Family-specific Polymerase Chain Reaction Research Articles

Determination of VH Family Usage in B-Cell Malignancies via the BIOMED-2 IGH PCR Clonality Assay.

To determine whether V H family usage in B-cell lymphoproliferative disorders can be deduced from polymerase chain reaction (PCR) product-length information obtained through the BIOMED-2 (Invivoscribe, San Diego, CA) clonality assay. We develop an algorithm that uses the sizing information of the BIOMED-2 immunoglobulin heavy chain (IGH) clonality assay to deduce V H family usage. PCR with family-specific primers on 51 clinical samples containing 54 rearranged alleles were used to validate the algorithm. The clonal PCR products in different framework reactions contain the same NDN segment (because they are from the same allele). Subtracting the size of the framework III product from the size of the framework I and II products yields the relative position of the framework primer binding sites for the V H segment used. The V H family can be assigned with these relative positions because they are V H family specific in the BIOMED-2 assay. The V H family assigned by the algorithm was concordant with family-specific PCR results for 49 (96%) of the 51 specimens. We have developed an algorithm that can correctly assign V H family usage when all three BIOMED-2 framework reactions produced clonal products. Given the wide adoption of BIOMED-2 assay, the algorithm can facilitate collection of IGH V H usage data without additional cost to the laboratories.

Occurrence of Chlamydiaceae in non-symptomatic free-living raptors in Spain

Few studies have investigated the role of raptors as natural reservoirs of Chlamydiaceae spp. and the preferred anatomical sites where these bacteria can be detected in non-symptomatic wild birds. We investigated the occurrence of Chlamydiaceae in 54 non-symptomatic adult free-living birds belonging to 14 species sampled upon reception in a raptor rehabilitation centre in Spain, and ten juvenile birds from five species born and reared in the centre for subsequent release into the wild. Swabs from conjunctivae, choanae and cloacae were taken to detect Chlamydiaceae DNA by a family-specific polymerase chain reaction (PCR) and a nested genus- and species-specific PCR. Chlamydiaceae DNA was detected in adult raptors belonging to 12 species (85.7%), mainly in conjunctival (40.6%) and, to a lesser extent, choanal (17.2%) swabs, but never in cloacal samples. Neither the genus nor the species of Chlamydiaceae could be confirmed by the nested PCR assay. Our results suggest that most of the raptor species investigated, especially the Common Kestrel (Falco tinnunculus) and Eurasian Griffon Vulture (Gyps fulvus), can be natural reservoirs of Chlamydiaceae spp. in the wild. Failure to identify the organisms at genus and species level might have been due to the poor quality and low concentration of DNA in the samples or to the presence of hitherto unclassified Chlamydiaceae species.

Immunoglobulin Mutational Status Detected through Single-Round Amplification of Partial V H Region Represents a Good Prognostic Marker for Clinical Outcome in Chronic Lymphocytic Leukemia

The immunoglobulin (Ig) mutational status in B-cell chronic lymphocytic leukemia (CLL) distinguishes two subsets of patients with different prognosis. Ig status detection is commonly performed with a panel of V(H) family-specific primers. Although this method detects clonal VDJ rearrangement in virtually all cases, it is technically cumbersome and therefore not widely used clinically. Here, we describe a simple and rapid method to establish the mutational status of IgV(H) in CLL. The method is based on a consensus V(H) FR2 primer, used in both polymerase chain reaction (PCR) and sequencing reactions. Overall, monoclonal B-cell populations were detected in 163 of 189 CLL patients (86%). The prognostic value of IgV(H) mutational status was then evaluated by analyzing survival in 146 CLL cases using different V(H) homology cutoffs. CLL prognostic groups were best separated by the classical 98% cutoff: median survival was 127 and 206 months in unmutated and mutated CLL cases, respectively (P = 0.0023). V(H) FR2 consensus and V(H) family PCR were compared in 41 cases, correctly assigning all cases by both methods. Therefore, we suggest a sequential strategy to detect immunoglobulin mutational status in CLL patients by first using the approach described in this study followed by alternative V(H) family-specific PCRs for negative cases.

