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Year 2019, , 120 - 126, 01.07.2019
https://doi.org/10.31127/tuje.472328

Abstract

References

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  • Audibert, C., Stuntz M., and Glass, D. (2018). "Treatment Sequencing in Advanced BRAF-Mutant Melanoma Patients: CurrentPractice in the United States", Journal of Pharmacy Technology, Vol.34, No.1, pp. 17–23.
  • Bolger, A.M., Lohse M., Usadel B. (2014). "Trimmomatic: a flexible trimmer for Illumina sequence data", Bioinformatics, Vol. 30, No.15, pp. 2114-2120.
  • Bukowski, R, Guo, X, Lu Y, et al. (2017) “Construction of the third-generation Zea mays haplotype map.” Gigascience. Vol. 7, No. 4, pp. 1-12.
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  • Ebbert, M.T., Wadsworth, M.E., Staley, L.A., et al. (2016) "Evaluating the necessity of PCR duplicate removal from next-generation sequencing dat aand a comparison of approaches", BMC Bioinformatics. Vol.17, No. 7, pp. 239.
  • Gao, J., Wan C., Zhang H., et al.(2017) "Anaconda: AN automated pipeline for somatic COpyNumber variation Detection and Annotation from tumor exome sequencing data", BMC Bioinformatics, Vol.18, No.1, pp:436.
  • Griffiths-Jones, S., Grocock, R. J., Dongen, S., Bateman, A., Enright, A. J. (2006). "miRBase: microRNA sequences, targets and gene nomenclature", Nucleic Acids Research, Vol.34, No.1, pp.140–144.
  • Haberer, G., Spannagl, M., "Hands-on Tutorial on SNP Calling" Plant Genome and Systems Biology Group/PGSB (Access Date: 01.11.2018)
  • Hsu, Y.C., Hsiao, Y.T., Kao, T.Y., Chang, J.G., Shieh, G.S. (2017). Detection of Somatic Mutations in Exome Sequencing of Tumor-Only Samples", Scientific Reports 7, 15959.
  • Kearse, M., Moir, R., Wilson, A., et al. (2012). "Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data." Bioinformatics, Vol.28, No.12, pp. 1647–1649.
  • Koboldt, D. C., Steinberg, K. M., Larson, D. E., Wilson, R. K., & Mardis, E. R. (2013). “The next-generation sequencing revolution and its impact on genomics.” Cell, Vol.155, No.1, pp. 27-38.
  • Koboldt, D.C., Chen, K, Wylie, et al. (2009). “VarScan: variant detection in massively parallel sequencing of individual and pooled samples.” Bioinformatics Vol. 25, No. 17, pp. 2283-2285.
  • Kroigard, A.B.,Thomassen M., Lænkholm A-V., Kruse T.A., Larsen M.J. (2016) "Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exomeand Targeted Deep Sequencing Data." PLoS One. Vol.11, No.3, e0151664.
  • Laila, N., Kelsey, M., Jordan, R., (2016). "Cytology Sample Based Next-Generation Sequencing for Metastatic Melanoma: A Feasible and UsefulTool", Journal of the American Society of Cytopathology, Vol.5, No.5, p. 67.
  • Larson, D.E., Harris C.C., Chen K., et al. (2011). "Somatic Sniper: identification of somatic point mutations in whole genome sequencing data." Bioinformatics. Vol.28, No.3, pp. 311-7.
  • Leipzig, J. (2016). "A review of bioinformatic pipeline frameworks", Brief Bioinform. Vol.18, No. 3, pp. 530-536.
  • Li, H., Handsaker, B., Wysoker, A., et al. (2009). "The Sequence Alignment/Map format and SAM tools", Bioinformatics. Vol. 25, No. 16, pp. 2078-2079.
  • McCormick, R.F., Truong, S.K., Mullet, J.E. (2015). "RIG: Recal ibration and inter relation of genomic sequence data with the GATK", G3 (Bethesda). Vol.5, No. 4, pp. 655-665.
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  • Ogasawara, T., Cheng, Y., Tzeng, T-H.K. (2016) "Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools." PLoS One. Vol. 11, no.11,. e0167100.
  • Peter, J. A., Cock, T.A., Jeffrey, T., et al. (2009). “Biopython: freely available Python tools for computational molecular biology and bioinformatics.” Bioinformatics, Vol.25, No. 11, pp. 1422–1423.
  • Rihtman, B., Meaden, S., Clokie, M.R., Koskella, B., Millard, A.D. (2016). "Assessing Illumina technology for the high-through put sequencing of bacteriophage genomes." PeerJ. Vol. 4, e2055.
  • Saunders, C.T., Wong, W.S., Swamy, S., Becq, J., Murray, L,J,, Cheetham, R.K. (2012). "Strelka: accurate somatic small variant calling from sequenced tumor-normal sample pairs." Bioinformatics, Vol.28, No. 14, pp. 1811-1817.
  • Sipos, B., Massingham, T., Stütz, A.M., Goldman N. (2012) "An Improved Protocol for Sequencing of Repetitive Genomic Regions and Structural Variations Using Muta genes is and Next Generation Sequencing." PLoS One Vol. 7, No. 8, e43359.
  • Sun, Z., Bhagwate, A., Prodduturi, N., Yang, P., Kocher, J. P.A. (2017) "Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations", Briefings in Bioinformatics, Vol. 18, No. 6, pp. 973–983.
  • Vogelstein, B., Papadopoulos, N., Velculescu, V.E., Zhou, S, Diaz LA, Kinzler KW. (2013). “Cancer genome landscapes.” Science. Vol. 339, No. 6127, pp. 1546-1558.
  • Walker, B.J., Abeel, T., Shea, T., et al. (2014) "Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement." PLoSOne. Vol. 9, No. 11, e112963.
  • Yang, H., Wang, K. (2015). "Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR", NatProtoc. Vol.10, No.10, pp. 1556-66.
  • Zhang J., Chiodini, R., Badr, A., Zhang, G. (2011). "The impact of next-generation sequencing on genomics." J Genet Genomics. Vol. 38, No. 3, pp.95-109.

