Volume 16 Supplement 1

Selected articles from the 2nd International Genomic Medicine Conference (IGMC 2013): Genomics

Open Access

Characterization of familial breast cancer in Saudi Arabia

  • Adnan Merdad1,
  • Mamdooh A Gari2,
  • Shireen Hussein2,
  • Shadi Al-Khayat3,
  • Hana Tashkandi1,
  • Jaudah Al-Maghrabi4,
  • Fatma Al-Thubaiti1,
  • Ibtessam R Hussein2,
  • Taha Koumosani5,
  • Nehad Shaer6,
  • Adeel G Chaudhary2,
  • Adel M Abuzenadah2, 6,
  • Mohammed H Al-Qahtani2 and
  • Ashraf Dallol2, 6Email author
BMC Genomics201516(Suppl 1):S3

DOI: 10.1186/1471-2164-16-S1-S3

Published: 15 January 2015

Abstract

Background

The contribution of genetic factors to the development of breast cancer in the admixed and consanguineous population of the western region of Saudi Arabia is thought to be significant as the disease is early onset. The current protocols of continuous clinical follow-up of relatives of such patients are costly and cause a burden on the usually over-stretched medical resources. Discovering the significant contribution of BRCA1/2 mutations to breast cancer susceptibility allowed for the design of genetic tests that allows the medical practitioner to focus the care for those who need it most. However, BRCA1/2 mutations do not account for all breast cancer susceptibility genes and there are other genetic factors, known and unknown that may play a role in the development of such disease. The advent of whole-exome sequencing is offering a unique opportunity to identify the breast cancer susceptibility genes in each family of sufferers. The polymorphisms/mutations identified will then allow for personalizing the genetic screening tests accordingly. To this end, we have performed whole-exome sequencing of seven breast cancer patients with positive family history of the disease using the Agilent SureSelect™ Whole-Exome Enrichment kit and sequencing on the SOLiD™ platform.

Results

We have identified several coding single nucleotide variations that were either novel or rare affecting genes controlling DNA repair in the BRCA1/2 pathway.

Conclusion

The disruption of DNA repair pathways is very likely to contribute to breast cancer susceptibility in the Saudi population.

Keywords

hereditary breast cancer DNA repair whole-exome sequencing

Background

The discovery of the BRCA1 and BRCA2 genes as major breast cancer susceptibility genes led to great advances in the genetic screening for the disease and the understanding of its inheritance [1, 2]. Several other genes were found to play a role in increasing susceptibility to breast cancer but at a markedly lower frequency and penetrance. These genes include ATM, TP53, CHECK2, PTEN, STK11, PALB2, BRIP and the RAD51 genes [311]. GWAS studies led to the identification of 21 susceptibility loci that are considered only as low risk alleles [9, 1217]. All these factors combined can account for only 35% of heritable breast cancer with the majority of cases remain with an unknown genetic etiology [18]. This problem is confounded for the admixed and consanguineous population of the western region of Saudi Arabia where virtually no research has been done so far to elucidate the genetic background of heritable breast cancer. A remarkable characteristic of breast cancer in this population is the relatively younger age of onset of the disease where the majority of cases (sporadic or familial) are diagnosed with invasive ductal carcinoma before they are 50 years old [19]. This early onset could be attributed, at least partly, to undetermined genetic susceptibility factors accumulating in the population due to consanguineous marriages and increased exposure to environmental insults due to life-style shifts in the past two decades.

Sanger sequencing of all known breast cancer susceptibility genes could be a daunting task. Developments in massively parallel sequencing technology and whole-exome sequencing alleviate many of the problems associated with such approach and allow for the simultaneous determination of known factors as well as the discovery of novel ones. And in the age of personalized medicine, whole-exome sequencing of each breast cancer patient is fast becoming a standard approach towards genetic diagnosis [20]. In the present study we employed whole-exome sequencing of seven cases diagnosed with familial breast cancer and with unknown BRCA1 or BRCA2 status. We determined the BRCA1 and BRCA2 status in these cases and report the identification of several rare variants that can potentially explain breast cancer susceptibility in each case analyzed.

