Supplementary Table 2: Genomic alterations in breast hyperplasia: literature review
Reference and
method
O’Connell 1994
LOH at 4
microsatellite loci
with FFPE
dissection
Lesions
Findings
Comments
Proliferative
disease without
atypia and ADH
N=21
LOH in DCIS 6-33% at each locus
LOH in DCIS in at least 1 locus in 63% of
specimens
50% of hyperplastic lesions share LOH
pattern with concurrent more advanced
lesions
Micale 1994
FISH with FFPE
centromeres 1, 16,
17, 18, X
Dietrich 1995
Karyotype of
primary culture
Moderate to
florid
hyperplasia
N=5
Diffuse benign
proliferative
breast disease
N=10
Moderate-florid
ductal
hyperplasia
N=3
UDH
N=51
LOH at 2pter in 4/21 lesions (19%)
LOH at 4q25-q34 in 3/21 lesions (9%)
LOH at 16q21 in 3/19 lesions (16%)
LOH at 17q21 in 5/20 lesions (25%)
LOH in at least 1 locus in 63% of
specimens
Loss of 17 in 1 lesion
Borderline loss of 16, 18, X in one lesion
each
Clonal cytogenetic abnormalities in 7/10
(5 UDH, 2 ADH)
Also in 4/5 papillary
And 5/15 fibroadenomas
No chromosomal gains or losses
LCIS: aneusomy in 6/9
DCIS: aneusomy in 7/10
LOH at 16q in 1/22 lesions (4.5%)
LOH at 17p in 2/3 lesions (4.7%)
LOH at 17q in 3/23 lesions (13%)
LOH at 13q in 0/18 lesions (0%)
No LOH in apocrine change (0/34) or
papillomas (0/11)
Prior studies:
LOH in ADH 17p: 25%, 16q: 55%
LOH in DCIS 11-55% at 16q, 17p, 17q
LOH in 3/6 (50%) DCIS
LOH in 6/16 (37%) IDC
Tested hyperplasias only from patients
Visscher 1996
FISH for 1, 7, 8, 16,
17, X with FFPE
Lakhani 1996
LOH at 4 loci
with FFPE, blade
dissection
Ahmadian 1997
LOH of 4
microsatellites at
Intraductal
hyperplasia
N=8 from 7
LOH in 2/8 (25%)
Same allele lost as corresponding DCIS,
IDC
3p12-21, with
FFPE;
Kasami 1997
MSI & LOH for10
loci with FFPE,
blade dissection
Dillon 1997
LOH and MSI at 8
loci with FFPE
O’connell 1998
LOH at 15
microsatellites with
FFPE, blade
dissection
patients
with known LOH in DCIS/IDC
Hyperplasia
N=13 lesions
from 5 patients
MSI in one hyperplasia without atypia
6 papillomas without LOH or MSI
MSI & LOH in one hyperplasia with atypia
Epithelial
hyperplasia
N=18 (11 with
cancer)
UDH
N=163 without
cancer
N=48 with
concurrent
cancer
Any microsatellite alteration in 33%
MSI in 1 lesion at 1 locus
LOH in 0-2 lesions at each locus (overall
LOH at 7/88 informative loci)
LOH at >=1 locus: 37% of specimens
without cancer (range: 1-4 loci/specimen)
15% of loci shared by multiple
concurrent UDH lesions
LOH at >=1 locus: 40% of specimens with
cancer (range:1-3 loci/specimen)
37% of LOH loci shared with concurrent
cancer
20q13 gain in 4/5
DCIS: microsatellite alteration in 32%
IMC: microsatellite alteration in 65%
Patients without cancer: No LOH (N=3
epithelial hyperplasia).
Patients with ipsilateral or contralateral
cancer: LOH in 4/6; proportion=0.46
LOH=0.57 in cancer
LOH in cancer but not benign in 27% loci
LOH in benign but not cancer in 20% loci
LOH in both in 27% loci, but in 3/4 parental
allele lost differs
Intraductal
Werner 1999
CGH & FISH 20q13 hyperplasia with
with FFPE, LCM
DCIS, IDC +/ADH
N=5 patients
Benign breast
Euhus 1999
Chromosome 3p
biopsies
LOH at 6 micro(epithelial
satellites with FFPE, hyperplasia,
pipet dissection of
atypical
H&E slides
hyperplasia,
adenosis,
fibroadenoma)
ADH LOH at >=1 locus: 42-44% of
specimens with-without cancer (range: 1-4
loci/specimen); 45% loci shared with cancer
DCIS LOH at >=1 locus: 70-93% of
specimens (range: 1-6 loci/specimen)
DCIS (2-LG, 2-HG): 20q13 gain in 5/5
IMC G2-3: 20q13 gain in 5/5 with higher
level amplification
Cummings 2000
FISH chromosome
1 centromere with
FFPE
Aubele 2000 (ACP)
CGH with FFPE,
LCM dissection
Aubele 2000
(DMP)
CGH with FFPE
LCM dissection
Washington 2000
LOH for 14 markers
with FFPE scalpel
dissection
Burbano 2000
Karyotype of
primary cultures
Hyperplasia
(illustration is
CCL) some with
cancer
N=7
Ductal
hyperplasia with
DCIS
N=9 samples
from 2 patients
Simple ductal
hyperplasia
N= 5 patients
Chromosome 1 copy number intermediate
between normal and ductal carcinoma
(mean 1.56)
Normal: 1.13 copy number
ADH: 1.50 copy number
DCIS: 1.95 copy number
IMC: 1.79 copy number
