Fig 1.
Overview of patient samples and sequencing methods.
Sequencing for the AmpliSeq CCP samples was done using the Ion 318 Chip and whole exome sequencing was preformed using the Genome Analyzer II or HiSeq 2000, both from Illumina.
Table 1.
Patient demographics and clinical information.
Fig 2.
Summary of mutated AmpliSeq CCP genes.
Genes containing variants and the associated sequencing platforms are shown. Most variants were associated with ExomeSeq data and there were a total of 409 genes on the AmpliSeq CCP.
Fig 3.
Read alignment view of PTCH1 (A) and NF1 (B) genes zoomed in to individual base level.
(A) View displayed spans chr9: 98,209,620–98,209,640 of PTCH1; variant base is G to A mutation located at base 98,209,634 in primary tumor of patient UH1. (B) View displayed spans chr17: 29,585,500–29,585,530 of NF1; variant is G to A mutation located at base 29,585,518 in recurrent tumor of patient UH3. The variant base is located between the two vertical lines crossing the reads.
Fig 4.
Read alignment view of PTEN (A) and TP53 (B) genes zoomed out to exon level.
The AmpliSeq data did not produce any reads covering the variant base in PTEN; however, a single read not shown in the graphic did cover the variant base in TP53 in the recurrent tumor. Data from primary tumors are shown. (A) View displayed spans chr10: 89,653,700–89,653,900 of PTEN; variant is T to G mutation located at base 89,653,783. (B) View of TP53 displays region of chr17: 7,578,400–7,578,600; variant is G to A mutation located at base 7,578,475. The location of the variant base is indicated by the vertical line crossing the reads.
Table 2.
Variants identified in Ion AmpliSeq Comprehensive Cancer Panel Genes.