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Whole-genome sequencing as a first-tier diagnostic framework for rare genetic diseases.

Experimental biology and medicine (Maywood, N.J.)

Nisar H, Wajid B, Shahid S, Anwar F, Wajid I, Khatoon A, Sattar MU, Sadaf S.
PMID: 34521224
Exp Biol Med (Maywood). 2021 Dec;246(24):2610-2617. doi: 10.1177/15353702211040046. Epub 2021 Sep 15.

Rare diseases affect nearly 300 million people globally with most patients aged five or less. Traditional diagnostic approaches have provided much of the diagnosis; however, there are limitations. For instance, simply inadequate and untimely diagnosis adversely affects both the...

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Nisar H, Wajid B, Shahid S, et al. Whole-genome sequencing as a first-tier diagnostic framework for rare genetic diseases. Exp Biol Med (Maywood). 2021;246(24):2610-2617doi: 10.1177/15353702211040046.
Nisar, H., Wajid, B., Shahid, S., Anwar, F., Wajid, I., Khatoon, A., Sattar, M. U., & Sadaf, S. (2021). Whole-genome sequencing as a first-tier diagnostic framework for rare genetic diseases. Experimental biology and medicine (Maywood, N.J.), 246(24), 2610-2617. https://doi.org/10.1177/15353702211040046
Nisar, Haseeb, et al. "Whole-genome sequencing as a first-tier diagnostic framework for rare genetic diseases." Experimental biology and medicine (Maywood, N.J.) vol. 246,24 (2021): 2610-2617. doi: https://doi.org/10.1177/15353702211040046
Nisar H, Wajid B, Shahid S, Anwar F, Wajid I, Khatoon A, Sattar MU, Sadaf S. Whole-genome sequencing as a first-tier diagnostic framework for rare genetic diseases. Exp Biol Med (Maywood). 2021 Dec;246(24):2610-2617. doi: 10.1177/15353702211040046. Epub 2021 Sep 15. PMID: 34521224; PMCID: PMC8669166.
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Copy-Number Variants Detection by Low-Pass Whole-Genome Sequencing.

Current protocols in human genetics

Dong Z, Xie W, Chen H, Xu J, Wang H, Li Y, Wang J, Chen F, Choy KW, Jiang H.
PMID: 28696555
Curr Protoc Hum Genet. 2017 Jul 11;94:8.17.1-8.17.16. doi: 10.1002/cphg.43.

Emerging studies have demonstrated that whole-genome sequencing (WGS) is an efficient tool for copy-number variants (CNV) detection, particularly in probe-poor regions, as compared to chromosomal microarray analysis (CMA). However, the cost of testing is beyond economical for routine usage...

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Dong Z, Xie W, Chen H, et al. Copy-Number Variants Detection by Low-Pass Whole-Genome Sequencing. Curr Protoc Hum Genet. 2017;94:8.17.1-8.17.16doi: 10.1002/cphg.43.
Dong, Z., Xie, W., Chen, H., Xu, J., Wang, H., Li, Y., Wang, J., Chen, F., Choy, K. W., & Jiang, H. (2017). Copy-Number Variants Detection by Low-Pass Whole-Genome Sequencing. Current protocols in human genetics, 948.17.1-8.17.16. https://doi.org/10.1002/cphg.43
Dong, Zirui, et al. "Copy-Number Variants Detection by Low-Pass Whole-Genome Sequencing." Current protocols in human genetics vol. 94 (2017): 8.17.1-8.17.16. doi: https://doi.org/10.1002/cphg.43
Dong Z, Xie W, Chen H, Xu J, Wang H, Li Y, Wang J, Chen F, Choy KW, Jiang H. Copy-Number Variants Detection by Low-Pass Whole-Genome Sequencing. Curr Protoc Hum Genet. 2017 Jul 11;94:8.17.1-8.17.16. doi: 10.1002/cphg.43. PMID: 28696555.
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Kronos: a workflow assembler for genome analytics and informatics.

GigaScience

Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP.
PMID: 28655203
Gigascience. 2017 Jul 01;6(7):1-10. doi: 10.1093/gigascience/gix042.

BACKGROUND: The field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into...

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Taghiyar MJ, Rosner J, Grewal D, et al. Kronos: a workflow assembler for genome analytics and informatics. Gigascience. 2017;6(7):1-10doi: 10.1093/gigascience/gix042.
Taghiyar, M. J., Rosner, J., Grewal, D., Grande, B. M., Aniba, R., Grewal, J., Boutros, P. C., Morin, R. D., Bashashati, A., & Shah, S. P. (2017). Kronos: a workflow assembler for genome analytics and informatics. GigaScience, 6(7), 1-10. https://doi.org/10.1093/gigascience/gix042
Taghiyar, M Jafar, et al. "Kronos: a workflow assembler for genome analytics and informatics." GigaScience vol. 6,7 (2017): 1-10. doi: https://doi.org/10.1093/gigascience/gix042
Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP. Kronos: a workflow assembler for genome analytics and informatics. Gigascience. 2017 Jul 01;6(7):1-10. doi: 10.1093/gigascience/gix042. PMID: 28655203; PMCID: PMC5569921.
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Clustering Analysis Supports the Detection of Biological Processes Related to Autism Spectrum Disorder.

