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Clinical Research Papers:

Prevalence and spectrum of BRCA germline variants in mainland Chinese familial breast and ovarian cancer patients

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Oncotarget. 2016; 7:9600-9612. https://doi.org/10.18632/oncotarget.7144

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Yeong C. Kim, Linli Zhao, Hanwen Zhang, Ye Huang, Jian Cui, Fengxia Xiao, Bradley Downs and San Ming Wang _

Abstract

Yeong C. Kim1,*, Linli Zhao1,*, Hanwen Zhang1,*, Ye Huang1, Jian Cui1, Fengxia Xiao1, Bradley Downs1 and San Ming Wang1

1 Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA

* These authors have contributed equally to the study

Correspondence to:

San Ming Wang, email:

Keywords: germline variant, BRCA1, BRCA2, mainland Chinese, familial breast and ovarian cancer

Received: September 28, 2015 Accepted: January 18, 2016 Published: February 02, 2016

Abstract

Germline mutations in BRCA1 and BRCA2 are the most penetrating genetic predispositions for breast and ovarian cancer, and their presence is largely ethnic-specific. Comprehensive information about the prevalence and spectrum of BRCA mutations has been collected in European and North American populations. However, similar information is lacking in other populations, including the mainland Chinese population despite its large size of 1.4 billion accounting for one fifth of the world’s population. Herein, we performed an extensive literature analysis to collect BRCA variants identified from mainland Chinese familial breast and ovarian cancer patients. We observed 137 distinct BRCA1 variants in 409 of 3,844 and 80 distinct BRCA2 variants in 157 of 3,024 mainland Chinese patients, with an estimated prevalence of 10.6% for BRCA1 and 5.2% for BRCA2. Of these variants, only 40.3% in BRCA1 and 42.5% in BRCA2 are listed in current Breast Cancer Information Core database. We observed higher frequent variation in BRCA1 exons 11A, 11C, 11D, and 24 and BRCA2 exon 10 in Chinese patients than in the patients of other populations. The most common pathogenic variant in BRCA1 wasc.981_982delAT in exon 11A, and in BRCA2 c.3195_3198delTAAT in exon 11B and c.5576_5579delTTAA in exon 11E; the most common novel variant in BRCA1 was c.919A>G in exon 10A, and in BRCA2 c.7142delC in exon 14. None of the variants overlap with the founder mutations in other populations. Our analysis indicates that the prevalence of BRCA variation in mainland Chinese familial breast and ovarian cancer patients is at a level similar to but the spectrum is substantially different from the ones of other populations.


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Introduction

BRCA1 and BRCA2 (BRCA) are rapidly evolving genes with high levels of variation across primate species [1-3]. Germline mutations in BRCA predispose individuals for breast and ovarian cancer [4-5]. Extensive efforts have been made to determine the prevalence and spectrum of germline mutations in both genes to aid clinical diagnosis of and prevent the disease [6-8].

Increasing evidence indicates that the presence of BRCA germline mutations in human familial breast and ovarian cancer is largely ethnic-specific [9]. For example, 185delAG [c.66_67delAG according to human genome variation society (HGVS) nomenclature] and 5382insC (c.5263_5264insC) in BRCA1 and 6174delT (c.5946delT) in BRCA2 are highly prevalent in Ashkenazi Jews [10]; c.4153delA (c.4035delA), C61G (c.-58C>G), and 5382insC (c.5263_5264insC) in BRCA1 are common in Polish familial breast cancer patients [11]; c.303T>G, c.5324T>G, c.1623dupG, and c.4122_4123delTG in BRCA1 are frequently present in the familial breast cancer patients of African ancestry [12]; ex9-12del in BRCA1 is often seen in Mexican familial breast and ovarian cancer patients [13], and c.7480C>T in BRCA2 is enriched in Korean familial breast cancer patients [14].

BRCA mutations have been extensively analyzed in European and North American populations, but much less are known about them in Asian, African, and Latin American populations, although these contribute most of the total human population. Using the data from Western populations to interpret BRCA mutations in non-Western patients can be inaccurate and lead to misdiagnoses. Therefore, knowledge of ethnic-specific BRCA mutations is urgently demanding and will be highly beneficial for the patients.

