US20140018261A9

US20140018261A9 - Focused libraries of genetic packages

Info

Publication number: US20140018261A9
Application number: US13/754,261
Authority: US
Inventors: Robert Charles Ladner
Original assignee: Dyax Corp
Current assignee: Takeda Pharmaceutical Co Ltd
Priority date: 2000-12-18
Filing date: 2013-01-30
Publication date: 2014-01-16
Also published as: JP4860098B2; US10604753B2; US20100292103A1; EP1360288B1; ATE498718T1; WO2002061071A3; US20120021952A1; DK1360288T3; JP2008183014A; US9803190B2; HK1156660A1; EP1360288A2; US20120028841A1; US20060257937A1; ES2360479T3; JP4855436B2; CA2432377C; US20030119056A1; US8895475B2; US9617536B2

Abstract

Focused libraries of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of antibody peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. The libraries have length and sequence diversities that mimic that found in native human antibodies.

Description

This application is a continuation of U.S. application Ser. No. 12/762,051, filed on Apr. 16, 2010, now published, which is a continuation of U.S. application Ser. No. 11/416,460, filed on May 1, 2006, now abandoned, which is a continuation of U.S. application Ser. No. 10/026,925, filed on Dec. 18, 2001, now abandoned, which claims the benefit under 35 USC §120 of U.S. provisional application 60/256,380, filed Dec. 18, 2000 the entire content of each of which is herein incorporated by reference. The provisional application and the Tables attached to it are specifically incorporated by reference herein.
The present invention relates to focused libraries of genetic packages that each display, display and express, or comprise a member of a diverse family of peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. The focused diversity of the libraries of this invention comprises both sequence diversity and length diversity. In a preferred embodiment, the focused diversity of the libraries of this invention is biased toward the natural diversity of the selected family. In more preferred embodiment, the libraries are biased toward the natural diversity of human antibodies and are characterized by variegation in their heavy chain and light chain complementarity determining regions (“CDRs”).
The present invention further relates to vectors and genetic packages (e.g., cells, spores or viruses) for displaying, or displaying and expressing a focused diverse family of peptides, polypeptides or proteins. In a preferred embodiment the genetic packages are filamentous phage or phagemids or yeast. Again, the focused diversity of the family comprises diversity in sequence and diversity in length.
The present invention further relates to methods of screening the focused libraries of the invention and to the peptides, polypeptides and proteins identified by such screening.

BACKGROUND OF THE INVENTION

It is now common practice in the art to prepare libraries of genetic packages that individually display, display and express, or comprise a member of a diverse family of peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the amino acid diversity of the family. In many common libraries, the peptides, polypeptides or proteins are related to antibodies (e.g., single chain Fv (scFv), Fv, Fab, whole antibodies or minibodies (i.e., dimers that consist of V_Hlinked to V_L)). Often, they comprise one or more of the CDRs and framework regions of the heavy and light chains of human antibodies.
Peptide, polypeptide or protein libraries have been produced in several ways in the prior art. See e.g., Knappik et al., J. Mol. Biol., 296, pp. 57-86 (20004, which is incorporated herein by references. One method is to capture the diversity of native donors, either naive or immunized. Another way is to generate libraries having synthetic diversity. A third method is combination of the first two. Typically, the diversity produced by these methods is limited to sequence diversity, i.e., each member of the library differs from the other members of the family by having different amino acids or variegation at a given position in the peptide, polypeptide or protein chain. Naturally diverse peptides, polypeptides or proteins, however, are not limited to diversity only in their amino acid sequences. For example, human antibodies are not limited to sequence diversity in their amino acids, they are also diverse in the lengths of their amino acid chains.
For antibodies, diversity in length occurs, for example, during variable region rearrangements. See e.g., Corbett et al., J. Mol. Biol., 270, pp. 587-97 (1997). The joining of V genes to J genes, for example, results in the inclusion of a recognizable D segment in CDR3 in about half of the heavy chain antibody sequences, thus creating regions encoding varying lengths of amino-acids. The following also may occur during joining of antibody gene segments: (i) the end of the V gene may have zero to several base deleted or changed; (ii) the end of the D segment may have zero to many bases removed or changed; (iii) a number of random bases may be inserted between V and D or between D and J; and (iv) the 5′ end of J may be edited to remove or to change several bases. These rearrangements result in antibodies that are diverse both in amino acid sequence and in length.
Libraries that contain only amino acid sequence diversity are, thus disadvantaged in that they do not reflect the natural diversity of the peptide, polypeptide or protein that the library is intended to mimic. Further, diversity in length may be important to the ultimate functioning of the protein, peptide or polypeptide. For example, with regard to a library comprising antibody regions, many of the peptides, polypeptides, proteins displayed, displayed and expressed, or comprised by the genetic packages of the library may not fold properly or their binding to an antigen may be disadvantaged, if diversity both in sequence and length are not represented in the library.
An additional disadvantage of prior art libraries of genetic packages that display, display and express, or comprise peptides, polypeptides and proteins is that they are not focused on those members that are based on natural occurring diversity and thus on members that are most likely to be functional. Rather, the prior art libraries, typically, attempt to include as much diversity or variegation at every amino acid residue as possible. This makes library construction time-consuming and less efficient than possible. The large number of members that are produced by trying to capture complete diversity also makes screening more cumbersome than it needs to be This is particularly true given that many members of the library will not be functional.

SUMMARY OF THE INVENTION

One objective of this invention is focused libraries of vectors or genetic packages that encode members of a diverse family of peptides, polypeptides or proteins wherein the libraries encode populations that are diverse in both length and sequence. The diverse length comprising components contain motifs that are likely to fold and function in the context of the parental peptide, polypeptide or protein.
Another object of this invention is focused libraries of genetic packages that display, display and express, or comprise a member of a diverse family of peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. These libraries are diverse not only in their amino acid sequences, but also in their lengths. And, their diversity is focused so as to more closely mimic or take into account the naturally-occurring diversity of the specific family that the library represents.
Another object of this invention is diverse, but focused, populations of DNA sequences encoding peptides, polypeptides or proteins suitable for display or display and expression using genetic packages (such as phage or phagemids) or other regimens that allow selection of specific binding components of a library.
A further object of this invention is focused libraries comprising the CDRs of human antibodies that are diverse in both their amino acid sequence and in their length (examples of such libraries include libraries of single chain Fv(scFv), Fv, Fab, whole antibodies or minibodies (i.e., dimers that consist of V_Hlinked to V_L). Such regions may be from the heavy or light chains or both and may include one or, more of the CDRs of those chains. More preferably, they diversity or variegation occurs in all of the heavy chain and light chain CDRs.
It is another object of this invention to provide methods of making and screening the above libraries and the peptides, polypeptides and proteins obtained in such screening.
Among the preferred embodiments of this invention are the following:
1. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a heavy chain CDR1 selected from the group consisting of:

- (1) <1>₁Y₂<1>₃M₄<1>₅(SEQ ID NO:100), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y;
- (2) (S/T)₁(S/G/X)₂(S/G/X)₃Y₄Y₅W₆(S/G/X)₇(SEQ ID NO:101) wherein (S/T) is a 1:1 mixture of S and T residues, (S/G/X) is a mixture of 0.2025 S, 0.2025 G and 0.035 of each of amino acid residues A, D, E, F, H, I, K, L, H, N, P, Q, R, T, V, W, and Y;
- (3) V₁S₂G₃G₄S₅I₆S₇<1>₈<1>₉<1>₁₀Y₁₁Y₁₂W₁₃<1>₁₄(SEQ ID NO:1), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and
- (4) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio: HC CDR1s (1):(2):(3)::0.80:0.17:0.02.

2. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express or comprise at least a portion of the diversity of the antibody facility, the vectors or genetic packages being characterized by variegated DNA sequences that encode a heavy chain CDR2 selected from the group consisting of:

- (1) <2>I<2><3>SGG<1>T<1>YADSVKG (SEQ ID NO:2), wherein <1> is an equimolar mixture of each of amino acid residues 2¹1, 0, E, F, G, H, I, K, L, M, N, P, 0, P, S, T, V, W, and Y; <2> is an equimolar mixture of each of amino acid residues Y, R, W, V, G, and S; and <3> is an equimolar mixture of each of amino acid residues P, S, and G or an equimolar mixture of P and S;
- (2) <1>I<4><1><1><G><5><1><1><1>YADSVKG (SEQ ID NO:3), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; <4> is an equimolar mixture of residues D, I, N, S, W, Y; and <5> is an equimolar mixture of residues S, G, D and N;
- (3) <1>I<4><1><1>G<5><1><1>YNPSLKG (SEQ ID NO:4), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N; P, Q, R, S, T, V, W and Y, and <4> and <5> are as defined above;

(4) <1>I<8>S<1><1><1>GGYY<1>YAASVKG (SEQ ID NO:5), wherein <1> is an equimolar mixture of each amino acid residues A, D, E, F, Gill, I, K, L, M, N, P, Q, R, S, T, V, and Y; <8> is 0.27 R and 0.027 of each of ADEFGHIKLMNPQSTVWY; and

- (5) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio: HC CDR2s: (1)/(2) (equimolar): (3):(4)::0.54:0.43:0.03.

3. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a heavy chain CDR3 was selected from the group consisting of:

- (1) YYCA21111YFDYWG (SEQ ID NO:6), Wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R;
- (2) YYCA2111111YFDYWG (SEQ ID NO:7), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R;
- (3) YYCA211111111YFDAYTG (SEQ ID NO:8), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, 1, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R;
- (4) YYCAR111S2S3111YFDYWG (SEQ ID NO:9), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of S and G; and 3 is an equimolar mixture of Y and W;
- (5) YYCA2111CSG11CY1YFDYWG (SEQ ID NO:10), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R;
- (6) YYCA211S1TIFG11111YFDYWG (SEQ ID NO:11), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R.
- (7) YYCAR111YY2S3344111YFDYWG (SEQ ID NO:12), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; 2 is an equimolar mixture of D and S; and 3 is an equimolar mixture of S and G;
- (8) YYCAR1111YC2231CY111YFDYWG (SEQ ID NO:13), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; 2 is an equimolar mixture of S and G; and 3 is an equimolar mixture of T, D and G; and
- (9) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably the HC CDR3s (1) through (8) are in the following proportions in the mixture:

(1) 0.10
(2) 0.14
(3) 0.25
(4) 0.13

- (5) 0.13

(6) 0.11
(7) 0.04 and
(8) 0.10; and more preferably the HC CDR3s (1) through (8) are in the following proportions in the mixture:
(1) 0.02
(2) 0.14
(3) 0.25
(4) 0.14

- (5) 0.14
- (6) 0.12
- (7) 0.08 and
- (8) 0.11.

Preferably, 1 in one or all of HC CDR3s (1) through (8) is 0.095 of each of G and Y and 0.048 of each of A, D, E, F H, 1, K, L, M, N, P, Q, R, S, T, V, and W.
4. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encodes a kappa light chain CDR1 selected from the group consisting of:
(1) RASQ<1>V<2><2><3>LA (SEQ ID NO:14)
(2) RASQ<1>V<2><2><2><3>LA (SEQ ID NO:15); wherein <1> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY; <2> is 0.2 S and 0.044 of each of ADEFGHIKLMNPQRTVWY; and <3> is 0.2Y and 0.044 each of ADEFGHIKLMNPQRTVW and S; and
(3) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio CDR1s (1):(2)::0.68:0.32.
5. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the-antibody family the vectors or genetic packages being characterized by variegated DNA sequences that encode a kappa light-chain CDR2 having the sequence:

- <1>AS<2>R<4><1> (SEQ ID NO:102), wherein <1> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY; <2> is 0.2 S and 0.044 of each of ADEFGHIKLMNPQRTVWY; and <4> is 0.2.A and 0.044 each of DEFGHIKLMNPQRSTVWY.

6. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a kappa light chain CDR3 selected from the groups consisting of:

- (1) QQ<3><1><1><1>P<1>T (SEQ ID NO:16), wherein <1> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY; <3> is 0.2 Y and 0.044 each of ADEFGHIKIMNPQRTVW;
- (2) QQ33111P (SEQ ID NO:103), wherein 1 and 3 are as defined in (1) above;
- (3) QQ3211PP1T (SEQ ID NO:17), wherein 1 and 3 are as defined in (1) above and 2 is 0.2 S and 0.044 each of ADEFGHIKLMNPQRTVWY; and
- (4) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio CDA3s (1):(2):(3)::0.65:0.1:0.25.

7. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a lambda light chain CDR1 selected from the group consisting of:

- (1) TG<1>SS<2>VG<1><3><2><3>VS (SEQ ID NO:18), wherein <1> is 0.27 T, 0.27 G and 0.027 each of ADEFRIKLMNPQRSVWY: <2> is 0.27 D, 0.27 N and 0.027 each of AEFGHIKLMPQRSTVWY, and <3> is 0.36 Y and 0.036 each of ADEFGHIKLMNPQRSTVW;
- (2) G<2><4>L<4><4><4><3><4><4> (SEQ ID NO:104), wherein <2> is as defined in (1) above and <4> is an equimolar mixture of amino acid residues ADEFGHIKIMNPQRSTVWY; and
- (3) mixtures of vectors or genetic packages 5 characterized by any of the above DNA sequences, preferably in the ratio CDR1 (1):(2)::0.67:0.33;

8. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a lambda light chain CDR2 has the sequence:

- <4><4><4><2>RPS (SEQ ID NO:105) wherein <2> is 0.27 D, 0.27 N, and 0.027 each of AEFGHIKIMPQRSTVWY and <4> is an equimolar mixture of amino acid residues ADEFGHIKLONPQRSTVW.

9. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a lambda light chain CDR3 selected from the group consisting of:

- (1) <4><5><4><2><4>S<4><4><4><4>V (SEQ ID NO:106), wherein <2> is 0.27 D, 0.27 N, and 0.027 each of AEFGHIKIMPQRSTVWY; <4> is an equimolar mixture of amino acid residues ADEFGHIKLMVPQRSTVW; and <5> is 0.36 S and 0.6355 each of ADEFGHIKLMNPQRTVWY;

(2) <5>SY<1><5>S<5><1><4>V (SEQ ID NO:19), wherein <1> is an equimolar mixture of ADEFGHIKLMNPQRSTVWY; and <4> and 5 <5> are as defined in (1) above; and

- (3) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio CDR3s

10. A focused library comprising variegated-DNA sequences that encode a heavy chain CDR selected from the group consisting of:

- (1) one or more of the heavy chain CDR's of paragraph 1 above;
- (2) one or more of the heavy chin CDR2s of paragraph 2 above;
- (3) one or more of the heavy chain CDR3s of paragraph 3 above; and
- (4) mixtures of vectors or genetic-packages characterized by (1), (2) and (3).

11. The focused library comprising one or more of the variegated DNA sequences that encodes a heavy chain CDR of paragraphs 1, 2 and 3 and further comprising variegated DNA sequences that encodes a light chain CDR selected from the group consisting of

- (1) one or more the kappa light chain CDR1s of paragraph 4;
- (2) the kappa light chain. CDR2 of paragraph 5;
- (3) one or more of the kappa light chain CDR3s of paragraph 6;
- (4) one or more of the kappa light chain CDR1s of paragraph 7;
- (5) the lambda light chain ‘CDR2’ of paragraph 8
- (6) one or more of the lambda light chain CDR3s of paragraph. 9; and
- (7) mixtures of vectors and genetic packages characterized by one or more of (1) through (6).

12. A population of variegated DNA sequences as. described in paragraphs 1-11 above.
13. A population of vectors comprising the variegated DNA sequences as described in paragraphs 1-11 above.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

Antibodies (“Ab”) concentrate their diversity into those regions that are involved in determining affinity and specificity of the Ab for particular targets. These regions may be diverse in sequence or in length. Generally, they are diverse In both ways. However, within families of human antibodies the diversities, both in sequence and in length, are not truly random. Rather, some amino acid residues are preferred at certain positions of the CDRs and some CDR lengths are preferred. These preferred diversities account for the natural diversity of the antibody family.
According to this invention, and as more fully described below, libraries of vectors and genetic packages that more closely mirror the natural diversity, both in sequence and in length, of antibody families, or portions thereof are prepared and used.

Human Antibody Heavy Chain Sequence and Length Diversity

(a) Framework
The heavy chain (“HC”) Germ-Line Gene (GLG) 3-23 (also known as 1/1)-47) accounts for about 12% of all human Abs and is preferred as the framework in the preferred embodiment of the invention. It should, however, be understood that other well-known frameworks, such as 4-34, 3-30, 3-30.3 and 4-30.1, may also be used without departing from the principles of the focused diversities of this invention.
In addition, JH4(YFDYWGQGTLVTVSS; SEQ ID NO:20) occurs more often than JH3 in native antibodies. Hence, it is preferred for the focused libraries of this invention. However, JH3 (AFDIWGQGTMVTVSS; SEQ ID NO:21) could as well be used.

(b) Focused Length Diversity: CDR1, 2 and 3

(i) CDR1
For CDR1, GLGs provide CDR1s only Of the lengths 5, 6, and 7. Mutations during the maturation of the v-domain gene, however, can lead to CDR1s having lengths as short as 2 and as long as 16. Nevertheless, length 5, predominates. Accordingly, in the preferred embodiment of this invention the preferred HC CDR1 is 5 amino acids, with less preferred CDR1s having lengths of 7 and 14. In the most preferred libraries of this invention, all three lengths are used in proportions similar to those found in natural antibodies.
(ii) CDR2
GLGs provide CDR2s only of the lengths 15:19, but mutations during maturation may result in CDR2s of lengths from 16 to 28 amino acids. The lengths 16 and 17 predominate in mature Ab genes. Accordingly, length 17 is the preferred length for HC CDR2 of the present invention. Less preferred HC CDR2s of this invention have lengths 16 and 19. In the most preferred focused libraries of this invention, all three lengths are included in proportions similar to those found in natural antibody families.
(iii) CDR3
HC CDR3s vary in length. About half of human HCs consist of the components: V::nz::D::ny::JHn where V is a V gene, nz is a series of bases (mean 12) that are essentially random, D is a D segment, often with heavy editing at both ends, ny is a series of bases (mean 6) that are essentially random, and JH is one of the six JH segments, often with heavy editing at the 5′ end. The D segments appear to provide spacer segments that allow folding of the IgG. The greatest diversity is at the junctions of y with D and of D with JH.
In the preferred-libraries of this invention both types of HC CDR3s are used. In HC CDR3s that have no identifiable D segment, the structure is V::nz::JHn where JH is usually edited at the 5′ end. In HC CDR3s that have an identifiable D segment, the structure is V::nz::D::ny::JHn.
(c) Focused Sequence Diversity: CDR1, 2 and 3
(i) CDR1
In 5 amino acid length CDR1, examination of a 3D model of a humanized Ab showed that the side groups of residues 1, 3, and 5 were directed toward the combining pocket. Consequently, in the focused libraries of this invention, each of these positions may be selected from any of the native amino acid residues, except cysteine (“C”). Cysteine can form disulfide bonds, which are an important component of the canonical Ig fold. Having free thiol groups Could, thus, interfere with proper folding of the HC and could lead to problems in production or manipulation of selected Abs. Thus, in the focused libraries of this invention cysteine is excluded from positions 1; 3 and 5 of the preferred 5 amino acid CDR1s. The other 19 natural amino acids residues may be used at positions 1, 3 and 5. Preferably, each is present in equimolar ratios in the variegated libraries of this invention.
3D modeling also suggests that the side groups of residue 2 in a 5 amino acid CDR1 are directed away from the combining pocket. Although this position shows substantial diversity, both in GLG and mature genes, in the focused libraries of this invention this residue is preferably Tyr (Y) because it occurs in 681/820 mature antibody genes. However, any of the other native amino acid residues, except Cys (C), could also be used at this position.
For position 4, there is also some diversity in GLG and mature antibody genes. However, almost all mature genes have uncharged hydrophobic amino acid residues: A, G, L, P, F, M, W, I, V, at this position. Inspection of a 3D model also shows that the side group of residue 4 is packed into the innards of the HC. Thus, in the preferred embodiment of this invention which uses framework 3-23, residue 4 is preferably Met because it Is likely to fit very well into the framework of 3-23. With other frameworks, a similar fit consideration is used to assign residue 4.
Thus, the most preferred HC CDR1 of this invention consists of the amino acid sequence <1>Y<I>M<1> where <1> can be any one of amino acid residues: A, D, E, G, H, I, K, L, M, N, R, Q, S, T, V, W, Y. (not C), preferably present at each position in an equimolar amount. This diversity is shown in the context of a framework 3-23:JH4 in Table 1. It has a diversity of 6859-fold.
The two less preferred HC CDR1s of this invention have length 7 and length 14. For length 7, a preferred variegation is (S/T)₁(S/G/<1>)₂(S/G/<1>)₃Y₄Y₅W₆(S/G/<1>)₇(SEQ ID NO:107); where (S/T) indicates an equimolar mixture of Ser and Thr codons; (S/G/<1>) indicates a mixture Of 0.2025 S, 0.2025 G, and 0.035 for each of A, D, E, F, H, I, K, L, M, N, P, Q, R, T, V, W, Y. This design gives a predominance of Ser and Gly at positions 2, 3, and 7, as occurs in mature HC genes. For length 14, a preferred variegation is VSGGSIS<1><1><1>YYW<1> (SEQ ID NO:108), where <1> is an equimolar mixture of the 19 native amino acid residues, except Cys (C).
The DNA that encodes these preferred HC CDR1s is preferably synthesized using trinucleotide building blocks so that each amino acid residue ii present in essentially equimolar or other described amounts. The preferred codons for the <1> amino acid residues are gct, gat, gag, ttt, ggt, cat, att, aag, ctt, atg, aat, cct, cag, cgt, tct, act, gtt, tgg, and tat. Of course, other codons for the chosen amino acid residue could also be used.
The diversity oligonucleotide (ON) is preferably synthesized from BspEI to BstXI (as shown in Table 1) and can, therefore, be incorporated either by PCR synthesis using overlapping ONs or introduced by ligation of BspEI/BstXI-cut fragments. Table 2 shows the oligonucleotides that embody the specified variegations of the preferred length 5 HC CDR1s of this invention. PCR using ON-R1V1vg, ON-R1top, and ON-R1bot gives a dsDNA product of 73 base-pairs, cleavage with 14spEI and BstXI trims 11 and 13 bases from the ends and provides cohesive ends that can be ligated to similarly cut vector having the 3-23 domain shown in Table 1. Replacement of ON-R1V1vg with either ONR1V2vg or ONR1V3vg (see Table 2) allows synthesis of the two alternative diversity patterns—the 7 residue length and the 14 residue length HC CDR1.
The more preferred libraries of this invention comprise the 3 preferred HC CDR1 length diversities. Most preferably, the 3 lengths should be incorporated in approximately the ratios in which they are observed in antibodies selected without reference to the length of the CDRs. For example, one sample of 1095 HC genes have the three lengths present in the ratio: L=5:L=7:L=14::820:175:23::0.80:0.17:0.02. This is the preferred ratio in accordance with this invention.
(ii) CDR2
Diversity in HC CDR2 was designed with the same considerations as for HC CORI: GLG sequences, mature sequences and 3D structure. A preferred length for CDR2 is 17, as shown in Table 1. For this preferred 17 length CDR2, the preferred variegation in accordance with the invention is: <2>I<2><3>SGG<1>T<1>YADSVKG (SEQ ID NO:2), where <2> indicates any amino acid residue selected from the group of Y, R, W, V, G and S (equimolar mixture), <3> is P, S and G or P and S only (equimolar mixture), and <1> is any native amino acid residue except C (equimolar mixture).
ON-R2V1vg shown in Table 3 embodies this diversity pattern. It is preferably synthesized so that fragments of dsDNA containing the BstXI and XbaI site can be generated by PCR. PCR with ON-R2V1vg, ON-R2top, and ONR2bot gives a dsDNA product of 122 base pairs. Cleavage with BstXI and XbaI removes about 10 bases from each end and produces cohesive ends that can be ligated to similarly cut vector that contains the 3-23 gene-shown in Table 1.
In an alternative embodiment for a 17 length HC CDR2, the following variegation may be used; <1>I<4><1><1>G<5><1><1><1>YADSVKG (SEQ ID NO:3), where <1> is as described above for the more preferred alternative of HC CDR2; <4> indicates an equimolar mixture of DINSWY, and <5> indicates an equimolar mixture of SGDN. This diversity pattern is embodied in ON-R2V2vg shown in Table 3. Preferably, the two embodiments are used in equimolar mixtures in the libraries of this invention.
Other preferred HC CDR2s have lengths 16 and 19.
(SEQ ID NO: 4)

Length 16: <1>I<4><1><1>G<5<1><1>YNPSLKG;

(SEQ ID NO: 5)

Length: 19: <1>I<8>S<1><1><1>GGYY<1>YAASVKG,

wherein <1> is an equimolar mixture of all native amino acid residues except C; <4> is a equimolar mixture of DINSWY; <5> is an equimolar mixture of SGDN; and <8> is 0.27 R and 0:0 7 of each of residues ADEFGHIKLMNPQSTVWY. Table 3 shows ON-R2V3vg which embodies a preferred aDR2 variegation of length 16 and ON7R2V4vg which embodies a preferred CDR2 variegation of length 19. To prepare these variegations ON-R2V3vg may be PCR amplified with ON-A2top and ON-R2bo3 and ON-R2V4vg may be PCR amplified with ON-R2top and ON-R2-bo4. See Table 3. In the most preferred embodiment of this invention, all three HC CDR2 lengths are used. Preferably, they are present in a ratio 17:16:19::579:464:31::0.54:0.43:0.03.
(iii) CDR3
The preferred libraries of this invention comprise several BC CDR3 components. Some of these will have only sequence diversity. Others will have sequence diversity with embedded D segments to extend the length, while also incorporating sequences known to allow Igs to fold. The HC CDR3 components of the preferred libraries of this invention and their diversities are depicted in Table 4: Components 1-8.
This set of components was chosen after studying the sequences of 1383 human BC sequences. The proposed components are meant to fulfill the following goals:
1) approximately the same distribution of lengths as seen in native Ab genes;
2) high level of sequence diversity at places having high diversity in native Ab genes; and
3) incorporation of constant sequences often seen in native Ab genes.
Component 1 represents all the genes having lengths 0 to 8 (counting from the YYCAR motif at the end of FR3 to the WG dipeptide motif near the start of the J region, i.e., FR4). Component 2 corresponds the all the genes having lengths 9 or 10. Component 3.corresponds to the genes having lengths 11 or 12 plus half the genes having length 13. Component 4 corresponds to those having length 14 plus half those having length 13. Component 5 corresponds to the genes having length 15 and half of those having length 16. Component. 6 corresponds to genes of length 17 plus half of those with length 16. Component 7 corresponds to those with length 18. Component 8 corresponds to those having length 19 and greater. See Table 4.
For each HC CDR3 residue having the diversity <1>, equimolar ratios are preferably not used. Rather, the following ratios are used 0.095 [G and Y] and 0.048 [A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, and W]. Thus, there is a double dose of G and Y with the other residues being in equimolar ratios. For the other diversities, e.g., KR or SG, the residues are present in equimolar mixtures.
In the preferred libraries of this invention the eight components are present in the following fractions: 1 (0.10), 2 (0.14), 3 (0.25), 4 (0.13), 5 (0.13), 6 (0.11), 7 (0.04) and 8 (0.10). See Table 4.
In the more preferred embodiment of this invention, the amounts of the eight components is adjusted because the first component is not complex enough to justify including it as 10% of the library. For example, if the final library were to have 1×10⁹members, then 1×10⁸sequences would come from component 1, but it has only 2.6×10⁵CDR3 sequences so that each one would occur in ˜385 CDR1/2 contexts. Therefore, the more preferred amounts of the eight components are 1 (0.02), 2 (0.14), 3 (0.25), 4 (0.14), 510.14), 6 (0.12), 7 (0.68), 8 (0.11). In accordance with the more preferred embodiment component 1 occurs in ˜77 CDR1/2 contexts and the other, longer CDR3s occur more often.
Table 5 shows vgDNA that embodies each of the eight HC CDR3 components shown in Table 4. In Table 5, the oligonucleotides (ON) Ctop25, CtprmA, C8prmB, and CBot25 allow PCR amplification of each of the variegated ONs (vgDNA): C1t08, C2t10, C3t12, C4t14, C5t15, C6t17, C7t18, and C8t19. After amplification, the dsDNA can be cleaved with AfiII and BstEII (or KpnI) and ligated to similarly cleaved vector that contains the remainder of the 3-23 domain. Preferably, this vector already contains diversity in one, or both, of CDR1 and CDR2 as disclosed herein. Most preferably, it contains diversity in both the CDR1 and CDR2 regions. It is, of course, to be understood that the various diversities can be incorporated into the vector in any order.
Preferably, the recipient vector originally contains a stuffer in place of CDR1, CDR2 and CDR3 so that there will be no parental sequence that would then occur in the resulting library. Table 6 shows a version of the V3-23 gene segment with each CDR replaced by a short segment that contains both stop codons and restriction sites that will allow specific cleavage of any vector that does not have the stuffer removed. The stuffer can either be short and contain a restriction enzyme site that will not occur in the finished library, allowing removal of vectors that are not cleaved by both AfiII and BstEII (or AionI) and religated. Alternatively, the stuffer could be 200-400 bases long so that uncleaned or once-cleaved vector can be readily separated from doubly cleaved vector.

