Germline Structural Variant Identification and Functional Determination in Childhood Cancer

儿童癌症的种系结构变异鉴定和功能测定

• 批准号: 10646500
• 负责人: OWEN Robert HIRSCHI
• 金额: $ 4.53万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10646500
• 关键词: Adult; Algorithms; Alveolar Rhabdomyosarcoma; Artificial Intelligence; Bioinformatics; Biological Assay; CRISPR/Cas technology; Cancer Biology; Cancer Patient; Cell Proliferation; Characteristics; Child; Childhood; Childhood Ependymoma; Cohort Studies; DNA biosynthesis; Data; Databases; Detection; Dinoprostone; Embryonal Rhabdomyosarcoma; Engineering; Enhancers; Ependymal Cell; Ependymoma; Event; Exons; Fellowship; Funding; Genetic; Graph; Hereditary Nonpolyposis Colorectal Neoplasms; Heterozygote; Inherited; Interleukin-6; Link; MSH2 gene; Malignant Childhood Neoplasm; Malignant Neoplasms; Malignant neoplasm of pancreas; Methodology; Methods; Neuroglia; Oxidoreductase; Parents; Pathogenicity; Patients; Philadelphia Chromosome; Play; Posterior Fossa; Predisposition; Promoter Regions; Prostaglandins; Proteins; Radial; Recurrence; Reporting; Rhabdomyosarcoma; Role; Running; STAT3 gene; Sensitivity and Specificity; Signal Transduction; Solid; Stat3 Signaling Pathway; Syndrome; Techniques; Testing; Training; Training Activity; Tumor Promoters; United States National Institutes of Health; Up-Regulation; Validation; Variant; Visualization; analysis pipeline; bioinformatics tool; cancer care; cancer predisposition; cancer prevention; cancer risk; cell type; clinical care; cohort; ethnic diversity; exome; exome sequencing; functional gain; genome sequencing; genomic data; improved; leukemia; malignant breast neoplasm; malignant stomach neoplasm; nerve stem cell; novel; participant enrollment; pediatric patients; proband; promoter; racial diversity; stem cells; t(9; 22)(q34; q11); tool; transcriptome; transcriptome sequencing; tumor; variant detection; whole genome

Abstract A few germline pathogenic structural variants (SV) have been identified in cancer predisposition syndromes, e.g., MSH2 inversion in Lynch syndrome. The advent of short-read whole-genome sequencing (WGS) has facilitated the detection of SVs. However, a pitfall of this sequencing methodology is the inability to capture all SVs, given the reads do not map well to low complexity regions, and current algorithms used to identify SVs from short-read data have very low sensitivity and very high false-positive rates. One of the objectives of this fellowship is to optimize and implement an SV calling pipeline that utilizes multiple algorithms to increase the sensitivity and specificity of variant identification from germline short-read WGS trios. This pipeline is currently being developed and tested on pediatric cancer patients enrolled in the NIH-funded Baylor Advancing Sequencing into Childhood Cancer Care (BASIC3) exome study, which consists of ethnically and racially diverse pediatric patients with solid (CNS and non-CNS) tumors. This BASIC3 subset includes 63 proband/parent trios who have subsequently undergone germline short-read WGS. Five SV callers are run and then filtered using either a percent reciprocal overlap filter or a proposed Artificial Intelligence-based proximity graph filter to identify de novo and inherited SVs. This cohort has recently been selected for a long-read sequencing pilot, data which serves as the gold standard for SV detection. Comparison of short-read WGS generated SV calls with the long- read data will help determine the sensitivity and specificity of variant calls and further improve the short read pipeline (Aim 1A). Once optimized this short-read WGS SV pipeline will be applied to the Kids First Genetics of Embryonal and Alveolar Rhabdomyosarcoma cohort (n=900), as an independent assessment of the method and also to identify recurrent germline SVs in this cancer which has not yet been well characterized (Aim 1B). The second training and scientific objective is to explore the functional effect of a novel de novo SV identified through the initial analysis. A de novo germline duplication of the Prostaglandin Reductase 2 (PTGR2) enhancer and promoter region was found in a pediatric Posterior Fossa subtype A (PF–A) ependymoma patient. Transcriptome data from the patient’s tumor revealed increased PTGR2 expression. The PTGR2 protein converts 15-keto- prostaglandin E2 to 15-keto-13,14-dihydro-PGE2. Studies in adult malignancies suggest that increased 15-keto- 13,14-dihydro-PGE2 is associated with cancer risk potentially through the STAT3 signaling pathway. Increased STAT3 signaling is reported as a distinct feature of PF-A ependymoma. The identified partial duplication of PTGR2 will be engineered into ependymoma progenitor cells, to functionally assess the effects on STAT3 signaling, cell proliferation, and DNA synthesis. In parallel, further analysis of PTGR2 expression and structural variants will be analyzed in pediatric ependymoma cohorts (Aim 2). Completion of this experimental plan and described training activities under Drs. Plon and Milosavljevic will provide Owen Hirschi highly interdisciplinary training in analysis of genomic data, structural variation, and the downstream effects on pediatric cancer biology.

