Table 3.

List of most frequent chromosomal regions of gain or loss in patients with BE or EA

(A) Most commonly altered regions in patients with BE
ChromosomeStartEndPatients with gain (%)Patients with loss (%)Genes in region
<HGD1163,432,534163,614,1111.624.2LMX1A
1*184,717,073186,846,0601.437.5PTGS2 (COX2), PLA2G4A
874,754,21874,913,3261.617.5STAU2
8101,279,027101,431,7722.041.2SPAG1, RNF19A
910,400,06711,764,217018.3PTPRD
9*21,210,77122,953,086042.9MTAP, CDKN2A, CDKN2B, others
9*25,425,78627,582,822019.4TUSC1, PLAA, IFT74, TEK
10108,165,938109,275,992012.7SORCS1
10114,856,262115,024,106028.1TCF7L2
11474,042626,401012.7RNH1, HRAS, RASSF7, MUPCDH, SCT and others
172,912,0163,092,3542.815.3olfactory receptor genes
19*8,714,3318,864,039012.5MBD3L1, MUC16
22*22,795,27022,989,794018.0CABIN1, GGTLA1
17*836,3301,008,12829.20ABR, TIMM22
18168,38375,965,50229.21.5BCL2, MADH2, MADH4, DCC, DPC4, PI5, others
HGD146,425,20246,624,292045.5RAD54L
1*184,717,073186,846,060027.3PTGS2 (COX2), PLA2G4A
550,107,903180,611,420027.3PLK2, CCNB1, XRCC4, APC, RAD50, others
7*156,680,451158,620,885018.2PTPRN2, NCAPG2
838,227,28138,404,631018.2PPAPDC1B, WHSC1L1, FGFR1
9222,26838,427,295045.5MTAP, CDKN2A, CDKN2B, others
10109,092,539133,471,230018.2BUB3, C10orf119, NANOS1, others
11149,5206,642,613036.4MUC6, RHOG, others
118,555,4858,795,697018.2STK33, ST5
11120,168,346133,686,875018.2CHEK1, TIRAP, ETS1, others
1458,681,498106,175,5069.136.4MLH3, M AX, FOXN3, others
1677,215,30277,345,302018.2WWOX
1718,863,80719,044,654036.4GRAP
18600,984771,9709.127.3TYMS, ENOSF1, YES1
1817,908,96076,089,909036.4SMAD2, SMAD4, SMAD7, DCC, others
8*7,156,8237,328,29918.29.1DEFB103A
1422,278,37023,705,61218.29.1MMP14, PCK2, others
1817,274,43818,073,47118.29.1MIB1, microRNAs
19*48,859,09750,122,98627.30ERCC2, multiple zinc finger proteins
5561,58443,795,93728.654.5POLS, NDUFS6, SLC6A19, others
8101,279,027101,431,77211.111.1SPAG1, RNF19A
172,912,0163,092,35418.227.3Olfactory receptor genes
EA550,107,903180,611,420764PLK2, CCNB1, XRCC4, APC, RAD50, others
8*304,1591,524,873053FBXO25
819,651,02626,038,8501340ADAM28, LOXL2, FGF17, others
9222,26830,116,164773MTAP, CDKN2A, CDKN2B, others
10214,3998,156,3911347GATA3, NET1, others
15*19,138,46520,536,973067TUBGCP5
1677,215,30277,345,302060WWOX
172,912,0163,092,354760
1712,002,24519,044,654047COX10, FLCN, others
1822,533,01176,089,9092067SMAD2, SMAD4, SMAD7, DCC, others
2114,850,74146,912,065767ANA, PCNT, TIAM1, others
2215,756,12249,441,6201357BIK, NF2, CHEK2, others
7835,958107,941,3028013EGFR, CDK6, SMURF1, ABCB1, others
8114,955,242141,809,1176013ASAP1, MYC, WISP1, PTK2, others
1583,671,081100,021,9434720FES, PRC1, others
1730,441,73930,442,082530
1817,274,43820,423,4144727GATA6, RBBP8, others
1933,315,12163,560,2136027CCNE1, CEACAM5, XRCC1, others
209,94362,430,3626720ZNF217, TOP1, DNMT3B, PCNA, other
(B) Regions of high-level amplification
Chromosome
High amplification start
High amplification end
Patients affected
Log 2 ratio
643,262,02143,439,93521.53
651,252,52751,423,71122.53
753,704,72553,864,62131.61
755,238,30455,381,99944.41
8128,612,329128,822,82722.11
1125,048,81925,049,17744.32
1610,944,01411,549,68921.63
1734,979,16636,924,02163.87
1934,301,92434,664,14822.52
  • NOTE: Chromosome regions that contain at least one known CNV thought to be present in >10% of populations analyzed are indicated by an asterisk. Normal font indicates regions of loss, boldface font indicates regions of gain, italics indicate regions for which different populations having gain or loss were identified. Genes in region is a subjective list of genes in the altered region that may be of interest for additional studies and is not meant to be exhaustive, particularly in larger regions (e.g., chromosome 18). Start and end of altered region is given in base pairs based on the locations of the BACs that bound the region being altered. Percentage of patients with gains and losses represent the maximum percentage within the region listed. High level amplification was defined as having a log 2 ratio >1.5. All high level amplification was found in EA samples, with the exception of a single patient with HGD, who subsequently went on to develop EA, having the amplification on chromosome 17. Log 2 ratio indicates the maximum value observed across all patients with that amplification.