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LitCoin-sentences  

PubMed:20126413 JSONTXT 42 Projects

Annnotations TAB TSV DIC JSON TextAE Lectin_function IAV-Glycan

Id Subject Object Predicate Lexical cue
T1 0-89 Sentence denotes U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line.
T2 90-216 Sentence denotes U87MG is a commonly studied grade IV glioma cell line that has been analyzed in at least 1,700 publications over four decades.
T3 217-483 Sentence denotes In order to comprehensively characterize the genome of this cell line and to serve as a model of broad cancer genome sequencing, we have generated greater than 30x genomic sequence coverage using a novel 50-base mate paired strategy with a 1.4kb mean insert library.
T4 484-600 Sentence denotes A total of 1,014,984,286 mate-end and 120,691,623 single-end two-base encoded reads were generated from five slides.
T5 601-754 Sentence denotes All data were aligned using a custom designed tool called BFAST, allowing optimal color space read alignment and accurate identification of DNA variants.
T6 755-1008 Sentence denotes The aligned sequence reads and mate-pair information identified 35 interchromosomal translocation events, 1,315 structural variations (>100 bp), 191,743 small (<21 bp) insertions and deletions (indels), and 2,384,470 single nucleotide variations (SNVs).
T7 1009-1180 Sentence denotes Among these observations, the known homozygous mutation in PTEN was robustly identified, and genes involved in cell adhesion were overrepresented in the mutated gene list.
T8 1181-1319 Sentence denotes Data were compared to 219,187 heterozygous single nucleotide polymorphisms assayed by Illumina 1M Duo genotyping array to assess accuracy:
T9 1320-1435 Sentence denotes 93.83% of all SNPs were reliably detected at filtering thresholds that yield greater than 99.99% sequence accuracy.
T10 1436-1572 Sentence denotes Protein coding sequences were disrupted predominantly in this cancer cell line due to small indels, large deletions, and translocations.
T11 1573-1779 Sentence denotes In total, 512 genes were homozygously mutated, including 154 by SNVs, 178 by small indels, 145 by large microdeletions, and 35 by interchromosomal translocations to reveal a highly mutated cell line genome.
T12 1780-1884 Sentence denotes Of the small homozygously mutated variants, 8 SNVs and 99 indels were novel events not present in dbSNP.
T13 1885-2002 Sentence denotes These data demonstrate that routine generation of broad cancer genome sequence is possible outside of genome centers.
T14 2003-2124 Sentence denotes The sequence analysis of U87MG provides an unparalleled level of mutational resolution compared to any cell line to date.