Genes

Emberti Gialloreti L, Enea R, Di Micco V, Di Giovanni D, Curatolo P.
PMID: 33316975
Genes (Basel). 2020 Dec 09;11(12). doi: 10.3390/genes11121476.

Genome sequencing has identified a large number of putative autism spectrum disorder (ASD) risk genes, revealing possible disrupted biological pathways; however, the genetic and environmental underpinnings of ASD remain mostly unanswered. The presented methodology aimed to identify genetically related...

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Emberti Gialloreti L, Enea R, Di Micco V, et al. Clustering Analysis Supports the Detection of Biological Processes Related to Autism Spectrum Disorder. Genes (Basel). 2020;11(12)doi: 10.3390/genes11121476.
Emberti Gialloreti, L., Enea, R., Di Micco, V., Di Giovanni, D., & Curatolo, P. (2020). Clustering Analysis Supports the Detection of Biological Processes Related to Autism Spectrum Disorder. Genes, 11(12), . https://doi.org/10.3390/genes11121476
Emberti Gialloreti, Leonardo, et al. "Clustering Analysis Supports the Detection of Biological Processes Related to Autism Spectrum Disorder." Genes vol. 11,12 (2020). doi: https://doi.org/10.3390/genes11121476
Emberti Gialloreti L, Enea R, Di Micco V, Di Giovanni D, Curatolo P. Clustering Analysis Supports the Detection of Biological Processes Related to Autism Spectrum Disorder. Genes (Basel). 2020 Dec 09;11(12). doi: 10.3390/genes11121476. PMID: 33316975; PMCID: PMC7763205.
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From exomes to genomes: challenges and solutions in population-based genetic association studies.

European journal of human genetics : EJHG

Auer PL, Leal SM.
PMID: 28120836
Eur J Hum Genet. 2017 Apr;25(4):395-396. doi: 10.1038/ejhg.2016.206. Epub 2017 Jan 25.

No abstract available.

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Auer PL, Leal SM. From exomes to genomes: challenges and solutions in population-based genetic association studies. Eur J Hum Genet. 2017;25(4):395-396doi: 10.1038/ejhg.2016.206.
Auer, P. L., & Leal, S. M. (2017). From exomes to genomes: challenges and solutions in population-based genetic association studies. European journal of human genetics : EJHG, 25(4), 395-396. https://doi.org/10.1038/ejhg.2016.206
Auer, Paul L, and Leal, Suzanne M. "From exomes to genomes: challenges and solutions in population-based genetic association studies." European journal of human genetics : EJHG vol. 25,4 (2017): 395-396. doi: https://doi.org/10.1038/ejhg.2016.206
Auer PL, Leal SM. From exomes to genomes: challenges and solutions in population-based genetic association studies. Eur J Hum Genet. 2017 Apr;25(4):395-396. doi: 10.1038/ejhg.2016.206. Epub 2017 Jan 25. PMID: 28120836; PMCID: PMC5386426.
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The nuanced negative: Meanings of a negative diagnostic result in clinical exome sequencing.

Sociology of health & illness

Skinner D, Raspberry KA, King M.
PMID: 27538589
Sociol Health Illn. 2016 Nov;38(8):1303-1317. doi: 10.1111/1467-9566.12460. Epub 2016 Aug 19.

Genomic sequencing technology is moving rapidly from the research setting into clinical medicine but significant technological and interpretive challenges remain. Exome sequencing (ES) in its recent clinical application provides a genetic diagnosis in about 25 per cent of cases...

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Skinner D, Raspberry KA, King M. The nuanced negative: Meanings of a negative diagnostic result in clinical exome sequencing. Sociol Health Illn. 2016;38(8):1303-1317doi: 10.1111/1467-9566.12460.
Skinner, D., Raspberry, K. A., & King, M. (2016). The nuanced negative: Meanings of a negative diagnostic result in clinical exome sequencing. Sociology of health & illness, 38(8), 1303-1317. https://doi.org/10.1111/1467-9566.12460
Skinner, Debra, et al. "The nuanced negative: Meanings of a negative diagnostic result in clinical exome sequencing." Sociology of health & illness vol. 38,8 (2016): 1303-1317. doi: https://doi.org/10.1111/1467-9566.12460
Skinner D, Raspberry KA, King M. The nuanced negative: Meanings of a negative diagnostic result in clinical exome sequencing. Sociol Health Illn. 2016 Nov;38(8):1303-1317. doi: 10.1111/1467-9566.12460. Epub 2016 Aug 19. PMID: 27538589; PMCID: PMC5089912.
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Ensemble outlier detection and gene selection in triple-negative breast cancer data.