Human Antibody Light Chain: Sequence and Length Diversity

(i) Kappa Chain
(a) Framework
In the preferred embodiment of this invention, the kappa light chain is built in an A27 framework with a JK1 region. These are the most common V and J regions in the native genes. Other frameworks, such as 012, L2, and All, and other J regions, such as JK4, however, may be used without departing from the scope of this invention.
(b) CDR1
In native human kappa chains, CDR1s with lengths of 11, 12, 13, 16, and 17 were observed with length 11 being predominant and length 12 being well represented. Thus, in the preferred embodiments of this invention LC CDR1s of length 11 and 12 are used in an and mixture similar to that observed in native antibodies), length 11 being most preferred. Length 11 has the following sequence: RASQ<1>V<2><2><3>LA (SEQ ID NO:14) and Length 12 hag the following sequence: RASQ<1>V<25<2><2><3>LA (SEQ ID NO:15), wherein <1> is an equimolar mixture of ill of the native-amino acid residues, except C, <2> is 0.2 S and 0.044 of each of ADEFGHIKLMNPQRTVWY, and <3> is 0.2.Y and 0.044 each of A, D, E, F, G, H, 1, K, L, M, N, Q, R, T, V, W and S. In the most preferred embodiment of this invention, both CDR1. lengths are used. Preferably, they are present in a ratio of 11:12::154:73:0.68:0.32.
(c) CDR2
In native kappa, CDR2 exhibits only length 7. This length is used in the preferred embodiments of-this invention. It has the sequence <1>AS<2>R<4><1>, wherein <1> is an-equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY; <2> is 0.2 S and 0.004 of each of ADEFGHIKLMNPQRTVWY; and <4> is 0.2 A and 0.044 of each of DEFGHIKLMNPQRSTUWY.
(d) CDR3
In native kappa, CDR3 exhibits lengths of 4, 6, 7; 8, 9, 10, 11, 12, 13, 0 and 19. While any of these lengths and mixtures of them can be employed in this invention, we prefer lengths 8, 9 and 10, length 9 being more preferred. For the preferred Length 9, the sequence is, QQ<3><1><1><1>P<1>T, wherein <1> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY and <3> is 0.2? and 0.044 each of ADEFGHIKLWQRSVW. Length 8 is preferably QQ33111P and Length 10 is Preferably QQ3211PP1T, wherein 1 and 3 are as defined for Length 9 and 2 is S (0.2) and 0.044 each of ADEFGHIKLMNPQRTVWY. A mixture of all 3 lengths being most preferred (ratios as in native antibodies), i.e., 8:9:10i28:166:63::0.1:0.65:0.25.
Table 7 shows a kappa chain gene of this invention, including a PlacZ promoter a ribosome-binding site, and signal sequence (MI3 III signal). The DNA sequence encodes the GLG amino acid sequence but does not comprise the GLG DNA sequence. Restriction sites are designed to fall within each framework region so that diversity can be cloned into the CDRs. XmaI and Espl are in FR1, SexAI is in FR2, RsrII is in FR3, and KpnI (or Acc65I), are in FR4. Additional sites are provided in the constant kappa chain to facilitate construction of the gene.
Table 7 also shows a suitable scheme of variegation for kappa. In CDR1, the most preferred length 11 is depicted. However, most preferably both lengths 11 and 12 are used. Length 12 in CDR1 can be construed by introducing codon 51 as <2> (i.e. a Ser-biased mixture). CDR2 of kappa is always 7 codons. Table 7 shows a preferred variegation scheme for CDR2. Table 7 Shows a variegation scheme for the most preferred CDR3 (length 9). Similar variegations can be lied for CDRs of length 8 and 10. In the preferred embodiment of this invention, those three lengths (8, 9 and 10) are included in the libraries of this invention in the native ratios, as described above.
Table 9 shows series of diversity oligonucleotides and primers that may be used to construct the kappa chain diversities depicted in Table 7.
(ii) Lambda Chain
(a) Framework
The lambda chain is preferably built in a 2a2 framework with an L2J region. These are the most common V and J regions in the native genes. Other frameworks, such as 31, 4b, 1a and 6a, and other J regions, such as L1J, L3J and L7J, however, may be used without departing from the scope of this invention.
(b) CDR1
In native human lambda chains, CDR1s with length 14 predominate, lengths 11, 12 and 13 also occur. While any of these can be used in this invention, lengths 11 and 14 are preferred. For length 11 the sequence is: TG<2><4>L<4><4><4><3><4><4> (SEQ ID NO:22) and for Length 14 the sequence is: TG<1>SS<2>VG<1><3><2><3>VS (SEQ ID NO:18), wherein <1> is 0.27 T, 0.21 G and 0.027 each of ADEFHIKLMNPQRSVWY; <2> is 0.27 D, 0.27 N and 0.027 each of AEFGHIKLMPQRSTVWY; <3> is 0.36 Y and 0.0355 each of ADEFGHIKLMNPQRSTVW; and <4> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY. Most preferably, Mixtures (similar to those occurring in native antibodies) preferably, the ratio is 11:14::23:46::0.33:0.67 of the three lengths are used.
(c) CDR2
In native human lambda chains₄.CDR2s with length 7 are by far the most common. This length is preferred in this invention. The sequence of this Length 7 CDR2 is <4><4><4><2>RPS, wherein <2> is 0.27 D, 0.27 N, and 0.027 each of AEFGHIKLMPQRTVWY and <4> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVW.
(d) CDR3
In native human lambda chains, CDR3s of length 10 and 11 predominate, while length 9 is also common. Any of these three lengths can be used in the invention. Length 11 is preferred and mixtures of 10 and 11 more preferred. The sequence of Length 11 is <4><5><4><2><4>S<4><4><4><4>V, where <2> and <4> are as defined for the lambda CORI and <5> is 0.36 S and 0.0355 each of ADFFGHIKLMNFORTVWY. The sequence of Length 10 is <5>SY<1><5>S<5><1><4>V (SEQ ID NO:19), wherein <1> is an equimolar mixture of ADEFGHIKLMNPQRSTVWY; and <4> and <5> are as defined for Length 11. The preferred mixtures of this invention comprise an equimolar mixture of Length 10 and Length 11. Table 8 shows a preferred focused lambda light chain diversity in accordance with this invention.
Table 9 shows a series of diversity oligonucleotides and primers that may be used to construct 10 the lambda chain diversities depicted in Table 7.

Method of Construction of the Genetic Package

The diversities of heavy chain and the kappa and lambda light chains are best constructed in separate vector's. First a synthetic gene is designed to embody each of the synthetic variable domains. The light chains are bounded by restriction sites for ApaLI (positioned at the very end of the signal sequence) and AscI (positioned after the stop codon). The heavy chain is bounded by SfiI (positioned within the PelB signal sequence) and NotI (positioned in the linker between CH1 and the anchor protein). Signal sequences other than PelB may also need, e.g., a M13 pIII signal sequence.
The initial genes are made with “stuffer” sequences in place of the desired CDRs. A “stuffer” is a sequence that is to be cut away and replaced by diverse DNA but which does not allow expression ‘of a functional antibody gene. For example, the stuffer may contain several stop codons and restriction sites that will not occur in the correct finished library vector. For example, in Table 10, the stuffer for CDR1 of kappa A27 contains a StuI site. The vgDNA for CDR1 is introduced as a cassette from EspI, XmaI, or Af1II to dither SexAI or KasI. After the ligation, the DNA is cleaved with Still; there should be no StuI sites in the desired vectors.
The sequences of the heavy chain gene with stuffers is depicted in Table 6. The sequences of the kappa light chain gene with stuffers is depicted in Table 10. The sequence of the lambda light chain gene with stuffers is depicted in Table 11.
In another embodiment of the present invention the diversities of heavy chain and the kappa or lambda light chains are constructed in a single vector or genetic packages (e.g., for display or display and expression) having appropriate restriction sites that allow cloning of these chains. The processes to construct such vectors are well known and widely used in the art. Preferably, a heavy chain and Kappa light Chain library and a heavy chain and lambda light chain library would be prepared separately. The two libraries, most preferably, will then be mixed in equimolar amounts to attain maximum diversity.
Most preferably, the display is had on the surface of a derivative of M13 phage. The most preferred vector contains all the genes of M13, an antibiotic resistance-gene, and the display cassette. The preferred vector is provided with restriction sites that allow introduction and excision of members of the diverse family of genes, as cassettes. The preferred vector is stable against rearrangement under the growth conditions used to amplify phage.
In another embodiment of this invention, the diversity captured by the methods of the present invention may be displayed and/or expressed in a phagemid vector (e.g., pCES1) that displays and/or expresses the peptide, polypeptide or protein. Such vectors may also be used to store the diversity for subsequent display and/or expression using other vectors or phage.
In another embodiment of this invention, the diversity captured by the methods of the present invention may be displayed and/or expressed in a yeast vector.

TABLE 1

3-23:JH4 CDR1/2 diversity = 1.78 × 10⁸

		FR1 (VP47/V3-23)---------------
	20 21 22	23 24 25 26 27 28 29 30
(SEQ ID NO: 99)	A M A	E V Q L L E S G
ctgtctgaac	cc atg gcc	gaa/gtt/caa/ttg/tta/gag/tct/ggt/
Scab.....	NcoI....	MfeI

---------- FR1---------------------------------

31 32 33 34 35 36 37 38 39 40 41 42 43 44 45

G G L V Q P G G S L R L S C A

/ggc/ggt/ctt/gtt/cag/cct/ggt/ggt/tct/tta/cgt/ctt/tct/tgc/gct/

Sites of variegation <1><1> <1> <1> 6859-fold diversity

----FR1------------- >/ .. CDR1........... ./---FR2-----

46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

A S G F T F S - Y - M - W V R

/gct/tcc/gga/ttc/act/ttc/tct/ - /tac/ - /atg/ - /tgg/gtt/cgc/

BspEI BsiWI BstXI.

Sites of variegation-><2> <2> <3>

-----FR2-------------------- >/ ..CDR2

61 62 63 64 65 66 67 68 69 70 71 72 73 74 75

Q A P G K G L E W V S - I - -

/caa/gct/cct/gtt/aaa/ggt/ttg/gag/tgg/gtt/tct/ - /atc/ - / - /

...BstXI

<1> <1> 25992-fold diversity in DCR2

...CDR2..................................... /---FR3-----

76 77 78 79 80 81 82 83 84 85 86 87 88 89 90

S G G - T - Y A D S V K G R F

/tct/ggt/ggc/ - /act/ - /tat/gct/gac/tcc/gtt/aaa/ggt/cgc/ttc/

-- - - FR3-------------------------------------------------

91 92 93 94 95 96 97 98 99 100 101 102 103 104 105

T I S R D N S K N T L Y L Q M

/act/atc/tct/aga/gac/aac/tct/aag/aat/act/ctc/tac/ttg/cag/atg/

XbaI

---FR3------------------------------------------------------

106 107 108 109 110 111 112 113 114 115 116 117 118 119 120

N S L R A E D T A V Y Y C A K

/aac/agc/tta/agg/gct/gag/gac/acc/gct/gtc/tac/tac/tgc/gcc/aaa/

Af1II

.....CDR3................../ Replaced by the various components!

121 122 123 124 125 126 127

D Y E G T G Y (SEQ ID NO: 24)

/gac/tat/gaa/ggt/act/ggt/tat/ (SEQ ID NO: 23)

/---------- fr4 ---(JH4)--------------------------------------------------

Y F D Y W G Q G T L V T V S S (SEQ ID NO: 26)

/tat/ttc/gat/tat/tgg/ggt/caa/ggt/acc/ctg/gtc/acc/gtc/tct/agt/.(SEQ ID NO: 25)

KpnI BstEII

<1> = Codons for ADEFGHIKLMNPQRSTVWY (equimolar mixture)

<2> = Codons for YRWVGS (equimolar mixture)

<3> = Codons for PS or PS and G (equimolar mixture)

TABLE 2

Oligonucleotides used to variegate CDR1 of human HC

CDR1-5 residues

	(ON-R1V1vg):	5′-ct/tcc/gga/ttc/act/ttc/tct/<1>/tac/<1>/atg/<1>/tgg/gtt/cgc/caa/gct/cct/gg-3′
		(SEQ ID NO: 27)

<1> = Codons of ADEFGHIKLMNPQRSTVWY 1:1

	(ON-Rltop):	5′-cctactgtct/tcc/gga/ttc/act/ttc/tct-3′ (SEQ ID NO: 28)

	(ON-Rlbot) [RC]:	5′-′tgg/gtt/cgc/caa/gct/cct/ggttgctcactc-3′ (SEQ ID NO: 29)

CDR1-7 residues

	(ON-R1V2vg):	5′-ct/tcc/gga/ttc/act/ttc/tcty/<6>/<7>/<7>/tac/tac/tgg/<7>/tgg/gtt/cgc/caa/gct/
		cct/gg-3′ (SEQ ID NO: 30)

	<6> = Codons for ST, 1:1
	<7> 0.2025(Codons for SG) + 0.035(Codons for ADEFHIKLMNPQRTVWY)

CDR1-14 residues

	(ON-R1V3vg):	5′-ct/tcc/gga/ttc/act/ttc/tct/atc/agc/ggt/ggt/tct/atc/tcc/<1>/<1>/<1>/-
		tac/tac/tgg/<1>/tgg/gtt/cgc/caa/gct/cct/gg-3′ (SEQ ID NO: 31)

<1> = Codons for ADEFGHIKLMNPQRSTVWY 1:1

TABLE 3

Oligonucleotides used to variegate CDR2 of human HC

CDR2-17 residues

(ON-R2V1vg):	5′-ggt/ttg/gag/tgg/gtt/tct/<2>/atc/<2>/<3>/tct/ggt/ggc/<1>/act/<1>/tat/gct/-
	gac/tcc/gtt/aaa/gg-3′ (SEQ ID NO: 32)

(ON-R2top):	5′-ct/tgg/gtt/cgc/caa/gct/cct/ggt/aaa/ggt/ttg/gag/tgg/gtt/tct-3′
	(SEQ ID NO: 33)

(ON-R2bot) [RC]:	5′-tat/gct/gac/tcc/gtt/aaa/ggt/cgc/ttc/act/atc/tct/aga/
	ttcctgtcac-3′ (SEQ ID NO: 34)

<I> = Codons for A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y (equimolar mixture)

<2> = Codons for Y, R, W, V, G and S (equimolar mixiure)

<a> = Codons for P and S (equimolar mixture) or P, S and G (equimolar mixture)

(ON-R2V2vg):	5′-ggt/ttg/gag/tgg/gtt/tct/<1>/atc/<4>/<1>/<1>/ggt/<5>/<1>/<1>/<1>/tat/gct/-
	gac/tcc/gtt/aaa/gg-3′ (SEQ ID NO: 35)

<4> = Codons for DINSWY (equimolar mixture)

<5> = Codons for SGDN, (equimolar mixture)

CDR2-16 residues

(ON-R2V3vg):	5′-ggt/ttg/gag/tgg/gtt/tct/<1>/att/<4>/<1>/<1>/ggt/
	<5>/<1>/<1>/tat/aac/cct/tcc/ctt/aag/gg-3′ (SEQ ID NO: 36)

(ON-R2bo3) [RC]:	5′-tat/aac/cct/tcc/ctt/aag/ggt/cgc/ttc/act/atc/tct/aga/ttcctgtcac-3′
	(SEQ ID NO: 37)

CDR2 19 residues

(ON-R2V4vg):	5′-ggt/ttg/gag/tgg/gtt/tct/<1>/atc/<8>/agt/<1>/<1>/
	<1>/ggt/ggt/act/act/<1>/tat/gcc/gct/tcc/gtt/aag/gg-3′ (SEQ ID NO: 38)

(ON-R2bo4) [RC]:	5′-tat/gcc/gct/tcc/gtt/aag/ggt/cgc/ttc/act/atc/tct/aga/ttcctgtcac′-3′
	(SEQ ID NO: 39)

<1>, <2>, <3>, <4> and <5> are as defined above

<8> is 0.27 R and 0.027 each of ADEFGHIKLMNPQSTVWY

TABLE 4

Preferred Components

			Fraction	Preferred
			of	Adjusted
Component	Length	Complexity	Library	Fraction

1	YYCA21111YFDYWG. 8	2.6 × 10⁵	.10	.02
	(SEQ ID NO: 6)
	(1 = any amino acid residue,
	except C; 2 = K and R)

2	YYCA2111111YFDYWG. 10	9.4 × 10⁷	.14	.14
	(SEQ ID NO: 7)
	(1 = any amino acid residue,
	except C; 2 = K and R)

3	YYCA211111111YFDYTG. 12	3.4 × 10¹⁰	.25	.25
	(SEQ ID NO: 8)
	(1 = any amino acid residue,
	except C; 2 = K and R)

4	YYCAR111S2S3111YFDYWG. 14	1.9 × 10⁸	.13	.14
	(SEQ ID NO: 9)
	(1 = any amino acid residue,
	except C; 2 = S and G
	3 = Y and W)

5	YYCA2111CSG11CY1YFDYWG. 15	9.4 × 10⁷	.13	.14
	(SEQ ID NO: 10)
	(1 = any amino acid residue
	except C; 2 = K and R)

6	YYCA211S1TIFG11111YFDYWG. 17	1.7 × 10¹⁰	.11	.12
	(SEQ ID NO: 11)
	(1 = any amino acid residue,
	except C; 2 = K and R)

7	YYCAR111YY2S33YY111YFDYMG. 18	3.8 × 10⁸	.04	.08
	(SEQ ID NO: 12)
	(1 = any amino acid residue,
	except C; 2 = D or G;
	3 = S and G)

8	YYCAR1111YC2231CY111YFDYWG. 19	2.0 × 10¹¹	.10	.11
	(SEQ ID NO: 13)
	(1 = any amino acid residue,
	except C; 2 = S and G;
	3 = T, D, and G)

TABLE 5

Oligonucleotides used to variegate the eight components of HC CDR3

(Ctop25): 5′-gctctggtcaac/tta/agg/gct/gag/g-3′ (SEQ ID NO: 40)

(CtprmA): 5′-gctctggtcaac/tta/agg/gct/gag/gac/acc/gct/gtc/tac/tac/tgc/gcc-3′

AflLL. . . (SEQ ID NO: 41)

(CBprmB)[RC]: 5′-/tac/ttc/gat/tac/tgg/ggc/caa/ggt/acc/ctg/gtc/acc/tcgctccacc-3′

(SEQ ID NO: 42) BstEII...

(CBot25)[RC]: 5′-/ggt/acc/ctg/gtc/acc/tcgctccacc-3′ (SEQ ID NO: 43)

The 20 bases at 3′ end of CtprmA are identical to the most 5′ 20 bases

of each of the vgDNA molecules.

Ctop25 is identical to the most 5′ 25 bases of CtprmA.

The 23 most 3′ bases of CBprmB are the reverse complement of the

most 3′ 23 bases of each of the vgDNA molecules.

CBot25 is identical to the 25 bases at the 5′ end of CBprmB.

Component 1

(C1t08):

5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/<1>/<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′

(SEQ ID NO: 44)

<1> = 0.095 Y + 0.095 G + 0.048 each of the residues ADEFHIKLMNPQRSTVW, no C;

<2> = K and R (equimolar mixture)

component 2

(C2t10):

5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/<1>/<1>/<1>/<1>/tac/ttc/gat/tac/tgg/ggc/caa/

gg-3′ (SEQ ID NO: 45)

<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C;

<2> = K and R (equimolar mixture)

Component 3

(C3t12):

5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/<1>/<1>/<1>/<1>/<1>/<1>/tac/ttc/gat/tac/-

tgg/ggc/caa/gg-3′ (SEQ ID NO: 46)

<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C;

<2> = K and R (equimolar mixture)

Component 4

(C4t140):

5′-cc/gct/gtc/tac/tac/tgc/gcc/cgt/<1>/<1>l<l>/tct/<2>/tct/<3>/<1>/<1>/<1>/tac/ttc/gat/-

tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 47)

<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C;

<2> = S and G (equimolar mixture);

<3> = Y and W (equimolar mixture)

Component 5

(C5t15):

5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/<1>/tgc/tct/ggt/<1>/<1>/tgc/tat/<1>/tac/-

ttc/gat/tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 48)

<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C;

<2> = K and R (equimolar mixture)

Component 6

(C6t17):

5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/tct/<1>/act/atc/ttc/ggt/<1>/<1>/<1>/<1>/-

<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 49)

<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C;

<2> = K and R (equimolar mixture)

Component 7

(C7t18):

5′-cc/gct/gtc/tac/tac/tgc/gcc/cgt/<1>/<1>/<1>/tat/tac/<2>/tct/<3>/<3>/tac/tat/-

<1>/<1>/<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 50)

<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = D and G

(equimolar mixture); <3> = S and G (equimolar mixture)

Component 8

(c8t19):

5′-cc/gct/gtc/tac/tac/tgc/gcc/cgt/<1>/<1>/<1>/<1>/tat/tgc/<2>/<2>/<3>/<1>/tgc/tat/-

<1>/<1>/<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′(SEQ ID NO: 51)

<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C;

<2> = S and G (equimolar mixture);

<3> = TDG (equimolar mixture);

TABLE 6

3-23:: JH4 Stuffers in place of CDRs

FR1(DP47/V3-23)------------------------

20 21 22 23 24 25 26 27 28 29 30

A M A E V Q L L E S G

ctgtctgaac cc atg gcc gaa/gtt/caa/ttg/tta/gag/tct/ggt/

(SEQ ID NO: 99)

Scab .......NcoI.... MfeI

---------------------------- FR1----------------------------

31 32 33 34 35 36 37 38 39 40 41 42 43 44 45

G G L V Q P G G S L R L S C A

/ggc/ggt/ctt/gtt/cag/cct/ggt/ggt/tct/tta/cgt/ctt/tct/tgc/gct/

---FR1--------------------->/...CDR1 stuffer..../---FR2------

46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

A S G F T F S S Y A / / W V R

/gct/tcc/gga/ttc/act/ttc/tct/tcg/tac/gct/tag/taa/tgg/gtt/cgc/

BspEI BsiWI BstXI.

-------FR2-------------------------------->/...CDR2 stuffer.

61 62 63 64 65 66 67 68 69 70 71 72 73 74 75

Q A P G K G L E W V S / P R /

/caa/gct/cct/ggt/aaa/ggt/ttg/gag/tgg/gtt/tct/taa/cct/agg/tag/

...BstXI AvrII..

....CDR2 stuffer...................................../---FR3---

91 92 93 94 95 96 97 98 99 100 101 102 103 104 105

T I S R D N S K N T L Y L Q M

/act/atc/tct/aga/gac/aac/tct/aag/aat/act/ctc/tac/ttg/cag/atg/

XbaI

--FR3------------..> CDR3 Stuffer ------------>/

106 107 108 109 110

N S L R A (SEQ ID NO: 53)

/aac/agc/tta/agg/gct/tag taa agg cct taa (SEQ ID NO: 52)

AflII StuI...

/-----FR4 ---(JH4)-------------------------------------------

Y F D Y W G Q G T L V T V S S (SEQ ID NO: 26)

/tat/ttc/gat/tat/tgg/ggt/caa/ggt/acc/ctg/gtc/acc/gtc/tct/agt/... (SEQ ID NO: 25)

KpnI BstEII

TABLE 7

A27:JH1 Human Kappa light chain gene

gaggacc attgggcccc ctccgagact ctcgagcgca

Scab ......Eco0109I XhoI

ApaI

acgcaattaa tgtgagttag ctcactcatt aggcacccca ggctttacac tttatgcttc

..-35.. Plac ..-10.

cggctcgtat gttgtgtgga attgtgagcg gataacaatt tcacacagga

aacagctatg accatgatta

cgccaagctt tggagccttt tttttggaga ttttcaac (SEQ ID NO: 54)

pflMI.......

Hind III

M13 III signal sequence (AA seg) ------------------------------

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

M K K L L F A I P L V V P F Y

gtg aag aag ctc cta ttt gct atc ccg ctt gtc gtt ccg ttt tac

--Signal-->FR1--------------------------------------------->

16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

S H S A Q S V L T Q S P G T L

/agc/cat/agt/gca/caa/tcc/gtc/ctt/act/caa/tct/cct/ggc/act/ctt/

ApaLI...

---- FR1 -------------------------------------->/ CDR1---->

31 32 33 34 35 36 37 38 39 40 41 42 43 44 45

S L S P G E R A T L S C R A S (SEQ ID NO: 55)

/tcg/cta/agc/ccg/ggt/gaa/cgt/gct/acc/tta/agt/tgc/cgt/gct/tcc/ (SEQ ID NO: 54; Cont′d)

EspI..... AflII ...

XmaI...

For CDR1:

<1> ADEFGHIKLMNPQRSTVWY 1:1

<2> S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)

<3> Y(0.2) ADEFGHIKLMNPQRSTVW (0.044 each)

(CDR1 installed as AflII-(SexAI or KasI) cassette.) For the most preferred 11 length codon 51

(XXX) is omitted; for the preferred 12 length this codon is <2>

------ CDR1--------------------- --->/--- FR2------------->

<1> <2> <2> xxx <3>

46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Q - V - - - - L A W Y Q Q K P (SEQ ID NO: 55; Cont′d)

/cag/ - /gtt/ - / - / - / - /ctt/gct/tgg/tat/caa/cag/aaa/cct/(SEQ ID NO: 54; Cont′d)

SexAI....

For CDR2:

<1> ADEFGHIKLMNPQRSTVWY 1:1

<2> S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)

<4> A(0.2) DEFGHIKLMNPQRSTVWY (0.044 each)

CDR2 installed as (SexAI or KasI) to (BamHI or RsrII) cassette.)

----- FR2 ------------------------->/------CDR2----------->

<1> <2> <4>

61 62 63 64 65 66 67 68 69 70 71 72 73 74 75

G Q A P R L L I Y - A S - R - (SEQ ID NO: 55; Cont′d)

/ggt/cag/gcg/ccg/cgt/tta/ctt/att/tat/ - /gct/tct/ - /cgc/ - (SEQ ID NO: 54; Cont′d)

SexAI.... KasI....

CDR2-->/--- FR3 ------------------------------------------->

<1>

76 77 78 79 80 81 82 83 84 85 86 87 88 89 90

- G I P D R F S G S G S G T D

/ - /ggg/atc/ccg/gac/cgt/ttc/tct/ggc/tct/ggt/tca/ggt/act/gac/

BamHI

RsrII.....

--------FR3------------------------------------------------>

91 92 93 94 95 96 97 98 99 100 101 102 103 104 105

F T L T I S R L E P E D F A V (SEQ ID NO: 55′ Cont′d)

/ttt/acc/ctt/act/att/tct/aga/ttg/gaa/cct/gaa/gac/ttc/gct/gtt/ (SEQ ID NO: 54; Cont′d)

XbaI

For CDR3 (Length 9):

<1> ADEFGHIKLMNPQRSTVWY 1:1

<3> Y(0.2) ADEFGHIKLMNPQRTVW (0.044 each)

For CDR3 (Length 8): QQ33111P

1 and 3 as defined for Length 9

For CDR3 (Length 10): QQ3211PP1T

1 and 3 as defined for Length 9

2 S(0.2) and 0.044 each of ADEFGHIKLMNPQRTVWY

CDR3 installed as XbaI to (Styl Or BsiWI)cassette.

------------->/----CDR3-------------------------->/----FR4--->

<3> <1> <1> <1> <1>

106 107 108 109 110 111 112 113 114 115 116 117 118 119 120

Y Y C Q Q - - - - P - T F G Q (SEQ ID NO: 55; Cont′d)

/tat/tat/tgc/caa/cag/ - / - / - / - /cct/ - /act/ttc/ggt/caa/ (SEQ ID NO: 54; Cont′d)

BstXI.........

----FR4-------------------->/ <-------Ckappa -------------

121 122 123 124 125 126 127 128 129 130 131 132 133 134

G T K V E I K R T V A A P S

/ggt/acc/aag/gtt/gaa/atc/aag/ /cgt/acg/gtt/gcc/gct/cct/agt/

StyI.... BsiWI..

135 136 137 138 139 140 141 142 143 144 145 146 147 148 149

V F I F P P S D E Q L K S G T

/gtg/ttt/atc/ttt/cct/cct/tct/gac/gaa/caa/ttg/aag/tca/ggt/act/

MfeI...

150 151 152 153 154 155 156 157 158 159 160 161 162 163 164

A S V V C L L N N F Y P R E A (SEQ ID NO: 55; Cont′d)

/gct/tct/gtc/gta/tgt/ttg/ctc/aac/aat/ttc/tac/cct/cgt/gaa/gct/ (SEQ ID NO: 54; Cont′d)

BssSI..

165 166 167 168 169 170 171 172 173 174 175 176 177 178 179

K V Q W K V D N A L Q S G N S

/aaa/gtt/cag/tgg/aaa/gtc/gat/aac/gcg/ttg/cag/tcg/ggt/aac/agt/

MluI....

180 181 182 183 184 185 186 187 188 189 190 191 192 193 194

Q E S V T E Q D S K D S T Y S

/caa/gaa/tcc/gtc/act/gaa/cag/gat/agt/aag/gac/tct/acc/tac/tct/

195 196 197 198 199 200 201 202 203 204 205 206 207 208 209

L S S T L T L S K A D Y E K H

/ttg/tcc/tct/act/ctt/act/tta/tca/aag/gct/gat/tat/gag/aag/cat/

210 211 212 213 214 215 216 217 218 219 220 221 222 223 224

K V Y A C E V T H Q G L S S P (SEQ ID NO: 55; Cont′d)

/aag/gtc/tat/GCt/TGC/gaa/gtt/acc/cac/cag/ggt/ctg/agc/ttc/cct/ (SEQ ID NO: 54; Cont′d)

SacI....

225 226 227 228 229 230 231 232 233 234

V T K S F N R G E C (SEQ ID NO: 55; Cont′d)

/gtt/acc/aaa/agt/ttc/aac/cgt/ggt/gaa/tgc/taa/tag ggcgcgcc

DsaI.... AscI....

BssHII

acgcatctctaa gcggccgc aacaggaggag (SEQ ID NO: 54; Cont′d)

NotI....

TABLE 8

2a2:JH2 Human lambda-chain gene

gaggaccatt gggcccc ttactccgtgac

Scab...... Eco0109I

---------FR1-------------------------------------------->

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

S A Q S A L T Q P A S V S G S P G (SEQ ID NO: 57)

agt/gca/caa/tcc/gct/ctc/act/cag/cct/gct/agc/gtt/tcc/ggg/tca/cct/ggt/ (SEQ ID NO: 56)

ApaLI... NheI... BstEII...

SexAI....

For CDR1 (length 14):

<1> = 0.27 T, 0.27 G, 0.027 each of ADEFHIKLMNPQRSVWY, no C

<2> = 0.27 D, 0.27 N,.0.027 each of AEFGHIKLMPQRSTVWY, no C

<3> = 0.36 Y, 0.0355 each of ADEFGHIKLMNPQRSTVW, no C

T G <1> S S <2> V G

-----FR1 ----------------> /---CDR1-----------------------

16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

Q S I T I S C T G - S S - V G

/caa/agt/atc/act/att/tct/tgt/aca/ggt/ - /tct/tct/ - /gtt/ggc/

BsrGI..

<1> <3> <2> <3> V S = vg Scheme #1, length = 14

-----CDR1 -------------> /------------- FR2-----------------

31 32 33 34 35 36 37 38 39 40 41 42 43 44 45

- - - - V S W Y Q Q H P G K A (SEQ ID NO: 57; Cont′d)

/ - / - / - / - /gtt/tct/tgg/tat/caa/caa/cac/ccg/ggc/aag/gcg/ (SEQ ID NO: 56; Cont′d)

XmaI.... KasI.....

AvaI....

A second Vg scheme for CDR1 gives segments of length 11:

T₂₂G<2><4>L<4><4><4><3><4><4> where

<4> = equimolar mixture of each of ADEFGHIKLMNPQRSTVWY, no C

<3> = as defined above for the alternative CDR1

For CDR2:

<2> and <4> 8 are the same variegation as for CDR1

<4> <4> <4> <2> R P S

--FR2---------------> /-------CDR2--------- ----->/------FR3-

46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

P K L M I Y - - - - R P S G V

/ccg/aag/ttg/atg/atc/tac/ - / - / - / - /cgt/cct/tct/ggt/gtt/

KasI....

