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Showing 1 to 12 of 15 entries
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Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimages.

BMC bioinformatics

Dander A, Baldauf M, Sperk M, Pabinger S, Hiltpolt B, Trajanoski Z.
PMID: 25230706
BMC Bioinformatics. 2014 Sep 18;15:306. doi: 10.1186/1471-2105-15-306.

BACKGROUND: Cancer immunotherapy has recently entered a remarkable renaissance phase with the approval of several agents for treatment. Cancer treatment platforms have demonstrated profound tumor regressions including complete cure in patients with metastatic cancer. Moreover, technological advances in next-generation...

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Dander A, Baldauf M, Sperk M, et al. Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimages. BMC Bioinformatics. 2014;15:306doi: 10.1186/1471-2105-15-306.
Dander, A., Baldauf, M., Sperk, M., Pabinger, S., Hiltpolt, B., & Trajanoski, Z. (2014). Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimages. BMC bioinformatics, 15306. https://doi.org/10.1186/1471-2105-15-306
Dander, Andreas, et al. "Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimages." BMC bioinformatics vol. 15 (2014): 306. doi: https://doi.org/10.1186/1471-2105-15-306
Dander A, Baldauf M, Sperk M, Pabinger S, Hiltpolt B, Trajanoski Z. Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimages. BMC Bioinformatics. 2014 Sep 18;15:306. doi: 10.1186/1471-2105-15-306. PMID: 25230706; PMCID: PMC4261581.
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Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk.

International journal of cancer

Dai J, Huang M, Amos CI, Hung RJ, Tardon A, Andrew A, Chen C, Christiani DC, Albanes D, Rennert G, Fan J, Goodman G, Liu G, Field JK, Grankvist K, Kiemeney LA, Le Marchand L, Schabath MB, Johansson M, Aldrich MC, Johansson M, Caporaso N, Lazarus P, Lam S, Bojesen SE, Arnold S, Landi MT, Risch A, Wichmann HE, Bickeboller H, Brennan P, Shete S, Melander O, Brunnstrom H, Zienolddiny S, Woll P, Stevens V, Hu Z, Shen H.
PMID: 31577861
Int J Cancer. 2020 May 15;146(10):2855-2864. doi: 10.1002/ijc.32698. Epub 2019 Oct 31.

Genome-wide association studies (GWAS) have identified 45 susceptibility loci associated with lung cancer. Only less than SNPs, small insertions and deletions (INDELs) are the second most abundant genetic polymorphisms in the human genome. INDELs are highly associated with multiple...

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Dai J, Huang M, Amos CI, et al. Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk. Int J Cancer. 2019;146(10):2855-2864doi: 10.1002/ijc.32698.
Dai, J., Huang, M., Amos, C. I., Hung, R. J., Tardon, A., Andrew, A., Chen, C., Christiani, D. C., Albanes, D., Rennert, G., Fan, J., Goodman, G., Liu, G., Field, J. K., Grankvist, K., Kiemeney, L. A., Le Marchand, L., Schabath, M. B., Johansson, M., Aldrich, M. C., Johansson, M., Caporaso, N., Lazarus, P., Lam, S., Bojesen, S. E., Arnold, S., Landi, M. T., Risch, A., Wichmann, H. E., Bickeboller, H., Brennan, P., Shete, S., Melander, O., Brunnstrom, H., Zienolddiny, S., Woll, P., Stevens, V., Hu, Z., & Shen, H. (2020). Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk. International journal of cancer, 146(10), 2855-2864. https://doi.org/10.1002/ijc.32698
Dai, Juncheng, et al. "Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk." International journal of cancer vol. 146,10 (2020): 2855-2864. doi: https://doi.org/10.1002/ijc.32698
Dai J, Huang M, Amos CI, Hung RJ, Tardon A, Andrew A, Chen C, Christiani DC, Albanes D, Rennert G, Fan J, Goodman G, Liu G, Field JK, Grankvist K, Kiemeney LA, Le Marchand L, Schabath MB, Johansson M, Aldrich MC, Johansson M, Caporaso N, Lazarus P, Lam S, Bojesen SE, Arnold S, Landi MT, Risch A, Wichmann HE, Bickeboller H, Brennan P, Shete S, Melander O, Brunnstrom H, Zienolddiny S, Woll P, Stevens V, Hu Z, Shen H. Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk. Int J Cancer. 2020 May 15;146(10):2855-2864. doi: 10.1002/ijc.32698. Epub 2019 Oct 31. PMID: 31577861; PMCID: PMC7101262.
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RNAIndel: discovering somatic coding indels from tumor RNA-Seq data.

