| WEEK # | TOPICS | READINGS |
|---|---|---|
| 1 |
Introduction | No Readings |
| 2 |
Classical approaches to Sequencing |
Maxam, A. M., and W. Gilbert. "A New Method for Sequencing DNA." Proceedings of the National Academy of Sciences of the United States of America 74, no. 2 (1977): 560–4. Sanger, F., S. Nicklen, et al. "DNA Sequencing with Chain-Terminating Inhibitors." Proceedings of the National Academy of Sciences of the United States of America 74, no. 12 (1977): 5463–7. |
| 3 |
Contemporary Sequencing Methods |
Li, R., A. Montpetit, et al. "Somatic Point Mutations Occurring Early in Development: A Onozygotic Twin Study." Journal of Medical Genetics 51, no. 1 (2014): 28–34. Quail, M. A., M. Smith, et al. "A Tale of Three Next Generation Sequencing Platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers." BMC Genomics 13 (2012): 341. |
| 4 |
Single nucleotide polymorphisms |
Vance, C., A. Al-Chalabi, et al. "Familial Amyotrophic Lateral Sclerosis with Frontotemporal Dementia is Linked to a Locus on Chromosome 9p13.2–21.3." Brain 129, no. 4 (2006): 868–76. DeJesus-Hernandez, M., I. R. Mackenzie, et al. "Expanded GGGGCC Hexanucleotide Repeat in Non-Coding Region of C9ORF72 Causes Chromosome 9p-Linked Frontotemporal Dementia and Amyotrophic Lateral Sclerosis." Neuron 72, no. 2 (2011): 245–56. |
| 5 |
Copy Number Variation |
Blauw, H. M., C. P. Barnes, et al. "SMN1 Gene Duplications are Associated with Sporadic ALS." Neurology 78, no. 11 (2012): 776–80. Nishiguchi, K. M., R. G. Tearle, et al. "Whole Genome Sequencing in Patients with Retinitis Pigmentosa Reveals Pathogenic DNA Structural Changes and NEK2 as a New Disease Gene." Proceedings of the National Academy of Sciences of the United States of America 110, no. 40 (2013): 16139–44. |
| 6 |
Tracing human populations |
Elhaik, E., E. Greenspan, et al. "The GenoChip: A New Tool for Genetic Anthropology." Genome Biology and Evolution 5, no. 5 (2013): 1021–31. Moodley, Y., B. Linz, et al. "The Peopling of the Pacific from a Bacterial Perspective." Science 323, no. 5913 (2009): 527–30. |
| 7 |
Genome wide association |
Nuinoon, M., W. Makarasara, et al. "A Genome-Wide Association Identified the Common Genetic Variants Influence Disease Severity in Beta0-Thalassemia / Hemoglobin E." Human Genetics 127, no. 3 (2010): 303–14. Rydz, N., L. L. Swystun, et al. "The C-type Lectin Receptor CLEC4M Binds, Internalizes, and Clears Von Willebrand Factor and Contributes to the Variation in Plasma Von Willebrand Factor Levels." Blood 121, no. 26 (2013): 5228–37. |
| 8 |
Field trip | No Readings |
| 9 |
Genomic analysis and targeted therapies |
Zhang, J., P. Meltzer, et al. "Application of Chromosome Microdissection Probes for Elucidation of BCR-ABL Fusion and Variant Philadelphia Chromosome Translocations in Chronic Myelogenous Leukemia." Blood 81, no. 12 (1993): 3365–71. Shah, N. P., J. M. Nicoll, et al. "Multiple BCR-ABL Kinase Domain Mutations Confer Polyclonal Resistance to the Tyrosine Kinase Inhibitor Imatinib (STI571) in Chronic Phase and Blast Crisis Chronic Myeloid Leukemia." Cancer Cell 2, no. 2 (2002): 117–25. |
| 10 |
From rare mutation to mainstream drug target |
Kotowski, I. K., A. Pertsemlidis, et al. "A Spectrum of PCSK9 Alleles Contributes to Plasma Levels of Low-Density Lipoprotein Cholesterol." American Journal of Human Genetics 78, no. 3 (2006): 410–22. Stein, E. A., S. Mellis, et al. "Effect of a Monoclonal Antibody to PCSK9 on LDL Cholesterol." New England Journal of Medicine 366, no. 12 (2012): 1108–18. |
| 11 |
Mosaics and chimeras: when genetic analysis goes astray |
O'Huallachain, M., K. J. Karczewski, et al. "Extensive Genetic Variation in Somatic Human Tissues." Proceedings of the National Academy of Sciences of the United States of America 109, no. 44 (2012): 18018–23. Ng, B. G., K. J. Buckingham, et al. "Mosaicism of the UDP-Galactose Transporter SLC35A2 Causes a Congenital Disorder of Glycosylation." American Journal of Human Genetics 92, no. 4 (2013): 632–6. |
| 12 |
Crowdsourcing genetic studies |
Do, C. B., J. Y. Tung, et al. "Web-Based Genome-Wide Association Study Identifies Two Novel Loci and A Substantial Genetic Component for Parkinson's Disease." PLoS Genetics 7 no. 6 (2011): e1002141. Kwak, D., A. Kam, et al. "Open-Phylo: A Customizable Crowd-Computing Platform for Multi Sequence Alignment." Genome Biology 14, no. 10 (2013): R116. |
| 13 |
Understanding the causes of rare diseases |
Chen, Z., J. L. Wang, et al. "Using next-Generation Sequencing as a Genetic Diagnostic Tool in Rare Autosomal Recessive Neurologic Mendelian Disorders." Neurobiology of Aging 34, no. 10 (2013): 2442.e11–7. Bainbridge, M. N., W. Wiszniewski, et al. "Whole-Genome Sequencing for Optimized Patient Management." Science Translational Medicine 3, no. 87 (2011): 87re3. |
| 14 |
Final Presentations | No Readings |
