refs.bib

@article{turajlic_resolving_2019,
	title = {Resolving genetic heterogeneity in cancer},
	volume = {20},
	copyright = {2019 Springer Nature Limited},
	issn = {1471-0064},
	url = {https://www.nature.com/articles/s41576-019-0114-6},
	doi = {10.1038/s41576-019-0114-6},
	abstract = {To a large extent, cancer conforms to evolutionary rules defined by the rates at which clones mutate, adapt and grow. Next-generation sequencing has provided a snapshot of the genetic landscape of most cancer types, and cancer genomics approaches are driving new insights into cancer evolutionary patterns in time and space. In contrast to species evolution, cancer is a particular case owing to the vast size of tumour cell populations, chromosomal instability and its potential for phenotypic plasticity. Nevertheless, an evolutionary framework is a powerful aid to understand cancer progression and therapy failure. Indeed, such a framework could be applied to predict individual tumour behaviour and support treatment strategies.},
	language = {en},
	number = {7},
	urldate = {2025-01-16},
	journal = {Nature Reviews Genetics},
	author = {Turajlic, Samra and Sottoriva, Andrea and Graham, Trevor and Swanton, Charles},
	month = jul,
	year = {2019},
	note = {Publisher: Nature Publishing Group},
	keywords = {Cancer genetics, Cancer genomics, Evolutionary theory, Genetic variation, Genomic instability, Molecular evolution, Tumour heterogeneity},
	pages = {404--416},
	file = {Full Text PDF:/home/villena/Zotero/storage/ZNPBFB5L/Turajlic et al. - 2019 - Resolving genetic heterogeneity in cancer.pdf:application/pdf},
}

@article{collins_new_2015,
	title = {A {New} {Initiative} on {Precision} {Medicine}},
	volume = {372},
	issn = {0028-4793, 1533-4406},
	url = {http://www.nejm.org/doi/10.1056/NEJMp1500523},
	doi = {10.1056/NEJMp1500523},
	language = {en},
	number = {9},
	journal = {New England Journal of Medicine},
	author = {Collins, Francis S. and Varmus, Harold},
	month = feb,
	year = {2015},
	pages = {793--795},
	file = {PDF:/home/villena/Zotero/storage/6ZA6G9HA/Collins y Varmus - 2015 - A New Initiative on Precision Medicine.pdf:application/pdf},
}

@article{shendure_genomic_2019,
	title = {Genomic {Medicine}–{Progress}, {Pitfalls}, and {Promise}},
	volume = {177},
	issn = {0092-8674},
	url = {https://www.sciencedirect.com/science/article/pii/S0092867419301527},
	doi = {10.1016/j.cell.2019.02.003},
	abstract = {In the wake of the Human Genome Project (HGP), strong expectations were set for the timeline and impact of genomics on medicine—an anticipated transformation in the diagnosis, treatment, and prevention of disease. In this Perspective, we take stock of the nascent field of genomic medicine. In what areas, if any, is genomics delivering on this promise, or is the path to success clear? Where are we falling short, and why? What have been the unanticipated developments? Overall, we argue that the optimism surrounding the transformational potential of genomics on medicine remains justified, albeit with a considerably different form and timescale than originally projected. We also argue that the field needs to pivot back to basics, as understanding the entirety of the genotype-to-phenotype equation is a likely prerequisite for delivering on the full potential of the human genome to advance the human condition.},
	number = {1},
	urldate = {2025-01-16},
	journal = {Cell},
	author = {Shendure, Jay and Findlay, Gregory M. and Snyder, Matthew W.},
	month = mar,
	year = {2019},
	pages = {45--57},
	file = {ScienceDirect Full Text PDF:/home/villena/Zotero/storage/ZFGIH4UM/Shendure et al. - 2019 - Genomic Medicine–Progress, Pitfalls, and Promise.pdf:application/pdf;ScienceDirect Snapshot:/home/villena/Zotero/storage/LSWP58GL/S0092867419301527.html:text/html},
}

@article{carrasco-ramiro_human_2017,
	title = {Human genomics projects and precision medicine},
	volume = {24},
	copyright = {2017 Macmillan Publishers Limited, part of Springer Nature.},
	issn = {1476-5462},
	url = {https://www.nature.com/articles/gt201777},
	doi = {10.1038/gt.2017.77},
	abstract = {The completion of the Human Genome Project (HGP) in 2001 opened the floodgates to a deeper understanding of medicine. There are dozens of HGP-like projects which involve from a few tens to several million genomes currently in progress, which vary from having specialized goals or a more general approach. However, data generation, storage, management and analysis in public and private cloud computing platforms have raised concerns about privacy and security. The knowledge gained from further research has changed the field of genomics and is now slowly permeating into clinical medicine. The new precision (personalized) medicine, where genome sequencing and data analysis are essential components, allows tailored diagnosis and treatment according to the information from the patient’s own genome and specific environmental factors. P4 (predictive, preventive, personalized and participatory) medicine is introducing new concepts, challenges and opportunities. This review summarizes current sequencing technologies, concentrates on ongoing human genomics projects, and provides some examples in which precision medicine has already demonstrated clinical impact in diagnosis and/or treatment.},
	language = {en},
	number = {9},
	urldate = {2025-01-16},
	journal = {Gene Therapy},
	author = {Carrasco-Ramiro, F. and Peiró-Pastor, R. and Aguado, B.},
	month = sep,
	year = {2017},
	note = {Publisher: Nature Publishing Group},
	keywords = {Biological techniques, Diseases, Genomics, Personalized medicine},
	pages = {551--561},
	file = {Full Text PDF:/home/villena/Zotero/storage/CUFGRP8I/Carrasco-Ramiro et al. - 2017 - Human genomics projects and precision medicine.pdf:application/pdf},
}

@article{johannessen_progress_2017,
	series = {Regulatory and metabolic networks • {Cancer} and systemic diseases},
	title = {Progress towards precision functional genomics in cancer},
	volume = {2},
	issn = {2452-3100},
	url = {https://www.sciencedirect.com/science/article/pii/S2452310017300410},
	doi = {10.1016/j.coisb.2017.02.002},
	abstract = {The notion of cancer precision medicine is appealingly simple; given the complete catalog of mutations and cell types present in each patient's tumor, along with sufficient prior knowledge, it should be possible to design a therapeutic strategy that improves outcomes. However, most cancer patients do not yet benefit from cancer precision medicine. A central bottleneck is that most recurrently mutated genes in cancer are found mutated in fewer than 5\% of patients and most individual variants are found at exceedingly rare frequencies. As a result, how most of these individual variants function is currently unknown. Improving future clinical predictions requires overcoming this challenge. Here, we describe the current state of the emerging field of “precision functional genomics” which stands to complement existing approaches to improve the interpretation of cancer genomes.},
	urldate = {2025-01-16},
	journal = {Current Opinion in Systems Biology},
	author = {Johannessen, Cory M. and Boehm, Jesse S.},
	month = apr,
	year = {2017},
	keywords = {Allele interpretation, Cancer, High-throughput screening, Mutant protein, Precision functional genomics, Variant characterization, Variant of unclear significance},
	pages = {74--83},
	file = {ScienceDirect Full Text PDF:/home/villena/Zotero/storage/58QMZAHN/Johannessen y Boehm - 2017 - Progress towards precision functional genomics in cancer.pdf:application/pdf;ScienceDirect Snapshot:/home/villena/Zotero/storage/HBAMIZUK/S2452310017300410.html:text/html},
}

@misc{nci_what_2007,
	type = {{cgvArticle}},
	title = {What {Is} {Cancer}? - {NCI}},
	shorttitle = {What {Is} {Cancer}?},
	url = {https://www.cancer.gov/about-cancer/understanding/what-is-cancer},
	abstract = {Explanations about what cancer is, how cancer cells differ from normal cells, and genetic changes that cause cancer to grow and spread.},
	language = {en},
	urldate = {2025-01-16},
	month = sep,
	year = {2007},
	note = {Archive Location: nciglobal,ncienterprise},
	file = {Snapshot:/home/villena/Zotero/storage/L4LWTY26/what-is-cancer.html:text/html},
}

@article{sicklick_molecular_2019,
	title = {Molecular profiling of cancer patients enables personalized combination therapy: the {I}-{PREDICT} study},
	volume = {25},
	copyright = {2019 The Author(s), under exclusive licence to Springer Nature America, Inc.},
	issn = {1546-170X},
	shorttitle = {Molecular profiling of cancer patients enables personalized combination therapy},
	url = {https://www.nature.com/articles/s41591-019-0407-5},
	doi = {10.1038/s41591-019-0407-5},
	abstract = {Cancer treatments have evolved from indiscriminate cytotoxic agents to selective genome- and immune-targeted drugs that have transformed the outcomes of some malignancies1. Tumor complexity and heterogeneity suggest that the ‘precision medicine’ paradigm of cancer therapy requires treatment to be personalized to the individual patient2–6. To date, precision oncology trials have been based on molecular matching with predetermined monotherapies7–14. Several of these trials have been hindered by very low matching rates, often in the 5–10\% range15, and low response rates. Low matching rates may be due to the use of limited gene panels, restrictive molecular matching algorithms, lack of drug availability, or the deterioration and death of end-stage patients before therapy can be implemented. We hypothesized that personalized treatment with combination therapies would improve outcomes in patients with refractory malignancies. As a first test of this concept, we implemented a cross-institutional prospective study (I-PREDICT, NCT02534675) that used tumor DNA sequencing and timely recommendations for individualized treatment with combination therapies. We found that administration of customized multidrug regimens was feasible, with 49\% of consented patients receiving personalized treatment. Targeting of a larger fraction of identified molecular alterations, yielding a higher ‘matching score’, was correlated with significantly improved disease control rates, as well as longer progression-free and overall survival rates, compared to targeting of fewer somatic alterations. Our findings suggest that the current clinical trial paradigm for precision oncology, which pairs one driver mutation with one drug, may be optimized by treating molecularly complex and heterogeneous cancers with combinations of customized agents.},
	language = {en},
	number = {5},
	urldate = {2025-01-16},
	journal = {Nature Medicine},
	author = {Sicklick, Jason K. and Kato, Shumei and Okamura, Ryosuke and Schwaederle, Maria and Hahn, Michael E. and Williams, Casey B. and De, Pradip and Krie, Amy and Piccioni, David E. and Miller, Vincent A. and Ross, Jeffrey S. and Benson, Adam and Webster, Jennifer and Stephens, Philip J. and Lee, J. Jack and Fanta, Paul T. and Lippman, Scott M. and Leyland-Jones, Brian and Kurzrock, Razelle},
	month = may,
	year = {2019},
	note = {Publisher: Nature Publishing Group},
	keywords = {Cancer genomics, Clinical trials, Targeted therapies},
	pages = {744--750},
	file = {Full Text PDF:/home/villena/Zotero/storage/QGN59NSP/Sicklick et al. - 2019 - Molecular profiling of cancer patients enables personalized combination therapy the I-PREDICT study.pdf:application/pdf},
}