Bioinformatics (Oxford, England)

Hagiwara K, Ding L, Edmonson MN, Rice SV, Newman S, Easton J, Dai J, Meshinchi S, Ries RE, Rusch M, Zhang J.
PMID: 31593214
Bioinformatics. 2020 Mar 01;36(5):1382-1390. doi: 10.1093/bioinformatics/btz753.

MOTIVATION: Reliable identification of expressed somatic insertions/deletions (indels) is an unmet need due to artifacts generated in PCR-based RNA-Seq library preparation and the lack of normal RNA-Seq data, presenting analytical challenges for discovery of somatic indels in tumor transcriptome.RESULTS:...

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Hagiwara K, Ding L, Edmonson MN, et al. RNAIndel: discovering somatic coding indels from tumor RNA-Seq data. Bioinformatics. 2020;36(5):1382-1390doi: 10.1093/bioinformatics/btz753.
Hagiwara, K., Ding, L., Edmonson, M. N., Rice, S. V., Newman, S., Easton, J., Dai, J., Meshinchi, S., Ries, R. E., Rusch, M., & Zhang, J. (2020). RNAIndel: discovering somatic coding indels from tumor RNA-Seq data. Bioinformatics (Oxford, England), 36(5), 1382-1390. https://doi.org/10.1093/bioinformatics/btz753
Hagiwara, Kohei, et al. "RNAIndel: discovering somatic coding indels from tumor RNA-Seq data." Bioinformatics (Oxford, England) vol. 36,5 (2020): 1382-1390. doi: https://doi.org/10.1093/bioinformatics/btz753
Hagiwara K, Ding L, Edmonson MN, Rice SV, Newman S, Easton J, Dai J, Meshinchi S, Ries RE, Rusch M, Zhang J. RNAIndel: discovering somatic coding indels from tumor RNA-Seq data. Bioinformatics. 2020 Mar 01;36(5):1382-1390. doi: 10.1093/bioinformatics/btz753. PMID: 31593214; PMCID: PMC7523641.
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dbCID: a manually curated resource for exploring the driver indels in human cancer.

Briefings in bioinformatics

Yue Z, Zhao L, Cheng N, Yan H, Xia J.
PMID: 30016397
Brief Bioinform. 2019 Sep 27;20(5):1925-1933. doi: 10.1093/bib/bby059.

While recent advances in next-generation sequencing technologies have enabled the creation of a multitude of databases in cancer genomic research, there is no comprehensive database focusing on the annotation of driver indels (insertions and deletions) yet. Therefore, we have...

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Yue Z, Zhao L, Cheng N, et al. dbCID: a manually curated resource for exploring the driver indels in human cancer. Brief Bioinform. 2019;20(5):1925-1933doi: 10.1093/bib/bby059.
Yue, Z., Zhao, L., Cheng, N., Yan, H., & Xia, J. (2019). dbCID: a manually curated resource for exploring the driver indels in human cancer. Briefings in bioinformatics, 20(5), 1925-1933. https://doi.org/10.1093/bib/bby059
Yue, Zhenyu, et al. "dbCID: a manually curated resource for exploring the driver indels in human cancer." Briefings in bioinformatics vol. 20,5 (2019): 1925-1933. doi: https://doi.org/10.1093/bib/bby059
Yue Z, Zhao L, Cheng N, Yan H, Xia J. dbCID: a manually curated resource for exploring the driver indels in human cancer. Brief Bioinform. 2019 Sep 27;20(5):1925-1933. doi: 10.1093/bib/bby059. PMID: 30016397.
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MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations.

BMC medical genomics

Doan RN, Miller MB, Kim SN, Rodin RE, Ganz J, Bizzotto S, Morillo KS, Huang AY, Digumarthy R, Zemmel Z, Walsh CA.
PMID: 33579278
BMC Med Genomics. 2021 Feb 12;14(1):47. doi: 10.1186/s12920-021-00893-3.

BACKGROUND: Mosaic mutations contribute to numerous human disorders. As such, the identification and precise quantification of mosaic mutations is essential for a wide range of research applications, clinical diagnoses, and early detection of cancers. Currently, the low-throughput nature of...

