Identification of Medically Actionable Secondary Findings in the 1000 Genomes

The American College of Medical Genetics and Genomics (ACMG) recommends that clinical sequencing laboratories return secondary findings in 56 genes associated with medically actionable conditions. Our goal was to apply a systematic, stringent approach consistent with clinical standards to estimate the prevalence of pathogenic variants associated with such conditions using a diverse sequencing reference sample. Candidate variants in the 56 ACMG genes were selected from Phase 1 of the 1000 Genomes dataset, which contains sequencing information on 1,092 unrelated individuals from across the world. These variants were filtered using the Human Gene Mutation Database (HGMD) Professional version and defined parameters, appraised through literature review, and examined by a clinical laboratory specialist and expert physician. Over 70,000 genetic variants were extracted from the 56 genes, and filtering identified 237 variants annotated as disease causing by HGMD Professional. Literature review and expert evaluation determined that 7 of these variants were pathogenic or likely pathogenic. Furthermore, 5 additional truncating variants not listed as disease causing in HGMD Professional were identified as likely pathogenic. These 12 secondary findings are associated with diseases that could inform medical follow-up, including cancer predisposition syndromes, cardiac conditions, and familial hypercholesterolemia. The majority of the identified medically actionable findings were in individuals from the European (5/379) and Americas (4/181) ancestry groups, with fewer findings in Asian (2/286) and African (1/246) ancestry groups. Our results suggest that medically relevant secondary findings can be identified in approximately 1% (12/1092) of individuals in a diverse reference sample. As clinical sequencing laboratories continue to implement the ACMG recommendations, our results highlight that at least a small number of potentially important secondary findings can be selected for return. Our results also confirm that understudied populations will not reap proportionate benefits of genomic medicine, highlighting the need for continued research efforts on genetic diseases in these populations.     

Recombinant plasmid conferring proline overproduction and osmotic tolerance.

A recombinant plasmid carrying the proBA (pro-74) mutant allele which governs osmotic tolerance and proline overproduction was constructed by using the broad-host-range plasmid vector pQSR49. The physiological, biochemical, and genetic properties of strains carrying the pQSR49 derivatives pMJ101 and pMJ1, mutant and wild type, respectively, were investigated. pMJ101 conferred enhanced osmotolerance compared with strains carrying the wild type, pMJ1. These results are in contrast to those obtained previously with strains carrying recombinant plasmids based on pBR322 that failed to confer the osmotic tolerance phenotype. gamma-Glutamyl kinase (first step in proline biosynthesis) from strains carrying pMJ101 was 200-fold less sensitive to feedback inhibition than was the wild-type enzyme. As expected, the intracellular proline levels of strains carrying pMJ101 were more than an order of magnitude higher than those of the wild type. An analysis of copy number revealed that the pQSR49 constructs were present in the cell at a level six- to eightfold lower than those of the pBR322 recombinants, which may account for the difference in phenotype. We found that the genetic stability of the pQSR49 derivative in a variety of gram-negative bacteria was dependent on the insert orientation and the presence of foreign DNA on the plasmid. These factors may be significant in future studies aimed at expanding the osmotolerance phenotype to a broad range of gram-negative bacteria.     

ADAPTATIONS TO CLIFF-NESTING IN SOME ARCTIC GULLS (LARUS)