Mainland China has a population size of nearly 1.4 billion, accounting for one fifth of the human population worldwide. However, limited information about BRCA mutations in this large population is available in current BRCA variation databases. For example, only 13 of the 1,791 BRCA1 variants and three of the 2,000 BRCA2 variants in the Breast Cancer Information Core (BIC) database were derived exclusively from mainland Chinese patients [15]. We hypothesized that 1) BRCA variation may be common in this population, and 2) many variants representing potential mutations may have already been identified but this information is unknown outside the Chinese scientific community, because many Chinese scientists publish in Chinese rather than in English and most Chinese medical and health science journals are not included in international journal databases [16]. To test our hypothesis, we performed an extensive survey of Chinese and English scientific literature to collect BRCA variant data derived solely from mainland Chinese familial breast and ovarian cancer patients (Figure 1).

Outline

Figure 1: Outline of the study. It shows the steps taken to extract information about BRCA variation in mainland Chinese familial breast and ovarian cancer patients.

Results and discussion

Identification of publications

We identified 32 Chinese publications, including 24 peer-reviewed papers and eight graduate theses (Supplementary Table 1), and 11 peer-reviewed English papers. This totaled 43 publications covering between 2003 and 2015 reported BRCA variants from mainland Chinese familial breast and ovarian cancer patients [17-59].

From these publications, we identified familial breast cancer cases using the inclusion criteria described in each publication: at least one first-degree relative with breast cancer irrespective of age; breast cancer diagnosed before the age of 35 years with a family history of breast and/or ovarian cancer; at least one or two first- or second-degree relatives diagnosed with breast cancer at any age; at least three relatives affected by breast cancer or breast and ovarian cancer; triple-negative breast cancer patients diagnosed before the age of 45 years; bilateral breast cancer diagnosed before the age of 50 years; one or more primary breast/ovarian cancers in first- or second-degree relatives; and at least one relative with cancer other than breast and ovarian cancer that is known to be BRCA1-related. From these publications, we also collected pedigree and genotype information available from family members although most publications only analyzed the proband without such information (Supplementary Table 2).

We identified a total of 3,844 familial breast and ovarian cancer cases from the original studies. All of these were analyzed for BRCA1 (3,129 covered all exons), and 3,024 were analyzed for BRCA2 (2,854 covered all exons); 92% of the 3,844 cases were Han Chinese and the rest were from other ethnic groups (Hui, Mongol, Uyghur, Kazakh, and Russian) (Table 1). These studies were performed in 15 provinces or cities in mainland China, mostly in the densely populated, economically advanced eastern coast area, with the exception of Xinjiang and Ningxia regions (Figure 2). The information highlights the need to analyze the population in so far uncovered regions to fully determine the prevalence and spectrum of BRCA mutations in the entire mainland Chinese population.

Table 1: Publications reporting BRCA mutations in mainland Chinese patients

Year

Location

Ethnicity

Cases

Targeted exons

Published in

Methods*

References

 

 

 

 

BRCA1

BRCA2

Chinese

English

 

 