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Doan RN, Miller MB, Kim SN, et al. MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations. BMC Med Genomics. 2021;14(1):47doi: 10.1186/s12920-021-00893-3.
Doan, R. N., Miller, M. B., Kim, S. N., Rodin, R. E., Ganz, J., Bizzotto, S., Morillo, K. S., Huang, A. Y., Digumarthy, R., Zemmel, Z., & Walsh, C. A. (2021). MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations. BMC medical genomics, 14(1), 47. https://doi.org/10.1186/s12920-021-00893-3
Doan, Ryan N, et al. "MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations." BMC medical genomics vol. 14,1 (2021): 47. doi: https://doi.org/10.1186/s12920-021-00893-3
Doan RN, Miller MB, Kim SN, Rodin RE, Ganz J, Bizzotto S, Morillo KS, Huang AY, Digumarthy R, Zemmel Z, Walsh CA. MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations. BMC Med Genomics. 2021 Feb 12;14(1):47. doi: 10.1186/s12920-021-00893-3. PMID: 33579278; PMCID: PMC7881461.
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Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels.

PloS one

Faircloth BC, Glenn TC.
PMID: 22900027
PLoS One. 2012;7(8):e42543. doi: 10.1371/journal.pone.0042543. Epub 2012 Aug 10.

Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing is a popular and efficient way to obtain sequence data from many individual samples. Tag sequences should be numerous and sufficiently different...

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Faircloth BC, Glenn TC. Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLoS One. 2012;7(8):e42543doi: 10.1371/journal.pone.0042543.
Faircloth, B. C., & Glenn, T. C. (2012). Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PloS one, 7(8), e42543. https://doi.org/10.1371/journal.pone.0042543
Faircloth, Brant C, and Glenn, Travis C. "Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels." PloS one vol. 7,8 (2012): e42543. doi: https://doi.org/10.1371/journal.pone.0042543
Faircloth BC, Glenn TC. Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLoS One. 2012;7(8):e42543. doi: 10.1371/journal.pone.0042543. Epub 2012 Aug 10. PMID: 22900027; PMCID: PMC3416851.
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MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations.

BMC medical genomics

Doan RN, Miller MB, Kim SN, Rodin RE, Ganz J, Bizzotto S, Morillo KS, Huang AY, Digumarthy R, Zemmel Z, Walsh CA.
PMID: 33579278
BMC Med Genomics. 2021 Feb 12;14(1):47. doi: 10.1186/s12920-021-00893-3.

BACKGROUND: Mosaic mutations contribute to numerous human disorders. As such, the identification and precise quantification of mosaic mutations is essential for a wide range of research applications, clinical diagnoses, and early detection of cancers. Currently, the low-throughput nature of...

Cite
Doan RN, Miller MB, Kim SN, et al. MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations. BMC Med Genomics. 2021;14(1):47doi: 10.1186/s12920-021-00893-3.
Doan, R. N., Miller, M. B., Kim, S. N., Rodin, R. E., Ganz, J., Bizzotto, S., Morillo, K. S., Huang, A. Y., Digumarthy, R., Zemmel, Z., & Walsh, C. A. (2021). MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations. BMC medical genomics, 14(1), 47. https://doi.org/10.1186/s12920-021-00893-3
Doan, Ryan N, et al. "MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations." BMC medical genomics vol. 14,1 (2021): 47. doi: https://doi.org/10.1186/s12920-021-00893-3
Doan RN, Miller MB, Kim SN, Rodin RE, Ganz J, Bizzotto S, Morillo KS, Huang AY, Digumarthy R, Zemmel Z, Walsh CA. MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations. BMC Med Genomics. 2021 Feb 12;14(1):47. doi: 10.1186/s12920-021-00893-3. PMID: 33579278; PMCID: PMC7881461.
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Interstitial Deletions Generating Fusion Genes.

Cancer genomics & proteomics

Panagopoulos I, Heim S.
PMID: 33893073
Cancer Genomics Proteomics. 2021 May-Jun;18(3):167-196. doi: 10.21873/cgp.20251.

A fusion gene is the physical juxtaposition of two different genes resulting in a structure consisting of the head of one gene and the tail of the other. Gene fusion is often a primary neoplasia-inducing event in leukemias, lymphomas,...

