104 Matching Annotations
  1. Apr 2021
    1. where hereditary CRC syndromes have been excluded

      molecularly excluded?

      We see these patients and follow up had been one off at 50 but now they get 5 yearly until 50

      standard surveillance - scope every year for 3 years?

    2. We recommend that deficient MMR tumours without hypermethylation/BRAF mutation and without a germline pathogenic variant in MMR genes should undergo somatic tumour testing with a CRC gene panel

      Zosia's point to discuss

      Small number of cases. ? pickup rate

      ? funding source

      ? needed for amsterdam

    3. We recommend screening for H elicobacter pylori in patients with LS and subsequent eradication therapy if indicated. (GRADE of evidence: low; Strength of recommendation: strong)

      explore in audit ? engagement with the GP (subgroup? i.e. males?)

    4. We recommend that gastric, small bowel, or pancreatic surveillance in LS patients is only performed in the context of a clinical trial

      Should we be identifying these trials and offering recruitment locally? maybe others already do?

      now not done, previously had been done over 50.

      something for the audit - to exclude some individuals

    5. We recommend that age of onset of surveillance colonoscopy should be stratified according to the LS-associated gene. We recommend colonoscopy from age 25 years for MLH1 and MSH2 mutation carriers and 35 years for MSH6 and PMS2 mutation carriers

      as per lynch specific CGG guidelines

    6. all people when first diagnosed with CRC

      I thought we were only doing <60/65 years. Mol path showed the marked drop off in pick-up above this age with huge increase in work load

      Scottish guideline in place. done under 70 but maybe all is getting done anyway. future clarity likely

    7. moderate their consumption

      what would you describe as moderate 2 meals a week? 1/2 processed meat portions a week?

      reduce it regardless or <500g/week

      Lifestyle discussion day

    8. A relative threshold for genetic testing was agreed for people with a 10% or greater probability of having a germline pathogenic variant in a cancer susceptibility gene in accordance with previous UK guidelines.3 4

      Target yield

    9. We recommend that patients with a moderate familial CRC risk should have a one-off colonoscopy at age 55 years. (GRADE of evidence: moderate; Strength of recommendation: strong)

      No longer mod and high-mod just moderate.

    10. We recommend that the moderate risk category of family history of CRC (FHCC) is the minimum threshold for referral from primary care (GRADE of evidence: very low; Strength of recommendation: strong

      this does not happen in practice, due to population risk referrals. Audit from the past - FHx Questions can modify risk up and down. WHen do you put in the extra effort to confirm? Bounce referrals with letters? Where can we direct GPs to for accurate referral info?

    11. In the interim clinicians may consider 150 mg aspirin in the context of LS outside of a clinical trial, with 300 mg doses in those with a BMI above 25 kg/m2.

      aspirin

    12. but not those with dMMR non-LS

      unpack - is this stating that, using somatic testing to find a second hit, you can reduce the risk profile of FDRs for CRC with dMRR.

    13. In a study by Bapat et al of 3143 CRC patients, dMMR tumours were associated with increasing numbers of FDRs with CRC (p=0.002); this association disappeared, however, when dMMR cases meeting Amsterdam criteria were removed from the analysis

      OR 4 when 3 FDRs and dMMR - if disappears then after removing Amsterdam. ? threshold for ISD request to push over the line

    14. across at least two generations

      I assume the flexibility of the guidelines would allow for clinical decision when 3 FDRs are all on one generation

    15. Moderate risk FHCC:One FDR diagnosed with CRC under 50 years, orTwo FDRs (in first degree kinship) diagnosed with CRC at any age, of whom the patient under assessment is an FDR of at least one affected individual.

      moderate

    16. Familial clusters (or aggregations) are of affected family members with CRC who are FDRs of each other.

      clusters

    17. metachronous adenomas

      must have more than one colonoscopy or if they are of differing size to suggest metachronous?

    18. one or two should be offered an index colonoscopic screening

      point for discussion

    19. an LS constitutional panel test

      Would the practice be better to do the whole CRC panel and extend from lynch if lynch analysis is negative?

    20. FIT (faecal immunochemical test), MR or CT colonography

      Is this likely to change? studies on going, improved tech?

    21. improve patient experience

      input from our visiting colleagues about sedation options for nervous patients

    22. a cluster of 3× FDRs with CRC across >1 generation

      cluster = connected sequence of 3 FDR

    23. surveillance recommendations

      surveillance recommendations

    24. 80% agreement, and consensus of over 70% was accepted if the GDG felt a statement was required for clinical practice

      thresholds for consensus statements

    25. UKCGG steering group, ACPGBI, BSG, the European Hereditary Tumour Group (EHTG) and the European Society of Gastrointestinal Endoscopy (ESGE) to participate in the modified Delphi process. We included additional patient and public involvement in the Delphi process by inviting participants through the national charities Bowel Cancer UK and Lynch Syndrome UK

      participants

    26. modified in cases where objective risk assessment was difficult to attain, and clinicians had sufficient clinical suspicion of risk

      flexibility

  2. Sep 2020
  3. Feb 2020
    1. The parametervector for a classcis~θc={θc1,θc2,...,θcn}

      needed for CNB formula

    2. However, the class probabilities tend to beoverpowered by the combination of word probabilities,so we use a uniform prior estimate for simplicity

      what is the uniform prior estimate for the class?