--------FR3-------------------------------------------------

61 62 63 64 65 66 67 68 69 70 71 72 73 74 75

S N R F S G S K S G N T A S L (SEQ ID NO: 57; Cont′d)

/agc/aat/cgt/ttc/tcc/gga/tct/aaa/tcc/ggt/aat/acc/gca/agc/tta/ (SEQ ID NO: 56; Cont′d)

BspEI.. HindIII.

BsaBI..............(blunt)

-------FR3------------------------------------------------->

76 77 78 79 80 81 82 83 84 85 86 87 88 89 90

T I S G L Q A E D E A D Y Y C (SEQ ID NO: 57; Cont′d)

/act/atc/tct/ggt/ctg/cag/gct/gaa/gac/gag/gct/gac/tac/tat/tgt/ (SEQ ID NO: 56; Cont′d)

PstI...

CDR3 (Length 11):

<2> and <4> are the same variegation as for CDR1

<5> = 0.36 S, 0.0355 each of ADEFGHIKLMNPQRTVWY no C

CDR3 (Length 10):

<5> SY <1> <5> S <5> <1> <4> V

<1> is an equimolar mixture of ADEFGHIKLMNPQRSTVWY, no C

<4> and <5> are as defined for Length 11

<4> <5> <4> <2> <4> S <4> <4> <4> <4> V

------CDR3--------------------------------->/----FR4-------

91 92 93 94 95 96 97 98 99 100 101 102 103 104 105

- - - - - S - - - - V F G G G

/ - / - / - / - / - /tct/ - / - / - / - /gtc/ttc/ggc/ggt/ggt/

KpnI..

-------FR4------------->

106 107 108 109 110 111 112 113 114 115 116 117 118 119 120

T K L T V L G Q P K A A P S V

/acc/aaa/ctt/act/gtc/ctc/ggt/caa/cct/aag/gct/gct/cct/tcc/gtt/

KpnI... HincII..

Bsu36I...

121 122 123 124 125 126 127 128 129 130 131 132 133 134 135

T L F P P S S E E L Q A N K A (SEQ ID NO: 57; Cont′d)

/act/ctc/ttc/cct/cct/agt/tct/gaa/gag/ctt/caa/gct/aac/aag/gct/ (SEQ ID NO: 56; Cont′d)

SapI.....

136 137 138 139 140 141 142 143 144 145 146 147 148 149 150

T L V C L I S D F Y P G A V T

/act/ctt/gtt/tgc/ttg/atc/agt/gac/ttt/tat/cct/ggt/gct/gtt/act/

BclI....

151 152 153 154 155 156 157 158 159 160 161 162 163 164 165

V A W K A D S S P V K A G V E

/gtc/gct/tgg/aaa/gcc/gat/tct/tct/cct/gtt/aaa/gct/ggt/gtt/gag/

BsmBI...

166 167 168 169 170 171 172 173 174 175 176 177 178 179 180

T T T P S K Q S N N K Y A A S

/acg/acc/act/cct/tct/aaa/caa/tct/aac/aat/aag/tac/gct/gcg/agc/

BsmBI... SacI....

181 182 183 184 185 186 187 188 189 190 191 192 193 194 195

S Y L S L T P E Q W K S H K S (SEQ ID NO: 57; Cont′d)

/tct/tat/ctt/tct/ctc/acc/cct/gaa/caa/tgg/aag/tct/cat/aaa/tcc/ (SEQ ID NO: 56; Cont′d)

SacI...

196 197 198 199 200 201 202 203 204 205 206 207 208 209 210

Y S C Q V T H E G S T V E K T

/tat/tcc/tgt/caa/gtt/act/cat/gaa/ggt/tct/acc/gtt/gaa/aag/act/

BspHI...

211 212 213 214 215 216 217 218 219

V A P T E C S (SEQ ID NO: 57; Cont′d)

/gtt/gcc/cct/act/gag/tgt/tct/tag/tga/ggcgcgcc

AscI....

BssHII

aacgatgttc aag gcggccgc aacaggaggag (SEQ ID NO: 56; Cont′d)

NotI.... Scab.......

TABLE 9

Oligonucleotides For Kappa and Lambda Light Chain Variegation

(Ctop25): 5′-gctctggtcaac/tta/agg/gct/gag/g-3′ (SEQ ID NO: 58)

(SEQ ID NO: 59) AflII...

(CBprmB)[RC]: 5′-/tac/ttc/gat/tac/ttg/ggc/caa/ggt/acc/ctg/gtc/acc/tcgctccacc-3′

(SEQ ID NO: 60) BstEII...

(CBot25) [RC]: 5′-/ggt/acc/ctg/gtc/acc/tcgaccacc-3′ (SEQ ID NO: 61)

Kappa chains: CDR1 (“1”), CDR2 (“2”), CDR1 (“3”)

CDR1

(KalTop610): 5′-ggtctcagttg/cta/agc/ccg/ggt/gaa/cgt/gct/acc/tta/agt/tgc/cgt/gct/tcc/cag-3′

(SEQ ID NO: 62)

(KalSTp615): 5′-ggtctcagttg/cta/agc/ccg/ggt/g-3′ (SEQ ID NO: 63)

(KalBot620) [RC]: ′5′-ctt/gct/tgg/tat/caa/cag/aaa/cct/ggt/cag/gcg/ccaagtcgtgtc-3′

(SEQ ID NO: 64)

(KalSB625) [RC]: 5′-cct/ggt/cag/gcg/ccaagtcgtgtc-3′ (SEQ ID NO: 65)

(Kalvg600): 5′-gct/acc/tta/agt/tgc/cgt/gct/tcc/cag-

/<1>/gtt/<2>/<2>/<3>/ctt/gct/tgg/tat/caa/cag/aaa/cc-3′ (SEQ ID NO: 66)

(Kalvg600-12): 5′-gct/acc/tta/agt/tgc/cgt/gct/tcc/cag-

/<1>/gtt/<2>/<2>/<2>/<3>/ctt/gct/tgg/tat/caa/cag/aaa/cc-3′ (SEQ ID NO: 67)

CDR2

(Ka2Tshort657): 5′-cacgagtccta/cct/ggt/cag/gc-3′ (SEQ ID NO: 68)

(Ka2Tlong655): 5′-cacgagtccta/cct/ggt/cag/gcg/ccg/cgt/tta/ctt/att/tat-3′ (SEQ ID NO: 69)

(Ka2Bshort660): [RC]: 5′-/gac/cgt/ttc/tct/ggt/tctcacc-3′ (SEQ ID NO: 70)

(Ka2vg650): 5′-cag/gcg/ccg/cgt/tta/ctt/att/tat/<1>/gct/tct/<2>/-

/cgc/<4>/<1>/ggg/atc/ccg/gac/cgt/ttc/tct/ggt/tctcacc-3′ (SEQ ID NO: 71)

CDR3

(Ka3Tlon672): 5′-gacgagtocttct/aga/ttg/gaa/cct/gaa/gac/ttc/gct/gtt/tat/tat/tgc/caa/c-3′

(SEQ ID NO: 72)

(Ka3BotL682)[RC]: 5′-act/ttc/ggt/caa/ggt/acc/aag/gtt/gaa/atc/aag/cgt/acg/tcacaggtgag-3′

(SEQ ID NO: 73)

(Ka3Bsho694) [RC]: 5′-gaa/atc/aag/cgt/acg/tcacaggtgag-3′(SEQ ID NO: 74)

(Ka3vg670): 5′-gac/ttc/gct/gtt/ -

/tat/tat/tgc/caa/cag/<3>/<1>/<1>/<1>/cct/<1>/act/ttc/ggt/caa/-

/ggt/acc/aag/gtt/g-3′ (SEQ ID NO: 75)

(Ka3v670-8): 5′-gac/ttc/gct/gtt/-

/tat/tat/tgc/caa/cag/<3>/<3>/<1>/<1>/<1>/cct/ttc/ggt/caa/-

/ggt/acc/aag/gtt/g-3′ (SEQ ID NO: 76)

(Ka3vg670-10): 5′-gac/ttc/gct/gtt/tat/-

/tat/tgc/caa/cag/<3>/<2>/<1>/<1>/cct/cct/<1>/act/ttc/ggt/caa/-

/ggt/acc/aag/gtt/g-3′ (SEQ ID NO: 77)

Lambda Chains: CDR1 (“1”), CDR2 (“2”), CDR3(“3”)

CDR1

(LmlTPri75): 5′-gacgagtcctgg/tca/cct/ggt/-3′ (SEQ ID NO: 78)

(Lm1t1o715): 5′-gacgagtcctgg/tca/cct/ggt/caa/agt/atc/act/att/tct/tgt/aca/ggt-3′

(SEQ ID NO: 79)

(Lm1b1o724)[rc]: 5′-/gtt/tct/tgg/tat/caa/caa/cac/ccg/ggc/aag/gcg/agatcttcacaggtgag-3′

(SEQ ID NO: 80)

(Lm1bsh737)[rc]: 5′-gc/aag/gcg/agatcttcacaggtgag-3′ (SEQ ID NO: 81)

(Lm1vg710b): 5′-gt/atc/act/att/tct/tgt/aca/ggt/<2>/<4>/ctc/<4>/<4>/<4>/-

/<3>/<4>/<4>/tgg/tat/caa/caa/cac/cc-3′ (SEQ ID NO: 82)

(Lmlvg710): 5′-gt/atc/act/att/tct/tgt/aca/ggt/<1>/tct/tct/<2>/gtt/ggc/-

/<1>/<3>/<2>/<3>/gtt/tct/tgg/tat/caa/caa/cac/cc-3′ (SEQ ID NO: 83)

CDR2

(Lm2TSh757): 5′-gagcagaggac/ccg/ggc/aag/gc-3′(SEQ ID NO: 84)

(Lm2TLo753): 5′-gagcagaggac/ccg/ggc/aag/gcg/ccg/aag/ttg/atg/atc/tac/-3′ (SEQ ID NO: 85)

(Lm2BLo762) [RC]: 5′-cgt/cct/tct/ggt/gtc/agc/aat/cgt/ttc/tcc/gga/tcacaggtgag-3′

(SEQ ID NO: 86)

(Lm2Bsh765) [RC]: 5′-cgt/ttc/tcc/gga/tcacaggtgag-3′ (SEQ ID NO: 87)

(Lm2vg750): 5′-g/ccg/aag/ttg/atg/atc/tac/-

<4>/<4>/<4>/<2>/cgt/cct/tct/ggt/gtc/agc/aat/c-3′ (SEQ ID NO: 88)

CDR3

(Lm3TSh822): 5′-ctg/cag/gct/gaa/gac/gag/gct/gac-3′ (SEQ ID NO: 89)

(Lm3TLo819): 5′-ctg/cag/gct/gaa/gac/gag/gct/gac/tac/tat/tgt/-3′ (SEQ ID NO: 90)

(Lm3BLo825) [RC]: 5′-gtc/ttc/ggc/ggt/ggt/acc/aaa/ctt/act/gtc/ctc/ggt/caa/cct/aag/g-

acacaggtgag-3′ (SEQ ID NO: 91)

(Lm3BSh832) (RC]: 5′ c/ggt/caa/cct/aag/gacacaggtgag (SEQ ID NO: 92)

(Lm3vg17): 5′-gac/gag/gct/gac/tac/tat/tgt/-/

<4>/<5>/<4>/<2>/<4>/tct/<4>/<4>/<4>/<4>/-

Gtc/ttc/ggc/ggt/ggt/acc/aaa/ctt/ac-3′ (SEQ ID NO: 93)

(Lm3vg817-10): 5′- gac/gag/gct/gac/tac/tat/tgt/-

/<5>/agc/tat/<1>/<5>/tct/<5>/<1>/<4>/gtc/ttc/ggc/ggt/ggt/-

/acc/aaa/ctt/ac-3′ (SEQ ID NO: 94)

TABLE 10

A27:JH1 Kappa light chain gene with stuffers in place of CDRs
Each stuffer contains at least one stop codon and a
restriction site that will be unique within the diversity vector.

gaggacc attgggcccc ctccgagact ctcgagcgca

Scab..... EcoO109I

ApaI. XhoI..

acgcaattaa tgtgagttag ctcactcatt aggcacccca ggctttacac tttatgcttc

..−35.. Plac ..−10.

cggctcgtat gttgtgtgga attgtgagcg gataacaatt tcacacagga aacagctatgac

catgatta cgccaagctt tggagccttt tttttggaga ttttcaac (SEQ ID NO:95)

Pf1MI .............

Hind3.

M13 III signal sequence (AA seq)-------------------------->

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

M K K L L F A I P L V V P F Y

gtg aag aag ctc cta ttt gct atc ccg ctt gtc gtt ccg ttt tac

--Signal--> FR1--------------------------------------------

16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

S H S A Q S V L T Q S P G T L

/agc/cat/agt/gca/caa/tcc/gtc/ctt/act/caa/tct/cct/ggc/act/ctt/

ApaLI...

----- FR1------------------- -------------->/---------Stuffer->

31 32 33 34 35 36 37 38 39 40 41 42 43

S L S P G E R A T L S / / (SEQ ID NO: 96)

/tcg/cta/agc/ccg/ggt/gga/cgt/gct/acc/tta/agt/tag/taa/gct/ccc/ (SEQ ID NO: 95; Cont′d)

EspI..... AflII...

XmaI....

- Stuffer for CDR1--> FR2 --------------- FR2--- >/ Stuffer for CDR2

59 60 61 62 63 64 65 66

K P G Q A P R

/agg/cct/ctt/tga/tct/g/aaa/cct/ggt/cag/gcg/ccg/cgt/taa/tga/aagcgctaatggccaacagtg

StuI... SexAI... KasI.... AfeI.. MscI..

Stuffer-->/--- FR3 ------------------------------------------->

76 77 78 79 80 81 82 83 84 85 86 87 88 89 90

T G I P D R F S G S G S G T D (SEQ ID NO: 96; Cont′d)

/act/ggg/atc/ccg/gac/cgt/ttc/tct/ggc/tct/ggt/tca/ggt/act/gac/ (SEQ ID NO: 95; Cont′d)

BamHI...

RsrII............

--------FR3------>----------------STUFFER for CDR3------------------->

91 92 93 94 95 96 97

F T L T I S R / /

/ttt/acc/ctt/act/att/tct/aga/taa/tga/ gttaac tag acc tacgta acc tag

XbaI... HpaI.. SnaBI.

----------------------CDR3 stuffer---------------->/------FR4------->

118 119 120

F G Q

/ttc/ggt/caa/

-----FR4--------------------> <--------Ckappa -----------

121 122 123 124 125 126 127 128 129 130 131 132 133 134

G T K V E I K R T V A A P S (SEQ ID NO: 96; Cont′d)

/ggt/acc/aag/gtt/gaa/atc/aag/ /cgt/acg/gtt/gcc/gct/cct/agt/

StyI.... BsiWI.. (SEQ ID NO: 95; Cont′d)

135 136 137 138 139 140 141 142 143 144 145 146 147 148 149

V F I F P P S D E Q L K S G T (SEQ ID NO: 96; Contfd)

/gtg/ttt/atc/ttt/cct/cct/tct/gac/gaa/caa/ttg/aag/tca/ggt/act/

MfeI...

acgcatctctaa gcggccgc aacaggaggag (SEQ ID NO: 95; Cont′d)

NotI....

EagI..

TABLE 11

2a2:JH2 Human lambda-chain gene with stuffers in place of CDR3

gaggaccatt gggcccc ttactccgtgac

Scab..... EcoO109I

ApaI

----------FR1-------------- ------------------------------>

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

S A Q S A L T Q P A S V S G S P G

agt/gca/caa/tcc/gct/ctc/act/cag/cct/gct/agc/gtt/tcc/ggg/tca/cct/ggt/

ApaLI... NheI... BstEll...

SexAI....

-------FR1----------------> /---------stuffer for CDR1 ---------

16 17 18 19 20 21 22 23

Q S I T I S C T (SEQ ID NO: 98)

/caa/agt/atc/act/att/tct/tgt/aca/tct tag tga ctc (SEQ ID NO: 97)

BsrGI..

----Stuffer----------------------------->--------FR2------->

31 32 33 34 35 36 37 38 39 40 41 42 43 44 45

R S / / P / H P G K A

aga tct taa tga ccg tag cac/ccg/ggc/aag/gcg/

BglII XmaI.... KasI.....

AvaI....

--/-------------Stuffer for CDR2--------------------------------->

P

/ccg/taa/tga/atc tcg tac g ct/ggt/gtt/

KasI.... BsiWI...

-------FR3------------------------------------------------

61 62 63 64 65 66 67 68 69 70 71 72 73 74 75

S N R F S G S K S G N T A S L (SEQ ID NO: 98; Cont′d)

/agc/aat/cgt/ttc/tcc/gga/tct/aaa/tcc/ggt/aat/acc/gca/agc/tta/ (SEQ ID NO: 97; Cont′d)

BseEI.. HindIII.

BsaBI..........(blunt)

------FR3------------->/--Stuffer for ODR3------------------>/

76 77 78 79 80 81 82 83 84 85 86 87 88 89 90

T I S G L Q

/act/atc/tct/ggt/ctg/cag/gtt ctg tag ttc caattg ctt tag tga ccc

PstI... MfeI..

-----Stuffer------------------------------->/---FR4---------

103 104 105

G G G

/ggc/ggt/ggt/

KpnI...

--------FR4-------------->

106 107 108 109 110 111 112 113 114 115 116 117 118 119 120

T K L T V L G Q P K A A P S (SEQ ID NO: 98; Cont′d)

V/acc/aaa/ctt/act/gtc/ctc/ggt/caa/cct/aag/gct/gct/cct/tcc/gtt/ (SEQ ID NO: 97; Cont′d)

KpnI... HincII..

Bsu36I...

121 122 123 124 125 126 127 128 129 130 131 132 133 134 135

T L F P P S S E E L Q A N K A

/act/ctc/ttc/cat/cct/agt/tct/gaa/gag/ctt/caa/gct/aac/aag/gct/

SapI.....

136 137 138 139 140 141 142 143 144 145 146 147 148 149 150

T L V C L I S D F Y P G A V T (SEQ ID NO: 98; Cont′d)

/act/cct/gtt/tgc/ttg/atc/agt/gac/ttt/tat/cct/ggt/gct/gtt/act/ (SEQ ID NO: 97; Cont′d)

Bc1I....

The invention relates to generation of useful diversity in synthetic antibody (Ab) gene, especially to Ab genes having frameworks derived from human Abs.

BACKGROUND OF THE INVENTION

Antibodies are highly useful molecules because of their ability to bind almost any substance with high specificity and affinity and their ability to remain in circulation in blood for prolonged periods as therapeutic or diagnostic agents. For treatment of humans, Abs derived from human Abs are much preferred to avoid immune response to the Ab. For example, murine Abs very often cause Human Anti Mouse Antibodies (HAMA) which at a minimum prevent the therapeutic effects of the murine Ab. For many medical applications, monoclonal Abs are preferred. Nowadays the preferred method of obtaining a human Ab having a particular binding specificity is to select the Ab from a library of human-derived Abs displayed on a genetic package, such as filamentous phage.
Libraries of phage-displayed Fabs and scFvs have been produced in several ways. One method is to capture the diversity of donors, either naive or immunized. Another way is to generate libraries having synthetic diversity. The present invention relates to methods of generating useful diversity in human Ab scaffolds.
As is well known, typical Abs consist of two heavy chains (HC) and two light chains (LC). There are several types of HCs: gamma, mu, epsilon, delta, etc. Each type has an N-terminal V domain followed by three or more constant domains. The LCs comprise an N-terminal V domain followed by a constant domain. LCs come in two types: kappa and lambda.
Within each V domain (LC or HC) there are seven canonical regions, named FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4, where “FR” stands for “Framework Region” and “CDR” stands for “Complementarity Determining Region”. For LC and HC, the FR and CDR GLGs have been selected over time to be secretable, stable, non-antigenic and these properties should be preserved as much as possible. Actual Ab genes contain mutations in the FR regions and some of these mutations contribute to binding, but such useful FR mutations are rare and are not necessary to obtain high-affinity binding. Thus, the present invention will concentrate diversity in the CDR regions.
In LC, FR1 up to FR3 and part of CDR3 comes from a genomic collection of genes called “V-genes”. The remainder of CDR3 and FR4 comes from a genomic collection of genes called “J-genes”. The joining may involve a certain degree of mutation, allowing diversity in CDR3 that is not present in the genomic sequences. After the LC gene is formed, somatic mutations can give rise to mature, rearranged LC genes that have higher affinity for an antigen (Ag) than does any LC encoded by genomic sequences. A large fraction of somatic mutations occur in CDRs.
The HC V region is more complicated. A V gene is joined to a J gene with the possible inclusion of a D segment. About half of HC Abs sequences contain a recognizable D segment in CDR3. The joining is achieved with an amazing degree of molecular sloppiness. Roughly, the end of the V gene may have zero to several bases deleted or changed, the D segment may have zero to many bases removed or changed at either end, a number of random bases may be inserted between V and D or between D and J, and the 5′ end of J may be edited to remove or change several bases. Withal, it is amazing that human heavy chains work, but they do. The upshot is that the CDR3 is highly diverse both in encoded amino-acid sequences and in length. In designing synthetic libraries, there is the temptation to just throw in a high degree of synthetic diversity and let the phage sort it out. Nevertheless, D regions serve a function. They cause the Ab repertoire to be rich in sequences that a) allow Abs to fold correctly, and b) are conducive to binding to biological molecules, i.e. antigens.
One purpose of the present invention is to show how a manageable collection of diversified sequences can confer these advantages on synthetic Ab libraries. Another purpose of the present invention is to disclose analysis of known mature Ab sequences that lead to improved designs for diversity in the CDR1 and CDR2 of HC and the three CDRs of lambda and kappa chains.

BRIEF STATEMENT OF THE INVENTION

The invention is directed to methods of preparing synthetically diverse populations of Ab genes suitable for display on genetic packages (such as phage or phagemids) or for other regimens that allow selection of specific binding. Said populations concentrate the diversity into regions of the Ab that are likely to be involved in determining affinity and specificity of the Ab for particular targets. In particular, a collection of actual Ab genes has been analyzed and the sites of actual diversity have been identified. In addition, structural considerations were used to determine whether the diversity is likely to greatly influence the binding activity of the Ab. Schemes of variegation are presented that encode populations in which the majority of members will fold correctly and in which there is likely to be a plurality of members that will bind to any given Ag. Specifically, a plan of variegation is presented for each CDR of the human heavy chain, kappa light chain, and lambda light chain. The variegated CDRs are presented in synthetic HC and LC frameworks.
In one embodiment, the invention involves variegation of human HC variable domains based on a synthetic 3-23 domain joined to a JH4 segment in which the variability in CDR1 and CDR2 comprises sequence variation of segments of fixed length while in CDR3 there are several components such that the population has lengths roughly corresponding to lengths seen in human Abs and having embedded D segments in a portion of the longer segments. In the light chains, the kappa chain is built in an A27 framework and a JK1 while lambda is built in a 2a2 framework with an L2 J region.

Examples

Choice of a Heavy-Chain V Domain

The HC Germ-Line Gene (GLG) 3-23 (also known as VP-47) accounts for about 12% of all human Abs and it suitable for the framework of the library. Certain types of Ags elicit Abs having particular types of VH genes; in some cases, the types elicited are otherwise rarely found. This apparent Ag/Ab type specificity has been ascribed to possible structural differences between the various families of V genes. It is also possible that the selection has to do with the availability of particular AA types in the GLG CDRs. Suppose, for example, that the sequence YR at positions 4 and 5 of CDR2 is particularly effective in binding a particular type of Ag. Only the V gene 6-1 provides this combination. Most Abs specific for the Ag will come from GLG 6-1. If Y4-R5 were provided in other frameworks, then other frameworks are likely to be as effective in binding the Ag.

Analysis of HC CDR1 and CDR2:

In CDR1 and CDR2 of HCs, the GLGs provide limited length diversity as shown in Table 15P. Note that GLGs provide CDR1s only of the lengths 5, 6, and 7. Mutations during the maturation of the V-domain gene leads to CDR1s having lengths as short as 2 and as long as 16. Nevertheless, length 5 predominates. The preferred length for the present invention is 5 AAs in CDR1 with a possible supplemental components having lengths of 7 and 14.
GLGs provide CDR2s only of the lengths 15-19, but mutations during maturation result in CDR2s of length from 16 to 28 AAs. The lengths 16 and 17 predominate in mature Ab genes and length 17 is the most preferred length for the present invention. Possible supplementary components of length 16 and 19 may also be incorporated.
Table 20P shows the AA sequences of human GLG CDR1s and CDR2. Table 21P shows the frequency of each amino-acid type at each position in the GLGs. The GLGs as shown in Table 20P have been aligned by inserting gaps near the middle of the segment so that the ends align.
The 1398 mature V-domain genes used in studying D segments (vide infra) were scanned for examples in which CDR1 and CDR2 could be readily identified. Of this sample 1095 had identifiable CDR1, 2, and 3. The CDRs were identified by finding subsequences of the GLGs in an open reading frame. There are 51 human HC V genes. At the end of FR1, there are 20 different 9-mers. At the start of FR2, there are 11 different 9-mers. At the end of FR2 there are 14 different 9-mers. At the start of FR3, there are 14 different 9-mers. At the end of FR3, there are 13 different 9-mers. At the start of JH, there are three different 9-mers. These motifs were compared to the reported gene in frame and a match, at the site of maximum similarity, of seven out of nine was deemed acceptable. Only when all three CDRs were identified were any of the CDRs included in the analysis. In addition, the type of the gene was determined by comparing the framework regions to the GLG frameworks; the results are shown in Table 22P.

Design of HC CDR1 and CDR2 Diversity.

Diversity in CDR1 and CDR2 was designed from: a) the diversity of the GLGs, b) observed diversity in mature HC genes, and c) structural considerations. In CDR1, examination of a 3D model of a humanized Ab showed that the side groups of residues 1, 3, and 5 were directed toward the combining pocket. Consequently, we allow each of these positions to be any amino-acid type except cysteine. Cysteine can form disulfide bonds. Disulfide bonds are an important component of the canonical Ig fold. Having free thiol groups could interfere with proper folding of the HC and could lead to problems in production or manipulation of selected Abs. Thus, I exclude cysteine from the menu. The side groups of residue 2 is directed away from the combining pocket. Although this position shows substantial diversity, both in GLG and mature genes, I fixed this residue as Tyr because it occurs in 681/820 mature genes (Table 21P). Position 4 is fixed as Met. There is some diversity here, but almost all mature genes have uncharged hydrophobic AA types: M, W, I, V, etc. (Table 21P). Inspection of a 3D model shows that the side group of residue 4 is packed into the innards of the HC. Since we are using a single framework (3-23), we retain the Met that 3-23 has because it is likely to fit very well into the framework of 3-23. Thus, the most preferred CDR1 library consists of XYXMX (SEQ ID NO:109) where X can be any one of [A,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y] (no C). The DNA that encodes this is preferably synthesized using trinucleotide building blocks so that each AA type is present in essentially equimolar amounts. Specifically, the X codons are synthesized using a mixture of the codons [gct, gat, gag, ttt, ggt, cat, att, aag, atg, aat, cct, cag, cgt, tct, act, gtt, tgg, tat]. This diversity is shown in the context of a synthetic 3-23 gene in Table 18P. The diversity oligonucleotide (ON) is synthesized from BspEI to BstXI and can be incorporated either by PCR synthesis using overlapping ONs or introduced by ligation of BspEI/BstXI-cut fragments. Table 22P shows ONs that embody the specified variegation. PCR using ON-R1V1vg, ON-R1top, and ON-R1bot gives a dsDNA product of 73 base pairs, cleavage with BspEI and BstXI trims 11 and 13 bases from the ends and provides cohesive ends that can be ligated to similarly cut vector having the synthetic 3-23 domain shown in Table 18P. Replacement of ON-R1V1vg with either ONR1V2vg or ONR1V3vg allows synthesis of the two alternative diversity patterns given below.
Alternatively, one can include CDR1s of length 7 and/or 14. For length 7, a preferred diversity is (S/T)₁(S/G/x)₂(S/G/x)₃Y₄Y₅W₆(S/G/x)₇(SEQ ID NO:107); where (S/T) indicates an equimolar mixture of Ser and Thr codons; (S/G/x) indicates a mixture of 0.2025 S, 0.2025 G, and 0.035 for each of A, D, E, F, H, I, K, L, M, N, P, Q, R, T, V, W, Y. Other proportions could be used. The design gives a predominance of Ser and Gly at positions 2, 3, and 7, as occurs in mature HC genes. For length 14, a preferred pattern of diversity is VSGGSISXXXYYWX (SEQ ID NO:1) where X can be any AA type except Cys. This pattern appears to arise by insertions into the GLG sequences (SGGYYWS; SEQ ID NO:110, (4-30.1 and 4-31) and similar sequences. There is a preference for a hydrophobic residue at position 1 (V or C) with a second insertion of SISXXX (SEQ ID NO:111) between GG and YY. Diversity ONs having CDR1s of length 7 or 14 are synthesized from BspEI to BstXI and introduced into the library in appropriate proportions to the CDR1 of length 5. The components should be incorporated in approximately the ratios in which they are observed in antibodies selected without reference to the length of the CDRs. For example, the sample of 1095 HC genes examined here have them in the ratios (L=5:L=7:L=14::820:175:23::0.80:0.17:0.02).

CDR2

Diversity at CDR2 was designed with the same considerations: GLG sequences, mature sequences and 3D structure. A preferred length for CDR2 is 17, as shown in Table 18P. Examination of a 3D model suggests that the residues shown as varied in Table 18P are the most likely to interact directly with Ag. Thus a preferred pattern of variegation is: <2>I<2><3>SGG<1>T<1>YADSVKG (SEQ ID NO:2), where <2> indicates a mixture of YRWVGS, <3> is a mixture of P and S, and <1> is a mixture of ADEFGHIKLMNPQRSTVWY (no C). ON-R2V1vg shown in Table 22P embodies this diversity pattern. PCR with ON-R2V1vg, ON-R2top, and ONR2bot gives a dsDNA product of 122 base pairs. Cleavage with BstXI and XbaI removes about 10 bases from each end and produces cohesive ends that can be ligated to similarly cut vector that contains the 3-23 gene shown in Table 18P.
An alternative pattern would include the variability seen in mature CDR2s as shown in Table 21P: <1>I<4><1><1>G<5><1><1><1>YADSVKG (SEQ ID NO:3), where <4> indicates a mixture of DINSWY, and <5> indicates a mixture of SGDN. This diversity pattern is embodied in ON-R2V2vg shown in Table 22P. For either case, the variegated ONs would be synthesized so that fragments of dsDNA containing the BstXI and XbaI site can be generated by PCR. ON-R2V2vg embodies this diversity pattern.
Alternatively, one can allow shorter or longer CDR2s. Table 22P shows ON-R2V3vg which embodies a CDR2 of length 16 and ON-R2V4vg which embodies a CDR2 of length 19. Table 22P shows ON-R2V3vg is PCR amplified with ON-R2top and ON-R2bo3 while ON-R2V4vg is amplified with ON-R2top and ONR2-bo4.

