@article {112,
	title = {Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.},
	journal = {Cell},
	volume = {182},
	year = {2020},
	month = {2020 07 09},
	pages = {145-161.e23},
	abstract = {<p>Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.</p>},
	keywords = {Alleles, Crops, Agricultural, Cytochrome P-450 Enzyme System, Ecotype, Epistasis, Genetic, Fruit, Gene Duplication, Gene Expression Regulation, Plant, Genome, Plant, Genomic Structural Variation, Genotype, Inbreeding, Lycopersicon esculentum, Molecular Sequence Annotation, Phenotype, Plant Breeding, Quantitative Trait Loci},
	issn = {1097-4172},
	doi = {10.1016/j.cell.2020.05.021},
	author = {Alonge, Michael and Wang, Xingang and Benoit, Matthias and Soyk, Sebastian and Pereira, Lara and Zhang, Lei and Suresh, Hamsini and Ramakrishnan, Srividya and Maumus, Florian and Ciren, Danielle and Levy, Yuval and Harel, Tom Hai and Shalev-Schlosser, Gili and Amsellem, Ziva and Razifard, Hamid and Caicedo, Ana L and Tieman, Denise M and Klee, Harry and Kirsche, Melanie and Aganezov, Sergey and Ranallo-Benavidez, T Rhyker and Lemmon, Zachary H and Kim, Jennifer and Robitaille, Gina and Kramer, Melissa and Goodwin, Sara and McCombie, W Richard and Hutton, Samuel and Van Eck, Joyce and Gillis, Jesse and Eshed, Yuval and Sedlazeck, Fritz J and van der Knaap, Esther and Schatz, Michael C and Lippman, Zachary B}
}
@article {40,
	title = {Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line.},
	journal = {Genome Res},
	volume = {28},
	year = {2018},
	month = {2018 08},
	pages = {1126-1135},
	abstract = {<p>The SK-BR-3 cell line is one of the most important models for HER2+ breast cancers, which affect one in five breast cancer patients. SK-BR-3 is known to be highly rearranged, although much of the variation is in complex and repetitive regions that may be underreported. Addressing this, we sequenced SK-BR-3 using long-read single molecule sequencing from Pacific Biosciences and develop one of the most detailed maps of structural variations (SVs) in a cancer genome available, with nearly 20,000 variants present, most of which were missed by short-read sequencing. Surrounding the important  oncogene (also known as ), we discover a complex sequence of nested duplications and translocations, suggesting a punctuated progression. Full-length transcriptome sequencing further revealed several novel gene fusions within the nested genomic variants. Combining long-read genome and transcriptome sequencing enables an in-depth analysis of how SVs disrupt the genome and sheds new light on the complex mechanisms involved in cancer genome evolution.</p>},
	keywords = {Breast Neoplasms, Female, Gene Amplification, Gene Rearrangement, Genome, Human, Genomic Structural Variation, High-Throughput Nucleotide Sequencing, Humans, MCF-7 Cells, Oncogenes, Receptor, ErbB-2, Repetitive Sequences, Nucleic Acid, Transcriptome},
	issn = {1549-5469},
	doi = {10.1101/gr.231100.117},
	author = {Nattestad, Maria and Goodwin, Sara and Ng, Karen and Baslan, Timour and Sedlazeck, Fritz J and Rescheneder, Philipp and Garvin, Tyler and Fang, Han and Gurtowski, James and Hutton, Elizabeth and Tseng, Elizabeth and Chin, Chen-Shan and Beck, Timothy and Sundaravadanam, Yogi and Kramer, Melissa and Antoniou, Eric and McPherson, John D and Hicks, James and McCombie, W Richard and Schatz, Michael C}
}
