Cancer cells display complex genomic aberrations that include large-scale genetic
rearrangements and epigenetic modulation that are not easily characterized by short-read
sequencing. We present a method for simultaneous profiling of long-range
genetic/epigenetic changes in matched cancer samples. Clear cell renal cell carcinoma
(ccRCC) is the most common subtype of kidney cancer. Most ccRCC cases demonstrate
somatic genomic alterations involving the short arm of chromosome 3 (3p), most often …