Analysis of HC CDR3:

CDR3s of HC vary in length and in sequence. About half of human HCs consist of the components: V::nz::D::ny::JHn where V is a V gene, nz is a series of bases (mean 12) that are essentially random, D is a D segment, often with heavy editing at both ends, ny is a series of bases (mean 6) that are essentially random, and JH is one of the six JH segments, often with heavy editing at the 5′ end. In HCs that have no identifiable D segment, the structure is V::nz::JHn where JH is usually edited at the 5′ end. Our goal is to mimic the diversity of CDR3, but not to duplicate it (which would be impossible). The D segments appear to provide spacer segments that allow folding of the IgG. The greatest diversity is at the junctions of V with D and of D with JH. The planned CDR3 library will consist of several components. Some of these will have only sequence diversity. Others will have sequence diversity with embedded D segments to extend the length while incorporating sequences known to allow Igs to fold.
There are many papers on D segments. Corbett et al. (1997) show which D segments are used in which reading frames. My analysis basically confirms their findings. They did not report, however, the level of editing of each D segment and this information is needed for design of an effective library.
The following diversified sequences would be incorporated in the indicated proportions: “1” stands for 0.095 [G, Y] and 0.048 [A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W]; double dose of Gly and Tyr plus all other AAs except Cys at equal level.
The amount of each component is assigned from the tabulation of lengths of the collection of natural VH genes. Component 1 represents all the genes having length 0 to 8 (counting from the YYCAR (SEQ ID NO:112) motif to the WG dipeptide motif). Component 2 corresponds the all the chains having length 9 or 10. Component 3 corresponds to the genes having length 11 or 12 plus half the genes having length 13. Component 4 corresponds to those having length 14 plus half those having length 13. Component 5 corresponds to the genes having length 15 and half of those having length 16. Component 6 corresponds to genes of length 17 plus half of those with length 16. Component 7 corresponds to those with length 18. Component 8 corresponds to those having length 19 and greater.
The composition has been adjusted because the first component is not complex enough to justify including it as 10% of the library. If the final library were to be 1. E 9, then 1. E 8 sequences would come from component 1, but it has only 2.6 E 5 CDR3 sequences so that each one would occur in ˜385 CDR1/2 contexts. I think it better to have this short CDR3 diversity occur in ˜77 CDR1/2 contexts and have the other, longer CDR3s occur more often.
The ONs would be PCR amplified with the primers CtprmA and CBprmB, cut with AflII and BstEII, and ligated to similarly cut V3-23.
This set of components was designed after studying the sequences of 1383 human HC sequences as described below. The proposed components are meant to fulfill the goals:
1) approximately the same distribution of lengths as seen in real Ab genes,
2) high level of sequence diversity at places having high diversity in real Ab genes, and
3) incorporation of constant sequences often seen in real Ab genes.
Note that the design uses JH4 (YFDYWGQGTLVTVSS; SEQ ID NO:20), which is found more often, instead of JH3 (AFDIWGQGTMVTVSS; SEQ ID NO:21). This involves three changes in AA sequence, shown as double underscored bold. An alternative JH segment is shown.
How the Library Components were Designed:
The processing of sequence data was accomplished by a series of custom-written FORTRAN programs, each of which carries out a fairly simple transformation on the data and writes its results as one or more ASCII files. The next program then uses these files as input.
A set of 2049 human heavy-chain genes was selected from the version of GenBank that was available at Dyax on the Sun server on 26 Jun. 2000. A program named “Reformat” changed the format of the files to that of GenBank from the GCG format, creating one file per sequence. A second program named “IDENT_CDR3” processed each of these files as follows. Files were tested for duplication by previous entries, duplicates were discarded. Each reading frame was tested. Most entries had a single open reading frame (ORF), none had two, and some had none. Entries with multiple stops in every reading frame were discarded because this indicates poor quality of sequencing. The sequence was written in triplets in the ORF or in all three reading frames if no ORF was found. The sequence was examined for three motifs: a) AA sequence=“YYCxx”, b) DNA sequence=“tgg ggc (=WG)”, and DNA sequence=“g gtc acc (=BstEII)”. FR3 ends with a conserved motif YYCAR or a close approximation. When writing the DNA sequence, IDENT_CDR3 prints the DNA mostly in lower case. Cysteine codons (TGT or TGC) are printed in uppercase. When the motif “tay tay tgy” is found, IDENT_CDR3 starts a new line that contains “< > xxx xxx xxx xxx xxx” where the xxx's stand for the actual five codons that encode YYC and the next two codons (most often AR or AK). The following DNA is printed in triplets on new lines. A typical processed entry appears as in Table 1P.
Following the YYC motif, IDENT_CDR3 seeks the sequence “TGG GGC” (the “WG” motif) in the correct reading frame, 5/6 bases is counted as a hit. If found, the DNA is made uppercase. Following the WG motif (if found) or the YYC motif (if no WG found), IDENT_CDR3 seeks the sequence “G GTC ACC” (the BstEII site) in the correct reading frame, 6/7 bases is counted as a hit. If found, the bases are made upper case. If either the WG or BstEII motif are not found, a note is inserted saying that the feature was not identified. The output of IDENT_CDR3 was processed by hand. In many cases, the lacking YYC motif could be seen as a closely related sequence, such as YFC, FYC, or HYC. When this was supported by an appropriately positioned WG and/or BstEII site, the effective YYC site was marked and the sequence retained for further analysis. If the YYC motif could not be identified or if the WG or BstEII sites could not be found, the entry was discarded. For example, the entry in Table 2P had no YYC motif.
The double underscored sequence encodes YHCAS and is taken as the end of FR3. Note that there is a WG motif at bases 403-408 (bold upper case) and a BstEII site at bases 420-426 (bold upper case). Using WordPerfect, I first made all occurrences of TGC and TGT bold. I then searched for “YYC not found”. If I could see the “YYC”-related sequence quickly, I edited the entry so that a YYC was shown. The entry above would be converted to that shown in Table 3P. This processing reduced the list of entries to 1669.
A third program named “New_DJ” processed the output of IDENT_CDR3. The end of the YYC motif (including the two codon following TGy=Cys) was taken as the end of FR3. The WG motif was taken as the end of the region that might contain a D segment. If WG was not observed and BstEII was, the WG site was assumed to be 17 bases upstream of BstEII. Using the WG motif for alignment, the sequence was compared to each human GLG JH segment (1-6) and the best one identified (New_DJ always assigned a JH segment). Starting from the WG motif of JH and moving toward the 5′ end, the program looked for the first codon having more than one mismatch. The region from YYCxx (SEQ ID NO:113) to this codon was taken as the region that might contain a D segment.
The region that might contain a D segment was tested against all the germ-line genes (GLGs) of human D segments and the best D segment was identified. The scoring involved matching the observed sequence to the GLG sequence in all possible ways. Starting at each base, multiply by 4 for a match and divide by 4 for a mismatch. Record the maximum value obtained for this function. The match was deemed significant if 7/7, 8/9, 9/11, etc. or more bases matched. Of the 1383 sequences examined for D segments,
“Assign_D” processes the output of New_DJ. For each sequence that had a significant match with a GLG D segment, a file was written containing the putative D segment, the DJ segment, the identified GLG D segment, the identified JH segment, the phase of the match between observed and GLG gene. For example, “D1_—1-01_Phz0_hsa239356.txt” is a file recording the match of entry hsa239356 with D1-01 in phase 0. The file contains the information shown in Table 4P. The final DV of the second sequence immediately precedes the WG in JH and is ascribed to JH3. Other files that begin D1_—1-01_Phz0 match the same GLG D segment and these can be aligned by sliding amino-acid sequences across each other.
Table 5P shows how sequence hs6d4xb7 is first assigned to JH4 and then to D3-22. Note that the DNA sequence TGGGGG is aligned to the TGG GGC of the GLG and that the sequence is truncated on the left to fit. The program finds that JH4 has the best fit (5 misses and 18 correct out of 23). From the right, the program sees that DYWGQ (underscored) come from JH, but then the match drops off and the rest of the sequence on the left comes either from added bases or a D segment.
The lower part of Table 5P shows that the possible D segment matches D#13 (3-23) is a very good match.
Of 1383 files accepted by Assign_D, 757 had identifiable D segments. The tally of JHs in Table 6P shows that JH4 is by far the most common.
JH4 is most common, JH6 next, followed by JH3 and JH5. JH1 and JH2 are seldom used. Table 7P shows the length distributions of each JH class; they do not differ significantly class to class. These lengths count only amino-acids that are not accounted for by JH and so are shorter that the lengths given in Table 8P which cover from YYCAR (SEQ ID NO:112) to WG.
Table 8P contains the distribution of lengths for a) all the CDR3 segments, b) the CDR3 segments with identified D segments, and c) the CDR3 segments having no identifiable D segment. The CDR3s with identifiable D segments (13.9) are systematically longer than are those that lack D segments (11.2).
The identified CDR3 segments can be collated in two ways: aligned to the left (looking for a pattern following YYCAR; SEQ ID NO:112) or aligned to the right (looking for a pattern preceding WG). Table 9P shows the collation of left-aligned sequences while Table 10P shows the right-aligned sequences. For each position, I have tabulated the frequency of each AA type (A-M in the first block and N-Y in the second). The column headed “#” shows how many sequences have some AA at that position. The final column shows all of the AA types seen at that position with the most frequent first and the least frequent last. In the left-aligned sequences, we see that Gly is highly over-represented in the first seven positions while Tyr is over-represented at positions 8-16.
In Table 11P, I have tabulated the AA frequencies for the sequences having between 7 and 15 AAs between YYCAR (SEQ ID NO:112) and WG. The last four positions can be viewed as coming from JH and so would be given lower levels of diversity than would earlier positions. From these tabulations, I conclude that most AA types are allowed at all the positions, but there is a fairly strong tendency to have Gly at the early positions and to end in Asp-Tyr (DY). We could use these tendencies in designing a pattern of variegation. I would not exclude any AA except Cys, but I might increase the frequency of Gly in the first several positions and Tyr in the last few.
There are 80 sequences (5.8%) having a pair of cysteines in CDR3. It is more surprising that 53 (3.8%) have a single Cys in CDR3.
MS-DOS was used to make a list of the files written by Assign_D. “Filter” converts the output of MS-DOS Dir into a form that can be read into WordPerfect and sorted to bring a files belonging to the same D region together.
“Filter2” collects the sequences and produces a draft table of sequences, grouped by the D-segment used, and written so that the sequences can be aligned. The output of Filter2 were edited by hand. For each group, the translation of the GLG was inserted and the collection of observed sequences was aligned to the conserved part of the GLG. “Filter3” collated the aligned sequences. Table 12P shows an example of an alignment and the tabulation of AA types. The entries are as follows: “Entry” is the name used in the data base, “Seq1” is the sequence from the YYCAR (SEQ ID NO:112) motif to the first amino acid not assigned to JH and “L1” is the length of the segment. The segments are shown aligned to the identified D segment. Seq2 is the sequence from the YYCAR (SEQ ID NO:112) motif to the WG motif (i.e. including part of JH) and “L2” is the length of that sequence. JH is the identified JH segment for this sequence. “P” is the phase of the match. For positive values of P, P bases are found in the observed sequence that do not correspond to any from the GLG, i.e. the observed sequence has had that many bases inserted. For negative values of P, there are |P| bases in the GLG sequence for which there are no corresponding bases in the observed sequence. “Score” is approximately 1/(probability of accidental match). This is calculated by looking at all possible alignments. For each alignment, the score is first set to 1.0. Base by base, the score is multiplied by 4. if the bases match and divided by 4. if they do not. This is done for all starting points and ending points and the maximum value is recorded.
Table 13P is a summary of how often each D segment was identified and in which reading frame. I have not been consistent with Corbett et al. in assigning the phases of the GLG D segments. The MRC Web page that I took the GLGs from did not have D segments D1-14, D4-11, D5-18, or D6-25. None of these contribute to any great extent and this omission is unlikely to have any serious effect on the conclusions. The column headed “%” contains the percentage of the sequences examined here. The column headed “C %” contains the percentage reported by Corbett et al. I assume that the data used in Corbett et al. is mostly included in my collection. Nevertheless, the observed frequencies differ in detail. For example, my compilation shows that 10.7% of the collection contains a D segment encoding two cysteines while they have only 4.16% in this category. In D3 phase “0”, I see 19.4% of the collection while they report 11.8%.
The most common actual D segments were further analyzed. The GLGs are heavily edited at either end. The aligned sequences were aligned. For each D-segment having more than seven examples, Filter3 produced a table of the frequency of each amino-acid type at each position. From these tabulations, library components shown in Table 17P were designed. At each position where at least half the examples have an amino acid, I entered either the dominant AA type or “x”. An AA type was “dominant” if it occurred more than 50% of the time. L is the length and f is the number of sequences observed that have related sequences.
Table 14P shows possible library components for a library of CDR3's. “L” is the length of the insert and “f” is the frequency of the motif in the assayed collection. Table 17P shows vgDNA that embodies each of the components shown in Table 14P. In Table 17P, the oligonucleotides (ON) Ctop25, CtprmA, CBprmB, and CBot25 allow PCR amplification of each of the variegated ONs (vgDNA): C1t08, C2t10, C3t12, C4t14, C5t15, C6t17, C7t18, and c8t19. After amplification, the dsDNA can be cleaved with AflII and BstEII (or KpnI) and ligated to similarly cleaved vector that contains the remainder of the 3-23 synthetic domain. Preferably, this vector already contains diversity in CDR1 and CDR2 as disclosed herein. Preferably, the recipient vector contains a stuffer in place of CDR3 so that there will be no parental sequence that would then occur in the resulting library. Table 50P shows a version of the V3-23 gene segment with each CDR replaced by a short segment that contains both stop codons and restriction sites that will allow specific cleavage of any vector that does not have the stuffer removed. The stuffer can either be short and contain a restriction enzyme site that will not occur in the finish library, allowing removal of vectors that are not cleaved by both AflII and BstEII (or KpnI) and religated. Alternatively, the stuffer could be 200-400 bases long so that uncleaved or once cleaved vector can be readily separated from doubly cleaved vector.
In the vgDNA for HC CDR3, <1> means a mixture comprising 0.27 Y, 0.27 G, and 0.027 of each of the amino-acid codons {A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W}; <2> means an equimolar mixture of K and R; and <3> means an equimolar mixture of S and G.

Analysis of Human Kappa Light Chains and Preferred Variegation Scheme:

A collection of 285 human kappa chains was assembled from the public data base. Table 27 shows the names of the entries used. The GLG sequences of nine bases at each end of the framework regions were used to find the FR/CDR junctions. Only in cases where all six junctions could be found was the sequences included. Table 25P shows the distribution of lengths in CDRs in human kappas. CDR1s with lengths of 11, 12, 13, 16, and 17 were observed with 11 being predominant and 12 well represented. CDR2 exhibits only length 7. CDR3 exhibits lengths of 1, 4, 6, 7, 8, 9, 10, 11, 12, 13, and 19. Essentially all examples are in the 8, 9, or 10 length groups.
Table 26P shows the distribution of V and J genes seen in the sample. A27 is the most common V and JK1 is the most common J. Thus, a suitable synthetic kappa gene comprises A27 joined to JK1. Table 30P shows a suitable synthetic kappa chain gene, including a PlacZ promoter, ribosome-binding site, and signal sequence (M13 III signal). The DNA sequence encodes the GLG amino-acid sequence, but does not comprise the GLG DNA sequence. Restriction sites are designed to fall within each framework region so that diversity can be cloned into the CDRs. XmaI and EspI are in FR1, SexAI is in FR2, RsrII is in FR3, and KpnI (or Acc65I) are in FR4. Additional sites are provided in the constant kappa chain to facilitate construction of the gene.
Table 30P also shows a suitable scheme of variegation for kappa. In CDR1, a preferred length is 11 codons. The A27 GLG has a CDR1 of 12 codons, but the sample of mature kappa chains has length 11 predominating. One could also introduce a component of kappas having length 12 in CDR1 by introducing codon 52 as <2> (i.e. a Ser-biased mixture). CDR2 of kappa is always 7 codons. Table 31P shows a tally of 285 CDR2s and a preferred variegation scheme for CDR2. The predominant length of CDR3 in kappa chains is 9 codons. Table 32P shows a tally of 166 CDR3s from human kappas and a preferred variegation scheme (which is also shown in Table 30P).

Analysis of Lambda Chains and Preferred Variegation Scheme:

A collection of 158 lambda sequences was obtained from the public data base. Of these 93 contained sequences in which the FR/CDR boundaries could be identified automatically. Table 33P shows the distribution of lengths of CDRs.

Method of Construction:

The diversity of HC, kappa, and lambda are best constructed in separate vectors. First a synthetic gene is designed to embody each of the synthetic variable domains. The light chains are bounded by restriction sites for ApaLI (positioned at the very end of the signal sequence) and AscI (positioned after the stop codon). The heavy chain is bounded by SfiI (positioned within the PelB signal sequence) and NotI (positioned in the linker between CH1 and the anchor protein. The initial genes are made with “stuffer” sequences in place of the desired CDRs. A “Stuffer” is a sequence the is to be cut away and replaced by diverse DNA but which does not allow expression of a functional antibody gene. For example, the stuffer may contain several stop codons and restriction sites that will not occur in the correct finished library vector. In Table 40P, the stuffer for CDR1 of kappa A27 contains a StuI site. The vgDNA for CDR1 is introduced as a cassette from EspI, XmaI, or AflII to either SexAI or KasI. After the ligation, the DNA is cleaved with StuI; there should be no StuI sites in the desired vectors.

REFERENCES

Corbett, S J, Tomlinson, I M, Sonnhammer, E L L, Buck, D, Winter, G. “Sequences of the Human Immunoglobulin Diversity (D) Segment Locus: A Systematic Analysis Provides No Evidence for the Use of DIR Segments, Inverted D Segments, ‘Minor’ D Segments or D-D Recombination”. J Molec Biol (1997) 270:587-597.

Tables

TABLE 1P

Typical entry in which YYC motif is found.

++++C:\tmp\haj10335.txt

LOCUS	HAJ10335 306 bp mRNA PRI 18 AUG. 1998
DEFINITION	Homo sapiens mRNA for immunoglobulin heavy chain
	variable region, clone ELD16/6.
ACCESSION	AJ010335
VERSION	AJ010335.1 GI:3445266
Ngene =	306

Stop codons in reading frame 1

49 115 124 253 277

No stops in reading frame 2

Stop codons in reading frame 3

12 60 81 147 204 213

1 t ttg ggg tcc ctg aga ctc tcc TGT gca gcc tct gga ttc acc

44 gtc agt agc aac tac atg acc tgg gtc cgc cag gct cta ggg aag

89 ggg ctg gag tgg gtc tca gtt att tat agc ggt ggt agc aca tac

134 tac gca gac tcc gtg aag ggc gga ttc acc atc tcc aga gac aat

179 tcc aag aac aca ctg tat ctt caa atg aac agc ctg aga ccc gag

224 gac acg gct gtg

< > TAT TAC TGT gcg aca

251 ggt aat cgc ctg gaa atg gct gca att aac TGG GGC caa gga acc

263 ctG GTC ACC aa (SEQ ID NO: 113)

TABLE 2P

entry in which YYC motif was not automatically identified

++C:\tmp\hs202g3.txt

!!NA_SEQUENCE 1.0

LOCUS	HS202G3 522 bp mRNA PRI 03 AUG. 1995
DEFINITION	H. sapiens mRNA for immunoglobulin variable
	region (clone 202-G3).
ACCESSION	Z47259
VERSION	Z47259.1 GI:619470

Ngene =	522

No stops in reading frame 1

Stop codons in reading frame 2

89 110 305 314

Stop codons in reading frame 3

84 192 321 351 369

1 atg gac tgg acc tgg agg ttc ctc ttt gtg gtg gca gca gct aca

46 ggt gtc cag tcc cag gtg cag ctg gtg cag tct ggg gct gag gtg

91 aag aag cct ggg tcc tcg gtg aag gtc tcc TGC aag gct tct gga

136 ggc acc ttc agc agc tat gct atc agc tgg gtg cga cag gcc cct

181 gga caa ggg ctt gag tgg atg gga ggg atc atc cct atc ttt ggt

226 aca gca aac tac gca cag aag ttc cag ggc aga gtc acg att acc

271 gcg gac gaa tcc acg agc aca gcc tac atg gag ctg agc agc ctg

316 aga tct gag gac acg gcc gtg tat cac TGT gcg agt gag gga tgg

361 gag agt TGT agt ggt ggt ggc TGC tac gac ggt atg gac gtc TGG

406 GGC caa ggg acc acG GTC ACC gtc tcc tca gct tcc acc aag ggc

451 cca tcg gtc ttc ccc ctg gcg ccc TGC tcc agg agc acc tct ggg

496 ggc aca gcg gcc ctg ggc TGC ctg (SEQ ID NO: 114)

YYC not found !!!

TABLE 3P

Entry of Table 2P after editting.

++C:\tmp\hs202g3.txt

!!NA SEQUENCE 1.0

LOCUS	HS202G3 522 bp mRNA PRI 03 AUG. 1995
DEFINITION	H. sapiens mRNA for immunoglobulin variable region
	(clone 202-G3).
ACCESSION	247259
VERSION	247259.1 GI:619470

Ngene = 522

No stops in reading frame 1

Stop codons in reading frame 2

89 110 305 314

Stop codons in reading frame 3

84 192 321 351 369

1 atg gac tgg acc tgg agg ttc ctc ttt gtg gtg gca gca gct aca

46 ggt gtc cag tcc cag gtg cag ctg gtg cag tct ggg gct gag gtg

91 aag aag cct ggg tcc tcg gtg aag gtc tcc TGC aag gct tct gga

136 ggc acc ttc agc agc tat gct atc agc tgg gtg cga cag gcc cct

181 gga caa ggg ctt gag tgg atg gga ggg atc atc cct atc ttt ggt

226 aca gca aac tac gca cag aag ttc cag ggc aga gtc acg att acc

271 gcg gac gaa tcc acg agc aca gcc tac atg gag ctg agc agc ctg

316 aga tct gag gac acg gcc gtg

<YHCAS> tat cac TGT gcg agt

(SEQ ID NO: 116)

gag gga tgg

361 gag agt TGT agt ggt ggt ggc TGC tac gac ggt atg gac gtc TGG

406 GGC caa ggg acc acG GTC ACC gtc tcc tca gct tcc acc aag ggc

451 cca tcg gtc ttc ccc ctg gcg ccc TGC tcc agg agc acc tct ggg

496 ggc aca gcg gcc ctg ggc TGC ctg (SEQ ID NO: 115)

YYC not found !!!

TABLE 4P

contents of file D1_1-01_Phz0_hsa239356.txt

	DRGGKYQLAPKGGM (SEQ ID NO: 117)

	DRGGKYQLAPKGGMDV (SEQ ID NO: 118)
	JH3 D#1 Phase 15 Score 6.55D+04

TABLE 5P

alignment of a CDR3::JH segment to GLG JHs and D-segments.

+C:\tmp\hs6d4xb7.txt

	1 1 2 2 3 3 3
	1234567890 5 0 5 0 5 9
Observed	tatgatagtagtgggtcatactccgactacTGGGGGcag (SEQ ID NO: 119)

JH1	------------gctgaatacttccagcactggggccagggcaccctggtcaccgtctcctcag--	Miss = 9	Nt = 27
	(SEQ ID NO: 120)

JH2	-----------ctactggtacttcgatctctggggccgtggcaccctggtcactgtctcctcag--	Miss = 13	Nt = 28
	(SEQ ID NO: 121)

JH3	--------------tgatgcttttgatatctggggccaagggacaatggtcaccgtctcttcag--	Miss = 14	Nt = 25
	(SEQ ID NO: 122)

JH4	----------------actactttgactactggggccagggaaccctggtcaccgtctcctcag--	Miss = 5	Nt = 23
	(SEQ ID NO: 123)

JH5	-------------acaactggttcgacccctggggccagggaaccctggtcaccgtctcctcag--	Miss = 11	Nt = 26
	(SEQ ID NO: 124)

JH6	-attactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcag--	Miss = 23	Nt = 38
	(SEQ ID NO: 125)

4	tat gat agt agt ggg tca TAC Tcc GAC TAC TGG GGg CAG (SEQ ID NO: 126)
	Y D S S G S Y S D Y W G Q (SEQ ID NO: 127)

JH4	--- --- --- --- --- -ac tac ttt gac tac tgg ggc cag gga acc ctg gtc acc gtc tcc tca g--
	(SEQ ID NO: 128)
	- - - - - - Y F D Y W G Q G T L V T V S S -
	(SEQ ID NO: 129)

Fract = 0.783 = 18/23

Matching the rest to D segments:

D#13 --------gtattactatgatagtagtggttattactac GLG (SEQ ID NO: 130)

gatcgccacaattactatgatagtagtgggtcatactcc Observed (SEQ ID NO: 131)

--------gt...................t.at....a. . = match

D#13 Phase = 9 Score = 4.3980E+12

TABLE 6P

Number of sequences identified as
having JH derived from GLG JHn

JH	1	2	3	4	5	6

# sequences	17	40	198	707	160	261

TABLE 7P

Distribution of CDR3 fragments that might contain D segments.

For JH1

0	1	2	3	4	5	6	7	8	9	10	11	12	13
0	0	1	1	3	1	1	2	0	3	1	1	1	2

Total = 17 Median = 8.0

For JH2

0	1	2	3	4	5	6	7	8	9	10	11	12	13	14
0	0	0	0	0	2	4	6	2	6	3	4	5	2	3
15	16	17	18
2	0	0	1

Total = 40 Median = 9.0

For JH3

0	1	2	3	4	5	6	7	8	9	10	11	12	13	14
0	0	2	6	16	12	17	17	15	22	20	20	18	13	4
15	16	17	18	19
8	3	2	1	2

Total = 198 Median = 8.6

For JH4

0	1	2	3	4	5	6	7	8	9	10	11	12	13	14
0	0	7	15	19	40	63	82	81	77	81	53	57	44	30
15	16	17	18	19	20	21	22	23	24	25	26	27	28	29
15	23	8	3	5	2	0	1	0	0	0	0	0	0	0
30	31	32	33	34	35
0	0	0	0	0	1

Total = 707 Median = 8.6

For JH5

0	1	2	3	4	5	6	7	8	9	10	11	12	13	14
0	0	0	3	4	6	13	19	12	14	22	18	10	18	10
15	16	17	18	19	20	21	22	23	24	25	26	27	28	29
5	1	1	0	0	1	1	0	0	0	0	0	0	0	0
30	31	32	33	34	35	36	37	38	39	40	41	42	43	44
0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
45	46
0	1

Total = 160 Median = 9.4

For JH6

0	1	2	3	4	5	6	7	8	9	10	11	12	13	14
2	0	1	2	5	15	20	18	22	29	29	28	23	16	10
15	16	17	18	19	20
14	9	9	4	2	3

Total = 261 Median = 9.6

TABLE 8P

Lengths of CDR3 segments from YYCAR to WG.

Distribution of lengths from end of FR3 to WG motif all sequences.

L	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14
N	6	0	0	4	2	9	13	38	61	88	101	118	154	150	118
Sum(N)	6	6	6	10	12	21	34	72	133	221	322	440	594	744	862
f	.004	.004	.004	.007	.009	.015	.025	.052	.096	.160	.233	.318	.430	.538	.623
L	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29
N	125	105	84	61	46	42	16	17	7	9	2	1	0	2	1
SN	987	1092	1176	1237	1283	1325	1341	1358	1365	1374	1376	1377	1377	1379	1380
f	.714	.790	.850	.894	.928	.958	.970	.982	.987	.993	.995	.996	.996	.997	.998
L	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44
N	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0
SN	1380	1380	1380	1380	1380	1380	1380	1381	1381	1381	1381	1381	1382	1382	1382
f	.998	.998	.998	.998	.998	.998	.998	.999	.999	.999	.999	.999	.999	.999	.999
L	45	46
N	0	1
SN	1382	1383
f	.999	1.0

Median = 12.65

Distribution of lengths from end of FR3 to WG motif with assigned D.

L	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14
N	3	0	0	0	0	0	3	9	21	15	39	64	77	97	72
SN	3	3	3	3	3	3	6	15	36	51	90	154	231	328	400
f	.004	.004	.004	.004	.004	.004	.008	.019	.046	.065	.115	.196	.294	.418	.510
L	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29
N	77	75	63	45	35	38	15	15	6	9	2	1	0	1	1
SN	477	552	615	660	695	733	748	763	769	778	780	781	781	782	783
f	.608	.703	.783	.841	.885	.934	.953	.972	.980	.991	.994	.995	.995	.996	.997
L	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44
N	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
SN	783	783	783	783	783	783	783	784	784	784	784	784	784	784	784
f	.997	.997	.997	.997	.997	.997	.997	.999	.999	.999	.999	.999	.999	.999	.999
L	45	46
N	0	1
SN	784	785
f	.999	1.0

Median = 13.90

Distribution of lengths from end of FR3 to WG motif with no assigned D.

