Prostate cancer risk group classification shifts between NCCN and EAU 2025

nccn_eau_2025.clj

(ns eau-nccn
  "Script to explore how different patient groups are classified
  according to the 2025 EAU Guidelines for Prostate Cancer and the
  NCCN.
  
  It starts by creating a list of all the permutations of the
  relevant markers, then applying the different classifications to each permutation.

  Finally, we calculate the % of each classification and the frequency
  of each EAU<>NCCN combination.

  The Sankey diagram can be accessed via this public link:
  https://sankeymatic.com/build/?i=PTAEFEDsBcFMCdQDEA2B7A7gZ1AI1tBrLJKAHJoAmsWANKCgJYDWso0AFo1gFwBQIUEOHCAymgCu8AMZsA2gEEAsgHkAqmQAqAXVCaAhvADmBPnzIBhC2VAAZTKHjdmoOQBZd4BWrsOnWZnMrGyR9ADdJeH1cFHkAVk9vZHDI6Nig61A1SAAzFKk0%2BQBGAA5En2y8iIKY2AybAAlGIw5HZ1cigGYAJnLQJpa2gLNLTNDqqNqOvoHW%2D0DRm0r8ydjXAE4%2B8dTa%2BqzclcKOopnmueczM0EATUlQaX1SLAJQfXIqWAByHGk0dHh6ExWOwuLwBGAeAAhCSUEzQUAAYgADHEAOzgkSY4QAOlxaEQb1%2B%2D1AOXxr1AWEYkCMa1QmH4gmhsJechOoBUnAQ5FgsiwlOgjBoiIAbEjhVcwAAiOQAKm0ktAAFtYI8cJK1M9XpAAJ6vRWSGAMWA5eFoMIISUMsBMuGuOWgUThKlGLASrKazn3NAweB%2DHD4dAYdhoe4SLDQNCKxgALzqgm1kVAlEY%2BiMUUV31eAAcsyqopBZLjsXxKbHQEHRUi%2BEJWpW%2BIrDEYqQxQEVutXHK320J4aUO7hQN0q7gjF7iQicpOpx3oPmsFnDCR4WQ%2BJAPuWux3WnEq0J5%2DppM7QKi4v38dRELuQbBla8O0SyQiSs%2BXx20AvD9BdUU%2BDlA6H4DCfRoCkNgkWxU8hCpDgEEYaAcl9RVQEkaBKWoABaKl7z%2BR91jw%2DC3w%2DODdXAtxTxQfQEwkU14AvV5qMjYDGGkDsACswwFHIEycJtIBwFchHY8NGC4khKH4jt4Fgc14GeNN9CzVoBNeaBoAPLgC0jLNYjgcMQ0gPMaGgPgKIDH4cMQZEkWs6yt0YahyDslomBaeFwJPDtSRgPJZApVV0OeJwcg7JgDP3Q9qVAcDu0cWAKIFc1SzYIoiivBsjEgETv1s0y4sgfRbwU3NDBwa4OyS1txSEIgznhNwcuiOKgJQCQ2CKvNSs8iQUBQLMpMPSlvVAMqhCzNB%2BUYIaA0wDsatc0B6qrXLevGuDJtIfQGP0FzSCvLBpBgwqGM8xhZPhfBSSk%2DspP0ZgxqpeFOj4ZrWpJfEG3hT5aGxT4Oz641GAAD1AT5fr3CRJyBkHfs5ZU0EnZ54TedZ%2Byi%2B9QCeoRKAx%2BsCDeZUYHWrBHlYbUPuYxyhCYYTFVwbbHl5YagA
  ")


(def perms
  (for [psa [9 15 21]
        biopsy [1 2]
        isup [1 2 3 4 5]
        t-stage [1 2 3 4 5 6]]
    {:psa psa
     :biopsy biopsy
     :isup isup
     :t-stage t-stage}))