2003

Beijing

Han

9

All

+

a

17

2003

Beijing

Han

26

All

+

a

18

2003

Jiangsu

Han

23

All but 1, 4

+

a

19

2003

Shanghai

Han

20

All

+

a

20

2003

Beijing

Han

15

4, 8, 11, 18, 19, 20

All but 15, 16, 25, 26

+

b

21

2004

Shanghai

Han

645

All

All

+

b

22

2005

Shanghai

Han

13

All

All

+

a

23

2005

Anhui

Han

76

All but 1, 3, 4, 6, 7, 10, 14, 19, 21-24

+

a

24

2006

Shanghai

Han

35

All

All

+

a

25

2006

Shanghai

Han

33

All

All

+

a

26

2007

Hebei

Han

18

2, 11A, 11B, 20

Not specified 4 mutations

+

c

27

2007

Shanghai Liaoning Shadong

Han

177

Not specified 7 mutations

+

a

28

2007

Shanghai Liaoning Shadong

Han

39

All

+

a

29

2007

Shanghai Liaoning Shadong

Han

60

1100delAT, IVS17-1G>T, IVS21+1G>C, 5640delA

+

a

30

2007

Shanghai Liaoning Shadong

Han

139

All

All

+

a

31

2007

Guangdong

Han

17

All

+

a

32

2008

Shanghai Liaoning Shandong

Han

115

All

All

+

a

33

2008

Shanghai Liaoning Shadong

Han

489

All

All

+

d

34

2008

Shandong

Han

25

All

All

+

a

35

2008

Shanghai Guangdong Liaoning

Han

219

All

All

+

a

36

2009

Shandong

Han

25

All

+

a

37

2009

Beijing

Han

139

All

+

a

38

2009

Hunan

Han

26

All

All

+

a

39

2009

Fujian

Han

20

11

+

b

40

2009

Tianjin

Han

5

1, 11, 16, 20

+

a

41

2009

Shandong

Han

30

2, 20

+

a

42

2010

Heilongjiang

Han

54

All but 1, 4

+

c

43

2011

Shandong

Han

8

2, 11

+

b

44

2012

Hebei

Han

13

2, 11, 20

11

+

c

45

2012

Hebei

Han

64

All

All

+

a

46

2012

Ningxia

Hui

7

5, 11, 18, 20, 24

10, 11

+

b

47

2012

Guangdong

Han

92

All but 1, 4

+

b

48

2012

Beijing

Han

409

All

All

+

b

49

2012

Zhejiang

Han

92

3, 8, 11, 12, 13, 24

3, 5, 6, 10, 11, 18, 22, 23

+

b

50

2013

Zhejiang

Han

62

All

All

+

b

51

2013

Xinjiang

Han

30

All

All

+

a

52

2013

Xinjiang

Han

79

All

All

+

a

53

2014

Xinjiang

Han Mongol Hui Uygur

214

All

All

+

a

54

2014

Xinjiang

Han

25

Not specified

Not specified

+

a

55

2014

Shanghai

Han

2

All

All

+

e

56

2015

Xinjiang

Han Mongol Hui Uygur Kazakh Russian

82

All

All

+

a

57

2015

Beijing

Han

109

All

All

+

b

58

2015

Shanghai

Han

64

All

All

+

e

59

Total

 

 

3,844

3844

3024

32

11

 

43

*a. DHPLC, Sanger sequencing; b. Sanger sequencing; c. SSCP, Sanger sequencing; d. SSCP, DHPLC, Sanger sequencing; e. NGS, Sanger sequencing

Geographic

Figure 2: Geographic locations of the original studies. The original studies were performed in 15 provinces and cities in mainland China. Of these, 13 were in east coast area of Han Chinese and two were in Xinjiang and Ningxia of other ethnic groups.

Multiple assays including hetero-duplex formation, single-strand conformation polymorphism (SSCP), denaturing high-performance liquid chromatography (DHPLC), and Sanger sequencing were used in the original studies. All BRCA1 and BRCA2 variants collected in our current study were identified by either direct Sanger sequencing or by Sanger sequencing validation for the results from other assays (Table 1).

BRCA variants identified from publications

By mining the variant data from the 3,844 cases, we identified a total of 137 distinct BRCA1 variants in 409 cases, and 80 distinct BRCA2 variants in 157 cases (Table 2, Supplementary Table 3; Table 3, Supplementary Table 4). Of the 137 BRCA1 variants, 33 (24.6%) were detected by at least two different studies; of the 80 BRCA2 variants, 22 (27.2%) were detected by at least two different studies.

Table 2: Examples of BRCA1 variants identified in mainland Chinese familial breast and ovarian cancer patients*

Class (BIC)

Exon

HGVS annotation

Variation type

Total case

Carrier

 

 

cDNA

Protein

 

 

 