L	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14
N	3	0	0	4	2	9	10	29	40	73	62	54	77	53	46
SN	3	3	3	7	9	18	28	57	97	170	232	286	363	416	462
f	.005	.005	.005	.012	.015	.030	.047	.095	.162	.284	.388	.478	.607	.696	.773
L	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29
N	48	30	21	16	11	4	1	2	1	0	0	0	0	1	0
SN	510	540	561	577	588	592	593	595	596	596	596	596	596	597	597
f	.853	.903	.938	.965	.983	.990	.992	.995	.997	.997	.997	.997	.997	.998	.998
L	30	31	32	33	34	35	36	37	38	39	40	41	42
N	0	0	0	0	0	0	0	0	0	0	0	0	1
SN	597	597	597	597	597	597	597	597	597	597	597	597	598
f	.998	.998	.998	.998	.998	.998	.998	.998	.998	.998	.998	.998	1.0

Median = 11.17

L is the length
N is the number of examples
Sum(N) = SN is the sum of the Ns
f is the cumulative fraction seen

TABLE 9P

Tally of left-aligned CDR3 sequences

	A	C	D	E	F	G	H	I	K	L	M	#

1	74	6	278	109	11	319	50	18	11	60	8	1383	GDERVASLHTNQPIWYFKMCX
2	50	9	64	32	29	249	43	42	41	109	22	1377	GRPSLDVYTANHIQKEFMWCX
3	81	18	74	39	25	214	29	42	16	83	19	1377	GSYRTVLADPIWEQHNFMCK\|
4	70	23	92	49	50	228	23	58	21	70	16	1373	GSYDRVALTIPFEWNCHQKMX
5	86	28	106	32	59	217	21	41	16	72	19	1371	GYSDAVTLRFIPWNECHMQK\|X
6	88	17	104	28	94	171	17	48	12	50	17	1362	GYSDFATVRWPLINEQCHMK\|
7	69	15	110	21	89	176	22	50	15	81	12	1349	GSYDFVLTAPRWINHEQCKM\|X
8	53	19	141	17	90	150	18	47	17	68	11	1311	YSGDFLTVWAPIRNCHEKQM\|
9	44	21	120	24	102	174	24	36	20	71	11	1250	YGSDFLNVRTAWPIEHCKQM\|
10	39	31	129	23	124	116	23	42	9	58	32	1162	YDFGSLIARPTVWNMCEHQK
11	36	12	158	17	137	83	13	18	10	40	21	1061	YDFGSPLVANWMTRIEHCKQX
12	34	11	164	10	82	74	34	30	1	31	20	943	YDFGPSVAHLINMRTWCEQKX
13	32	2	121	6	84	56	10	26	7	43	32	789	YDFGLSPVAMIWRTHNKQEC
14	23		131	5	59	65	10	16	4	25	34	639	YDGFMVLAPISWNRHTQEKX
15	15	4	107	5	43	42	1	23		20	34	521	YDFGVMILWAPRSENCQTH\|
16	4	2	80	3	33	26	4	5	1	10	29	396	YDVFMGPSLNTRIWAHECQ\|K
17	3	1	63		19	19	9	13		12	21	291	DYVMFGILHPSTWAQRCNX
18	3		47		16	13	1	4		7	23	207	DYVMFGPSLTIAHN
19	5	1	39	1	4	13	3	3		1	14	146	DYVMGAFHINRSCELPQW
20	2		17		4	5		3		4	12	100	VYDMGFLIPSARWQ
21			17		3	8	1	1			4	58	DVGYMFHINTW
22	1		7		6	1		1			5	42	VDFMYSAGITW
23			9			1		1		1	1	25	DVYGILMPS
24	1		2				1			1	1	18	VYDAHLMPT
25			1			3						9	GVDPSY
26						2					2	7	GMSTV
27			2						1		1	6	DKMST
28	1		1			1						6	VADGS
29					1							4	DPSV
30					1							3	FST
31									1	1		3	KLV
32					1	1						3	FGP
33						1						3	PG
34							1			1		3	HLS
35	1											3	AVW
36			1		1							3	DFP
37												3	PSY
38										1		2	LS
39		1							1			2	AK
40												2	PS
41												2	ST
42												2	S
43		1										1	K
44												1	S
45												1	T
46												1	S
	816	220	2186	421	1166	2428	358	568	205	920	421


	N	P	Q	R	S	T	V	W	Y	\|	X	#

1	35	23	31	108	63	50	94	16	13		6	1383	GDERVASLHTNQPIWYFKMCX
2	44	114	42	169	114	59	62	21	60		2	1377	GRPSLDVYTANHIQKEFMWCX
3	26	73	37	110	140	97	89	42	122	1		1377	GSYRTVLADPIWEQHNFMCK\|
4	48	51	22	79	141	65	77	49	139		2	1373	GSYDRVALTIPFEWNCHQKMX
5	37	41	18	61	157	75	85	38	158	2	2	1371	GYSDAVTLRFIPWNECHMQK\|X
6	32	54	23	67	152	80	78	64	165	1		1362	GYSDFATVRWPLINEQCHMK\|
7	44	59	18	58	157	73	85	54	139	1	1	1349	GSYDFVLTAPRWINHEQCKM\|X
8	38	48	14	41	167	68	59	59	185	1		1311	YSGDFLTVWAPIRNCHEKQM\|
9	52	40	14	47	123	45	48	41	192	1		1250	YGSDFLNVRTAWPIEHCKQM\|
10	33	37	12	39	73	36	36	35	235			1162	YDFGSLIARPTVWNMCEHQK
11	33	49	7	20	68	21	37	29	251		1	1061	YDFGSPLVANWMTRIEHCKQX
12	30	53	10	19	45	19	42	18	215		1	943	YDFGPSVAHLINMRTWCEQKX
13	10	34	7	22	40	15	33	25	184			789	YDFGLSPVAMIWRTHNKQEC
14	13	22	6	12	15	10	26	14	148		1	639	YDGFMVLAPISWNRHTQEKX
15	5	12	3	12	12	3	40	20	119	1		521	YDFGVMILWAPRSENCQTH\|
16	10	24	2	6	12	7	49	5	82	2		396	YDVFMGPSLNTRIWAHECQ\|K
17	1	8	2	2	8	5	42	4	58		1	291	DYVMFGILHPSTWAQRCNX
18	1	13			8	5	31		35			207	DYVMFGPSLTIAHN
19	2	1	1	2	2		24	1	29			146	DYVMGAFHINRSCELPQW
20		3	1	2	3		23	2	19			100	VYDMGFLIPSARWQ
21	1					1	14	1	7			58	DVGYMFHINTW
22					2	1	12	1	5			42	VDFMYSAGITW
23		1			1		5		5			25	DVYGILMPS
24		1				1	5		5			18	VYDAHLMPT
25		1			1		2		1			9	GVDPSY
26					1	1	1					7	GMSTV
27					1	1						6	DKMST
28					1		2					6	VADGS
29		1			1		1					4	DPSV
30					1	1						3	FST
31							1					3	KLV
32		1										3	FGP
33		2										3	PG
34					1							3	HLS
35							1	1				3	AVW
36		1										3	DFP
37		1			1				1			3	PSY
38					1							2	LS
39												2	AK
40		1			1							2	PS
41					1	1						2	ST
42					2							2	S
43												1	K
44					1							1	S
45						1						1	T
46					1							1	S
	495	769	270	876	1518	741	1104	540	2572	10	17		18621

TABLE 10P

Tally of right-aligned sequences

	A	C	D	E	F	G	H	I	K	L	M	#

5						1						1	G
6												1	S
7						1						1	G
8						1						1	G
9												2	RV
10												2	RV
11						1		1				2	GI
12												2	V
13												2	TY
14			1			1						3	DGN
15								1				3	ISY
16			1									3	DSY
17	1											3	APY
18			1		1						1	3	DFM
19			2			1						3	DG
20								1		1		3	ILV
21												3	WP
22						3						4	GS
23						2	1					6	GHQSV
24	1					3				1		6	GALR
25	1		2					1				7	DTAIS
26	1	1	1			1			1	1	1	9	ACDGKLMST
27	2		5	1		2		1		1		18	DAGVEILNQRS
28			2	2		3		1		2		25	TGQSDELPRIV
29	3		5	6		7			1	1	1	42	GEDVAPQRSKLMTY\|
30	2		9		1	9	1	4		5	2	58	DGRLSIVPAMQTFHNY
31	4	2	19	9	2	18	1	2	1	3		100	DGSERVYALPTCFINHKW
32	10	5	18	5	3	16	3	3	2	14	1	146	DGLRVAPYSTCEQFHINWKM
33	20		18	10	7	34	7	8	2	9	1	207	GARDPSYTEVIFHLQWKM
34	13	4	31	18	9	37	8	16	4	14	4	291	GDRYPVEILASTFHQWCKMNX\|
35	17	5	32	23	10	70	12	10	6	25	1	396	GRSDYLEVTPAHNFIWKCQM\|
36	23	6	51	21	9	79	19	15	14	36	9	521	GDSYRLTVPAEHIKNFMWCQ\|
37	35	12	56	23	15	110	14	17	5	24	4	639	GYDVRSTAPLEIFHNCWQKMX
38	28	19	68	27	29	133	26	31	12	43	7	789	GSYDVRLPTIFAEHCNWKQM
39	51	25	80	27	33	162	16	30	18	55	15	943	GSDRYVLATPFWIECKHMQNX
40	44	14	73	36	46	161	27	32	17	59	8	1061	GSRDYVTLPFAEIWHQNKCM
41	54	21	74	25	23	178	23	52	15	57	11	1162	GSYTDRVLPAIWNQEFHCKMX\|
42	57	13	82	40	42	190	14	39	15	82	15	1250	GSYDLVRTANPFEIWQKMHC\|
43	75	18	54	25	35	242	13	29	18	49	12	1311	GYSTARVPDLWNFIQECKHM\|
44	63	17	79	15	43	197	20	38	14	76	8	1349	YGSTDLRAPVWNFIQHCEKM
45	59	16	69	35	55	165	26	23	23	75	9	1362	YGSLRTDNAFPVWEHIKCQM
46	41	19	125	26	27	208	31	14	16	38	8	1371	YGDSNRWATLPHFEVQCKIM
47	160	10	24	13	53	332	36	16	11	40	10	1373	GYAWPSFRLHTVNDIEKCMQX
48	21	4	8	5	680	27	4	44	5	145	288	1377	FMLISGVYPAWTDNQREKCHX
49	23	2	1181	29	1	30	15	4	2	8	1	1377	DGEAHNQSYVLPTIRCKW\|FMX
50	7	7	15		42	3	41	135	3	59	4	1383	YVIPSLFHNDTACXMGKQRW\|
	816	220	2186	421	1166	2428	358	568	205	920	421


	N	P	Q	R	S	T	V	W	Y	\|	X	#

5												1	G
6					1							1	S
7												1	G
8												1	G
9				1			1					2	RV
10				1			1					2	RV
11												2	GI
12							2					2	V
13						1			1			2	TY
14	1											3	DGN
15					1				1			3	ISY
16					1				1			3	DSY
17		1							1			3	APY
18												3	DFM
19												3	DG
20								1				3	ILV
21		1							2			3	WP
22					1							4	GS
23			1		1		1					6	GHQSV
24				1								6	GALR
25					1	2						7	DTAIS
26					1	1						9	ACDGKLMST
27	1		1	1	1		2					18	DAGVEILNQRS
28		2	3	2	3	4	1					25	TGQSDELPRIV
29		3	3	2	2	1	5		1	1		42	GEDVAPQRSKLMTY\|
30	1	3	2	7	5	2	4		1			58	DGRLSIVPAMQTFHNY
31	2	3		7	10	3	7	1	6			100	DGSERVYALPTCFINHKW
32	3	9	4	12	8	6	12	3	9			146	DGLRVAPYSTCEQFHINWKM
33		16	6	19	15	12	10	3	13			207	GARDPSYTEVIFHLQWKM
34	2	20	5	31	12	12	20	5	23	1	2	291	GDRYPVEILASTFHQWCKMNX\|
35	12	18	5	39	35	19	23	7	26	1		396	GRSDYLEVTPAHNFIWKCQM\|
36	11	24	6	42	47	29	28	7	44	1		521	GDSYRLTVPAEHIKNFMWCQ\|
37	14	33	9	54	52	37	55	11	58		1	639	GYDVRSTAPLEIFHNCWQKMX
38	18	33	12	46	77	32	58	17	73			789	GSYDVRLPTIFAEHCNWKQM
39	11	38	12	70	94	42	61	33	68		2	943	GS DRYVLATPFWIECKHMQNX
40	24	52	27	74	140	61	66	29	71			1061	GSRDYVTLPFAEIWHQNKCM
41	31	55	29	70	156	76	61	51	97	1	2	1162	GSYTDRVLPAIWNQEFHCKMX\|
42	48	47	24	68	171	68	70	39	125	1		1250	GSYDLVRTANPFEIWQKMHC\|
43	38	58	28	73	164	76	66	43	194	1		1311	GYSTARVPDLWNFIQECKHM\|
44	48	60	24	69	131	86	57	52	252			1349	YGSTDLRAPVWNFIQHCEKM
45	62	51	16	75	116	74	50	39	324			1362	YGSLRTDNAFPVWEHIKCQM
46	97	38	21	55	110	39	26	55	377			1371	YGDSNRWATLPHFEVQCKIM
47	25	54	9	44	54	34	32	122	292		2	1373	GYAWPSFRLHTVNDIEKCMQX
48	8	22	7	6	28	10	25	16	23		1	1377	FMLISGVYPAWTDNQREKCHX
49	15	6	13	4	13	5	9	2	11	2	1	1377	DGEAHNQSYVLPTIRCKW\|FMX
50	23	122	3	3	67	9	350	3	480	1	6	1383	YVIPSLFHNDTACXMGKQRW\|
50	495	769	270	876	1518	741	1104	540	2572	10	17		18621

TABLE 11P

Tallies of AA frequencies in all CDR3 by length

Tally of sequences of length 7 # = 38

	A	C	D	E	F	G	H	I	K	L	M	#

1	1		8	1	1	14	1		1	5		38	GDLRWAEFHKS
2	1		1		2	6	3		2	1	1	38	RGNHVFKTYADLMW
3	1		4		1	5	1	2		2		38	GSDWYPVILTAFHN
4	3		1		1	12	1	1		1		38	GYSANRVDFHILPT
5	2			1	14	3		4	1	3	3	38	FIGLMARVYEKP
6			26				1	1				38	DVPTHISWY
7	1		2				2	3		1		38	YVINDHSALR
	9		42	2	19	40	9	11	4	13	4

	N	P	Q	R	S	T	V	W	Y	\|	X	#

1				3	1			2				38	GDLRWAEFHKS
2	6			7		2	3	1	2			38	RGNHVFKTYADLMW
3	1	3			5	2	3	4	4			38	GSDWYPVILTAFHN
4	2	1		2	4	1	2		6			38	GYSANRVDFHILPT
5		1		2			2		2			38	FIGLMARVYEKP
6		2			1	2	3	1	1			38	DVPTHISWY
7	3			1	2		7		16			38	YVINDHSALR
	12	7		15	13	7	20	8	31			266

Tally of sequences of length 8 # = 61

	A	C	D	E	F	G	H	I	K	L	M	#

1	3		7	3		14	2	2		5		61	GDLTVRSAEHINWPQY
2	1		9	1	1	15		1	2	1		61	GDTNRSVKWYAEFILPQ
3	2		3		1	10	1	1		7	1	61	GLSTYVDPRAFHIMNQW
4	4	1	3	1	1	15	1			4		61	GYRALQDSWVCEFHNPT
5	10		2	1		9	5		1	5	1	61	AGYHLTPRVDSEKMW
6	5	1			24	2		7		5	2	61	FIALPSVYGMCQRW
7	5		37	2			4	1		2		61	DAHSELNVIP\|
8	1		2		3		1	12		3		61	YISFLVDNAHPRT
	31	2	63	8	30	65	14	24	3	32	4

	N	P	Q	R	S	T	V	W	Y	\|	X	#

1	2	1	1	4	4	5	5	2	1			61	GDLTVRSAEHINWPQY
2	6	1	1	4	3	8	3	2	2			61	GDTNRSVKWYAEF I LPQ
3	1	3	1	3	7	7	5	1	7			61	GLSTYVDPRAFHIMNQW
4	1	1	4	5	3	1	2	3	11			61	GYRALQDSWVCEFHNPT
5		4		4	2	5	4	1	7			61	AGYHLTPRVDSEKMW
6		3	1	1	3		3	1	3			61	FIALPSVYGMCQRW
7	2	1			4		2			1		61	DAHSELNVIPI
8	2	1		1	7	1	3		24			61	YISFLVDNAHPRT
	14	15	8	22	33	27	27	10	55	1		488

Tally of sequences of length 9 # = 88

	A	C	D	E	F	G	H	I	K	L	M	#

1	9		12	4		21	1	1	2	5		88	GDARNVLEQTKWHIPSY
2	2		2	3	3	13	4		3	7	2	88	GPSRLNTHEFKYADMQW
3	4	2	3	3	3	15				1	1	88	GTPSQNRVWYADEFCLM
4	5	1	6	3	6	22	2	4	1	6	1	88	GSDFLARITYENPWHVCKM
5	7	1	4	3	4	14	2			7	2	88	GSYALNDFVERWHMQTCP
6	13		2	1	3	13	6	2	1	4	1	88	YAGHNLPSVFTWDIEKMQR
7	4		2		41	2		3	1	14	5	88	FLMAPWIDGSVKNQTY
8	1	1	73	2		2	1			2		88	DEGLSACHNQRV
9		1	1		4	1	3	8		2		88	YVISFHPLNTCDGR
	45	6	105	19	64	103	19	18	8	48	12

	N	P	Q	R	S	T	V	W	Y	\|	X	#

1	7	1	3	8	1	3	7	2	1			88	GDARNVLEQTKWHIPSY
2	5	11	2	10	11	5		2	3			88	GPSRLNTHEFKYADMQW
3	5	7	6	5	7	11	5	5	5			88	GTPSQNRVWYADEFCLM
4	3	3		5	7	4	2	3	4			88	GSDFLARITYENPWHVCKM
5	6	1	2	3	12	2	4	3	11			88	GSYALNDFVERWHMQTCP
6	5	4	1	1	4	3	4	3	17			88	YAGHNLPSVFTWDIEKMQR
7	1	4	1		2	1	2	4	1			88	FLMAPWIDGSVKNQTY
8	1		1	1	2		1					88	DEGLSACHNQRV
9	2	3		1	8	2	9		43			88	YVISFHPLNTCDGR
	35	34	16	34	54	31	34	22	85			792

Tally of sequences of length 10 # = 101

	A	C	D	E	F	G	H	I	K	L	M	#

1	8	1	19	7	1	16	3		2	3	2	101	DGNAERTSQVHLWKMYCF
2	3		8	3	5	13		5		15	2	101	LGRDSPVFINTAEQYMW
3	6		9		1	26	1	3	1	4	1	101	GSYDAVTLNRIPWFHKMQ
4	7		6		1	25	1	5		4	1	101	GSYARDINPLTVWQFHM
5	6		5	9	4	16	1		3	4		101	GYTESANDPRFLVKQWH
6	6	1	6	5	4	23	2	4	3	3	1	101	GYRSWADEFINKLTHCMQV
7	13		3	1	5	9	3	1		4	1	101	YASGPRWFTVLDHNEIMQ
8	2	1		1	57	3		4		15	4	101	FLIMSGWANPVCEY
9	3		78	2		6		1	1	1		101	DGAQENIKLPRSW
10			3		4		4	13		1		101	YIPSVFHNDL
	54	3	137	28	82	137	15	36	10	54	12

	N	P	Q	R	S	T	V	W	Y	\|	X	#

1	9		4	6	5	6	4	3	2			101	DGNAERTSQVHLWKMYCF
2	5	6	3	11	8	4	6	1	3			101	LGRDSPVFINTAEQYMW
3	4	3	1	4	14	5	6	2	10			101	GSYDAVTLNRIPWFHKMQ
4	5	5	3	7	11	4	4	4	8			101	GSYARDINPLTVWQFHM
5	6	5	2	5	8	10	4	2	11			101	GYTESANDPRFLVKQWH
6	4		1	8	7	3	1	7	12			101	GYRSWADEFINKLTHCMQV
7	2	7	1	7	11	5	5	6	17			101	YASGPRWFTVLDHNEIMQ
8	2	2			4		2	3	1			101	FLIMSGWANPVCEY
9	2	1	3	1	1			1				101	DGAQENIKLPRSW
10	4	8			7		5		52			101	YIPSVFHNDL
	43	37	18	49	76	37	37	29	116			1010

Tally of sequences of length 11 # = 118

	A	C	D	E	F	G	H	I	K	L	M	#

1	7	1	21	11		23	5	2		7		118	GDEVRALQHSPTINCWY
2	1	2	9	1	1	24	5	6	2	7	3	118	GSRDYLPIVHQTMNCKWAEFX
3	4		4	2	4	13	2	3	1	7	2	118	SGTVRLYWADFNQIEHMKP
4	10		3	3	2	25	1	2		4	3	118	SGARTWYLVDEMQFINPH
5	5	2	10	1	4	24	2		1	5	1	118	GSVYDTNALRFWCHQEKM
6	6		4	2	7	19	2	3	1	5	1	118	GSYWTFAVLRDINEHQKMP
7	4	1	8	5	2	20	4	1		2	1	118	GYSNRDWTEPAHFLQVCIM
8	13	2	6	1	8	12	4		2	7		118	YAGWFLDPRSTHCKVE
9	2		2		68	2		5		14	7	118	FLMYVITADGP
10	2	1	100	5		3	2			1	1	118	DEGAHCLMNPQ
11			2		6		1	7	1	6	1	118	YPVISFLNDHKM
	54	9	169	31	102	165	28	29	8	65	20

	N	P	Q	R	S	T	V	W	Y	\|	X	#

1	2	4	7	8	5	3	10	1	1			118	GDEVRALQHSPTINCWY
2	3	7	4	10	11	4	6	2	9		1	118	GSRDYLPIVHQTMNCKWAEFX
3	4	1	4	8	25	12	9	6	7			118	SGTVRLYWADFNQIEHMKP
4	2	2	3	9	26	8	4	6	5			118	SGARTWYLVDEMQFINPH
5	6		2	5	15	9	11	4	11			118	GSVYDTNALRFWCHQEKM
6	3	1	2	5	16	9	6	11	15			118	GSYWTFAVLRDINEHQKMP
7	9	5	2	9	11	6	2	7	19			118	GYSNRDWTEPAHFLQVCIM
8		6		5	5	5	2	11	29			118	YAGWFLDPRSTHCKVE
9		1				4	6		7			118	FLMYVITADGP
10	1	1	1									118	DEGAHCLMNPQ
11	3	13			7		11		60			118	YPVISFLNDHKM
	33	41	25	59	121	60	67	48	163		1	1298

Tally of sequences of length 12 # = 154

	A	C	D	E	F	G	H	I	K	L	M	#

1	5		31	12		37	6	1	1	7	3	154	GDRESVLHAPMNQTWYIK
2	5	1	7	6	1	25	3	7	3	13	2	154	GSRLPDIQEAVYHKNTMWCF
3	10	2	7	5	1	19		5	4	12	2	154	GRSYLATVPDQEIKWCMNF
4	8		9	6	8	27		6	5	6	1	154	GVSDNAFRTYEILKWPQM
5	18	1	8	5	6	42	1	9	1	7	3	154	GSAIDYLFPTEQVMNWCHK
6	13		12	4	10	23	1	7		8	1	154	GAVDSFYTLPRWINEQHM
7	11	2	4	3	10	15	1	4		12		154	YGSPLRAFWTNVDIECQH
8	3	2	18	3	3	25	4	2	5	6		154	YGDSNLTKRWHPAEFCIQV
9	15	1	2		8	33	4	7	1	5	1	154	GYWARFISPLHTDQCKMN
10	1	1	2	1	79	1	2	5	1	19	26	154	FMLIPYDHVWACEGKNQRST
11	2		135	2		4	2					154	DGYAEHSVNR
12		1	1		6	1	9	16		4		154	YVPIHFSLNCDGW
	91	11	236	47	132	252	33	69	21	99	39

	N	P	Q	R	S	T	V	W	Y	\|	X	#

1	3	4	3	14	10	3	10	2	2			154	GDRESVLHAPMNQTWYIK
2	3	11	7	22	24	3	5	2	4			154	GSRLPDIQEAVYHKNTMWCF
3	2	8	6	17	17	9	9	4	15			154	GRSYLATVPDQEIKWCMNF
4	9	4	4	7	17	7	18	5	7			154	GVSDNAFRTYEILKWPQM
5	3	6	4		20	6	4	2	8			154	GSAIDYLFPTEQVMNWCHK
6	5	8	3	8	11	9	13	8	10			154	GAVDSFYTLPRWINEQHM
7	5	14	2	12	15	6	5	9	24			154	YGSPLRAFWTNVDIECQH
8	10	4	2	5	15	6	2	5	34			154	YGDSNLTKRWHPAEFCIQV
9	1	6	2	10	7	3		18	30			154	GYWARFISPLHTDQCKMN
10	1	4	1	1	1	1	2	2	3			154	FMLIPYDHVWACEGKNQRST
11	1			1	2		2		3			154	DGYAEHSVNR
12	2	18			5		32	1	58			154	YVPIHFSLNCDGW
	45	87	34	97	144	53	102	58	198

Tally of sequences of length 13 # = 150

	A	C	D	E	F	G	H	I	K	L	M	#

1	4	2	28	9	3	37	8	3	3	5		150	GDTESHRVLPAQFIKCNW
2	11	4	4	1	2	32	3	1	5	11	3	150	GRSPALTKVCDYHMQWFEIN
3	7	2	8	4	4	23	11	1	4	6	2	150	GSYHQTDPRAVLEFKNCMWI
4	6	2	6	4	6	30	1	8		6	1	150	GSWYTIADFLPVEQRCHMNX
5	8		10	4	2	28	1	2		22	3	150	GLSYDATWPREQMNVFIH
6	10	2	11	1	6	21		2	2	5	1	150	GYSPTDAQVFRLNWCIKEM
7	5	1	8	1	4	19	1	6	5	21	2	150	LGYSTDPIRVAKFNWMQCEH
8	7	5	22	5	3	12	3	3	3	8	1	150	YDSGLARTCEQVNPFHIKWM
9	1	2	12	3	1	26	7	2	4	7	2	150	NGYDSWHLPRKETVCIMAFQ
10	19	1	2	2	17	24	5	2		5	1	150	YGAFWHLPTNSVDEIQRCM
11	1			1	105	2		2	1	13	14	150	FMLYGIVAEKPQRSWX
12			130	3		5	1					150	DGYEQNHT
13	1		2		5		5	14		18	1	150	YVLIPSFHTDAMN
	80	21	243	38	158	259	46	46	27	127	31

	N	P	Q	R	S	T	V	W	Y	\|	X	#

1	2	5	4	8	9	11	8	1				150	GDTESHRVLPAQFIKCNW
2	1	13	3	20	17	7	5	3	4			150	GRSPALTKVCDYHMQWFEIN
3	3	8	11	8	16	11	7	2	12			150	GSYHQTDPRAVLEFKNCMWI
4	1	6	4	4	18	10	6	16	14		1	150	GSWYTIADFLPVEQRCHMNX
5	3	6	4	5	19	8	3	7	15			150	GLSYDATWPREQMNVFIH
6	3	15	8	6	16	13	8	3	17			150	GYSPTDAQVFRLNWCIKEM
7	4	7	2	6	15	14	6	4	19			150	LGYSTDPIRVAKFNWMQCEH
8	4	4	5	7	15	7	5	2	29			150	YDSGLARTCEQVNPFHIKWM
9	31	5	1	5	10	3	3	9	16			150	NGYDSWHLPRKETVCIMAFQ
10	3	5	2	2	3	4	3	15	35			150	YGAFWHLPTNSVDEIQRCM
11		1	1	1	1		2	1	3		1	150	FMLYGIVAEKPQRSWX
12	2		3			1			5			150	DGYEQNHT
13	1	14			13	4	21		51			150	YVLIPSFHTDAMN
	58	89	48	72	152	93	77	63	220		2	1950

Tally of sequences of length 14 # = 118

	A	C	D	E	F	G	H	I	K	L	M	#

1	6		29	7	2	32	8	1	1	2		118	GDVHERTAFLPSIKNQ
2	4		10	1	5	22	7	3	4	7		118	GPDRYSVHLFAKIQTENW
3	11	2	7	2	3	25		5	1	9	2	118	GVARYLSDITFWCEMPK
4	5	2	7	7	3	12	4	4	3	6		118	SGVYPDELRTANHIFKWC
5	6	5	12		2	18	2	2	2	4	1	118	GYSDTVARCLPFHIKNWMQ
6	6		10	5	4	16		5	3	2	1	118	YGSTDRAEIFVKWLPQMN
7	4		4	1	4	32	2	2	2		1	118	GSVTYNADFHIKPQRWEM
8	6	1	5	1	4	18	2	5		3	2	118	GSYTWAPRDIFNVLHMCE
9	5	2	4	1	2	11	2	1	5	9	1	118	YSGTLVAKNRDWCFHPEIM
10	2	5	9	2	3	21		2	2	4		118	YGSDNTCQLRFWAEIKPV
11	12		1	3	5	25	2			2	1	118	YGWAPVFNEHLTDMQR
12	1				64	5	1	5		12	16	118	FMLGIPSVAHQTY
13	3		97	4		5	1	1	1	1		118	DGEANQHIKLV
14	2				3		4	12		6		118	YVPILHFANS
73	73	17	195	34	104	242	35	48	24	67	25

	N	P	Q	R	S	T	V	W	Y	\|	X	#

1	1	2	1	7	2	7	10					118	GDVHERTAFLPSIKNQ
2	1	13	2	10	8	2	8	1	10			118	GPDRYSVHLFAKIQTENW
3		2		11	8	4	13	3	10			118	GVARYLSDITFWCEMPK
4	5	8		6	13	6	12	3	12			118	SGVYPDELRTANHIFKWC
5	2	3	1	6	15	10	7	2	18			118	GYSDTVARCLPFHIKNWMQ
6	1	2	2	7	16	12	4	3	19			118	YGSTDRAEIFVKWLPQMN
7	5	2	2	2	18	12	13	2	10			118	GSVTYNADFHIKPQRWEM
8	4	6		6	16	12	4	9	14			118	GSYTWAPRDIFNVLHMCE
9	5	2		5	14	10	8	4	27			118	YSGTLVAKNRDWCFHPEIM
10	6	2	5	4	13	6	2	3	27			118	YGSDNTCQLRFWAEIKPV
11	4	7	1	1		2	6	14	32			118	YGWAPVFNEHLTDMQR
12		4	1		4	1	3		1			118	FMLGIPSVAHQTY
13	2		2				1					118	DGEANQHIKLV
14	2	14			2		20		53			118	YVPILHFANS
	38	67	17	65	129	84	111	44	233			1652

Tally of sequences of length 15 # = 125

	A	C	D	E	F	G	H	I	K	L	M	#

1	7		26	8	3	29	1	3		10		125	GDLREASTVNFIPYH
2	6		2	3		22	3	4	1	9		125	RGPLNSTYAVIQEHWDK
3	4	4	5	7	2	19	2	6	2	9	2	125	GRYLSVEPIDTACQWFHKMN
4	7	4	14	6	6	15	2	7	5	7	4	125	GDYAILVEFRKSTCMNPWHQ
5	6	3	10	2	5	18		4	2	3	2	125	GSYVDRWAFTICLNEKMP
6	6	2	7	2	5	10	1	5		7	1	125	SRYGTDLWAPFIVNCEQHM
7	8	4	14	2	2	22	3	3	1	9	1	125	GSDLAVRPYCTHIWEFNKM
8	6	2	4			22		2	2	3		125	GYSVWRATDNPLCIKQ
9	4	3	8		4	20	4	3	1	6		125	YGSDLPTRVAFHQCINKW
10	3	4	5	8	8	17	1	3		7		125	YGEFNTLSRDVCPAIWH
11	4	2	15	3	3	17	1	1	1			125	YGDSNPAWEFRTCQHIKV
12	22	3			2	31	3	1		3	3	125	GYAWPSNCHLMFQRVITX
13					71	1		4		6	30	125	FMLISQTVGPRY
14			115	2	1	1	1					125	DNEFGHPQ
15		3			5	1	1	20		7	1	125	YVILPFSCNGHMQ
	83	34	225	43	117	245	23	66	15	86	44