Materials and methods

Patients’ samples

Patients were selected for this study if they have a first-degree relative(s) diagnosed with breast cancer. Peripheral blood was obtained from the patients following obtaining their informed consent and their family history of breast cancer. Patients’ recruitment and blood sampling was all performed according to the institutional ethical procedures (Additional file 1 Figure S1). Genomic DNA was prepared using the Qiagen QIAamp DNA Blood Mini kit according to the manufacturer’s recommendations.

Whole-exome sequencing and SNP genotyping

Three micrograms of genomic DNA was sheared using the Covaris S2 system. Exome capture was performed on seven cases and six non-cancer controls using the SureSelect Whole-Exome Enrichment version 2 kit from Agilent. Fragment libraries were prepared from the captured exomes for sequencing on the SOLiD 4 platform (AB). Sequencing for each library was performed on one part of the quad slide and fragments were sequenced in in single reads of 50 bp. Sequence capture and primary analysis were performed by the instruments ICS and SETS softwares. SNP genotyping using Taqman was performed using assay ID (C___7530120_20) from Life Technologies targeting the rs1799950 SNP. Genotyping was performed on DNA from peripheral blood of breast cancer patients or non-cancer controls.

Analysis pipeline

Color-space sequences in .csfasta and .qual files were exported to LifeScope software were mapping to the human genome version 19 (hg19) was performed using standard settings. Identification of single nucleotide polymorphisms was achieved by the diBayes software incorporated in the LifeScope pipeline. Variant call format (vcf) files were analyzed using the SNPs & Variation Suite 7 (SVS7) from Golden Helix where short-listing of candidate SNVs was performed by filtering the detected SNVs to include only those with more than 10x coverage and MQV of >=20. Rare variants were identified by filtering out SNVs present in the 1000genomes or NHLBI Exome sequencing data. Disease-associated SNVs were determined following filtering out rare SNVs found in the 6 non-cancer control cases from the same ethnic background. Damaging nonsynonymous variations were determined by the SIFT, PolyPhen or Mutation Taster softwares within the SVS7 suite.

Results

Exome sequencing revealed several single nucleotide variants affecting key genes that could be involved in increased susceptibility to breast cancer. The single nucleotide variants or short indels obtained for every sample were filtered against the NHLBI Exome project and the 1000genomes project databases. Novel or rare variants (MAF of <0.01) were filtered against our in-house database of exome sequencing of non-cancer patients or healthy individuals. The statistics of each breast cancer exome sequenced are shown in Table 1. The mutational status of BRCA1 and BRCA2 in the sequenced samples was unknown. Therefore, variants affecting those genes were analyzed first. We have identified one novel frameshift mutation affecting BRCA2 caused by an -/AC insertion affecting one patient only (Table 2). Other BRCA1 or BRCA2 variants identified were previously reported in dbSNP137. However, the nonsense variant represented by SNP rs80358972 is very rare and no information about its MAF could be found. We have found this variant in one BC patient only. Other Missense single nucleotide variants affecting BRCA1 and BRCA2 were identified. However, when selection is based on rarity and degree of predicted damage to the protein, SNP rs1799950 is found in one patient. In order to determine the frequency of the rs1799950 SNP in our cohort, we performed Taqman® SNP genotyping assay on DNA obtained from the peripheral blood of 204 breast cancer patients samples as well as 120 non-cancer controls. The rs1799950 SNP was in a highly significant Hardy-Weinberg disequilibrium in the patient group (X2=133.124) compared to the control group (X2=0.108). The GG state of the rs1799950 SNP is significantly associated with breast cancer compared to the AA and AG states combined (p=0.0003, OR=22.79, CI=1.366-380.1).
Table 1

Next-generation run statistics for breast cancer exomes.

