Development and performance of a next generation sequencing (NGS) assay for monitoring of dd-cfDNA post solid organ transplantation.

The aim of this study was to evaluate the analytical performance of a novel NGS assay, intended for monitoring of donor-derived cell-free DNA (dd-cfDNA), and describe its validity in clinical plasma samples from kidney transplanted patients. Artificial and clinical samples with increasing amounts of patient DNA were evaluated using NGS analysis of indel markers. Monitoring of dd-cfDNA with the NGS assay presented herein demonstrated a sensitivity of ≥0.1% dd-cfDNA and excellent accuracy (R2 0.99) throughout an extensive range of dd-cfDNA (0.1-30%). The precision of the test was determined for two levels (0.1% (LoD) and 1%) of dd-cfDNA. The between run precision (CV%) for the respective level was 16% and 9% and the corresponding result for the within run precision was 19% and 7%. To evaluate performance of the assay in clinical samples, 507 retrospective monitoring samples from 21 patients transplanted either with kidneys from living or deceased donors were analyzed. Monitoring samples were sampled at multiple time points from 24 h up to 90 days post-transplantation. We show that in one patient, increase of dd-cfDNA preceded increase of creatinine caused by acute cellular rejection by several days. In conclusion, the NGS assay displayed a combination of high sensitivity with good accuracy and precision in both artificial and clinical dd-cfDNA samples.

Development and performance of a next generation sequencing (NGS) assay for monitoring of mixed chimerism.

The aim of this study was to evaluate the performance of a novel NGS-based assay to monitor mixed chimerism (MC) and compare its technical capacity to established techniques for chimerism analysis. Artificial and clinical samples with increasing amounts of patient DNA were compared using real-time PCR detection of indels and SNP, fragment analysis of short-tandem repeats (STR) and NGS analysis of indels. Real-time PCR displayed excellent sensitivity (>0,01%) but poor accuracy (>20 CV% at MC > 20%), while fragment analysis exhibited good accuracy (<5 CV% at MC > 20%) with limited sensitivity (>2,5%). In contrast, NGS chimerism demonstrated a sensitivity (>0,1%) equal to real-time PCR and an accuracy equal or better than STR analysis throughout an extensive range of mixed chimerism (0,1 - 100%). To evaluate performance of the separate techniques for chimerism determination, 75 retrospective patient monitoring samples (3-7 weeks post-HSCT) with low (<5%), intermediate (5-20%) or high mixed chimerism (>20%) were analyzed. The between run precision for the NGS assay varied from 0,72% (>20% MC) to 7,38% (MC < 5%). In conclusion, NGS displayed a combination of high sensitivity with good accuracy in both artificial and clinical chimerism samples.

Midgut Carcinoids and Solid Carcinomas of the Intestine: Differences in Endocrine Markers and p53 Mutations.

Fifteen midgut carcinoid tumors and 5 solid carcinomas of the intestine with carcinoid-like morphological features were evaluated histochemically and immunohistochemically with respect to various endocrine markers and expression of mutant p53 protein. Direct sequencing of the p53 gene after PCR amplification was carried out on microdissected cells from all tumors. All investigated carcinoid tumors showed chromogranin and argentaffin reaction, but lacked nuclear immunostaining with p53 antibodies. In 14 immunohistochemically negative midgut carcinoid tumors, no mutations were identified. One carcinoid tumor devoid of p53 staining was, however, found to contain mutation in exon 6 of the p53 gene. In contrast, the solid carcinomas were essentially chromogranin negative but all displayed clearly positive p53 staining in a variable number of cell nuclei. Sequence analysis of exons 5-8 of the p53 gene in the 5 carcinomas showed mutations in exons 6 and 7 in 2 tumors and in exon 8 in 2 other tumors, while no mutation was detected in the fifth tumor. The carcinoid tumors and the solid carcinomas of the small intestine are thought to derive histogenetically from endocrine cells and enterocytes, respectively. The present results substantiate that divergent mechanisms operate in the development of the two tumor types.