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: 8143191
• 负责人: PATRICIA K DONAHOE
• 金额: $ 37.29万
• 依托单位: MASSACHUSETTS GENERAL HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-01 至 2016-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8143191
• 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确定候选CDH基因）Charies Lee博士正在完成一个广泛的平台比较，以评估从阵列CGH平台得出的拷贝数变化（CNV），以及与Affymetrix 6.0阵列平台的平台。 这项工作是通过Lee实验室，Sanger Consorslum和多伦多大学的Sherer实验室合作进行的，现在正在准备出版结果。我们预计该分析将为各自平台对CNV的未来解释提供指导。我们将使用高分辨率安捷伦IM阵列CGH研究我们的孤立和综合症CDH患者，以鉴定新的候选基因座。将分析家长/患者三重奏，以确定未报告的CNV是从头开始还是继承。由于预计诸如CDH之类的先天缺陷将是多基因，因此我们应该预期，遗传性的CNV组合患者与对照组的频率增加将是强大的促成因素。 Affymetrix 6.0芯片将用于研究多重CDH家族，以识别链接块和杂合性损失的区域，当与整个外部测序结合使用时，可以揭示新的候选CDH基因。然后，为这项研究创建的生物信息学算法CNV Connect将优先考虑CNV基因座中的所有基因，以及从杂合性的区域丧失衍生的基因，以选择与其他基因相互作用的人，从而有助于CDH。 随着新兴测序平台的成本逐渐降低，我们计划对50例sydromic或复杂CDH患者进行整个外部测序。我们的假设是，共同基因座的变体对于心脏和隔膜缺陷的合并症患者而言是病因。我们还假设，同样的是，有限的数量甚至单个变体将导致具有CDH表型与其他明显的先天性异常的各种综合症CDH患者。我们预测，筛查这一特殊群体的患者将增加揭示新的因果变异的可能性。 为了对较大的孤立先天性diaphragmargmantic疝的较大患者组进行亚遗传学测序。 Lee和Donahoe实验室将创建患者特定的DNA库。然后，Lee实验室将在捕获过滤器上加入所有由Pober博士在项目I中选择的候选基因并杂交患者DNA样本。洗脱后，将采用下一代测序技术来对150例分离CDH患者的整个队列中的所有候选基因进行测序。 通过SEIDMAN实验室的咨询以及他与Sanger和多伦多财团的广泛宣传，具有Lee实验室的专业知识，这给我们的平台选择提供了额外的有效性，并保证这些技术将被适当地选择，使用和解释，并希望影响患者护理的应用。