Targeted Sequencing Of Chromosome 9 Genes Associated With Papillary Type 1 Renal Cell Carcinoma

Open Access
Author:
Belsky, Michael Alan
Area of Honors:
Biomedical Engineering
Degree:
Bachelor of Science
Document Type:
Thesis
Thesis Supervisors:
  • William O Hancock, Thesis Supervisor
  • Peter J Butler, Honors Advisor
  • Dr William A La Framboise, Faculty Reader
Keywords:
  • Cancer
  • next generation sequencing
  • renal cell carcinoma
  • targeted sequencing
  • papillary type 1
Abstract:
We have completed a targeted sequencing study of 6 patient Papillary Type 1 tumors. Fragment libraries were created for 456 exons of 43 genes on the p-arm of chromosome 9 between reference positions 1,051,050-14,150,350 using biotinylated DNA hybridization probes to enrich 112.5 kb of sequence. The selected fragments were collected, concentrated, and subjected to a second round of hybridization, capture, wash, and amplification followed by sequencing on the Ion Torrent PGM using the 318 v2 chip. Analysis was performed using the GenomAnalytics (GenomOncology, Westlake, OH) server and all findings were confirmed by manual curation of the sequence using the Integrated Genome Viewer (Broad Institute, Canbridge, MA). We previously identified significant copy number losses specific to Papillary Type 2 renal tumors in the GLDC, SLC1A1, and CDC37L1 genes of each tumor. Also, we identified 3 single nucleotide substitutions that were identical in every tumor sample within the coding regions of 3 genes (TPD52L3, PDCD1LG2 and KIAA0020) in this genomic domain. Papillary Type 1 tumors were sequenced to determine if they exhibit different single nucleotide and copy number variants than those identified in Papillary Type 2 samples. The long-range goal is to develop a low cost, high- resolution test requiring minimal substrate to rapidly distinguish among Papillary Type 1 and Type 2 cancers using small biopsy specimens or fine needle aspirates.