Various aspects of the breeding of three gulls, Larus thayeri, glaucoides and hyperboreus, which nested in colonies both on cliff ledges and on level ground in the eastern Canadian Arctic, were compared with those of the ground-nesting L. argentatus and the cliff-nesting Rissa tridactyla. As the result of adaptation to cliff ledge nesting, many aspects of the breeding biology of R. tridactyla were strikingly different from those of the ground-nesting European L. argentatus, but the behaviour of L. thayeri, glaucoides and hyperboreus clearly spanned these differences. Cliff-nesting individuals of thayeri and glaucoides were most like Rissa; ground-nesting individuals of these species were most like argentatus. L. thayeri was more like Rissa than was glaucoides. With but few exceptions, both cliff- and ground-nesting individuals of hyperboreus were most like argentatus. The factors responsible for the intra-specific differences between cliff- and ground-nesters of thayeri and glaucoides are not clear. Limited gene exchange between cliff and ground colonies occurs. Because of physical features of the nest, first-laid eggs were more liable to fall from ledges than second or third eggs. L. thayeri and glaucoides have evolved separate mechanisms to cope with this problem. Egg shape was multimodal in thayeri and glaucoides. Long pyriform eggs were less liable to fall from ledges than eggs of other shapes. L. thayeri laid more long pyriform eggs as first eggs than did glaucoides. L. thayeri lost fewer eggs than did glaucoides, but glaucoides replaced all lost eggs while thayeri did not. Delayed follicular atresia provided glaucoides with insurance of egg replacement. In thayeri, accessory follicles were reabsorbed after the first egg was laid; in argentatus, after the second egg, and in glaucoides after the third egg. At the approach of a predator, it was advantageous for cliff-dwelling chicks to remain motionless but for ground-dwelling chicks to flee their nests and to hide. Among the cliff-nesters, the “freezing in place” reaction of chicks was best developed in thayeri, to a lesser extent in glaucoides, and least in hyperboreus. Among the ground-nesters, chicks of glaucoides and hyperboreus behaved like those of argentatus and fled their nests when disturbed, but chicks of thayeri froze like their cliff-dwelling siblings. Reciprocal transfers of eggs and chicks between cliff and ground colonies indicated that in argentatus, glaucoides and hyperboreus, the factors determining a chick's reaction to disturbance came into play between hatching and the eighth day. In thayeri, the reaction appeared to be effectively innate. Chicks of glaucoides showed a greater predisposition to this behaviour than chicks of argentatus after both had received identical experience on cliff ledges. In thayeri, stereotypy of the freezing reaction has probably been a factor limiting the colonisation of areas where cliffs are scarce but predators present. In argentatus, lack of perfection of this behaviour (compared to glaucoides and thayeri) has probably been a factor preventing argentatus from attaining cliff ledges. L. hyperboreus, although nowhere abundant, is a widespread species nesting on level ground and on cliff ledges but lacking the modifications observed in glaucoides and thayeri; this is due to its size and aggressiveness, the fact that it picks nest-sites before glaucoides and thayeri arrive in the colonies, and that on cliffs it chooses the largest and most level ledges.     

ANALYSIS OF MICROTUBULE STRUCTURE IN EUGLENA GRANULATA

The microtubules associated with the pellicle, reservoir and locomotory flagellum of Euglena granulata were subjected to rotational analysis using the technique of Markham et al. The results indicate that the microtubules have 11-14 subunits when viewed in transverse section. Rotational analysis of the entire locomotory flagellum was also conducted to better demonstrate the nature of the arms extending from the peripheral microtubules.     

2-Deoxy-D-galactose metabolism in ascites hepatoma cells results in phosphate trapping and glycolysis inhibition.

The metabolism of 2-deoxy-D-galactose has been studied in AS-30D rat ascites hepatoma cells in suspension. Using 2-deoxy-D-(1-14C)galactose and an alkaline ethanol deproteinization procedure, the quantitatively identified metabolites included 2-deoxy-D-galactose 1-phosphate comprising 99.3%, and UDP-2-deoxy-D-galactose and UDP-2-deoxy-D-glucose, together amounting to 0.4% of the total metabolites. After incubation for 5 h in the presence of 2-deoxy-D-galactose (1 mmo1/1), the content of 2-deoxy-D-galactose 1-phosphate reached 35 mmo1x(kg cells)-1. The rate of phosphorylation of 2-deoxy-D-galactose was rapid during the first 30 min and decreased to approximately 20% of this rate during the subsequent hours. The rapid trapping of Pi in the form of 2-deoxy-D-galactose 1-phosphate resulted in a depression of free intracellular Pi in spite of a concomitant increase in net 32Pi uptake from the medium and a decrease of ATP and other 5'-nucleotides. The rates of glucose utilization and lactate production were depressed by more than 80% in the presence of 2-deoxy-D-galactose (1 mmo1/1). Interruption of Pi trapping by removal of 2-deoxy-D-galactose from the medium reversed the depressions of Pi and ATP and resulted in a rapid but incomplete relief of glycolysis inhibition. Crossover analysis of glycolytic intermediates indicated an inhibition at the 6-phosphofructokinase step. The depression of glucose utilization may be mediated by the increased level of glucose 6-phosphate, a potent inhibitor of hexokinase. An additional inhibitory effect of a metabolite of 2-deoxy-D-galactose at the 6-phosphofructokinase step was indicated by crossover analysis after reversal of Pi and ATP depressions in the presence of a high intracellular content of 2-deoxy-D-glactose 1-phosphate. The quantitative analysis of the metabolites of 2-deoxy-D-galactose demonstrated the predominance of the monophosphate and the negligible formation of UPD derivatives of this sugar analog in AS-30D hepatoma cells. This provides a system for the investigation of a galactose analog as a phosphate-trapping agent in the virtual absence of uridylate trapping.