Genetic analysis of 10 pedigrees with inherited retinal degeneration by exome sequencing and phenotype-genotype association.

Our purpose was to identify causative mutations and characterize the phenotype associated with the genotype in 10 unrelated families with autosomal recessive retinal degeneration. Ophthalmic evaluation and DNA isolation were carried out in 10 pedigrees with inherited retinal degenerations (IRD). Exomes of probands from eight pedigrees were captured using Nimblegen V2/V3 or Agilent V5+UTR kits, and sequencing was performed on Illumina HiSeq. The DHDDS gene was screened for mutations in the remaining two pedigrees with Ashkenazi Jewish ancestry. Exome variants were filtered to detect candidate causal variants using exomeSuite software. Segregation and ethnicity-matched control sample analysis were performed by dideoxy sequencing. Retinal histology of a patient with DHDDS mutation was studied by microscopy. Genetic analysis identified six known mutations in ABCA4 (p.Gly1961Glu, p.Ala1773Val, c.5461-10T>C), RPE65 (p.Tyr249Cys, p.Gly484Asp), PDE6B (p.Lys706Ter) and DHDDS (p.Lys42Glu) and ten novel potentially pathogenic variants in CERKL (p.Met323Val fsX20), RPE65 (p.Phe252Ser, Thr454Leu fsX31), ARL6 (p.Arg121His), USH2A (p.Gly3142Ter, p.Cys3294Trp), PDE6B (p.Gln652Ter), and DHDDS (p.Thr206Ala) genes. Among these, variants/mutations in two separate genes were observed to segregate with IRD in two pedigrees. Retinal histopathology of a patient with a DHDDS mutation showed severe degeneration of retinal layers with relative preservation of the retinal pigment epithelium. Analysis of exome variants in ten pedigrees revealed nine novel potential disease-causing variants and nine previously reported homozygous or compound heterozygous mutations in the CERKL, ABCA4, RPE65, ARL6, USH2A, PDE6B, and DHDDS genes. Mutations that could be sufficient to cause pathology were observed in more than one gene in one pedigree.

Validation of a home food inventory among low-income Spanish- and Somali-speaking families.

OBJECTIVE: To refine and validate an existing home food inventory (HFI) for low-income Somali- and Spanish-speaking families. DESIGN: Formative assessment was conducted using two focus groups, followed by revisions of the HFI, translation of written materials and instrument validation in participants' homes. SETTING: Twin Cities Metropolitan Area, Minnesota, USA. SUBJECTS: Thirty low-income families with children of pre-school age (fifteen Spanish-speaking; fifteen Somali-speaking) completed the HFI simultaneously with, but independently of, a trained staff member. Analysis consisted of calculation of both item-specific and average food group kappa coefficients, specificity, sensitivity and Spearman's correlation between participants' and staff scores as a means of assessing criterion validity of individual items, food categories and the obesogenic score. RESULTS: The formative assessment revealed the need for few changes/additions for food items typically found in Spanish-speaking households. Somali-speaking participants requested few additions, but many deletions, including frozen processed food items, non-perishable produce and many sweets as they were not typical food items kept in the home. Generally, all validity indices were within an acceptable range, with the exception of values associated with items such as 'whole wheat bread' (k = 0.16). The obesogenic score (presence of high-fat, high-energy foods) had high criterion validity with k = 0.57, sensitivity = 91.8%, specificity = 70.6% and Spearman correlation = 0.78. CONCLUSIONS: The revised HFI is a valid assessment tool for use among Spanish and Somali households. This instrument refinement and validation process can be replicated with other population groups.