@article{moorcraft_understanding_2015,
	title = {Understanding next generation sequencing in oncology: {A} guide for oncologists},
	volume = {96},
	issn = {1040-8428},
	shorttitle = {Understanding next generation sequencing in oncology},
	url = {https://www.sciencedirect.com/science/article/pii/S1040842815001250},
	doi = {10.1016/j.critrevonc.2015.06.007},
	abstract = {DNA sequencing is now faster and cheaper than ever before, due to the development of next generation sequencing (NGS) technologies. NGS is now widely used in the research setting and is becoming increasingly utilised in clinical practice. However, due to evolving clinical commitments, increased workload and lack of training opportunities, many oncologists may be unfamiliar with the terminology and technology involved. This can lead to oncologists feeling daunted by issues such as how to interpret the vast amounts of data generated by NGS and the differences between sequencing platforms. This review article explains common concepts and terminology, summarises the process of DNA sequencing (including data analysis) and discusses the main factors to consider when deciding on a sequencing method. This article aims to improve oncologists’ understanding of the most commonly used sequencing platforms and the ongoing challenges faced in expanding the use of NGS into routine clinical practice.},
	number = {3},
	urldate = {2025-01-16},
	journal = {Critical Reviews in Oncology/Hematology},
	author = {Moorcraft, Sing Yu and Gonzalez, David and Walker, Brian A.},
	month = dec,
	year = {2015},
	keywords = {Bioinformatics, Genetics, Next generation sequencing, NGS},
	pages = {463--474},
	file = {ScienceDirect Snapshot:/home/villena/Zotero/storage/3FPQNC7V/S1040842815001250.html:text/html},
}

@article{jeon_comparison_2021,
	title = {Comparison between {MGI} and {Illumina} sequencing platforms for whole genome sequencing},
	volume = {43},
	issn = {2092-9293},
	url = {https://doi.org/10.1007/s13258-021-01096-x},
	doi = {10.1007/s13258-021-01096-x},
	abstract = {Illumina next generation sequencing (NGS) systems are the major sequencing platform in worldwide next-generation sequencing market. On the other hand, MGI Tech launched a series of new NGS equipment that promises to deliver high-quality sequencing data faster and at lower prices than Illumina’s sequencing instruments.},
	language = {en},
	number = {7},
	urldate = {2025-01-16},
	journal = {Genes \& Genomics},
	author = {Jeon, Sol A. and Park, Jong Lyul and Park, Seung-Jin and Kim, Jeong Hwan and Goh, Sung-Ho and Han, Ji-Youn and Kim, Seon-Young},
	month = jul,
	year = {2021},
	keywords = {Benchmarking, DNBSEQ-T7, MGISEQ-2000, NovaSeq 6000, Platform, WGS},
	pages = {713--724},
}

@article{logsdon_long-read_2020,
	title = {Long-read human genome sequencing and its applications},
	volume = {21},
	copyright = {2020 Springer Nature Limited},
	issn = {1471-0064},
	url = {https://www.nature.com/articles/s41576-020-0236-x},
	doi = {10.1038/s41576-020-0236-x},
	abstract = {Over the past decade, long-read, single-molecule DNA sequencing technologies have emerged as powerful players in genomics. With the ability to generate reads tens to thousands of kilobases in length with an accuracy approaching that of short-read sequencing technologies, these platforms have proven their ability to resolve some of the most challenging regions of the human genome, detect previously inaccessible structural variants and generate some of the first telomere-to-telomere assemblies of whole chromosomes. Long-read sequencing technologies will soon permit the routine assembly of diploid genomes, which will revolutionize genomics by revealing the full spectrum of human genetic variation, resolving some of the missing heritability and leading to the discovery of novel mechanisms of disease.},
	language = {en},
	number = {10},
	urldate = {2025-01-16},
	journal = {Nature Reviews Genetics},
	author = {Logsdon, Glennis A. and Vollger, Mitchell R. and Eichler, Evan E.},
	month = oct,
	year = {2020},
	note = {Publisher: Nature Publishing Group},
	keywords = {Genetic variation, Genomics, Sequencing},
	pages = {597--614},
	file = {Full Text PDF:/home/villena/Zotero/storage/U3ZFS6KB/Logsdon et al. - 2020 - Long-read human genome sequencing and its applications.pdf:application/pdf},
}

@misc{zhang_single-molecule_2024,
	title = {A single-molecule nanopore sequencing platform},
	copyright = {© 2024, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/2024.08.19.608720v1},
	doi = {10.1101/2024.08.19.608720},
	abstract = {Nanopore sequencing, a third-generation sequencing technology, has revolutionized the gene sequencing industry with its advantages of long reads, fast speed, real-time sequencing and analysis, and potential in detecting base modifications. This technology allows researchers to sequence longer DNA fragments in a single read, providing more comprehensive genomic information compared to previous methods. Nanopore sequencing operates on electrical signals generated by a nanopore embedded in a membrane separating two electrolyte-filled chambers. When single-stranded DNA (ssDNA) passes through the nanopore, it creates variations in the current that correspond to different DNA bases. By analyzing these current fluctuations with machine learning algorithms, the DNA sequence can be determined. In this study, we introduced several improvements to nanopore sequencing, including nanopore local chemistry sequencing, novel motor and pore proteins, chip design, and basecalling algorithms. Our new nanopore sequencing platform, CycloneSEQ, demonstrated long-duration sequencing (107 hours) on a single chip with high yield ({\textgreater}50 Gb). In human genomic DNA sequencing, CycloneSEQ was able to produce long reads with N50 33.6 kb and modal identity 97.0\%. Preliminary findings on human whole-genome de novo assembly, variant calling, metagenomics sequencing, and single-cell RNA sequencing have further highlighted CycloneSEQ’s potential across different areas of genomics.},
	language = {en},
	urldate = {2025-01-16},
	publisher = {bioRxiv},
	author = {Zhang, Jia-Yuan and Zhang, Yuning and Wang, Lele and Guo, Fei and Yun, Quanxin and Zeng, Tao and Yan, Xu and Yu, Lei and Cheng, Lei and Wu, Wei and Shi, Xiao and Chen, Junyi and Sun, Yuhui and Yang, Jingnan and Guo, Rongrong and Zhang, Xianda and Kong, Liu’er and Wang, Zong’an and Yao, Junlei and Tan, Yangsheng and Shi, Liuxin and Zhao, Zhentao and Feng, Zhongwang and Yu, Xiaopeng and Li, Chuang and Zhan, Wu and Ren, Yulin and Yang, Fan and Liu, Zhenjun and Fan, Guangnan and Zhong, Weilian and Li, Dachang and He, Lei and Qi, Yanwei and Zhang, Meng and Zhu, Yening and Chi, Heng and Zhao, Ziyu and Wei, Zhuofang and Song, Ziqi and Ju, Yanmei and Guo, Ruijin and Xiao, Liang and Lin, Xiumei and Chen, Liang and Yang, Chentao and Li, Qiye and Wang, Ou and Jin, Xin and Ni, Ming and Zhang, Wenwei and Liu, Longqi and Gu, Ying and Wang, Jian and Li, Yuxiang and Xu, Xun and Dong, Yuliang},
	month = aug,
	year = {2024},
	note = {Pages: 2024.08.19.608720
Section: New Results},
	file = {Full Text PDF:/home/villena/Zotero/storage/SK5YE8KU/Zhang et al. - 2024 - A single-molecule nanopore sequencing platform.pdf:application/pdf},
}

@article{chaisson_genetic_2015,
	title = {Genetic variation and the de novo assembly of human genomes},
	volume = {16},
	copyright = {2015 Springer Nature Limited},
	issn = {1471-0064},
	url = {https://www.nature.com/articles/nrg3933},
	doi = {10.1038/nrg3933},
	abstract = {Complete de novo assembly of a genome is guaranteed to allow assessment of the full range of genetic variation, although the only mammalian genome assemblies completed to date are for human and mouse. Assemblies using massively parallel sequencing (MPS) have increased the diversity of draft genomes that are available but do not completely resolve genomes.When designing a de novo assembly project, the most-suitable assembly approach to use differs depending on the characteristics of the sequencing reads. MPS methods have relied on de Bruijn graphs, whereas single-molecule sequencing (SMS) reads require pairwise overlaps encoded in overlap or string graphs.A component of 'missing heritability' is missed sequence variation. Approximately 5–40 Mb of sequence are absent from any given human reference genome owing to structural polymorphism, and standard resequencing has missed detection of diseases such as medullary cystic kidney disease type 1, amyotrophic lateral sclerosis and facioscapulohumeral muscular dystrophy.Single-molecule long-read sequencing is currently driving gains in genome assembly accuracy and completeness, but new technologies are being developed to generate long-range information, such as optical maps and dilution pool sequencing, that may aid in scaffolding complex regions.},
	language = {en},
	number = {11},
	urldate = {2025-01-16},
	journal = {Nature Reviews Genetics},
	author = {Chaisson, Mark J. P. and Wilson, Richard K. and Eichler, Evan E.},
	month = nov,
	year = {2015},
	note = {Publisher: Nature Publishing Group},
	keywords = {Genome, Genome assembly algorithms, Genome informatics, Medical genomics, Next-generation sequencing},
	pages = {627--640},
	file = {Full Text PDF:/home/villena/Zotero/storage/WSB5ZQ7K/Chaisson et al. - 2015 - Genetic variation and the de novo assembly of human genomes.pdf:application/pdf},
}

@article{ho_structural_2020,
	title = {Structural variation in the sequencing era},
	volume = {21},
	copyright = {2019 Springer Nature Limited},
	issn = {1471-0064},
	url = {https://www.nature.com/articles/s41576-019-0180-9},
	doi = {10.1038/s41576-019-0180-9},
	abstract = {Identifying structural variation (SV) is essential for genome interpretation but has been historically difficult due to limitations inherent to available genome technologies. Detection methods that use ensemble algorithms and emerging sequencing technologies have enabled the discovery of thousands of SVs, uncovering information about their ubiquity, relationship to disease and possible effects on biological mechanisms. Given the variability in SV type and size, along with unique detection biases of emerging genomic platforms, multiplatform discovery is necessary to resolve the full spectrum of variation. Here, we review modern approaches for investigating SVs and proffer that, moving forwards, studies integrating biological information with detection will be necessary to comprehensively understand the impact of SV in the human genome.},
	language = {en},
	number = {3},
	urldate = {2025-01-16},
	journal = {Nature Reviews Genetics},
	author = {Ho, Steve S. and Urban, Alexander E. and Mills, Ryan E.},
	month = mar,
	year = {2020},
	note = {Publisher: Nature Publishing Group},
	keywords = {DNA sequencing, Genetic variation, Genomics, Next-generation sequencing, Structural variation},
	pages = {171--189},
	file = {Full Text PDF:/home/villena/Zotero/storage/VRSUICX2/Ho et al. - 2020 - Structural variation in the sequencing era.pdf:application/pdf},
}

@article{espinosa_advancements_2024,
	title = {Advancements in long-read genome sequencing technologies and algorithms},
	volume = {116},
	issn = {0888-7543},
	url = {https://www.sciencedirect.com/science/article/pii/S0888754324000636},
	doi = {10.1016/j.ygeno.2024.110842},
	abstract = {The recent advent of long read sequencing technologies, such as Pacific Biosciences (PacBio) and Oxford Nanopore technology (ONT), have led to substantial improvements in accuracy and computational cost in sequencing genomes. However, de novo whole-genome assembly still presents significant challenges related to the quality of the results. Pursuing de novo whole-genome assembly remains a formidable challenge, underscored by intricate considerations surrounding computational demands and result quality. As sequencing accuracy and throughput steadily advance, a continuous stream of innovative assembly tools floods the field. Navigating this dynamic landscape necessitates a reasonable choice of sequencing platform, depth, and assembly tools to orchestrate high-quality genome reconstructions. This comprehensive review delves into the intricate interplay between cutting-edge long read sequencing technologies, assembly methodologies, and the ever-evolving field of genomics. With a focus on addressing the pivotal challenges and harnessing the opportunities presented by these advancements, we provide an in-depth exploration of the crucial factors influencing the selection of optimal strategies for achieving robust and insightful genome assemblies.},
	number = {3},
	urldate = {2025-01-16},
	journal = {Genomics},
	author = {Espinosa, Elena and Bautista, Rocio and Larrosa, Rafael and Plata, Oscar},
	month = may,
	year = {2024},
	keywords = {Genome assembly, Hybrid assembly, Long reads},
	pages = {110842},
	file = {ScienceDirect Full Text PDF:/home/villena/Zotero/storage/CZMNPBTR/Espinosa et al. - 2024 - Advancements in long-read genome sequencing technologies and algorithms.pdf:application/pdf;ScienceDirect Snapshot:/home/villena/Zotero/storage/QYKXB47U/S0888754324000636.html:text/html},
}