 

case_193

case_195

case_264

case_320

case_573

case_574

case_903

Total reads

108,381,083

84,054,514

95,591,607

89,014,487

107,417,081

89,456,100

62,675,973

Mappable reads (%)

73%

67%

72%

73%

78%

64%

78%

Mappable yield (bp)

3,958,042,800

2,795,592,150

3,425,085,950

3,231,704,750

4,145,428,250

2,865,812,200

2,459,039,800

On-target yield (bp) (%)

46%

61%

74%

47%

63%

68%

52%

Coverage of target region (>10x)

71.24

67.68

67.21

64.93

80.59

70.16

64.64

Mean read depth of targeted region

34.63

33.02

45.09

28.08

49.87

37.42

24.14

Mean read depth of called variants

36.54

72.34

68.94

39.41

56.47

44.61

33.35

Number of high quality variants

23959

1788

5823

10019

18691

14113

9623

Number of missense, nonsense, splice, and indel variants

1861

154

352

619

1240

1035

616

Number of filtered damaging rare variants

53

6

21

39

105

91

45

Number of filtered damaging novel variants

141

46

108

80

116

129

71

Number of filtered damaging novel indels

85

38

129

55

54

38

123

Table 2

Detection of single nucleotide variations and short indels in the BRCA1 and BRCA2 genes in familial breast cancer cases

Gene

dbSNP137

Genomic Position

AA Change

Nucleotide change

SIFT Prediction

MAF

Occurrence

BRCA1

rs799917

Chr17:41244936

p.Pro871Leu

c.2894G>A

Tolerated

0.483

4/7

 

rs4986852

Chr17:41244429

p.Ser1040Asn

c.3351 G>A

Tolerated

0.012

1/7

 

rs1799966

Chr17:41223094

p.Ser1613Gly

c.5096A>G

Damaging

0.327

3/7

 

rs16941

Chr17:41244435

p.Glu1038Gly

c.3345A>G

Damaging

0.303

3/7

 

rs1799950

Chr17:41246481

p.Gln356Arg

c.1299A>G

Damaging

0.028

1/7

 

rs16942

Chr17:41244000

p.Lys1183Arg

c.3780A>G

Tolerated

0.324

2/7

BRCA2

rs144848

Chr13:32906729

p.Asn372His

c.1341A>C

Tolerated

0.240

4/7

 

rs766173

Chr13:32906480

p.Asn289His

c.1092A>C

Damaging

0.058

1/7

 

rs169547

Chr13:32929387

p.Val2466Ala

c.7397C>T

Tolerated

0.022

5/7

 

rs80358972

Chr13:32930609

p.Arg2494Stop

c.7707C>T

NA

NA

1/7

 

rs4987117

Chr13:32914236

p.Thr1915Met

c.5971C>T

Tolerated

0.011

1/7

 

Novel

Chr13:32906700

p.Thr363fs

c.1084_1085insAC

NA

NA

1/7

Predisposition to breast cancer is often caused by genetic defects in DNA repair mechanisms. Therefore, SNVs affecting known genes with DNA repair function were examined (Table 3). In addition, SNVs were also identified affecting the APC, EGF and EGFR genes. An interesting mutation c.148G>A / p.Ala62Thr is found affecting the PARP1-interacting region of the Cockayne Syndrome group B (ERCC6) gene. Analysis of DNA from the family of the affected female revealed that this mutation segregated in the heterozygous state in one sibling affected with breast cancer as well as in the mother who also suffered from breast cancer. The father did not harbor this mutation (Figure 1). This SNV was recently reported by the 1000Genome project (rs186839348) where it was found only once in 1094 individuals. We could not detect this SNV in 228 non-cancer control samples from Saudi Arabia.
Table 3

Candidate breast cancer genetic risk factors

Chr.

