FACETS

Overview

Allele-specific copy-number and clonality inference tool for tumor/normal NGS data.

Used by

  • PMID:36493333 — used to assess clonality in the appendiceal adenocarcinoma MSK-IMPACT cohort, supporting the molecular subtyping of mucinous appendiceal adenocarcinoma into RAS-mut, GNAS-mut, and TP53-mut predominant lineages PMID:36493333.
  • PMID:37682528 — used to derive allele-specific copy-number calls from MSK-IMPACT in 1,507 urothelial carcinoma tumors, supporting assessment of CDKN2A/CDKN2B co-alteration patterns in FGFR3-altered disease PMID:37682528.
  • PMID:37651310 — FACETS used for copy-number analysis in 1,882 endometrial carcinoma patients sequenced by MSK-IMPACT; supported identification of CN-H/TP53abn molecular subtype enriched in Black patients PMID:37651310.
  • PMID:38630790 — FACETS used to assess tumor purity and detect genomic near-haploidization (LOH >80%) in 210 evaluable diffuse pleural mesothelioma patients from MSK-IMPACT sequencing PMID:38630790.
  • PMID:38758238 — FACETS v0.5.6 used for allele-specific copy-number and LOH inference in pituitary neuroendocrine tumors; identified rcLOH pattern in 11/14 treatment-refractory corticotroph PitNETs PMID:38758238.
  • PMID:38949888 — FACETS v0.5.6 used for copy-number analysis in 3,244 prostate cancer tumors from 2,257 patients sequenced by MSK-IMPACT PMID:38949888.
  • PMID:39753968 — FACETS v0.5.14 used in a two-step pipeline for allele-specific copy-number inference in 2,336 PDAC patients sequenced with MSK-IMPACT; 1,555 of 2,322 tumors passed copy-number QC; FACETS output enabled classification of KRAS allelic imbalance events (focal/arm amplifications, gains, CNLOH, LOH, post-WGD loss) and showed that KRAS mutant-allele dosage gains independently predict shorter OS across all clinical stages PMID:39753968.
  • Used to assess tumor purity (>=25% threshold) in 22 primary-metastasis WES pairs for bladder cancer clonal evolution analysis PMID:36543146
  • FACETS used for allele-specific copy-number estimation and clonality assessment in 151 advanced head and neck tumors sequenced with MSK-IMPACT; identified whole-genome duplication in 25% of HNSC cases and quantified 3p deletions enriched in recurrent HPV-positive disease PMID:27442865
  • Applied FACETS algorithm to infer somatic copy number alterations and tumor purity/ploidy from sequencing data PMID:28336552
  • Used to estimate cancer cell fraction and clonality of alterations in MSK-IMPACT-sequenced prostate cancer tumors (504 tumors from 451 patients); identified TP53 and BRCA2 somatic alterations as early truncal clonal events in patients who later developed metastasis PMID:28825054
  • FACETS v0.5.0 used for allele-specific copy-number analysis from WES in 68 melanoma biopsies; identified focal CDKN2A loss emerging on-therapy in 4 progressive-disease patients PMID:29033130
  • FACETS used for allele-specific copy-number estimation and tumor purity calculation in 295 metastatic EGC samples; ERBB2 amplification level by FACETS-based NGS predicted trastuzumab PFS better than IHC/FISH PMID:29122777
  • FACETS v0.3.9 used to estimate copy number, purity, and ploidy in SUMMIT basket-trial patients; integrated with ABSOLUTE v1.0.6 for HER2 mutation clonality estimates (95% of HER2 mutations were clonal) PMID:29420467
  • FACETS v0.5.10 applied to 1,013 prostate tumor/normal pairs for allele-specific copy number, purity, ploidy, and clonality (cancer-cell fraction) estimation PMID:29610475

Notes

  • In the appendiceal cohort, FACETS-derived clonality was paired with aneuploidy scoring (segment-length-weighted copy-number deviation from diploid), where TP53-mut predominant tumors were highly aneuploid and aneuploidy was independently associated with poor prognosis (P=.001) PMID:36493333.

Sources

This page was processed by crosslinker on 2026-05-04. - PMID:36543146

This page was processed by wiki-cli on 2026-05-05. - PMID:27442865

This page was processed by entity-page-writer on 2026-05-15. - PMID:28336552

This page was processed by wiki-cli on 2026-05-14. - PMID:28825054

This page was processed by entity-page-writer on 2026-05-15. - PMID:29033130

This page was processed by entity-page-writer on 2026-05-15. - PMID:29122777

This page was processed by entity-page-writer on 2026-05-15. - PMID:29420467

This page was processed by wiki-cli on 2026-05-15. - PMID:29610475

This page was processed by wiki-cli on 2026-05-15.