Journal: Veterinary ophthalmology

Article Title: O ptic nerve hypoplasia in miniature poodle dogs: a preliminary genetic and candidate gene association study

doi: 10.1111/vop.12691

Figure Lengend Snippet: All sampled animals are related to a single founder male born more than 40 years ago. For simplicity, the pedigree only shows prior generations tracing back to that founder. No examination records were available for animals with a dot in the center of the symbol. Parents of affected dogs either had an unknown status, were normal or diagnosed with Mp. Dogs sequenced by Sanger sequencing and the Illumina CanineHD BeadChip that were used for candidate gene sequencing and haplotype analysis are marked with an oblique arrow. The control dog that was only sequenced by Sanger sequencing is marked with an asterisk.

Article Snippet: Haplotypes for candidate genes sequenced by Sanger sequencing (A), and haplotypes for candidate genes genotyped with Illumina CanineHD BeadChip (B1, B2).

Techniques: Sequencing

Journal: Veterinary ophthalmology

Article Title: O ptic nerve hypoplasia in miniature poodle dogs: a preliminary genetic and candidate gene association study

doi: 10.1111/vop.12691

Figure Lengend Snippet: Haplotypes for the candidate genes studied for ONH affected and control dogs. Note that haplotype analysis was only carried out in normal control and ONH affected dogs, and not in dogs with Mp. Haplotypes for candidate genes sequenced by Sanger sequencing (A), and haplotypes for candidate genes genotyped with Illumina CanineHD BeadChip (B1, B2). Phenotypic status was assigned as detailed in Materials and Methods. Haplotypes for genes with informative SNPs are shown in animals used for association study. Haplotypes of HESX1 and TUBA8 are not shown as all animals shared the same homozygous wildtype haplotype. SNP IDs for SNPs located in dbSNP are given next to the variant base pair position.

Article Snippet: Haplotypes for candidate genes sequenced by Sanger sequencing (A), and haplotypes for candidate genes genotyped with Illumina CanineHD BeadChip (B1, B2).

Techniques: Sequencing, Variant Assay

Journal: Current epidemiology reports

Article Title: Neighborhoods to Nucleotides – Advances and gaps for an obesity disparities systems epidemiology model

doi: 10.1007/s40471-019-00221-5

Figure Lengend Snippet: Outcomes measured in the Neighborhoods to Nucleotides sample (n=209) across seven domains.

Article Snippet: Epigenomic/Transcriptomic DNA methylation Illumina Infinium MethylationEpic BeadChip Kits (>850,000 methylation sites at single-nucleotide resolution) mRNA & miRNA Illumina Next Generation Sequencing HiSeq4000 Microbiome Diversity 16S rRNA gene amplicon sequencing for calculating alpha diversity (diversity within each sample) such as the Shannon index Dissimilarity Metrics of beta diversity such as UniFrac calculated from the 16S rRNA data Taxonomy Assignment of each 16S rRNA read to a bacterial taxon, at multiple levels (typically from the phylum to the genus) Nutrition 24 hour recall Nutrition Data Systems for Research 24 hour food recalls (total calories, fats, fiber, number of food types e.g. vegetables or fruit) Food frequency VioScreen food frequency questionnaire (instances of food types eaten over past weeks/months) Biomarker Clinical BMI, waist-hip circumference, medications Urine Metabolomics Blood Metabolomics, hormone, adipokines, biomarkers of inflammation, glycemic regulation, lipid metabolism, liver health Behavior Accelerometer Physical activity (bouts, total duration, daily patterns), sedentary behavior (bouts, total duration, daily patterns), sleep time, sleep quality, machine learned behaviors (biking, running, walking, in vehicle) GPS Time spent indoor/outdoor, dynamic exposure measures to all environmental features (e.g., total air pollution participant is exposed to measured by movement) Self-report Questionnaires on health, physical functioning, sleep, etc.

Techniques: DNA Methylation Assay, Methylation, Next-Generation Sequencing, Amplification, Sequencing, Biomarker Assay, Activity Assay