Genomic DNA from reported samples underwent whole-exome sequencing (WES) as described previously and below11 (link),14 (link). The SeqCap EZ Exome v2.0 (Roche Life Science), xGen Exome Research Panel (Integrated DNA Technologies), or SeqCap EZ MedExome (Roche Life Science) kit was used for capture. After library preparation, sequencing was performed on the Illumina HiSeq platform (RRIDs: SCR_016386, SCR_016383, SCR_016387) with paired-end 74 or 100 base pair reads. The tumor and blood samples were sequenced to a target depth of 185 and 85 reads, respectively. Sequenced reads were aligned to the human reference genome (GRCh37) using BWA-mem (version 0.7.15)58 . PCR duplicates were marked with Picard (version 2.17.11, RRID:SCR_006525)59 , followed by local realignment and base quality recalibration using Genome Analysis Toolkit (GATK, version 3.4, RRID:SCR_001876)60 (link).
Youngblood M.W., Erson-Omay Z., Li C., Najem H., Coșkun S., Tyrtova E., Montejo J.D., Miyagishima D.F., Barak T., Nishimura S., Harmancı A.S., Clark V.E., Duran D., Huttner A., Avşar T., Bayri Y., Schramm J., Boetto J., Peyre M., Riche M., Goldbrunner R., Amankulor N., Louvi A., Bilgüvar K., Pamir M.N., Özduman K., Kilic T., Knight J.R., Simon M., Horbinski C., Kalamarides M., Timmer M., Heimberger A.B., Mishra-Gorur K., Moliterno J., Yasuno K, & Günel M. (2023). Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas. Nature Communications, 14, 6279.
Other organizations :
Yale Cancer Center, Northwestern University, Neurological Surgery, Bahçeşehir University, Marmara University, University of Bonn, Sorbonne Université, Assistance Publique – Hôpitaux de Paris, University Hospital Cologne, University of Pennsylvania, Yale University, Kent Hastanesi, Acıbadem Adana Hospital
Sequencing depth for tumor samples (target depth of 185 reads)
Sequencing depth for blood samples (target depth of 85 reads)
control variables
Exome capture kit (SeqCap EZ Exome v2.0, xGen Exome Research Panel, or SeqCap EZ MedExome)
Sequencing platform (Illumina HiSeq)
Paired-end 74 or 100 base pair reads
Alignment to human reference genome (GRCh37) using BWA-mem
PCR duplicate marking using Picard
Local realignment and base quality recalibration using GATK
controls
Positive control: None specified
Negative control: None specified
Annotations
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