Genomic Approaches to Defining Inherited Basis of Childhood Cancer

确定负责癌症易感性的特定基因中的突变会影响以下决策： 对患者的治疗以及允许增加对高危家庭的监测和预防方法 成员此外，对儿童恶性肿瘤遗传易感性的了解， 深入了解癌症的机制以及儿童和成人癌症患者的潜在治疗靶点 在一般人群中。目前利用高通量测序方法进行编码改变 一直专注于肿瘤组织中的体细胞突变，相反， 癌症易感性集中在对癌症风险影响很小的共同变异上。 我们提出了一个项目在这两种不同的方法的交叉点。我们计划使用大规模并行 有病史和家族史的儿童癌症患者的组成DNA序列分析 表明是癌症易感综合征在目标1中，我们将重点关注具有一致性的家庭群体， 和特定的表型，例如，40岁时患有儿童肉瘤和第二恶性肿瘤的先证者 其中对充分表征的癌症相关基因的彻底分析一直是阴性的。分子 生殖系DNA的分析将包括两种综合方法：（1）捕获所有编码外显子， 通过在密集覆盖下测序以鉴定突变致病性突变（缺失、无义、移码或 剪接位点）影响编码序列（全外显子组）和（2）配对末端全基因组测序 在较低覆盖率的文库中鉴定拷贝数变化和新的重排。在目标2中，我们将携带 我们使用原始的基因组数据，对罕见或新的错义等位基因进行了信息统计和生物信息学分析。 方法，涉及优化的对齐深度为基础的功能性研究的演变。在目标3中， 通过全基因组测序分析拷贝数变化和重排将包括额外的 患有儿童癌症和先天性异常或发育迟缓的受试者队列，以发现新的 邻接基因或重排综合征。这些初始队列的结果将通过以下方法进行验证： 对其他儿童癌症先证者和家族中的相关基因进行靶向测序。 为了完成这个翻译，跨学科的项目，我们包括合作者从儿科癌症 得克萨斯大学医学博士安德森癌症中心和卫生部得克萨斯儿童医院的遗传学项目 圣安东尼奥科学中心和费城儿童医院，人类基因组测序 中心和莱斯大学统计系。临床中心从种族上招募家庭 与医学数据相关的不同人群，以及建立永生化细胞系以促进 功能和临床相关数据的生成。我们计划彻底审问 基因组将推进国家癌症研究所战略计划的目标， 了解高度受影响的儿童癌症家族中癌症遗传易感性的谱。 1

Identification of mutations in specific genes responsible for cancer susceptibility impacts decisions about treatment of the patient as well as allowing increased surveillance and prevention approaches for at-risk family members. In addition, knowledge of inherited predisposition to pediatric malignancies has provided important insights into the mechanisms of cancer and potential therapeutic targets in both children and adults with cancer in the general population. Current utilization of high-throughput sequencing methodologies for coding changes has been focused on somatic mutations in tumor tissue, and conversely; genome-wide association studies of cancer susceptibility have focused on common variations that individually have small impacts on cancer risk. We propose a project at the intersection of these two different approaches. We plan to use massively parallel sequence analyses of constitutional DNA from childhood cancer patients with medical and family history suggestive of a cancer susceptibility syndrome. In Aim 1 we will focus on cohorts of families with consistent and specific phenotypes, for example, probands with childhood sarcomas and second malignancies by age 40 where thorough analysis of well-characterized cancer-associated genes has been negative. The molecular analyses of germline DNA will include two comprehensive approaches (1) capture of all coding exons followed by sequencing at dense coverage to identify mutations pathogenic mutations (deletion, nonsense, frameshift or splice site) that impact coding sequence (whole exome) and (2) whole genome sequencing of paired-ends libraries at lower coverage to identify copy number changes and novel rearrangements. In Aim 2, we will carry out informative statistical and bioinformatics analysis of rare or novel missense alleles, using original methodology involving optimization of alignment depths for evolution-based studies of functionality. In Aim 3, analyses of copy number change and rearrangement by whole genome sequencing will include an additional cohort of subjects with childhood cancer and congenital anomalies or developmental delay to uncover novel contiguous gene or rearrangement syndromes. Results from these initial cohorts will then be validated by targeted sequencing of implicated genes in additional childhood cancer probands and families. To complete this translational, cross-disciplinary project we include collaborators from pediatric cancer genetics programs at Texas Children's Hospital, University of Texas MD Anderson Cancer Center and Health Science Center at San Antonio and the Children's Hospital of Philadelphia, the Human Genome Sequencing Center and the Department of Statistics at Rice University. The clinical centers enroll families from ethnically diverse populations with linkage to medical data, and establishment of immortalized cell lines to facilitate the generation of functionally and clinically relevant data. Our plan to thoroughly interrogate the constitutional genome will advance the goals of the National Cancer Institute's Strategic Plan on gaining a fuller understanding of the spectrum of genetic susceptibility to cancer in highly affected childhood cancer families. 1