Clonal T-cell composition detected by family specific polymerase chain reaction of the T-cell receptor beta chain is exclusively present in dilated cardiomyopathy

Clonal T-cell composition detected by family specific polymerase chain reaction of the T-cell receptor beta chain is exclusively present in dilated cardiomyopathy

High detection rate of T-cell receptor beta chain rearrangements in T-cell lymphoproliferations by family specific polymerase chain reaction in combination with the GeneScan technique and DNA sequencing

AbstractThe distinction between benign polyclonal and malignant monoclonal lymphoid disorders by morphology or immunophenotyping is frequently difficult. Therefore, the demonstration of clonal B-cell or T-cell populations by detecting identically rearranged immunoglobulin (Ig) or T-cell receptor (TCR) genes is often used to solve this diagnostic problem. Whereas the detection of rearranged Ig genes is well established, TCR gamma (γ) and beta (β) gene rearrangements often escape detection with the currently available polymerase chain reaction (PCR) assays. To establish a sensitive, specific, and rapid method for the detection of rearranged TCR-β genes, we developed a new PCR approach with family-specific Jβ primers and analyzed the resulting PCR products by high-resolution GeneScan technique. The superior efficiency of this new method was demonstrated by investigating 132 DNA samples extracted from lymph node and skin biopsy specimens (mostly formalin fixed) and blood samples of 62 patients who had a variety of T-cell lymphomas and leukemias. In all but 1 of the tumor samples (98.4%) a clonal amplificate was detectable after TCR-β PCR and the same clonal T-cell population was also found in 15 of 18 (83%) of the regional lymph nodes and in 7 of 11 (64%) of the peripheral blood samples. Direct comparison of these results with those obtained currently by the most widely applied TCR-γ PCR revealed an approximate 20% lower detection rate in the same set of samples than with the TCR-β PCR method. These results indicate that the new TCR-β PCR is most suitable for a rapid and reliable detection of clonal T-cell populations.

High detection rate of T-cell receptor beta chain rearrangements in T-cell lymphoproliferations by family specific polymerase chain reaction in combination with the GeneScan technique and DNA sequencing

The distinction between benign polyclonal and malignant monoclonal lymphoid disorders by morphology or immunophenotyping is frequently difficult. Therefore, the demonstration of clonal B-cell or T-cell populations by detecting identically rearranged immunoglobulin (Ig) or T-cell receptor (TCR) genes is often used to solve this diagnostic problem. Whereas the detection of rearranged Ig genes is well established, TCR gamma (γ) and beta (β) gene rearrangements often escape detection with the currently available polymerase chain reaction (PCR) assays. To establish a sensitive, specific, and rapid method for the detection of rearranged TCR-β genes, we developed a new PCR approach with family-specific Jβ primers and analyzed the resulting PCR products by high-resolution GeneScan technique. The superior efficiency of this new method was demonstrated by investigating 132 DNA samples extracted from lymph node and skin biopsy specimens (mostly formalin fixed) and blood samples of 62 patients who had a variety of T-cell lymphomas and leukemias. In all but 1 of the tumor samples (98.4%) a clonal amplificate was detectable after TCR-β PCR and the same clonal T-cell population was also found in 15 of 18 (83%) of the regional lymph nodes and in 7 of 11 (64%) of the peripheral blood samples. Direct comparison of these results with those obtained currently by the most widely applied TCR-γ PCR revealed an approximate 20% lower detection rate in the same set of samples than with the TCR-β PCR method. These results indicate that the new TCR-β PCR is most suitable for a rapid and reliable detection of clonal T-cell populations.

Clonal evolution as judged by immunoglobulin heavy chain gene rearrangements in relapsing precursor-B acute lymphoblastic leukemia.

