1,580 Matching Annotations
  1. Oct 2024
    1. Disease: Von-Willebrand Disorder

      Patient 2 Variant(s):

      VWF NM_000552.5: c.4135C>T p.(Arg1379Cys) Exon 28 VWF NM_000552.5: c.4130C>T p.(Ala1377Val) Exon 28 VWF NM_000552.5: c.3797C>T p.(Pro1266Leu) Exon 28 VWF NM_000552.5: c.3835G>A p.(Val1279Ile) Exon 28

      Note: Pro1266Leu and Val1279Ile are in trans with Ala1377Val and Arg1379Cys

      Note2: MAF of Ala1377Val is present in Exome Variant Server (<0.01) and 1000 Genomes database (<0.02), designated as rare variant, typically found in indiv with African ethnicity

      Family: Relatives molecular analysis showed Arg1379 and Ala1377Val variants mentioned above were in cis

      Patient 2 Phenotype: Mild bleeding symptom Nearly normal VWF:Ag value, reduced VWF:RCo value slight loss of HMWM with smear decreased/slightly decreased proteolysis Slightly reduced RIPA VWFpp/VWF:Ag ratio shows increased VWF clearance VWF platelet levels reduced reduced rBpIba binding in VWF plasma VWF:GPIbM values slightly increased

      Note: Treated with desmopressin in case of minor surgeries or delivery

      Note 2: Slightly decreased RIPA may be explained by presence of 2B New York Variant (Pro1266Leu) that mitigates RIPA assay in 2M phenotype.

      In silico analysis available:

      I-Mutant 3.0 states decrease in A1 domain stability for both mutations (Ala1377Val = -0.91, Arg1379Cys = -1.36)

      PYMOL predicts Ala1377Val does not alter formation of hydrogen bonds with Arg1374 residue and water. Predicts substitution of ARG 1379 with a cysteine results in the loss of hydrogen bonds with Lys1407 and Lys1408, predicted change in secondary structure of A1 domain

      Ala1377Val was previously reported in 3 other patients Publications:

      Millar CM, Riddel AF, Mellors G, Yee TT. The spectrum of VWD type 2 phenotypes associated with A1 domain mutations posters. J Thromb Haemost 2009; 7: 531–2.

      Logsdon BA, Dai JY, Auer PL et al. A variational Bayes discrete mixture test for rare variant association. Genet Epidemiol 2014; 38: 21–30.

      Final note: Authors suggest patients' 2M phenotype is due to the presence of Ala1377Val and Arg1379Cys together to create synergistic effect. Though difficult to discern with this specific patient having two other variants in addition to the two mentioned above.

  2. Apr 2024
    1. In at least one other published version the first two items on this list are not peacock fans and Japanese screens but “ormolu garden gates, handleless cups”. The Oxford Book of Victorian Ghost Stories, ed. Michael Cox and R.A. Gilbert

      Ormolu is the gilding technique of applying finely ground, high-carat gold–mercury amalgam to an object of bronze, and for objects finished in this way. The mercury is driven off in a kiln leaving behind a gold coating. The French refer to this technique as "bronze doré"; in English, it is known as "gilt bronze". https://en.wikipedia.org/wiki/Ormolu?wprov=sfti1

  3. Jun 2023
  4. Oct 2022
    1. peacock fans, Japanese screens,

      In at least one other published version the first two items on this list are not peacock fans and Japanese screens but “ormolu garden gates, handleless cups”. The Oxford Book of Victorian Ghost Stories, ed. Michael Cox and R.A. Gilbert

      Ormolu is the gilding technique of applying finely ground, high-carat gold–mercury amalgam to an object of bronze, and for objects finished in this way. The mercury is driven off in a kiln leaving behind a gold coating. The French refer to this technique as "bronze doré"; in English, it is known as "gilt bronze". https://en.wikipedia.org/wiki/Ormolu?wprov=sfti1

  5. Aug 2022
    1. Lucas, C., Vogels, C. B. F., Yildirim, I., Rothman, J. E., Lu, P., Monteiro, V., Gelhausen, J. R., Campbell, M., Silva, J., Tabachikova, A., Peña-Hernandez, M. A., Muenker, M. C., Breban, M. I., Fauver, J. R., Mohanty, S., Huang, J., Shaw, A. C., Ko, A. I., Omer, S. B., … Iwasaki, A. (2021). Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity. Nature, 1–9. https://doi.org/10.1038/s41586-021-04085-y

    1. Kustin, T., Harel, N., Finkel, U., Perchik, S., Harari, S., Tahor, M., Caspi, I., Levy, R., Leschinsky, M., Dror, S. K., Bergerzon, G., Gadban, H., Gadban, F., Eliassian, E., Shimron, O., Saleh, L., Ben-Zvi, H., Amichay, D., Ben-Dor, A., … Stern, A. (2021). Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals. MedRxiv, 2021.04.06.21254882. https://doi.org/10.1101/2021.04.06.21254882

