This study was conducted under an institutional review board–approved protocol at Yale University. The patient's blood and tumor tissue were collected after obtaining written informed consent. Histopathology, including immunohistochemical studies, was evaluated by a board-certified oncologic surgical pathologist.
WES and analysis was performed in accordance with our previously described methods at the Yale Cancer for Genome Analysis (YCGA) (Fomchenko et al. 2019 (link)). Briefly, genomic DNA from the tumor and blood were isolated and exome captured with IDT xGen Exome Research Panel v1 (Integrated DNA Technologies) and then sequenced on the Illumina NovaSeq6000 WES platform with 2 × 100 base pair reads. Downstream analysis of raw reads, including alignment, duplicate marking, realignment, and base quality recalibration was performed according to “GATK Best Practice” recommendations (v.4.1.9, Grch37). Somatic SNVs, indels, and copy-number variations (CNVs) were identified as previously described (Fomchenko et al. 2019 (link)). Mean coverage of 139.4× was achieved for blood and 240× for tumor tissue (Supplemental Table 1 ).
WES and analysis was performed in accordance with our previously described methods at the Yale Cancer for Genome Analysis (YCGA) (Fomchenko et al. 2019 (link)). Briefly, genomic DNA from the tumor and blood were isolated and exome captured with IDT xGen Exome Research Panel v1 (Integrated DNA Technologies) and then sequenced on the Illumina NovaSeq6000 WES platform with 2 × 100 base pair reads. Downstream analysis of raw reads, including alignment, duplicate marking, realignment, and base quality recalibration was performed according to “GATK Best Practice” recommendations (v.4.1.9, Grch37). Somatic SNVs, indels, and copy-number variations (CNVs) were identified as previously described (Fomchenko et al. 2019 (link)). Mean coverage of 139.4× was achieved for blood and 240× for tumor tissue (
