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.     

Photoperiod control of birth timing in the harbour seal (Phoca vitulina)

The harbour seal ( Phoca vitulina ) has delayed implantation, precise annual birth timing, and significant latitudinal variation in birth timing. The birth timing patterns of four distinct groups of seals, including colonies of P. v. vitulina and colonies and captive individuals of P. v. richardsi , were examined using population-based photoperiod analysis to assess the role of photoperiod in setting annual birth timing. This analysis simultaneously determined the time, relative to birth, at which photoperiod response was likely to occur and the critical photoperiod.
Despite marked differences in birth timing patterns, a high level of agreement was found among groups for the timing of photoperiod response. The two subspecies, however, demonstrated significantly divergent critical photoperiods. Eastern Atlantic harbour seals were exposed to a common critical photoperiod of 11.7 h/day on the 268th pre-partum day. Wild Pacific harbour seals were exposed to 14.3 h/day on the 283rd pre-partum day. These times corresponded to the estimated occurrence of blastocyst implantation.
Using the above information, three small captive populations were subjected to artificially prolonged photoperiods during the period of embryonic diapause to test whether subsequent birth timing could be delayed. Technical difficulties invalidated results at two sites. At the third and largest colony, the mean pupping date of six individuals was significantly delayed by 10.7days.
The precision and latitudinal variation of annual birth timing in the harbour seal are due to a response to photoperiod which occurs immediately prior to blastocyst implantation. The critical photoperiod, however, is divergent among subspecies and, thus, has probably evolved allowing seasonal adaptation. Similar environmental signalling has been described for California sea lions and northern fur seals and represents the likely timing mechanism for most pinniped species.     

The influence of postnatal nutritional deprivation on the phospholipid content of developing rat lung.

It has been previously reported that fasting may result in decreased lung surfactant production. In order to investigate this relationship and the role of nutrition in lung phospholipid synthesis, 21-day-old rats were exposed for 60 h to one of five dietary regimens: standard rat chow (controls), fasting, pure glucose, pure fat, or pure protein. After the period of fasting there was a 33% decrease in lung protein content, but there was no change in DNA content. Exposure to any of the experimental diets resulted in a decrease in tissue total phospholipid and phosphatidylcholine content per lung, but not per unit lung protein. Similarly lung lavage phospholipid and phosphatidylcholine content was decreased by 25% after fasting when expressed per lung or per unit DNA, but not per unit protein. Pulmonary cholinephosphotransferase (EC 2.7.8.2) activity was decreased in the fasted animals and those fed the protein diet, but not in the glucose or fat-fed animals. The activities of acetyl-CoA carboxylase (EC 6.4.1.2) and microsomal fatty acid elongation were decreased in all the experimental groups except for the glucose-fed group. It is concluded that fasting results in a decrease in lung cell size but not in lung cell number. Total phospholipid and phosphatidylcholine content in lung tissue and lung lavage is decreased per cell but not per unit cell mass.     

Human hypoxanthine-guanine phosphoribosyltransferase

A mutant form of human hypoxanthine-guanine phosphoribosyltransferase (HPRTToronto) was isolated from erythrocytes of a male patient with gout due to a partial deficiency of enzyme activity. The tryptic peptides of HPRTToronto were mapped by reverse-phase high pressure liquid chromatography in an attempt to define the precise abnormality in its primary structure. Sequence analysis of the single aberrant peptide in HPRTToronto revealed an arginine to glycine amino acid substitution at position 50. A single nucleotide change in the codon for arginine 50 (CGA leads to GGA) could explain this substitution.     

The preparation and kinetics of lactate dehydrogenase attached to water-insoluble particles and sheets

1. The preparation of lactate dehydrogenase covalently attached to anion-exchange cellulose particles and sheets by use of a dichloro-sym-triazinyl dyestuff, Procion brilliant orange MGS, is described. 2. The stability and kinetic properties of these preparations were investigated. 3. An equation is derived to describe the change in concentration of a substrate when passed through a uniform bed of a substrate-inhibited enzyme. A number of theoretical curves are shown to illustrate the system. 4. A titrimetric assay for lactate dehydrogenase is described, and shown to be stoicheiometric over the range pH5.0-9.2. 5. The results are discussed in relation to previous work, and the effects of charged groups on the support, and of the diffusion film surrounding any particle in suspension, are treated qualitatively.