DETERMINATION OF MALIGNANT MELANOMA BY ANALYSIS OF VARIATION VALUES

Year 2019, , 120 - 126, 01.07.2019
https://doi.org/10.31127/tuje.472328

Abstract

Melanoma is a serious disease associated with mutation-based cancer cells. Genetic structure and hereditary condition play important role to understand the underlying reasons of the diseases caused by Deoxiribole Nucleic Acid (DNA). In order to identify mutation carriers and to analyze disease, researchers tend to find various gene determinations methods. Nowadays, Next Generation Sequencing (NGS) is emerging as a valuable and powerful platform to detect gene-based diseases by entiring human genome. In this study, we aimed to propose a bioinformatics application workflow to distinguish between insertions/deletions and somatic/germline mutations, by using NGS methods. We carried this study out on a data set containing 100 human genomes data (20 training, 80 testing) for the detection of Malignant Melanoma. We found that the results of diagnosis performance were 92.50% accuracy, 94.03% precision, 96.92% sensitivity and 95.45% F1 score. These results show the potential for proposed application based on NGS to improve Melanoma detection. 

References

  • Andrea, F., Franz, J.H., Tobias, S., et. al. (2018). "Next-generation-sequencing of advanced melanoma: Which genetic alterations have an impact on systemic therapy response?" J Clin Oncol, Vol.36, No.15, suppl. e21557-e21557.
  • Audibert, C., Stuntz M., and Glass, D. (2018). "Treatment Sequencing in Advanced BRAF-Mutant Melanoma Patients: CurrentPractice in the United States", Journal of Pharmacy Technology, Vol.34, No.1, pp. 17–23.
  • Bolger, A.M., Lohse M., Usadel B. (2014). "Trimmomatic: a flexible trimmer for Illumina sequence data", Bioinformatics, Vol. 30, No.15, pp. 2114-2120.
  • Bukowski, R, Guo, X, Lu Y, et al. (2017) “Construction of the third-generation Zea mays haplotype map.” Gigascience. Vol. 7, No. 4, pp. 1-12.
  • Bulmer, M. G. (1971). "The Effect of Selection on Genetic Variability," The American Naturalist, Vol.105, No. 943, pp. 201-211.
  • Ebbert, M.T., Wadsworth, M.E., Staley, L.A., et al. (2016) "Evaluating the necessity of PCR duplicate removal from next-generation sequencing dat aand a comparison of approaches", BMC Bioinformatics. Vol.17, No. 7, pp. 239.
  • Gao, J., Wan C., Zhang H., et al.(2017) "Anaconda: AN automated pipeline for somatic COpyNumber variation Detection and Annotation from tumor exome sequencing data", BMC Bioinformatics, Vol.18, No.1, pp:436.
  • Griffiths-Jones, S., Grocock, R. J., Dongen, S., Bateman, A., Enright, A. J. (2006). "miRBase: microRNA sequences, targets and gene nomenclature", Nucleic Acids Research, Vol.34, No.1, pp.140–144.
  • Haberer, G., Spannagl, M., "Hands-on Tutorial on SNP Calling" Plant Genome and Systems Biology Group/PGSB (Access Date: 01.11.2018)
  • Hsu, Y.C., Hsiao, Y.T., Kao, T.Y., Chang, J.G., Shieh, G.S. (2017). Detection of Somatic Mutations in Exome Sequencing of Tumor-Only Samples", Scientific Reports 7, 15959.
  • Kearse, M., Moir, R., Wilson, A., et al. (2012). "Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data." Bioinformatics, Vol.28, No.12, pp. 1647–1649.
  • Koboldt, D. C., Steinberg, K. M., Larson, D. E., Wilson, R. K., & Mardis, E. R. (2013). “The next-generation sequencing revolution and its impact on genomics.” Cell, Vol.155, No.1, pp. 27-38.
  • Koboldt, D.C., Chen, K, Wylie, et al. (2009). “VarScan: variant detection in massively parallel sequencing of individual and pooled samples.” Bioinformatics Vol. 25, No. 17, pp. 2283-2285.
