Article

Novel BRCA1 and BRCA2 genomic rearrangements in Southern Chinese breast/ovarian cancer patients

Department of Surgery, The University of Hong Kong, Hong Kong SAR, China, .
Breast Cancer Research and Treatment (Impact Factor: 3.94). 10/2012; 136(3). DOI: 10.1007/s10549-012-2292-1
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Available from: James Ford, Dec 30, 2013
LETTER TO THE EDITOR
Novel BRCA1 and BRCA2 genomic rearrangements in Southern
Chinese breast/ovarian cancer patients
Ava Kwong
Enders K. O. Ng
Fian B. F. Law
H. N. Wong
Anna Wa
Chris L. P. Wong
Allison W. Kurian
Dee W. West
James M. Ford
Edmond S. K. Ma
Received: 4 October 2012 / Accepted: 4 October 2012 / Published online: 26 October 2012
Ó The Author(s) 2012. This article is published with open access at Springerlink.com
To the Editor,
Breast cancer is the most frequently occurring malignancy
in not only Western but also Asian women. Germline
mutations in the breast cancer susceptibility genes, BRCA1
and BRCA2, are found in a significant proportion of
patients affected by hereditary breast/ovarian cancer [1].
Pathogenic mutations in BRCA1 and BRCA2 are predom-
inantly small deletions, insertions, and point mutations
resulting in frame shift, nonsense, premature termination,
or splice site alterations, which lead to the formation of a
truncated BRCA protein. Owing to the richness of Alu
sequences [2]inBRCA1 and BRCA2, albeit to a lesser
extent in the latter gene, it is not surprising that BRCA1/2
genomic rearrangements are known to be mediated through
Alu repeat sequences. Large genomic rearrangements
(LGRs) have been increasingly reported and more than 80
different LGRs have been characterized in BRCA1, but less
in BRCA2 [35]. One study in the United States reported that
genetic testing, as currently carried out, did not provide all
available information to women at risk. Their findings
indicated that 12 % of those high-risk breast cancer patients
with negative genetic test results for BRCA1 and BRCA2
actually carried large genomic arrangement in one of these
genes [3]. These results are consistent with previous studies
specifically of BRCA1 in various European populations [6,
7]. Over the past decade, a large number of techniques have
become available for detecting large deletions and duplica-
tions. Multiplex ligation-dependent probe amplification
(MLPA) is one of the most commonly used assays for this
purpose [4, 811]. The prevalence of LGRs varies between
different populations ranging from 0 to 27 % of BRCA1
mutation-positive families from French Canadian and Dutch
populations, respectively [10, 12]. Founder LGRs have also
been identified. However, in many countries; breast cancer
patients without family history are generally not tested for
LGRs. Lack of a family history may relate to small family
size, non-penetrance, premature death, loss of contact with
family members, and inadequate information [13]. Alterna-
tively, lack of family history can also be explained by new
germline mutations that found in the probands, but not in any
of their family members. De novo mutations are very rare,
but reported among BRCA genes [1417]. Previously, we
reported a de novo mutation in which multiple exons were
deleted from BRCA1 in a Chinese breast cancer patient [18].
To date, the spectrum of LGR in Chinese population is lar-
gely unknown. In this study, MLPA analysis was employed
together with full gene sequencing to determine the fre-
quency and spectrum of
BRCA1/2 LGRs in a group of
Chinese breast cancer patients from Southern China.
A. Kwong E. K. O. Ng H. N. Wong A. Wa
Department of Surgery, The University of Hong Kong,
Hong Kong SAR, China
A. Kwong
Cancer Genetics Center, Hong Kong Sanatorium & Hospital,
Hong Kong SAR, China
A. Kwong (&) C. L. P. Wong E. S. K. Ma
Hong Kong Hereditary Breast Cancer Family Registry,
Hong Kong SAR, China
e-mail: akwong@asiabreastregistry.com
A. Kwong A. W. Kurian D. W. West J. M. Ford
Departments of Medicine, Oncology, and Health Research and
Policy, Stanford University School of Medicine, Palo Alto,
CA, USA
E. K. O. Ng F. B. F. Law C. L. P. Wong E. S. K. Ma
Department of Molecular Pathology, Hong Kong Sanatorium &
Hospital, Hong Kong SAR, China
123
Breast Cancer Res Treat (2012) 136:931–933
DOI 10.1007/s10549-012-2292-1
Page 1
A total of 555 clinically high-risk breast and/or ovarian
cancer probands (520 female and 35 male), referred to the
Hong Kong Hereditary and High Risk Breast Cancer Pro-
gramme (www.HRBCP.org) from March 2007 to Novem-
ber 2011, were recruited [18, 19]. Based on the lower
incidence of breast cancer in Asia cohorts, clinically high-
risk patients included in this study were defined as those
who (1) had at least one first- or second-degree relative
with breast and/or ovarian cancer, regardless of age; (2)
were less than 50 years of age at diagnosis; (3) had bilat-
eral breast cancer; (4) had triple negative (TN) or medul-
lary type pathology; (5) had at least one relative with
cancers other than breast and ovarian cancer that are known
to be related to BRCA mutations; or (6) they were ovarian
cancer patients with a family history of breast cancer. The
mean age at diagnosis of breast cancer was 45-years (range
18–82) and that of ovarian cancer was 44-years (range
19–64). All probands were from Chinese ancestry and over
90 % were from Guangdong province of Southern China.
