From a36fe4c39043d71e5cf64fe03ad5918079a5e009 Mon Sep 17 00:00:00 2001 From: Kyle Belanger Date: Sun, 11 Sep 2022 16:19:11 -0400 Subject: [PATCH] update chapter 2 and index --- chapter2.qmd | 61 +++++++++++++++++---------- extras/Draft Research Questions.docx | Bin 12749 -> 0 bytes index.qmd | 26 +++--------- references.bib | 14 ++++++ 4 files changed, 60 insertions(+), 41 deletions(-) delete mode 100644 extras/Draft Research Questions.docx diff --git a/chapter2.qmd b/chapter2.qmd index 49d6bcf..fdf2354 100644 --- a/chapter2.qmd +++ b/chapter2.qmd @@ -112,31 +112,48 @@ computed by aggregating the errors across the entire validation data set ### Machine Learning in the Clinical Laboratory - + -| **Author and Year** | **Objective and Machine Learning Task** | **Best Model** | **Major Themes** | -|-------------|---------------------------------|-------------|-------------| -| Azarkhish (2012) | Predict iron deficiency anemia and serum iron levels from CBC indices | Neural Network | Prediction | - -Cao (2012) \| - - Triage manual review for urinalysis samples | - - Tree-based | Automation | - -| - -Yang (2013) \| - - Predict normal reference ranges of ESR for various laboratories based on geographic and other clinical features | - - Neural Network | - - Interpretation | +| **Author and Year** | **Objective and Machine Learning Task** | **Best Model** | **Major Themes** | +|---------------|-----------------------------|---------------|---------------| +| Azarkhish (2012) | Predict iron deficiency anemia and serum iron levels from CBC indices | Neural Network | Prediction | +| Cao (2012) | Triage manual review for urinalysis samples | Tree-based | Automation | +| Yang (2013) | Predict normal reference ranges of ESR for various laboratories based on geographic and other clinical features | Neural Network | Interpretation | : Table 1. Summary of characteristics of machine learning algorithms [@rabbani2022]. -### + -#### +## Reflex Testing + +The laboratory diagnosis of thyroid dysfunction relies on the +measurement of circulating concentrations of thyrotropin (TSH), free +thyroxine (fT4), and, in some cases, free triiodothyronine (fT3). TSH +measurement is generally regarded as the most sensitive initial +laboratory test for screening individuals for thyroid hormone +abnormalities [@woodmansee2018]. TSH and fT4 have a complex, nonlinear +relationship, such that small changes in fT4 result in relatively large +changes in TSH [@plebani2020]. Many clinicians and laboratories check +TSH alone as the initial test for thyroid problems and then only add a +Free T4 measurement if the TSH is abnormal (outside the laboratory +normal reference range), this is known as reflex testing +[@woodmansee2018]. Reflex testing became possible with the advent of +laboratory information systems (LIS) that were sufficiently flexible to +permit modification of existing test requests at various stages of the +analytical process [@srivastava2010]. Reflex testing is widely used, the +major aim being to optimize the use of laboratory tests. However the +common practice of reflex testing relies simply on hard coded rules that +allow no flexibility. For instance in the case of TSH, free T4 will be +added to the patient order whenever the value falls outside of the +established laboratory reference range. This bring into the fold the +issue that the thresholds used to trigger reflex addition of tests vary +widely. In a study by Murphy he found the hypocalcaemic threshold to +trigger magnesium measurement varied from 1.50 mmol/L up to 2.20 mmol/L +[-@murphy2021]. Even allowing for differences in the nature, size and +staffing of hospital laboratories, and populations served, the extent of +the observed variation invites scrutiny [@murphy2021]. + + + + diff --git a/extras/Draft Research Questions.docx b/extras/Draft Research Questions.docx deleted file mode 100644 index 1febaf6d8952d45da22ad5378170b8d6b855b1d8..