  • Kroigard, A.B.,Thomassen M., Lænkholm A-V., Kruse T.A., Larsen M.J. (2016) "Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exomeand Targeted Deep Sequencing Data." PLoS One. Vol.11, No.3, e0151664.
  • Laila, N., Kelsey, M., Jordan, R., (2016). "Cytology Sample Based Next-Generation Sequencing for Metastatic Melanoma: A Feasible and UsefulTool", Journal of the American Society of Cytopathology, Vol.5, No.5, p. 67.
  • Larson, D.E., Harris C.C., Chen K., et al. (2011). "Somatic Sniper: identification of somatic point mutations in whole genome sequencing data." Bioinformatics. Vol.28, No.3, pp. 311-7.
  • Leipzig, J. (2016). "A review of bioinformatic pipeline frameworks", Brief Bioinform. Vol.18, No. 3, pp. 530-536.
  • Li, H., Handsaker, B., Wysoker, A., et al. (2009). "The Sequence Alignment/Map format and SAM tools", Bioinformatics. Vol. 25, No. 16, pp. 2078-2079.
  • McCormick, R.F., Truong, S.K., Mullet, J.E. (2015). "RIG: Recal ibration and inter relation of genomic sequence data with the GATK", G3 (Bethesda). Vol.5, No. 4, pp. 655-665.
  • McKenna, A., Hanna, M., Banks, E., et al. (2010). “The Genome Analysis Toolkit: A Map Reduce framework for analyzing next-generation DNA sequencing data.” Genome Research. Vol.20, No. 9, pp. 1297-1303.
  • Moore, J.H., Asselbergs, F.W., Williams, S.M. (2010) "Bioinformatics challenges for genome-wide association studies." Bioinformatics, Vol.26, No.4, pp. 445–455.
  • Nielsen, R., Paul, J. S., Albrechtsen, A., Song, Y. S. (2011). "Geno type and SNP calling from next-generation sequencing data" Nat Rev Genet. Vol.12, No. 6, pp. 443-451.
  • Ogasawara, T., Cheng, Y., Tzeng, T-H.K. (2016) "Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools." PLoS One. Vol. 11, no.11,. e0167100.
  • Peter, J. A., Cock, T.A., Jeffrey, T., et al. (2009). “Biopython: freely available Python tools for computational molecular biology and bioinformatics.” Bioinformatics, Vol.25, No. 11, pp. 1422–1423.
  • Rihtman, B., Meaden, S., Clokie, M.R., Koskella, B., Millard, A.D. (2016). "Assessing Illumina technology for the high-through put sequencing of bacteriophage genomes." PeerJ. Vol. 4, e2055.
  • Saunders, C.T., Wong, W.S., Swamy, S., Becq, J., Murray, L,J,, Cheetham, R.K. (2012). "Strelka: accurate somatic small variant calling from sequenced tumor-normal sample pairs." Bioinformatics, Vol.28, No. 14, pp. 1811-1817.
  • Sipos, B., Massingham, T., Stütz, A.M., Goldman N. (2012) "An Improved Protocol for Sequencing of Repetitive Genomic Regions and Structural Variations Using Muta genes is and Next Generation Sequencing." PLoS One Vol. 7, No. 8, e43359.
  • Sun, Z., Bhagwate, A., Prodduturi, N., Yang, P., Kocher, J. P.A. (2017) "Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations", Briefings in Bioinformatics, Vol. 18, No. 6, pp. 973–983.
  • Vogelstein, B., Papadopoulos, N., Velculescu, V.E., Zhou, S, Diaz LA, Kinzler KW. (2013). “Cancer genome landscapes.” Science. Vol. 339, No. 6127, pp. 1546-1558.
  • Walker, B.J., Abeel, T., Shea, T., et al. (2014) "Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement." PLoSOne. Vol. 9, No. 11, e112963.
  • Yang, H., Wang, K. (2015). "Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR", NatProtoc. Vol.10, No.10, pp. 1556-66.
  • Zhang J., Chiodini, R., Badr, A., Zhang, G. (2011). "The impact of next-generation sequencing on genomics." J Genet Genomics. Vol. 38, No. 3, pp.95-109.
There are 32 citations in total.

