COMPLETE VARIANT PROFILING OF ALL KNOWN BREAST CANCER GENES

所有已知乳腺癌基因的完整变异分析

基本信息

批准号：
9330794
负责人：
MARY-CLAIRE KING
金额：
$ 60.39万
依托单位：
UNIVERSITY OF WASHINGTON
依托单位国家：
美国
项目类别：
财政年份：
2013
资助国家：
美国
起止时间：
2013-09-30 至 2019-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9330794
关键词：
Affect Age Alleles BARD1 gene BRCA1 gene BRCA2 gene Bar Codes Bioinformatics Biological Assay Biopsy Specimen Blood Breast Cancer Detection Breast Cancer Treatment Breast Cancer gene CDH1 gene CHEK1 gene CHEK2 gene Candidate Disease Gene Code Custom DNA DNA Damage DNA Repair Exons Family Family Study Fanconi Anemia-BRCA Pathway Frequencies Gene Frequency Gene Targeting Genes Genetic Predisposition to Disease Genomics Germ-Line Mutation Goals Hybrids Information Technology Inherited Intercistronic Region Introns Lead Libraries Loss of Heterozygosity Massive Parallel Sequencing Missense Mutation Modality Modeling Mutation Nonsense Mutation Operative Surgical Procedures PPM1D gene PTEN gene Patient Care Patients RAD51C gene RNA RNA Splicing Recording of previous events Relative Risks Reverse Transcriptase Polymerase Chain Reaction Risk STK11 gene Sample Size Sampling Side TP53 gene Testing Time Translations Variant Woman XRCC2 gene Yeasts actionable mutation base case control clinical care clinically actionable effective therapy enzyme activity gene function genetic variant genotyped patients loss of function mutation malignant breast neoplasm p53-binding protein 1 premature public health relevance response tool tumor

项目摘要

DESCRIPTION (provided by applicant): The goal of this project is to identify and characterize clinically actionable mutations in all known breast cancer genes so that they can be incorporated into clinical care. DNA samples from 3000 cases and 2000 ancestry matched controls will be sequenced for all known breast cancer genes. Germline mutations will be evaluated with respect to function and relative risk of breast cancer. The discovery and characterization of clinically actionable variants in breast cancer genes involves three aims. In AIM 1, we will sequence all 18 known breast cancer genes in DNA samples from 3000 women with breast cancer and 2000 ancestry-matched controls. In parallel, we will similarly evaluate 6 new candidate genes for inherited breast cancer that have emerged from our independent family studies. For all characterizations, we will use our recently developed approach for simultaneous capture and multiplexed sequencing, to >300-fold median coverage, of exons, introns, regulatory, and flanking intergenic regions of breast cancer genes. In AIM 2, we will identify all variants predicted to lead to loss of gene function, including truncating mutations (whether nonsense, frameshifts, disrupting CNV and so on), complete genomic deletions, and putatively damaging missense mutations. We will assess all variants for effect on gene function using bioinformatics tools. Variants with possible splice effects will be evaluated by RT-PCR of patient RNA and ex vivo minigenes. The most promising missense alleles will be tested experimentally for DNA damage response, loss of enzyme activity and other functional assays as appropriate. In AIM 3, we will test the strength of association of breast cancer with each of the 24 genes, based on the combined frequency of unambiguous loss-of-function mutations in cases vs controls. Relative risks will be estimated for each gene. The challenge of integrating genomics into clinical care is timely now for inherited predisposition to breast cancer, because multiple causal genes are known, specialized breast screening modalities are available, risk- reducing surgery is effective, and treatment of breast cancer is influenced by the patient's genotype. The goal of this project is to provide the information and technology necessary for this translation.

描述（由申请人提供）：该项目的目标是识别和表征所有已知乳腺癌基因中临床上可操作的突变，以便将它们纳入临床护理中。来自 3000 个病例和 2000 个血统匹配对照的 DNA 样本将对所有已知的乳腺癌基因进行测序。将根据功能和乳腺癌的相对风险评估种系突变。乳腺癌基因中临床上可行的变异的发现和表征涉及三个目标。在 AIM 1 中，我们将对来自 3000 名乳腺癌女性和 2000 名血统匹配对照者的 DNA 样本中的所有 18 个已知乳腺癌基因进行测序。与此同时，我们将类似地评估从我们的独立家庭研究中发现的 6 个新的遗传性乳腺癌候选基因。对于所有表征，我们将使用我们最近开发的方法对乳腺癌基因的外显子、内含子、调控和侧翼基因间区域进行同步捕获和多重测序，中值覆盖率>300倍。在 AIM 2 中，我们将识别所有预计会导致基因功能丧失的变异，包括截短突变（无论是无义突变、移码突变、破坏 CNV 等）、完全基因组缺失以及假定的破坏性错义突变。我们将使用生物信息学工具评估所有变异对基因功能的影响。具有可能剪接效应的变体将通过患者 RNA 和离体小基因的 RT-PCR 进行评估。最有希望的错义等位基因将通过实验测试 DNA 损伤反应、酶活性丧失和其他适当的功能测定。在 AIM 3 中，我们将根据病例与对照中明确功能丧失突变的组合频率来测试乳腺癌与 24 个基因中每一个的关联强度。将估计每个基因的相对风险。对于乳腺癌的遗传易感性来说，将基因组学整合到临床护理中的挑战现在是及时的，因为已知多种致病基因，可以使用专门的乳房筛查方式，降低风险的手术是有效的，并且乳腺癌的治疗受到患者基因型的影响。该项目的目标是提供翻译所需的信息和技术。