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Panagopoulos I, Heim S. Interstitial Deletions Generating Fusion Genes. Cancer Genomics Proteomics. 2021;18(3):167-196doi: 10.21873/cgp.20251.
Panagopoulos, I., & Heim, S. (2021). Interstitial Deletions Generating Fusion Genes. Cancer genomics & proteomics, 18(3), 167-196. https://doi.org/10.21873/cgp.20251
Panagopoulos, Ioannis, and Heim, Sverre. "Interstitial Deletions Generating Fusion Genes." Cancer genomics & proteomics vol. 18,3 (2021): 167-196. doi: https://doi.org/10.21873/cgp.20251
Panagopoulos I, Heim S. Interstitial Deletions Generating Fusion Genes. Cancer Genomics Proteomics. 2021 May-Jun;18(3):167-196. doi: 10.21873/cgp.20251. PMID: 33893073; PMCID: PMC8126330.
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Relative impact of indels versus SNPs on complex disease.

Genetic epidemiology

Gagliano SA, Sengupta S, Sidore C, Maschio A, Cucca F, Schlessinger D, Abecasis GR.
PMID: 30565766
Genet Epidemiol. 2019 Feb;43(1):112-117. doi: 10.1002/gepi.22175. Epub 2018 Nov 22.

It is unclear whether insertions and deletions (indels) are more likely to influence complex traits than abundant single-nucleotide polymorphisms (SNPs). We sought to understand which category of variation is more likely to impact health. Using the SardiNIA study as...

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Gagliano SA, Sengupta S, Sidore C, et al. Relative impact of indels versus SNPs on complex disease. Genet Epidemiol. 2018;43(1):112-117doi: 10.1002/gepi.22175.
Gagliano, S. A., Sengupta, S., Sidore, C., Maschio, A., Cucca, F., Schlessinger, D., & Abecasis, G. R. (2019). Relative impact of indels versus SNPs on complex disease. Genetic epidemiology, 43(1), 112-117. https://doi.org/10.1002/gepi.22175
Gagliano, Sarah A, et al. "Relative impact of indels versus SNPs on complex disease." Genetic epidemiology vol. 43,1 (2019): 112-117. doi: https://doi.org/10.1002/gepi.22175
Gagliano SA, Sengupta S, Sidore C, Maschio A, Cucca F, Schlessinger D, Abecasis GR. Relative impact of indels versus SNPs on complex disease. Genet Epidemiol. 2019 Feb;43(1):112-117. doi: 10.1002/gepi.22175. Epub 2018 Nov 22. PMID: 30565766; PMCID: PMC6330128.
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Dynamics of Indel Profiles Induced by Various CRISPR/Cas9 Delivery Methods.

Progress in molecular biology and translational science

Kosicki M, Rajan SS, Lorenzetti FC, Wandall HH, Narimatsu Y, Metzakopian E, Bennett EP.
PMID: 29150004
Prog Mol Biol Transl Sci. 2017;152:49-67. doi: 10.1016/bs.pmbts.2017.09.003. Epub 2017 Nov 06.

The introduction of CRISPR/Cas9 gene editing in mammalian cells is a scientific breakthrough, which has greatly affected basic research and gene therapy. The simplicity and general access to CRISPR/Cas9 reagents has in an unprecedented manner "democratized" gene targeting in...

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Kosicki M, Rajan SS, Lorenzetti FC, et al. Dynamics of Indel Profiles Induced by Various CRISPR/Cas9 Delivery Methods. Prog Mol Biol Transl Sci. 2017;152:49-67doi: 10.1016/bs.pmbts.2017.09.003.
Kosicki, M., Rajan, S. S., Lorenzetti, F. C., Wandall, H. H., Narimatsu, Y., Metzakopian, E., & Bennett, E. P. (2017). Dynamics of Indel Profiles Induced by Various CRISPR/Cas9 Delivery Methods. Progress in molecular biology and translational science, 15249-67. https://doi.org/10.1016/bs.pmbts.2017.09.003
Kosicki, Michael, et al. "Dynamics of Indel Profiles Induced by Various CRISPR/Cas9 Delivery Methods." Progress in molecular biology and translational science vol. 152 (2017): 49-67. doi: https://doi.org/10.1016/bs.pmbts.2017.09.003
Kosicki M, Rajan SS, Lorenzetti FC, Wandall HH, Narimatsu Y, Metzakopian E, Bennett EP. Dynamics of Indel Profiles Induced by Various CRISPR/Cas9 Delivery Methods. Prog Mol Biol Transl Sci. 2017;152:49-67. doi: 10.1016/bs.pmbts.2017.09.003. Epub 2017 Nov 06. PMID: 29150004.
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Filtering de novo indels in parent-offspring trios.

