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Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing.

Genome medicine

O'Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, Bodily P, Tian L, Hakonarson H, Johnson WE, Wei Z, Wang K, Lyon GJ.
PMID: 23537139
Genome Med. 2013 Mar 27;5(3):28. doi: 10.1186/gm432. eCollection 2013.

BACKGROUND: To facilitate the clinical implementation of genomic medicine by next-generation sequencing, it will be critically important to obtain accurate and consistent variant calls on personal genomes. Multiple software tools for variant calling are available, but it is unclear...

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O'Rawe J, Jiang T, Sun G, et al. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013;5(3):28doi: 10.1186/gm432.
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. (2013). Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome medicine, 5(3), 28. https://doi.org/10.1186/gm432
O'Rawe, Jason, et al. "Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing." Genome medicine vol. 5,3 (2013): 28. doi: https://doi.org/10.1186/gm432
O'Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, Bodily P, Tian L, Hakonarson H, Johnson WE, Wei Z, Wang K, Lyon GJ. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013 Mar 27;5(3):28. doi: 10.1186/gm432. eCollection 2013. PMID: 23537139; PMCID: PMC3706896.
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Widespread intron retention diversifies most cancer transcriptomes.

Genome medicine

Dvinge H, Bradley RK.
PMID: 26113877
Genome Med. 2015 May 15;7(1):45. doi: 10.1186/s13073-015-0168-9. eCollection 2015.

BACKGROUND: Somatic mutations affecting components of the RNA splicing machinery occur with high frequencies across many tumor types. These mutations give rise to distinct alterations in normal splice site and exon recognition, such as unusual 3' splice site preferences,...

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Dvinge H, Bradley RK. Widespread intron retention diversifies most cancer transcriptomes. Genome Med. 2015;7(1):45doi: 10.1186/s13073-015-0168-9.
Dvinge, H., & Bradley, R. K. (2015). Widespread intron retention diversifies most cancer transcriptomes. Genome medicine, 7(1), 45. https://doi.org/10.1186/s13073-015-0168-9
Dvinge, Heidi, and Bradley, Robert K. "Widespread intron retention diversifies most cancer transcriptomes." Genome medicine vol. 7,1 (2015): 45. doi: https://doi.org/10.1186/s13073-015-0168-9
Dvinge H, Bradley RK. Widespread intron retention diversifies most cancer transcriptomes. Genome Med. 2015 May 15;7(1):45. doi: 10.1186/s13073-015-0168-9. eCollection 2015. PMID: 26113877; PMCID: PMC4480902.
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Enabling multiscale modeling in systems medicine.

Genome medicine

Wolkenhauer O, Auffray C, Brass O, Clairambault J, Deutsch A, Drasdo D, Gervasio F, Preziosi L, Maini P, Marciniak-Czochra A, Kossow C, Kuepfer L, Rateitschak K, Ramis-Conde I, Ribba B, Schuppert A, Smallwood R, Stamatakos G, Winter F, Byrne H.
PMID: 25031615
Genome Med. 2014 Mar 21;6(3):21. doi: 10.1186/gm538. eCollection 2014.

No abstract available.

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Wolkenhauer O, Auffray C, Brass O, et al. Enabling multiscale modeling in systems medicine. Genome Med. 2014;6(3):21doi: 10.1186/gm538.
Wolkenhauer, O., Auffray, C., Brass, O., Clairambault, J., Deutsch, A., Drasdo, D., Gervasio, F., Preziosi, L., Maini, P., Marciniak-Czochra, A., Kossow, C., Kuepfer, L., Rateitschak, K., Ramis-Conde, I., Ribba, B., Schuppert, A., Smallwood, R., Stamatakos, G., Winter, F., & Byrne, H. (2014). Enabling multiscale modeling in systems medicine. Genome medicine, 6(3), 21. https://doi.org/10.1186/gm538
Wolkenhauer, Olaf, et al. "Enabling multiscale modeling in systems medicine." Genome medicine vol. 6,3 (2014): 21. doi: https://doi.org/10.1186/gm538
Wolkenhauer O, Auffray C, Brass O, Clairambault J, Deutsch A, Drasdo D, Gervasio F, Preziosi L, Maini P, Marciniak-Czochra A, Kossow C, Kuepfer L, Rateitschak K, Ramis-Conde I, Ribba B, Schuppert A, Smallwood R, Stamatakos G, Winter F, Byrne H. Enabling multiscale modeling in systems medicine. Genome Med. 2014 Mar 21;6(3):21. doi: 10.1186/gm538. eCollection 2014. PMID: 25031615; PMCID: PMC4062045.
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Transferring genomics to the clinic: distinguishing Burkitt and diffuse large B cell lymphomas.