MLPA analysis and full BRCA1/2 sequencing of the 555
probands were conducted. Overall, we identified 69
(69/555, 12.4 %) deleterious BRCA gene mutations. Of the
69 deleterious mutations, 29 were in BRCA1 and 40 in
BRCA2. Among the 69 mutations, 29 of them were novel in
which 12 were in BRCA1 and 17 were in BRCA2.
Intriguingly, we also identified 7 out of the 35 male pro-
bands who carried only BRCA2 deleterious mutations.
Most importantly, among the 29 novel mutations, 4 of them
are LGRs (2 in BRCA1 and 2 in BRCA2) and all were only
detected by MLPA, but not sequencing. Overall it
accounted for 5.8 % (4/69) of all BRCA mutations in our
cohort, 6.9 % (2/29) of all BRCA1 mutations and 5 %
(2/40) of all BRCA2 mutations. Except for the one we
previously reported [18], all remaining LGRs identified in
this study are novel mutations and not found in BIC entries.
The characteristics of the probands and characterization
of the LGRs are described in Table 1. Based on MLPA
analysis, female proband (TWH9701) was found to have a
large BRCA1 deletion of exons 1–12. We have previously
reported this patient who carried a de novo BRCA1 LGR
because none of her parents carried the mutation [18].
Although we could not determine the LGR breakpoints by
cDNA sequencing, qRT-PCR analysis has shown that this
novel germline mutation resulted in the downregulation of
BRCA1 gene expression, suggesting that there is no expres-
sion of truncated RNA transcript. Female proband
(TWH5901) was found to have a BRCA1 deletion spanning
exons 17–20. Sequence analysis of amplified cDNA revealed
a deletion of 291 bp with breakpoints located at c.4987_
5277. The loss of exons 17–20 caused an in-frame deletion
and truncation of the BRCA1 protein (p.M1663_
K1759del97). Male proband (HKSH9601) and a family
member were identified to carry a BRCA2 deletion of exons
15–16 only by MLPA. Sequencing of amplified cDNA
revealed a deletion of 370 bp with breakpoints located at
c.7436_7805. This deletion produced a shift in the reading
frame and truncation of BRCA2 protein (p.Asp2479Gly-
fsX46). Female proband (HKSH1001) was found to carry a
BRCA2 deletion of exons 21 and sequence analysis revealed
that a deletion of 122 bp with breakpoints located at c.8633_
8754. The loss of exon 21 caused a shift in the reading frame
and truncation of BRCA2 protein (p.Glu2878GlyfsX5).
Importantly, we have recently confirmed by haplotype
analysis that the recurrent LGR (c.7436_7805del370) found
in the male proband (HKSH9601) and his family member is a
founder mutation [20]. Thus, we are the first to report that
male breast cancer in this Chinese family has the BRCA2
founder LGR.
In conclusion, overall BRCA1/2 mutation prevalence
among this cohort was 12.4 % (69/555). Four novel LGRs
Table 1 BRCA genomic rearrangements of the probands
Exon
deletion
Breakpoints
a
(cDNA)
Predicted amino
acid change
Case no. Gender Family
history
of BC
BC and other
cancers (age at
diagnosis)
Other tumors in
proband family
BIC
entries
1–12
(BRCA1)
No transcript Uncertain TWH9701 F No BC (30) Bone, leukemia,
liver, pancreas
None
17–20
(BRCA1)
c.4987_5277del291 p.M1663_K1759del97 TWH5901 F Yes BC (36); OC (45) Esophagus,
stomach
None
15–16
(BRCA2)
c.7436_7805del370 p.Asp2479GlyfsX46 HKSH9601 M Yes BC (55); GC (54);
HCC (50)
Esophagus None
21
(BRCA2)
c.8633_8754del122 p.Glu2878GlyfsX5 HKSH1001 F Yes BC (39) None
BC breast cancer, GC gastric cancer, HCC hepatocellular carcinoma, OC ovarian cancer, BIC breast cancer information core
a
All mutations are named according to the recommendations for the description of sequence variants of Human Genome Variation Society
(HGVS)
932 Breast Cancer Res Treat (2012) 136:931–933
123
Page 2
(2 in BRCA1 and 2 in BRCA2) were detected only by
MLPA, which accounted for 6.9 % (2/29) of all BRCA1
mutations and 5 % (2/40) of all BRCA2 mutations. These
findings highlight the LGR spectrum of BRCA1 and
BRCA2 genes in Southern Chinese breast cancer patients
and the ethnic specificity of these rearrangements. Con-
sistent with the literature, we recommend LGR testing
together with BRCA1/2 full gene sequencing for the pur-
pose of comprehensive BRCA1/2 analysis in the clinical
setting.
