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Table-S1: Clinicopathological parameters of the breast lesions

Clinical features / No. of
samples / Mean age
(years) / Age range
(years) / ER/PR status1 (n=83) / P value
+ / -
Menopausal status
Premenopausal / 62 / 41 / 20-45 / 10 (25%) / 30 (75%) / 0.106
Postmenopausal / 58 / 45 / 44-77 / 18 (43%) / 24 (57%)
Clinical Stage2
TNM Stage I+II / 40 / 46 / 23-61 / 17(55%) / 14 (45%) / 0.008*
TNM Stage III + IV / 85 / 47 / 20-72 / 11 (26%) / 34 (74%)
Tumor Grade3
Grade I / 15 / 39 / 20-61 / 5 (56%) / 4 (44%)
Grade II / 71 / 41 / 23-72 / 20 (41%) / 29 (59%) / 0.01*
Grade III / 35 / 46 / 25-77 / 3 (12%) / 22 (88%)
Lymph node status4
Positive / 90 / 46 / 23-77 / 22 (35%) / 40 (65%) / 0.606
Negative / 33 / 43 / 20-65 / 6 (28%) / 15 (72%)

1ER/PR status were determined for 83 samples; 2exludes one fibroadenoma and one atypical ductal hyperplasia sample; 3tumor grade was not determined for five samples; 4lymph node status not applicable to two samples; ‘*’ indicates significant P value (≤0.05).

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Table-S2: Summary of oligonucleotides used in the study

Primers / Location / Analytical purpose / Forward Primer / Reverse Primer / Size (bp)
D8S1742 / 8p23.1 / Deletion analysis / 5'-cccccaccaagacaca-3' / 5'-ctcaagggatatgaagggca-3' / 130
D8S277 / 8p23.1 / Deletion analysis / 5'-ccaggtgagtttatcaattcctgag-3' / 5'-tgagaggtctgagtgacatccg-3' / 148
D11S2179 / 11q22.3 / Deletion analysis / 5'-taggcaatacagcaagaccctg-3' / 5'-gcactggaatacgattctagcac-3' / 130
MCPH1 Ex- 2 / 8p23.1 / HD/HED, Mutation / 5-aaatctattgggcaggggatg-3' / 5'-cagaagactgtcatatgaatcaaca-3' / 200
D8S557 / 8q24.22 / Deletion control / 5'-tccaggggcttaaactttac-3' / 5'-ggggtcctagagatttagagg-3' / 139
MCPH1Ex-12-13 / Coding regions of exons / Q-PCR / 5'-agccgttcgaactgtctcac-3' / 5'-gttcacagagcttggccact-3' / 156
ATM Ex-58-59 / Coding regions of exons / Q-PCR / 5'-tggatccagctatttggtttga-3' / 5'-ccaagtatgtaaccaacaatagaagaagtag-3' / 82
β2 Microglobulin / 15q21-q22.2 / Q-PCR / 5'-gtgctcgcgctactctctct-3' / 5'-tcaatgtcggatggatgaaa-3' / 153
β-3A-adaptin (K1) / 5q14.1 / DNA cleavage control / 5'-tgccctctggactggaacct-3' / 5'-cctgagcccagcccaagtc-3' / 445
RARβ2 (K2) / 3p24.2 / DNA integrity control / 5'-agagtttgatggagttgggt-3' / 5'-cattcggtttgggtcaatcc-3' / 229
MCPH1 promoter / -1 to + 41 bp / Methylation by MSRA / 5'-ccgcctcacctacagagaaa-3' / 5'-gcagcaggaagtacctcacc-3' / 190
ATM promoter / -644 to -416 bp / Methylation by MSRA / 5'-aatgctctttcaggggtcct-3' / 5'-tagggaagctttggggtttt-3' / 229
MCPH1-U / -169 to + 24 bp / Methylation by MSP / 5'-gtttagttttttttagttttttgt-3' / 5'-acctttcaaaataaaaaccacc-3' / 193
MCPH1-M / -173 to + 27 bp / Methylation by MSP / 5'-gggggtttagttttttttagtttttc-3' / 5'-ctcacctttcaaaataaaaaccg-3' / 200
ATM-U / -592 to -424 bp / Methylation by MSP / 5'-atttgttttaggtgttttattttga-3' / 5'-ctttaaaattttacctcccaacttaca-3' / 169
ATM-M / -592 to -426 bp / Methylation by MSP / 5'-attcgttttaggtgttttatttcga -3' / 5'-ttaaaattttacctcccaacttacg-3' / 167
MCPH1 Ex- 1 / Coding regions of exons / Mutation / 5'-ccgcctcacctacagagaaa-3' / 5'-gcagcaggaagtacctcacc-3' / 190
MCPH1 Ex- 3 / Coding regions of exons / Mutation / 5'-cattttgttttctgcattttgtc-3' / 5'-tggttctgcgatctgtgaaa-3' / 231
MCPH1 Ex- 4 / Coding regions of exons / Mutation / 5'-catgtgcagatttagtgctgtg-3' / 5'-tcctaattgccattatctacattga-3' / 203
MCPH1 Ex- 5 / Coding regions of exons / Mutation / 5'-gggctttttctcctgcctta-3' / 5'-ggtgtatggacacaaatgcaa-3' / 219
MCPH1 Ex- 9 / Coding regions of exons / Mutation / 5'-ggcctataacttcctgtttcca-3' / 5'-cccaggtatcagcatttgaa-3' / 268
MCPH1 Ex- 10 / Coding regions of exons / Mutation / 5'-ttacagtttatttctgtgggaaaaa-3' / 5'-caggacagattgacaagttgc-3' / 215
MCPH1 Ex- 11 / Coding regions of exons / Mutation / 5'-aatttttcccccgatttgac -3' / 5'-cctcagggtgacccactcta-3' / 251
MCPH1 Ex- 12 / Coding regions of exons / Mutation / 5'-ttggtttattgcctgctaagg-3' / 5'-gcaaactgcatttaccatcg-3' / 181
MCPH1 Ex- 13 / Coding regions of exons / Mutation / 5'-ggagtggtcccacctctgta -3' / 5'-cgtctgtgtgcctggattc -3' / 305
MCPH1 Ex- 14 / Coding regions of exons / Mutation / 5'-cacagctcttggctatttgtttt-3' / 5'-accacaggccagtgaggtc-3' / 194

