The goal of this project is to identify new genes for inherited susceptibility to breast cancer. DNA capture and massively parallel sequencing technologies will be exploited to identify these genes in a cohort of 1822 families, each with at least four relatives with breast cancer. The genetic causes of breast cancer in more than 1500 of these families remain unresolved. Discovery of new breast cancer genes in these families involves three aims.
In AIM 1, all known genes for inherited predisposition to breast cancer will be fully sequenced in all affected relatives from 150 of the families. The probands of all unresolved families have wildtype sequences at BRCA1, BRCA2, CHEK2, PALB2, CHEK2, BRIP1, p53, and PTEN. However, other affected family members may carry mutations in these genes, and the proband may be a sporadic case. Constitutional DNA of affected relatives will be used to prepare paired-end libraries, which will be hybridized to custom oligonucleotide pools to capture all known breast cancer susceptibility genes, then the enriched libraries will be bar-coded and sequenced in a multiplex design on an Illumina GAIIx genome analyzer. Mutations will be validated by Sanger sequencing.
In AIM 2, the Illumina platform will be used again, to fully sequence the entire exomes of all women in the screen with wildtype sequences at all known breast cancer genes. Variants will be filtered to identify rare nonsense mutations, frameshifts, splice site mutations, and genomic deletions and duplications that disrupt genes. Filtered mutations will be validated and tested for co-inheritance with breast cancer. Multiple deleterious mutations are a hallmark of all known genes for inherited breast cancer and are the strongest proof of functional consequence of new breast cancer genes.
In Aim 3 A, the most promising candidate genes will be fully sequenced in DNA samples from an independent series of familial breast cancer patients to reveal additional mutations.
In Aim 3 B, potentially functional mutations in these genes will be genotyped by TaqMan assays in large follow-up series to estimate individual and gene-wide mutation frequencies and relative risks. Discovery of new breast cancer susceptibility genes will allow prevention strategies to be extended to families for which causal genes are currently unknown, to better identify women at risk, to allow closer medical surveillance of these women, to stimulate design of new prevention strategies based on genetic evidence, and to offer a better understanding of the biological pathways involved in breast cancer development.

Public Health Relevance

The goal of this project is to identify new genes for inherited susceptibility to breast cancer using DNA capture and next generation sequencing technologies. Discovery of new breast cancer susceptibility genes will allow prevention strategies to be extended to families for which causal genes are currently unknown.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA157744-03
Application #
8444635
Study Section
Genetics of Health and Disease Study Section (GHD)
Program Officer
Schully, Sheri D
Project Start
2011-03-01
Project End
2016-02-29
Budget Start
2013-03-01
Budget End
2014-02-28
Support Year
3
Fiscal Year
2013
Total Cost
$491,748
Indirect Cost
$176,525
Name
University of Washington
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
605799469
City
Seattle
State
WA
Country
United States
Zip Code
98195
Norquist, Barbara M; Harrell, Maria I; Brady, Mark F et al. (2016) Inherited Mutations in Women With Ovarian Carcinoma. JAMA Oncol 2:482-90
Levy-Lahad, Ephrat; Lahad, Amnon; King, Mary-Claire (2015) Precision medicine meets public health: population screening for BRCA1 and BRCA2. J Natl Cancer Inst 107:420
Churpek, Jane E; Walsh, Tom; Zheng, Yonglan et al. (2015) Inherited predisposition to breast cancer among African American women. Breast Cancer Res Treat 149:31-9
Antoniou, Antonis C; Casadei, Silvia; Heikkinen, Tuomas et al. (2014) Breast-cancer risk in families with mutations in PALB2. N Engl J Med 371:497-506
Gabai-Kapara, Efrat; Lahad, Amnon; Kaufman, Bella et al. (2014) Population-based screening for breast and ovarian cancer risk due to BRCA1 and BRCA2. Proc Natl Acad Sci U S A 111:14205-10
Pritchard, Colin C; Salipante, Stephen J; Koehler, Karen et al. (2014) Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. J Mol Diagn 16:56-67
Pennington, Kathryn P; Walsh, Tom; Harrell, Maria I et al. (2014) Germline and somatic mutations in homologous recombination genes predict platinum response and survival in ovarian, fallopian tube, and peritoneal carcinomas. Clin Cancer Res 20:764-75
King, Mary-Claire; Levy-Lahad, Ephrat; Lahad, Amnon (2014) Population-based screening for BRCA1 and BRCA2: 2014 Lasker Award. JAMA 312:1091-2
Shirts, Brian H; Salipante, Stephen J; Casadei, Silvia et al. (2014) Deep sequencing with intronic capture enables identification of an APC exon 10 inversion in a patient with polyposis. Genet Med 16:783-6
King, Mary-Claire (2014) "The race" to clone BRCA1. Science 343:1462-5

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