摘要 在癌症易感综合征中已经鉴定出一些生殖系致病性结构变异体（SV）， 例如，在一个实施例中，Lynch综合征中的MSH 2倒置短读全基因组测序（WGS）的出现 有助于检测SV。然而，这种测序方法的一个缺陷是无法捕获所有的 考虑到读段不能很好地映射到低复杂度区域，并且用于从序列中识别SV的当前算法是不可行的。 短读取数据具有非常低灵敏度和非常高的假阳性率。这个奖学金的目标之一 是优化和实现SV调用流水线，该流水线利用多种算法来增加灵敏度 和来自种系短读WGS三重体的变体鉴定的特异性。该管道目前正在 在参加NIH资助的Baylor Advancing Sequencing的儿科癌症患者中开发和测试， 儿童癌症护理（BASIC 3）外显子组研究，包括种族和种族多样的儿童 实体（CNS和非CNS）肿瘤患者。这个BASIC 3子集包括63个先证者/父母三人组， 随后进行种系短读WGS。运行五个SV调用程序，然后使用 百分比倒数重叠过滤器或建议的基于人工智能的邻近图过滤器，以识别de 新生儿和遗传性SV。该队列最近被选为长读序试验，数据 作为SV检测的金标准。短读WGS生成的SV调用与长读WGS生成的SV调用的比较。 读段数据将有助于确定变异识别的灵敏度和特异性， 管道（目标1A）。一旦优化，这个短读WGS SV管道将应用于Kids First Genetics， 胚胎和腺泡状横纹肌肉瘤队列（n=900），作为该方法的独立评估， 还鉴定了这种癌症中的复发性生殖系SV，其尚未得到很好的表征（目的1B）。的 第二个培训和科学目标是探索通过以下方法鉴定的新型新生SV的功能效应： 初步分析。前列腺素还原酶2（PTGR 2）增强子的从头生殖系复制， 启动子区被发现在儿科后颅窝亚型A（PF-A）室管膜瘤患者。转录组 来自患者肿瘤的数据显示PTGR 2表达增加。PTGR 2蛋白将15-酮基- 前列腺素E2至15-酮基-13，14-二氢-PGE 2。成人恶性肿瘤的研究表明，增加15-酮- 13，14-二氢-PGE 2可能通过STAT 3信号通路与癌症风险相关。增加 据报道，STAT 3信号传导是PF-A室管膜瘤的一个独特特征。已发现的部分重复 PTGR 2将被工程化到室管膜瘤祖细胞中，以在功能上评估对STAT 3的影响。 信号传导、细胞增殖和DNA合成。同时，进一步分析PTGR 2表达和结构， 将在儿科室管膜瘤队列中分析变异体（Aim 2）。完成本实验计划， 在Plon和Milosavljevic博士的指导下所描述的培训活动将为Owen Hirschi提供高度跨学科的培训。 基因组数据分析、结构变异和对儿科癌症生物学的下游影响方面的培训。