Recommendations for Specimen and Therapy Selection in Colorectal Cancer.

INTRODUCTION: Next-generation sequencing has emerged as a clinical tool for the identification of actionable mutations to triage advanced colorectal cancer patients for targeted therapies. The literature is conflicted as to whether primaries or their metastases should be selected for sequencing. Some authors suggest that either site may be sequenced, whereas others recommend sequencing the primary, the metastasis, or even both tumors. Here, we address this issue head on with a meta-analysis and provide for the first time a set of sensible recommendations to make this determination. METHODS: From our own series, we include 43 tumors from 13 patients including 14 primaries, 10 regional lymph node metastases, 17 distant metastases, and two anastomotic recurrences sequenced using the 50 gene Ion AmpliSeq cancer NGS panel v2. RESULTS: Based on our new cohort and a meta-analysis, we found that ~ 77% of patient-matched primary-metastatic pairs have identical alterations in these 50 cancer-associated genes. CONCLUSIONS: Low tumor cellularity, tumor heterogeneity, clonal evolution, treatment status, sample quality, and/or size of the sequencing panel accounted for a proportion of the differential detection of mutations at primary and metastatic sites. The therapeutic implications of the most frequently discordant alterations (TP53, APC, PIK3CA, and SMAD4) are discussed. Our meta-analysis indicates that a subset of patients who fail initial therapy may benefit from sequencing of additional sites to identify new actionable genomic abnormalities not present in the initial analysis. Evidence-based recommendations are proposed.

Comparison of Large, Medium, and Small Solid Tumor Gene Panels for Detection of Clinically Actionable Mutations in Cancer.

BACKGROUND: Next-generation sequencing of gene panels has supplanted single-gene testing for cancer molecular diagnostics in many laboratories. Considerations for the optimal number of genes to assess in a panel depend on the purpose of the testing. OBJECTIVE: To address the optimal size for the identification of clinically actionable variants in different-sized solid tumor sequencing panels. PATIENTS AND METHODS: Sequencing results from 480 patients with a large, 315 gene, panel were compared against coverage of a medium, 161 gene, and small, 50 gene, panel. RESULTS: The large panel detected a total of 2072 sequence variants in 480 patient specimens; 61 (12.7%) contained variants for which there is therapy approved by the US Food and Drug Administration, 89 (18.5%) had variants associated with an off-label therapy, and 312 (65.0%) contained variants eligible for a genomically matched clinical trial. The small panel covered only 737 of the 2072 variants (35.5%) and somewhat fewer therapy-related variants (on-label 88.5%, off-label 60.7%). The medium-size panel included 1354 of the 2072 (65.3%) variants reported by the large panel. All 318 patients with a clinically actionable variant would have been identified by the medium panel. CONCLUSIONS: The results demonstrate that a carefully designed medium size gene panel is as effective as a large panel for the detection of clinically actionable variants and can be run by most molecular pathology laboratories.

Next-Generation Sequencing: A Novel Approach to Distinguish Multifocal Primary Lung Adenocarcinomas from Intrapulmonary Metastases.

Distinguishing between multiple lung primary tumors and intrapulmonary metastases is imperative for accurate staging. The American Joint Committee on Cancer (AJCC) criteria are routinely used for this purpose but can yield equivocal conclusions. This study evaluated whether next-generation sequencing (NGS) using the 50-gene AmpliSeq Cancer Hotspot Panel version 2 can help facilitate this distinction. NGS was performed on known primary-metastatic pairs (8 patients) and multiple lung adenocarcinomas (11 patients). Primary-metastatic pairs had high mutational concordance. Seven pairs shared mutations, and 1 was concordant for having no mutations. Driver mutations in KRAS (n = 4), EGFR (n = 2), and BRAF (n = 1) were always concordant. Multiple lung tumors from 3 patients were completely concordant and predicted by NGS to be intrapulmonary metastases, whereas 8 had completely discordant mutations and were predicted to be independent primary tumors. The NGS prediction correlated with the AJCC (eighth edition) prediction in all patients for whom the latter was unequivocal (8 of 11). Furthermore, it separated patients by overall survival. Patients with predicted multiple independent primary tumors by NGS had better survival than those with distant metastases (P = 0.016, log-rank test), whereas those with predicted intrapulmonary metastases had no difference (P = 0.527). With further validation, the 50-gene panel has the potential to serve as an adjunct to the AJCC criteria.