@article{loman_complete_2015,
	title = {A complete bacterial genome assembled de novo using only nanopore sequencing data},
	volume = {12},
	copyright = {2015 Springer Nature America, Inc.},
	issn = {1548-7105},
	url = {https://www.nature.com/articles/nmeth.3444},
	doi = {10.1038/nmeth.3444},
	abstract = {By error-correcting long nanopore reads and calling a consensus sequence using nanopore signal data, an entire bacterial genome is assembled de novo.},
	language = {en},
	number = {8},
	urldate = {2025-01-16},
	journal = {Nature Methods},
	author = {Loman, Nicholas J. and Quick, Joshua and Simpson, Jared T.},
	month = aug,
	year = {2015},
	note = {Publisher: Nature Publishing Group},
	keywords = {DNA sequencing, Genome informatics, Nanopores},
	pages = {733--735},
	file = {Full Text PDF:/home/villena/Zotero/storage/CFG6ZXFZ/Loman et al. - 2015 - A complete bacterial genome assembled de novo using only nanopore sequencing data.pdf:application/pdf},
}

@article{nurk_complete_2022,
	title = {The complete sequence of a human genome},
	copyright = {Copyright © 2022 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works},
	url = {https://www.science.org/doi/10.1126/science.abj6987},
	doi = {10.1126/science.abj6987},
	abstract = {Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8\% of the genome, the Telomere-to-Telomere (T2T) ...},
	language = {EN},
	urldate = {2025-01-16},
	journal = {Science},
	author = {Nurk, Sergey and Koren, Sergey and Rhie, Arang and Rautiainen, Mikko and Bzikadze, Andrey V. and Mikheenko, Alla and Vollger, Mitchell R. and Altemose, Nicolas and Uralsky, Lev and Gershman, Ariel and Aganezov, Sergey and Hoyt, Savannah J. and Diekhans, Mark and Logsdon, Glennis A. and Alonge, Michael and Antonarakis, Stylianos E. and Borchers, Matthew and Bouffard, Gerard G. and Brooks, Shelise Y. and Caldas, Gina V. and Chen, Nae-Chyun and Cheng, Haoyu and Chin, Chen-Shan and Chow, William and Lima, Leonardo G. de and Dishuck, Philip C. and Durbin, Richard and Dvorkina, Tatiana and Fiddes, Ian T. and Formenti, Giulio and Fulton, Robert S. and Fungtammasan, Arkarachai and Garrison, Erik and Grady, Patrick G. S. and Graves-Lindsay, Tina A. and Hall, Ira M. and Hansen, Nancy F. and Hartley, Gabrielle A. and Haukness, Marina and Howe, Kerstin and Hunkapiller, Michael W. and Jain, Chirag and Jain, Miten and Jarvis, Erich D. and Kerpedjiev, Peter and Kirsche, Melanie and Kolmogorov, Mikhail and Korlach, Jonas and Kremitzki, Milinn and Li, Heng and Maduro, Valerie V. and Marschall, Tobias and McCartney, Ann M. and McDaniel, Jennifer and Miller, Danny E. and Mullikin, James C. and Myers, Eugene W. and Olson, Nathan D. and Paten, Benedict and Peluso, Paul and Pevzner, Pavel A. and Porubsky, David and Potapova, Tamara and Rogaev, Evgeny I. and Rosenfeld, Jeffrey A. and Salzberg, Steven L. and Schneider, Valerie A. and Sedlazeck, Fritz J. and Shafin, Kishwar and Shew, Colin J. and Shumate, Alaina and Sims, Ying and Smit, Arian F. A. and Soto, Daniela C. and Sović, Ivan and Storer, Jessica M. and Streets, Aaron and Sullivan, Beth A. and Thibaud-Nissen, Françoise and Torrance, James and Wagner, Justin and Walenz, Brian P. and Wenger, Aaron and Wood, Jonathan M. D. and Xiao, Chunlin and Yan, Stephanie M. and Young, Alice C. and Zarate, Samantha and Surti, Urvashi and McCoy, Rajiv C. and Dennis, Megan Y. and Alexandrov, Ivan A. and Gerton, Jennifer L. and O’Neill, Rachel J. and Timp, Winston and Zook, Justin M. and Schatz, Michael C. and Eichler, Evan E. and Miga, Karen H. and Phillippy, Adam M.},
	month = apr,
	year = {2022},
	note = {Publisher: American Association for the Advancement of Science},
	file = {PubMed Central Full Text PDF:/home/villena/Zotero/storage/3NZQPEPN/Nurk et al. - 2022 - The complete sequence of a human genome.pdf:application/pdf;Snapshot:/home/villena/Zotero/storage/QY4253FW/science.html:text/html},
}

@article{zahn_filling_2022,
	title = {Filling the gaps},
	volume = {376},
	url = {https://www.science.org/doi/10.1126/science.abp8653},
	doi = {10.1126/science.abp8653},
	number = {6588},
	urldate = {2025-01-16},
	journal = {Science},
	author = {Zahn, Laura M.},
	month = apr,
	year = {2022},
	note = {Publisher: American Association for the Advancement of Science},
	pages = {42--43},
	file = {Full Text PDF:/home/villena/Zotero/storage/P4JNNE8L/Zahn - 2022 - Filling the gaps.pdf:application/pdf},
}

@article{rhie_complete_2023,
	title = {The complete sequence of a human {Y} chromosome},
	volume = {621},
	copyright = {2023 This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/s41586-023-06457-y},
	doi = {10.1038/s41586-023-06457-y},
	abstract = {The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1–3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.},
	language = {en},
	number = {7978},
	urldate = {2025-01-16},
	journal = {Nature},
	author = {Rhie, Arang and Nurk, Sergey and Cechova, Monika and Hoyt, Savannah J. and Taylor, Dylan J. and Altemose, Nicolas and Hook, Paul W. and Koren, Sergey and Rautiainen, Mikko and Alexandrov, Ivan A. and Allen, Jamie and Asri, Mobin and Bzikadze, Andrey V. and Chen, Nae-Chyun and Chin, Chen-Shan and Diekhans, Mark and Flicek, Paul and Formenti, Giulio and Fungtammasan, Arkarachai and Garcia Giron, Carlos and Garrison, Erik and Gershman, Ariel and Gerton, Jennifer L. and Grady, Patrick G. S. and Guarracino, Andrea and Haggerty, Leanne and Halabian, Reza and Hansen, Nancy F. and Harris, Robert and Hartley, Gabrielle A. and Harvey, William T. and Haukness, Marina and Heinz, Jakob and Hourlier, Thibaut and Hubley, Robert M. and Hunt, Sarah E. and Hwang, Stephen and Jain, Miten and Kesharwani, Rupesh K. and Lewis, Alexandra P. and Li, Heng and Logsdon, Glennis A. and Lucas, Julian K. and Makalowski, Wojciech and Markovic, Christopher and Martin, Fergal J. and Mc Cartney, Ann M. and McCoy, Rajiv C. and McDaniel, Jennifer and McNulty, Brandy M. and Medvedev, Paul and Mikheenko, Alla and Munson, Katherine M. and Murphy, Terence D. and Olsen, Hugh E. and Olson, Nathan D. and Paulin, Luis F. and Porubsky, David and Potapova, Tamara and Ryabov, Fedor and Salzberg, Steven L. and Sauria, Michael E. G. and Sedlazeck, Fritz J. and Shafin, Kishwar and Shepelev, Valery A. and Shumate, Alaina and Storer, Jessica M. and Surapaneni, Likhitha and Taravella Oill, Angela M. and Thibaud-Nissen, Françoise and Timp, Winston and Tomaszkiewicz, Marta and Vollger, Mitchell R. and Walenz, Brian P. and Watwood, Allison C. and Weissensteiner, Matthias H. and Wenger, Aaron M. and Wilson, Melissa A. and Zarate, Samantha and Zhu, Yiming and Zook, Justin M. and Eichler, Evan E. and O’Neill, Rachel J. and Schatz, Michael C. and Miga, Karen H. and Makova, Kateryna D. and Phillippy, Adam M.},
	month = sep,
	year = {2023},
	note = {Publisher: Nature Publishing Group},
	keywords = {Chromosomes, Genetic variation, Genome, Genome informatics, Genomics},
	pages = {344--354},
	file = {Full Text PDF:/home/villena/Zotero/storage/NT25JIN2/Rhie et al. - 2023 - The complete sequence of a human Y chromosome.pdf:application/pdf},
}

@misc{oxford_nanopore_technologies_nanopore_nodate,
	title = {Nanopore store: {PromethION} 2 {Solo}},
	shorttitle = {Nanopore store},
	url = {https://store.nanoporetech.com/eu/p2-solo.html},
	urldate = {2025-01-16},
	author = {{Oxford Nanopore Technologies}},
	file = {Snapshot:/home/villena/Zotero/storage/UVTZZJVN/p2-solo.html:text/html},
}

@misc{noauthor_vega_nodate,
	title = {Vega benchtop system},
	url = {https://www.pacb.com/vega/},
	abstract = {The Vega benchtop system - The first HiFi benchtop system - bringing industry-leading and exceptionally accurate long-reads to your lab.},
	language = {en-US},
	urldate = {2025-01-16},
	journal = {PacBio},
	file = {Snapshot:/home/villena/Zotero/storage/I248YHE8/vega.html:text/html},
}

@article{wang_nanopore_2021,
	title = {Nanopore sequencing technology, bioinformatics and applications},
	volume = {39},
	copyright = {2021 Springer Nature America, Inc.},
	issn = {1546-1696},
	url = {https://www.nature.com/articles/s41587-021-01108-x},
	doi = {10.1038/s41587-021-01108-x},
	abstract = {Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.},
	language = {en},
	number = {11},
	urldate = {2025-01-16},
	journal = {Nature Biotechnology},
	author = {Wang, Yunhao and Zhao, Yue and Bollas, Audrey and Wang, Yuru and Au, Kin Fai},
	month = nov,
	year = {2021},
	note = {Publisher: Nature Publishing Group},
	keywords = {Bioinformatics, Genome informatics, Sequencing},
	pages = {1348--1365},
	file = {Full Text PDF:/home/villena/Zotero/storage/63PBLLFM/Wang et al. - 2021 - Nanopore sequencing technology, bioinformatics and applications.pdf:application/pdf},
}

