The primary cause of poor outcome following allogeneic hematopoietic cell transplantation (HCT) for chronic lymphocytic leukemia (CLL) is disease recurrence. Detection of increasing minimal residual disease (MRD) following HCT may permit early intervention to prevent clinical relapse; however, MRD quantification remains an uncommon diagnostic test because of logistical and financial barriers to widespread use. Here we describe a method for quantifying CLL MRD using widely available consensus primers for amplification of all Ig heavy chain (IGH) genes in a mixture of peripheral blood mononuclear cells, followed by high-throughput sequencing (HTS) for disease-specific IGH sequence quantification. To achieve accurate MRD quantification, we developed a systematic bioinformatic methodology to aggregate cancer clone sequence variants arising from systematic and random artifacts occurring during IGH-HTS. We then compared the sensitivity of IGH-HTS, flow cytometry, and allele-specific oligonucleotide PCR for MRD quantification in 28 samples collected from 6 CLL patients following allogeneic HCT. Using amplimer libraries generated with consensus primers from patient blood samples, we demonstrate the sensitivity of IGH-HTS with 454 pyrosequencing to be 10, with a high correlation between quantification by allele-specific oligonucleotide PCR and IGH-HTS (r = 0.85). From the same dataset used to quantify MRD, IGH-HTS also allowed us to profile IGH repertoire reconstitution after HCT-information not provided by the other MRD methods. IGH-HTS using consensus primers will broaden the availability of MRD quantification in CLL and other B cell malignancies, and this approach has potential for quantitative evaluation of immune diversification following transplant and nontransplant therapies.next-generation sequencing | consensus-primed polymerase chain reaction | immune reconstitution C hronic lymphocytic leukemia (CLL) is the most common adult leukemia in the United States, with ∼15,500 new cases and 4,400 deaths per year (1). Despite improvements in treatment responses using multiagent therapy, CLL remains incurable with available immunochemotherapy regimens (2). Patients with relapsed CLL and those with high-risk features at presentation, such as 17p deletions or unmutated Ig heavy chain (IGH) regions, are generally referred for allogeneic hematopoietic cell transplantation (allo-HCT) (3, 4). Fifty percent of CLL patients undergoing allo-HCT experience long-term disease-free survival (DFS) and may be cured. Nevertheless, 50% of patients will experience disease recurrence (5, 6). Quantification of CLL MRD has prognostic value because achievement of MRD negativity 1 y after HCT is associated with long-term DFS (6-13). Furthermore, strategies for treating post-HCT relapse, including additional chemotherapy, donor lymphocyte infusions, and cell vaccines, may be more effective when CLL progression is detected with low tumor burden.Validated methods for MRD assessment include allele-specific oligonucleotide PCR (ASO-PCR) and flow cy...