Immunologic parameters and viral infections in patients desensitized with intravenous immunoglobulin and rituximab.

Desensitization with IVIG and rituximab followed by transplantation with alemtuzumab or daclizumab induction is an effective clinical protocol. Here, we examined the effects of this protocol on immune cell number, T cell function by Cylex ImmuKnow®, CMV-specific CD8+ T cell (CMV-Tc) activity, total and viral-specific immunoglobulin levels and viral infections. In 17 highly HLA-sensitized (HS) patients who received desensitization, CD19+ cells were undetectable immediately after desensitization, while other immune cells were unchanged. No alteration in Cylex or CMV-Tc levels was seen. In separate 14 HS patients who were desensitized followed by transplantation, T cell numbers were near zero after alemtuzumab, while NK cell reduction was minimal. Early B cell recovery was not a risk for antibody-mediated rejection. Total IgG, IgM, and IgA remained in the normal range up to 12.6 months post-transplant, and CMV IgG level did not change. CMV-Tc activity was eliminated post-transplant in some patients, but recovered by 4 months post-transplant. None of them developed CMV infection. In conclusion, IVIG-rituximab-desensitization does not significantly alter T cell function pre-transplant, or reduce Ig levels below the normal range post-transplant. Although post-transplant induction therapy is associated with a transient depletion of viral-specific CD8+ memory cells, it does not increase risks for viral infections.

Cellular allo reactivity against paternal HLA antigens in normal multiparous females as detected by intracellular cytokine flow cytometry remains elevated over years despite diminution of anti-HLA antibody levels.

BACKGROUND: Sensitization to allo-antigens (Ags) resulting from previous transplants, blood transfusion or pregnancy (PG), is a significant obstacle to kidney transplantation and risk factor for antibody-mediated rejection (AMR). We have previously shown that allo-Ag-specific CD3 negative (-) cells as analyzed by cytokine flow cytometry (CFC) are elevated in many highly HLA-sensitized (HS) patients, but not most normal individuals. HS patients with high(+) CFC, especially to donor Ags, may be at high risk for AMR and may need additional pre-transplant desensitization. Here, we investigate allo-sensitization that results from paternal HLA (pHLA) Ag exposure in normal multiparous females and assess the utility of the CFC assay in detecting allo-Ag-specific immune cell activity. METHODS: Whole blood from 8 normal females with previous PG (pPG), 8 normal females without pPG and 5 normal males were incubated with irradiated normal peripheral blood mononuclear cells (PBMC). IFNgamma+/CD3- cells were enumerated and results expressed as a ratio against un-stimulated cells. RESULTS: 4/8 females with pPG showed elevated CFC reactivity against at least 1 PBMC tested (ratio 4.7+/-1.4), while the remaining 4 (0.76+/-0.42), 8 females without pPG (0.65+/-0.24) and 5 males (0.99+/-0.59) showed minimal reactivity. The reactivity against the same PBMC was fairly consistent over months and years. Anti-HLA antibody was detected in females with elevated CFC, but the levels as analyzed by ELISA did not correlate with CFC reactivity. Individuals with minimal reactivity consistently show negative anti-HLA antibody levels. Two females with pPG with elevated CFC (#1 and #2) showed high reactivity to PBMC from their husbands, one offspring and 3rd-party normals carrying antigenic pHLA-Ags (#1: 13.2, 9.4 and 22.9; #2: 8.2, 8.0 and 8.8-12.6, respectively). Antibody specificity for antigenic pHLA-Ags was found by Luminex in anti-HLA antibody(+) samples in these 2 females. CONCLUSIONS: 1) The CFC is a novel way to measure allo-specific CD3- cell responses and can detect allo-sensitization resulting from PG, 2) the CFC detects allo-specific memory cell activity as reactivity is consistent over years regardless of anti-HLA antibody levels, 3) high(+) CFC in normal multiparous females may explain increased risk for AMR in female HS patients, and 4) analysis of donor- or allo-specific CFC in multiparous females awaiting kidney transplant may identify those at risk for AMR.