Items where Subject is "Investigative techniques and equipment > whole exome sequencing
Investigative techniques and equipment > assays > whole exome sequencing"

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Number of items at this level: 52.

B

Berstein, Y., McCarthy, S., Kramer, M., Zandi, P., Goes, F., Potash, J., McCombie, R. (October 2017) RARE VARIANT DETECTION IN COMPLEX DISORDERS USING THE BIRTHDAY MODEL. European Neuropsychopharmacology, 27 (Supple). S367-S368, Meeting Abstract 2. ISSN 0924-977X

C

Cleary, S. P., Jeck, W. R., Zhao, X. B., Chen, K., Selitsky, S. R., Savich, G. L., Tan, T. X., Wu, M. C., Getz, G., Lawrence, M. S., Parker, J. S., Li, J. Y., Powers, S., Kim, H., Fischer, S., Guindi, M., Ghanekar, A., Chiang, D. Y. (November 2013) Identification of Driver Genes in Hepatocellular Carcinoma by Exome Sequencing. Hepatology, 58 (5). pp. 1693-1702. ISSN 0270-9139

Cleary, S. P., Jeck, W. R., Zhao, X. B., Selitsky, S. R., Savich, G. L., Tan, T. X., Wu, M. C., Getz, G., Lawrence, M. S., Parker, J. S., Li, J. Y., Powers, S., Kim, H., Fischer, S. E., Guindi, M., Ghanekar, A., Chiang, D. Y. (April 2013) Identification of driver genes in hepatocellular carcinoma by exome sequencing. Cancer Research, 73 (8 (Sup). p. 4598. ISSN 0008-5472

E

Erlich, Y., Edvardson, S., Hodges, E., Zenvirt, S., Thekkat, P., Shaag, A., Dor, T., Hannon, G. J., Elpeleg, O. (May 2011) Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. Genome Research, 21 (5). pp. 658-664. ISSN 1088-9051

F

Fairfield, H., Gilbert, G. J., Barter, M., Corrigan, R. R., Curtain, M., Ding, Y. M., D'Ascenzo, M., Gerhardt, D. J., He, C., Huang, W. H., Richmond, T., Rowe, L., Probst, F. J., Bergstrom, D. E., Murray, S. A., Bult, C., Richardson, J., Kile, B. T., Gut, I., Hager, J., Sigurdsson, S., Mauceli, E., Di Palma, F., Lindblad-Toh, K., Cunningham, M. L., Cox, T. C., Justice, M. J., Spector, M. S., Lowe, S. W., Albert, T., Donahue, L. R., Jeddeloh, J., Shendure, J., Reinholdt, L. G. (2011) Mutation discovery in mice by whole exome sequencing. Genome Biology, 12 (9). ISSN 1474-7596

Fang, Han, Lyon, Gholson J. (November 2014) Reducing INDEL calling errors in whole genome and exome sequencing data. In: Cold Spring Harbor Laboratory Personal Genomes Meeting, November 2014, Cold Spring Harbor, NY . (Unpublished)

Fang, Han, Lyon, Gholson J. (November 2014) Reducing INDEL calling errors in whole genome and exome sequencing data. In: Cold Spring Harbor Laboratory Biological Data Science Meeting, November 8, 2014, Cold Spring Harbor, NY. (Unpublished)

Fang, Han, Wu, Yiyang, Narzisi, G., O'Rawe, Jason, Jimenez Barron, Laura, Rosenbaum, J., Ronemus, M., Iossifov, I., Schatz, M. C., Lyon, Gholson J. (2014) Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Med, 6 (10). p. 89.

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Glessner, J. T., Bick, A. G., Ito, K., Homsy, J. G., Rodriguez-Murillo, L., Fromer, M., Mazaika, E., Vardarajan, B., Italia, M., Leipzig, J., DePalma, S. R., Golhar, R., Sanders, S. J., Yamrom, B., Ronemus, M., Iossifov, I., Willsey, A. J., State, M. W., Kaltman, J. R., White, P. S., Shen, Y., Warburton, D., Brueckner, M., Seidman, C., Goldmuntz, E., Gelb, B. D., Lifton, R., Seidman, J., Hakonarson, H., Chung, W. K. (October 2014) Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data. Circulation Research, 115 (10). pp. 884-96. ISSN 0009-7330

Goes, F., Pirooznia, M., Parla, J., Melissa, K., Monson, E., Willour, V., Boenkhe, M., Scotts, L., Stahl, E., Purcell, S., Sklar, P., Zandi, P., McCombie, W., Potash, J. (October 2017) EXOME SEQUENCING OF BIPOLAR DISORDER: FAMILY AND CASE-CONTROL RESULTS SHOW OVERLAP WITH GENES IMPLICATED IN AUTISM AND SCHIZOPHRENIA. European Neuropsychopharmacology, 27 (Supple). Abstract 17; S148-S148. ISSN 0924-977X

