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This laboratory-developed NGS test protocol is based on a well-validated research use-only kit that targets 54 genes, including all exons of 15 genes (BCOR, BCORL1, CDKN2A, CEBPA, CUX1, DNMT3A, ETV6, EZH2, IKZF1, KDM6A, PHF6, RAD21, RUNX1, STAG2, and ZRSR2) and hot spot exons/regions of 39 genes (ABL1, ASXL1, ATRX, BRAF, CALR, CBL, CBLB, CBLC, CSF3R, FBXW7, FLT3, GATA1, GATA2, GNAS, HRAS, IDH1, IDH2, JAK2, JAK3, KIT, KMT2A/MLL, KRAS, MPL, MYD88, NOTCH1, NPM1, NRAS, PDGFRA, PTEN, PTPN11, SETBP1, SF3B1, SMC1A, SMC3, SRSF2, TET2, TP53, U2AF1, and WT1).
If KDM6A is a gene that prevents uncontrolled cell division (a tumor-suppressor gene) a mutation of that gene could enable cancer development because there would be no curb on cell proliferation.
One of the genes on the now-active X chromosome is a "good" copy of KDM6A that keeps the cell from becoming cancerous.
There are findings indicating that the molecular pathology in KS is caused by mutations in genes involved in histone modification and responsible for the production of histone methyltransferase and histone demethylase (MLL2 and KDM6A, respectively).
MLL2 and KDM6A mutations that are thought to be responsible for KS generally create an early stop codon and truncate the protein before it is functional.
This left 24 distinct mutations, including 16 missense mutations in these genes: CBL, FLT3, IDH2, KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog), NRAS [neuroblastoma RAS viral (v-ras) oncogene homolog], TP53, RUNX1, SRSF2, TET2, KDM6A [lysine (K)-specific demethylase 6A (also known as UTX)], and ZRSR2.
a) Gene class Gene Selected exons Signaling BRAF 11, 15 CBL 8, 9 ETV6 Complete FLT3 20 JAK2 12, 14 KIT 8, 17 KRAS 2, 3 SH2B3 2 MPL 10 NRAS 2, 3 Transcription CEBPA Complete NPM1 11 RUNX1 Complete TP53 Complete WT1 7, 9 Epigenetics ASXL1 12 DNMT3A Complete EZH2 Complete IDH1 4 IDH2 4 TET2 Complete KDM6A Complete RNA splicing SF3B1 12, 13, 14, 15, 16 SRSF2 1, 2 U2AF1 2, 6 ZRSR2 Complete (a) BRAF, v-raf murine sarcoma viral oncogene homolog B1 (synonym: BRAF1); ETV6, ets variant 6 (synonym: TEL); KIT, v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (synonyms: c-Kit, CD117, SCFR); SH2B3, SH2B adaptor protein 3 (synonyms: IDDM20, LNK); WT1, Wilms tumor 1 (synonyms: AWT1, WAGR, ).
Recently, recurrent mutations in several genes encoding histone regulators, including ASXL1, EZH2, SUZ12, and KDM6A (also known as UTX), have been identified.
Example genes included in this group: ASXL1, EZH2, SUZ12, and KDM6A.
18,19) The most-common, biologically relevant alterations were alterations in TP53 (n = 15; 75%), MYC (n = 6; 30%), MLL2 (n = 6; 30%), and KDM6A (n = 2; 10%).
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