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Home > Platforms > Medical Sequencing
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Medical Sequencing
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| With the completion of the reference human genome sequence, researchers can begin to answer questions about individual human genomic variation, both in the context of normal variation and of disease onset, progression and prognosis. Over the past year, the GSC has developed a high-throughput pipeline for PCR-based genomic re-sequencing, including infrastructure to design and test primer pairs, automation to achieve 384-well plate-based sample processing, and barcode-based sample tracking. We also have developed robust procedures and QC checks throughout the pipeline. At present, human re-sequencing data is actively being produced with this pipeline for multiple genes using DNA from a variety of patient-derived tissues. Our corresponding sequence analysis pipeline utilizes the polyphred/consed suite of informatics tools for mutation detection of the assembled sequence reads, and we are developing a Gbrowse-based viewer that illustrates polymorphisms and somatic mutations in the context of relevant genome annotation. As such, the GSC has put in place a comprehensive mechanism for human re-sequencing that has the potential to increase in scale according to demand. Please contact Robert Fulton for more detailed information. |
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| Medical Sequencing Projects
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| Medical Sequencing Information
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| Medical Sequencing Contact |
Robert Fulton
Group Leader of Sequencing Improvement
Send email
Washington University School of Medicine
The Genome Center
4444 Forest Park Ave
St. Louis, Missouri 63108
USA
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| Selected Medical Sequencing Publications
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Title
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Distinct patterns of mutations occurring in de novo AML versus AML arising in the setting of severe congenital neutropenia.
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Authors
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Daniel C. Link, Ghada Kunter, Yumi Kasai, Yu Zhao, Tracie Miner, Michael D. McLellan, Rhonda E. Ries, Deepak Kapur, Rakesh Nagarajan, David C. Dale, Audrey Anna Boylard, Laurence A. Boxer, Karl Welte, Cornelia Zeidler, Jean Donadieu, Christine Bellanne-Chantelot, James W. Vardiman, Michael A. Caligiuri, Clara D. Bloomfield, John F. DiPersio, ... |
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Blood. 2007 Sep 1;110(5):1648-55. Epub 2007 May 9. |
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DCLink_TJLey primers
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DCLink_TJLey protocols
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Title
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Mutational Analysis of EGFR and Related Signaling Pathway Genes in Lung Adenocarcinomas Identifies a Novel Somatic Kinase Domain Mutation in FGFR4
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Authors
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Jenifer L. Marks, Michael D. McLellan, Maureen F. Zakowski, Alex Lash, Yumi Kasai, Stephen Broderick, Inderpal S. Sarkaria, DuyKhanh Pham, Bhuvanesh Singh, Tracie L. Miner, Ginger A. Fewell, Lucinda L. Fulton, Elaine R. Mardis, Richard K. Wilson, Mark G. Kris, Valerie W. Rusch, Harold Varmus, William Pao |
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PLoS ONE. 2007 May 9;2:e426. |
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JLMarks_WPao primers
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JLMarks_WPao protocols
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Title
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PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data.
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Authors
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Chen K, McLellan MD, Ding L, Wendl MC, Kasai Y, Wilson RK, Mardis ER. |
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Genome Res. 2007 Apr 6; |
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Title
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Low frequency of telomerase RNA mutations among children with aplastic anemia or myelodysplastic syndrome.
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Authors
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Field JJ, Mason PJ, An P, Kasai Y, McLellan M, Jaeger S, Barnes YJ, King AA, Bessler M, Wilson DB. |
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J Pediatr Hematol Oncol. 2006 Jul;28(7):450-3. |
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Title
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Use of cigarette-smoking history to estimate the likelihood of mutations in epidermal growth factor receptor gene exons 19 and 21 in lung adenocarcinomas.
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Authors
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Pham D, Kris MG, Riely GJ, Sarkaria IS, McDonough T, Chuai S, Venkatraman ES, Miller VA, Ladanyi M, Pao W, Wilson RK, Singh B, Rusch VW. |
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J Clin Oncol. 2006 Apr 10;24(11):1700-4. Epub 2006 Feb 27. |
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Title
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EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib.
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Authors
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Pao W, Miller V, Zakowski M, Doherty J, Politi K, Sarkaria I, Singh B, Heelan R, Rusch V, Fulton L, Mardis E, Kupfer D, Wilson R, Kris M, Varmus H. |
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Proc Natl Acad Sci U S A. 2004 Sep 7;101(36):13306-11. |
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Title
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A pilot study of high-throughput, sequence-based mutational profiling of primary human acute myeloid leukemia cell genomes.
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Authors
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Ley TJ, Minx PJ, Walter MJ, Ries RE, Sun H, McLellan M, DiPersio JF, Link DC, Tomasson MH, Graubert TA, McLeod H, Khoury H, Watson M, Shannon W, Trinkaus K, Heath S, Vardiman JW, Caligiuri MA, Bloomfield CD, Milbrandt JD, ... |
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Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):14275-80. Epub 2003 Nov 12. |
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