@article{kolmogorov_scalable_2023,
	title = {Scalable {Nanopore} sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation},
	volume = {20},
	copyright = {2023 The Author(s), under exclusive licence to Springer Nature America, Inc.},
	issn = {1548-7105},
	url = {https://www.nature.com/articles/s41592-023-01993-x},
	doi = {10.1038/s41592-023-01993-x},
	abstract = {Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for population-scale projects, being a combination of too expensive, not scalable enough or too error-prone. Here we develop an efficient and scalable wet lab and computational protocol, Napu, for Oxford Nanopore Technologies long-read sequencing that seeks to address those limitations. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the National Institutes of Health Center for Alzheimer’s and Related Dementias. Using a single PromethION flow cell, we can detect single nucleotide polymorphisms with F1-score comparable to Illumina short-read sequencing. Small indel calling remains difficult within homopolymers and tandem repeats, but achieves good concordance to Illumina indel calls elsewhere. Further, we can discover structural variants with F1-score on par with state-of-the-art de novo assembly methods. Our protocol phases small and structural variants at megabase scales and produces highly accurate, haplotype-specific methylation calls.},
	language = {en},
	number = {10},
	urldate = {2025-01-16},
	journal = {Nature Methods},
	author = {Kolmogorov, Mikhail and Billingsley, Kimberley J. and Mastoras, Mira and Meredith, Melissa and Monlong, Jean and Lorig-Roach, Ryan and Asri, Mobin and Alvarez Jerez, Pilar and Malik, Laksh and Dewan, Ramita and Reed, Xylena and Genner, Rylee M. and Daida, Kensuke and Behera, Sairam and Shafin, Kishwar and Pesout, Trevor and Prabakaran, Jeshuwin and Carnevali, Paolo and Yang, Jianzhi and Rhie, Arang and Scholz, Sonja W. and Traynor, Bryan J. and Miga, Karen H. and Jain, Miten and Timp, Winston and Phillippy, Adam M. and Chaisson, Mark and Sedlazeck, Fritz J. and Blauwendraat, Cornelis and Paten, Benedict},
	month = oct,
	year = {2023},
	note = {Publisher: Nature Publishing Group},
	keywords = {Epigenomics, Genomics, Haplotypes},
	pages = {1483--1492},
	file = {Full Text PDF:/home/villena/Zotero/storage/GKWRYL4V/Kolmogorov et al. - 2023 - Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved va.pdf:application/pdf},
}

@article{sakamoto_phasing_2022,
	title = {Phasing analysis of lung cancer genomes using a long read sequencer},
	volume = {13},
	copyright = {2022 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-022-31133-6},
	doi = {10.1038/s41467-022-31133-6},
	abstract = {Chromosomal backgrounds of cancerous mutations still remain elusive. Here, we conduct the phasing analysis of non-small cell lung cancer specimens of 20 Japanese patients. By the combinatory use of short and long read sequencing data, we obtain long phased blocks of 834 kb in N50 length with {\textgreater}99\% concordance rate. By analyzing the obtained phasing information, we reveal that several cancer genomes harbor regions in which mutations are unevenly distributed to either of two haplotypes. Large-scale chromosomal rearrangement events, which resemble chromothripsis events but have smaller scales, occur on only one chromosome, and these events account for the observed biased distributions. Interestingly, the events are characteristic of EGFR mutation-positive lung adenocarcinomas. Further integration of long read epigenomic and transcriptomic data reveal that haploid chromosomes are not always at equivalent transcriptomic/epigenomic conditions. Distinct chromosomal backgrounds are responsible for later cancerous aberrations in a haplotype-specific manner.},
	language = {en},
	number = {1},
	urldate = {2025-01-16},
	journal = {Nature Communications},
	author = {Sakamoto, Yoshitaka and Miyake, Shuhei and Oka, Miho and Kanai, Akinori and Kawai, Yosuke and Nagasawa, Satoi and Shiraishi, Yuichi and Tokunaga, Katsushi and Kohno, Takashi and Seki, Masahide and Suzuki, Yutaka and Suzuki, Ayako},
	month = jun,
	year = {2022},
	note = {Publisher: Nature Publishing Group},
	keywords = {Cancer epigenetics, Cancer genomics, DNA sequencing, Medical genomics, Non-small-cell lung cancer},
	pages = {3464},
	file = {Full Text PDF:/home/villena/Zotero/storage/RJMAF29E/Sakamoto et al. - 2022 - Phasing analysis of lung cancer genomes using a long read sequencer.pdf:application/pdf},
}

@article{schaal_migrating_2022,
	title = {Migrating to {Long}-{Read} {Sequencing} for {Clinical} {Routine} {BCR}-{ABL1} {TKI} {Resistance} {Mutation} {Screening}},
	volume = {21},
	issn = {1176-9351},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9290162/},
	doi = {10.1177/11769351221110872},
	abstract = {Objective:
The aim of this project was to implement long-read sequencing for BCR-ABL1 TKI resistance mutation screening in a clinical setting for patients undergoing treatment for chronic myeloid leukemia.

Materials and Methods:
Processes were established for registering and transferring samples from the clinic to an academic sequencing facility for long-read sequencing. An automated analysis pipeline for detecting mutations was established, and an information system was implemented comprising features for data management, analysis and visualization. Clinical validation was performed by identifying BCR-ABL1 TKI resistance mutations by Sanger and long-read sequencing in parallel. The developed software is available as open source via GitHub at https://github.com/pharmbio/clamp

Results:
The information system enabled traceable transfer of samples from the clinic to the sequencing facility, robust and automated analysis of the long-read sequence data, and communication of results from sequence analysis in a reporting format that could be easily interpreted and acted upon by clinical experts. In a validation study, all 17 resistance mutations found by Sanger sequencing were also detected by long-read sequencing. An additional 16 mutations were found only by long-read sequencing, all of them with frequencies below the limit of detection for Sanger sequencing. The clonal distributions of co-existing mutations were automatically resolved through the long-read data analysis. After the implementation and validation, the clinical laboratory switched their routine protocol from using Sanger to long-read sequencing for this application.

Conclusions:
Long-read sequencing delivers results with higher sensitivity compared to Sanger sequencing and enables earlier detection of emerging TKI resistance mutations. The developed processes, analysis workflow, and software components lower barriers for adoption and could be extended to other applications.},
	urldate = {2025-01-16},
	journal = {Cancer Informatics},
	author = {Schaal, Wesley and Ameur, Adam and Olsson-Strömberg, Ulla and Hermanson, Monica and Cavelier, Lucia and Spjuth, Ola},
	month = jul,
	year = {2022},
	pmid = {35860345},
	pmcid = {PMC9290162},
	pages = {11769351221110872},
	file = {PubMed Central Full Text PDF:/home/villena/Zotero/storage/LG5D7PRE/Schaal et al. - 2022 - Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening.pdf:application/pdf},
}

@article{li_genome_2024,
	title = {Genome assembly in the telomere-to-telomere era},
	volume = {25},
	copyright = {2024 Springer Nature Limited},
	issn = {1471-0064},
	url = {https://www.nature.com/articles/s41576-024-00718-w},
	doi = {10.1038/s41576-024-00718-w},
	abstract = {Genome sequences largely determine the biology and encode the history of an organism, and de novo assembly — the process of reconstructing the genome sequence of an organism from sequencing reads — has been a central problem in bioinformatics for four decades. Until recently, genomes were typically assembled into fragments of a few megabases at best, but now technological advances in long-read sequencing enable the near-complete assembly of each chromosome — also known as telomere-to-telomere assembly — for many organisms. Here, we review recent progress on assembly algorithms and protocols, with a focus on how to derive near-telomere-to-telomere assemblies. We also discuss the additional developments that will be required to resolve remaining assembly gaps and to assemble non-diploid genomes.},
	language = {en},
	number = {9},
	urldate = {2025-01-16},
	journal = {Nature Reviews Genetics},
	author = {Li, Heng and Durbin, Richard},
	month = sep,
	year = {2024},
	note = {Publisher: Nature Publishing Group},
	keywords = {DNA sequencing, Genome assembly algorithms, Genome informatics, Software},
	pages = {658--670},
	file = {Full Text PDF:/home/villena/Zotero/storage/E7UBR8YY/Li y Durbin - 2024 - Genome assembly in the telomere-to-telomere era.pdf:application/pdf},
}

@misc{koren_gapless_2024,
	title = {Gapless assembly of complete human and plant chromosomes using only nanopore sequencing},
	copyright = {© 2024, Posted by Cold Spring Harbor Laboratory. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license},
	url = {https://www.biorxiv.org/content/10.1101/2024.03.15.585294v2},
	doi = {10.1101/2024.03.15.585294},
	abstract = {The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, this approach for complete, “telomere-to-telomere” genome assembly relies on multiple sequencing platforms, limiting its accessibility.
ONT “Duplex” sequencing reads, where both strands of the DNA are read to improve quality, promise high per-base accuracy. To evaluate this new data type, we generated ONT Duplex data for three widely-studied genomes: human HG002, Solanum lycopersicum Heinz 1706 (tomato), and Zea mays B73 (maize). For the diploid, heterozygous HG002 genome, we also used “Pore-C’’ chromatin contact mapping to completely phase the haplotypes.
We found the accuracy of Duplex data to be similar to HiFi sequencing, but with read lengths tens of kilobases longer, and the Pore-C data to be compatible with existing diploid assembly algorithms. This combination of read length and accuracy enables the construction of a high-quality initial assembly, which can then be further resolved using the ultra-long reads, and finally phased into chromosome-scale haplotypes with Pore-C. The resulting assemblies have a base accuracy exceeding 99.999\% (Q50) and near-perfect continuity, with most chromosomes assembled as single contigs. We conclude that ONT sequencing is a viable alternative to HiFi sequencing for de novo genome assembly, and has the potential to provide a single-instrument solution for the reconstruction of complete genomes.},
	language = {en},
	urldate = {2025-01-16},
	publisher = {bioRxiv},
	author = {Koren, Sergey and Bao, Zhigui and Guarracino, Andrea and Ou, Shujun and Goodwin, Sara and Jenike, Katharine M. and Lucas, Julian and McNulty, Brandy and Park, Jimin and Rautiainen, Mikko and Rhie, Arang and Roelofs, Dick and Schneiders, Harrie and Vrijenhoek, Ilse and Nijbroek, Koen and Ware, Doreen and Schatz, Michael C. and Garrison, Erik and Huang, Sanwen and McCombie, W. Richard and Miga, Karen H. and Wittenberg, Alexander H. J. and Phillippy, Adam M.},
	month = mar,
	year = {2024},
	note = {Pages: 2024.03.15.585294
Section: New Results},
	file = {Full Text PDF:/home/villena/Zotero/storage/ZEH4A48J/Koren et al. - 2024 - Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.pdf:application/pdf},
}

@article{li_patterns_2020,
	title = {Patterns of somatic structural variation in human cancer genomes},
	volume = {578},
	copyright = {2020 The Author(s)},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/s41586-019-1913-9},
	doi = {10.1038/s41586-019-1913-9},
	abstract = {A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments that range in size from kilobases to whole chromosomes1–7. Here we develop methods to group, classify and describe somatic structural variants, using data from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumour types8. Sixteen signatures of structural variation emerged. Deletions have a multimodal size distribution, assort unevenly across tumour types and patients, are enriched in late-replicating regions and correlate with inversions. Tandem duplications also have a multimodal size distribution, but are enriched in early-replicating regions—as are unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy-number gains and frequent inverted rearrangements. One prominent structure consists of 2–7 templates copied from distinct regions of the genome strung together within one locus. Such cycles of templated insertions correlate with tandem duplications, and—in liver cancer—frequently activate the telomerase gene TERT. A wide variety of rearrangement processes are active in cancer, which generate complex configurations of the genome upon which selection can act.},
	language = {en},
	number = {7793},
	urldate = {2025-01-16},
	journal = {Nature},
	author = {Li, Yilong and Roberts, Nicola D. and Wala, Jeremiah A. and Shapira, Ofer and Schumacher, Steven E. and Kumar, Kiran and Khurana, Ekta and Waszak, Sebastian and Korbel, Jan O. and Haber, James E. and Imielinski, Marcin and Weischenfeldt, Joachim and Beroukhim, Rameen and Campbell, Peter J.},
	month = feb,
	year = {2020},
	note = {Publisher: Nature Publishing Group},
	keywords = {Cancer genomics, Genomic instability},
	pages = {112--121},
	file = {Full Text PDF:/home/villena/Zotero/storage/LHUNW9CL/Li et al. - 2020 - Patterns of somatic structural variation in human cancer genomes.pdf:application/pdf},
}