Position

Gene Name

Refseq

Nucleotide change

Amino acid change

9

133748391

ABL1

NM_007313

c.1109T>C

p.Met370Thr

4

41015755

APBB2

NM_001166050

c.680C>G

p.Ser227*

5

112157653

APC

NM_001127511

c.1319T>C

p.Phe440Ser

5

112175675

APC

NM_001127511

c.4330A>G

p.Lys1444Glu

X

55028750

APEX2

NM_014481

c.308T>G

p.Phe103Cys

2

68740731

APLF

NM_173545

c.541G>A

p.Glu181Lys

9

32987778

APTX

NM_001195249

c.247C>A

p.Pro83Thr

7

97498324

ASNS

NM_133436

c.145C>T

p.Arg49Trp

3

48506356

ATRIP

NM_032166

c.2101C>T

p.His701Tyr

12

56994493

BAZ2A

NM_013449

c.4580G>A

p.Arg1527Gln

11

117261519

CEP164

NM_014956

c.1961C>T

p.Ala654Val

11

72070023

CLPB

NM_030813

c.766A>C

p.Asn256His

11

61097050

DDB1

NM_001923

c.334A>T

p.Ile112Phe

11

61099086

DDB1

NM_001923

c.139G>A

p.Glu47Lys

1

10529353

DFFA

NM_004401

c.179C>T

p.Thr60Ile

11

46396161

DGKZ

NM_201532

c.1517T>C

p.Phe506Ser

1

44680377

DMAP1

NM_001034023

c.200A>T

p.Asp67Val

4

110901232

EGF

NM_001178130

c.2158C>T

p.Arg720Cys

4

110915959

EGF

NM_001178130

c.2805T>A

p.Cys935*

7

55231449

EGFR

NM_201282

c.1655A>C

p.Asn552Thr

10

50740827

ERCC6

NM_000124

c.184G>A

p.Ala62Thr

16

89851328

FANCA

NM_000135

c.1404G>T

p.Lys468Asn

6

30521271

GNL1

NM_005275

c.664C>G

p.Leu222Val

10

96306191

HELLS

NM_018063

c.89T>A

p.Met30Lys

1

153742705

INTS3

NM_023015

c.2421G>C

p.Gln807His

1

153744835

INTS3

NM_023015

c.2740A>T

p.Lys914*

6

42985075

KLHDC3

NM_057161

c.145T>G

p.Phe49Val

17

8273384

KRBA2

NM_213597

c.547C>T

p.Arg183*

3

49167350

LAMB2

NM_002292

c.1327C>T

p.His443Tyr

6

52129538

MCM3

NM_002388

c.2275C>A

p.His759Asn

6

52148114

MCM3

NM_002388

c.169A>T

p.Lys57*

7

99691911

MCM7

NM_182776

c.1205C>A

p.Ala402Asp

6

30675438

MDC1

NM_014641

c.2918C>G

p.Ala973Gly

12

68719303

MDM1

NM_017440

c.551A>C

p.Asn184Thr

1

46073578

NASP

NM_001195193

c.803A>C

p.Gln268Pro

13

25049687

PARP4

NM_006437

c.1837C>T

p.Leu613Phe

22

38461037

PICK1

NM_001039583

c.182A>C

p.Asp61Ala

12

133237560

POLE

NM_006231

c.3055A>G

p.Ser1019Gly

12

133240651

POLE

NM_006231

c.2645A>G

p.Asn882Ser

6

43550079

POLH

NM_006502

c.23T>G

p.Val8Gly

11

7660974

PPFIBP2

NM_003621

c.1248C>A

p.Phe416Leu

11

7670122

PPFIBP2

NM_003621

c.1889T>C

p.Leu630Pro

2

1670120

PXDN

NM_012293

c.1157A>T

p.Asp386Val

2

1680732

PXDN

NM_012293

c.815A>T

p.Asn272Ile

19

13063505

RAD23A

NM_005053

c.816A>T

p.Gln272His

12

110957646

RAD9B

NM_152442

c.815T>A

p.Ile272Asn

4

39310618

RFC1

NM_001204747

c.1523A>C

p.Gln508Pro

9

94486015

ROR2

NM_004560

c.2761C>T

p.Pro921Ser

9

135171409

SETX

NM_015046

c.5956A>T

p.Arg1986Trp

9

135205531

SETX

NM_015046

c.1454G>C

p.Trp485Ser

6

146244812

SHPRH

NM_001042683

c.3512A>G

p.Lys1171Arg

10

69672638

SIRT1

NM_012238

c.1765G>T

p.Glu589*

16

18846451

SMG1

NM_015092

c.8093C>A

p.Thr2698Lys

12

104376700

TDG

NM_003211

c.602A>C

p.Lys201Thr

14

24711133

TINF2

NM_001099274

c.260T>C

p.Phe87Ser

17

38546386

TOP2A

NM_001067

c.4298A>C

p.Lys1433Thr

17

18178184

TOP3A

NM_004618

c.2938A>T

p.Lys980*

18

662218

TYMS

NM_001071

c.352T>G

p.Leu118Val

15

70971987

UACA

NM_001008224

c.812T>C

p.Val271Ala