Oligoclonality and ongoing clonal evolution are common features in patients with precursor-B (pre-B) acute lymphoblastic leukemia (ALL), as judged by immunoglobulin heavy chain (IgH) gene rearrangement analysis. These features are considered to be results of secondary rearrangements after malignant transformation or emergence of new tumor clones. In the present study we analyzed the IgH gene rearrangement status in 18 cases with relapsing pre-B ALL using variable heavy chain (V(H)) gene family specific polymerase chain reaction (PCR) amplification and single stranded conformation polymorphism (SSCP) analysis. Clonal IgH rearrangements were displayed in all leukemias but one, and altered rearrangement patterns occurred in five cases (29%), which were selected for detailed nucleotide sequence analysis. In one case, multiple subclones at diagnosis were suggested to be derived from a progenitor clone through joining of different V(H) germline gene segments to a pre-existing D-J(H) complex (V(H) to D-J(H) joining). Evidence for V(H) gene replacement with identical N-sequences at the V(H)-D junction and a common D-J(H) region was observed in one case. Diversification at the V(H)-D junction consisting of heterogeneous N-sequences were observed in one case. This molecular modification of the V(H)-D region could fit a hypothesized "open-and-shut" mechanism. Nevertheless, despite these ongoing events at least one IgH rearrangement remained unchanged throughout the disease in most patients, indicating that the immunoglobulin heavy chain locus can be a suitable marker for detection of minimal residual disease (MRD).

V(H) gene family utilization in different B-cell lymphoma subgroups.

V(H) gene family specific polymerase chain reaction (PCR) amplification was performed in 87 B-cell lymphoma samples from 4 different subgroups. No apparent restriction in the VH gene usage was found in follicular lymphomas, lymphoplasmacytoid lymphomas or large B-cell lymphomas, whereas a biased VH1 utilization was shown in patients with chronic lymphocytic leukemia. Eleven of 18 chronic lymphocytic leukemia cases utilized the VH1 gene family, and nucleotide sequencing of the VH1 gene rearrangements revealed that a majority utilized the DP10 (51p1) germline gene, which has been reported to be strongly associated with autoimmune disease. No VH5 or VH6 rearrangements were amplified in the chronic lymphocytic leukemia subgroup, 2 gene families which previously have been found to be over-represented in these patients. In a high proportion (40%) of large B-cell lymphomas, VH gene family-specific PCR failed to amplify any rearrangement. Using primers hybridizing to the framework regions 2 and 3 and Southern blot analysis of the immunoglobulin heavy chain locus, clonal rearrangements were displayed in two-thirds of these PCR negative cases. However, the rearrangement status could not be elucidated in 5 of 35 patients with large B-cell lymphoma.

Immunoglobulin V H gene replacements in a T-cell lymphoblastic lymphoma

We have analysed the rearrangement status of the immunoglobulin heavy (IgH) chain locus during progression of a T-cell lymphoblastic lymphoma displaying multiple IgH rearrangements as demonstrated by variable heavy (V h ) gene family specific polymerase chain reaction (PCR) analysis. The tumor was found to undergo diversification at the IgH locus between diagnosis and relapse through a mechanism of V h to V h DJ h replacement. In subsets of the tumor at relapse, two separate V h gene segments were found to have replaced the V h gene utilized by a V h DJ h rearrangement identified at diagnosis. The observed V h gene replacement events appear to have been mediated by a heptamer sequence homologous to the heptamer of the recombination signal sequence (RSS) located internally in the V h gene segment. These results support the notion that V h replacements contribute to the diversification of immunoglobulin genes.

Use of family specific leader region primers for PCR amplification of the human heavy chain variable region gene repertoire

We have designed a set of six, non-degenerate oligonucleotide primers, corresponding to the 5' leader regions of each of the six human V H gene families. A general strategy for family specific polymerase chain reaction amplification is described using these primers and a conserved 3' primer corresponding to frame work 3, J H, or constant region. This strategy was used to isolate and sequence novel human germline V H genes belonging to the V H2 and V H4 families. Under certain conditions, chimeric V H sequences were created by a “jumping polymerase chain reaction”, combining DNA segments from different germline genes, but this could be avoided by limiting the number of amplification cycles. PCR amplification with these family specific primers will facilitate studies of the repertoire of germline V H genes as well as studies on V H gene usage in normal and aberrant (B cell malignancies, autoimmune diseases, etc.) B cell populations.