@article{menghi_tandem_2018,
	title = {The {Tandem} {Duplicator} {Phenotype} {Is} a {Prevalent} {Genome}-{Wide} {Cancer} {Configuration} {Driven} by {Distinct} {Gene} {Mutations}},
	volume = {34},
	issn = {1535-6108},
	url = {https://www.sciencedirect.com/science/article/pii/S1535610818302654},
	doi = {10.1016/j.ccell.2018.06.008},
	abstract = {The tandem duplicator phenotype (TDP) is a genome-wide instability configuration primarily observed in breast, ovarian, and endometrial carcinomas. Here, we stratify TDP tumors by classifying their tandem duplications (TDs) into three span intervals, with modal values of 11 kb, 231 kb, and 1.7 Mb, respectively. TDPs with ∼11 kb TDs feature loss of TP53 and BRCA1. TDPs with ∼231 kb and ∼1.7 Mb TDs associate with CCNE1 pathway activation and CDK12 disruptions, respectively. We demonstrate that p53 and BRCA1 conjoint abrogation drives TDP induction by generating short-span TDP mammary tumors in genetically modified mice lacking them. Lastly, we show how TDs in TDP tumors disrupt heterogeneous combinations of tumor suppressors and chromatin topologically associating domains while duplicating oncogenes and super-enhancers.},
	number = {2},
	urldate = {2025-01-16},
	journal = {Cancer Cell},
	author = {Menghi, Francesca and Barthel, Floris P. and Yadav, Vinod and Tang, Ming and Ji, Bo and Tang, Zhonghui and Carter, Gregory W. and Ruan, Yijun and Scully, Ralph and Verhaak, Roel G. W. and Jonkers, Jos and Liu, Edison T.},
	month = aug,
	year = {2018},
	keywords = {BRCA1, CCNE1, CDK12, genome instability, ovarian carcinoma, tandem duplication, TP53, triple-negative breast cancer},
	pages = {197--210.e5},
	file = {ScienceDirect Full Text PDF:/home/villena/Zotero/storage/98BFFS28/Menghi et al. - 2018 - The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct G.pdf:application/pdf;ScienceDirect Snapshot:/home/villena/Zotero/storage/VBJ9BAVM/S1535610818302654.html:text/html},
}

@article{cameron_comprehensive_2019,
	title = {Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software},
	volume = {10},
	copyright = {2019 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-019-11146-4},
	doi = {10.1038/s41467-019-11146-4},
	abstract = {In recent years, many software packages for identifying structural variants (SVs) using whole-genome sequencing data have been released. When published, a new method is commonly compared with those already available, but this tends to be selective and incomplete. The lack of comprehensive benchmarking of methods presents challenges for users in selecting methods and for developers in understanding algorithm behaviours and limitations. Here we report the comprehensive evaluation of 10 SV callers, selected following a rigorous process and spanning the breadth of detection approaches, using high-quality reference cell lines, as well as simulations. Due to the nature of available truth sets, our focus is on general-purpose rather than somatic callers. We characterise the impact on performance of event size and type, sequencing characteristics, and genomic context, and analyse the efficacy of ensemble calling and calibration of variant quality scores. Finally, we provide recommendations for both users and methods developers.},
	language = {en},
	number = {1},
	urldate = {2025-01-16},
	journal = {Nature Communications},
	author = {Cameron, Daniel L. and Di Stefano, Leon and Papenfuss, Anthony T.},
	month = jul,
	year = {2019},
	note = {Publisher: Nature Publishing Group},
	keywords = {Computational biology and bioinformatics, Genetics, Medical genomics},
	pages = {3240},
	file = {Full Text PDF:/home/villena/Zotero/storage/ERYE93KS/Cameron et al. - 2019 - Comprehensive evaluation and characterisation of short read general-purpose structural variant calli.pdf:application/pdf},
}

@article{abel_mapping_2020,
	title = {Mapping and characterization of structural variation in 17,795 human genomes},
	volume = {583},
	copyright = {2020 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/s41586-020-2371-0},
	doi = {10.1038/s41586-020-2371-0},
	abstract = {A key goal of whole-genome sequencing for studies of human genetics is to interrogate all forms of variation, including single-nucleotide variants, small insertion or deletion (indel) variants and structural variants. However, tools and resources for the study of structural variants have lagged behind those for smaller variants. Here we used a scalable pipeline1 to map and characterize structural variants in 17,795 deeply sequenced human genomes. We publicly release site-frequency data to create the largest, to our knowledge, whole-genome-sequencing-based structural variant resource so far. On average, individuals carry 2.9 rare structural variants that alter coding regions; these variants affect the dosage or structure of 4.2 genes and account for 4.0–11.2\% of rare high-impact coding alleles. Using a computational model, we estimate that structural variants account for 17.2\% of rare alleles genome-wide, with predicted deleterious effects that are equivalent to loss-of-function coding alleles; approximately 90\% of such structural variants are noncoding deletions (mean 19.1 per genome). We report 158,991 ultra-rare structural variants and show that 2\% of individuals carry ultra-rare megabase-scale structural variants, nearly half of which are balanced or complex rearrangements. Finally, we infer the dosage sensitivity of genes and noncoding elements, and reveal trends that relate to element class and conservation. This work will help to guide the analysis and interpretation of structural variants in the era of whole-genome sequencing.},
	language = {en},
	number = {7814},
	urldate = {2025-01-16},
	journal = {Nature},
	author = {Abel, Haley J. and Larson, David E. and Regier, Allison A. and Chiang, Colby and Das, Indraniel and Kanchi, Krishna L. and Layer, Ryan M. and Neale, Benjamin M. and Salerno, William J. and Reeves, Catherine and Buyske, Steven and Matise, Tara C. and Muzny, Donna M. and Zody, Michael C. and Lander, Eric S. and Dutcher, Susan K. and Stitziel, Nathan O. and Hall, Ira M.},
	month = jul,
	year = {2020},
	note = {Publisher: Nature Publishing Group},
	keywords = {Genome, Genomics, Structural variation},
	pages = {83--89},
	file = {Full Text PDF:/home/villena/Zotero/storage/YC3AEAH6/Abel et al. - 2020 - Mapping and characterization of structural variation in 17,795 human genomes.pdf:application/pdf},
}

@article{rausch_long-read_2023,
	title = {Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures},
	volume = {3},
	issn = {2666-979X},
	url = {https://www.sciencedirect.com/science/article/pii/S2666979X23000411},
	doi = {10.1016/j.xgen.2023.100281},
	abstract = {Cancer genomes harbor a broad spectrum of structural variants (SVs) driving tumorigenesis, a relevant subset of which escape discovery using short-read sequencing. We employed Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic and post-therapy medulloblastoma to unravel the haplotype-resolved somatic genetic and epigenetic landscape. We assembled complex rearrangements, including a 1.55-Mbp chromothripsis event, and we uncover a complex SV pattern termed templated insertion (TI) thread, characterized by short (mostly {\textless}1 kb) insertions showing prevalent self-concatenation into highly amplified structures of up to 50 kbp in size. TI threads occur in 3\% of cancers, with a prevalence up to 74\% in liposarcoma, and frequent colocalization with chromothripsis. We also perform long-read-based methylome profiling and discover allele-specific methylation (ASM) effects, complex rearrangements exhibiting differential methylation, and differential promoter methylation in cancer-driver genes. Our study shows the advantage of long-read sequencing in the discovery and characterization of complex somatic rearrangements.},
	number = {4},
	urldate = {2025-01-16},
	journal = {Cell Genomics},
	author = {Rausch, Tobias and Snajder, Rene and Leger, Adrien and Simovic, Milena and Giurgiu, Mădălina and Villacorta, Laura and Henssen, Anton G. and Fröhling, Stefan and Stegle, Oliver and Birney, Ewan and Bonder, Marc Jan and Ernst, Aurelie and Korbel, Jan O.},
	month = apr,
	year = {2023},
	keywords = {cancer genomics, chromothripsis, complex rearrangements, epigenetic signatures, long read sequencing, Nanopore methylation calling, templated insertions},
	pages = {100281},
	file = {ScienceDirect Full Text PDF:/home/villena/Zotero/storage/ZKH4Y9R3/Rausch et al. - 2023 - Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement pat.pdf:application/pdf;ScienceDirect Snapshot:/home/villena/Zotero/storage/6Q6YK2DJ/S2666979X23000411.html:text/html},
}

@article{valle-inclan_ongoing_2025,
	title = {Ongoing chromothripsis underpins osteosarcoma genome complexity and clonal evolution},
	volume = {0},
	issn = {0092-8674, 1097-4172},
	url = {https://www.cell.com/cell/abstract/S0092-8674(24)01418-1},
	doi = {10.1016/j.cell.2024.12.005},
	language = {English},
	number = {0},
	urldate = {2025-01-16},
	journal = {Cell},
	author = {Valle-Inclan, Jose Espejo and Noon, Solange De and Trevers, Katherine and Elrick, Hillary and Belzen, Ianthe A. E. M. van and Zumalave, Sonia and Sauer, Carolin M. and Tanguy, Mélanie and Butters, Thomas and Muyas, Francesc and Rust, Alistair G. and Amary, Fernanda and Tirabosco, Roberto and Giess, Adam and Sosinsky, Alona and Elgar, Greg and Flanagan, Adrienne M. and Cortés-Ciriano, Isidro},
	month = jan,
	year = {2025},
	pmid = {39814020},
	note = {Publisher: Elsevier},
	keywords = {breakage-fusion-bridge cycles, cancer evolution, chromosomal instability, chromothripsis, complex genome rearrangements, extrachromosomal DNA, genomic instability, osteosarcoma, TP53, whole-genome duplication},
	file = {Full Text PDF:/home/villena/Zotero/storage/SDRWW7RD/Valle-Inclan et al. - 2025 - Ongoing chromothripsis underpins osteosarcoma genome complexity and clonal evolution.pdf:application/pdf},
}

@misc{oxford_nanopore_technologies_unlocking_2024,
	title = {Unlocking comprehensive genome for large-scale projects},
	url = {https://www.youtube.com/watch?v=nRmm13IAFcg},
	abstract = {Comprehensive genome analyses that provide information on single-nucleotide polymorphisms, structural variants, copy number variations and epigenetic markers are changing the landscape of genomics.
In this webinar, you’ll discover projects from Genomics England and deCODE genetics that are using nanopore sequencing to identify novel and known variants and provide greater insights into hundreds to thousands of samples.},
	urldate = {2025-01-16},
	author = {{Oxford Nanopore Technologies}},
	month = sep,
	year = {2024},
}

