Educational Immersion Experience Title: Genome Sequencing Center
Mentor(s): Elaine Mardis, Ph.D., and Richard Wilson, Ph.D.
Location: 4444 Forest Park Blvd., Genome Sequencing Center (floors 3 and 4)
Overall Educational Goals:
1) Understand various strategies and corresponding technologies for sequencing of patient samples.
2) Appreciate the range of considerations for how the sequence data are analyzed, in the context of
patient-specific (e.g. somatic vs. germline) variants and in the context of the impact of mutation on
protein protducts
3) Understand the logistics and underlying imfrastructure required for high throughput genomics, and
its ultimate impact on the practice of medicine.
4) Introduction to the next generation sequencing technologies and high-throughput genotyping, the
applications of these technologies, and how they will change genomics and medical practice.
Educational Goals by Week:
Weeks 1-3:
- Introduction to the organization and infrastructure of the GSC (meet with various group leaders to
discuss their roles and associated methods, 3 hours/week)
- Meet with Drs. Wilson and Mardis to review progress and answer questions (1 hour/week)
- Read background manuscripts to understand the clinical context of training project
- Attend weekly medical sequencing progress review meeting
Weeks 3-6:
- Begin work on medical sequencing project with introduction to pipetting robotics, thermal cyclers,
DNA sequencing instrumentation (3 hours per week), then review primer validation pipeline and
metrics, shadow an active technician performing medical sample PCR and sequencing.
- Meet with Dr. Mark Watson to understand the logistics and underpinning principles needed for
successful high fidelity sample banking (1 hour/week)
- Attend weekly medical sequencing progress review meeting
- Meet with Drs. Wilson and Mardis (1 hour/week)
Weeks 7-9:
- Train in Medical Sequencing Informatics group to understand data analysis approaches and tools (5
hours/week)
- Import data produced on sequencing project to Consed database, analyze through variant detection
pipeline and analyze data (5 hours/week)
- Meet with Drs. Wilson and Mardis (1 hour/week)
- Attend weekly medical sequencing progress review meeting
- Review variant validation pipeline approaches, including 454 sequencing-based approaches and
conventional pipeline (1 hour/week)
Weeks 10-12:
- Introduction to next generation sequencing instrument processes and procedures (4 hours/week)
- Review currently literature on next generation sequencing and functional annotation of the human
genome (1 hour/week)
- Introduction to genome-wide genotyping and copy number polymorphism platforms
(Affymetrix/Illumina), including workflow and data analysis pipelines (3 hours/week)
- Meet with Drs. Wilson and Mardis (1 hour/week)
- Attend weekly medical sequencing progress review meeting
- Present a 45 minute seminar on project and results obtained during GSC training
Suggested readings:
1. Xiang Z, Zhao Y, Mitaksov V, Fremont DH, Kasai Y, Molitoris A, Ries RE, Miner TL, McLellan MD,
Dipersio JF, Link DC, Payton JE, Graubert TA, Watson M, Shannon W, Heath SE, Naggarajan R,
Mardis ER, Wilson RK, Ley TJ, Tomasson MH. Identification of somatic JAK1 mutations in patients
with acute myeloid leukemia. Blood 2007. Epub.
2. Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, Lin WM, Province MA, Kraja A, Johnson
LA, Shah K, Sato M, Thomas RK, Barletta JA, Borecki IB, Broderick S, Chang AC, Chiang DY, Chirieac
LR, Cho J, Fujii Y, Gazdar AF, Giordano T, Greulich H, Hanna M, Johnson BE, Kris MG, Lash A, Lin L,
Lindeman N, Mardis ER, McPherson JD, Minna JD, Morgan MB, Nadel M, Orringer MB, Osborne JR,
Ozenberger B, Ramos AH, Robinson J, Roth JA, Rusch V, Sasaki H, Shepherd F, Sougnez C, Spitz
MR, Tsao MS, Twomey D, Verhaak RG, Weinstock GM, Wheeler DA, Winckler W, Yoshizawa A, Yu S,
Zakowski MF, Zhang Q, Beer DG, Wistuba II, Watson MA, Garraway LA, Ladanyi M, Travis WD, Pao W,
Rubin MA, Gabriel SB, Gibbs RA, Varmus HE, Wilson RK, Lander ES, Meyerson M. Characterizing the
cancer genome in lung adenocarcinoma. Nature 2007. 450: 893-8.
3. Link DC, Kunter G, Kasai Y, Zhao Y, Miner T, McLellan MD, Ries RE, Kapur D, Nagarajan R, Dale DC,
Bolyard AA, Boxer LA, Welte K, Zeidler C, Donadieu J, Bellanne-Chantelot C, Vardiman JW, Caligiuri
MA, Bloomfield CD, DiPersio JF, Tomasson MH, Graubert TA, Westervelt P, Watson M, Shannon W,
Baty J, Mardis ER, Wilson RK and Ley, TJ. Distinct patterns of mutations occurring in de novo AML
versus AML arising in the setting of severe congenital neutropenia. Blood 2007. 110: 1648-55.
4. Marks JL, McLellan MD, Zakowski MF, Lash AE, Kasai Y, Broderick S, Sarkaria IS, Pham D, Singh B,
Miner TL, Fewell GA, Fulton LL, Mardis ER, Wilson RK, Kris MG, Rusch VW, Varmus H, and Pao W.
Mutational analysis of EGFR and related signaling pathway genes in lung adenocarcinomas identifies a
novel somatic kinase domain mutation in FGFR4. PLoS ONE 2007. 2: e426.
5. Chen K, McLellan M, Ding L, Wendl MC, Kasai Y, Wilson RK and Mardis ER. PolyScan: An automatic
indel and SNP detection approach to the analysis of human resequencing data. Genome Research
2007: 17: 659-66.
6. Elizur A, Orscheln RC, Ferkol TW, Atkinson JJ, Dunne WM Jr, Buller RS, Armstrong JR, Mardis ER,
Storch GA, Cannon CL. Panton-Valentine leukocidin-positive Methicillin-resistant Staphylococcus
aureus lung infections in patients with cystic fibrosis. Chest 2007. 131: 1718-25.
7. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al. 2007. Genome-wide maps of chromatin
state in pluripotent and lineage-committed cells. Nature 448: 553-60.
8. Johnson DS, Mortazavi A, Myers RM, Wold B. 2007. Genome-wide mapping of in vivo protein-DNA
interactions. Science 316: 1497-502.
9. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, et al. 2007. Genome-wide profiles of STAT1
DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods
4: 651-7