Class 5

11A

c.981_982delAT

p.Cys328*

Frameshift

1142

18

Class 5

11A

c.1116G>A

p.Trp372*

Nonsense

480

5

Class 5

11B

c.2110_2111delAA

p.Asn704Cysfs*7

Frameshift

822

8

Class 5

11B

c.2275C>T

p.Gln759*

Nonsense

473

5

Class 5

11B

c.1556delA

p.Lys519Argfs*13

Frameshift

7

2

Class 5

11B

c.2138C>G

p.Ser713*

Nonsense

50

2

Class 5

11D

c.3531delT

p.Phe1177Leufs*33

Frameshift

7

6

Class 5

11D

c.3916_3917delTT

p.Leu1306Aspfs*23

Frameshift

518

3

Class 5

11D

c.3640G>T

p.Glu1214*

Nonsense

239

3

Class 5

11D

c.3607C>T

p.Arg1203*

Nonsense

239

2

Class 5

11D

c.4065_4068delTCAA

p.Asn1355Lysfs*10

Frameshift

171

2

Class 5

11D

c.3770_3771delAG

p.Glu1257Glyfs*9

Frameshift

548

2

Class 5

19

c.5154G>A

p.Trp1718*

Nonsense

62

2

Pending

I-5

c.212+1G>T

-

IVS

214

3

Pending

11A

c.1064A>G

p.Lys355Arg

Missense

92

8

Pending

11B

c.2077G>A

p.Asp693Asn

Missense

214

3

Pending

11B

c.1934C>A

p.Ser645Tyr

Missense

214

2

Pending

11C

c.3113A>G

p.Glu1038Gly

Missense

437

31

Pending

11C

c.3119G>A

p.Ser1040Asn

Missense

667

3

Pending

11D

c.3548A>G

p.Lys1183Arg

Missense

439

34

Pending

11D

c.3508A>T

p.Ile1170Phe

Missense

76

2

Pending

I-16

c.4986+1G>A

-

IVS

101

2

Pending

16

c.4837A>G

p.Ser1613Gly

Missense

302

17

Pending

22

c.5363G>T

p.Gly1788Val

Missense

548

2

Pending

24

c.5470_5477delATTGGGCA

p.Ile1824Aspfs*3

Frameshift

1505

20

Pending

24

c.5521delA

p.Ser1841Valfs*2

Frameshift

1272

8

Pending

24

c.5503C>T

p.Arg1835*

Nonsense

173

2

Novel

2

c.-1A>T

-

IVS

76

2

Novel

11A

c.919A>G

p.Lys307Glu

Missense

92

10

Novel

11A

c.1660G>T

p.Glu554*

Nonsense

628

3

Novel

11B

c.2073delA

p.Arg691Serfs*10

Frameshift

430

5

Novel

11B

c.2248_2252delCTCAT

p.Leu750Valfs*10

Frameshift

518

2

Novel

11C

c.2572C>T

p.Gln858*

Nonsense

782

4

Novel

11C

c.3122C>G

p.Ser1041*

Nonsense

743

4

Novel

11C

c.2798_2799delGT

p.Gly933Alafs*4

Missense

743

3

Novel

11C

c.3294delT

p.Pro1099Leufs*10

Frameshift

239

3

Novel

11C

c.2939T>A

p.Ile980Lys

Missense

214

2

Novel

11C

c.2941C>G

p.Pro981Ala

Missense

214

2

Novel

11C

c.2603C>A

p.Ser868*

Nonsense

480

2

Novel

11D

c.3363_3367delTACAG

p.Asn1121Lysfs*10

Frameshift

1186

7

Novel

11D

c.3359_3363delTTAAT

p.Val1120Aspfs*11

Frameshift

1226

5

Novel

11D

c.3432G>C

p.Gln1144His

Missense

7

3

Novel

11D

c.3450delT

p.Asp1151Metfs*4

Frameshift

519

3

Novel

11D

c.3952A>C

p.Ile1318Leu

Missense

20

2

Novel

11D

c.3433delG

p.Val1145Phefs*10

Frameshift

7

2

Novel

I-23

c.5468-1_5474delGCAATTGG

-

IVS

823

8

* The table lists the variants detected in at least two cases in each class

Table 3: Examples of BRCA2 variants identified in mainland Chinese familial breast and ovarian cancer patients*

Class (BIC)

Exon

HGVS annotation

Variant type

Total cases

Carrier

 

 

cDNA

Protein

 

 

 

