A similar procedure was followed to develop the predictor for resistance by comparing patients with extensive residual disease (RCB-III) after neoadjuvant chemotherapy treatment versus remaining patients. The final predictor of extensive residual disease used 73 and 54 probe sets for ER+/HER2−and ER−/HER2− subsets respectively (
Residual Cancer
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Specimens were retrieved via endoscopic biopsy at the time of diagnosis, screening laparoscopy or at the time of surgical resection at the Walter C Mackenzie Health Sciences Centre or Royal Alexandra Hospital. Normal biopsies were obtained from gastric mucosa greater than 5 cm away from the cancerous lesion or associated gastritis. The initial study protocol retrieved two tissue biopsies for permanent pathology, however, following interim review four biopsies were retrieved thereafter. The presence of cancer in specimens was confirmed by a gastrointestinal pathologist. In the absence of cancer, clinical formalin-fixed paraffin-embedded pathology blocks were retrieved when available. In clinical samples with treatment effect, residual cancer cells were detected using anti-pan cytokeratin (Abcam, clone C-11, ab7753) IHC staining followed by the manual assembly of tissue microarray (TMA) blocks with 4mm cores of regions containing residual tumour.
Our primary outcome for all patients was the difference in expression of selected biomarkers between normal and cancer tissue. In the subgroup of patients receiving neoadjuvant chemotherapy, our primary outcome was the difference in expression between tumour treatment response and incomplete treatment response. We also evaluated the difference in expression of biomarkers in paired samples before and after chemotherapy treatment.
Treatment response was retrieved from clinical pathology reports. The Tumour Regression Score was graded according to the College of American Pathologists and National Comprehensive Cancer Network protocol on a 4-point scale (0 = Complete response, 1 = near complete response, 2 = partial response, 3 = poor or no response)[40 (link)]. In accordance with prior studies, treatment response was expressed as a binary variable consisting of response and incomplete response categories[12 (link)]. Responsive tumours included complete and near-complete responses, whereas incomplete responses included partial, and poor no response. Patients who progressed to metastasis while receiving neoadjuvant treatment were classified as an incomplete response.
The primary tumor response was assessed according to the iRECIST criteria[19 (link)]. Acute toxicity was graded according to the NCI Common Terminology Criteria for Adverse Events 4.0[20 (link)]. After every one or two cycles of neoadjuvant immunotherapy, all patients had complete assessment including computed tomography (CT), magnetic resonance imaging, PET-CT, blood counts, renal biochemistry, hepatobiliary function, thyroid function, cardiac function, and tumor markers (carcinoembryonic antigen and carbohydrate antigen 19-9) to evaluate the general condition and treatment response. The determination of clinical complete response (cCR) was based on Memorial Sloan Kettering Cancer Center standard[21 (link)] and International Watch & Wait Database[22 (link)]. The cCR was defined as no evidence of residual tumor determined by rectum MRI, abdomen/pelvis CT and chest CT, endoscopic physical examination, nomarl CEA and/or digital rectal exam. Pathological staging was based on the 8th edition of the American Joint Committee on Cancer TNM staging system[23 (link)]. Post-treatment response was assessed by NCCN grading: 0 = complete response (ypCR) with no detectable cancer cells; 1 = major response with few residual cancer cells; 2 = partial response; 3 = no or very little response[24 (link)].
Postoperative complications were classified according to the Clavien–Dindo classification[24 (link)].
Schematic overview of the algorithm.
ICD-10: C349X (lung cancer recurrence diagnosis);
ICD-10: C76*-C79* or C34xM (metastasis diagnosis) and no new primary cancer registered after the conclusion of primary lung cancer treatment;
SNOMED morphology codes M8*-M9* and 7 (malignant recurrence) in the fifth digit;
SNOMED morphology codes M8*-M9* and 4 (direct spread to surrounding tissue) or 6 (malignant metastasis) in the fifth digit and a morphology similar to a morphology code registered within 90 days of the primary lung cancer diagnosis date or date of lung cancer surgery;
Radiotherapy or chemotherapy procedure codes combined with a diagnosis code indicating lung cancer (ICD-10: C34*);
Radiotherapy or chemotherapy procedure codes combined with a diagnosis code indicating metastases (ICD-10: C76*-C79* or C34xM) and no new primary cancer registered after the conclusion of primary lung cancer treatment.
biopsy samples included assessments of stromal TILs and the nuclear and
histologic grades of each breast carcinoma sample. The levels of TILs are
expressed as percentages, as described by the International TIL Working
Group.17 (link) The residual cancer burden (RCB) score,
Miller-Payne grade, residual tumor size, and TILs of the surgical specimens
were determined.18 (link),19 (link) The tumor bed area in samples of patients who
achieved pCR group was marked and collected for high-throughput NGS.
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