	N	P	Q	R	S	T	V	W	Y	\|	X	#

1	4	3		10	7	6	6		2			125	GDLREASTVNFIPYH
2	8	11	4	23	7	7	5	3	7			125	RGPLNSTYAVIQEHWDK
3	2	7	3	13	9	5	8	3	13			125	GRYLSVEPIDTACQWFHKMN
4	4	4	1	6	5	5	7	3	13			125	GDYAILVEFRKSTCMNPWHQ
5	3	2		8	18	5	11	8	15			125	GSYVDRWAFTICLNEKMP
6	3	6	2	12	24	9	4	7	12			125	SRYGTDLWAPFIVNCEQHM
7	2	6		7	21	4	8	3	5			125	GSDLAVRPYCTHIWEFNKM
8	4	4	2	7	19	5	12	10	21			125	GYSVWRATDNPLCIKQ
9	3	6	4	5	19	6	5	1	23			125	YGSDLPTRVAFHQCINKW
10	8	4		6	7	8	5	2	29			125	YGEFNTLSRDVCPAIWH
11	7	5	2	3	14	3	1	4	39			125	YGDSNPAWEFRTCQHIKV
12	4	7	2	2	6	1	2	8	24		1	125	GYAWPSNCHLMFQRVITX
13		1	2	1	4	2	2		1			125	FMLISQTVGPRY
14	3	1	1									125	DNEFGHPQ
15	2	7	1		5		33		39			125	YVILPFSCNGHMQ
	57	74	24	103	165	66	109	52	243		1	1875

Distribution of D-JH with number of cys′s

0 1 2 3 4

1248 53 80 1 1

Tally of AAs in the YYCar motif

	A	C	D	E	F	G	H	I	K	L	M	#

1			1	1	14		1					1383	YFDEH
2		4	1		92		11			4		1383	YFHCLSWDR
3		1379
4	1207		3		2	12		2		2		1383	AVTSGNDFILRQX
5	14			1	4	18	17	9	187	4	1	1383	RKTSGHAIVNFLQYPEMI
	1221	1383	5	2	112	30	29	11	187	10	1

	N	P	Q	R	S	T	V	W	Y	\|	X	#

1									1366			1383	YFDEH
2				1	3			2	1265			1383	YFHCLSWDR
3				2	2							1383	CRS
4	4		1	2	17	51	79				1	1383	AVTSGNDFILRQX
5	7	2	3	992	55	56	9		3	1		1383	RKTSGHAIVNFLQYPEMI
	11	2	4	997	77	107	88	2	2634	1	1	6915

TABLE 12P

Alignment and tabulation of sequences having 3-22 D segments

D3:3-22_Phz0 YYYDSSGYYY (SEQ ID NO: 448) = GLG

	Entry	Seq1	L1	Seq2	L2	JH	P	Score

1	hs3d6hcv	GRDYYDSGGYFT	12	GRDYYDSGGYFTVAFDI	17	3	6	1.76D + 13
		(SEQ ID NO: 334)		(SEQ ID NO: 335)

2	hs6d4xb7	DRHNYYDSSGSYS	13	DRHNYYDSSGSYSDY	15	4	9	4.40D + 12
		(SEQ ID NO: 336)		(SEQ ID NO: 337)

3	hs6d4xg3	DCPAPAKMYYYGSGICT	17	DCPAPAKMYYYGSGICTFDY	20	4	3	6.55D + 04
		(SEQ ID NO: 338)		(SEQ ID NO: 339)

4	hs83x6f2	AFYDSAD	7	AFYDSADDY	9	4	−4	2.62D + 05
		(SEQ ID NO: 340)		(SEQ ID NO: 341)

5	hsa230644	RDYYDSSGPEAG	12	RDYYDSSGPEAGFDI	15	3	3	6.87D + 10
		(SEQ ID NO: 342)		(SEQ ID NO: 343)

6	hsa239386	DGTLIDTSAYYYL	13	DGTLIDTSAYYYLY	14	4	6	6.87D + 10
		(SEQ ID NO: 344)		(SEQ ID NO: 345)

7	hsa234232	NSSDSS	6	NSSDSSVLDV	10	6	−4	6.55D + 04
		(SEQ ID NO: 346)		(SEQ ID NO: 347)

8	hsa239378	DQVFDSGGYNHR	12	DQVFDSGGYNHRFDS	15	4	3	1.07D + 09
		(SEQ ID NO: 348)		(SEQ ID NO: 349)

9	hsa239367	DLEYYYDSGGHYSP	14	DLEYYYDSGGHYSPFHY	17	4	9	1.10D + 12
		(SEQ ID NO: 350)		(SEQ ID NO: 351)

10	hsa239339	DDSSGY	6	DDSSGYYYIDY	11	4	−10	1.72D + 10
		(SEQ ID NO: 352)		(SEQ ID NO: 353)

11	hsa245311	GHYYDSPGQYSYS	13	GHYYDSPGQYSYSEY	15	4	3	1.07D + 09
		(SEQ ID NO: 354)		(SEQ ID NO: 355)

12	hsa240578	GGFRPPPYDYESSAYRTYR	19	GGFRPPPYDYESSAYRTYRLDF	22	4	21	2.75D + 11
		(SEQ ID NO: 356)		(SEQ ID NO: 357)

13	hsa245359	DSDTRAY	7	DSDTRAYYWYFDL	13	2	−7	1.68D + 07
		(SEQ ID NO: 358)		(SEQ ID NO: 359)

14	hsa245028	GRHYYDSSGYYSTPE	15	GRHYYDSSGYYSTPENYFDY	20	4	6	1.80D + 16
		(SEQ ID NO: 360)		(SEQ ID NO: 361)

15	hsa245019	DPSYYYDSSGLPL	13	DPSYYYDSSGLPLHGMDV	18	6	9	4.40D + 12
		(SEQ ID NO: 362)		(SEQ ID NO: 363)

16	hsa244991	TYYYDSSGYLLTR	13	TYYYDSSGYLLTRYFQH	17	1	3	4.50D + 15
		(SEQ ID NO: 364)		(SEQ ID NO: 365)

17	hsa244945	NAPHYDSSGYYQT	13	NAPHYDSSGYYQTFDY	16	4	6	7.04D + 13
		(SEQ ID NO: 366)		(SEQ ID NO: 367)

18	hsa244943	GYHSSSYA	8	GYHSSSYADAFDI	13	3	−7	6.71D + 07
		(SEQ ID NO: 368)		(SEQ ID NO: 369)

19	hsa245289	PIGYCSGGSC	10	PIGYCSGGSCYSFDY	15	4	−4	2.62D + 05
		(SEQ ID NO: 370)		(SEQ ID NO: 371)

20	hsa240554	THGTYVTSGYYPKI	14	THGTYVTSGYYPKI	14	4	6	2.68D + 08
		(SEQ ID NO: 372)		(SEQ ID NO: 373)

21	hsa279533	GATYYYESSGNYP	13	GATYYYESSGNYPDY	15	4	9	7.04D + 13
		(SEQ ID NO: 374)		(SEQ ID NO: 375)

22	hsa389177	AFYHYDSTGYPNRRY	15	AFYHYDSTGYPNRRYYFDY	19	4	6	4.29D + 09
		(SEQ ID NO: 376)		(SEQ ID NO: 377)

23	hsa7321	SYSYYYDSSGYWGG	14	SYSYYYDSSGYWGGYFDY	18	4	9	4.50D + 15
		(SEQ ID NO: 378)		(SEQ ID NO: 379)

24	hsaj2772	LSPYYYDSSSYH	12	LSPYYYDSSSYHDAFDI	17	3	6	2.62D + 05
		(SEQ ID NO: 380)		(SEQ ID NO: 381)

25	hsb7g4f08	EEDYYDSSGQAS	12	EEDYYDSSGQASYNWFXP	18	5	6	2.75D + 11
		(SEQ ID NO: 382)		(SEQ ID NO: 383)

26	hsb7g3b02	ETNYYDSGGYPG	12	ETNYYDSGGYPGFDF	15	4	6	4.40D + 12
		(SEQ ID NO: 384)		(SEQ ID NO: 385)

27	hsb7g3c12	GDHYYDRSGYRH	12	GDHYYDRSGYRHSYYYYAMDV	21	6	6	2.75D + 11
		(SEQ ID NO: 386)		(SEQ ID NO: 387)

28	hsb8g3b07	DRSSGN	6	DRSSGNYFDGMDV	13	6	−10	6.55D + 04
		(SEQ ID NO: 388)		(SEQ ID NO: 389)

29	hsfog1h	GRSRYSGYG	9	GRSRYSGYGFYSGMDV	16	6	−4	2.62D + 05
		(SEQ ID NO: 390)		(SEQ ID NO: 391)

30	hsgvh0209	DDTSGYGP	8	DDTSGYGPYYFYYGMDV	17	6	−10	2.68D + 08
		(SEQ ID NO: 392)		(SEQ ID NO: 393)

31	hsgvh55	RAYYDTSFYFEY	12	RAYYDTSFYFEYY	13	4	3	1.72D + 10
		(SEQ ID NO: 394)		(SEQ ID NO: 395)

32	hsgvh0304	DRIDYYKSGYYLGSA	15	DRIDYYKSGYYLGSADS	17	4	6	1.68D + 07
		(SEQ ID NO: 396)		(SEQ ID NO: 397)

33	hsgvh0332	DTDSSSHYG	9	DTDSSSHYGRFDP	13	5	−7	1.68D + 07
		(SEQ ID NO: 398)		(SEQ ID NO: 399)

34	hsgvh0328	VSISHYDSSGRPQRVF	16	VSISHYDSSGRPQRVFYGMDV	21	6	9	1.07D + 09
		(SEQ ID NO: 400)		(SEQ ID NO: 401)

35	hsgvh536	QARENVFYDSSGPTAP	16	QARENVFYDSSGPTAPFDH	19	4	15	1.72D + 10
		(SEQ ID NO: 402)		(SEQ ID NO: 403)

36	hshcmg42	VPAGNYYDTSGPDN	14	VPAGNYYDTSGPDNAD	16	4	12	1.72D + 10
		(SEQ ID NO: 404)		(SEQ ID NO: 405)

37	hsig001vh	WYYFDTSGYYPRNFYYMDV	19	WYYFDTSGYYPRNFYYMDV	19	4	3	2.81D + 14
		(SEQ ID NO: 406)		(SEQ ID NO: 407)

38	hsig13g10	GYYYDSGGNYNG	12	GYYYDSGGNYNGDY	14	4	3	1.10D + 12
		(SEQ ID NO: 408)		(SEQ ID NO: 409)

39	hsighpat3	DLRSYDPSGYYN	12	DLRSYDPSGYYNDGFDI	17	3	6	2.75D + 11
		(SEQ ID NO: 410)		(SEQ ID NO: 411)

40	hsigh13g7	GYYYDRGGNCNG	12	GYYYDRGGNCNGDY	14	4	3	6.87D + 10
		(SEQ ID NO: 412)		(SEQ ID NO: 413)

41	hsigh13g1	GYYYDRGGNYNG	12	GYYYDRGGNYNGDY	14	4	3	1.10D + 12
		(SEQ ID NO: 414)		(SEQ ID NO: 415)

42	hsighxx20	THYDSSGL	8	THYDSSGLDAFDI	13	3	−4	1.72D + 10
		(SEQ ID NO: 416)		(SEQ ID NO: 417)

43	hsihr9	DDSSGS	6	DDSSGSYYFDY	11	4	−10	1.07D + 09
		(SEQ ID NO: 418)		(SEQ ID NO: 419)

44	hsihv11	LSGGYYS	7	LSGGYYSDFDY	11	4	−13	2.68D + 08
		(SEQ ID NO: 420)		(SEQ ID NO: 421)

45	hs ej1f	GDYSDSSDSYI	11	GDYSDSSDSYIDAFDV	16	3	3	1.10D + 12
		(SEQ ID NO: 422)		(SEQ ID NO: 423)

46	hsmvh51	GETYYYDSRGYA	12	GETYYYDSRGYAFDH	15	4	6	2.62D + 05
		(SEQ ID NO: 424)		(SEQ ID NO: 425)

47	hsmvh517	PTRDSSGY	8	PTRDSSGYYVGY	12	4	−4	1.07D + 09
		(SEQ ID NO: 426)		(SEQ ID NO: 427)

48	hsmvh0406	GSFYYDSSGYPP	12	GSFYYDSSGYPPFDC	15	4	6	6.87D + 10
		(SEQ ID NO: 428)		(SEQ ID NO: 429)

49	hst14x14	GPYYYDSSGYYL	12	GPYYYDSSGYYLLDY	15	4	6	1.80D + 16
		(SEQ ID NO: 430)		(SEQ ID NO: 431)

50	hsvhig2	EEGYYDSSGYYSLGA	15	EEGYYDSSGYYSLGASDY	18	4	6	4.50D + 15
		(SEQ ID NO: 432)		(SEQ ID NO: 433)

51	hsvhia2	RPDSSGSRW	9	RPDSSGSRWYFDY	13	4	−7	6.71D + 07
		(SEQ ID NO: 434)		(SEQ ID NO: 435)

52	hsy14936	GYYDISGYYF	10	GYYDISGYYFDAFNI	15	3	−4	2.81D + 14
		(SEQ ID NO: 436)		(SEQ ID NO: 437)

53	hsy14934	DRGYDSSGYYGN	12	DRGYDSSGYYGNLDC	15	4	3	1.76D + 13
		(SEQ ID NO: 438)		(SEQ ID NO: 439)

54	hsy14935	DRGYDSIGYYGN	12	DRGYDSIGYYGNLDC	15	4	3	1.10D + 12
		(SEQ ID NO: 440)		(SEQ ID NO: 441)

55	hsz80519	AEDLTYYYDRSGWGVHGLL	19	AEDLTYYYDRSGWGVHGLLYYFDY	24	4	15	4.40D + 12
		(SEQ ID NO: 442)		(SEQ ID NO: 443)

56	hsz80429	LYPHYDSSGYYYV	13	LYPHYDSSGYYYVLDY	16	4	6	4.50D + 15
		(SEQ ID NO: 444)		(SEQ ID NO: 445)

57	hsz80461	DRVGYYDSSGYPPGSP	16	DRVGYYDSSGYPPGSPLDY	19	4	9	1.76D + 13
		(SEQ ID NO: 446)		(SEQ ID NO: 447)

Frequency of each AA type at each position in 57 Sequences having D3-22 segments

Pos	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y	\|	X	#

1						1																	1

2						1																	1

3	1				1									1									3

4	1			1											1			1					4

5			5			1				1			2		1	1		1					12

6	3		3	4		6				3		1	2		2	2	1			1			28	x

7	1		5	4	1	7	2	1		1		1	3		5	3	4	1	1	1			41	x

8	2	1	4		1	5	3	1				4	4	1	3	1	3	1		14			48	x

9			4		2	3	5	1		1			1		2	2	2	1		28			52	Y

10	1		4		2	1		1					1		1	4	1			40			56	Y

11			46	2			1			1			1		2			1		3			57	D

12	1	1	1					1	1				1		4	39	7			1			57	S

13	1					8		1	1				1		1	43	1						57	S

14	3		2		1	45					1				1	3							56	G

15						2	2			2		5	3	2	1	4			1	33			55	Y

16	2	1	1	1	2	3	1			1		1	6		3	1	1		1	24			49	x

17	3	1		1	1	5	2	1		4		6	6	2		7	2	1	1	3			46	x

18						8	1		1	2		2	2		4		3	1		3			27

19						2		1				1	1		3	4		1					13

20	2			1	2	1				1			1							1			9

21								1		1										1			3

22		1																		1			2

23											1						1						2

24			1																				1

25																		1					1

Average Dseg = 11.9 Average DJ = 15.7
Median D = 12 12 Shortest 6 Longest 19
Median DJ = 15 15 Shortest 9 Longest 24

TABLE 13P

Frequency of D-segments. “\|” stands for a stop codon.

D seg

“0”

%

C %

GLG

“1”

%

C %

GLG

“2”

%

C %

GLG

1-01	1	0.13	0	VQLERX(SEQ ID	4	0.53	0.22	GTTGTX(SEQ ID	5	0.66	0.34	YNWND(SEQ ID
				NO: 132)				NO: 133)				NO: 134)

1-07	0	0	0	V\|LELX(SEQ ID	3	0.4	0.11	GITGTX(SEQ ID	9	1.19	0.34	YNWNY(SEQ ID
				NO: 135)				NO: 136)				NO: 137)

1-20	0	0	0	V\|LERX(SEQ ID	1	0.13	0.22	GITGTX(SEQ ID	4	0.53	0.45	YNWND(SEQ ID
				NO: 138)				NO: 139)				NO: 140)

1-26	4	0.53	0	V\|WELLX(SEQ ID	13	1.72	0.90	GIVGATX(SEQ ID	36	4.76	0.78	YSGSYY(SEQ ID
				NO: 141)				NO: 142)				NO: 143)

2-02	31	4.1	2.47	GYCSSTSCYT(SEQ	4	0.53	0.22	RIL\|\|YQLLYX(SEQ	9	1.19	2.47	DIVVVPAAIX(SEQ
				ID NO: 144)				ID NO: 145)				ID NO: 146)

2-08	5	0.66	0.56	GYCTNGVCYT(SEQ	0	0	0	RILY\|WCMLYX(SEQ	3	0.4	0.56	DIVLMVYAIX(SEQ
				ID NO: 147)				ID NO: 148)				ID NO: 149)

2-15	29	3.83	1.57	GYCSGGSCYS(SEQ	2	0.26	0.11	RIL\|WW\|LLLX(SEQ	7	0.92	1.57	DIVVVVAATX(SEQ
				ID NO: 150)				ID NO: 151)				ID NO: 152)

2-21	16	2.11	0.67	AYCGGDCYS(SEQ	0	0	0	SILWW\|LLFX(SEQ	7	0.92	0.67	HIVVVTAIX(SEQ
				ID NO: 153)				ID NO: 154)				ID NO: 155)

3-03	32	4.23	2.80	YYDFWSGYYT(SEQ	7	0.92	0.90	VLRFLEWLLYX(SEQ	27	3.57	1.12	ITIFGVVIIX(SEQ
				ID NO: 156)				ID NO: 157)				ID NO: 158)

3-09	13	1.72	1.35	YYDILTGYYN(SEQ	5	0.66	0.78	VLRYFDWLL\|X(SEQ	0	0	0	ITIF\|LVIIX(SEQ
				ID NO: 159)				ID NO: 160)				ID NO: 161)

3-10	42	5.55	4.26	YYYGSGSYYN(SEQ	13	1.72	0.89	VLLWFGELL\|X(SEQ	11	1.45	2.91	ITMVRGVIIX(SEQ
				ID NO: 162)				ID NO: 163)				ID NO: 164)

3-16	18	2.38	0.67	YYDYVWGSYRYT	8	1.06	0	VL\|LRLGELSLYX	5	0.66	0.34	IMITFGGVIVIX
				(SEQ ID				(SEQ ID NO: 166)				(SEQ ID
				NO: 165)								NO: 167)

3-22	57	7.53	3.36	YYYDSSGYYY(SEQ	1	0.13	0.11	VLL\|\|\|WLLLX	6	0.79	0.34	ITMIVVVITX(SEQ
				ID NO: 168)				(SEQ ID				ID NO: 170)
								NO: 169)

4-04	5	0.66	0.28	DYSNY(SEQ ID	2	0.26	0	\|LQ\|LX(SEQ ID	2	0.26	0.06	TTVTX(SEQ ID
				NO: 171)				NO: 172)				NO: 173)

4-17	29	3.83	1.45	DYGDY(SEQ ID	0	0	0	\|LR\|LX(SEQ ID	20	2.64	0.90	TTVTX(SEQ ID
				NO: 174)				NO: 175)				NO: 176)

4-23	10	1.32	0.56	DYGGNS(SEQ ID	1	0.13	0	\|LRW\|LX(SEQ ID	4	0.53	0.56	TTVVTX(SEQ ID
				NO: 177)				NO: 178)				NO: 179)

5-05	3	0.4	0.06	WIQLWLX(SEQ ID	10	1.32	0.39	VDTAMVX(SEQ ID	31	4.1	0.73	GYSYGY(SEQ ID
				NO: 180)				NO: 181)				NO: 182)

5-12	0	0	0	WI\|WLRLX(SEQ	8	1.06	0.45	VDIVATIX(SEQ	14	1.85	1.12	GYSGYDY(SEQ ID
				ID NO: 183)				ID NO: 184)				NO: 185)

5-24	11	1.45	0	\|RWLQLX(SEQ ID	5	0.66	0.34	VEMATIX(SEQ ID	13	1.72	0.44	RDGYNY(SEQ ID
				NO: 186)				NO: 187)				NO: 188)

6-06	11	1.45	0.78	SIAARX(SEQ ID	9	1.19	0.48	EYSSSS(SEQ ID	1	0.13	0.11	V\|QLVX(SEQ ID
				NO: 189)				NO: 190)				NO: 191)

6-13	19	2.51	1.01	GIAVAGX(SEQ ID	35	4.62	2.13	GYSSSWY(SEQ ID	2	0.26	0.31	V\|QQLVX(SEQ ID
				NO: 192)				NO: 193)				NO: 194)

6-19	14	1.85	2.12	GIAVAGX(SEQ ID	48	6.34	2.02	GYSSGWY(SEQ ID	4	0.53	0.56	V\|QWLVX(SEQ ID
				NO: 195)				NO: 196)				NO: 197)

D7:7-	1	0.13	0	\|LGX	2	0.26	0.68	LTGX(SEQ ID	2	0.26	0.22	NWG
27								NO: 198)

Total = 757

TABLE 14P

Possible library components.

	Component	L	f

D2_2-02_Phz0	xxxYCSSTSCxxx	13,	31,	(SEQ ID NO: 199)

D3_3-16_Phz0	xxxxYVWGSYxxx	13,	18,	(SEQ ID NO: 200)

D5_5-12_Phz2	xxxxxxxSGYxxx	13,	14,	(SEQ ID NO: 201)

D3_3-09_Phz0	xxxYDILTGYYxx	13,	13,	(SEQ ID NO: 202)

D2_2-02_Phz2	xxxVVVPAAxxxx	13,	9,	(SEQ ID NO: 203)

D3_3-22_Phz0	xxxYYDSSGYxx	12,	57,	(SEQ ID NO: 204)

D3_3-03_Phz0	xxxDFWSGxxxx	12,	32,	(SEQ ID NO: 205)

D3_3-03_Phz2	xxxTIFGVxxxx	12,	27,	(SEQ ID NO: 206)

D5_5-12_Phz1	xxxxIVATxxxx	12,	8,	(SEQ ID NO: 207)

D3_3-10_Phz0	xxxYGSGSYYx	11,	42,	! could add one x at either end (SEQ ID NO:208)

D5_5-05_Phz2	xxxxYSYGxxx	11,	31,	(SEQ ID NO: 209)

D2_2-15_Phz0	xxxCSGxxCYx	11,	29,	(SEQ ID NO: 210)

D6_6-13_Phz0	xxxxAAAGxxx	11,	19,	(SEQ ID NO: 211)

D4_4-23_Phz0	xGxxxGGNxxx	11,	10,	(SEQ ID NO: 212)

D1_1-26_Phz2	xxxSGSYxxx	10,	35,	(SEQ ID NO: 213)

D6_6-13_Phz1	xxxSSSWxxx	10,	35,	(SEQ ID NO: 214)

D4_4-17_Phz2	xxxxTTVTTx	10,	20,	(SEQ ID NO: 215)

D2_2-21_Phz0	xxxC(SG)GDxCx	10,	16,	(SEQ ID NO: 216)

D6_6-19_Phz0	xxx(IV)AVAGxx	10,	14,	(SEQ ID NO: 217)

D3_3-10_Phz1	xxLWFGELxx	10,	13,	(SEQ ID NO: 218)

D5_5-24_Phz0	GxxWLxxxxF	10,	11,	(SEQ ID NO: 219)

D5_5-05_Phz1	xxxDTxMVxx	10,	10,	(SEQ ID NO: 220)

D3_3-16_Phz1	xxxxxGExxx	10,	8,	(SEQ ID NO: 221)

D6_6-19_Phz1	xxxxSGWxx	9,	48,	(SEQ ID NO: 222)

D5_5-24_Phz2	xxxxGYNxx	9,	13,	(SEQ ID NO: 223)

D3_3-10_Phz2	xxxVRGVxx	9,	11,	(SEQ ID NO: 224)

D6_6-06_Phz0	xxxIAAxxx	9,	11,	(SEQ ID NO: 225)

D1_1-07_Phz2	xxYxWNxxx	9,	9,	(SEQ ID NO: 226)

D4_4-17_Phz0	xxxYGDxx	8,	29,	(SEQ ID NO: 227)

D1_1-26_Phz1	xxVGATxx	8,	13,	(SEQ ID NO: 228)

D6_6-06_Phz1	xxxYSSSx	8,	9,	(SEQ ID NO: 229)

TABLE 15P

Lengths of CDRs: 1095 actual VH domains and 51 VH GLGs.

Length	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17

CDR1	0	0	10	0	1	820	38	175	1	1	5	1	11	0	23	1	7	0

GLG

0

38

3

10

0

0 . . .

CDR2	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	464	579
GLG	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	17	28
CDR3	0	0	0	4	2	8	6	28	40	65	77	90	117	117	88	105	86	81

Length	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	(33 or more)

CDR2

9

31

1

3

1

0

2

0

0 . . .

GLG

1

4

0

0 . . .

CDR3	45	36	36	16	16	8	8	2	3	0	2	1	0	0	1	5

TABLE 16P

Library of HC CDR3

Component	Fraction of	Length	#X	Complexity	library	Adjusted

1:	YYCA21111YFDYWG.	8	4	2.6 E 5	.10 (0-8)	.02
	(2 = KR; SEQ ID NO: 6)

2:	YYCA2111111YFDYWG.	10	6	9.4 E 7	.14 (9-10)	.14
	(2 = KR; SEQ ID NO: 7)

3:	YYCA211111111YFDYTG.	12	8	3.4 E 10	.25 (11 + 12 + 13/2)	.25
	(2 = KR; SEQ ID NO: 8)

4:	YYCAR111S2S3111YFDYWG.	14	6	1.9 e 8	.13 (14 + 13/2)	.14
	(2 = SG 3 = YW; SEQ ID NO: 9)

5:	YYCA2111CSG11CY1YFDYWG.	15	6	9.4 E 7	.13 (15 + 16/2)	.14
	(2 = KR; SEQ ID NO: 10)

6:	YYCA211S1TIFG11111YFDYWG.	17	8	1.7 E 10	.11 (17 + 16/2)	.12
	(2 = KR; SEQ ID NO: 11)

7:	YYCAR111YY2S33YY111YFDYWG.	18	6	3.8 E 8	.04 (18)	.08
	(2 = D\|G; 3 = S\|G; SEQ ID NO: 12)

8:	YYCAR1111YC2231CY111YFDYWG.	19	8	2.0 E 11	.10 (19 on)	.11
	(2 = S G; 3 = T D G; SEQ ID NO: 13)

Allowed lengths: 8, 10, 12, 14, 15, 17, 18, & 19

TABLE 17P

vgDNA encoding the CDR3 elements of the library

! CDR3 library components

(Ctop25) 5′-gctctggtcaa C|TTA|AGg|gct|gag|g-3′ (SEQ ID NO:40)

(CtprmA) 5′-gctctggtcaa C|TTA|AGg|gct|gag|gac-

! AflII . . .

	\|acc\|gct\|gtc\|tac\|tac\|tgc\|gcc-3′ (SEQ ID NO: 41)

(CBprmB)[RC] 5′-|tac|ttc|gat|tac|ttg|ggc|caa|GGT|ACC|ctG|GTC|ACC|tcgctccacc-3′(SEQ ID NO: 42)

! BstEII . . .

(CBot25)[RC] 5′-|GGT|ACC|ctG|GTC|ACC|tcgctccacc-3′(SEQ ID NO: 43)

!

! N.B. [RC] means the the actual oligonucleotide is the reverse complement

! of the one shown.

! N.B. The 20 bases at 3′ end of CtprmA are identical to the most 5′ 20 bases

! of each of the vgDNA molecules.

! N.B. Ctop25 is identical to the most 5′ 25 bases of CtprmA.

! N.B. The 23 most 3′ bases of CBprmB are the reverse complement of the

! most 3′ 23 bases of each of the vgDNA molecules.

! N.B. CBot25 is identical to the 25 bases at the 5′ end of CBprmB.

!

(C1t08)	5′-cc\|gct\|gtc\|tac\|tac\|tgc\|gcc\|-
	<2>\|<1>\|<1>\|<1>\|<1>-
	\|tac\|ttc\|gat\|tac\|ttg\|ggc\|caa\|GG-3′ (SEQ ID NO: 44)

! 2 = KR, 1 = 0.27Y + 0.27G + 0.027 {ADEFHIKLMNPQRSTVW} no C

!

(C2t10)	5′-cc\|gct\|gtc\|tac\|tac\|tgc\|gcc\|-
	<2>\|<1>\|<1>\|<1>\|<1>\|<1>\|<1>\|-
	tac\|ttc\|gat\|tac\|ttg\|ggc\|caa\|GG-3′ (SEQ ID NO: 45)

! 2 = KR, 1 = 0.27Y + 0.27G + 0.027 {ADEFHIKLMNPQRSTVW} no C

!

(C3t12)	5′-cc\|gct\|gtc\|tac\|tac\|tgc\|gcc\|-
	<2>\|<1>\|<1>\|<1>\|<1>\|<1>\|<1>\|<1>\|<1>\|-
	tac\|ttc\|gat\|tac\|ttg\|ggc\|caa\|GG-3′ (SEQ ID NO: 46)

! 2 = KR, 1 = 0.27Y + 0.27G + 0.027 {ADEFHIKLMNPQRSTVW} no C

!

(C4t14)	5′-cc\|gct\|gtc\|tac\|tac\|tgc\|gcc\|cgt\|-
	\|<1>\|<1>\|<1>\|tct\|<2>\|tct\|<3>\|<1>\|<1>\|<1>\|-
	tac\|ttc\|gat\|tac\|ttg\|ggc\|caa\|GG-3′ (SEQ ID NO: 47)

! 2 = SG, 1 = 0.27Y + 0.27G + 0.027 {ADEFHIKLMNPQRSTVW} no C, 3 = YW

!

(C5t15)	5′-cc\|gct\|gtc\|tac\|tac\|tgc\|gcc\|-
	<2>\|<1>\|<1>\|<1>\|tgc\|tct\|ggt\|<1>\|<1>\|tgc\|tat\|<1>\|-
	tac\|ttc\|gat\|tac\|ttg\|ggc\|caa\|GG-3′ (SEQ ID NO: 48)

! 2 = KR, 1 = 0.27Y + 0.27G + 0.027 {ADEFHIKLMNPQRSTVW} no C

!