@article{kurtin_relapsed_2013,
	title = {Relapsed or {Relapsed}/{Refractory} {Multiple} {Myeloma}},
	abstract = {Multiple myeloma (MM) is a malignant plasma cell disorder with potential secondary organ effects including renal, bone, and bone marrow effects as well as neurologic and immune dysfunction. Diagnostic evaluation of MM includes laboratory and radiologic studies along with bone marrow biopsy to confirm diagnosis. Multiple myeloma is a clonal plasma cell malignancy that results from complex interactions between malignant progenitor cells, bone marrow stromal cells, and the bone marrow microenvironment. Multiple myeloma is clinically and pathologically heterogeneous, which results in variability in treatment response and survival. The disease trajectory varies for each patient, but relapses are inevitable and many patients become refractory to treatments. Management of relapsed and refractory (RR) MM requires careful evaluation of individual patient characteristics and the course of the disease. When determining treatment options for patients with RR MM, comorbidities, the frailty and vulnerability of the patient, and the specific adverse event profile associated with each treatment should be considered, as well as the patient's goals. The goal of therapy for patients with RR MM is to achieve disease control with acceptable toxicity and quality of life, which may be accomplished with novel agents, most likely in combination regimens. The integration of these novel agents into the treatment paradigm has shifted the perception of MM from incurable to a disease that may be considered chronic in the near future with a hope for long-term survival and maintained quality of life.},
	language = {en},
	number = {6},
	author = {Kurtin, Sandra E},
	year = {2013},
	file = {PDF:/home/villena/Zotero/storage/73IQDUU7/Kurtin - 2013 - Relapsed or RelapsedRefractory Multiple Myeloma.pdf:application/pdf},
}

@misc{noauthor_usage_nodate,
	title = {Usage - {CNIO} {Bioinformatics} {Unit} documentation},
	url = {https://cnio-bu.github.io/hpc/usage/},
	urldate = {2025-01-16},
	file = {Usage - CNIO Bioinformatics Unit documentation:/home/villena/Zotero/storage/8T4S7FDN/usage.html:text/html},
}

@article{wick_badread_2019,
	title = {Badread: simulation of error-prone long reads},
	volume = {4},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	issn = {2475-9066},
	shorttitle = {Badread},
	url = {http://joss.theoj.org/papers/10.21105/joss.01316},
	doi = {10.21105/joss.01316},
	number = {36},
	urldate = {2025-01-16},
	journal = {Journal of Open Source Software},
	author = {Wick, Ryan},
	month = apr,
	year = {2019},
	pages = {1316},
	file = {Texto completo:/home/villena/Zotero/storage/9838KSY6/Wick - 2019 - Badread simulation of error-prone long reads.pdf:application/pdf},
}

@article{liu_numerous_2024,
	title = {The numerous facets of 1q21$^{\textrm{+}}$ in multiple myeloma: {Pathogenesis}, clinicopathological features, prognosis and clinical progress ({Review})},
	volume = {27},
	issn = {1792-1074},
	shorttitle = {The numerous facets of 1q21$^{\textrm{+}}$ in multiple myeloma},
	url = {https://www.spandidos-publications.com/10.3892/ol.2024.14391},
	doi = {10.3892/ol.2024.14391},
	abstract = {Multiple myeloma (MM) is a malignant neoplasm characterized by the clonal proliferation of abnormal plasma cells (PCs) in the bone marrow and recurrent cytogenetic abnormalities. The incidence of MM worldwide is on the rise. 1q21$^{\textrm{+}}$ has been found in {\textasciitilde}30‑40\% of newly diagnosed MM (NDMM) patients.1q21$^{\textrm{+}}$ is associated with the pathophysiological mechanisms of disease progression and drug resistance in MM. In the present review, the pathogenesis and clinicopathological features of MM patients with 1q21$^{\textrm{+}}$ were studied, the key data of 1q21$^{\textrm{+}}$ on the prognosis of MM patients were summarized, and the clinical treatment significance of MM patients with 1q21$^{\textrm{+}}$ was clarified, in order to provide reference for clinicians to develop treatment strategies targeting 1q21$^{\textrm{+}}$.},
	number = {6},
	urldate = {2025-01-16},
	journal = {Oncology Letters},
	author = {Liu, Na and Xie, Zhanzhi and Li, Hao and Wang, Luqun},
	month = jun,
	year = {2024},
	note = {Publisher: Spandidos Publications},
	pages = {1--17},
	file = {Full Text PDF:/home/villena/Zotero/storage/JMP3VQWN/Liu et al. - 2024 - The numerous facets of 1q21+ in multiple myeloma Pathogenesis, clinicopathological featu.pdf:application/pdf},
}

@article{aksenova_genome_2021,
	title = {Genome {Instability} in {Multiple} {Myeloma}: {Facts} and {Factors}},
	volume = {13},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2072-6694},
	shorttitle = {Genome {Instability} in {Multiple} {Myeloma}},
	url = {https://www.mdpi.com/2072-6694/13/23/5949},
	doi = {10.3390/cancers13235949},
	abstract = {Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.},
	language = {en},
	number = {23},
	urldate = {2025-01-16},
	journal = {Cancers},
	author = {Aksenova, Anna Y. and Zhuk, Anna S. and Lada, Artem G. and Zotova, Irina V. and Stepchenkova, Elena I. and Kostroma, Ivan I. and Gritsaev, Sergey V. and Pavlov, Youri I.},
	month = jan,
	year = {2021},
	note = {Number: 23
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{kataegis}, chromothripsis, DNA repair, editing deaminases, genome instability, multiple myeloma, translocations},
	pages = {5949},
	file = {Full Text PDF:/home/villena/Zotero/storage/2DDIEQ7M/Aksenova et al. - 2021 - Genome Instability in Multiple Myeloma Facts and Factors.pdf:application/pdf},
}

@article{dagogo-jack_tumour_2018,
	title = {Tumour heterogeneity and resistance to cancer therapies},
	volume = {15},
	copyright = {2017 Springer Nature Limited},
	issn = {1759-4782},
	url = {https://www.nature.com/articles/nrclinonc.2017.166},
	doi = {10.1038/nrclinonc.2017.166},
	abstract = {Genomic instability fosters genetic diversity by providing the raw material for the generation of tumour heterogeneityTumours with high levels of intratumoural heterogeneity might predispose patients to inferior clinical outcomesUnder therapeutic selective pressure, resistance to treatment can emerge as a result of the expansion of pre-existing subclonal populations or from the evolution of drug-tolerant cellsSerial characterization of genetic variants in plasma samples has the potential to provide information on spatial and temporal heterogeneity on a scale that cannot easily be achieved through analyses of tumour biopsy samples aloneMultiregion sampling, research autopsies, and single-cell sequencing are all emerging informative platforms that have the potential to enable decoding of complex clonal relationships at a high level of resolutionCombinatorial approaches that pair therapies targeting the predominant, drug-sensitive population of clones in addition to the various subsets of drug-resistant and drug-tolerant cells seem likely to induce the most-durable responses},
	language = {en},
	number = {2},
	urldate = {2025-01-16},
	journal = {Nature Reviews Clinical Oncology},
	author = {Dagogo-Jack, Ibiayi and Shaw, Alice T.},
	month = feb,
	year = {2018},
	note = {Publisher: Nature Publishing Group},
	keywords = {Cancer therapeutic resistance, Non-small-cell lung cancer, Targeted therapies, Tumour heterogeneity},
	pages = {81--94},
	file = {Full Text PDF:/home/villena/Zotero/storage/AJ5MFNT9/Dagogo-Jack y Shaw - 2018 - Tumour heterogeneity and resistance to cancer therapies.pdf:application/pdf},
}

@misc{noauthor_ligation_2022,
	title = {Ligation sequencing {gDNA} {V14} — human sample ({N50} 10 kb) on {PromethION} ({SQK}-{LSK114})},
	url = {https://nanoporetech.com/document/ligation-sequencing-gdna-v14-10-kb-human-sample-on-promethion-sqk-lsk114},
	abstract = {- This protocol uses N50 of 10 kb genomic DNA extracted from human cell lines
- Sample preparation time: {\textasciitilde}220 minutes and library preparation time: {\textasciitilde}60 minutes
- Data analysis: 1-2 hours
- No PCR
- Compatible with R10.4.1 flow cells

For Research Use Only},
	language = {en-GB},
	urldate = {2025-01-16},
	journal = {Oxford Nanopore Technologies},
	month = oct,
	year = {2022},
	file = {Snapshot:/home/villena/Zotero/storage/ZZNWPQE4/ligation-sequencing-gdna-v14-10-kb-human-sample-on-promethion-sqk-lsk114.html:text/html},
}

@misc{oxford_nanopore_technologies_epi2me_nodate,
	title = {{EPI2ME} {Desktop}},
	url = {https://labs.epi2me.io/about/},
	abstract = {Tutorials and workflows for nanopore sequencing.},
	language = {en},
	urldate = {2025-01-16},
	journal = {EPI2ME Labs},
	author = {{Oxford Nanopore Technologies}},
	file = {Snapshot:/home/villena/Zotero/storage/7HKYR8E8/about.html:text/html},
}

@misc{noauthor_display_nodate,
	title = {Display {IDs} instead of gene names when loading .gff3 and .gtf files · {Issue} \#43 · kcleal/gw},
	url = {https://github.com/kcleal/gw/issues/43},
	urldate = {2025-01-16},
	file = {Display IDs instead of gene names when loading .gff3 and .gtf files · Issue #43 · kcleal/gw:/home/villena/Zotero/storage/D2WB9VVW/43.html:text/html},
}

@misc{noauthor_saving_nodate,
	title = {Saving to pdf from the main program · {Issue} \#59 · kcleal/gw},
	url = {https://github.com/kcleal/gw/issues/59},
	urldate = {2025-01-16},
	file = {Saving to pdf from the main program · Issue #59 · kcleal/gw:/home/villena/Zotero/storage/PRIC2TPJ/59.html:text/html},
}

@misc{noauthor_error_nodate,
	title = {Error: skia {GrGLInterface} was not valid · {Issue} \#38 · kcleal/gw},
	url = {https://github.com/kcleal/gw/issues/38},
	urldate = {2025-01-16},
	file = {Error\: skia GrGLInterface was not valid · Issue #38 · kcleal/gw:/home/villena/Zotero/storage/NEHUDIY7/38.html:text/html},
}

@misc{noauthor_add_nodate,
	title = {Add parameter logging to {VISOR} {LASeR} output · {Issue} \#42 · davidebolo1993/{VISOR}},
	url = {https://github.com/davidebolo1993/VISOR/issues/42},
	urldate = {2025-01-16},
	file = {Add parameter logging to VISOR LASeR output · Issue #42 · davidebolo1993/VISOR:/home/villena/Zotero/storage/BEM93MPN/42.html:text/html},
}

@article{english_truvari_2022,
	title = {Truvari: refined structural variant comparison preserves allelic diversity},
	volume = {23},
	issn = {1474-760X},
	shorttitle = {Truvari},
	url = {https://doi.org/10.1186/s13059-022-02840-6},
	doi = {10.1186/s13059-022-02840-6},
	abstract = {The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same. Common approaches for comparing SVs were developed alongside technologies which produce ill-defined boundaries. As SV detection becomes more exact, algorithms to preserve this refined signal are needed. Here, we present Truvari—an SV comparison, annotation, and analysis toolkit—and demonstrate the effect of SV comparison choices by building population-level VCFs from 36 haplotype-resolved long-read assemblies. We observe over-merging from other SV merging approaches which cause up to a 2.2× inflation of allele frequency, relative to Truvari.},
	number = {1},
	urldate = {2025-01-16},
	journal = {Genome Biology},
	author = {English, Adam C. and Menon, Vipin K. and Gibbs, Richard A. and Metcalf, Ginger A. and Sedlazeck, Fritz J.},
	month = dec,
	year = {2022},
	keywords = {Structural variation, SV annotation, SV benchmarking, SV comparison, SV merging},
	pages = {271},
	file = {Full Text PDF:/home/villena/Zotero/storage/MVH2F4K9/English et al. - 2022 - Truvari refined structural variant comparison preserves allelic diversity.pdf:application/pdf;Snapshot:/home/villena/Zotero/storage/AJ7GWM99/s13059-022-02840-6.html:text/html},
}