Genome medicine

Sha C, Barrans S, Care MA, Cunningham D, Tooze RM, Jack A, Westhead DR.
PMID: 26207141
Genome Med. 2015 Jul 01;7(1):64. doi: 10.1186/s13073-015-0187-6. eCollection 2015.

BACKGROUND: Classifiers based on molecular criteria such as gene expression signatures have been developed to distinguish Burkitt lymphoma and diffuse large B cell lymphoma, which help to explore the intermediate cases where traditional diagnosis is difficult. Transfer of these...

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Sha C, Barrans S, Care MA, et al. Transferring genomics to the clinic: distinguishing Burkitt and diffuse large B cell lymphomas. Genome Med. 2015;7(1):64doi: 10.1186/s13073-015-0187-6.
Sha, C., Barrans, S., Care, M. A., Cunningham, D., Tooze, R. M., Jack, A., & Westhead, D. R. (2015). Transferring genomics to the clinic: distinguishing Burkitt and diffuse large B cell lymphomas. Genome medicine, 7(1), 64. https://doi.org/10.1186/s13073-015-0187-6
Sha, Chulin, et al. "Transferring genomics to the clinic: distinguishing Burkitt and diffuse large B cell lymphomas." Genome medicine vol. 7,1 (2015): 64. doi: https://doi.org/10.1186/s13073-015-0187-6
Sha C, Barrans S, Care MA, Cunningham D, Tooze RM, Jack A, Westhead DR. Transferring genomics to the clinic: distinguishing Burkitt and diffuse large B cell lymphomas. Genome Med. 2015 Jul 01;7(1):64. doi: 10.1186/s13073-015-0187-6. eCollection 2015. PMID: 26207141; PMCID: PMC4512160.
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A missing link in the bench-to-bedside paradigm: engaging regulatory stakeholders in clinical genomics research.

Genome medicine

O'Daniel JM, Berg JS.
PMID: 27655359
Genome Med. 2016 Sep 21;8(1):95. doi: 10.1186/s13073-016-0351-7.

For genomic medicine research to be fully translated into clinical care, it is critical for researchers to engage stakeholders who ultimately regulate the use of genomic technologies and therapeutics within healthcare practice. Herein, we describe an example of how...

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O'Daniel JM, Berg JS. A missing link in the bench-to-bedside paradigm: engaging regulatory stakeholders in clinical genomics research. Genome Med. 2016;8(1):95doi: 10.1186/s13073-016-0351-7.
O'Daniel, J. M., & Berg, J. S. (2016). A missing link in the bench-to-bedside paradigm: engaging regulatory stakeholders in clinical genomics research. Genome medicine, 8(1), 95. https://doi.org/10.1186/s13073-016-0351-7
O'Daniel, Julianne M, and Berg, Jonathan S. "A missing link in the bench-to-bedside paradigm: engaging regulatory stakeholders in clinical genomics research." Genome medicine vol. 8,1 (2016): 95. doi: https://doi.org/10.1186/s13073-016-0351-7
O'Daniel JM, Berg JS. A missing link in the bench-to-bedside paradigm: engaging regulatory stakeholders in clinical genomics research. Genome Med. 2016 Sep 21;8(1):95. doi: 10.1186/s13073-016-0351-7. PMID: 27655359; PMCID: PMC5031300.
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Reconciling evidence-based medicine and precision medicine in the era of big data: challenges and opportunities.

Genome medicine

Beckmann JS, Lew D.
PMID: 27993174
Genome Med. 2016 Dec 19;8(1):134. doi: 10.1186/s13073-016-0388-7.

This era of groundbreaking scientific developments in high-resolution, high-throughput technologies is allowing the cost-effective collection and analysis of huge, disparate datasets on individual health. Proper data mining and translation of the vast datasets into clinically actionable knowledge will require...

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Beckmann JS, Lew D. Reconciling evidence-based medicine and precision medicine in the era of big data: challenges and opportunities. Genome Med. 2016;8(1):134doi: 10.1186/s13073-016-0388-7.
Beckmann, J. S., & Lew, D. (2016). Reconciling evidence-based medicine and precision medicine in the era of big data: challenges and opportunities. Genome medicine, 8(1), 134. https://doi.org/10.1186/s13073-016-0388-7
Beckmann, Jacques S, and Lew, Daniel. "Reconciling evidence-based medicine and precision medicine in the era of big data: challenges and opportunities." Genome medicine vol. 8,1 (2016): 134. doi: https://doi.org/10.1186/s13073-016-0388-7
Beckmann JS, Lew D. Reconciling evidence-based medicine and precision medicine in the era of big data: challenges and opportunities. Genome Med. 2016 Dec 19;8(1):134. doi: 10.1186/s13073-016-0388-7. PMID: 27993174; PMCID: PMC5165712.
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Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study.

