Minimal Residual Disease as a Possible Predictive Factor for Relapse in Patients With AL Amyloidosis

Overview

This protocol will assess patients with AL amyloidosis who achieve a complete response (CR) or very good partial response (VGPR) to therapy for minimal residual disease (MRD). Three approaches to MRD testing will be used since there is no established method. The investigators will clone and sequence each patient's light chain (LC) gene and design patient-specific primers to evaluate genomic DNA from future marrow specimens. Whole genome sequencing (WGS) will be used to test baseline and follow-up marrow cell DNA, seeking copy number variations in chromosomes 1 and 2 or 22, and structural variations in chromosomes 11 and 14, consistent with the known genetic abnormalities in AL and with clonal LC gene use. Plasma protein analysis by mass spectrometry will also be used to look for fragmentary protein sequences associated with the culprit LC gene of each subject. The feasibility and predictive value of these three approaches in patients achieving CR or VGPR will be evaluated. This protocol will help provide insight into the ways that the disease changes and progresses. MRD testing is likely an important next step in AL management.

This protocol will assess AL amyloidosis patients who achieve a CR or VGPR to first-line therapy for evidence of MRD by Q-PCR, NGS, and plasma protein analysis by mass spectrometry using marrow cells obtained annually at times of standard clinical evaluations. A bone marrow aspirate sample from diagnosis will be used to create a baseline profile of each patient's disease. This sample will allow the investigators to create the primer-probe sets required for MRD testing by Q-PCR, which will be conducted after the patient has achieved a CR or VGPR. A baseline bone marrow biopsy sample will either be taken at the time of consent or can be taken from storage if the patient has previously consented to have their marrow cells banked for research purposes. An extra 15 mL of aspirate will be taken from their diagnostic bone marrow biopsy, which is routinely conducted on newly diagnosed patients for clinical purposes. Annual bone marrow aspirates will not be taken for research purposes until after the patient has responded. Patients will remain on protocol, but only begin MRD testing after achieving a CR or VGPR to first-line therapy at which point annual marrow collections for MRD testing will begin. In the event the patient does not reach a CR or VGPR to first-line therapy, the baseline bone marrow aspirate from diagnosis will be discarded. Patients who choose to allow their marrow to be used in this study will sign a consent form specifically for this study. At the time of consent, three green top tubes of peripheral blood will be obtained for WGS of non-tumor cells. No further blood samples will be required for this study. After achieving a CR or VGPR, patients will be completely re-staged as is standard of care at annual intervals. Samples to test for the presence of MRD in their marrows will be obtained at these times of clinical re-staging for up to 3 years after their response to therapy. Both blood and bone marrow samples for this study will be immediately taken to an on-site laboratory where they will be briefly stored before testing. This will ensure no study samples interfere with routine clinical care. In order to test for the presence of MRD, three techniques will be used: Q-PCR, WGS, and plasma protein analysis by mass spectrometry. Both Q-PCR and WGS will use genomic DNA from marrow aspirate samples. To make primer-probe sets for Q-PCR, bone marrow samples from baseline will be used to create individualized primer-probe sets that can recognize the genetically unique LC gene that causes each patient's disease. To perform WGS, genomic DNA will be supplied to the core genetics laboratory for creation of a library and multiplex next generation sequencing. To perform plasma protein analysis, plasma will be isolated from a portion of each subject's peripheral blood and bone marrow aspirate samples in an on-site laboratory. Each subject's de-identified LC gene sequence and their de-identified plasma samples will then be sent to Memorial Sloan-Kettering Cancer Center (MSKCC) for mass spectrometry to look for fragmentary protein sequences associated with the culprit LC gene of each subject. After reaching a CR or VGPR, at annual evaluations for up to 3 years, the genomic DNA from the research sample of bone marrow collected during standard of care clinical procedures will be used to confirm maintenance of response by testing for the presence of MRD with each of the 3 methods (Q-PCR, WGS, and plasma protein analysis) noted above. Marrow material collected for the purposes of this study will not be stored after analysis, and primer-probe set design will be conducted entirely within Tufts Medical Center. Any marrow samples not fully consumed during analysis will be destroyed. By using these three methods this protocol will determine whether one method is superior to the others and whether the three methods produce results that correlate with each other. The decision to discontinue participation in MRD testing will be made by the patient and the physician on an individual basis. Patients who have relapse or hematologic progression of disease during the three year period by standard blood and urine tests will no longer have testing for MRD.