N250 Targeted Panel

Overview

The N250 targeted panel is a 250 cancer-gene targeted sequencing assay using NimbleGen SeqCap EZ Choice capture technology, achieving mean coverage of approximately 400x. It was used at Weill Cornell Medicine as an orthogonal validation platform alongside whole-exome sequencing (EXaCT-1) in urothelial carcinoma studies.

Used by

  • N250 targeted panel (250 cancer genes, SeqCap EZ Choice, mean 400x coverage) used as orthogonal validation of EXaCT-1 WES variant calls in 72 urothelial carcinoma tumours from 32 patients; Pearson r=0.93 with WES VAFs (P<10⁻¹⁷¹), confirming high concordance between platforms. PMID:27749842

Notes

  • 250 cancer-relevant genes captured with NimbleGen SeqCap EZ Choice.
  • Mean coverage ~400x — substantially deeper than the paired EXaCT-1 WES (~85x), enabling sensitive subclonal variant detection.
  • Demonstrated high concordance with WES VAFs (Pearson r=0.93), validating EXaCT-1 as a reliable exome-scale platform for clonal architecture studies.

Sources

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