BMC bioinformatics

Liu Y, Liu J, Wang Y.
PMID: 33323105
BMC Bioinformatics. 2020 Dec 16;21:547. doi: 10.1186/s12859-020-03900-z.

BACKGROUND: Identification of de novo indels from whole genome or exome sequencing data of parent-offspring trios is a challenging task in human disease studies and clinical practices. Existing computational approaches usually yield high false positive rate.RESULTS: In this study,...

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Liu Y, Liu J, Wang Y. Filtering de novo indels in parent-offspring trios. BMC Bioinformatics. 2020;21:547doi: 10.1186/s12859-020-03900-z.
Liu, Y., Liu, J., & Wang, Y. (2020). Filtering de novo indels in parent-offspring trios. BMC bioinformatics, 21547. https://doi.org/10.1186/s12859-020-03900-z
Liu, Yongzhuang, et al. "Filtering de novo indels in parent-offspring trios." BMC bioinformatics vol. 21 (2020): 547. doi: https://doi.org/10.1186/s12859-020-03900-z
Liu Y, Liu J, Wang Y. Filtering de novo indels in parent-offspring trios. BMC Bioinformatics. 2020 Dec 16;21:547. doi: 10.1186/s12859-020-03900-z. PMID: 33323105; PMCID: PMC7739476.
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One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation.

Genetics in medicine : official journal of the American College of Medical Genetics

Lincoln SE, Hambuch T, Zook JM, Bristow SL, Hatchell K, Truty R, Kennemer M, Shirts BH, Fellowes A, Chowdhury S, Klee EW, Mahamdallie S, Cleveland MH, Vallone PM, Ding Y, Seal S, DeSilva W, Tomson FL, Huang C, Garlick RK, Rahman N, Salit M, Kingsmore SF, Ferber MJ, Aradhya S, Nussbaum RL.
PMID: 34007000
Genet Med. 2021 Sep;23(9):1673-1680. doi: 10.1038/s41436-021-01187-w. Epub 2021 May 18.

PURPOSE: To evaluate the impact of technically challenging variants on the implementation, validation, and diagnostic yield of commonly used clinical genetic tests. Such variants include large indels, small copy-number variants (CNVs), complex alterations, and variants in low-complexity or segmentally...

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Lincoln SE, Hambuch T, Zook JM, et al. One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation. Genet Med. 2021;23(9):1673-1680doi: 10.1038/s41436-021-01187-w.
Lincoln, S. E., Hambuch, T., Zook, J. M., Bristow, S. L., Hatchell, K., Truty, R., Kennemer, M., Shirts, B. H., Fellowes, A., Chowdhury, S., Klee, E. W., Mahamdallie, S., Cleveland, M. H., Vallone, P. M., Ding, Y., Seal, S., DeSilva, W., Tomson, F. L., Huang, C., Garlick, R. K., Rahman, N., Salit, M., Kingsmore, S. F., Ferber, M. J., Aradhya, S., & Nussbaum, R. L. (2021). One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation. Genetics in medicine : official journal of the American College of Medical Genetics, 23(9), 1673-1680. https://doi.org/10.1038/s41436-021-01187-w
Lincoln, Stephen E, et al. "One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation." Genetics in medicine : official journal of the American College of Medical Genetics vol. 23,9 (2021): 1673-1680. doi: https://doi.org/10.1038/s41436-021-01187-w
Lincoln SE, Hambuch T, Zook JM, Bristow SL, Hatchell K, Truty R, Kennemer M, Shirts BH, Fellowes A, Chowdhury S, Klee EW, Mahamdallie S, Cleveland MH, Vallone PM, Ding Y, Seal S, DeSilva W, Tomson FL, Huang C, Garlick RK, Rahman N, Salit M, Kingsmore SF, Ferber MJ, Aradhya S, Nussbaum RL. One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation. Genet Med. 2021 Sep;23(9):1673-1680. doi: 10.1038/s41436-021-01187-w. Epub 2021 May 18. PMID: 34007000; PMCID: PMC8460443.
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Showing 1 to 12 of 15 entries