Class 5

3

c.262_263delCT

p.Leu88Alafs*12

Frameshift

518

2

Class 5

10

c.1832C>A

p.Ser611*

Nonsense

518

4

Class 5

10

c.1399A>T

p.Lys467*

Nonsense

191

3

Class 5

19

c.8485C>T

p.Gln2829*

Nonsense

99

2

Class 5

11B

c.3195_3198delTAAT

p.Asn1066Leufs*10

Frameshift

1226

5

Class 5

11B

c.2808_2811delACAA

p.Ala938Profs*21

Frameshift

708

2

Class 5

11C

c.3744_3747delTGAG

p.Ser1248Argfs*10

Frameshift

708

2

Class 5

11D

c.5164_5165delAG

p.Ser1722Tyrfs*4

Frameshift

518

4

Class 5

11E

c.5576_5579delTTAA

p.Ile1859Lysfs*3

Frameshift

1302

5

Class 5

11E

c.5682C>G

p.Tyr1894*

Nonsense

99

2

Class 5

11F

c.6591_6592delTG

p.Glu2198Asnfs*4

Frameshift

409

3

Class 5

23

c.9098_9099insA

p.Gln3034Serfs*10

Frameshift

518

4

Pending

10

c.865A>C

p.Asn289His

Missense

321

13

Novel

10

c.1303dupA

p.Arg435Lysfs*17

Frameshift

708

2

Novel

10

c.1881delA

p.Pro628Hisfs*16

Frameshift

708

2

Novel

11A

c.2442delC

p.Met815Trpfs*10

Frameshift

708

2

Novel

11E

c.5864C>G

p.Ser1955*

Nonsense

409

2

Novel

11F

c.6645_6648CTCC

p.Tyr2215*

Nonsense

375

3

Novel

11F

c.6150_6151insT

p.Asn2051*

Nonsense

109

2

Novel

14

c.7142delC

p.Pro2381Hisfs*13

Frameshift

99

5

Novel

18

c.8172delG

p.Trp2725Glyfs*8

Frameshift

109

3

Novel

18

c.8234dupT

p.Thr2746Aspfs*18

Frameshift

708

2

Novel

19

c.8400_8403del4ins5

p.Phe2801Leufs*10

Nonsense

409

2

Novel

20

c.8517C>A

p.Tyr2839*

Nonsense

181

2

Novel

22

c.8820_8823del

p.Gln2941Leufs*34

Frameshift

1013

3

Novel

22

c.8950delT

p.Ser2984Glnfs*4

Frameshift

604

2

Novel

23

c.9105dup

p.Gln3036Serfs*8

Frameshift

109

4

Novel

24

c.9253delA

p.Thr3085Glnfs*19

Frameshift

375

3

* The table lists the variants detected in at least two cases in each class.

Prevalence assessment

The prevalence of the variant carriers was 10.6% (409/3,844) for BRCA1 and 5.2% (157/3,024) for BRCA2 (Of the 3,844 cases, all were used for BRCA1, but 3,024 were used for BRCA2). The total number of cases used for all exon analysis was 3,129 in BRCA1 and 2,854 in BRCA2. Thus, the total number of cases in the BRCA2 group accounted for 91.2% of the BRCA1 (2,854/3,129). Therefore, the different prevalence of BRCA1 and BRCA2 variations is unlikely caused by the analysis of different cases in each group but instead reflects the fact that BRCA1 has a higher prevalence than BRCA2 in Chinese population. This pattern differs from that in the neighboring Korean population, which has a much higher prevalence of BRCA2 variation than BRCA1 variation [14]. The variation types included frameshift, nonsense, missense, and splicing changes. Majority of the variants except a few do not have frequency information in genome databases, indicating that the variants are mostly rare in human population (Supplementary Table 3, Supplementary Table 4).