@article{koster_snakemakescalable_2012,
	title = {Snakemake—a scalable bioinformatics workflow engine},
	volume = {28},
	issn = {1367-4803},
	url = {https://doi.org/10.1093/bioinformatics/bts480},
	doi = {10.1093/bioinformatics/bts480},
	abstract = {Summary: Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. It is the first system to support the use of automatically inferred multiple named wildcards (or variables) in input and output filenames.Availability:  http://snakemake.googlecode.com.Contact:  johannes.koester@uni-due.de},
	number = {19},
	urldate = {2025-01-16},
	journal = {Bioinformatics},
	author = {Köster, Johannes and Rahmann, Sven},
	month = oct,
	year = {2012},
	pages = {2520--2522},
	file = {Full Text PDF:/home/villena/Zotero/storage/EGHRTEIQ/Köster y Rahmann - 2012 - Snakemake—a scalable bioinformatics workflow engine.pdf:application/pdf;Snapshot:/home/villena/Zotero/storage/2AZ8FDM3/290322.html:text/html},
}

@article{bolognini_visor_2020,
	title = {{VISOR}: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing},
	volume = {36},
	issn = {1367-4803},
	shorttitle = {{VISOR}},
	url = {https://doi.org/10.1093/bioinformatics/btz719},
	doi = {10.1093/bioinformatics/btz719},
	abstract = {VISOR is a tool for haplotype-specific simulations of simple and complex structural variants (SVs). The method is applicable to haploid, diploid or higher ploidy simulations for bulk or single-cell sequencing data. SVs are implanted into FASTA haplotypes at single-basepair resolution, optionally with nearby single-nucleotide variants. Short or long reads are drawn at random from these haplotypes using standard error profiles. Double- or single-stranded data can be simulated and VISOR supports the generation of haplotype-tagged BAM files. The tool further includes methods to interactively visualize simulated variants in single-stranded data. The versatility of VISOR is unmet by comparable tools and it lays the foundation to simulate haplotype-resolved cancer heterogeneity data in bulk or at single-cell resolution.VISOR is implemented in python 3.6, open-source and freely available at https://github.com/davidebolo1993/VISOR. Documentation is available at https://davidebolo1993.github.io/visordoc/.Supplementary data are available at Bioinformatics online.},
	number = {4},
	urldate = {2025-01-16},
	journal = {Bioinformatics},
	author = {Bolognini, Davide and Sanders, Ashley and Korbel, Jan O and Magi, Alberto and Benes, Vladimir and Rausch, Tobias},
	month = feb,
	year = {2020},
	pages = {1267--1269},
	file = {Full Text PDF:/home/villena/Zotero/storage/RP29CT49/Bolognini et al. - 2020 - VISOR a versatile haplotype-aware structural variant simulator for short- and long-read sequencing.pdf:application/pdf;Snapshot:/home/villena/Zotero/storage/6R4VM4N4/5582674.html:text/html},
}

@article{li_minimap2_2018,
	title = {Minimap2: pairwise alignment for nucleotide sequences},
	volume = {34},
	issn = {1367-4803},
	shorttitle = {Minimap2},
	url = {https://doi.org/10.1093/bioinformatics/bty191},
	doi = {10.1093/bioinformatics/bty191},
	abstract = {Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15\%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments. It is 3–4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment.https://github.com/lh3/minimap2Supplementary data are available at Bioinformatics online.},
	number = {18},
	urldate = {2025-01-16},
	journal = {Bioinformatics},
	author = {Li, Heng},
	month = sep,
	year = {2018},
	pages = {3094--3100},
	file = {Full Text PDF:/home/villena/Zotero/storage/JIELNJUW/Li - 2018 - Minimap2 pairwise alignment for nucleotide sequences.pdf:application/pdf},
}

@article{danecek_twelve_2021,
	title = {Twelve years of {SAMtools} and {BCFtools}},
	volume = {10},
	issn = {2047-217X},
	url = {https://doi.org/10.1093/gigascience/giab008},
	doi = {10.1093/gigascience/giab008},
	abstract = {SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines.Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed \>1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.},
	number = {2},
	urldate = {2025-01-16},
	journal = {GigaScience},
	author = {Danecek, Petr and Bonfield, James K and Liddle, Jennifer and Marshall, John and Ohan, Valeriu and Pollard, Martin O and Whitwham, Andrew and Keane, Thomas and McCarthy, Shane A and Davies, Robert M and Li, Heng},
	month = feb,
	year = {2021},
	pages = {giab008},
	file = {Full Text PDF:/home/villena/Zotero/storage/S9SEAZHP/Danecek et al. - 2021 - Twelve years of SAMtools and BCFtools.pdf:application/pdf;Snapshot:/home/villena/Zotero/storage/WKTVEIMY/6137722.html:text/html},
}

@misc{elrick_savana_2024,
	title = {{SAVANA}: reliable analysis of somatic structural variants and copy number aberrations in clinical samples using long-read sequencing},
	copyright = {© 2024, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
	shorttitle = {{SAVANA}},
	url = {https://www.biorxiv.org/content/10.1101/2024.07.25.604944v1},
	doi = {10.1101/2024.07.25.604944},
	abstract = {Accurate detection of somatic structural variants (SVs) and copy number aberrations (SCNAs) is critical to inform the diagnosis and treatment of human cancers. Here, we describe SAVANA, a computationally efficient algorithm designed for the joint analysis of somatic SVs, SCNAs, tumour purity and ploidy using long-read sequencing data. SAVANA relies on machine learning to distinguish true somatic SVs from artefacts and provide prediction errors for individual SVs. Using high-depth Illumina and nanopore whole-genome sequencing data for 99 human tumours and matched normal samples, we establish best practices for benchmarking SV detection algorithms across the entire genome in an unbiased and data-driven manner using simulated and sequencing replicates of tumour and matched normal samples. SAVANA shows significantly higher sensitivity, and 9- and 59-times higher specificity than the second and third-best performing algorithms, yielding orders of magnitude fewer false positives in comparison to existing long-read sequencing tools across various clonality levels, genomic regions, SV types and SV sizes. In addition, SAVANA harnesses long-range phasing information to detect somatic SVs and SCNAs at single-haplotype resolution. SVs reported by SAVANA are highly consistent with those detected using short-read sequencing, including complex events causing oncogene amplification and tumour suppressor gene inactivation. In summary, SAVANA enables the application of long-read sequencing to detect SVs and SCNAs reliably in clinical samples.},
	language = {en},
	urldate = {2025-01-16},
	publisher = {bioRxiv},
	author = {Elrick, Hillary and Sauer, Carolin M. and Valle-Inclan, Jose Espejo and Trevers, Katherine and Tanguy, Melanie and Zumalave, Sonia and Noon, Solange De and Muyas, Francesc and Cascão, Rita and Afonso, Angela and Amary, Fernanda and Tirabosco, Roberto and Giess, Adam and Freeman, Timothy and Sosinsky, Alona and Piculell, Katherine and Miller, David T. and Faria, Claudia C. and Elgar, Greg and Flanagan, Adrienne M. and Cortes-Ciriano, Isidro},
	month = jul,
	year = {2024},
	note = {Pages: 2024.07.25.604944
Section: New Results},
	file = {Full Text PDF:/home/villena/Zotero/storage/HXTW39BV/Elrick et al. - 2024 - SAVANA reliable analysis of somatic structural variants and copy number aberrations in clinical sam.pdf:application/pdf},
}

@misc{keskus_severus_2024,
	title = {Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads},
	copyright = {© 2024, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
	shorttitle = {Severus},
	url = {https://www.medrxiv.org/content/10.1101/2024.03.22.24304756v1},
	doi = {10.1101/2024.03.22.24304756},
	abstract = {Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvements in germline SV detection. However, current long-read SV detection methods do not generalize well to the analysis of somatic SVs in tumor genomes with complex rearrangements, heterogeneity, and aneuploidy. Here, we present Severus: a method for the accurate detection of different types of somatic SVs using a phased breakpoint graph approach. To benchmark various short- and long-read SV detection methods, we sequenced five tumor/normal cell line pairs with Illumina, Nanopore, and PacBio sequencing platforms; on this benchmark Severus showed the highest F1 scores (harmonic mean of the precision and recall) as compared to long-read and short-read methods. We then applied Severus to three clinical cases of pediatric cancer, demonstrating concordance with known genetic findings as well as revealing clinically relevant cryptic rearrangements missed by standard genomic panels.},
	language = {en},
	urldate = {2025-01-16},
	publisher = {medRxiv},
	author = {Keskus, Ayse and Bryant, Asher and Ahmad, Tanveer and Yoo, Byunggil and Aganezov, Sergey and Goretsky, Anton and Donmez, Ataberk and Lansdon, Lisa A. and Rodriguez, Isabel and Park, Jimin and Liu, Yuelin and Cui, Xiwen and Gardner, Joshua and McNulty, Brandy and Sacco, Samuel and Shetty, Jyoti and Zhao, Yongmei and Tran, Bao and Narzisi, Giuseppe and Helland, Adrienne and Cook, Daniel E. and Chang, Pi-Chuan and Kolesnikov, Alexey and Carroll, Andrew and Molloy, Erin K. and Pushel, Irina and Guest, Erin and Pastinen, Tomi and Shafin, Kishwar and Miga, Karen H. and Malikic, Salem and Day, Chi-Ping and Robine, Nicolas and Sahinalp, Cenk and Dean, Michael and Farooqi, Midhat S. and Paten, Benedict and Kolmogorov, Mikhail},
	month = mar,
	year = {2024},
	note = {Pages: 2024.03.22.24304756},
	file = {Full Text PDF:/home/villena/Zotero/storage/CD6XZ2RC/Keskus et al. - 2024 - Severus accurate detection and characterization of somatic structural variation in tumor genomes us.pdf:application/pdf},
}

@article{smolka_detection_2024,
	title = {Detection of mosaic and population-level structural variants with {Sniffles2}},
	volume = {42},
	copyright = {2024 The Author(s)},
	issn = {1546-1696},
	url = {https://www.nature.com/articles/s41587-023-02024-y},
	doi = {10.1038/s41587-023-02024-y},
	abstract = {Calling structural variations (SVs) is technically challenging, but using long reads remains the most accurate way to identify complex genomic alterations. Here we present Sniffles2, which improves over current methods by implementing a repeat aware clustering coupled with a fast consensus sequence and coverage-adaptive filtering. Sniffles2 is 11.8 times faster and 29\% more accurate than state-of-the-art SV callers across different coverages (5–50×), sequencing technologies (ONT and HiFi) and SV types. Furthermore, Sniffles2 solves the problem of family-level to population-level SV calling to produce fully genotyped VCF files. Across 11 probands, we accurately identified causative SVs around MECP2, including highly complex alleles with three overlapping SVs. Sniffles2 also enables the detection of mosaic SVs in bulk long-read data. As a result, we identified multiple mosaic SVs in brain tissue from a patient with multiple system atrophy. The identified SV showed a remarkable diversity within the cingulate cortex, impacting both genes involved in neuron function and repetitive elements.},
	language = {en},
	number = {10},
	urldate = {2025-01-16},
	journal = {Nature Biotechnology},
	author = {Smolka, Moritz and Paulin, Luis F. and Grochowski, Christopher M. and Horner, Dominic W. and Mahmoud, Medhat and Behera, Sairam and Kalef-Ezra, Ester and Gandhi, Mira and Hong, Karl and Pehlivan, Davut and Scholz, Sonja W. and Carvalho, Claudia M. B. and Proukakis, Christos and Sedlazeck, Fritz J.},
	month = oct,
	year = {2024},
	note = {Publisher: Nature Publishing Group},
	keywords = {Cancer, Genetics, Genome informatics, Software},
	pages = {1571--1580},
	file = {Full Text PDF:/home/villena/Zotero/storage/2BCVIHQ5/Smolka et al. - 2024 - Detection of mosaic and population-level structural variants with Sniffles2.pdf:application/pdf},
}