Goes, F. S., Pirooznia, M., Parla, J. S., Kramer, M., Ghiban, E., Mavruk, S., Chen, Y. C., Monson, E. T., Willour, V. L., Karchin, R., Flickinger, M., Locke, A. E., Levy, S. E., Scott, L. J., Boehnke, M., Stahl, E., Moran, J. L., Hultman, C. M., Landen, M., Purcell, S. M., Sklar, P., Zandi, P. P., McCombie, W. R., Potash, J. B. (July 2016) Exome Sequencing of Familial Bipolar Disorder. JAMA Psychiatry, 73 (6). pp. 590-597. ISSN 2168-6238 (Electronic)2168-622X (Linking)

Guo, Y., Ding, X., Shen, Y., Lyon, G. J., Wang, K. (September 2015) SeqMule: automated pipeline for analysis of human exome/genome sequencing data. Sci Rep, 5. p. 14283. ISSN 2045-2322 (Electronic)2045-2322 (Linking)

H

He, M., Person, T. N., Hebbring, S. J., Heinzen, E., Ye, Z., Schrodi, S. J., McPherson, E. W., Lin, S. M., Peissig, P. L., Brilliant, M. H., O'Rawe, J., Robison, R. J., Lyon, G. J., Wang, K. (January 2015) SeqHBase: a big data toolset for family based sequencing data analysis. Journal of Medical Genetics, 52 (4). pp. 282-288. ISSN 0022-2593

I

Iossifov, I. (November 2011) Talk from Ivan Iossifov at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Iossifov, I., Levy, D., Allen, J., Ye, K., Ronemus, M., Lee, Y. H., Yamrom, B., Wigler, M. (September 2015) Low load for disruptive mutations in autism genes and their biased transmission. Proc Natl Acad Sci U S A. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Irvine, D. V., Goto, D. B., Vaughn, M. W., Nakaseko, Y., McCombie, W. R., Yanagida, M., Martienssen, R. (June 2009) Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing. Genome research, 19 (6). pp. 1077-83. ISSN 1088-9051 (Print)1088-9051 (Linking)

K

Koren, S., Schatz, M. C., Walenz, B. P., Martin, J., Howard, J. T., Ganapathy, G., Wang, Z., Rasko, D. A., McCombie, W. R., Jarvis, E. D., Phillippy, A. M. (July 2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology, 30 (7). pp. 693-700. ISSN 1087-0156

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Lyon, Gholson J. (November 2013) Cambridge HealthTech Institute Clinical Genomics Podcast: Highlights from the Upcoming Clinical Exome Sequencing Conference. [Audio]

Lyon, Gholson J. (2012) Clinical Issues with the Return of Next-­Generation Sequencing Results. In: The Clinical Genome Conference, June 12th-13th 2012, San Francisco, CA. (Unpublished)

Lyon, Gholson J. (April 2013) Exome and Genome Sequencing. [Teaching Resource] (Unpublished)

Lyon, Gholson J. (May 2013) Exome and Genome Sequencing. [Teaching Resource] (Unpublished)

Lyon, Gholson J. (2011) Finding and Analyzing Human Genetic Variation in Neuropsychiatric Disorders. In: Faculty Recruitment Talk, Dec 2011, Cold Spring Harbor Laboratory. (Unpublished)

Lyon, Gholson J. (December 2013) Increasing Accuracy for Exome and Whole Genome Sequencing. In: Bio-IT World and Cambridge Healthtech Institute's Inaugural- Clinical Exome Sequencing, December 4-5th 2013, Lisbon, Portugal. (Unpublished)

Lyon, Gholson J. (April 2013) Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. In: COMPUTATIONAL BIOLOGY & BIOINFORMATICS SEMINAR SERIES, April 10th 2013, Cold Spring Harbor Laboratory. (Unpublished)

Lyon, Gholson J. (2011) Personal account of the discovery of a new disease using next-generation sequencing. Interview by Natalie Harrison. Pharmacogenomics, 12 (11). pp. 1519-1523. ISSN 1744-8042

Lyon, Gholson J. (September 2011) Returning Research Results from Next‐Generation Sequencing and Analysis to Patients with Idiopathic Disorders? In: Personal Genomes Meeting, Sept 30th - Oct 2nd 2011, Cold Spring Harbor Laboratory. (Unpublished)

Lyon, Gholson J. (November 2012) Software Considerations for Processing, Analyzing and Interpreting Exome & Genome Sequence Data in Clinical Settings. In: World Genome Data Analysis Summit: Pre Conference Workshop, Nov 27th 2012, San Francisco. (Unpublished)