8

103324043

UBR5

NM_015902

c.2338C>A

p.Gln780Lys

8

103359274

UBR5

NM_015902

c.433G>T

p.Gly145Cys

8

30949362

WRN

NM_000553

c.1846G>C

p.Ala616Pro

8

31030529

WRN

NM_000553

c.4210A>G

p.Lys1404Glu

12

58345668

XRCC6BP1

NM_033276

c.443C>T

p.Ala148Val

Figure 1

Identification of ERCC6 mutation p.Ala62Thr in a breast cancer family. (A) The pedigree of the family analyzed where the patient, marked with an arrow has a sister who was also diagnosed of breast cancer. The sisters’ mother and grandmother died of breast cancer. Their father died of unspecified lung disease. (B) Sequence chromatographs showing the heterozygous state of the c.148G>A p.Ala62Thr mutation and its segregation in the family. The sequence of the reverese strand is shown.

Discussion

Breast cancer incidence is on the rise in the Kingdom of Saudi Arabia with a remarkable number of those affected are being diagnosed before they are 50 years old [19]. The early-onset of the breast cancer in this population could be partly explained by the accumulation of breast cancer predisposition genetic factor(s) due to high incidence of consanguineous marriages. The effects of these genetic factor(s) is probably becoming more evident now due to the social and life-style changes brought upon by the relatively recent positive economical upheavals in the country. In order to identify such genetic factors, we performed a pilot whole-exome sequencing study on DNA obtained from the peripheral blood of seven cases suffering from hereditary breast cancer. First, the status of the known breast cancer predisposition factors, mainly BRCA1 and BRCA2, was determined. We could not identify recurrent BRCA1/2 mutations in our cohort. However, we identified a novel insertion that led to a frameshift mutation (p.Thr363fs) in BRCA2 causing the synthesis of a truncated and presumably dysfunctional protein. We identified another rare mutation in BRCA2 in one of our patients. Represented by the rs80358972 SNP, the p.Arg2494Stop affecting BRCA2 has been reported by the Breast Cancer Information Core submitted by Myriad Genetics as a direct result of their diagnostic services. Additionally, we have identified the relatively rare rs1799950 SNP in BRCA1 which is a p.Gln356Arg mutation reported by the 1000Genomes project to have an MAF of 0.026. We found this SNP in our cohort with a MAF of 0.058 (7 heterozygous cases in 120 non-cancer cases). The minor allele frequency of the rs1799950 SNP did not differ significantly from controls. However, we observed an increase in the number of breast cancer cases displaying the homozygous GG minor allele state that is not seen in the control cases. When the GG state is analyzed in comparison to the combined frequency of the AA and AG states, a highly significant association with breast cancer becomes evident. The rs1799950 SNP is one of 25 SNPs in cancer predisposition genes that were identified to confer minor but cumulatively significant risk of breast cancer [21]. However, a later study dismissed the association of the rs1799950 SNP with breast cancer [22]. Unfortunately, it is difficult to perform direct comparisons between our findings and reported studies due to the differences in sample size and the ethnic makeup of the cohorts analyzed.