@article{wang_novo_2024,
	title = {De novo and somatic structural variant discovery with {SVision}-pro},
	copyright = {2024 The Author(s)},
	issn = {1546-1696},
	url = {https://www.nature.com/articles/s41587-024-02190-7},
	doi = {10.1038/s41587-024-02190-7},
	abstract = {Long-read-based de novo and somatic structural variant (SV) discovery remains challenging, necessitating genomic comparison between samples. We developed SVision-pro, a neural-network-based instance segmentation framework that represents genome-to-genome-level sequencing differences visually and discovers SV comparatively between genomes without any prerequisite for inference models. SVision-pro outperforms state-of-the-art approaches, in particular, the resolving of complex SVs is improved, with low Mendelian error rates, high sensitivity of low-frequency SVs and reduced false-positive rates compared with SV merging approaches.},
	language = {en},
	urldate = {2025-01-16},
	journal = {Nature Biotechnology},
	author = {Wang, Songbo and Lin, Jiadong and Jia, Peng and Xu, Tun and Li, Xiujuan and Liu, Yuezhuangnan and Xu, Dan and Bush, Stephen J. and Meng, Deyu and Ye, Kai},
	month = mar,
	year = {2024},
	note = {Publisher: Nature Publishing Group},
	keywords = {Genetic variation, Genome informatics, Genomics, Machine learning, Software},
	pages = {1--5},
	file = {Full Text PDF:/home/villena/Zotero/storage/88ADEZI7/Wang et al. - 2024 - De novo and somatic structural variant discovery with SVision-pro.pdf:application/pdf},
}

@article{quinlan_bedtools_2010,
	title = {{BEDTools}: a flexible suite of utilities for comparing genomic features},
	volume = {26},
	issn = {1367-4803},
	shorttitle = {{BEDTools}},
	url = {https://doi.org/10.1093/bioinformatics/btq033},
	doi = {10.1093/bioinformatics/btq033},
	abstract = {Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner.Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets.Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtoolsContact:  aaronquinlan@gmail.com; imh4y@virginia.eduSupplementary information:  Supplementary data are available at Bioinformatics online.},
	number = {6},
	urldate = {2025-01-16},
	journal = {Bioinformatics},
	author = {Quinlan, Aaron R. and Hall, Ira M.},
	month = mar,
	year = {2010},
	pages = {841--842},
	file = {Full Text PDF:/home/villena/Zotero/storage/A5H22KZ4/Quinlan y Hall - 2010 - BEDTools a flexible suite of utilities for comparing genomic features.pdf:application/pdf;Snapshot:/home/villena/Zotero/storage/4G5ZI99D/244688.html:text/html},
}

@misc{cleal_gw_2024,
	title = {{GW}: ultra-fast chromosome-scale visualisation of genomics data},
	copyright = {© 2024, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
	shorttitle = {{GW}},
	url = {https://www.biorxiv.org/content/10.1101/2024.07.26.605272v5},
	doi = {10.1101/2024.07.26.605272},
	abstract = {Genome-Wide (GW) is an interactive genome browser that expedites analysis of aligned sequencing reads and data tracks, and introduces novel interfaces for exploring, annotating and quantifying data. GW’s high-performance design enables rapid rendering of data at speeds approaching the file reading rate, in addition to removing the memory constraints of visualizing large regions. We report substantial gains in performance and demonstrate GW’s utility in exploring massive genomic regions or chromosomes without requiring additional processing.},
	language = {en},
	urldate = {2025-01-16},
	publisher = {bioRxiv},
	author = {Cleal, Kez and Kearsey, Alexander and Baird, Duncan M.},
	month = sep,
	year = {2024},
	note = {Pages: 2024.07.26.605272
Section: New Results},
	file = {Full Text PDF:/home/villena/Zotero/storage/N5HDV5BS/Cleal et al. - 2024 - GW ultra-fast chromosome-scale visualisation of genomics data.pdf:application/pdf},
}

@article{perez_ucsc_2025,
	title = {The {UCSC} {Genome} {Browser} database: 2025 update},
	volume = {53},
	issn = {1362-4962},
	shorttitle = {The {UCSC} {Genome} {Browser} database},
	doi = {10.1093/nar/gkae974},
	abstract = {The UCSC Genome Browser (https://genome.ucsc.edu) is a widely utilized web-based tool for visualization and analysis of genomic data, encompassing over 4000 assemblies from diverse organisms. Since its release in 2001, it has become an essential resource for genomics and bioinformatics research. Annotation data available on Genome Browser includes both internally created and maintained tracks as well as custom tracks and track hubs provided by the research community. This last year's updates include over 25 new annotation tracks such as the gnomAD 4.1 track on the human GRCh38/hg38 assembly, the addition of three new public hubs, and significant expansions to the Genome Archive[GenArk) system for interacting with the enormous variety of assemblies. We have also made improvements to our interface, including updates to the browser graphic page, such as a new popup dialog feature that now displays item details without requiring navigation away from the main Genome Browser page. GenePred tracks have been upgraded with right-click options for zooming and precise navigation, along with enhanced mouseOver functions. Additional improvements include a new grouping feature for track hubs and hub description info links. A new tutorial focusing on Clinical Genetics has also been added to the UCSC Genome Browser.},
	language = {eng},
	number = {D1},
	journal = {Nucleic Acids Research},
	author = {Perez, Gerardo and Barber, Galt P. and Benet-Pages, Anna and Casper, Jonathan and Clawson, Hiram and Diekhans, Mark and Fischer, Clay and Gonzalez, Jairo Navarro and Hinrichs, Angie S. and Lee, Christopher M. and Nassar, Luis R. and Raney, Brian J. and Speir, Matthew L. and van Baren, Marijke J. and Vaske, Charles J. and Haussler, David and Kent, W. James and Haeussler, Maximilian},
	month = jan,
	year = {2025},
	pmid = {39460617},
	pmcid = {PMC11701590},
	keywords = {Animals, Computational Biology, Databases, Genetic, Genome, Human, Genomics, Humans, Internet, Molecular Sequence Annotation, Software, User-Computer Interface, Web Browser},
	pages = {D1243--D1249},
}

@misc{noauthor_releases_nodate,
	title = {Releases · fritzsedlazeck/{Sniffles}/releases/tag/v2.5},
	url = {https://github.com/fritzsedlazeck/Sniffles/releases/tag/v2.5},
	abstract = {Structural variation caller using third generation sequencing - fritzsedlazeck/Sniffles},
	language = {en},
	urldate = {2025-01-16},
	journal = {GitHub},
	file = {Snapshot:/home/villena/Zotero/storage/8M2B2TA6/v2.html:text/html},
}

@misc{oxford_nanopore_technologies_r103_2020,
	title = {R10.3: the newest nanopore for high accuracy nanopore sequencing},
	shorttitle = {R10.3},
	url = {https://nanoporetech.com/ja/news/news-r103-newest-nanopore-high-accuracy-nanopore-sequencing-now-available-store},
	abstract = {Latest chemistry retains the Q50 accuracy of R10 and provides increased throughput and capture, better raw read accuracy and compatibility with PromethION.\  Designed to improve on R10, which has recently reported at 99.995\% single molecule consensus accuracy with UMI method.    Flow cells using},
	language = {ja-JP},
	urldate = {2025-01-16},
	author = {{Oxford Nanopore Technologies}},
	month = jan,
	year = {2020},
	note = {Section: Technology},
	file = {Snapshot:/home/villena/Zotero/storage/7HA92JES/news-r103-newest-nanopore-high-accuracy-nanopore-sequencing-now-available-store.html:text/html},
}

@article{kuehl_multiple_2002,
	title = {Multiple myeloma: evolving genetic events and host interactions},
	volume = {2},
	copyright = {2002 Springer Nature Limited},
	issn = {1474-1768},
	shorttitle = {Multiple myeloma},
	url = {https://www.nature.com/articles/nrc746},
	doi = {10.1038/nrc746},
	abstract = {Multiple myeloma, which is located at multiple sites in the bone-marrow compartment, is a malignant plasma-cell tumour that is characterized by osteolytic bone lesions. It is a slowly proliferating tumour, typically with less than 1\% of tumour cells synthesizing DNA, until late in the disease, when multiple myeloma cells are often found outside the bone marrow. A pre-malignant lesion called monoclonal gammopathy of undetermined significance (MGUS), which is present in 1\% of adults, progresses to malignant multiple myeloma at a rate of 1\% per year. The karyotypes of multiple myeloma are complex, and more similar to those found in epithelial tumours and the blast phase of chronic myelogenous leukaemia than to those in other haematopoietic tumours. Primary translocations — mediated by errors in B-cell-specific DNA modification processes — juxtapose one or more oncogenes and immunoglobulin transcriptional regulatory regions in ∼50\% of MGUS and multiple myelomas. In contrast to other B-cell malignancies, these translocations simultaneously dysregulate a variety of oncogenes, such as the genes for cyclin D1 or D3, fibroblast growth factor receptor 3 (FGFR3) combined with the nuclear protein MMSET, and the transcription factor c-MAF. Secondary translocations that do not involve B-cell-specific processes contribute to progression by dysregulating other oncogenes. Although c-MYC is dysregulated by primary translocations in some B-cell malignancies, it is dysregulated by secondary translocations, often without involvement of an immunogloublin locus, as myeloma tumours become more proliferative at a late stage of progression. Genetic changes are similar in pre-malignant MGUS and multiple myeloma, although the latter is distinguished by the presence of activating mutations of NRAS or KRAS2, and also a higher incidence of monosomy 13, indicating a possible tumour-suppressor gene on chromosome 13. Normal plasma cells, as well as MGUS and multiple myeloma cells, are dependent on the bone-marrow microenvironment for survival, growth and differentiation. These processes are, in part, mediated by paracrine interleukin-6 and insulin-like growth factor 1. The evolving interaction of multiple myeloma cells with the bone-marrow microenvironment is also involved in the secondary effects of malignancy, including osteolysis, anaemia and immunodeficiency. Multiple myeloma is an incurable malignancy for which the median survival has remained fixed at about 3 years for the past decade. Although MGUS can be efficiently diagnosed by a simple blood test, it is not possible to prevent progression or even predict when progression to myeloma will occur. Recent advances in understanding the molecular pathogenesis of these tumours indicate that improved approaches for prevention and treatment should be possible in the near future.},
	language = {en},
	number = {3},
	urldate = {2025-01-16},
	journal = {Nature Reviews Cancer},
	author = {Kuehl, W. Michael and Bergsagel, P. Leif},
	month = mar,
	year = {2002},
	note = {Publisher: Nature Publishing Group},
	keywords = {Biomedicine, Cancer Research, general},
	pages = {175--187},
	file = {Full Text PDF:/home/villena/Zotero/storage/UAZLEBWV/Kuehl y Bergsagel - 2002 - Multiple myeloma evolving genetic events and host interactions.pdf:application/pdf},
}