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.
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