%0 Journal Article %J Nat Methods %D 2018 %T Accurate detection of complex structural variations using single-molecule sequencing. %A Sedlazeck, Fritz J %A Rescheneder, Philipp %A Smolka, Moritz %A Fang, Han %A Nattestad, Maria %A von Haeseler, Arndt %A Schatz, Michael C %K DNA Mutational Analysis %K Genome, Human %K Genomics %K High-Throughput Nucleotide Sequencing %K Humans %K Sequence Analysis, DNA %X

Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are a challenge with existing methods. Addressing this need, we introduce open-source methods for long-read alignment (NGMLR; https://github.com/philres/ngmlr ) and structural variant identification (Sniffles; https://github.com/fritzsedlazeck/Sniffles ) that provide unprecedented sensitivity and precision for variant detection, even in repeat-rich regions and for complex nested events that can have substantial effects on human health. In several long-read datasets, including healthy and cancerous human genomes, we discovered thousands of novel variants and categorized systematic errors in short-read approaches. NGMLR and Sniffles can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings.

%B Nat Methods %V 15 %P 461-468 %8 2018 06 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/29713083?dopt=Abstract %R 10.1038/s41592-018-0001-7 %0 Journal Article %J Genome Res %D 2018 %T Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. %A Nattestad, Maria %A Goodwin, Sara %A Ng, Karen %A Baslan, Timour %A Sedlazeck, Fritz J %A Rescheneder, Philipp %A Garvin, Tyler %A Fang, Han %A Gurtowski, James %A Hutton, Elizabeth %A Tseng, Elizabeth %A Chin, Chen-Shan %A Beck, Timothy %A Sundaravadanam, Yogi %A Kramer, Melissa %A Antoniou, Eric %A McPherson, John D %A Hicks, James %A McCombie, W Richard %A Schatz, Michael C %K Breast Neoplasms %K Female %K Gene Amplification %K Gene Rearrangement %K Genome, Human %K Genomic Structural Variation %K High-Throughput Nucleotide Sequencing %K Humans %K MCF-7 Cells %K Oncogenes %K Receptor, ErbB-2 %K Repetitive Sequences, Nucleic Acid %K Transcriptome %X

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.

%B Genome Res %V 28 %P 1126-1135 %8 2018 08 %G eng %N 8 %1 http://www.ncbi.nlm.nih.gov/pubmed/29954844?dopt=Abstract %R 10.1101/gr.231100.117