Use of Next Generation Sequencing and Single Nucleotide Polymorphism (SNP) Fingerprinting to Assess Post Transplant Engraftment Status

Introduction:

Hematopoietic stem-cell transplantation has become an essential component of the treatment of many malignant and nonmalignant disorders in children and in adult patients. For hematologic malignancies, post transplant surveillance is often accomplished by a combination of chimerism analysis and various assays for assessment of known disease associated molecular markers. The use of several methods for disease and engraftment monitoring can be laborious and expensive and may lack sufficient sensitivity and specificity to discriminate host from donor. In this study we describe the incorporation of single nucleotide polymorphisms (SNPs) fingerprinting to assess engraftment using next generation sequencing assays that are routinely utilized for concurrent assessment of mutations in hematologic malignancies.

Methods:

Blood and bone marrow samples from patients undergoing monitoring for myeloid neoplasms were collected. A total of 90 samples from 32 patients were analyzed which included the diagnostic baseline host, unrelated donor and up to 6 post transplant (PT) samples from each patient. The PT samples ranged from 3 months to 2 years at various time points. NGS data from two different clinical assays were used in the study: 1) A PCR amplicon based myeloid panel capturing certain exons of 28 genes based on Raindance technology 2) MSK-IMPACT-Heme, a hybridization-capture based panel interrogating coding exons of 400 genes. While MSK-IMPACT Heme targeted 1029 polymorphic SNP loci by design, 77 highly polymorphic SNP loci were identified in the regions captured by the amplicon-based assay. Genotypes of these SNP loci were used to identify homozygous and heterozygous status in respective assays. Source and percentage of DNA contribution in the PT sample was determined using genotype information. Routine EA was performed using standard short tandem repeat (STR) analysis (Promega GammaSTR and CTTv kits.).

Results:

Comparison of donor contribution to the PT sample between EA and NGS assays showed very highly concordant results (R2 = 0.99, p < 0.001). Furthermore, NGS assay results were more sensitive compared to the traditional STR approach as we were able to detect low levels of host contribution in the PT sample based on the alternate alleles fractions supporting the host alleles in samples which were assessed as "all donor" by STR analysis. In addition to the clinical cases, two proficiency samples were also evaluated and the engraftment assessment showed high concordance with the known results. Data from the MSK-IMPACT-Heme assay was concordant with both Raindance assay results and STR. We randomly downsampled the 1029 different SNP loci to identify the lower limit of detection of PT status with varying number of SNPs.

Conclusion:

We show that NGS based assays can be used to detect engraftment status in PT samples and they can be used as a robust monitoring technique. Since they include both somatic mutation assessment in PT samples and EA in a single assay, they are a much cheaper alternative to performing multiple assays for one specimen.