  4. Dec 2019
    1. ages 2–10 y
    2. average stature
    3. height velocity
    4. 0.8 cm/mo (10 cm/y)
    5. 1 y
    6. median height velocity
    7. 1 y of life
    8. infants
    9. ≈1.7 cm/mo (20 cm/y)
    10. ≈3.7 cm/mo (44 cm/y)
    11. shortly after birth
    12. average stature
    13. median height velocity
    14. average stature
    15. puberty
    16. infancy
    17. height velocity
    18. average stature
    19. height velocity
    20. average stature
    21. height
    22. average stature
    23. height
    24. 48.5 ± 0.1; n = 595
    25. 47.4 ± 0.2 cm; n = 242

      value, sd, n

    26. birth length
    27. average stature
    28. mean birth length
    29. average stature
    30. Height
    31. average-stature
    32. median weight-for-age
    33. average stature
    34. 5th
  5. Nov 2019
    1. Ref. [44], and for BioNLP, in Ref. [45].

      useful for me

    2. Add handling of negation and hedging

      key

    3. (or the entire document)

      hopefully

    4. affects recall

      halved

    5. ActualRelatedNot RelatedPredictedRelated2010Not Related2731Precision = 67%Recall = 43%

      i am not sure that this is an improvement if you are losing 57% of your recall! depends of what you value more, novel relationship discover or accuracy

    6. define a set of selected features for each one.

      what features? PO? symantics? entity patterns?

    7. OMIM MorbidMap

      not very surprising due to the size of omim and the inevitable gaps in the data

    8. The simple NER approach that we applied to medical records, leveraging Uruguayan terminology dictionaries from SNOMED CT, produced the results listed in Table 3 for the domains of disease and finding entities. A physician manually evaluated the expected vs. found entities for each medical record, considering an entity as correctly identified when its recognized name was exactly or nearly exactly as expected. We obtained a precision of 94% when counting entity repetitions (more than one mention), and 87% leaving repetitions apart

      not mentioning negation which is important

    9. Fig. 5. Structure of the mini ontology: A graph with nodes representing entities and edges representing relations between them.

      i note there is no connection between pubmed and phenotype which suggests that the genotype-phenotype is omim based. OMIM has quite shallow phenotyping as i am aware

    10. hipertensión arterial (English arterial hypertension), the dictionary-based approach correctly recognizes hipertensión arterial disease in Spanish, but the CoreNLP node recognized both hipertensión (English hypertension) and arterial only individually.

      sounds like a language incompatibility as arterial hypertension is not a term used in english medicine

    11. Since an actual set of medical records in Spanish was not available for research, we manually transcribed 109 clinical notes with physician observations, from actual patient cases, used for medical education.

      this type of case will be succinct and cherry picked for educational purposes - will need real life validation

    12. The knowledge base can be queried in two ways: 1) starting from the medical record, and leading to related entities (like genes); or 2) starting from genes of interest (previously obtained from patients genome or exome analysis), and leading to related diseases and substances

      This all sounds very useful as an approach to a new case clincally

    13. Mini Ontology, is permanently updated from a corpus that contains novel articles, on a daily basis

      contemperaneous

    14. {relation_type, entitity_1, entity_2}.

      must predefine the relations

    15. Wu et al. [22] compare alternatives based on word embeddings to improve NER results in BioNLP, against existent proposals based on CRF, MaxEnt, and SVM. Chiu et al. [23] devise guidelines for good word2vec based embeddings, both CBOW and skip-gram, working on PubMed and the PMC corpus. For auxiliary tasks, these authors use GeniaSS as a sentence splitter and NLTK [24] for word tokenizing

      The challenges of word embedding and text processing in a specialised domain

    16. GeniaSS as a sentence splitter

      Will be useful to add to my pipeline

    17. Genia Tagger [13] has been frequently used both for part of speech tagging and named entity recognition (NER) in the BioNLP domain. For Spanish medical documents, Genia Tagger has been used in conjunction with Freeling [14] for entity recognition and automatic annotation [15]

      NER annotations

    18. HGVS

      genomic variant ontolgy

    19. OMIM

      genotype phenotype ontology

    20. SNOMED CT,

      medical language ontology - very large

    21. The goal of this work is to provide tools for the medical geneticist that optimize his/her access to the latest research pertaining to a specific patient (or to specific genomic information)

      SUggesting the reverse and forward genetics genotype - phenotype (need high prob variants) phenotype - genotype (need good phenotyping) approaches

    22. This makes attempts to become properly acquainted with the latest findings that could be relevant to a specific patient particularly challenging

      Impossible?

    23. Are there known substance/drug interactions?;

      less relevant in clinical genetics

    24. Is this variant pathogenic?; With which phenotypes/diseases is this variant associated?;

      All relevant

    25. The literature requires reviewing in such a way that will allow the gathering of the latest findings

      Case reports sequencing cohorts case series reviews and meta-analysis contemporaneous literature is key for rare conditions

    26. A patient genome can be sequenced in a few hours or even minutes [1],

      Not much use without the analysis that supports any interpretation

    27. PubMed abstracts

      Key advantage we should have with full text analysis

  6. Jun 2019
  7. May 2019
  8. Apr 2019
    1. screening, surveillance, and interventional measures,

      will need to consider locally available options for all of these

    2. excess toxicities withparticular cytotoxic therapies

      indication for genetic testing

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