(defn t
  "
  Map t-stage to an integer for easier math.
  "
  [k]
  (let [t-stages [:t1 :t2a :t2b :t2c :t3 :t4]
        t-mapping (zipmap t-stages [1 2 3 4 5 6])]
    (if (contains? t-mapping k)
      (k t-mapping)
      (throw (ex-info (str t " is not a valid t-stage! Valid stages " t-stages)
                      {:k k :t-mapping t-mapping})))))


(defn eau-low
  [{:keys [psa isup t-stage]}]
  (and
    (= isup 1)
    (< psa 10)
    (<= t-stage (t :t2a))))


(defn eau-favorable
  [{:keys [psa isup t-stage]}]
  (or
    (and
      (= isup 2)
      (< psa 10)
      (<= t-stage (t :t2b)))
    (and
      (= isup 1)
      (<= 10 psa 20)
      (<= t-stage (t :t2b)))
    (and
      (= isup 1)
      (< psa 10)
      (= t-stage (t :t2b)))))


(defn eau-unfavorable
  [{:keys [psa isup t-stage]}]
  (or
    (and
      (= isup 2)
      (<= 10 psa 20)
      (<= t-stage (t :t2b)))
    (and
      (= isup 3)
      (<= t-stage (t :t2b)))))


(defn eau-high
  [{:keys [psa isup t-stage]}]
  (or
    (> isup 3)
    (> psa 20)
    (>= t-stage (t :t2c))))


(defn eau
  [m]
  (cond
    (eau-high m)          :high-risk
    (eau-low m)           :low-risk
    (eau-favorable m)     :favorable
    (eau-unfavorable m)   :unfavorable
    :else :uncategorized))


(def eau-freqs
  (->> perms
       (map #(assoc % :eau (eau %)))
       (map :eau)
       (frequencies)))


(defn add-percent
  [perms freqs]
  (reduce
    (fn [p c]
      (update p c (fn [v] [v (str (int (* (/ v (count perms)) 100)) "%")])))
    freqs
    (keys freqs)))


;; ----------------------------------------------------------------------------


(defn nccn-low
  [{:keys [psa isup t-stage]}]
  (and
    (= isup 1)
    (< psa 10)
    (<= t-stage (t :t2a))))


(def nccn-intermediate-factors
  [(fn [{:keys [isup]}]
     (<= 2 isup 3))
   (fn [{:keys [psa]}]
     (<= 10 psa 20))
   (fn [{:keys [t-stage]}]
     (<= (t :t2b) t-stage (t :t2c)))])


(defn nccn-n-intermediate-risk-factors
  [perm]
  (->> nccn-intermediate-factors
       (map #(% perm))
       (filter true?)
       (count)))


(defn nccn-favorable
  [{:keys [isup biopsy] :as perm}]
  (and
    (= (nccn-n-intermediate-risk-factors perm) 1)
    (< isup 3)
    (= biopsy 1)))


(defn nccn-unfavorable
  [{:keys [isup biopsy] :as perm}]
  (or
    (<= 2 (nccn-n-intermediate-risk-factors perm) 3)
    (= isup 3)
    (= biopsy 2)))


(defn nccn-high
  [{:keys [psa isup t-stage]}]
  (or
    (> isup 3)
    (> psa 20)
    (>= t-stage (t :t3))))


(defn nccn
  [m]
  (cond
    (nccn-high m)         :high-risk
    (nccn-low m)          :low-risk
    (nccn-favorable m)    :favorable
    (nccn-unfavorable m)  :unfavorable
    :else :uncategorized))


(def nccn-freqs
  (->> perms
       (map #(assoc % :nccn (nccn %)))
       (map :nccn)
       (frequencies)))


(def percentages
  {:eau (add-percent perms eau-freqs)
   :nccn (add-percent perms nccn-freqs)
   :combinations (->> perms
                      (map #(assoc % :eau (eau %)))
                      (map #(assoc % :nccn (nccn %)))
                      ;; (filter #(and (= (:eau %) :favorable)
                      ;;               (= (:nccn %) :unfavorable))))
                      (map #(assoc % :same? (= (:eau %) (:nccn %))))
                      (map (fn [p] [(:eau p) (:nccn p)]))
                      (frequencies))})


percentages