Lyon, Gholson J. (October 2012) Summary of Efforts to Achieve and Evaluate High-Quality Exomes and Genomes. In: Bio-IT Europe Pre-Conference Short Courses: Software Considerations for Processing, Analyzing and Interpreting Sequence Data , Oct 8th 2012, Vienna, Austria. (Unpublished)

Lyon, Gholson J., Jiang, Tao, Van Wijk, Richard, Wang, Wei, Bodily, Paul Mark, Xing, Jinchuan, Tian, Lifeng, Robison, Reid J., Clement, Mark, Lin, Yang, Zhang, Peng, Liu, Ying, Moore, Barry, Glessner, Joseph T., Elia, Josephine, Reimherr, Fred, van Solinge, Wouter W., Yandell, Mark, Hakonarson, Hakon, Wang, Jun, Johnson, William Evan, Wei, Zhi, Wang, Kai (2011) Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. Dscovery Medicine, 12 (62). pp. 41-55. ISSN 1944-7930

M

Malcolmson, J., Kleyner, R., Tegay, D., Adams, W., Ward, K., Coppinger, J., Nelson, L., Meisler, M. H., Wang, K., Robison, R., Lyon, G. J. (November 2016) SCN8A mutation in a child presenting with seizures and developmental delays. Cold Spring Harb Mol Case Stud, 2 (6). a001073. ISSN 2373-2873

Menges, F., Narzisi, G., Mishra, B. (September 2011) TotalReCaller: improved accuracy and performance via integrated alignment and base-calling. Bioinformatics, 27 (17). pp. 2330-2337. ISSN 1367-4803

Monson, E., Pirooznia, M., Parla, J., Kramer, M., Goes, F., Breen, M., Gaynor, S., de Klerk, K., Jancic, D., Karchin, R., McCombie, W., Zandi, P., Potash, J., Willour, V. (October 2017) ASSESSMENT OF WHOLE-EXOME SEQUENCE DATA IN ATTEMPTED SUICIDE WITHIN A BIPOLAR COHORT. European Neuropsychopharmacology, 27. Meeting Abstract 20; S267-S268. ISSN 0924-977X

Monson, E. T., Pirooznia, M., Parla, J., Kramer, M., Goes, F. S., Gaine, M. E., Gaynor, S. C., de Klerk, K., Jancic, D., Karchin, R., McCombie, W. R., Zandi, P. P., Potash, J. B., Willour, V. L. (July 2017) Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort. Mol Neuropsychiatry, 3 (1). pp. 1-11. ISSN 2296-9209 (Print)2296-9179

N

Narzisi, G., O'Rawe, Jason, Iossifov, I., Fang, Han, Lee, Y. H., Wang, Zihua, Wu, Yiyang, Lyon, Gholson J., Wigler, M. H., Schatz, M. C. (August 2014) Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nature Methods, 11 (10). pp. 1033-1036.

Navin, N., Hicks, J. B. (May 2011) Future medical applications of single-cell sequencing in cancer. Genome Medicine, 3 (5). ISSN 1756994X (ISSN)

O

O'Rawe, J., Jiang, T., Sun, G., Wu, Y., Wang, W., Hu, J., Bodily, P., Tian, L., Hakonarson, H., Johnson, W. E., Wei, Z., Wang, K., Lyon, G. J. (March 2013) Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med, 5 (3). p. 28. ISSN 1756-994X (Print)

Olson, A. J., Brennecke, J., Aravin, A. A., Hannon, G. J., Sachidanandam, R. (2008) Analysis of large-scale sequencing of small RNAs. Pacific Symposium on Biocomputing. pp. 126-136. ISSN 17935091 (ISSN)

P

Parla, J., Kramer, M. R., McCombie, W. R. (2011) High-Throughput Sequencing. In: Microbial Forensics (Second Edition). Academic Press, San Diego, pp. 461-478.

Parla, J. S., Iossifov, I., Grabill, I., Spector, M. S., Kramer, M., McCombie, W. R. (September 2011) A comparative analysis of exome capture. Genome Biology, 12 (9). R97. ISSN 1474-7596

Pirooznia, M., Goes, F., Parla, J., Kramer, M., Monson, E., Han, S., Jancic, D., Karchin, R., Willour, V., McCombie, W., Potash, J., Zandi, P. (October 2017) RARE BIPOLAR LOCI IDENTIFICATION THROUGH WHOLE EXOME SEQUENCING. European Neuropsychopharmacology, 27 (Supple). Abstract S242-S242. ISSN 0924-977X

Pond, S. K., Wadhawan, S., Chiaromonte, F., Ananda, G., Chung, W. Y., Taylor, J., Nekrutenko, A. (October 2009) Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Research, 19 (11). pp. 2144-2153.