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12749 zcmeHtg&06;zr0Dum74XGt!XX|WY z>#V2jVQ=E3!{}~fO_B=@Ns|qL1dso}|#a{yA6I09B-JDY@x~T9>|S0 z!8gB$2xpfSy%q+wKDTdjv*c5-un+W-j4gSMy=Dm~l2pRXn&F}@?al{slI>D7 z;?2jM%}DMa5F?4Di{AD@xwas;q!nQr8=+2qt(xjl6QHYT)mB%;Dzrhezb~0U)ATvU z%1!ncce9llS1tQtJLZ?r#c+f{M$3deq3I^9zku^?2%Wus`8);$KclN}y+EqF?DqaCSNm$S zRB_kymqKlE7)4O?-d~MB34$f-?x5 zTK+HA#lKCxEUpu*mI&`p1D^uN+Y}Z$aX_+6Mn4vD=3l+ml8{DUoU@#Le&U;(gVfnK z_%Jjv8UMr6DFf)TmY{Qnm!yIi-Uc^wr`x6V(CQ9I3~tS5ai6i@KuF)YF?|{&m!KUC zjL^UgAH#!<{TZ4v@(q2PPV{EG@Qno-?bwtNMJ*`PL1p$f#g{ERm1TOyQe4aHRSCaX zdkA66D6TKOsbF<78$(R=_mvu*ZsmjcCe|oR+G~0|Yi1_Oj99}mc)YXL@dHm#M`2G` zFg;ujTo}`Xx2ZOo=JRg&4z3{QDXB)C-nt!rhK|rB*h&4je$=){5W;|a8lV6G0>Ens zH#SZl7=FJ2IXzx{uUkwnkAGe1~_;@$uNsNfO5i_zZ&Xh~Jd zZjl?M9eeKO{azhEMVxk@L~ws+gT*9(VNIrC&p}9uJPc8fg!b)8R_>ThF{#B zR!oCUqoB9pglUrNL$(!;+Xgn~s_`gX`r_D1zc4Jh*o%H&~< zO(;F?9D^T`wV#ad0#HQ*Op%ZRxp7Gh8G}>!gShU!mS?jD^8av^i4gh62 znyzo>+9HQ-WDs>t25Jr^Eu@kmaScx33Zk8HN!F7@osJ5mbjrFWV>r8PwU@RO;vPA? 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In most current clinical laboratories, reflex testing is performed with a 'hard' cutoff, using a specifically -established range with no means of flexibility [@murphy2021]. - - - -This study will examine the use of Machine learning to develop -algorithms to allow flexibility for automatic reflex testing in clinical -chemistry. The goal is to fill the gap between hard coded reflex testing -and fully manual reflective testing using machine learning algorithms. - - +established range with no means of flexibility [@murphy2021]. This study +will examine the use of Machine learning to develop algorithms to allow +flexibility for automatic reflex testing in clinical chemistry. The goal +is to fill the gap between hard coded reflex testing and fully manual +reflective testing using machine learning algorithms. ## Statement of Problem @@ -77,15 +72,8 @@ widened to decrease the number of unnecessary Free T4 measurements performed. This reduction would reduce overall costs to the medical system without likely causing negative consequences of missing the detection of people with thyroid hormone abnormalities -[@whitneyw.woodmansee2018]. - - - -The reduction in testing aside, the hard-coded rule still exists. -Additionally, machine learning may predict missing values in a patient's -record or even suggest further testing on a particular patient. In a -study at Massachusetts General hospital, researchers predicted ferritin -results based on already run laboratory testing [@charnaalbert2020]. +[@woodmansee2018]. Even with the potential reduction in testing the +hard-coded reflex rule still exists. ## Purposed Study Set Up diff --git a/references.bib b/references.bib index 5535ea2..08815d3 100644 --- a/references.bib +++ b/references.bib @@ -214,3 +214,17 @@ PMID: 33045173} doi = {10.1214/ss/1009213726}, url = {http://dx.doi.org/10.1214/ss/1009213726} } + +@article{woodmansee2018, + title = {Determination of optimal TSH ranges for reflex Free T4 testing}, + author = {Woodmansee, Whitney W.}, + year = {2018}, + month = {02}, + date = {2018-02}, + journal = {Clinical Thyroidology for the Public}, + pages = {3--4}, + volume = {11}, + number = {2}, + url = {https://www.thyroid.org/patient-thyroid-information/ct-for-patients/february-2018/vol-11-issue-2-p-3-4/}, + langid = {canadian} +}