Cloning and Characterization of Canine \u3cem\u3ePAX6\u3c/em\u3e and Evaluation as a Candidate Gene in a Canine Model of Aniridia

Purpose: Mutations in PAX6 cause human aniridia. The small eye (sey) mouse represents an animal model for aniridia. However, no large animal model currently exists. We cloned and characterized canine PAX6, and evaluated PAX6 for causal associations with inherited aniridia in dogs. Methods: Canine PAX6 was cloned from a canine retinal cDNA library using primers designed from human and mouse PAX6 consensus sequences. An RH3000 radiation hybrid panel was used to localize PAX6 within the canine genome. Genomic DNA was extracted from whole blood of dogs with inherited aniridia, and association testing was performed using markers on CFA18. Fourteen PAX6 exons were sequenced and scanned for mutations, and a Southern blot was used to test for large deletions. Results: Like the human gene, canine PAX6 has 13 exons and 12 introns, plus an alternatively spliced exon (5a). PAX6 nucleotide and amino acid sequences were highly conserved between dog, human, and mouse. The canine PAX6 cDNA sequence determined in this study spans 2 large gaps present in the current canine genomic sequence. Radiation hybrid mapping placed canine PAX6 on CFA18 in a region with synteny to HSA11p13. Exon-scanning revealed single nucleotide polymorphisms, but no pathological mutations, and Southern blot analysis revealed no differences between normal and affected animals. Conclusions: Canine PAX6 was cloned and characterized, and results provide sequence information for gaps in the current canine genome sequence. Canine PAX6 nucleotide and amino acid sequences, as well as gene organization and map location, were highly homologous with that of the human gene. PAX6 was evaluated in dogs with an inherited form of aniridia, and sequence analysis indicated no pathological mutations in the coding regions or splice sites of aniridia-affected dogs, and Southern blot analysis showed no large deletions

Radiation Hybrid Mapping of Cataract Genes in the Dog

Purpose: To facilitate the molecular characterization of naturally occurring cataracts in dogs by providing the radiation hybrid location of 21 cataract-associated genes along with their closely associated polymorphic markers. These can be used for segregation testing of the candidate genes in canine cataract pedigrees. Methods: Twenty-one genes with known mutations causing hereditary cataracts in man and/or mouse were selected and mapped to canine chromosomes using a canine:hamster radiation hybrid RH5000 panel. Each cataract gene ortholog was mapped in relation to over 3,000 markers including microsatellites, ESTs, genes, and BAC clones. The resulting independently determined RH-map locations were compared with the corresponding gene locations from the draft sequence of the canine genome. Results: Twenty-one cataract orthologs were mapped to canine chromosomes. The genetic locations and nearest polymorphic markers were determined for 20 of these orthologs. In addition, the resulting cataract gene locations, as determined experimentally by this study, were compared with those determined by the canine genome project. All genes mapped within or near chromosomal locations with previously established homology to the corresponding human gene locations based on canine:human chromosomal synteny. Conclusions: The location of selected cataract gene orthologs in the dog, along with their nearest polymorphic markers, serves as a resource for association and linkage testing in canine pedigrees segregating inherited cataracts. The recent development of canine genomic resources make canine models a practical and valuable resource for the study of human hereditary cataracts. Canine models can serve as large animal models intermediate between mouse and man for both gene discovery and the development of novel cataract therapies

Identifying postoperative atrial fibrillation in cardiac surgical patients posthospital discharge, using iPhone ECG: a study protocol

Introduction: Postoperative atrial fibrillation (AF) occurs in 30–40% of patients after cardiac surgery. Identification of recurrent postoperative AF is required to initiate evidence-based management to reduce the risk of subsequent stroke. However, as AF is oftenasymptomatic, recurrences may not be detected after discharge. This study determines feasibility and impact of a self-surveillance programme to identify recurrence of postoperative AF in the month of posthospital discharge.Methods and analysis: This is a feasibility study, using a cross-sectional study design, of self-screening for AF using a hand-held single-lead iPhone electrocardiograph device (iECG). Participants will be recruited from the cardiothoracic surgery wards of the Royal North Shore Hospital and North Shore Private Hospital, Sydney, Australia. Cardiac surgery patients admitted in sinus rhythm and experiencing a transient episode of postoperative AF will be eligible for recruitment. Participants will be taught to take daily ECGrecordings for 1 month posthospital discharge using the iECG and will be provided education regarding AF, including symptoms and health risks. The primary outcome is the feasibility of patient self-monitoring for AF recurrence using an iECG. Secondary outcomesinclude proportion of patients identified with recurrent AF; estimation of stroke risk and patient knowledge. Process outcomes and qualitative data related to acceptability of patient’s use of the iECG and sustainability of the screening programme beyond thetrial setting will also be collected.Ethics and dissemination: Primary ethics approval was received on 25 February 2014 from Northern Sydney Local Health District Human Resource Ethics Committee, and on 17 July 2014 from North Shore Private Hospital Ethics Committee. Results will bedisseminated via forums including, but not limited to, peer-reviewed publications and presentation at national and international conferences

Towards a comprehensive structural variation map of an individual human genome

A comprehensive map of structural variation in the human genome provides a reference dataset for analyses of future personal genomes

Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing

Abstract Background To identify potential tumor suppressor genes, genome-wide data from exome and transcriptome sequencing were combined to search for genes with loss of heterozygosity and allele-specific expression. The analysis was conducted on the breast cancer cell line HCC1954, and a lymphoblast cell line from the same individual, HCC1954BL. Results By comparing exome sequences from the two cell lines, we identified loss of heterozygosity events at 403 genes in HCC1954 and at one gene in HCC1954BL. The combination of exome and transcriptome sequence data also revealed 86 and 50 genes with allele specific expression events in HCC1954 and HCC1954BL, which comprise 5.4% and 2.6% of genes surveyed, respectively. Many of these genes identified by loss of heterozygosity and allele-specific expression are known or putative tumor suppressor genes, such as BRCA1, MSH3 and SETX, which participate in DNA repair pathways. Conclusions Our results demonstrate that the combined application of high throughput sequencing to exome and allele-specific transcriptome analysis can reveal genes with known tumor suppressor characteristics, and a shortlist of novel candidates for the study of tumor suppressor activities

Using comparative genomics to reorder the human genome sequence into a virtual sheep genome

Using BAC-end sequences, a sparse marker map and the sequences of the human, dog and cow genomes, an accurate and detailed sub-gene level map of the sheep genome has been constructed

Canine Morphology: Hunting for Genes and Tracking Mutations

In this essay, Abigail Shearin and Elaine Ostrander discuss the proposed genomic mechanisms for the extraordinary level of phenotypic variation observed in the domestic dog and the evidence detailing the variants responsible for the many shapes, sizes, textures, and colors of man's best friend