PROJECT II: VARIANTS FROM COMPLEMENTARY GENOMIC TECHNOLOGIES WILL YIELD

项目二：互补基因组技术的变体将会产生

• 批准号: 8377164
• 负责人: PATRICIA K DONAHOE
• 金额: $ 42.3万
• 依托单位: MASSACHUSETTS GENERAL HOSPITAL
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8377164
• 关键词: Affect; Algorithms; Bioinformatics; Candidate Disease Gene; Collaborations; Comorbidity; Complex; Congenital Abnormality; Congenital diaphragmatic hernia; Consultations; Copy Number Polymorphism; Custom; DNA; DNA Library; DNA Sequence; Defect; Diaphragmatic Hernia; Family; Frequencies; Future; Gene Mutation; Genes; Genetic Screening; Genomics; Heart; Human; Individual; Inherited; Laboratories; Linkage Disequilibrium; Loss of Heterozygosity; Oligonucleotide Microarrays; Parents; Patient Care; Patients; Phenotype; Probability; Publications; Resolution; Respiratory Diaphragm; Sampling; Screening procedure; Susceptibility Gene; Techniques; Technology; Universities; Variant; Work; base; cohort; cost; dosage; exome; genome wide association study; genome-wide; next generation; novel; outreach; programs

In PROJECT II (Variants from Complementary Genomic Technologies will Identify Candidate Causative CDH Genes) Dr. Charies Lee is completing an extensive platform comparison to evaluate copy number variations (CNV) derived from array CGH platforms, with those from the Affymetrix 6.0 array platform. This work has been done in collaboration between the Lee laboratory, the Sanger Consorslum, and the Sherer laboratory in the University of Toronto, and results are now being readied for publication. We anticipate that this analysis will provide guidance for future interpretations of CNVs from the respective platforms. We will use the high resolution Agilent IM array CGH to study our patients with isolated and syndromic CDH to identify new candidate loci. Parent/patient trios will be analyzed to determine whether an unreported CNV is de novo or inherited. Since birth defects such as CDH are anticipated to be polygenic, we should anticipate that combinations of inherited CNVs which have an increased frequency in patients vs. controls will be strong contributing factors. Affymetrix 6.0 chips will be used to study multiplex CDH families to identify blocks of linkage and for regions of loss of heterozygosity, which, when combined with whole exomic sequencing, can reveal new candidate CDH genes. A bioinformatic algorithm created for this study, CNV connect, will then prioritize all the genes in the CNV loci and those derived from regions loss of heterozygosity to select those that significantly interact with other genes know to contribute to CDH. As the cost of emerging sequencing platforms is progressively reduced, we are planning to undertake whole exomic sequencing on 50 patients with sydromic or complex CDH. Our hypothesis is that variant in common loci will be causative In patients with comorbidities of heart and diaphragm defects. We also hypothesize that similarly, a limited number or even a single variant will be responsible for patients with various syndromic CDH who have a phenotype constellation of CDH with other significant congenital anomalies. We predict that screening this special group's of patients will increase the probability of revealing novel causal variants. For subgenomic sequencing of a larger cohort of patients with isolated Congenital Diaphragmatic Hernia. The Lee and Donahoe laboratories will create the patient specific DNA libraries. The Lee laboratory will then concatamerize on the capture filter all the candidate genes selected by Dr. Pober in Project I and hybridize the patient DNA samples. After elution, next generation sequencing techniques will be employed to sequence all the candidate genes in the entire cohort of 150 patients with isolated CDH. Having the expertise of the Lee laboratory with the consultation of the Seidman laboratory and with his extensive outreach to the Sanger and the Toronto consortia gives added validity to our choice of platforms and the assurity that these technologies will be appropriately selected, used, and interpreted, with the hope of affecting an application to patient care.

在项目 II（互补基因组技术的变体将识别候选致病 CDH 基因）中，Charies Lee 博士正在完成一项广泛的平台比较，以评估源自阵列 CGH 平台的拷贝数变异 (CNV) 与来自 Affymetrix 6.0 阵列平台的拷贝数变异 (CNV)。 这项工作是由 Lee 实验室、Sanger Consorslum 和多伦多大学 Sherer 实验室合作完成的，结果现已准备发表。我们预计该分析将为未来对各个平台的 CNV 的解释提供指导。我们将使用高分辨率安捷伦 IM 阵列 CGH 研究孤立性和综合征性 CDH 患者，以确定新的候选基因座。将分析父母/患者三人组，以确定未报告的 CNV 是新生的还是遗传的。由于 CDH 等出生缺陷预计是多基因的，因此我们应该预见到，与对照组相比，患者中出现频率增加的遗传性 CNV 组合将是强有力的影响因素。 Affymetrix 6.0 芯片将用于研究多重 CDH 家族，以识别连锁块和杂合性丢失区域，当与全外显子组测序相结合时，可以揭示新的候选 CDH 基因。为本研究创建的生物信息学算法 CNV connect 将优先考虑 CNV 位点中的所有基因以及源自杂合性缺失区域的基因，以选择那些与已知有助于 CDH 的其他基因显着相互作用的基因。 随着新兴测序平台的成本逐步降低，我们计划对 50 名患有综合征或复杂 CDH 的患者进行全外显子测序。我们的假设是，共同位点的变异将导致患有心脏和隔膜缺陷合并症的患者。同样，我们还假设，有限数量甚至单一变异将导致患有各种 CDH 综合征的患者，这些患者具有 CDH 表型星座并伴有其他显着的先天性异常。我们预测，对这一特殊患者群体进行筛查将增加揭示新的因果变异的可能性。 用于对更大范围的孤立性先天性膈疝患者进行亚基因组测序。 Lee 和 Donahoe 实验室将创建患者特异性 DNA 库。然后，Lee 实验室将在捕获过滤器上对 Pober 博士在项目 I 中选择的所有候选基因进行串联，并对患者 DNA 样本进行杂交。洗脱后，将采用下一代测序技术对整个 150 名分离的 CDH 患者队列中的所有候选基因进行测序。 拥有 Lee 实验室的专业知识、Seidman 实验室的咨询以及他与 Sanger 和多伦多财团的广泛联系，增加了我们选择平台的有效性，并确保这些技术将得到适当的选择、使用和解释，以期影响患者护理的应用。