(C6t17)	5′-cc\|gct\|gtc\|tac\|tac\|tgc\|gcc\|-
	<2>\|<1>\|<1>\|tct\|<1>\|act\|atc\|ttc\|ggt\|<1>\|<1>\|<1>\|<1>\|<1>\|-
	tac\|ttc\|gat\|tac\|ttg\|ggc\|caa\|GG-3′ (SEQ ID NO: 49)

! 2 = KR, 1 = 0.27Y + 0.27G + 0.027 {ADEFHIKLMNPQRSTVW} no C

!

(C7t18)

5′-cc|gct|gtc|tac|tac|tgc|gcc|cgt|-

|<1>|<1>|<1>|tat|tac|<2>|tct|<3>|<3>|tac|tat|<1>|<1>|<1>|-

tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 50)

! 2 = DG, 1 = 0.27Y + 0.27G + 0.027 {ADEFHIKLMNPQRSTVW} no C, 3 = SG

!

(c8t19)

5′-cc|gct|gtc|tac|tac|tgc|gcc|cgt|-

|<1>|<1>|<1>|<1>|tat|tgc|<2>|<2>|<3>|<1>|tgc|tat|<1>|<1>|<1>|-

tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 51)

! 2 = SG, 1 = 0.27Y + 0.27G + 0.027 {ADEFHIKLMNPQRSTVW} no C, 3 = TDG

!

-----------------------------------------------------------------------------

TABLE 19

Names of 1398 GeneBank entries examined

haj10335	hsa006165	hsa234190	hsa234288	hsa239366	hsa240594	hsa244963
hs201e3	hsa006167	hsa234191	hsa234290	hsa239367	hsa240595	hsa244965
hs201g1	hsa006169	hsa234193	hsa234291	hsa239368	hsa240599	hsa244966
hs201m2	hsa006171	hsa234194	hsa234294	hsa239369	hsa240604	hsa244967
hs202e2	hsa006173	hsa234196	hsa234296	hsa239370	hsa241344	hsa244968
hs202g3	hsa131921	hsa234197	hsa234298	hsa239371	hsa241345	hsa244969
hs202g9	hsa132847	hsa234199	hsa235649	hsa239372	hsa241346	hsa244970
hs202m3	hsa132849	hsa234202	hsa235658	hsa239373	hsa241347	hsa244971
hs203e1	hsa132850	hsa234203	hsa235662	hsa239375	hsa241348	hsa244972
hs203g1	hsa132851	hsa234205	hsa235664	hsa239376	hsa241349	hsa244973
hs203m5	hsa132852	hsa234206	hsa235665	hsa239377	hsa241350	hsa244974
hs204e1	hsa224746	hsa234207	hsa235667	hsa239378	hsa241351	hsa244975
hs204g1	hsa225092	hsa234208	hsa235671	hsa239379	hsa241353	hsa244976
hs3d6hcv	hsa225093	hsa234209	hsa235675	hsa239380	hsa241354	hsa244977
hs6d4xa7	hsa230634	hsa234211	hsa235677	hsa239381	hsa241355	hsa244978
hs6d4xb7	hsa230635	hsa234212	hsa238036	hsa239382	hsa241356	hsa244979
hs6d4xf1	hsa230636	hsa234214	hsa238037	hsa239383	hsa241357	hsa244980
hs6d4xf2	hsa230637	hsa234217	hsa238038	hsa239384	hsa241420	hsa244981
hs6d4xg3	hsa230638	hsa234221	hsa238039	hsa239385	hsa241421	hsa244982
hs6d4xh5	hsa230639	hsa234224	hsa238040	hsa239386	hsa242555	hsa244983
hs83x6b2	hsa230640	hsa234227	hsa238326	hsa239387	hsa242556	hsa244984
hs83x6b5	hsa230641	hsa234229	hsa238327	hsa239388	hsa243108	hsa244985
hs83x6c3	hsa230643	hsa234230	hsa238328	hsa239390	hsa243110	hsa244986
hs83x6c4	hsa230644	hsa234232	hsa239330	hsa239391	hsa244928	hsa244987
hs83x6c5	hsa230645	hsa234235	hsa239331	hsa240553	hsa244929	hsa244988
hs83x6d4	hsa230646	hsa234238	hsa239332	hsa240554	hsa244930	hsa244989
hs83x6f1	hsa230647	hsa234239	hsa239333	hsa240555	hsa244931	hsa244990
hs83x6f2	hsa230648	hsa234242	hsa239334	hsa240556	hsa244932	hsa244991
hs83x6f3	hsa230649	hsa234245	hsa239335	hsa240557	hsa244933	hsa244992
hs83x6f5	hsa230650	hsa234248	hsa239336	hsa240558	hsa244934	hsa244993
hs83x6h3	hsa230651	hsa234249	hsa239337	hsa240559	hsa244935	hsa244994
hs83x9a6	hsa230652	hsa234251	hsa239338	hsa240560	hsa244936	hsa244995
hs83x9b6	hsa230653	hsa234252	hsa239339	hsa240561	hsa244937	hsa244996
hs83x9b9	hsa230654	hsa234255	hsa239340	hsa240562	hsa244938	hsa244997
hs83x9c8	hsa230655	hsa234256	hsa239341	hsa240563	hsa244939	hsa244998
hs83x9d6	hsa230656	hsa234257	hsa239342	hsa240564	hsa244940	hsa244999
hs83x9d7	hsa230657	hsa234258	hsa239343	hsa240565	hsa244941	hsa245000
hs83x9e6	hsa230658	hsa234259	hsa239344	hsa240566	hsa244942	hsa245001
hs83x9e8	hsa234156	hsa234260	hsa239345	hsa240567	hsa244943	hsa245002
hs83x9e9	hsa234158	hsa234262	hsa239346	hsa240568	hsa244944	hsa245003
hs83x9f6	hsa234160	hsa234263	hsa239347	hsa240569	hsa244945	hsa245004
hs83x9g6	hsa234161	hsa234264	hsa239348	hsa240570	hsa244946	hsa245005
hs9d4x10	hsa234163	hsa234266	hsa239349	hsa240571	hsa244947	hsa245006
hs9d4x7	hsa234164	hsa234268	hsa239350	hsa240572	hsa244948	hsa245007
hs9d4x8	hsa234166	hsa234269	hsa239351	hsa240573	hsa244949	hsa245008
hs9d4x9	hsa234168	hsa234270	hsa239353	hsa240575	hsa244950	hsa245009
hs9d4xa6	hsa234169	hsa234272	hsa239354	hsa240576	hsa244951	hsa245010
hs9d4xa7	hsa234171	hsa234273	hsa239355	hsa240578	hsa244952	hsa245011
hs9d4xb6	hsa234172	hsa234274	hsa239356	hsa240580	hsa244953	hsa245012
hs9d4xc2	hsa234175	hsa234276	hsa239357	hsa240581	hsa244954	hsa245013
hs9d4xd6	hsa234178	hsa234277	hsa239358	hsa240582	hsa244955	hsa245014
hs9d4xe6	hsa234180	hsa234279	hsa239359	hsa240585	hsa244956	hsa245015
hs9d4xf3	hsa234181	hsa234281	hsa239360	hsa240586	hsa244957	hsa245016
hs9d4xh4	hsa234183	hsa234282	hsa239361	hsa240588	hsa244958	hsa245017
hs9d4xh5	hsa234184	hsa234283	hsa239362	hsa240589	hsa244959	hsa245018
hsa005975	hsa234186	hsa234284	hsa239363	hsa240590	hsa244960	hsa245019
hsa005977	hsa234187	hsa234286	hsa239364	hsa240592	hsa244961	hsa245020
hsa006161	hsa234189	hsa234287	hsa239365	hsa240593	hsa244962	hsa245021
hsa245022	hsa245217	hsa245305	hsa279524	hsabhiv8	hsb8g2g08	hsevh52a1
hsa245023	hsa245218	hsa245307	hsa279526	hsadeigvh	hsb8g3b07	hsevh52a2
hsa245024	hsa245219	hsa245309	hsa279527	hsaj2768	hsb8g3c07	hsevh52a3
hsa245025	hsa245220	hsa245311	hsa279528	hsaj2769	hsb8g3c08	hsevh52a4
hsa245026	hsa245221	hsa245312	hsa279529	hsaj2771	hsb8g3c12	hsevh52a5
hsa245027	hsa245222	hsa245313	hsa279530	hsaj2772	hsb8g3d03	hsevh52b1
hsa245028	hsa245223	hsa245315	hsa279531	hsaj2773	hsb8g3d04	hsevh53a1
hsa245029	hsa245224	hsa245317	hsa279532	hsaj2776	hsb8g3d07	hsevh53a2
hsa245030	hsa245225	hsa245318	hsa279533	hsaj2777	hsb8g3d08	hsfog1h
hsa245031	hsa245226	hsa245319	hsa279535	hsaj4083	hsb8g3e02	hsfog3h
hsa245032	hsa245228	hsa245320	hsa279536	hsaj4899	hsb8g3e03	hsfogbh
hsa245033	hsa245229	hsa245321	hsa279537	hsasighc	hsb8g3f03	hsfom1h
hsa245034	hsa245230	hsa245322	hsa279543	hsavh510	hsb8g3g01	hsfs10hc
hsa245035	hsa245231	hsa245323	hsa279544	hsavh512	hsb8g3g03	hsfs11hc
hsa245036	hsa245232	hsa245325	hsa279545	hsavh513	hsb8g3g05	hsfs9whc
hsa245037	hsa245233	hsa245326	hsa279552	hsavh514	hsb8g3g10	hsgad2h
hsa245039	hsa245234	hsa245338	hsa389169	hsavh515	hsb8g3h01	hsgvh0117
hsa245040	hsa245235	hsa245342	hsa389170	hsavh516	hsb8g4c02	hsgvh0118
hsa245041	hsa245236	hsa245343	hsa389171	hsavh517	hsb8g4e01	hsgvh0119
hsa245042	hsa245237	hsa245345	hsa389172	hsavh519	hsb8g4e05	hsgvh0120
hsa245043	hsa245238	hsa245346	hsa389173	hsavh520	hsb8g4f11	hsgvh0121
hsa245044	hsa245239	hsa245347	hsa389174	hsavh523	hsb8g4h09	hsgvh0122
hsa245045	hsa245240	hsa245348	hsa389175	hsavh524	hsb8g4h10	hsgvh0123
hsa245046	hsa245241	hsa245349	hsa389176	hsavh526	hsb8g5d10	hsgvh0124
hsa245047	hsa245246	hsa245350	hsa389177	hsavh529	hsb8g5h08	hsgvh0201
hsa245048	hsa245251	hsa245352	hsa389178	hsavh53	hsbel1	hsgvh0202
hsa245049	hsa245255	hsa245353	hsa389179	hsavh56	hsbel14	hsgvh0203
hsa245050	hsa245258	hsa245355	hsa389180	hsb3g4a07	hsbel28	hsgvh0204
hsa245051	hsa245260	hsa245356	hsa389181	hsb73g04n	hsbel29	hsgvh0205
hsa245052	hsa245261	hsa245357	hsa389182	hsb74a08n	hsbel3	hsgvh0206
hsa245053	hsa245262	hsa245358	hsa389183	hsb7g1a11	hsbel34	hsgvh0207
hsa245054	hsa245263	hsa245359	hsa389184	hsb7g2b01	hsbel43	hsgvh0208
hsa245055	hsa245265	hsa249378	hsa389185	hsb7g3a01	hsbel45	hsgvh0209
hsa245056	hsa245266	hsa249628	hsa389186	hsb7g3a05	hsbel5	hsgvh0210
hsa245057	hsa245268	hsa249629	hsa389187	hsb7g3a10	bsbel54	hsgvh0211
hsa245058	hsa245272	hsa249630	hsa389188	hsb7g3b02	bsbel69	hsgvh0213
hsa245059	hsa245273	hsa249631	hsa389190	hsb7g3b03	hsbo1vhig	hsgvh0214
hsa245060	hsa245275	hsa249632	hsa389191	hsb7g3b05	hsbo3vhig	hsgvh0215
hsa245061	hsa245277	hsa249633	hsa389192	hsb7g3c03	hsbr1vhig	hsgvh0216
hsa245062	hsa245278	hsa249634	hsa389193	hsb7g3c12	hsbradh3	hsgvh0217
hsa245063	hsa245279	hsa249635	hsa389194	hsb7g3d07	hscal4ghc	hsgvh0218
hsa245064	hsa245280	hsa249636	hsa389195	hsb7g3e01	hsd4xd10	hsgvh0219
hsa245065	hsa245281	hsa249637	hsa389927	hsb7g3f02	hsd4xf21	hsgvh0220
hsa245066	hsa245282	hsa271600	hsa389929	hsb7g3f10	hsd4xg2	hsgvh0221
hsa245067	hsa245283	hsa271601	hsa6351	hsb7g3g02	hsd4xi10	hsgvh0222
hsa245068	hsa245284	hsa271602	hsa7321	hsb7g3g04	hsd4xi4	hsgvh0223
hsa245069	hsa245285	hsa271603	hsa7322	hsb7g4a08	hsd4xk9	hsgvh0224
hsa245071	hsa245286	hsa271604	hsa7323	hsb7g4c05	hsd4xl3	hsgvh0302
hsa245072	hsa245287	hsa279513	hsa7325	hsb7g4d09	hsd5hc	hsgvh0304
hsa245073	hsa245288	hsa279514	hsa7326	hsb7g4f08	hsdo1vhig	hsgvh0306
hsa245201	hsa245289	hsa279515	hsa7328	hsb7g4g07	hseliepa1	hsgvh0307
hsa245203	hsa245290	hsa279516	hsa7438	hsb7g5g03	hseliepa3	hsgvh0308
hsa245204	hsa245291	hsa279517	hsa7440	hsb8g1c04	hseliepa4	hsgvh0309
hsa245208	hsa245292	hsa279519	hsa7441	hsb8g1e04	hseliepb2	hsgvh0310
hsa245209	hsa245294	hsa279520	hsa7442	hsb8g1f03	hseliepd2	hsgvh0311
hsa245210	hsa245298	hsa279521	hsa7443	hsb8g1g04	hselilpb1	hsgvh0312
hsa245214	hsa245299	hsa279522	hsa7444	hsb8g1h02	hsevh51a1	hsgvh0314
hsa245215	hsa245301	hsa279523	hsaarma1	hsb8g2f09	hsevh51b1	hsgvh0315
hsgvh0318	hsig001vh	hsighpat5	hsigvhc07	hsimghc1	hsmvh0401	hsrou233
hsgvh0320	hsig030vh	hsighpat6	hsigvhc08	hsimghc2	hsmvh0403	hsrt792hc
hsgvh0321	hsig033vh	hsighpat7	hsigvhc09	hsimghc3	hsmvh0404	hsrt79hc
hsgvh0322	hsig039vh	hsighpat8	hsigvhc10	hsimghc4	hsmvh0405	hssm1vhig
hsgvh0323	hsig040vh	hsighpat9	hsigvhc11	hsimghcS	hsmvh0406	hssp46a
hsgvh0324	hsig055vh	hsighpt11	hsigvhc12	hsin42p5	hsmvh0501	hst14vh
hsgvh0325	hsig057vh	hsighpt12	hsigvhc14	hsin51p7	hsmvh0502	hst14x1
hsgvh0326	hsig1059	hsighpta1	hsigvhc16	hsin51p8	hsmvh0503	hst14x10
hsgvh0327	hsig10610	hsighvb5	hsigvhc17	hsin78	hsmvh0504	hst14x11
hsgvh0328	hsig13g10	hsighvca	hsigvhc18	hsin87	hsmvh0505	hst14x12
hsgvh0329	hsig473	hsighvcb	hsigvhc19	hsin89p2	hsmvh0506	hst14x13
hsgvh0330	hsig7sa11	hsighvcc	hsigvhc20	hsin92	hsmvh0507	hst14x14
hsgvh0331	hsigaehc	hsighvcd	hsigvhc21	hsin98p1	hsmvh0508	hst14x15
hsgvh0332	hsigaf2h2	hsighvce	hsigvhc22	hsjac10h	hsmvh0509	hst14x16
hsgvh0333	hsigashc	hsighvm	hsigvhc23	hsjhba1f	hsmvh0510	hst14x17
hsgvh0334	hsigathc	hsighxx1	hsigvhc24	hsjhbr2f	hsmvh0511	hst14x18
hsgvh0335	hsigdvrhc	hsighxx10	hsigvhc25	hsjhej1f	hsmvh0513	hst14x19
hsgvh0336	hsigg1kh	hsighxx11	hsigvhc26	hsld1110	hsmvh0515	hst14x20
hsgvh0419	hsigg1kl	hsighxx12	hsigvhc27	hsld1117	hsmvh0529	hst14x21
hsgvh0420	hsigg1lh	hsighxx14	hsigvhc28	hsld152	hsmvh51	hst14x22
hsgvh0421	hsigghc85	hsighxx16	hsigvhc29	hsld21	hsmvh510	hst14x23
hsgvh0422	hsigghcv3	hsighxx18	hsigvhc30	hsld217	hsmvh511	hst14x24
hsgvh0423	hsigghevr	hsighxx2	hsigvhc31	hsld218	hsmvh512	hst14x25
hsgvh0424	hsiggvdj1	hsighxx20	hsigvhc32	hsld25	hsmvh515	hst14x3
hsgvh0428	hsiggvdj2	hsighxx21	hsigvhc33	hsmad2h	hsmvh516	hst14x6
hsgvh0429	hsiggvhb	hsighxx22	hsigvhc35	hsmbcl5h4	hsmvh517	hst14x7
hsgvh0430	hsiggvhc	hsighxx23	hsigvhc36	hsmica1h	hsmvh53	hst14x8
hsgvh0517	hsigh10g1	hsighxx25	hsigvhc37	hsmica3h	hsmvh54	hst14x9
hsgvh0519	hsigh10g2	hsighxx26	hsigvhc38	hsmica4h	hsmvh55	hst22x1
hsgvh0522	hsigh10g3	hsighxx28	hsigvhc39	hsmica5h	hsmvh56	hst22x11
hsgvh0523	hsigh10g4	hsighxx29	hsigvhc40	hsmica6h	hsmvh57	hst22x12
hsgvh0526	hsigh10g5	hsighxx3	hsigvhc41	hsmica7h	hsmvh58	hst22x13
hsgvh0527	hsigh10g7	hsighxx30	hsigvhc42	hsmt11ige	hsmvh59	hst22x14
hsgvh0531	hsigh10g8	hsighxx31	hsigvhc43	hsmt12ige	hsnamembo	hst22x15
hsgvh511	hsigh10g9	hsighxx32	hsigvhls	hsmt13ige	hsnpb346e	hst22x18
hsgvh512	hsigh13g1	hsighxx34	hsigvhttd	hsmt14ige	hsoak3h	hst22x20
hsgvh513	hsigh13g7	hsighxx36	hsigvp151	hsmt15ige	hsog31h	hst22x21
hsgvh515	hsigh14g1	hsighxx37	hsigvp152	hsmt16ige	hspag1h	hst22x22
hsgvh519	hsigh14g2	hsighxx38	hsigvp153	hsmt17ige	hsrael	hst22x23
hsgvh521	hsigh2f2	hsighxx5	hsigvp154	hsmt21ige	hsregah	hst22x25
hsgvh526	hsigh3135	hsighxx6	hsigvp155	hsmt22ige	hsrfabh37	hst22x26
hsgvh530	hsigh35	hsighxx7	hsigvp156	hsmt23ige	hsrighvja	hst22x27
hsgvh533	hsigh44	hsighxx8	hsigvp157	hsmt24ige	hsrighvjb	hst22x28
hsgvh534	hsigh4c2	hsighxx9	hsigvp158	hsmt25ige	hsrou10	hst22x30
hsgvh535	hsigh9e1	hsigkrf	hsigvp251	hsmt26ige	hsrou11	hst22x9
hsgvh536	hsighadi2	hsigmhavh	hsigvp255	hsmt27ige	hsrou111	hsu24687
hsgvh55	hsighadi3	hsigrhe15	hsigvp256	hsmutuiem	hsrou112	hsu24688
hsh217e	hsighcvr	hsigtgk1h	hsigvp257	hsmvh0001	hsrou119	hsu24690
hsh241e	hsighcza	hsigtgk4h	hsigvp360	hsmvh0002	hsrou122	hsu24691
hsh28e	hsighczb	hsigtgl9h	hsigvp363	hsmvh0003	hsrou126	hsv52a512
hsha3d1ig	hsighczc	hsigvarh1	hsigvp369	hsmvh0004	hsrou127	hsvdj10h
hshambh	hsighczd	hsigvhc	hsigvp39	hsmvh0005	hsrou129	hsvdj12h
hshcmg42	hsighczf	hsigvhc01	hsihr8	hsmvh0006	hsrou13	hsvgcg1
hshcmg43	hsighczg	hsigvhc02	hsihr9	hsmvh0007	hsrou131	hsvgcm1
hshcmg44	hsigheavy	hsigvhc03	hsihv1	hsmvh0009	hsrou18	hsvgcm2
hshcmg46	hsighpat2	hsigvhc04	hsihv11	hsmvh0010	hsrou219	hsvh1djh6
hshcmt42	hsighpat3	hsigvhc05	hsihv18	hsmvh0011	hsrou221	hsvh3djh4
hshcmt47	hsighpat4	hsigvhc06	hsim9vch	hsmvh0012	hsrou222	hsvh4dj
hsvh4djh6	hsvhic11	hsww1p10e	hsy14935	hsz80377	hsz80424	hsz80482
hsvh4r	hsvhic2	hsx98932	hsy14936	hsz80378	hsz80426	hsz80483
hsvh52a43	hsvhic3	hsx98933	hsy14937	hsz80383	hsz80427	hsz80487
hsvh52a55	hsvhid1	hsx98934	hsy14938	hsz80385	hsz80429	hsz80489
hsvh5dj	hsvhid5	hsx98935	hsy14939	hsz80386	hsz80433	hsz80492
hsvh5djh5	hsvhid7	hsx98936	hsy14940	hsz80388	hsz80436	hsz80495
hsvh710p1	hsvhid9	hsx98938	hsy14943	hsz80390	hsz80438	hsz80496
hsvheg7	hsvhie4	hsx98939	hsy14945	hsz80391	hsz80439	hsz80499
hsvhfa2	hsvhif10	hsx98940	hsy18120	hsz80392	hsz80441	hsz80500
hsvhfa7	hsvhif3	hsx98941	hsz74663	hsz80393	hsz80442	hsz80502
hsvhfb5	hsvhif7	hsx98943	hsz74665	hsz80394	hsz80443	hsz80504
hsvhfc2	hsvhig2	hsx98944	hsz74668	hsz80397	hsz80445	hsz80507
hsvhfd7	hsvhp2	hsx98945	hsz74671	hsz80400	hsz80458	hsz80509
hsvhfe5	hsvhp29	hsx98946	hsz74672	hsz80403	hsz80459	hsz80512
hsvhfg9	hsvhp30	hsx98947	hsz74682	hsz80406	hsz80460	hsz80513
hsvhgd8	hsvhp32	hsx98948	hsz74688	hsz80407	hsz80461	hsz80517
hsvhgd9	hsvhp34	hsx98950	hsz74690	hsz80409	hsz80462	hsz80519
hsvhgh7	hsvhp4	hsx98951	hsz74693	hsz80411	hsz80463	hsz80520
hsvhha10	hsvhp46	hsx98952	hsz74695	hsz80412	hsz80465	hsz80527
hsvhia2	hsvhp48	hsx98953	hsz80363	hsz80414	hsz80466	hsz80534
hsvhia5	hsvhp53	hsx98954	hsz80364	hsz80415	hsz80473	hsz80538
hsvhib12	hsvhp7	hsx98955	hsz80365	hsz80416	hsz80474	hsz80544
hsvhib6	hsvigd9	hsx98956	hsz80367	hsz80417	hsz80475	hsz80545
hsvhib8	hswad35vh	hsx98958	hsz80368	hsz80418	hsz80476
hsvhic1	hswanembo	hsx98963	hsz80372	hsz80421	hsz80477
hsvhic10	hswo1vhig	hsy14934	hsz80375	hsz80422	hsz80480

TABLE 20P

Human GLG CDR1 & CDR2 AA seqs

	CDR1		1 1 1
Name	1234567	CDR2	1234567890123456789

1-02	GYY-MH	(SEQ ID NO: 230)	WINPNSGG--TNYAQKFQG	(SEQ ID NO: 231)

1-03	SYA--MH	(SEQ ID NO: 232)	WINAGNGN--TKYSQKFQG	(SEQ ID NO: 233)

1-08	SYD--IN	(SEQ ID NO: 234)	WMNPNSGN--TGYAQKFQG	(SEQ ID NO: 235)

1-18	SYG--IS	(SEQ ID NO: 236)	WISAYNGN--TNYAQKLQG	(SEQ ID NO: 237)

1-24	ELS--MH	(SEQ ID NO: 238)	GFDPEDGE--TIYAQKFQG	(SEQ ID NO: 239)

1-45	YRY--LH	(SEQ ID NO: 240)	WITPFNGN--TNYAQKFQD	(SEQ ID NO: 241)

1-46	SYY--MH	(SEQ ID NO: 242)	IINPSGGS--TSYAQKFQG	(SEQ ID NO: 243)

1-58	SSA--VQ	(SEQ ID NO: 244)	WIVVGSGN--TNYAQKFQE	(SEQ ID NO: 245)

1-69	SYA--IS	(SEQ ID NO: 246)	GIIPIFGT--ANYAQKFQG	(SEQ ID NO: 247)

1-e	SYA--IS	(SEQ ID NO: 248)	GIIPIFGT--ANYAQKFQG	(SEQ ID NO: 249)

1-f	DYY--MH	(SEQ ID NO: 250)	LVDPEDGE--TIYAEKFQG	(SEQ ID NO: 251)

2-05	TSGVGVG	(SEQ ID NO: 252)	LIYWNDDK---RYSPSLKS	(SEQ ID NO: 253)

2-26	NARMGVS	(SEQ ID NO: 254)	HIFSNDEK---SYSTSLKS	(SEQ ID NO: 255)

2-70	TSGMRVS	(SEQ ID NO: 256)	RIDWDDDK---FYSTSLKT	(SEQ ID NO: 257)

3-07	SYW--MS	(SEQ ID NO: 258)	NIKQDGSE--KYYVDSVKG	(SEQ ID NO: 259)

3-09	DYA--MH	(SEQ ID NO: 260)	GISWNSGS--IGYADSVKG	(SEQ ID NO: 261)

3-11	DYY--MS	(SEQ ID NO: 262)	YISSSGST--IYYADSVKG	(SEQ ID NO: 263)

3-13	SYD--MH	(SEQ ID NO: 264)	AIGTAGD---TYYPGSVKG	(SEQ ID NO: 265)

3-15	NAW--MS	(SEQ ID NO: 266)	RIKSKTDGGTTDYAAPVKG	(SEQ ID NO: 267)

3-20	DYG--MS	(SEQ ID NO: 268)	GINWNGGS--TGYADSVKG	(SEQ ID NO: 269)

3-21	SYS--MN	(SEQ ID NO: 270)	SISSSSSY--IYYADSVKG	(SEQ ID NO: 271)

3-23	SYA--MS	(SEQ ID NO: 272)	AISGSGGS--TYYADSVKG	(SEQ ID NO: 273)

3-30	SYG--MH	(SEQ ID NO: 274)	VISYDGSN--KYYADSVKG	(SEQ ID NO: 275)

3303	SYA--MH	(SEQ ID NO: 276)	VISYDGSN--KYYADSVKG	(SEQ ID NO: 277)

3305	SYG--MH	(SEQ ID NO: 278)	VISYDGSN--KYYADSVKG	(SEQ ID NO: 279)

3-33	SYG--MH	(SEQ ID NO: 280)	VIWYDGSN--KYYADSVKG	(SEQ ID NO: 281)

3-43	DYT--MH	(SEQ ID NO: 282)	LISWDGGS--TYYADSVKG	(SEQ ID NO: 283)

3-48	SYS--MN	(SEQ ID NO: 284)	YISSSSST--IYYADSVKG	(SEQ ID NO: 285)

3-49	DYA--MS	(SEQ ID NO: 286)	FIRSKAYGGTTEYTASVKG	(SEQ ID NO: 287)

3-53	SNY--MS	(SEQ ID NO: 288)	VIYSGGS---TYYADSVKG	(SEQ ID NO: 289)

3-64	SYA--MH	(SEQ ID NO: 290)	AISSNGGS--TYYANSVKG	(SEQ ID NO: 291)

3-66	SNY--MS	(SEQ ID NO: 292)	VIYSGGS---TYYADSVKG	(SEQ ID NO: 293)

3-72	DHY--MD	(SEQ ID NO: 294)	RTRNKANSYTTEYAASVKG	(SEQ ID NO: 295)

3-73	GSA--MH	(SEQ ID NO: 296)	RIRSKANSYATAYAASVKG	(SEQ ID NO: 297)

3-74	SYW--MH	(SEQ ID NO: 298)	RINSDGSS--TSYADSVKG	(SEQ ID NO: 299)

3-d	SNE--MS	(SEQ ID NO: 300)	SISGGS----TYYADSRKG	(SEQ ID NO: 301)

4-04	SSNW-WS	(SEQ ID NO: 302)	EIYHSGS---TNYNPSLKS	(SEQ ID NO: 303)

4-28	SSNW-WG	(SEQ ID NO: 304)	YIYYSGS---TYYNPSLKS	(SEQ ID NO: 305)

4301	SGGYYWS	(SEQ ID NO: 306)	YIYYSGS---TYYNPSLKS	(SEQ ID NO: 307)

4302	SGGYSWS	(SEQ ID NO: 308)	YIYHSGS---TYYNPSLKS	(SEQ ID NO: 309)

4304	SGDYYWS	(SEQ ID NO: 310)	YIYYSGS---TYYNPSLKS	(SEQ ID NO: 311)

4-31	SGGYYWS	(SEQ ID NO: 312)	YIYYSGS---TYYNPSLKS	(SEQ ID NO: 313)

4-34	GYY--WS	(SEQ ID NO: 314)	EINHSGS---TNYNPSLKS	(SEQ ID NO: 315)

4-39	SSSYYWG	(SEQ ID NO: 316)	SIYYSGS---TYYNPSLKS	(SEQ ID NO: 317)

4-59	SYY--WS	(SEQ ID NO: 318)	YIYYSGS---TNYNPSLKS	(SEQ ID NO: 319)

4-61	SGSYYWS	(SEQ ID NO: 320)	YIYYSGS---TNYNPSLKS	(SEQ ID NO: 321)

4-b	SGYY-WG	(SEQ ID NO: 322)	SIYHSGS---TYYNPSLKS	(SEQ ID NO: 323)

5-51	SYW--IG	(SEQ ID NO: 324)	IIYPGDSD--TRYSPSFQG	(SEQ ID NO: 325)

5-a	SYW--IS	(SEQ ID NO: 326)	RIDPSDSY--TNYSPSFQG	(SEQ ID NO: 327)

6-1	SNSAAWN	(SEQ ID NO: 328)	RTYYRSKWY-NDYAVSVKS	(SEQ ID NO: 329)

74.1	SYA--MN	(SEQ ID NO: 330)	WINTNTGN--PTYAQGFTG	(SEQ ID NO: 331)

CDR1 of human GLGs

	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y	—	Consens.

