Comparison of B-cell clonality in BAL fluid, pulmonary biopsy, and blood. DNA from BAL fluid, biopsy, and blood samples was amplified, and PCR products were loaded on an ABI prism fragment size gel analysis. By using size marker (gray peak) and Genscan software, CDR3 size of the dominant peak could be determined and compared between different samples in a single patient. In case 1, the same dominant peak can be seen in PCR products obtained from BAL fluid and pulmonary biopsy but not from a blood sample, showing the presence of the same clonal B-cell population in both biopsy lymphocyte infiltrate and BAL fluid. In case 2, no dominant peak was detected in any analyzed tissue.