normal human genomic templates  (Promega)

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Novel secondary Ig VH gene rearrangement and in-frame Ig heavy chain complementarity-determining region III insertion/deletion variants in de novo follicular lymphoma.

doi: 10.4049/jimmunol.166.4.2235

Figure Lengend Snippet: FIGURE 1. IgH fingerprinting analysis of PCR-amplified CDR IIIH-encoding DNA fragments derived from the lymph node biopsy specimens of UPN 13, UPN 17, and UPN 49. The IgH fingerprinting technique was conducted using oligos 48 and either 15 with cDNA template or Fantl I with genomic DNA template. Serial biopsy specimens (Bx) are designated for UPN 13 as Bx1 (diagnosis) and Bx2 (progression), and for UPN 49 as Bx1 (diagnosis), Bx2 (3 years later), Bx3 (4.5 years later), and Bx4 (6.25 years later) The sample labeled Hyb for UPN 13 refers to template isolated from the heterohy- bridoma generated from Bx1 cells that yielded the tumor-derived Ig vaccine. All bands were aligned by their nucleotide lengths as determined by relative migration to a nucleotide sequencing ladder generated from a known VH sequence. For each patient the slower migrating upper band is designated the U band, while the faster migrating lower band is designated the L band.

Article Snippet: Using normal human placental genomic DNA template (Clontech, Palo Alto, CA), the RAG-1 probe was generated using oligos 118 and 121 to amplify RAG-1-coding sequence, mapping between positions 197 and 1067.

Techniques: Derivative Assay, Biomarker Discovery, Labeling, Isolation, Generated, Migration, Sequencing

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Novel secondary Ig VH gene rearrangement and in-frame Ig heavy chain complementarity-determining region III insertion/deletion variants in de novo follicular lymphoma.

doi: 10.4049/jimmunol.166.4.2235

Figure Lengend Snippet: FIGURE 2. Nucleotide and translated protein sequences of the VH rearrangement associated with each CDR IIIH-encoding species revealed by IgH fingerprinting analysis in UPN 13 (A), UPN 17 (B), and UPN 49 (C). For each patient, the U and L designations at the left of each line of sequence, respectively, refer to VH region sequence associated with the U and L band CDR IIIH encoding DNA fragments shown in Fig. 1. The sequence derived from the U band in all three cases is written as the consensus sequence against which the sequence derived from the L band is aligned. The VH region sequence was obtained from cloned PCR-amplified fragments using antisense oligo 15 with oligos 62, 73, and 85 for UPN 17, UPN 13, and UPN 49, respectively. VH3D and D3JH recombination joints are, respectively, indicated as gaps separating residues 94/95 and 100B/100C (A), 100A(G)/ 100A(GT) (B), and 100C/100D (C). Codon 94 encodes the amino acid Arg in sequences L, Lmicro, and LBX2 in A. Dashes indicate identity with the consensus sequence, and base substitutions and amino acid replacements are indicated. Residues representing apparent somatic mutations in germline- encoded JH sequences are highlighted on a black background. No homologies to any D minigenes were found using the criteria of Corbett et al. (58).

Article Snippet: Using normal human placental genomic DNA template (Clontech, Palo Alto, CA), the RAG-1 probe was generated using oligos 118 and 121 to amplify RAG-1-coding sequence, mapping between positions 197 and 1067.

Techniques: Sequencing, Derivative Assay, Clone Assay

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Novel secondary Ig VH gene rearrangement and in-frame Ig heavy chain complementarity-determining region III insertion/deletion variants in de novo follicular lymphoma.

doi: 10.4049/jimmunol.166.4.2235

Figure Lengend Snippet: FIGURE 3. Southern blotting analysis of Ig light chain rearrangements to the J-Cl2 segment in UPN 13 tumor cells. A single blot containing genomic DNA isolated from UPN 13 tumor cells at diagnosis (UPN 13) or human placenta (Pla) that was digested with a combination of the EcoRI and HindIII restriction enzymes was sequentially hybridized to the J-Cl2/ J-Cl3 and J-Cl2 probes, respectively. The J-Cl2/J-Cl3 probe will detect rearrangements to either J-Cl segment, while the J-Cl2 probe uniquely hybridizes to J-Cl2 rearrangements. The positions of the bands derived from the Pla sample establish the migration of unrearranged segments. All band sizes are calculated from their migration relative to the l HindIII m.w. marker (MW marker). The 5.4-kb J-Cl2 hybridizing band has been observed in other patients and most likely corresponds to a genetic ampli- fication polymorphism in the Cl2-Cl3 region (31).

Article Snippet: Using normal human placental genomic DNA template (Clontech, Palo Alto, CA), the RAG-1 probe was generated using oligos 118 and 121 to amplify RAG-1-coding sequence, mapping between positions 197 and 1067.

Techniques: Southern Blot, Isolation, Biomarker Discovery, Derivative Assay, Migration, Marker