Whole-exome sequencing revealed several candidate risk factors for breast cancer. We made the assumption that the most likely risk factor is a gene(s) involved in DNA repair, cell cycle or apoptosis [18]. Applying this filter to the SNVs obtained reveal rare polymorphisms that could affect important genes such as WRN, APC, EGF, EGFR and ERCC6. The contribution of these SNVs towards increasing predisposition to breast cancer remains unknown. Therefore, we analyzed the segregation with breast cancer of the SNVs affecting ERCC6 (p.Ala62Thr) and WRN (p.Ala616Pro) in a family with reported breast cancer affecting three generations (case_574). The WRN p.Ala616Pro was detectable in the two siblings diagnosed with breast cancer. However, this SNV could not be found in the mother who died of breast cancer. In contrast, the ERCC6 p.Ala62Thr SNV segregated with breast cancer in the same family and it was not detectable in the father or control samples. This mutation affects the PARP1-interaction region of ERCC6, also known as Cockayne Syndrome group B (CSB) [23]. ERCC6-dependent activation of the poly(ADP-ribose)polymerases, or PARPs is an early event in the cellular response to genotoxic stress [24]. Carrying a variant ERCC6 therefore will cause a less-efficient DNA repair response and could therefore lead to an increased predisposition to breast cancer.

Conclusions

This is the first report on the breast cancer predisposition factors in the population of the Kingdom of Saudi Arabia. The high consanguinity and life-style shifts in this population are coupled to an early-onset breast cancer and the SNVs identified in this study could partly explain this phenomenon. We have identified a novel BRCA2 mutation as well as found a case with a very rare nonsense mutation truncating the BRCA2 protein. We demonstrate the potential importance of the homozygous risk allele to breast cancer predisposition in the Saudi population. We suggest that mutations in the ERCC6 gene could be considered as potential risk factors for breast cancer. Although no recurrent mutations were identified, this study validates the use of whole-exome sequencing for the determination of the “breast cancer predisposition genome”.

Declarations

Acknowledgements

The authors would like to extend their gratitude to Shylu Mathew, Lubna Mira, Manal Shabat and Nada Salem for their technical support. The authors would like to thank the patients recruited in this study for their support and understanding. The authors acknowledge the generous funding received through the Kingdom of Saudi Arabia’s National Science, Technology and Innovation Plan (NSTIP) Project No. 09-BIO-818-03.

Declarations

Publication charges for this article have been funded by the Center of Excellence in Genomic Medicine Research, King Abdulaziz University

This article has been published as part of BMC Genomics Volume 16 Supplement 1, 2015: Selected articles from the 2nd International Genomic Medical Conference (IGMC 2013): Genomics. The full contents of the supplement are available online at http://www.biomedcentral.com/bmcgenomics/supplements/16/S1.

Authors’ Affiliations

(1)
Department of Surgery, Faculty of Medicine, King Abdulaziz University
(2)
Center of Excellence in Genomic Medicine Research, King Abdulaziz University
(3)
Department of Medicine, King Abdulaziz University Hospital
(4)
Department of Pathology, King Abdulaziz University Hospital
(5)
Department of Biochemistry, Faculty of Science, King Abdulaziz University
(6)
KACST Technology Innovation Center in Personalized Medicine, King Abdulaziz University

