Figure 2
Figure 2. Amino acid sequence alignments of HCDR3 region from CLL-derived IGH rearrangements assigned to subset 6 and from healthy donor-derived IGH rearrangements identified with a semi-nested subset 6 specific primer approach. (A) Left column: the first number indicates sequence identification number (SIN.); DON1/2/3 indicate donor's source; x followed by a number (eg, x13) indicates the number of identical sequences (eg, 13 identical sequences) identified among different tumor rearrangements from CLL individuals or by cloning of PCR products from normal individuals. (.) indicates homology; and (−), lack of amino acid. Among CLL sequences represented with identical (GGx)YD motif in separate lines, different amino acids were observed at codon 111.2 and or N2 junctional region (codons 112.1-112). Among normal sequences, a different nucleotide sequence at codon 111.2, leading different amino acid translation outside primer sequence was observed between clones 3448 and 3450. Among the healthy donors, those amino acid sequences, identical from position 107 to 111.1 but different outside the represented amino acid sequence or in the degenerate prs6D3-16 primer sequence at position 111.2 in IGHD3-16 and/or 112-113 in the N2 junctional region, are indicated with different SIN. (B) Crude percent frequency by logo analysis representation. Top row: alignment for CLL subset 6 rearrangements. Bottom row: normal sequences identified by cloning after PCR amplification with HCDR2-J3 and subsequent semi-nested HCDR2-prs6D3-16 primers approach. Amino acid sequences are represented as sequence logos as described at http://weblogo.berkeley.edu/. The letters represent the amino acids used at each particular codon numbered according to IMGT criteria. When more than one amino acid was observed in a codon, the letters representing each change are displayed as a stack. The size of the amino acid symbol represents the crude percent frequency of any of the observed amino acid in that position. Sequences with no amino acid at a given position were excluded from the calculation of the frequency at that codon. Blank spaces represent absence of any amino acid in that particular position as a comparison between CLL and normal sequences. Codon numbering between IMGT positions 108 and 109 is omitted.

Amino acid sequence alignments of HCDR3 region from CLL-derived IGH rearrangements assigned to subset 6 and from healthy donor-derived IGH rearrangements identified with a semi-nested subset 6 specific primer approach. (A) Left column: the first number indicates sequence identification number (SIN.); DON1/2/3 indicate donor's source; x followed by a number (eg, x13) indicates the number of identical sequences (eg, 13 identical sequences) identified among different tumor rearrangements from CLL individuals or by cloning of PCR products from normal individuals. (.) indicates homology; and (−), lack of amino acid. Among CLL sequences represented with identical (GGx)YD motif in separate lines, different amino acids were observed at codon 111.2 and or N2 junctional region (codons 112.1-112). Among normal sequences, a different nucleotide sequence at codon 111.2, leading different amino acid translation outside primer sequence was observed between clones 3448 and 3450. Among the healthy donors, those amino acid sequences, identical from position 107 to 111.1 but different outside the represented amino acid sequence or in the degenerate prs6D3-16 primer sequence at position 111.2 in IGHD3-16 and/or 112-113 in the N2 junctional region, are indicated with different SIN. (B) Crude percent frequency by logo analysis representation. Top row: alignment for CLL subset 6 rearrangements. Bottom row: normal sequences identified by cloning after PCR amplification with HCDR2-J3 and subsequent semi-nested HCDR2-prs6D3-16 primers approach. Amino acid sequences are represented as sequence logos as described at http://weblogo.berkeley.edu/. The letters represent the amino acids used at each particular codon numbered according to IMGT criteria. When more than one amino acid was observed in a codon, the letters representing each change are displayed as a stack. The size of the amino acid symbol represents the crude percent frequency of any of the observed amino acid in that position. Sequences with no amino acid at a given position were excluded from the calculation of the frequency at that codon. Blank spaces represent absence of any amino acid in that particular position as a comparison between CLL and normal sequences. Codon numbering between IMGT positions 108 and 109 is omitted.

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