    1. Lauring, A. S., Tenforde, M. W., Chappell, J. D., Gaglani, M., Ginde, A. A., McNeal, T., Ghamande, S., Douin, D. J., Talbot, H. K., Casey, J. D., Mohr, N. M., Zepeski, A., Shapiro, N. I., Gibbs, K. W., Files, D. C., Hager, D. N., Shehu, A., Prekker, M. E., Erickson, H. L., … Self, W. H. (2022). Clinical severity of, and effectiveness of mRNA vaccines against, covid-19 from omicron, delta, and alpha SARS-CoV-2 variants in the United States: Prospective observational study. BMJ, 376, e069761. https://doi.org/10.1136/bmj-2021-069761

    1. Krause, P. R., Fleming, T. R., Peto, R., Longini, I. M., Figueroa, J. P., Sterne, J. A. C., Cravioto, A., Rees, H., Higgins, J. P. T., Boutron, I., Pan, H., Gruber, M. F., Arora, N., Kazi, F., Gaspar, R., Swaminathan, S., Ryan, M. J., & Henao-Restrepo, A.-M. (2021). Considerations in boosting COVID-19 vaccine immune responses. The Lancet, 4. https://doi.org/10.1016/S0140-6736(21)02046-8

    1. Sandra Ciesek. (2021, December 8). Unsere ersten Daten zur Neutralisation von Omicron versus Delta sind fertig: 2x Biontech, 2x Moderna, 1xAZ/1x Biontech nach 6 Monaten 0% Neutralisation bei Omicron, auch 3x Biontech 3 Monate nach Booster nur 25% NT versus 95% bei Delta. Bis zu 37fache Reduktion Delta vs. Omicron https://t.co/w0gHww26sg [Tweet]. @CiesekSandra. https://twitter.com/CiesekSandra/status/1468465347519041539

    1. Collier, A. Y., Brown, C. M., Mcmahan, K., Yu, J., Liu, J., Jacob-Dolan, C., Chandrashekar, A., Tierney, D., Ansel, J. L., Rowe, M., Sellers, D., Ahmad, K., Aguayo, R., Anioke, T., Gardner, S., Siamatu, M., Rivera, L. B., Hacker, M. R., Madoff, L. C., & Barouch, D. H. (2021). Immune Responses in Fully Vaccinated Individuals Following Breakthrough Infection with the SARS-CoV-2 Delta Variant in Provincetown, Massachusetts (p. 2021.10.18.21265113). https://doi.org/10.1101/2021.10.18.21265113

    1. Meng, B., Abdullahi, A., Ferreira, I. A. T. M., Goonawardane, N., Saito, A., Kimura, I., Yamasoba, D., Gerber, P. P., Fatihi, S., Rathore, S., Zepeda, S. K., Papa, G., Kemp, S. A., Ikeda, T., Toyoda, M., Tan, T. S., Kuramochi, J., Mitsunaga, S., Ueno, T., … Gupta, R. K. (2022). Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity. Nature, 1–1. https://doi.org/10.1038/s41586-022-04474-x

    1. Vöhringer, H. S., Sanderson, T., Sinnott, M., De Maio, N., Nguyen, T., Goater, R., Schwach, F., Harrison, I., Hellewell, J., Ariani, C. V., Gonçalves, S., Jackson, D. K., Johnston, I., Jung, A. W., Saint, C., Sillitoe, J., Suciu, M., Goldman, N., Panovska-Griffiths, J., … Gerstung, M. (2021). Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 1–11. https://doi.org/10.1038/s41586-021-04069-y

    1. Kai Kupferschmidt. (2021, December 10). “the severity profile of Omicron cases must be interpreted along with an understanding of its capacity to re-infect (and infect the vaccinated)“ This is what I have been trying to explain the last few days. As usual @nataliexdean does it better (and in color)! [Tweet]. @kakape. https://twitter.com/kakape/status/1469270407995867139

    1. Yaniv Erlich. (2021, December 8). Updated table of Omicron neuts studies with @Pfizer results (which did the worst job in terms of reporting raw data). Strong discrepancy between studies with live vs pseudo. Https://t.co/InQuWMAm4l [Tweet]. @erlichya. https://twitter.com/erlichya/status/1468580675007795204

    1. ReconfigBehSci. (2021, December 12). RT @ryan_landay: > A new diverse genome has appeared within the B.1.1.529 lineage that has all of the shared mutations of B.1.1.529, some o… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1470066521615605766

    1. ReconfigBehSci. (2021, November 26). vaccine equity has been a disaster, but I do wonder whether the exclusive focus on donations does the US/EU comparison justice. The EU allowed the export of huge numbers of EU produced doses at a time when the US did not (and EU itself was struggling to meet demand). [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1464255575416520749

    1. ReconfigBehSci. (2021, November 26). maybe this is a good moment to remind people that makers of mRNA vaccines have been extensively prepping for the possibility of new variants. Biontech/Pfizer have given a timeline of 100 days to the delivery of a retooled version of their vaccine [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1464225264523747359

