The overall goal of this proposal is to develop a strategy towards clinical resequencing of the human genome which we define as the application of human genome resequencing to large clinical populations for disease gene discovery research as well as a clinical application that has diagnostic potential. Our strategy relies on """"""""third generation"""""""" single molecule DNA sequencing as utilized by the Pacific Biosciences platform. We anticipate that single molecule DNA sequencing technology will ultimately be the sequencer of choice given these systems'rapid collection of massive amounts of DNA sequences from patient samples with clinical outcome annotation, and cost-effective operation at a fraction of the current costs of other sequencing technologies. This first goal focuses on developing what we term an intermittent segment resequencing approach. A set of interspersed reads will be generated from a single DNA molecule, much the same way as mate paired sequence works, but having internal interval sequences rather than a terminal sequence pair as generated by paired-end approaches. The second goal involves testing in-solution based approaches to increase substantially the fold coverage of genomics regions of high clinical interest in combination with genome shotgun sequencing. Given their random distribution of sequences, shotgun genome sequencing efforts treat all regions of the genome equally. Increasing the fold-coverage of these regions of interest selectively, in comparison to the rest of the genome, would improve the detection of important clinical variants.

Public Health Relevance

Creating a """"""""personalized"""""""" medicine strategy for each individual requires decoding the DNA sequence of a person's cancer that involves identifying genetic variations for any patient and discovering the clinical significance of these variants. The composition and spectrum of these variants can vary significantly from individual to individual, thus pointing out the importance of identifying all of the critical ones with clinical ramifications. New sequencing technologies have opened the way for creating personalized genetic signatures which can be used to tailor the clinical management of individuals but even more cost-effective approaches are needed given that thousands of individuals with specific disease have their genomes sequenced.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
High Impact Research and Research Infrastructure Programs (RC2)
Project #
1RC2HG005570-01
Application #
7855611
Study Section
Special Emphasis Panel (ZHG1-HGR-N (O2))
Program Officer
Schloss, Jeffery
Project Start
2009-09-25
Project End
2011-07-31
Budget Start
2009-09-25
Budget End
2010-07-31
Support Year
1
Fiscal Year
2009
Total Cost
$1,978,579
Indirect Cost
Name
Stanford University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305
Chen, Hao; Bell, John M; Zavala, Nicolas A et al. (2015) Allele-specific copy number profiling by next-generation DNA sequencing. Nucleic Acids Res 43:e23
Nadauld, Lincoln D; Garcia, Sarah; Natsoulis, Georges et al. (2014) Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer. Genome Biol 15:428
Grimes, Susan M; Ji, Hanlee P (2014) MendeLIMS: a web-based laboratory information management system for clinical genome sequencing. BMC Bioinformatics 15:290
Cushing, Anna; Flaherty, Patrick; Hopmans, Erik et al. (2013) RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing. BMC Res Notes 6:206
Natsoulis, Georges; Zhang, Nancy; Welch, Katrina et al. (2013) Identification of Insertion Deletion Mutations from Deep Targeted Resequencing. J Data Mining Genomics Proteomics 4:
Rodriguez, Jesse M; Bercovici, Sivan; Elmore, Megan et al. (2013) Ancestry inference in complex admixtures via variable-length Markov chain linkage models. J Comput Biol 20:199-211
Jensen, Michael A; Jauregui, Lauren; Davis, Ronald W (2012) A rapid, cost-effective method of assembly and purification of synthetic DNA probes >100 bp. PLoS One 7:e34373
Newburger, Daniel E; Natsoulis, Georges; Grimes, Sue et al. (2012) The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome. Nucleic Acids Res 40:D1137-43
Muralidharan, Omkar; Natsoulis, Georges; Bell, John et al. (2012) A cross-sample statistical model for SNP detection in short-read sequencing data. Nucleic Acids Res 40:e5
Kyriazopoulou-Panagiotopoulou, Sofia; Kashef Haghighi, Dorna; Aerni, Sarah J et al. (2011) Reconstruction of genealogical relationships with applications to Phase III of HapMap. Bioinformatics 27:i333-41

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