![Figure 4. Amino acid sequence alignments of 5 selected subsets defined by HCDR3 stereotypy. Sequence alignments for (A) subsets 1 and 28, (B) subset 2, (C) subset 4, (D) subset 14, and (E) subset 16 are represented as sequence logos85,86 to summarize a total of 106 sequences belonging to these selected subsets (Table S10). In each subset representation (ie, sequence logo), the colored letters above the line represent the amino acids used in that particular subset, and the gray letters shown upside-down below the line represent the germ line amino acid composition of the relevant IGHV gene. Each colored letter indicates an amino acid position where a mutation occurred. When more than one change was observed in a position, the letters representing each change are displayed as a stack. Thus, the size of the amino acid symbol represents the relative frequency of that amino acid at that position relative to all other mutations at that position in that subset. The height of the inverted germ line amino acid symbol is the sum of the heights of the upright amino acids. Blank spaces represent amino acids that are unchanged in the CLL IGHV sequence compared with the germ line sequence. Amino acids are colored based on their similarity in terms of their physicochemical properties: [GAPVLIM], blue; [FYW], purple; [STCNQ], green; [KRH], red; and [DE], orange. Sequence logos are vertically stretched so that the tallest upright stacks are of the same size, irrespective of the number of sequences. For example, in subset 4, 9 of 20 sequences carry E, whereas 5 of 20 sequences carry D at position IMGT/HCDR1-28 (Table S10); therefore, E is taller than D at that position in the sequence logo for subset 4 (C), whereas the height of the inverted germ line G is the sum of the heights of the upright D and E. Additional information about number of sequences with a certain amino acid change of total number of sequences in each subset can be found in Table 1 and Table S10. For clarity, only codons 27 to 104, corresponding to HCDR1-HFR3 of the V region, are shown. In panel B, the letter X denotes the serine deletion at IMGT/HCDR2 codon 59.](https://ash.silverchair-cdn.com/ash/content_public/journal/blood/111/3/10.1182_blood-2007-07-099564/6/zh80040813050004.jpeg?Expires=1723364482&Signature=CO4v96QgpWWl78eYoEct7mJAoJ1iYYzYZkZ-UiT2kg5pRlFUUdff-7PfFFdv1wvhLO~7JN7sEeNXdGwKEveXs95G6o~Lt49bsHEn5CbSEp0ZWS1ghQGIzkjGgcF9TtvU8P0JCt-I5iIcU00OxO-i7f~5G4SS0wRYPQf-lD6m0qj93bct4gTVaHP-iweCG3iBpZvY2Macuq1VyMCTcRgqu1FMNicm4Cqp2PP60zIe6Fig~x16xktkYfLYoi1XJegC6VmHcCFGfOcB-cOKPISznDuuLxWhHCZnUJ4-8arPc~fOdC6FhuioOyDPuxFG8m3TE~B9ddrHzzNvCIdP9gDUmQ__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA)
Amino acid sequence alignments of 5 selected subsets defined by HCDR3 stereotypy. Sequence alignments for (A) subsets 1 and 28, (B) subset 2, (C) subset 4, (D) subset 14, and (E) subset 16 are represented as sequence logos85,86 to summarize a total of 106 sequences belonging to these selected subsets (Table S10). In each subset representation (ie, sequence logo), the colored letters above the line represent the amino acids used in that particular subset, and the gray letters shown upside-down below the line represent the germ line amino acid composition of the relevant IGHV gene. Each colored letter indicates an amino acid position where a mutation occurred. When more than one change was observed in a position, the letters representing each change are displayed as a stack. Thus, the size of the amino acid symbol represents the relative frequency of that amino acid at that position relative to all other mutations at that position in that subset. The height of the inverted germ line amino acid symbol is the sum of the heights of the upright amino acids. Blank spaces represent amino acids that are unchanged in the CLL IGHV sequence compared with the germ line sequence. Amino acids are colored based on their similarity in terms of their physicochemical properties: [GAPVLIM], blue; [FYW], purple; [STCNQ], green; [KRH], red; and [DE], orange. Sequence logos are vertically stretched so that the tallest upright stacks are of the same size, irrespective of the number of sequences. For example, in subset 4, 9 of 20 sequences carry E, whereas 5 of 20 sequences carry D at position IMGT/HCDR1-28 (Table S10); therefore, E is taller than D at that position in the sequence logo for subset 4 (C), whereas the height of the inverted germ line G is the sum of the heights of the upright D and E. Additional information about number of sequences with a certain amino acid change of total number of sequences in each subset can be found in Table 1 and Table S10. For clarity, only codons 27 to 104, corresponding to HCDR1-HFR3 of the V region, are shown. In panel B, the letter X denotes the serine deletion at IMGT/HCDR2 codon 59.
