Discovering genomic rearrangements under selection in serious ovarian cancer

发现严重卵巢癌选择下的基因组重排

基本信息

批准号：
8976219
负责人：
Julia Salzman
金额：
$ 22.78万
依托单位：
STANFORD UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2014
资助国家：
美国
起止时间：
2014-01-01 至 2016-12-31
项目状态：
已结题

项目摘要

Recurrent gene fusions and internal tandem duplications are among the most tumor-specific molecular markers known and can provide the potential for therapeutic targets. With a few notable exceptions, however, relatively common recurrent gene fusions have not been identified in commonly occurring carcinomas, which often have multiple, complex chromosomal rearrangements that are difficult to analyze by traditional cytogenetic approaches. Complex tumor karyotpes make it difficult to identify gene fusions using cytogenetics, but suggest the possibility that recurrent rearrangements producing fusions or internal tandem duplications (ITDs) may be prevalent. This proposal aims to use deep sequencing and the novel analytic techniques described to study aspects of the serous ovarian cancer genome and transcriptome which have remained hidden due to limitations in technology or analytical methods, and to test intra-individual and inter-individual selective pressures on tumors. The aspects of this proposal are as follows 1) to further investigate the extent of gene rearrangements in ovarian cancer, focusing on discovering local rearrangements transcribed into RNA; 2) to determine the composition of a group of novel circular transcripts that I have recently found to be expressed at relatively high levels in normal and pathogenic human cells; 3) to characterize double minutes in ovarian cancer, combining bioinformatics to determine rearrangements in their sequence composition and statistical analysis to determine evolutionary pressures on their composition exerted by the tumors. The applicant has a track-record of success in discovering novel gene fusions with ultra-high throughput sequencing (the ESRRA-C11 orf20 fusion), as well as designing original rigorous statistical and bioinformatic methods for ultra-high throughput data. Under the mentorship of Dr. Patrick O. Brown, a pioneer in high throughput genomic technologies and statistical methods for analyzing them, the applicant will continue career development and training. The first aim of this project will be performed during the mentoring phase, and experiments for aims 2 and 3 will be piloted. The K99/R00 award will support the applicant in her development into an independent investigator.

复发基因融合和内部串联重复是最肿瘤特异性的分子之一已知的标记，可以提供治疗靶标的潜力。除了一些值得注意的例外，但是，在通常发生的情况下尚未发现相对常见的复发基因融合癌通常具有多个复杂的染色体重排，难以通过传统的细胞遗传学方法。复杂的肿瘤核核使很难识别使用的基因融合细胞遗传学，但建议复发重排产生融合或内部串联的可能性重复（ITD）可能很普遍。该建议旨在使用深层测序和新颖的分析描述的技术是研究浆液卵巢癌基因组和转录组的方面由于技术或分析方法的局限性，仍隐藏着隐藏，并测试个体内部和个体间肿瘤的选择性压力。该提案的各个方面如下1）进一步调查卵巢癌基因重排的程度，重点是发现局部重排转录为RNA； 2）确定我拥有的一组新型圆形转录本的组成最近发现在正常和致病性人类细胞中以相对较高的水平表达。 3）到表征卵巢癌的双分钟，结合生物信息学以确定重排它们的序列组成和统计分析以确定其组成的进化压力由肿瘤施加。申请人在发现新颖的基因融合方面拥有成功的轨道纪录超高吞吐量测序（ESRRA-C11 ORF20融合），并设计原始的严格超高吞吐量数据的统计和生物信息学方法。在高吞吐量基因组技术和分析统计方法的先驱帕特里克·O·布朗（Patrick O. Brown）的指导下，申请人将继续职业发展和培训。该项目的第一个目标将在指导阶段进行，目标2和3的实验将进行试验。 K99/R00奖将为申请人发展成为独立调查员的发展。

项目成果

期刊论文数量（8）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

ciRS-7 exonic sequence is embedded in a long non-coding RNA locus.

DOI：
10.1371/journal.pgen.1007114
发表时间：
2017-12
期刊：
PLoS genetics
影响因子：
4.5
作者：
Barrett SP;Parker KR;Horn C;Mata M;Salzman J
通讯作者：
Salzman J

Cell-type specific features of circular RNA expression.

DOI：
10.1371/journal.pgen.1003777
发表时间：
2013
期刊：
PLoS genetics
影响因子：
4.5
作者：
Salzman J;Chen RE;Olsen MN;Wang PL;Brown PO
通讯作者：
Brown PO

Circular RNA is expressed across the eukaryotic tree of life.

环状RNA在真核生命树中表达。

DOI：
10.1371/journal.pone.0090859
发表时间：
2014
期刊：
PloS one
影响因子：
3.7
作者：
Wang PL;Bao Y;Yee MC;Barrett SP;Hogan GJ;Olsen MN;Dinneny JR;Brown PO;Salzman J
通讯作者：
Salzman J

Circular RNA biogenesis can proceed through an exon-containing lariat precursor.