A genome-wide association study (GWAS) for bronchopulmonary dysplasia.

OBJECTIVE: Twin studies suggest that heritability of moderate-severe bronchopulmonary dysplasia (BPD) is 53% to 79%, we conducted a genome-wide association study (GWAS) to identify genetic variants associated with the risk for BPD. METHODS: The discovery GWAS was completed on 1726 very low birth weight infants (gestational age = 25(0)-29(6/7) weeks) who had a minimum of 3 days of intermittent positive pressure ventilation and were in the hospital at 36 weeks' postmenstrual age. At 36 weeks' postmenstrual age, moderate-severe BPD cases (n = 899) were defined as requiring continuous supplemental oxygen, whereas controls (n = 827) inhaled room air. An additional 795 comparable infants (371 cases, 424 controls) were a replication population. Genomic DNA from case and control newborn screening bloodspots was used for the GWAS. The replication study interrogated single-nucleotide polymorphisms (SNPs) identified in the discovery GWAS and those within the HumanExome beadchip. RESULTS: Genotyping using genomic DNA was successful. We did not identify SNPs associated with BPD at the genome-wide significance level (5 × 10(-8)) and no SNP identified in previous studies reached statistical significance (Bonferroni-corrected P value threshold .0018). Pathway analyses were not informative. CONCLUSIONS: We did not identify genomic loci or pathways that account for the previously described heritability for BPD. Potential explanations include causal mutations that are genetic variants and were not assayed or are mapped to many distributed loci, inadequate sample size, race ethnicity of our study population, or case-control differences investigated are not attributable to underlying common genetic variation.

High quality genome-wide genotyping from archived dried blood spots without DNA amplification.

Spots of blood are routinely collected from newborn babies onto filter paper called Guthrie cards and used to screen for metabolic and genetic disorders. The archived dried blood spots are an important and precious resource for genomic research. Whole genome amplification of dried blood spot DNA has been used to provide DNA for genome-wide SNP genotyping. Here we describe a 96 well format procedure to extract DNA from a portion of a dried blood spot that provides sufficient unamplified genomic DNA for genome-wide single nucleotide polymorphism (SNP) genotyping. We show that SNP genotyping of the unamplified DNA is more robust than genotyping amplified dried blood spot DNA, is comparable in cost, and can be done with thousands of samples. This procedure can be used for genome-wide association studies and other large-scale genomic analyses that require robust, high-accuracy genotyping of dried blood spot DNA.

Cell shape regulation by Gravin requires N-terminal membrane effector domains.

Gravin (AKAP12, SSeCKS) is a scaffolding protein that acts as a potent inhibitor of tumor metastasis in vivo and in vitro, and regulates morphogenesis during vertebrate gastrulation. Despite being implicated in many cellular processes, surprisingly little is known about the mechanism by which Gravin elicits cell shape changes. In this work, we use in vitro cell spreading assays to demonstrate that the Gravin N-terminus containing the three MARCKS-like basic regions (BRs) is necessary and sufficient to regulate cell shape in vitro. We show that the conserved phosphorylation sites in the BRs are essential for their function in these assays. We further demonstrate that the Gravin BRs are necessary for in vivo function during gastrulation in zebrafish. Together, these results provide an important step forward in understanding the mechanism of Gravin function in cell shape regulation and provide valuable insight into how Gravin acts as a cytoskeletal regulator.