EXaCT-1 (Exome Cancer Test 1)

Overview

EXaCT-1 is a New York State–approved CLIA-grade whole-exome sequencing assay developed at Weill Cornell Medicine. It uses Agilent HaloPlex Exome capture targeting 21,522 genes at mean coverage of approximately 85x. The CLIA certification allows results to be used clinically as well as for research. It was designed for paired tumour/normal somatic variant calling in cancer specimens.

Used by

• CLIA-grade EXaCT-1 WES (Agilent HaloPlex Exome, 21,522 genes, mean 85x coverage) applied to 72 urothelial carcinoma tumours from 32 patients to map clonal evolution pre- and post-platinum chemotherapy; validated orthogonally with an N250 targeted panel (Pearson r=0.93 with WES VAFs, P<10⁻¹⁷¹). PMID:27749842

Notes

• New York State CLIA-certification distinguishes EXaCT-1 from standard research WES platforms, enabling clinical-grade reporting.
• Mean coverage ~85x across 21,522 genes; Agilent HaloPlex library preparation.
• Variants called with MuTect and SNVseeqer; annotation with Oncotator.
• Validated against the N250 targeted panel (SeqCap EZ Choice, 400x mean coverage; Pearson r=0.93 with WES VAFs).

Sources

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