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.     

The economics of clinical genetics services. III. Cognitive genetics services are not self-supporting.

We investigated the amount of time required to provide, and the charges and reimbursement for, cognitive genetics services in four clinical settings. In a prenatal diagnostic center, a mean of 3 h/couple was required to provide counseling and follow-up services with a mean charge of $30/h and collection of $27/h. Only 49% of personnel costs were covered by income from patient charges. In a genetics clinic in a private specialty hospital, 5.5 and 2.75 h were required to provide cognitive services to each new and follow-up family, respectively. The mean charge for each new family was $25/h and for follow-up families $13/h. The amount collected was less than 25% of that charged. In a pediatric genetics clinic in a large teaching hospital, new families required a mean of 4 h and were charged $28/h; follow-up families also required a mean of 4 h, and were charged $15/h. Only 55% of the amounts charged were collected. Income from patient charges covered only 69% of personnel costs. In a genetics outreach setting, 5 and 4.5 h were required to serve new and follow-up families, respectively. Charges were $25/h and $12/h, and no monies were collected. In all clinic settings, less than one-half of the total service time was that of a physician, and more than one-half of the service time occurred before and after the clinic visit. In no clinic setting were cognitive genetics services self-supporting. Means to improve the financial base of cognitive genetics services include improving collections, increasing charges, developing fee schedules, providing services more efficiently, and seeking state, federal, and foundation support for services.     

Anthecology ofSchrankia nuttallii (Mimosaceae) on the tallgrass prairie

Schrankia nuttalii flowers through late spring on the tallgrass prairie. Although each stem produces an average of 26 capitate inflorescences only 12% of those inflorescences will open each day to disperse and receive polyads. Each inflorescence may live up to 48 hours but anthers abscise by late afternoon on the first day and the filaments change color and lose their scent. The 78–93 florets comprising each inflorescence open synchronously before dawn or during early morning hours. First day inflorescences ofS. nuttallii are herkogamous and fragrant. They are nectarless. Bombyliid flies and male bees are infrequent floral foragers so the major pollinators include female bees representing five families;Anthophoridae, Apidae, Colletidae, Halictidae, andMegachilidae. All foraging insects ignore second day inflorescences although stigmas are still receptive. Although 97% of all bees collected onS. nuttallii carrySchrankia polyads in their scopae or corbiculae 59% also carry the pollen/pollinaria of one or more coblooming angiosperms. At least 98% of all bees carrying mixed pollen loads incorporate the pollen/pollinaria of one or more nectariferous taxa (e.g.Asclepias spp.,Asteraceae, Convolvulaceae, Delphinium spec., etc.). Species of halictid bees are more likely to carry pure loads ofS. nuttallii polyads (70%) than bees of the four remaining families. Due to the nectarless florets and high degree of polylectic foraging bee-pollination inS. nuttallii converges more closely with the pollination systems of some AustralianAcacia spp. than with most other xeric/tropical genera of mimosoids studied in the western hemisphere.     

Pressure-Induced Alterations in the Protein Pattern of the Thermophilic Archaebacterium Methanococcus thermolithotrophicus

Elevated hydrostatic pressure has been shown to affect the growth rate of the thermophilic methanobacterium Methanococcus thermolithotrophicus without extending its temperature range of viability. Analysis of the cell inventory after ≈ 10 h of incubation at 65°C and 50 MPa (applying high-pressure liquid chromatography and two-dimensional gel electrophoresis) proved that pressure induces alterations in the protein pattern and the amino acid composition of the total cell hydrolysate. Gels showed that after pressurization a series of (basic) proteins with a molecular mass in the range of 38 and 70 kilodaltons occurs which is not detectable in cells grown at normal atmospheric pressure. The question of whether the observed alterations are caused by the perturbation of the balance of protein synthesis and turnover or by the pressure-induced synthesis of compounds analogous to heat shock proteins remains unanswered.     

Endoderm-secreted factor stimulates growth of embryonal carcinoma stem cells

Summary Stem cells of the embryonal carcinoma cell line called H6 can be induced to differnetiate to endoderm-like cells by retinoic acid (3×10⁻⁶ M). We have detected a diffusible and stable factor which is secreted by H6 endoderm-like cells and stimulates the growth of H6 stem cells. The stimulation by the endoderm-like cells is considereably greater than that by mouse fibroblasts or H6 stem cells themselves. No reciprocal stimulation of endoderm-like cells by stem cells occurs. Part but not all of the stimulation might be due to extracellular matrix proteins or to insulin-like growth factor type 2, each of which also stimulates the growth of H6 stem cells. Insulin causes no such stimulation. This work was supported by research rant no. CA-16754 from the National Cancer Institute to J. W. L. E. L. G. was supported by an American Heart Association Medical Student Research Award. Editor's Statement This paper presents a good example of cooperativity between undifferentiated teratoma stem cells and differentiated parietal endoderm-derived countrparts in terms of growth support. It raises the interesting question of the relationship between factors produced by paprietal and visceral endoderm cells. Gordon H. Sato     

Applications of fluorochromes to pollen biology. II. The DNA probes ethidium bromide and Hoechst 33258 in conjunction with the callose-specific aniline blue fluorochrome

Techniques are described for detection of pollen grain and pollen tube nuclei using the fluorescent DNA probes ethidium bromide or Hoechst 33258, in conjunction with the aniline blue fluorochrome sirofluor, which stains the callose component of pollen tube walls and plugs. The DNA probes, which may be used either as vital stains or following fixation, permit discrimination between vegetative and generative or sperm nuclei. Double staining with sirofluor allows location of nuclei within pollen tubes grown in vitro, and when used after pollination enables the viewer to discriminate between nuclei within the pollen tube vs. nuclei of the pistil tissue.