Altman, Russ |
| Advisor | Bejerano, Gill, 1970- |
| Advisor | Covert, Markus |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Lian Chye Winston Koh. |
|---|---|
| Note | Submitted to the Department of Bioengineering. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2015. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2015 by Lian Chye Winston Koh
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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