Acknowledgments We sincerely thank sDr Ellen Li Charitable
Foundation, The Kuok Foundation, National Institute of Health
1R03CA130065, and North California Cancer Center for support.
Conflict of interest None.
Open Access This article is distributed under the terms of the
Creative Commons Attribution Noncommercial License which per-
mits any noncommercial use, distribution, and reproduction in any
medium, provided the original author(s) and the source are credited.
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    • "However studies done in these populations are limited. Several deletions and duplications have been reported from Singapore [9], Korea [8], Malaysia [10] and China [11]. There are no published reports on the analysis of BRCA1 and BRCA2 large genomic rearrangements in Sri Lankans and this study examined the possibility of such genomic rearrangements in a cohort in which point mutations and sequence variants in BRCA1 and BRCA2 were previously described [5,6]. "
    [Show abstract] [Hide abstract] ABSTRACT: Background Majority of mutations found to date in the BRCA1/BRCA2 genes in breast and/or ovarian cancer families are point mutations or small insertions and deletions scattered over the coding sequence and splice junctions. Such mutations and sequence variants of BRCA1 and BRCA2 genes were previously identified in a group of Sri Lankan breast cancer patients. Large genomic rearrangements have been characterized in BRCA1 and BRCA2 genes in several populations but these have not been characterized in Sri Lankan breast cancer patients. Findings A cohort of familial breast cancer patients (N = 57), at risk individuals (N = 25) and healthy controls (N = 23) were analyzed using multiplex ligation-dependent probe amplification method to detect BRCA1 and BRCA2 large genomic rearrangements. One familial breast cancer patient showed an ambiguous deletion in exon 6 of BRCA1 gene. Full sequencing of the ambiguous region was used to confirm MLPA results. Ambiguous deletion detected by MLPA was found to be a false positive result confirming that BRCA1 large genomic rearrangements were absent in the subjects studied. No BRCA2 rearrangement was also identified in the cohort. Conclusion Thus this study demonstrates that BRCA1 and BRCA2 large genomic rearrangements are unlikely to make a significant contribution to aetiology of breast cancer in Sri Lanka.
    Full-text · Article · Jun 2014 · BMC Research Notes
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    • "Furthermore, LGRs account for 6.3% of the total mutations in BRCA1/2 genes in a Malaysian cohort [47]. A recent report from southern China found that 0.7% (4/555) of high-risk breast or ovarian cancer patients had LGRs in their BRCA genes, representing 5.8% of overall BRCA1/2 mutations in their cohort [48]. These studies suggest that LGRs in the BRCA genes of Asian high-risk patients amount to less than 7% of all BRCA mutations. "
    [Show abstract] [Hide abstract] ABSTRACT: Breast cancer is the most prevalent cancer in Asian females, and the incidence of breast cancer has been increasing in Asia. Because Asian patients develop breast cancer at a younger age than their Caucasian counterparts, the contributions of BRCA1 and BRCA2 (BRCA1/2) mutations in Asians are expected to be different than in Caucasians. The prevalence of BRCA1/2 mutations in the Asian population varies among countries and studies. Most Asian studies have reported more frequent mutations in BRCA2 than in BRCA1, with the exception of studies from India and Pakistan. In addition, the contribution of large genomic rearrangements of BRCA1/2 genes is relatively small in Asian populations in comparison to other ethnic populations. Various statistical models for the prediction of BRCA1/2 mutations have underestimated the risk of having these genetic mutations in Asians, especially in predicting BRCA2 gene mutation. Until recently, BRCA1/2 mutation analyses in Asia were mostly conducted by independent single institutions with different patient selection criteria and using various genotyping methods. However, a couple of Asian groups have initiated nationwide studies collecting BRCA1/2 mutational data. These national collaborative studies will help a comprehensive understanding of the prevalence of BRCA1/2 mutations in the Asian population.
    Full-text · Article · Dec 2013 · Journal of Breast Cancer
  • No preview · Article · Jul 2014 · Clinical Genetics
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