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BC samples / Methylation technique / MCPH1 / ATM
366 / MSRA
MSP
1183 / MSRA
MSP
1186 / MSRA
MSP
3069 / MSRA
MSP
1099 / MSRA
MSP
1818 / MSRA
MSP
1865 / MSRA
MSP
2766 / MSRA
MSP
3098 / MSRA
MSP
3158 / MSRA
MSP
4131 / MSRA
MSP
4272 / MSRA
MSP
4370 / MSRA
MSP
3156 / MSRA
MSP
2587 / MSRA
MSP
4187 / MSRA
MSP
5234 / MSRA
MSP
6285 / MSRA
MSP
1144 / MSRA
MSP
141 / MSRA
MSP
1590 / MSRA
MSP
MSRA
MCF-7 / MSP
% of methylation / MSRA / 68%, (15/22) / 77%, (17/22)
MSP / 68%, (15/22) / 64%, (14/22)
P value / 0.0002* / 0.003*

Table-S3:Correlation between MSRA and MSP analysis

Methylated CpG
Unmethylated CpG

MSRA: Methylation sensitive restriction analysis, MSP: Methylation specific PCR, *indicates significant P value.

Table-S4A: Association between (a) Deletion; (b) Methylation and (c) Alteration (deletion/methylation) of MCPH1and ATM in BC

(a) / ATM / (b) / ATM / (c) / ATM
D+ / D- / M+ / M- / A+ / A-
MCPH1 / D+ / 8 / 15 / MCPH1 / M+ / 14 / 6 / MCPH1 / A+ / 26 / 6
D- / 8 / 20 / M- / 24 / 4 / A- / 18 / 1
P-value / 0.76 / P-value / 0.28 / P-value / 0.23

Table-S4B: Association between (a) Deletion; (b) Methylation and (c) Alteration (deletion/methylation) of MCPH1and ATM in Early onset BC

(a) / ATM / (b) / ATM / (c) / ATM
D+ / D- / M+ / M- / A+ / A-
MCPH1 / D+ / 11 / 17 / MCPH1 / M+ / 29 / 8 / MCPH1 / A+ / 45 / 6
D- / 10 / 37 / M- / 32 / 6 / A- / 21 / 3
P-value / 0.11 / P-value / 0.56 / P-value / 1.00

Table-S4C: Association between (a) Deletion; (b) Methylation and (c) Alteration (deletion/methylation) of MCPH1and ATM in Late onset BC

(a) / ATM / (b) / ATM / (c) / ATM
D+ / D- / M+ / M- / A+ / A-
MCPH1 / D+ / 19 / 32 / MCPH1 / M+ / 43 / 14 / MCPH1 / A+ / 71 / 12
D- / 18 / 57 / M- / 56 / 10 / A- / 39 / 4
P-value / 0.11 / P-value / 0.25 / P-value / 0.57

Table-S4D: Association between (a) Deletion; (b) Methylation and (c) Alteration (deletion/methylation) of MCPH1and ATM in ER/PR + BC

(a) / ATM / (b) / ATM / (c) / ATM
D+ / D- / M+ / M- / A+ / A-
MCPH1 / D+ / 2 / 7 / MCPH1 / M+ / 7 / 2 / MCPH1 / A+ / 11 / 2
D- / 3 / 16 / M- / 16 / 3 / A- / 12 / 3
P-value / 1.00 / P-value / 1.00 / P-value / 1.00

Table-S4E: Association between (a) Deletion; (b) Methylation and (c) Alteration (deletion/methylation) of MCPH1and ATM in ER/PR- BC

(a) / ATM / (b) / ATM / (c) / ATM
D+ / D- / M+ / M- / A+ / A-
MCPH1 / D+ / 12 / 11 / MCPH1 / M+ / 18 / 9 / MCPH1 / A+ / 32 / 5
D- / 8 / 24 / M- / 23 / 5 / A- / 16 / 2
P-value / 0.05* / P-value / 0.22 / P-value / 1.00

D: deletion, M: methylation, A: Alteration, * indicates significant P value (≤0.05)

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MCPH1 / ATM
D+ / D- / D+ / D-
MCPH1 / M+ / 30 / 21 / ATM / M+ / 32 / 5
M- / 28 / 36 / M- / 72 / 17
P value / 0.13 / P value / 0.608

Table-S5: Association between deletion and methylation of MCPH1 and ATM

D: deletion, M: methylation