    1. ReconfigBehSci. (2021, December 13). RT @DrEricDing: 11) Omicron is doubling every 1.6 days in UK 🇬🇧 according to @DrWilliamKu’s figure. That’s way faster growth than in South… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1470451594378502154

    1. John Burn-Murdoch. (2021, November 25). Five quick tweets on the new variant B.1.1.529 Caveat first: Data here is very preliminary, so everything could change. Nonetheless, better safe than sorry. 1) Based on the data we have, this variant is out-competing others far faster than Beta and even Delta did 🚩🚩 https://t.co/R2Ac4e4N6s [Tweet]. @jburnmurdoch. https://twitter.com/jburnmurdoch/status/1463956686075580421

    1. ReconfigBehSci. (2021, December 9). a rather worrying development- a (local) newspaper “fact checking” the new German health minister simply by interviewing a virologist who happens to have a different view. There’s simply no established “fact” as to the severity of omicron in children at this point in time [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1469037817481334786

  6. Jun 2022
    1. whole-genome sequencing (WGS) provides the highest possible subtyping resolution improving the surveillance, outbreak investigation, source attribution, and microbial population studies

      Purpose of WGS in population epidemiology

      1. Surveillance
      2. Outbreak Investigation
      3. Source attribution
      4. Microbial population
  7. May 2022
    1. DICER1 syndrome is an autosomal-dominant, pleiotropic, tumor-predisposition disorder arising from pathogenic germline variants in DICER1, which encodes an endoribonuclease integral to processing microRNAs (1).

      Gene Name: DICER1 PMCID: PMC5443331 PMID: 28323992 HGNCID: not found Inheritance Pattern: autosomal dominant Disease Entity: thyroid cancer and familial multinodular doiter Mutation: germline loss-of-function mutation Zygosity: not provided Variant: c.1870C>T; p.Arg624a, c.1870C>T; p.Arg624a, c.1870C>T; p.Arg624a, c.1870C>T; p.Arg624a, c.3726C>A; p.Tyr1242a, c.3675C>G; p.Tyr1225a, c.3675C>G; p.Tyr1225a Family Information: 145 individuals with a DICER1 germline mutation and 135 controls from 48 families Case: family members used; both males and females used and no significant differences seen among sex; ages range from 20-40 with carriers being significantly younger than controls; no significant differences seen among ethnicity but participants located from the US, UK, and Great Britain CasePresentingHPOs: thyroid cancer or MNG diagnosis common to those with a DICER! mutation but with no chemotherapy or radiation treatment yet CasePreviousTesting: tested levels of thyroid-stimulating hormone, thyroxine, thyroxine-binding globulin, and serum albumin; thyroid palpation; thyroid ultrasound; Sanger or next-generation sequencing assays gnomAD: n/a Mutation Type: missense

    1. Pathogenic germline variants in DICER1 underlie an autosomal dominant, pleiotropic tumor-predisposition disorder.

      gene name: DICER 1 PMID (PubMed ID): 33570641 HGNCID: n/a Inheritance Pattern: autosomal dominant Disease Entity: benign and malignant tumor mutation Mutation: somatic Zygosity: heterozygous Variant: n/a Family Information: n/a Case: people of all sexes, ages, ethnicities and races participated CasePresentingHPOs: individuals with DICER1-associated tumors or pathogenic germline DICER1 variants were recruited to participate CasePreviousTesting: n/a gnomAD: n/a

  8. Apr 2022
    1. Kai Kupferschmidt. (2021, December 1). @DirkBrockmann But these kinds of models do help put into context what it means when certain countries do or do not find the the variant. You can find a full explanation and a break-down of import risk in Europe by airport (and the people who did the work) here: Https://covid-19-mobility.org/reports/importrisk_omicron/ https://t.co/JXsYdmTnNP [Tweet]. @kakape. https://twitter.com/kakape/status/1466109304423993348

    2. Kai Kupferschmidt. (2021, December 1). @DirkBrockmann That percentage number tells you “how likely an infected passenger from South Africa or Botswana travels to each country and exits the airport there”. So: “0.9% in Germany means that out of 1000 such individuals, 9 are expected to have Germany as their final destination.” [Tweet]. @kakape. https://twitter.com/kakape/status/1466107478807097354

    1. 🇺🇦 Meaghan Kall. (2022, January 27). NEW: 🏴󠁧󠁢󠁥󠁮󠁧󠁿 Vaccine effectiveness (symptomatic infection) data for BA.2 {Omicron’s more infectious sister} NO difference in VE between Omicron (BA.1) and BA.2 Possibly even higher VE for BA.2 but estimates overlap See full thread 🧵 from @freja_kirsebom https://t.co/bJ7uCn2cGV [Tweet]. @kallmemeg. https://twitter.com/kallmemeg/status/1486821549458001927