R

Rope, Alan F., Wang, Kai, Evjenth, Rune, Xing, Jinchuan, Johnston, Jennifer J., Swensen, Jeffrey J., Johnson, W. Evan, Moore, Barry, Huff, Chad D., Bird, Lynne M., Carey, John C., Opitz, John M., Stevens, Cathy A., Jiang, Tao, Schank, Christa, Fain, Heidi Deborah, Robison, Reid, Dalley, Brian, Chin, Steven, South, Sarah T., Pysher, Theodore J., Jorde, Lynn B., Hakonarson, Hakon, Lillehaug, Johan R., Biesecker, Leslie G., Yandell, Mark, Arnesen, Thomas, Lyon, Gholson J. (2011) Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. American Journal of Human Genetics, 89 (1). pp. 28-43. ISSN 0002-9297

Russnes, H. G., Navin, N., Hicks, J. B., Borresen-Dale, A. L. (October 2011) Insight into the heterogeneity of breast cancer through next-generation sequencing. Journal of Clinical Investigation, 121 (10). pp. 3810-3818. ISSN 0021-9738

S

Sabot, F., Picault, N., Elbaidouri, M., Llauro, C., Chaparro, C., Piegu, B., Roulin, A., Guiderdoni, E., Delabastide, M., McCombie, W. R., Panaud, O. (January 2011) Transpositional landscape of rice genome revealed by Paired-End Mapping of high-throughput resequencing data. Plant Journal, 66 (2). pp. 241-246. ISSN 0960-7412

Schatz, M. C., Witkowski, J., McCombie, W. R. (April 2012) Current challenges in de novo plant genome sequencing and assembly. Genome Biology, 13 (4). p. 243. ISSN 1474-7596

Sheikh, H., Pirooznia, M., Parla, J., Kramer, M., Goes, F., Jancic, D., Karchin, R., Willour, V., McCombie, W., Zandi, P., Potash, J. (October 2017) EXOME SEQUENCING IN BIPOLAR DISORDER WITH COMORBID PANIC: GENE SET AND PATHWAY BASED-ANALYSES SUGGEST A ROLE FOR GLUTAMATE AND CALCIUM SIGNALING. European Neuropsychopharmacology, 27. Abstract S157. ISSN 0924-977X

Spector, M. S., Iossifov, I., Kritharis, A., He, C., Kolitz, J. E., Lowe, S. W., Allen, S. L. (June 2012) Mast-cell leukemia exome sequencing reveals a mutation in the IgE mast-cell receptor beta chain and KIT V654A. Leukemia, 26 (6). pp. 1422-1425. ISSN 0887-6924

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Thomson, P. A., Parla, J. S., McRae, A. F., Kramer, M., Ramakrishnan, K., Yao, J., Soares, D. C., McCarthy, S., Morris, S. W., Cardone, L., Cass, S., Ghiban, E., Hennah, W., Evans, K. L., Rebolini, D., Millar, J. K., Harris, S. E., Starr, J. M., MacIntyre, D. J., McIntosh, A. M., Watson, J. D., Deary, I. J., Visscher, P. M., Blackwood, D. H., McCombie, W. R., Porteous, D. J. (June 2014) 708 Common and 2010 rare DISC1 locus variants identified in 1542 subjects: Analysis for association with psychiatric disorder and cognitive traits. Molecular Psychiatry, 19 (6). pp. 668-675. ISSN 14765578

Tilgner, H., Knowles, D. G., Johnson, R., Davis, C. A., Chakrabortty, S., Djebali, S., Curado, J., Snyder, M., Gingeras, T. R., Guigo, R. (September 2012) Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for IncRNAs. Genome Research, 22 (9). pp. 1616-1625. ISSN 1088-9051

Y

Yoon, S., Xuan, Z., Makarov, V., Ye, K., Sebat, J. (September 2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res, 19. p. 9.

Z

Zador, A. M., Dubnau, J., Oyibo, H. K., Zhan, H., Cao, G., Peikon, I. D. (October 2012) Sequencing the Connectome. PLoS Biology, 10 (10). ISSN 1544-9173

Zhang, T., Romanel, A., Kluk, M. J., Eng, K., Iossifov, I., Sboner, A., Lipkin, S., Pritchard, C., Beltran, H., Rubin, M., Demichelis, F., Elemento, O. (February 2016) Germline Variants and Secondary Findings in a Cancer Precision Medicine Cohort. Laboratory Investigation, 96. 461A-461A. ISSN 0023-6837

This list was generated on Sat Dec 15 14:45:26 2018 EST.
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