References

  1. Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, Tavtigian S, Liu Q, Cochran C, Bennett LM, Ding W, et al: A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science. 1994, New York, NY, 266 (5182): 66-71. 10.1126/science.7545954.
  2. Wooster R, Bignell G, Lancaster J, Swift S, Seal S, Mangion J, Collins N, Gregory S, Gumbs C, Micklem G: Identification of the breast cancer susceptibility gene BRCA2. Nature. 1995, 378 (6559): 789-792. 10.1038/378789a0.View ArticlePubMedGoogle Scholar
  3. Borresen AL, Andersen TI, Garber J, Barbier-Piraux N, Thorlacius S, Eyfjord J, Ottestad L, Smith-Sorensen B, Hovig E, Malkin D, et al: Screening for germ line TP53 mutations in breast cancer patients. Cancer research. 1992, 52 (11): 3234-3236.PubMedGoogle Scholar
  4. Lynch ED, Ostermeyer EA, Lee MK, Arena JF, Ji H, Dann J, Swisshelm K, Suchard D, MacLeod PM, Kvinnsland S, et al: Inherited mutations in PTEN that are associated with breast cancer, cowden disease, and juvenile polyposis. American journal of human genetics. 1997, 61 (6): 1254-1260. 10.1086/301639.PubMed CentralView ArticlePubMedGoogle Scholar
  5. Giardiello FM, Brensinger JD, Tersmette AC, Goodman SN, Petersen GM, Booker SV, Cruz-Correa M, Offerhaus JA: Very high risk of cancer in familial Peutz-Jeghers syndrome. Gastroenterology. 2000, 119 (6): 1447-1453. 10.1053/gast.2000.20228.View ArticlePubMedGoogle Scholar
  6. Meijers-Heijboer H, van den Ouweland A, Klijn J, Wasielewski M, de Snoo A, Oldenburg R, Hollestelle A, Houben M, Crepin E, van Veghel-Plandsoen M, et al: Low-penetrance susceptibility to breast cancer due to CHEK2(*)1100delC in noncarriers of BRCA1 or BRCA2 mutations. Nature genetics. 2002, 31 (1): 55-59. 10.1038/ng879.View ArticlePubMedGoogle Scholar
  7. Renwick A, Thompson D, Seal S, Kelly P, Chagtai T, Ahmed M, North B, Jayatilake H, Barfoot R, Spanova K, et al: ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles. Nature genetics. 2006, 38 (8): 873-875. 10.1038/ng1837.View ArticlePubMedGoogle Scholar
  8. Seal S, Thompson D, Renwick A, Elliott A, Kelly P, Barfoot R, Chagtai T, Jayatilake H, Ahmed M, Spanova K, et al: Truncating mutations in the Fanconi anemia J gene BRIP1 are low-penetrance breast cancer susceptibility alleles. Nature genetics. 2006, 38 (11): 1239-1241. 10.1038/ng1902.View ArticlePubMedGoogle Scholar
  9. Rahman N, Seal S, Thompson D, Kelly P, Renwick A, Elliott A, Reid S, Spanova K, Barfoot R, Chagtai T, et al: PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene. Nature genetics. 2007, 39 (2): 165-167. 10.1038/ng1959.PubMed CentralView ArticlePubMedGoogle Scholar
  10. Meindl A, Hellebrand H, Wiek C, Erven V, Wappenschmidt B, Niederacher D, Freund M, Lichtner P, Hartmann L, Schaal H, et al: Germline mutations in breast and ovarian cancer pedigrees establish RAD51C as a human cancer susceptibility gene. Nature genetics. 2010, 42 (5): 410-414. 10.1038/ng.569.View ArticlePubMedGoogle Scholar
  11. Loveday C, Turnbull C, Ramsay E, Hughes D, Ruark E, Frankum JR, Bowden G, Kalmyrzaev B, Warren-Perry M, Snape K, et al: Germline mutations in RAD51D confer susceptibility to ovarian cancer. Nature genetics. 2011, 43 (9): 879-882. 10.1038/ng.893.View ArticlePubMedGoogle Scholar
  12. Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, Ballinger DG, Struewing JP, Morrison J, Field H, Luben R, et al: Genome-wide association study identifies novel breast cancer susceptibility loci. Nature. 2007, 447 (7148): 1087-1093. 10.1038/nature05887.PubMed CentralView ArticlePubMedGoogle Scholar