Exon distribution of BRCA variants between Chinese and other patient populations

We compared exon distribution frequencies of BRCA variations between mainland Chinese patients and other patient populations represented in the BIC database. We compared the ratios calculated as: number of variation cases in each exon / total number of variation cases in each data set. The total number of variation cases (entries) in the BIC dataset was 15,311 for BRCA1 [61] and 14,914 for BRCA2 [62]; the total number of variation cases in this study was 409 for BRCA1 and 157 for BRCA2. The results showed that the distribution frequencies in 13 out of 24 BRCA1 exons were significantly different between between mainland Chinese and BIC populations (Figure 3A). Variants in mainland Chinese were particularly lower in exons 2 and 20 but higher in exons 11A, 11C, and 11D (exon 11 is arbitrarily divided into 11A, 11B, 11C, and 11D by the BIC database because of its large size) and exon 24 than in other populations. The variants in BRCA1 exons 11A, 11C, 11D and exon 24 occurred in 299 of the 409 (73.1%) Chinese BRCA1- variation cases. In BRCA2, the differences were smaller with only 6 out of 27 exons showed significant difference between mainland Chinese and BIC populations. Exon 10 was the highest in mainland Chinese with 44 of the 157 (28%) Chinese BRCA2-variation cases (Figure 3B). Therefore, BRCA1 exon 11A, 11C, 11D, exon 24, and BRCA2 exon 10 are the variation hot spots in mainland Chinese patients.

Comparison

Figure 3: Comparison of exon distribution frequencies of BRCA variation between mainland Chinese and BIC populations. Relative ratios between these two datasets were used for the comparison (see text for the details). Chi square (χ2) and Fisher exact test were used for statistics analysis. “*” refers to p < 0.05 (actual P values listed in Supplementary Table 5). A. Variant distribution in BRCA1. B. Variant distribution in BRCA2.

BIC-matched variants

Fifty-six (40.3%) BRCA1 and 34 (42.5%) BRCA2 variants exist in the BIC database (Figure 4). Of these, 27 BRCA1 and 23 BRCA2 variants are classified by BIC as Class 5 (Pathogenic), 27 BRCA1 and 9 BRCA2 variants as Pending [most were variants of unknown significance (VUS)], and two BRCA1 and two BRCA2 variants as Class 1 (Benign). The most common pathogenic BRCA1 variant was c.981_982delAT (p.Cys328*) in exon 11A (n = 18), confirming the previous observation in a smaller group of patients [30]. The frequency of this variant was substantially higher in mainland Chinese than in non-Chinese populations: 18 of 409 (4.4%) Chinese BRCA1 variant carriers carried this variant, compared with only 18 of 15,311 (0.1%) BRCA1 variant carriers in the BIC database. The most common BRCA1 Pending variant was c.3548A>G (p.Lys1183Arg) in exon 11D (n = 34; frequency in 1000 Genomes: 0.3526) and c.3113A>G (p.Glu1038Gly) in exon 11C (n = 31, frequency in 1000 Genomes: 0.3357, in Han Chinese Beijing: 0.689). Three Pending variants [c.5470_5477delATTGGGCA (p.Ile1824Aspfs*3), c.5503C>T (p.Arg1835*)] c.5521delA (p.Ser1841Valfs*2) with high frequencies were located at exon 24, which contributes to the BRCT domain of BRCA1 (Figure 3A). The most common Pathogenic BRCA2 variant was c.3195_3198delTAAT (p.Asn1066Leufs*10) in exon 11B (n = 5) and c.5576_5579delTTAA (p.Ile1859Lysfs*3) in exon 11E (n = 5), and the most common Pending variant was c.865A>C (p.Asn289His) in exon 10 (n = 13; frequency in 1000 Genomes: 0.0737). Except for the BRCA1 c.981_982delAT variant, other known pathogenic and Pending variants in either BRCA1 or BRCA2 are unlikely to be founder mutation candidates among mainland Chinese patients due to their lower prevalence or higher frequency in normal population.

No variants were found to overlap with other ethnic-specific BRCA founder mutations, including BRCA1 185delAG (c.66_67delAG, HGVS nomenclature) and 5382insC (c.5263_5264insC) and BRCA2 6174delT (c.5946delT) in Ashkenazi Jews [10]; BRCA1 c.4153delA (c.4035delA), C61G (c.-58C>G), and 5382insC (c.5263_5264insC) in Poles [11]; BRCA1 c.303T>G, c.5324T>G, c.1623dupG, and c.4122_4123delTG in Africans [12]; BRCA1 ex9-12del in Mexicans [13], and BRCA2 c.7480C>T in Koreans [14].

