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: 8708176
• 负责人: PATRICIA K DONAHOE
• 金额: $ 44.36万
• 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/8708176
• 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; Susceptibility Gene; Techniques; Technology; Universities; Variant; Work; base; cohort; congenital anomaly; cost; dosage; exome sequencing; genome wide association study; genome-wide; next generation; next generation sequencing; novel; outreach; programs; screening

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，以评价来自阵列CGH平台的拷贝数变异（CNV）与来自Affytron 6.0阵列平台的拷贝数变异。 这项工作是由李实验室、桑格财团和多伦多大学的谢勒实验室合作完成的，结果正在准备发表。我们预计，这一分析将为未来解释各自平台的CNV提供指导。我们将使用高分辨率Agilent IM阵列CGH研究我们的孤立和综合征型CDH患者，以确定新的候选基因座。将分析父母/患者三联体，以确定未报告的CNV是新发的还是遗传的。由于出生缺陷如CDH预计是多基因的，我们应该预期，与对照组相比，患者中频率增加的遗传性CNV的组合将是强有力的影响因素。 Affyester6.0芯片将用于研究多重CDH家族，以确定连锁区和杂合性缺失区，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和来自杂合性缺失区域的基因，以选择那些与已知导致CDH的其他基因显著相互作用的基因。 随着新兴测序平台的成本逐渐降低，我们计划对50名症状性或复杂性CDH患者进行全外显子组测序。我们的假设是，共同基因座的变异将是心脏和膈肌缺损合并症患者的病因。我们还假设，类似地，有限数量或甚至单个变体将负责各种综合征型CDH的患者，这些患者具有CDH与其他显著先天性异常的表型星座。我们预测，筛查这一特殊群体的患者将增加发现新的因果变异的可能性。 用于较大的孤立性先天性膈疝患者队列的亚基因组测序。Lee和Donahoe实验室将创建患者特异性DNA文库。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多联体化，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例孤立性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桑格和多伦多财团的广泛联系，为我们选择平台提供了更多的有效性，并确保这些技术将得到适当的选择、使用和解释，希望能影响患者护理的应用。