Genome medicine

Sanderson SC, Linderman MD, Kasarskis A, Bashir A, Diaz GA, Mahajan MC, Shah H, Wasserstein M, Zinberg RE, Zweig M, Schadt EE.
PMID: 24373383
Genome Med. 2013 Dec 30;5(12):113. doi: 10.1186/gm518. eCollection 2013.

BACKGROUND: Multiple laboratories now offer clinical whole genome sequencing (WGS). We anticipate WGS becoming routinely used in research and clinical practice. Many institutions are exploring how best to educate geneticists and other professionals about WGS. Providing students in WGS...

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Sanderson SC, Linderman MD, Kasarskis A, et al. Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study. Genome Med. 2013;5(12):113doi: 10.1186/gm518.
Sanderson, S. C., Linderman, M. D., Kasarskis, A., Bashir, A., Diaz, G. A., Mahajan, M. C., Shah, H., Wasserstein, M., Zinberg, R. E., Zweig, M., & Schadt, E. E. (2013). Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study. Genome medicine, 5(12), 113. https://doi.org/10.1186/gm518
Sanderson, Saskia C, et al. "Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study." Genome medicine vol. 5,12 (2013): 113. doi: https://doi.org/10.1186/gm518
Sanderson SC, Linderman MD, Kasarskis A, Bashir A, Diaz GA, Mahajan MC, Shah H, Wasserstein M, Zinberg RE, Zweig M, Schadt EE. Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study. Genome Med. 2013 Dec 30;5(12):113. doi: 10.1186/gm518. eCollection 2013. PMID: 24373383; PMCID: PMC3971344.
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Erratum to: a SNP profiling panel for sample tracking in whole-exome sequencing studies.

Genome medicine

Pengelly RJ, Gibson J, Andreoletti G, Collins A, Mattocks CJ, Ennis S.
PMID: 25949530
Genome Med. 2015 May 07;7(1):44. doi: 10.1186/s13073-015-0163-1. eCollection 2015.

This is an Erratum to Genome Medicine 2013, 5:89, highlighting an error in Table 1 of the original article. Please see related article: http://genomemedicine.com/content/5/9/89.[This corrects the article DOI: 10.1186/gm492.].

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Pengelly RJ, Gibson J, Andreoletti G, et al. Erratum to: a SNP profiling panel for sample tracking in whole-exome sequencing studies. Genome Med. 2015;7(1):44doi: 10.1186/s13073-015-0163-1.
Pengelly, R. J., Gibson, J., Andreoletti, G., Collins, A., Mattocks, C. J., & Ennis, S. (2015). Erratum to: a SNP profiling panel for sample tracking in whole-exome sequencing studies. Genome medicine, 7(1), 44. https://doi.org/10.1186/s13073-015-0163-1
Pengelly, Reuben J, et al. "Erratum to: a SNP profiling panel for sample tracking in whole-exome sequencing studies." Genome medicine vol. 7,1 (2015): 44. doi: https://doi.org/10.1186/s13073-015-0163-1
Pengelly RJ, Gibson J, Andreoletti G, Collins A, Mattocks CJ, Ennis S. Erratum to: a SNP profiling panel for sample tracking in whole-exome sequencing studies. Genome Med. 2015 May 07;7(1):44. doi: 10.1186/s13073-015-0163-1. eCollection 2015. PMID: 25949530; PMCID: PMC4422541.
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Returning individual research results for genome sequences of pancreatic cancer.

Genome medicine

Johns AL, Miller DK, Simpson SH, Gill AJ, Kassahn KS, Humphris JL, Samra JS, Tucker K, Andrews L, Chang DK, Waddell N, Pajic M, Pearson JV, Grimmond SM, Biankin AV, Zeps N.
PMID: 24963353
Genome Med. 2014 May 29;6(5):42. doi: 10.1186/gm558. eCollection 2014.

BACKGROUND: Disclosure of individual results to participants in genomic research is a complex and contentious issue. There are many existing commentaries and opinion pieces on the topic, but little empirical data concerning actual cases describing how individual results have...

