Genomic Approaches to Defining Inherited Basis of Childhood Cancer

描述（由申请人提供）：确定负责癌症易感性的特定基因突变，影响患者治疗决策，并允许增加对高危家庭成员的监测和预防方法。此外，对儿童恶性肿瘤的遗传易感性的了解为癌症的机制和儿童和成人癌症的潜在治疗靶点提供了重要的见解。目前对编码变化的高通量测序方法的利用主要集中在肿瘤组织中的体细胞突变上，反之亦然；癌症易感性的全基因组关联研究集中在个别对癌症风险影响较小的常见变异上。我们在这两种不同方法的交汇处提出了一个项目。我们计划使用大量的平行序列分析的体质DNA从儿童癌症患者的医疗和家族史提示癌症易感综合征。在目标1中，我们将重点关注具有一致和特定表型的家庭队列，例如，40岁前患有儿童肉瘤和第二恶性肿瘤的先证，其中对特征明确的癌症相关基因的彻底分析是阴性的。种系DNA的分子分析将包括两种综合方法：(1)捕获所有编码外显子，然后在密集覆盖范围内测序，以确定影响编码序列（整个外显子组）的突变致病突变（缺失、无义、移码或剪接位点）；(2)对低覆盖范围的配对端文库进行全基因组测序，以确定拷贝数变化和新的重排。在目标2中，我们将对罕见或新型错义等位基因进行信息统计和生物信息学分析，使用涉及优化基于进化的功能研究的对齐深度的原始方法。在Aim 3中，通过全基因组测序对拷贝数变化和重排的分析将包括另一组患有儿童癌症和先天性异常或发育迟缓的受试者，以发现新的连续基因或重排综合征。这些初始队列的结果将通过对其他儿童癌症先证者和家庭的相关基因进行靶向测序来验证。

DESCRIPTION (provided by applicant): 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. PUBLIC HEALTH RELEVANCE: Identification of mutations cancer susceptibility genes impacts decisions about treatment of the patient as well as allowing increased surveillance and prevention approaches for at-risk family members. We plan to use massively parallel sequence analyses of all coding regions in constitutional DNA from childhood cancer patients with medical and family history suggestive of a cancer susceptibility syndrome to identify novel cancer susceptibility genes and gain a fuller understanding of the spectrum of genetic susceptibility to cancer.