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Table 1 Summary of somatic copy number aberrations showing a difference in frequency between pure-cLCIS, inv-cLCIS and cILC

From: PIK3CA mutations are common in lobular carcinoma in situ, but are not a biomarker of progression

Chr Region Genes Type of SCNA PURE c-LCIS (27) INV-cLCIS (28) cILC (25) P_values
  Pure cLCIS vs INV-cLCIS INV-cLCIS vs cILC Across all 3 groups
5 39436375-39620648 (p13.1) LOC101926940 Gain 4 0 3 0.05 0.1 0.1
5 129741359-131422972 (q23.3 – q31.1) HINT1, LYRM7, CDC42SE2, RAPGEF6, FNIP1,MEIKIN, ACSL6, IL3, CSF2 Gain 4 0 2 0.05 0.2 0.09
6 82391438-171115067 (q14.1 – q27) Many including: MAP3K7, FOXO3, ESR1, IGF2R, MAP3K4, etc. Loss 0 2 10 0.5 0.007 0.00007
8 5412833-8927086 (p23.2-p23.1) MCPH1, ANGPT2, AGPAT5, XKR5, Defensins, FAM66B,SPAG11B &A,CLDN23, ERI1 Loss 1 2 9 1 0.04 0.002
10 75541103-76515425 (q22.2) CHCHD1,VCL,PLAU,ADK,AP3M1, CAMK2G, NDST2 Gain 2 0 5 0.2 0.05 0.03
11 68961001-71551048 (q13.3 – q13.4) CCND1, MYEOV, FGF4, FGF3 Gain (Amp) 0 4 (2) 6 (5) 0.1 0.1 0.02
17 29779560-29899917 (q11.2) RAB11FIP4 Gain (Amp) 5 (1) 0 0 0.02 0.005 0.005
18 727180-742194 (p11.32) YES1 Gain (Amp) 7 (1) 2 0 0.07 0.02 0.02
X 55670623-57693679 (p11.21) KLF8 Gain 10 0 1 0.0003 0.00004 0.00004
20 14695735-15225214 (p12.1) MACROD2 Gain 6 0 1 0.01 0.006 0.006
22 47751337-51304566 (q13.31 - q13.3) BRD1, HDAC10, MAPK12. MAPK11 …. Loss 2 4 13 0.6 0.005 0.0003
  1. Pure-cLCIS pure classic lobular carcinoma in situ, inv-cLCIS classic lobular carcinoma in situ associated with invasive lobular cancer, cILC classic invasive lobular cancer, Chr chromosome, SCNA somatic copy number aberration