BMC bioinformatics

Lopes MB, Veríssimo A, Carrasquinha E, Casimiro S, Beerenwinkel N, Vinga S.
PMID: 29728051
BMC Bioinformatics. 2018 May 04;19(1):168. doi: 10.1186/s12859-018-2149-7.

BACKGROUND: Learning accurate models from 'omics data is bringing many challenges due to their inherent high-dimensionality, e.g. the number of gene expression variables, and comparatively lower sample sizes, which leads to ill-posed inverse problems. Furthermore, the presence of outliers,...

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Lopes MB, Veríssimo A, Carrasquinha E, et al. Ensemble outlier detection and gene selection in triple-negative breast cancer data. BMC Bioinformatics. 2018;19(1):168doi: 10.1186/s12859-018-2149-7.
Lopes, M. B., Veríssimo, A., Carrasquinha, E., Casimiro, S., Beerenwinkel, N., & Vinga, S. (2018). Ensemble outlier detection and gene selection in triple-negative breast cancer data. BMC bioinformatics, 19(1), 168. https://doi.org/10.1186/s12859-018-2149-7
Lopes, Marta B, et al. "Ensemble outlier detection and gene selection in triple-negative breast cancer data." BMC bioinformatics vol. 19,1 (2018): 168. doi: https://doi.org/10.1186/s12859-018-2149-7
Lopes MB, Veríssimo A, Carrasquinha E, Casimiro S, Beerenwinkel N, Vinga S. Ensemble outlier detection and gene selection in triple-negative breast cancer data. BMC Bioinformatics. 2018 May 04;19(1):168. doi: 10.1186/s12859-018-2149-7. PMID: 29728051; PMCID: PMC5936001.
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Total number of reads affects the accuracy of fetal fraction estimates in NIPT.

Molecular genetics & genomic medicine

Miceikaitė I, Brasch-Andersen C, Fagerberg C, Larsen MJ.
PMID: 33687149
Mol Genet Genomic Med. 2021 Apr;9(4):e1653. doi: 10.1002/mgg3.1653. Epub 2021 Mar 09.

BACKGROUND: Sufficient fetal fraction (FF) is crucial for quality control of NIPT (Non-Invasive Prenatal Test) results. Different factors influencing bioinformatic estimation of FF should be considered when implementing NIPT. To what extent the total number of sequencing reads influences...

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Miceikaitė I, Brasch-Andersen C, Fagerberg C, et al. Total number of reads affects the accuracy of fetal fraction estimates in NIPT. Mol Genet Genomic Med. 2021;9(4):e1653doi: 10.1002/mgg3.1653.
Miceikaitė, I., Brasch-Andersen, C., Fagerberg, C., & Larsen, M. J. (2021). Total number of reads affects the accuracy of fetal fraction estimates in NIPT. Molecular genetics & genomic medicine, 9(4), e1653. https://doi.org/10.1002/mgg3.1653
Miceikaitė, Ieva, et al. "Total number of reads affects the accuracy of fetal fraction estimates in NIPT." Molecular genetics & genomic medicine vol. 9,4 (2021): e1653. doi: https://doi.org/10.1002/mgg3.1653
Miceikaitė I, Brasch-Andersen C, Fagerberg C, Larsen MJ. Total number of reads affects the accuracy of fetal fraction estimates in NIPT. Mol Genet Genomic Med. 2021 Apr;9(4):e1653. doi: 10.1002/mgg3.1653. Epub 2021 Mar 09. PMID: 33687149; PMCID: PMC8123752.
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A Simple Practical Guide to Genomic Diagnostics in a Pediatric Setting.

Genes

Taylor A, Alloub Z, Tayoun AA.
PMID: 34071827
Genes (Basel). 2021 May 27;12(6). doi: 10.3390/genes12060818.

With limited access to trained clinical geneticists and/or genetic counselors in the majority of healthcare systems globally, and the expanding use of genetic testing in all specialties of medicine, many healthcare providers do not receive the relevant support to...

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Taylor A, Alloub Z, Tayoun AA. A Simple Practical Guide to Genomic Diagnostics in a Pediatric Setting. Genes (Basel). 2021;12(6)doi: 10.3390/genes12060818.
Taylor, A., Alloub, Z., & Tayoun, A. A. (2021). A Simple Practical Guide to Genomic Diagnostics in a Pediatric Setting. Genes, 12(6), . https://doi.org/10.3390/genes12060818
Taylor, Alan, et al. "A Simple Practical Guide to Genomic Diagnostics in a Pediatric Setting." Genes vol. 12,6 (2021). doi: https://doi.org/10.3390/genes12060818
Taylor A, Alloub Z, Tayoun AA. A Simple Practical Guide to Genomic Diagnostics in a Pediatric Setting. Genes (Basel). 2021 May 27;12(6). doi: 10.3390/genes12060818. PMID: 34071827; PMCID: PMC8228870.
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Showing 1 to 9 of 9 entries