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Johns AL, Miller DK, Simpson SH, et al. Returning individual research results for genome sequences of pancreatic cancer. Genome Med. 2014;6(5):42doi: 10.1186/gm558.
Johns, A. L., Miller, D. K., Simpson, S. H., Gill, A. J., Kassahn, K. S., Humphris, J. L., Samra, J. S., Tucker, K., Andrews, L., Chang, D. K., Waddell, N., Pajic, M., Pearson, J. V., Grimmond, S. M., Biankin, A. V., & Zeps, N. (2014). Returning individual research results for genome sequences of pancreatic cancer. Genome medicine, 6(5), 42. https://doi.org/10.1186/gm558
Johns, Amber L, et al. "Returning individual research results for genome sequences of pancreatic cancer." Genome medicine vol. 6,5 (2014): 42. doi: https://doi.org/10.1186/gm558
Johns AL, Miller DK, Simpson SH, Gill AJ, Kassahn KS, Humphris JL, Samra JS, Tucker K, Andrews L, Chang DK, Waddell N, Pajic M, Pearson JV, Grimmond SM, Biankin AV, Zeps N. Returning individual research results for genome sequences of pancreatic cancer. Genome Med. 2014 May 29;6(5):42. doi: 10.1186/gm558. eCollection 2014. PMID: 24963353; PMCID: PMC4067993.
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From small studies to precision medicine: prioritizing candidate biomarkers.

Genome medicine

Gaile DP, Miecznikowski JC.
PMID: 24286480
Genome Med. 2013 Nov 29;5(11):104. doi: 10.1186/gm507. eCollection 2013.

There are still many open questions in data-analytic research pertaining to biomarker development in the era of personalized/precision medicine and big data. Among them is the question of what constitutes best practice for the extraction of prioritized lists of...

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Gaile DP, Miecznikowski JC. From small studies to precision medicine: prioritizing candidate biomarkers. Genome Med. 2013;5(11):104doi: 10.1186/gm507.
Gaile, D. P., & Miecznikowski, J. C. (2013). From small studies to precision medicine: prioritizing candidate biomarkers. Genome medicine, 5(11), 104. https://doi.org/10.1186/gm507
Gaile, Daniel P, and Miecznikowski, Jeffrey C. "From small studies to precision medicine: prioritizing candidate biomarkers." Genome medicine vol. 5,11 (2013): 104. doi: https://doi.org/10.1186/gm507
Gaile DP, Miecznikowski JC. From small studies to precision medicine: prioritizing candidate biomarkers. Genome Med. 2013 Nov 29;5(11):104. doi: 10.1186/gm507. eCollection 2013. PMID: 24286480; PMCID: PMC3978446.
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Whole-genome haplotyping approaches and genomic medicine.

Genome medicine

Glusman G, Cox HC, Roach JC.
PMID: 25473435
Genome Med. 2014 Sep 25;6(9):73. doi: 10.1186/s13073-014-0073-7. eCollection 2014.

Genomic information reported as haplotypes rather than genotypes will be increasingly important for personalized medicine. Current technologies generate diploid sequence data that is rarely resolved into its constituent haplotypes. Furthermore, paradigms for thinking about genomic information are based on...

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Glusman G, Cox HC, Roach JC. Whole-genome haplotyping approaches and genomic medicine. Genome Med. 2014;6(9):73doi: 10.1186/s13073-014-0073-7.
Glusman, G., Cox, H. C., & Roach, J. C. (2014). Whole-genome haplotyping approaches and genomic medicine. Genome medicine, 6(9), 73. https://doi.org/10.1186/s13073-014-0073-7
Glusman, Gustavo, et al. "Whole-genome haplotyping approaches and genomic medicine." Genome medicine vol. 6,9 (2014): 73. doi: https://doi.org/10.1186/s13073-014-0073-7
Glusman G, Cox HC, Roach JC. Whole-genome haplotyping approaches and genomic medicine. Genome Med. 2014 Sep 25;6(9):73. doi: 10.1186/s13073-014-0073-7. eCollection 2014. PMID: 25473435; PMCID: PMC4254418.
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Genomic data sharing for translational research and diagnostics.

Genome medicine

Robinson PN.
PMID: 25473437
Genome Med. 2014 Sep 26;6(9):78. doi: 10.1186/s13073-014-0078-2. eCollection 2014.

Translational genomics is changing, not only in the technology used but also in the sharing of data. The enormous potential for genomics technologies to improve patient care has been recognized, but it will not be reached unless powerful but...

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Robinson PN. Genomic data sharing for translational research and diagnostics. Genome Med. 2014;6(9):78doi: 10.1186/s13073-014-0078-2.
Robinson, P. N. (2014). Genomic data sharing for translational research and diagnostics. Genome medicine, 6(9), 78. https://doi.org/10.1186/s13073-014-0078-2
Robinson, Peter N. "Genomic data sharing for translational research and diagnostics." Genome medicine vol. 6,9 (2014): 78. doi: https://doi.org/10.1186/s13073-014-0078-2
Robinson PN. Genomic data sharing for translational research and diagnostics. Genome Med. 2014 Sep 26;6(9):78. doi: 10.1186/s13073-014-0078-2. eCollection 2014. PMID: 25473437; PMCID: PMC4254431.
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Showing 1 to 12 of 946 entries