Dataset Information

2013-11-19-17-24-36-breez-MB-2013-10-18-Whole_genome_DNAseq_Medulloblastoma_ICGC - samples

ABSTRACT: Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed.

OTHER RELATED OMICS DATASETS IN: PRJNA213744PRJNA213380PRJNA214321

PROVIDER: EGAD00001000697 | EGA |

REPOSITORIES: EGA

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Publications

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition.

Kool Marcel M Jones David T W DT Jäger Natalie N Northcott Paul A PA Pugh Trevor J TJ Hovestadt Volker V Piro Rosario M RM Esparza L Adriana LA Markant Shirley L SL Remke Marc M Milde Till T Bourdeaut Franck F Ryzhova Marina M Sturm Dominik D Pfaff Elke E Stark Sebastian S Hutter Sonja S Seker-Cin Huriye H Johann Pascal P Bender Sebastian S Schmidt Christin C Rausch Tobias T Shih David D Reimand Jüri J Sieber Laura L Wittmann Andrea A Linke Linda L Witt Hendrik H Weber Ursula D UD Zapatka Marc M König Rainer R Beroukhim Rameen R Bergthold Guillaume G van Sluis Peter P Volckmann Richard R Koster Jan J Versteeg Rogier R Schmidt Sabine S Wolf Stephan S Lawerenz Chris C Bartholomae Cynthia C CC von Kalle Christof C Unterberg Andreas A Herold-Mende Christel C Hofer Silvia S Kulozik Andreas E AE von Deimling Andreas A Scheurlen Wolfram W Felsberg Jörg J Reifenberger Guido G Hasselblatt Martin M Crawford John R JR Grant Gerald A GA Jabado Nada N Perry Arie A Cowdrey Cynthia C Croul Sydney S Zadeh Gelareh G Korbel Jan O JO Doz Francois F Delattre Olivier O Bader Gary D GD McCabe Martin G MG Collins V Peter VP Kieran Mark W MW Cho Yoon-Jae YJ Pomeroy Scott L SL Witt Olaf O Brors Benedikt B Taylor Michael D MD Schüller Ulrich U Korshunov Andrey A Eils Roland R Wechsler-Reya Robert J RJ Lichter Peter P Pfister Stefan M SM

Cancer cell 20140301 3

Smoothened (SMO) inhibitors recently entered clinical trials for sonic-hedgehog-driven medulloblastoma (SHH-MB). Clinical response is highly variable. To understand the mechanism(s) of primary resistance and identify pathways cooperating with aberrant SHH signaling, we sequenced and profiled a large cohort of SHH-MBs (n = 133). SHH pathway mutations involved PTCH1 (across all age groups), SUFU (infants, including germline), and SMO (adults). Children >3 years old harbored an excess of downstream ...[more]

PMID: 24651015

Publication: 1/4

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Project description:While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can cause base quality scores to underestimate the probability of error at certain genomic positions, resulting in false positive variant calls, particularly in mixtures such as samples with RNA editing, tumors, circulating tumor cells, bacteria, mitochondrial heteroplasmy, or pooled DNA. Most algorithms proposed for correction of SSEs require a training data set, which is typically either from a part of the data set being M-bM-^@M-^\recalibratedM-bM-^@M-^] (Genome Analysis ToolKit, or GATK) or from a separate data set with special characteristics (SysCall). Here, we combine the advantages of these approaches by adding synthetic RNA spike-in standards to human RNA, and use GATK to recalibrate base quality scores with reads mapped to the spike-in standards. Compared to conventional GATK recalibration that uses reads mapped to the genome, spike-ins improve the accuracy of Illumina base quality scores by a mean of 5 units, and by as much as 13 units M-BM- at CpG sites. In addition, since reads mapping to the genome are not used for recalibration, our method allows run-specific recalibration even for the many species without a comprehensive and accurate SNP database. We also use GATK with the spike-in standards to demonstrate that the Illumina RNA sequencing runs overestimate quality scores for AC, CC, GC, GG, and TC dinucleotides, while SOLiD has less dinucleotide SSEs but more SSEs for certain cycles. We conclude that using these DNA and RNA spike-in standards with GATK improves base quality score recalibration. Four human RNA samples with equimolar ERCC spike-in standards were sequenced on Illumina. Two human brain/liver/muscle RNA mixtures with dynamic range of ERCC spike-in standards were sequenced on SOLiD.

Dataset Information

2013-11-19-17-24-36-breez-MB-2013-10-18-Whole_genome_DNAseq_Medulloblastoma_ICGC - samples

Publications

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition.

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