Details

Primary Language English
Subjects Engineering
Journal Section Articles
Authors

Ahmet Kürşat Esim This is me 0000-0002-3458-2411

Hilal Kaya 0000-0003-4787-105X

Veysel Alcan This is me 0000-0002-7786-8591

Publication Date July 1, 2019
Published in Issue Year 2019

Cite

APA Esim, A. K., Kaya, H., & Alcan, V. (2019). DETERMINATION OF MALIGNANT MELANOMA BY ANALYSIS OF VARIATION VALUES. Turkish Journal of Engineering, 3(3), 120-126. https://doi.org/10.31127/tuje.472328
AMA Esim AK, Kaya H, Alcan V. DETERMINATION OF MALIGNANT MELANOMA BY ANALYSIS OF VARIATION VALUES. TUJE. July 2019;3(3):120-126. doi:10.31127/tuje.472328
Chicago Esim, Ahmet Kürşat, Hilal Kaya, and Veysel Alcan. “DETERMINATION OF MALIGNANT MELANOMA BY ANALYSIS OF VARIATION VALUES”. Turkish Journal of Engineering 3, no. 3 (July 2019): 120-26. https://doi.org/10.31127/tuje.472328.
EndNote Esim AK, Kaya H, Alcan V (July 1, 2019) DETERMINATION OF MALIGNANT MELANOMA BY ANALYSIS OF VARIATION VALUES. Turkish Journal of Engineering 3 3 120–126.
IEEE A. K. Esim, H. Kaya, and V. Alcan, “DETERMINATION OF MALIGNANT MELANOMA BY ANALYSIS OF VARIATION VALUES”, TUJE, vol. 3, no. 3, pp. 120–126, 2019, doi: 10.31127/tuje.472328.
ISNAD Esim, Ahmet Kürşat et al. “DETERMINATION OF MALIGNANT MELANOMA BY ANALYSIS OF VARIATION VALUES”. Turkish Journal of Engineering 3/3 (July 2019), 120-126. https://doi.org/10.31127/tuje.472328.
JAMA Esim AK, Kaya H, Alcan V. DETERMINATION OF MALIGNANT MELANOMA BY ANALYSIS OF VARIATION VALUES. TUJE. 2019;3:120–126.
MLA Esim, Ahmet Kürşat et al. “DETERMINATION OF MALIGNANT MELANOMA BY ANALYSIS OF VARIATION VALUES”. Turkish Journal of Engineering, vol. 3, no. 3, 2019, pp. 120-6, doi:10.31127/tuje.472328.
Vancouver Esim AK, Kaya H, Alcan V. DETERMINATION OF MALIGNANT MELANOMA BY ANALYSIS OF VARIATION VALUES. TUJE. 2019;3(3):120-6.
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