  13. Stacey SN, Manolescu A, Sulem P, Rafnar T, Gudmundsson J, Gudjonsson SA, Masson G, Jakobsdottir M, Thorlacius S, Helgason A, et al: Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nature genetics. 2007, 39 (7): 865-869. 10.1038/ng2064.View ArticlePubMedGoogle Scholar
  14. Ahmed S, Thomas G, Ghoussaini M, Healey CS, Humphreys MK, Platte R, Morrison J, Maranian M, Pooley KA, Luben R, et al: Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2. Nature genetics. 2009, 41 (5): 585-590. 10.1038/ng.354.PubMed CentralView ArticlePubMedGoogle Scholar
  15. Thomas G, Jacobs KB, Kraft P, Yeager M, Wacholder S, Cox DG, Hankinson SE, Hutchinson A, Wang Z, Yu K, et al: A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Nature genetics. 2009, 41 (5): 579-584. 10.1038/ng.353.PubMed CentralView ArticlePubMedGoogle Scholar
  16. Turnbull C, Ahmed S, Morrison J, Pernet D, Renwick A, Maranian M, Seal S, Ghoussaini M, Hines S, Healey CS, et al: Genome-wide association study identifies five new breast cancer susceptibility loci. Nature genetics. 2010, 42 (6): 504-507. 10.1038/ng.586.PubMed CentralView ArticlePubMedGoogle Scholar
  17. Ghoussaini M, Fletcher O, Michailidou K, Turnbull C, Schmidt MK, Dicks E, Dennis J, Wang Q, Humphreys MK, Luccarini C, et al: Genome-wide association analysis identifies three new breast cancer susceptibility loci. Nature genetics. 2012, 44 (3): 312-318. 10.1038/ng.1049.PubMed CentralView ArticlePubMedGoogle Scholar
  18. Gracia-Aznarez FJ, Fernandez V, Pita G, Peterlongo P, Dominguez O, de la Hoya M, Duran M, Osorio A, Moreno L, Gonzalez-Neira A, et al: Whole exome sequencing suggests much of non-BRCA1/BRCA2 familial breast cancer is due to moderate and low penetrance susceptibility alleles. PloS one. 2013, 8 (2): e55681-10.1371/journal.pone.0055681.PubMed CentralView ArticlePubMedGoogle Scholar
  19. Mehmood A, Te OB, Urcia JC, Khan A: Tumor Registry Annual Report. 2011, Kingdom of Saudi Arabia: King Faisal Specialist Hospital & Research CenterGoogle Scholar
  20. Chouchane L, Mamtani R, Dallol A, Sheikh JI: Personalized medicine: a patient-centered paradigm. Journal of translational medicine. 2011, 9: 206-10.1186/1479-5876-9-206.PubMed CentralView ArticlePubMedGoogle Scholar
  21. Johnson N, Fletcher O, Palles C, Rudd M, Webb E, Sellick G, dos Santos Silva I, McCormack V, Gibson L, Fraser A, et al: Counting potentially functional variants in BRCA1, BRCA2 and ATM predicts breast cancer susceptibility. Human molecular genetics. 2007, 16 (9): 1051-1057. 10.1093/hmg/ddm050.View ArticlePubMedGoogle Scholar
  22. Baynes C, Healey CS, Pooley KA, Scollen S, Luben RN, Thompson DJ, Pharoah PD, Easton DF, Ponder BA, Dunning AM: Common variants in the ATM, BRCA1, BRCA2, CHEK2 and TP53 cancer susceptibility genes are unlikely to increase breast cancer risk. Breast cancer research : BCR. 2007, 9 (2): R27-10.1186/bcr1669.PubMed CentralView ArticlePubMedGoogle Scholar
  23. Thorslund T, von Kobbe C, Harrigan JA, Indig FE, Christiansen M, Stevnsner T, Bohr VA: Cooperation of the Cockayne syndrome group B protein and poly(ADP-ribose) polymerase 1 in the response to oxidative stress. Molecular and cellular biology. 2005, 25 (17): 7625-7636. 10.1128/MCB.25.17.7625-7636.2005.PubMed CentralView ArticlePubMedGoogle Scholar
  24. Flohr C, Burkle A, Radicella JP, Epe B: Poly(ADP-ribosyl)ation accelerates DNA repair in a pathway dependent on Cockayne syndrome B protein. Nucleic acids research. 2003, 31 (18): 5332-5337. 10.1093/nar/gkg715.PubMed CentralView ArticlePubMedGoogle Scholar

Copyright

© Merdad et al; licensee BioMed Central Ltd. 2015

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Advertisement