Novel BRCA variants

Eighty-one (59.4%) BRCA1 variants and 46 (57.5%) BRCA2 variants are not recorded in the BIC database (Figure 4). A total of 19 of these 81 BRCA1 variants and 15 of the 46 BRCA2 variants were detected in at least two cases, with c.919A>G (p.Lys307Glu) in BRCA1 exon 11A (n = 10), c.7142delC (p.Pro2381Hisfs*13) in BRCA2 exon 14 (n = 5) having the highest frequencies. We compared these novel variants with the BRCA variant dataset from Asian populations [60], and identified 35 overlapping variants (18 in BRCA1 and 17 in BRCA2). Thirty-three (94.3%) of these overlapping variants were from Chinese ethnicity but not from other ethnicities (Supplementary Table 6), confirming that these novel variants are mainland Chinese-specific. The presence of multiple novel variants provides a rich resource to identify new BRCA pathogenic mutations in mainland Chinese population.

In conclusion, our study indicates that BRCA variations are common in mainland Chinese familial breast and ovarian cancer patients. The absence of such information in current international BRCA databases appears to largely reflect the poor communication between Western and Chinese scientific communities. Our study also indicates while the prevalence of BRCA variation is similar to that of other populations, the spectrum of BRCA variation in Chinese patients differs substantially with the hot spots of BRCA1 exons 11A, 11C, 11D, 24 and BRCA2 exon 10. Except the c.981_982delAT in BRCA1 exon 11A, there is no strong evidence showing the presence of common founder BRCA mutations in mainland Chinese patients, although such a possibility may exist in certain subpopulations of specific geographic regions or ethnic groups in mainland China.

Matching

Figure 4: Matching BRCA variants to the BIC database. The 137 BRCA1 and 80 BRCA2 distinct variants from mainland Chinese patients were compared with the 1,781 BRCA1 and 2,000 BRCA2 distinct variants in the BIC database. Of the Chinese variants, 56 BRCA1 and 34 BRCA2 variants were matched, whereas 82 BRCA1 and 46 BRCA2 variants were not.

materials and Methods

Information sources

We searched two major Chinese scientific databases, China National Knowledge Infrastructure (CNKI) [63] and WanFang [16], which comprehensively collect information from Chinese academic journals, dissertations, conference proceedings, and patents, by using the key words “breast cancer”, “BRCA1 mutation”, and “BRCA2 mutation” in Chinese characters. From the identified publications, we excluded those of sporadic breast cancer, animals, and those about patients marked with “early diagnosis”, “triple-negative”, and “bilateral” but without age indication, “male”, and from non-mainland Chinese. Using similar approaches but in English, we also searched the PubMed database to identify non-Chinese publications reporting BRCA mutations from mainland Chinese patients (Figure 1).

We applied multiple steps to ensure the reliability of the identified variants, including: 1) only including variants detected or validated by Sanger sequencing; 2) re-annotating all variants following HGVS nomenclature using the reference sequences U14680 for BRCA1 and U43746 for BRCA2, regardless of original annotation; 3) using the BIC database (13-Mar-2015 version) as a reference to classify variants as known variants with BIC designation or novel variants without BIC designation; 4) excluding synonymous variants and un-interpretable variants from analysis; and 5) annotating novel variants by referring to their effects on coding changes in BRCA1 and BRCA2. We used U14680 and U43746 as the reference sequences for BRCA1 and BRCA2 annotation, as they were used as the standard references by most of the cited publications and BIC database. However, different BRCA databases may use different BRCA reference sequences, which can generate differences for certain variants. For example, Clinvar database uses NM_007294 and NM_000059 as the references for BRCA1 and BRCA2 (64). To facilitate data comparison with BRCA variants annotated by Clinvar database, we also included the variants annotated by using these two references (Supplementary Tables 3, 4). All variants were annotated following HGVS nomenclature.

Abbreviations

BIC: Breast Cancer Information Core; BRCA1: breast cancer 1, early onset; BRCA2: breast cancer 2, early onset; HGVS: human genome variation society.

GRANT SUPPORT

The study was supported by an NIH grant CA180008 (SMW), an American Cancer Society Institutional Research Grant (YK), and Chinese Scholar Council fellowships (LZ, JC and FX).

CONFLICTS OF INTEREST

The authors declare no competing interests.

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