Average 5.6 alterations
Loss: 13q, 16p,
Gain: 1q, 6p, 11q, 20q
More heterogeneity as compared to DCIS,
but many alterations in common
Average 7.0 (± 1.8) alterations
Loss: 13q
Gain: 12q, 16p, 20q
Associated DCIS-HG: 12.7 (6 samples)
Associated IMC-G3: 15 (2 samples)
One patient with gain 6p in UDH but none of
DCIS/IMC
Ductal
hyperplasia
N=21 lesions
LOH in 4/21 lesions (each with 1, 2, 4, 5
alterations)
One hyperplasia shares 3/5 aberrant loci
with concurrent apocrine metaplasia
Clonal chromosomal abnormalities in 3/4
Loss of chromosome 9 in each
Chromosome 1 alterations in 2
Marinho 2000
FISH for
chromosome 1, 17
centromere with
FFPE
Epithelial or
‘fibroepithelial’
hyperplasia
N=4
Ductal
hyperplasia
N=9 (2 atypical)
in specimens
with cancer
Boecker 2001
CGH with FFPE
needle dissection of
Ductal
hyperplasia
N=14
Chromosome 1 aneusomy 55.6%
Chromosome 17 aneusomy 0%
No genomic changes in hyperplasia
Associated ADH: 9.3 (± 2.8) alterations
Associated DCIS: 11.4 (± 0.8) alterations
Associated IDC: 16.6 (± 1.3) alterations
Specimens with cancer
Adenosis: LOH in 4/23 (1-2 per lesion)
Apocrine metaplasia: LOH in 10/19 (1-5 per
lesion)
Specimens without cancer
Chromosome 1 aneusomy in 2/2 atypical
hyperplasia
DCIS: Chromosome 1 aneusomy 81.8%
Chromosome 17 aneusomy 90.9 %
IMC: Chromosome 1 aneusomy 87.5%
Chromosome 17 aneusomy 87.5%
DCIS: 5.9 alterations (n=52, Unrelated to
UDH except for 2)
No genomic changes in 22 papillary lesions
slides; FISH 8q24,
11q13, 17q12,
20q13.
Gong 2001
CGH with FFPE,
blade dissection of
unstained slides
Maitra 2001
Chromosome 3p
allotyping (LOH)
with FFPE, LCM
Kaneko 2002
LOH and MSI with
FFPE, dissected
Jones 2003
CGH with FFPE,
LCM
Simpson 2005
CGH with FFPE
LCM
Larson 2006
AI for 20
microsatellite
markers with FFPE
LCM
Xu 2008
CGH with frozen
UDH, some with UDH without ADH: 1/9 with copy number
concurrent ADH alterations (3 alterations)
N=18
UDH with ADH: 4/9 with copy number
alterations (range 0-8)
Loss: 16q, 17p
UDH, with
LOH in at least 1 locus in 7/25 (28%)
IMC, +/- DCIS
N=25
Hyperplasia:
mild &
moderate
N=17
HUT, bilateral
n=14x2
HUT
N=4 lesions
from 1 patient
UDH
N= 13 lesions
from 9
specimens
UDH
without
LOH of at least 1 locus: 8/17 (47%)
MSI of at least 1 locus: 1/17 (6%)
Copy number change
Mean=1.6 (range 0-5)
Loss: 1p, 16p, 17q, 19p, 22q
Gain: 13q
Loss of Xq in 1 lesion only
2/13 lesions with AI (mean 0.2/lesion)
Copy number change mean=1.95 (0-5
range)
UDH with ADH: 3 of 4 have subset of
alterations seen in ADH;
The UDH lesion with 8 alterations has no
copy number alterations in concurrent ADH
LOH in 12/13 DCIS
Of pre-neoplastic lesions (DCIS, papillary,
apocrine, UDH) 19/21 clonally relateddivergent vs IMC, 2/21 clonally unrelated
LOH of atypical categories: 14/18 (77%)
LOH of in situ carcinoma: 2/5 (40%)
LOH of invasive carcinoma: 6/8 (75%)
Specimens with cancer
Predominantly a study of CCL and
accompanying carcinoma
Concurrent lesions
ADH: 23/45 with AI (mean 1.3/lesion)
DCIS: 28/30 with AI (mean 4.2/lesion)
IDC: 17/18 with AI (mean 4.8/lesion)
Specimens with cancer
Copy number change in specimens unrelated
to UDH:
tissue, LCM
Newburger 2013
Whole genome
sequencing with
FFPE, core dissect
associated
cancer
N=20
Early neoplasia
without atypia
N=6 patients
Loss: 1p, 13q, 16q
Gain: 1q, 2q, 3p, 6p, 17p, 16q, 12q, 13q,
16p, 17q, 20q
Common ancestor of early neoplasia and
IMC in 1 patient
*see reference for other short segments of high level amplification
ADH: atypical ductal hyperplasia
AI: Allelic imbalance
FFPE: formalin fixed paraffin embedded
CGH: comparative genomic hybridization
DCIS: ductal carcinoma in situ
DIN: Ductal intraepithelial neoplasia
G1-2: grade 1-2
G3: grade 3
HG: high grade
H&E: hematoxylin and eosin stained
HRM: high resolution melting
LG: low grade
IMC: invasive mammary carcinoma
LCM: laser capture microdissection
LOH: loss of heterozygosity
MSI: microsatellite instability
UDH: usual ductal hyperplasia
ADH=9.5 (n=2)
DCIS=11 (n= 3 HG)
IMC =17.8 (n=5 G3)
Early neoplasia with atypia: common
ancestor with IMC in 3 additional patients
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