1			7	1		3						2				35	2			1		Sd x

2	2					6	1			1		4			1	7				29		Ysg x

3	11		3	1		10						2			1	6	1		5	11		YAGS x

4	1										2							1	2	7	38	—

5	1					2									1	1				5	41	—

6								6		1	28							4	12			Mwi

7			1			5	16					5		1		23						SHng

CDR2 of human GLGs

	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y	—	Consens.

1	3			2	1	5	1	2		3		1			7	4		6	7	9		X

2					1			46			1						2	1				I

3			4		1	1		2	2			8			3	12	1	1	1	15		ysn x

4	2					2	4					1	10	1		11	2	1	5	12		ysp x

5	1		8	2	1	6		2	4			8			1	17				1		sd x

6	3		7		2	26						3				8	2					Gsd x

7			4	1		17			1			2				24				1	1	SG x

8			1	3		3			3			10				9	4		1	2	15	—ns

9						2														3	46	—

10	1																3				47	—

11	2							4	5			1	1				35				3	T

12	1		2	2	1	3		2	1			11			2	3	1			22		Yn x

13																				51		Y

14	31											11	1			6	1	1				An x

15	4		16	1		1						1	14	11			2	1				dpq x

16						1			11				1			38						Sk

17					13					15					1			22				Vlf

18									37					13			1					Kq

19			1	1		34										14	1					GS

TABLE 21P

Tallies of Amino-acid frequencies in mature CDR1 and CDR2

Tally of 23 examples with length 14

	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y	\|	X

1		8								2								13
2	3															15	3	2
3	2			1		14										1		5
4			2		2	11										5				3
5						7						1	1			13				1
6	1				4	3		12		2								1
7						3		1	1			2	1		5	10
8					6	1				1		2			1	6	4	2
9					1	5		1				3	1		4	7	1
10	1		8			3						1	2		1	4	1			2
11	1				1		1	1								2		1		16
12	1		2	1		1	1					1				1			1	14
13											4							2	17
14	4		1			5						4				5	4

Tally of 11 examples with length 12

	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y	\|	X

1						4												7
2					1	4										4				2
3						7										4
4	1		1		1	5		2										1
5															1	9	1
6					2	1		3		2						3
7						3		1				3			1	3
8	1		3			2	1									2	2
9			1							1										9
10					1															10
11																			11
12						2						1				7	1

Tally of 175 examples with length 7

	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y	\|	X

1	2			1	1	2				1		3			2	153	10
2	3		2		1	87					1	10	1		5	61	2			2
3	3		26	1		54		1				5	1		2	76	3	1		2
4	6	1	1		6		1				2	1						11	1	145
5	5	2				13	2			2		3				6	2			140
6								1		1	1							13	159
7	2		1			67	1					10				88	5	1

Tally of 38 examples with length 6

	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y	\|	X

1												2				34	2
2	1		2		1	8						4				22
3							3					26								9
4					1		1												29	7
5																			38
6						10						3				22	3

Tally of 820 examples with length 5

	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y		Seen

1	8		81	10		151	4	8	5	3		100		4	15	364	55	8		4	SGNDT x	15
2	7	5	12		24	1	30	1	1	5		26		1	1	23	2			681	Y	15
3	202	4	24	13	13	133	10			2		7	5	2	3	32	14	13	112	231	YAGW x	17
4					6			172	2	7	409						3	16	205		MWI	8
5	8		6	1	1	49	241	2				79	1	3		367	56	2		4	SHNT x	14
CDR2

Tally of 31 examples with CDR2 of length 19

	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y	X

1					11					1		1		1	15	1	1					RF x
2	1							28									2					I
3									9	1					18	1	1			1		Rk
4						1			2			6				21	1					S
5			1	1		1			22		1			1	1	1	1			1		K x
6	16		1			1		1	1				3			1	6	1				A x
7	1		9									7				3	1			10		y x
8						23						1		1		5	1					G
9	2					18									1	1		1		7	1	G
10	4					1		1	1			1				1	21			1		T
11	1							3		1							26					T
12	2		11	9		1	1		1	1						2	1			2		x
13							1		1											29		Y
14	29												1				1					A
15	25		3	1										1			1					A
16									1				10			20						Sp
17										1	1							29				V
18				1					27					1	2							K
19			1			30																G

Tally of 579 (n > 50, bold; over 400, underscored) examples with length 17

	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y	X

1	44	1	1	2	11	81	5	69	1	14	6	41	1	4	34	30	19	118	66	31		VGIW x
2					7			522	1	10	17	1				3	8	10				I
3	3	1	22		5	7	6	51	25	1		76			8	262	19	1	46	46		SNI x
4	39	2	8	6	16	64	9	3	2	3		15	178	23	6	50	11	8	16	120		PYG x
5	3		194	6	1	70	6	44	6	4	1	55		4	8	133	9	7	1	27		DSGN x
6	3	1	75	4	45	326	1			6		43			1	63	8	1		2		GDS x
7	8		24	5		226	3	3	3	4		24		2	11	245	14	6		1		SG x
8	4	2	57	37	5	22	4	18	18	2	2	161	1	4	11	106	90	2	1	32		NST X
9	56			11		2		63	157	1	3	3	11	5	13	4	242	8				TKIA x
10	1		14	2	13	30	23	6	29	2	3	110		3	52	20	10	1	1	259		YNR x
11		1	2		7		5		1	4		3				5				551		Y
12	405			2		18		1		6		2	3		1	89	8	44				A
13	7		323	22		7	4			1		4	66	138	3			1		3		DQP x
14	2			5	6	3			123		1	4		2	7	421	1	2		2		SK x
15	1			1	188	2		1		22	3					1		357		2	1	VF
16	1			13		1	1		332	3	2	1	1	199	21		4					KQ x
17			11	1		565														1	1	G

Tally of 464 (over 50, bold; over 400, underscored)

	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y	X

1	5		13	184	8	1	7	1	2	15		6		3	26	65	9	14		105		EYSL x
2					6			429		3	4					1	2	19				I
3		1	13		13	4	10	5				154			1	12	1			250		YN x
4	1		12	2	6		199	2		1		3	4	5	2	19	28		15	165		YH x
5	5		20	1	1	18		4				9	1		22	365	16	1		1		S x
6			13	8		439						1					1	1	1			G
7			20	2		14	2	4	2			26	1		12	357	20	1		2	1	S x
8	13					2		4	8	1	2		4		3	6	420				1	T
9			10		4	1	10	1	8	1		245			13	9	3	1	1	157		NY x
10		6			2		2					2		1		7				444		Y
11	14		3				1	1	8			408	4			21	2			2		N
12	4		13			4				2		1	418			14	7	1				P
13	2				2								6			452	1			1		S
14					2			2		441					1			18				L
15				18					413		3	5		11	10	1	2	1				K
16	1		1			31		2				2			3	419	5					S

TABLE 22P

Tally of VH types

1-02	16	1-03	16	1-08	13	1-18	27	1-24	5
1-45	0	1-46	14	1-58	1	1-69	37	1-e	16
1-f	1	2-05	13	2-26	1	2-70	2	3-07	33
3-09	13	3-11	15	3-13	4	3-15	10	3-20	4
3-21	25	3-23	85	3-30	55	3303	59	3305	0
3-33	42	3-43	1	3-48	24	3-49	11	3-53	12
3-64	4	3-66	4	3-72	3	3-73	3	3-74	12
3-d	0	4-04	29	4-28	3	4301	46	4302	7
4304	37	4-31	0	4-34	184	4-39	65	4-59	45
4-61	9	4-b	11	5-51	55	5-a	13	6-1	7
74.1	3

TABLE 23P

Oligonucleotides used to variegate CDR1 and CDR2 of human HC

!(name) 5′-....DNA sequence....-3′

!everything to right of an exclamation point is commentary

![RC] means “reverse complement” of sequence shown

! If last non-comment and non-blank character is “-”, then continue

! on next line.

! Ignore case, “a” = “A”, “c” = “C”, etc.

! Ignore “|” and blanks.

! <number> means incorporate trinucleotide mixtue of given number.

!-------------------------------------------------------------------------

!

! CDR1

(ON-R1V1vg) 5′- ct|TCC|GGA|ttc|act|ttc|tct|-

<1>|tac|<1>|atg|<1>|- ! CDR1 of length 5, ON = 55 bases

tgg|gtt|cgC|CAa|gct|ccT|GG-3′ (SEQ ID NO: 27)

! <1> = ADEFGHIKLMNPQRSTVWY no C

!

(ON-R1top) 5′-cctactgtct |TCC|GGA|ttc|act|ttc|tct-3′ (SEQ ID NO: 28)

(ON-R1bot)[RC] 5′-tgg|gtt|cgC|CAa|gct|ccT|GG ttgctcactc-3′ (SEQ ID NO: 29)

(ON-R1V2vg) 5′- ct|TCC|GGA|ttc|act|ttc|tct|-

<6>|<7>|<7>|tac|tac|tgg|<7>|- ! CDR1 of length 7, ON = 61 bases

tgg|gtt|cgC|CAa|gct|ccT|GG-3′ (SEQ ID NO: 30)

! <6> = ST, 1:1

! <7> = 0.2025(SG) + 0.035(ADEFHIKLMNPQRTVWY) no C

(ON-R1V3vg) 5′-ct|TCC|GGA|ttc|act|ttc|tct|-

|atc|agc|ggt|ggt|tct|atc|tcc|<1>|<1>|<1>|tac|tac|tgg|<1>|- ! CDR1, L = 14

tgg|gtt|cgC|CAa|gct|ccT|GG-3′ (SEQ ID NO: 31) ! ON = 82 bases

! CDR2

(ON-R2V1vg) 5′-ggt|ttg|gag|tgg|gtt|tct|-

<2>|atc|<2>|<3>|tct|ggt|ggc|<1>|act|<1>|-

tat|gct|gac|tcc|gtt|aaa|gg-3′ (SEQ ID NO: 32)! ON = 68

bases, CDR2 = 17 AA

(ON-R2top) 5′-ct|tgg|gtt|cgC|CAa|gct|ccT|GGt|aaa|ggt|ttg|gag|tgg|gtt|tct-3′

(SEQ ID NO: 33)

(ON-R2bot)[RC] 5′-tat|gct|gac|tcc|gtt|aaa|ggt|-

cgc|ttc|act|atc|TCT|AGA|ttcctgtcac-3′ (SEQ ID NO: 34)! XbaI plus 10

bases of scab

(ON-R2V2vg) 5′-ggt|ttg|gag|tgg|gtt|tct|-

<1>|atc|<4>|<1>|<1>|ggt|<5>|<1>|<1>|<1>|-

tat|gct|gac|tcc|gtt|aaa|gg-3′ (SEQ ID NO: 35)! ON = 68

bases, CDR2 = 17 AA

! <4> = DINSWY, equimolar ! <5> = SGDN, equimolar

(ON-R2V3vg) 5′-ggt|ttg|gag|tgg|gtt|tct|-

<1>|atc|<4>|<1>|<1>|ggt|<5>|<1>|<1>|-

tat|aac|cct|tcc|ctt|aag|gg-3′ (SEQ ID NO: 36)! ON = 65

bases, CDR2 = 16 AA

(ON-R2bo3)[RC] 5′-tat|aac|cct|tcc|ctt|aag|ggt|-

cgc|ttc|act|atc|TCT|AGA|ttcctgtcac-3′ (SEQ ID NO: 37)! XbaI plus 10

bases of scab

(ON-R2V4vg) 5′-ggt|ttg|gag|tgg|gtt|tct|-

<1>|atc|<8>|agt|<1>|<1>|<1>|ggt|ggt|act|act|<1>

tat|gcc|gct|tcc|gtt|aag|gg-3′ (SEQ ID NO: 38)! ON = 74

bases, CDR2 = 19 AA

(ON-R2bo4)[RC] 5′-tat|gcc|gct|tcc|gtt|aag|ggt|-

cgc|ttc|act|atc|TCT|AGA|ttcctgtcac-3′ (SEQ ID NO: 39) ! XbaI plus

10 bases of scab

TABLE 25P

Lengths of CDRs in 285 human kappa chains

	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19

CDR1	0	0	0	0	0	0	0	0	0	0	0	154	73	3	0	0	28	27	0	0
CDR2	0	0	0	0	0	0	0	285	0	0	0	0	0	0	0	0	0	0	0	0
CDR3	0	5	0	0	1	0	3	2	28	166	63	12	1	1	0	0	0	0	0	1

TABLE 26P

Tally of kappa types: V and J

V genes:

O12	59	O2	0	O18	0	O8	0	A20	0
A30	0	L14	0	L1	2	L15	0	L4	2
L18	0	L5	4	L19	0	L8	4	L23	0
L9	1	L24	0	L11	4	L12	8	O11	10
O1	0	A17	5	A1	0	A18	3	A2	0
A19	13	A3	0	A23	4	A27	79	A11	26
L2	28	L16	0	L6	11	L20	0	L25	0
B3	22	B2	0	A26	0	A10	0	A14	0

JH#	1	2	3	4	5

tally	105	64	29	78	9

TABLE 27P

Names of Kappa chains analyzed

	AB022651
	AB022653
	AB022654
	AB022656
	AF007572
	AF021036
	AF103499
	AF103500
	AF103527
	AF103873
	AF107244
	AF107245
	AF107246
	AF107247
	AF115361
	AF165099
	AF165101
	AF165103
	AF165108
	AF165110
	AF165111
	AF184763
	AF184767
	hsa004955
	hsa004956
	hsa011133
	HSA241367
	HSA241375
	HSA388639
	HSA388640
	HSA388641
	HSA388642
	HSA388643
	HSA388644
	HSA388645
	HSA388646
	HSA388647
	HSA388648
	HSA388650
	HSA388651
	HSA388652
	HSA388653
	HSA388654
	HSA388655
	HSA388656
	HSA388657
	hsew1vk
	hsew3vk
	hsew4vk
	hsigdpk13
	hsigg1kl
	HSIGGVKA
	hsigk123
	hsigk319
	hsigklc14
	hsigklc28
	hsigklc5
	hsigklg31
	hsigklv01
	hsigklv02
	hsigklv03
	hsigklv04
	hsigklv05
	hsigklv06
	hsigklv07
	hsigklv09
	hsigklv10
	hsigklv12
	hsigklv13
	hsigklv14
	hsigklv15
	hsigklv16
	hsigklv17
	hsigklv18
	hsigklv19
	hsigklv20
	hsigklv21
	hsigklv22
	hsigklv23
	hsigklv24
	hsigklv25
	hsigklv27
	hsigklv28
	hsigklv29
	hsigklv31
	hsigklv32
	hsigklv33
	hsigklv34
	hsigklv35
	hsigklv36
	hsigklv37
	hsigklv38
	hsigklv39
	hsigklv40
	hsigklv41
	hsigklv42
	hsigklv43
	hsigklv44
	hsigklv45
	hsigklv46
	hsigklv49
	hsigklv50
	hsigklv51
	hsigklv52
	hsigklv53
	hsigklv54a
	hsigklv56
	hsigklv57
	hsigklv58
	hsigklv59
	hsigklv60
	hsigklv61
	hsigklv62
	hsigklv63
	hsigklv65
	hsigklv66
	hsigklv68
	hsigklv69
	hsigklv71
	hsigkvba
	hsigkvbb
	hsigkvbc
	hsigkvbd
	hsigkvbe
	hsigkvbf
	hsigkvc01
	hsigkvc03
	hsigkvc06
	hsigkvc11
	hsigkvc12
	hsigkvc20
	hsigkvc23
	hsigkvc27
	hsigkvc29
	hsigrklc
	hsikcvjp1
	hsikcvjp2
	hsikcvjp3
	hsikcvjp6
	hsikcvjp7
	hsld110vl
	hsld117vl
	hsld128vl
	hsld140vl
	hsld152vl
	hsld184vl
	hsld198vl
	hsld24vl
	hsmbcl1k1
	hsmbcl1k2
	hsmbcl2k2
	hsmbcl5k4
	hss10avl
	hss17bvl
	hss1a15vl
	HSU44792
	HSU44794
	HSU94422
	hsz84852
	hsz84853
	humigk1dm
	humigk3am
	humigk3bm
	humigk3cm
	humigkacoa
	humigkacob
	humigkacoc
	humigkacoe
	humigkacof
	humigkb1aa
	humigkb1ab
	humigkb1ac
	humigkvra
	humigkvrb
	humigkvrc
	humigkvrd
	humigkvre
	humigkvrg
	humigkvrh
	humigkvri
	humigkx
	humigky1
	humigky2
	humigky4
	humigky5
	humigky6
	humigl3ac
	humikc
	humikca
	humikcad
	humikcaf
	humikcag
	humikcah
	humikcai
	humikcaj
	humikcal
	humikcam
	humikcan
	humikcas
	humikcau
	humikcav
	humikcaw
	humikcax
	humikcay
	humikcaz
	humikcb
	humikcba
	humikcbb
	humikcbc
	humikcbd
	humikcbe
	humikcbf
	humikcbg
	humikcbh
	humikcbi
	humikcbj
	humikcbl
	humikcbm
	humikcbn
	humikcbo
	humikcbp
	humikcbq
	humikcbs
	humikcbt
	humikcbu
	humikcbv
	humikcbw
	humikcbx
	humikcbz
	humikcc
	humikcca
	humikccb
	humikccc
	humikccd
	humikcce
	humikccf
	humikccg
	humikcch
	humikcci
	humikccj
	humikcck
	humikcco
	humikccp
	humikccq
	humikccr
	humikccs
	humikcct
	humikccu
	humikccv
	humikccw
	humikcd
	humikcf
	humikcg
	humikch
	humikci
	humikck
	humikcm
	humikcn
	humikco
	humikcp
	humikcq
	humikcr
	humikcs
	humikct
	humikcu
	humikcv
	humikcva
	humikcvb
	humikcvc
	humikcvd
	humikcve
	humikcvf
	humikcvg
	humikcvh
	humikcvi
	humikcvj
	humikcw
	humikcx
	humikcy
	humikcz
	S46248
	S82746
	S82747
	SU96396
	SU96397

TABLE 28P

AA types seen in 154 kappa sequences having CDR1 of length 11 Tally

A

C

D

E

F

G

H

I

K

L

M

N

P

Q

R

S

T

V

W

Y

1												11	143						R
2	148										1			2	2	1			A
3														152	2				S
4		1	3			3						147							Q
5		12	1		27					7			3	99	4	1			S
6	1						81		1							71			V
7	2	4			18		5	1	2	9			12	97	3			1	S
8		3			5	1	2	1		31	1		10	87	12			1	S
9	2	7		10	1	6				29			1	8			13	77	Y
10				2					150					1		1			L
11	96				4	2				46				2	1	3			A

TABLE 30P

Synthetic Kappa light chain gene

!

! A27::JH1 with all CDRs replaced by stuffers.

! Each stuffer contains at least one stop codon and a

! restriction site that will be unique within the diversity vector.

!

1 GAGGACCATt GGGCCCC ctccgagact

! Scab...... Eco0109I

! ApaI.

!-----------------------------------

!

28 CTCGAG cgca

! XhoI..

!-----------------------------------

!

38 acgcaatTAA TGTgagttag ctcactcatt aggcacccca ggcTTTACAc tttatgcttc

! ..−35.. Plac ..−10.

!-----------------------------------

!

98 cggctcgtat gttgtgtgga attgtgagcg gataacaatt tc

!-----------------------------------

!

140 acacagga aacagctatgac

!-----------------------------------

!

160 catgatta cgCCAAGCTT TGGagccttt tttttggaga ttttcaac (SEQ ID NO: 54)

! PflMI.......

! Hind3.

!-----------------------------------

!

! M13 III signal sequence (AA seq)--------------------------->

! 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

! M K K L L F A I P L V V P F Y

206 gtg aag aag ctc cta ttt gct atc ccg ctt gtc gtt ccg ttt tac

!-----------------------------------

!

! --Signal--> FR1------------------------------------------->

! 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

! S H S A Q S V L T Q S P G T L

251|agc|cat|aGT|GCA|Caa|tcc|gtc|ctt|act|caa|tct|cct|ggc|act|ctt|

! ApaLI...

!-----------------------------------

!

! ----- FR1 ------------------------------------->| CDR1------>

! 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45

! S L S P G E R A T L S C R A S (SEQ ID NO: 55)

|tcG|CTA|AGC|CCG|GGt|gaa|cgt|gct|acC|TTA|AGt|tgc|cgt|gct|tcc| (SEQ ID NO: 54; Cont'd))

! EspI..... AflII...

! XmaI....

!

!----------------------------------

! For CDR1:

! <1> ADEFGHIKLMNPQRSTVWY equimolar

! <2> S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)

! <3> Y(0.2) ADEFGHIKLMNPQRSTVW (0.044 each)

! In a preferred embodiment, we omit codon 52 in vgDNA for CDR1.

!

! ------- CDR1 --------------------->|--- FR2 --------------->

! <1> <2> <2> xxx <3>

! 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

! Q S V S S S Y L A W Y Q Q K P

|cag|tct|gtt|tcc|tct|tct|tat|ctt|gct|tgg|tat|caa|cag|aaA|CCT|

! SexAI...

!

!----------------------------------

! For CDR2:

! <1> ADEFGHIKLMNPQRSTVWY equimolar

! <2> S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)

! <4> A(0.2) DEFGHIKLMNPQRSTVWY (0.044 each)

! ----- FR2 ------------------------->|------- CDR2 ---------->

! <1> <2> <4>

! 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75

! G Q A P R L L I Y G A S S R A

|GGT|caG|GCG|CCg|cgt|tta|ctt|att|tat|ggt|gct|tct|tcc|cgc|gct|

! SexAI.... KasI.... (CDR1 installed as AflII-(SexAI or KasI) cassette.)

!

!----------------------------------

!

! CDR2-->|--- FR3----------------------------------------------->

! <1>

! 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90

! T G I P D R F S G S G S G T D

| |act|gGG|ATC|CCG|GAC|CGt|ttc|tct|ggc|tct|ggt|tca|ggt|act|gac|

! BamHI...

! RsrII.....

! (CDR2 installed as (SexAI or KasI) to (BamHI or RsrII) cassette.)

!----------------------------------

!

! ------ FR3 ------------------------------------------------>

! 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105

! F T L T I S R L E P E D F A V

477 |ttt|acc|ctt|act|att|TCT|AGA|ttg|gaa|cct|gaa|gac|ttc|gct|gtt|

! XbaI...

!

!----------------------------------

!

! ----------->|----CDR3-------------------------->|-----FR4--->

! <3> <1> <1> <1> <1>

! 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120

! Y Y C Q Q Y G S S P E T F G Q

|tat|tat|tgC|CAa|cag|taT|GGt|tct|tct|cct|gaa|act|ttc|ggt|caa|

! BstXI...........

!

!----------------------------------

!

! -----FR4------------------->| <------- Ckappa ------------

! 121 122 123 124 125 126 127 128 129 130 131 132 133 134

! G T K V E I K R T V A A P S

510 |ggt|aCC|AAG|Gtt|gaa|atc|aag| |CGT|ACG|gtt|gcc|gct|cct|agt

! StyI.... BsiWI..

!

! (CDR3 installed as XbaI to (StyI or BsiWI) cassette.)

!

! 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149

! V F I F P P S D E Q L K S G T

552 |gtg|ttt|atc|ttt|cct|cct|tct|gac|gaa|CAA|TTG|aag|tca|ggt|act|

! MfeI...

!

! 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164

! A S V V C L L N N F Y P R E A

597 |gct|tct|gtc|gta|tgt|ttg|ctc|aac|aat|ttc|tac|cCT|CGT|Gaa|gct|

! BssSI...

!

! 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179

! K V Q W K V D N A L Q S G N S

642 |aaa|gtt|cag|tgg|aaa|gtc|gat|aAC|GCG|Ttg|cag|tcg|ggt|aac|agt|

! MluI....

!

! 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194

! Q E S V T E Q D S K D S T Y S

687 |caa|gaa|tcc|gtc|act|gaa|cag|gat|agt|aag|gac|tct|acc|tac|tct|

!

! 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209

! L S S T L T L S K A D Y E K H

732 |ttg|tcc|tct|act|ctt|act|tta|tca|aag|gct|gat|tat|gag|aag|cat|

!

! 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224

! K V Y A C E V T H Q G L S S P

777 |aag|gtc|tat|GCt|TGC|gaa|gtt|acc|cac|cag|ggt|ctG|AGC|TCc|cct|

! SacI....

!

! 225 226 227 228 229 230 231 232 233 234

! V T K S F N R G E C . . (SEQ ID NO: 332)

822 |gtt|acc|aaa|agt|ttc|aaC|CGT|GGt|gaa|tgc|taa|tag GGCGCGCC

! DsaI.... AscI....

! BssHII

866 acgcatctctaa GCGGCCGC aacaggaggag (SEQ ID NO: 333)

! NotI....

! EagI..

TABLE 31P

Tally of 285 CDR2s of length 7 in human kappa

Tally

A

C

D

E

F

G

H

I

K

L

M

N

P

Q

R

S

T

V

W

Y

1	51		62	7		95	1		11	15	2	1			2	6	6	3	22	1	x
2	225					18		5		5		2	1		1	3	16	9			A
3	2				9			1				2				267	2		1	1	S
4	2		1				5	4	9	1		77			4	93	80		2	7	Sx
5		1			2					80					200	2					R
6	162		7	36	4		4		1	3			3	63				2			Ax
7	5		1			3		1	1			2	2		1	125	144				x

TABLE 32P

Tally of 166 CDR3s of length 9 from human kappa.

Tally

A

C

D

E

F

G

H

I

K

L

M

N

P

Q

R

S

T

V

W

Y

1							4			8	21			131	1			1			Q
2				1			9		2	1				153							Q
3	14	4	4		3	6	4			1		1	3		21	16	3	4		82	Yx
4	1		9	1	2	37	4	2	2	15	1	33			2	20	7	1		29	x
5	2		2	6		3	4	5	3			28		17	7	65	19	1	1	3	x
6	7		1		11	2		3		8		1	4		3	41	33	5	28	19	x
7					1	2				6			146	2	2	5		2			P
8	2	4	1	2	21	7	3	5	1	38			7	4	25	1	3	1	16	25	x
9	3						2	1				1				2	157				T

TABLE 33P

lengths of CDRs in 93 human lambda chains

	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18+

CDR1	0	0	0	0	0	0	0	0	0	0	0	23	7	15	46	0	0	0	2
CDR2	5	0	0	1	0	0	0	80	2	0	0	1	4	0	0	0	0	0	1
CDR3	0	0	0	0	0	0	0	0	1	16	28	27	6	1	0	4	6	4	0

TABLE 34P

Tally of 46 CDR1s of length 14 from human lambda chains

Tally

A

C

D

E

F

G

H

I

K

L

M

N

P

Q

R

S

T

V

W

Y

1	2			2							1	41			T
2				43			3								G
3	2							1		1	6	36			TGx
4								1			45				S
5				5				1			40				S
6		39				1		4			2				DNx
7						8		1					37		V
8		1		42							2		1		G
9	4	1		35						1	2	3			TGx
10	1		1	3						1	2			38	Yx
11		4				1		35						6	DNx
12		3	1		2		1			1	2			36	Yx
13						1			2				43		V
14			1		4						41				S

TABLE 35P

Synthtic human lambda-chain gene

TABLE 36P

Tally of 23 CDR1s of length 11 from human lambda chains

Tally

A

C

D

E

F

G

H

I

K

L

M

N

P

Q

R

S

T

V

W

Y

1	1					6							10		6				x
2	1			1		21													G
3			15			1					7								DNx
4	2			1		1			3		7			1	8				X
5								7		16									L
6						11			1			2		8		1			X
7			1	1		1			2		2			1	14	1			X
8					1				10		1		1	1	2			7	X
9											2				6			15	Yx
10	11											1					11		X
11		3					7								9	2		2	X

TABLE 37P

Tally of 80 CDR2s of length 7 from human lambda chains

Tally

A

C

D

E

F

G

H

I

K

L

M

N

P

Q

R

S

T

V

W

Y

1	1	14	32	1	13			3		1		4	5	1	2		3	X
2		18	2					8		16					2	34		X
3	1	2					1			31				39	4		2	X
4		6	4			1		14	1	41		8	1	1	2		1	DNx
5								1	1				78					R
6									1		77			2				P
7	2													78				S

TABLE 38P

Tally of 27 CDR3s of length 11 from human lambda chains

Tally

A

C

D

E

F

G

H

I

K

L

M

N

P

Q

R

S

T

V

W

Y

1	4			5					6		5		4	3				X
2	3			1						2			14	5	2			Sx
3			1									7				13	6	X
4		19		2					1				1	4				DNx
5	1	4		2		2			2			1	13	2				X
6						1			3			1	21	1				S
7		1		7				12	1				4	2				X
8		2		1					10	1			6	6	1			X
9	3		1	8	10			3		1			1					X
10	1			4	1		1	1		3		1	1		6	5	3	X
11								2							25			V

TABLE 40P

Synthetic Kappa light chain gene with stuffers

TABLE 41P

Variegated DNA for kappa chains

!----------------------------------------------------------------

! Kappa chains

! For CDR1:

! <1> ADEFGHIKLMNPQRSTVWY equimolar

! <2> S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)

! <3> Y(0.2) ADEFGHIKLMNPQRSTVW (0.044 each)

! <4> A(0.2) DEFGHIKLMNPQRSTVWY (0.044 each)

(Kalvg600) 5′-gct|acC|TTA|AGt|tgc|cgt|gct|tcc|cag-

|<1>|gtt|<2>|<2>| <3>|ctt|gct|tgg|tat|caa|cag|aaA|CC-3′ (SEQ ID NO: 66)

(Ka2vg650) 5′-caG|GCG|CCg|cgt|tta|ctt|att|tat|<1>|gct|tct|<2>|cgc|<4>|-

|<1>|gGG|ATC|CCG|GAC|CGt|ttc|tct|ggt|tctcacc-3′ (SEQ ID NO: 71)

(Ka3vg670) 5′- gac|ttc|gct|gtt|-

|tat|tat|tgC|CAa|cag|<3>|<1>|<1>|<1>|cct|<1>|act|ttc|ggt|caa|-

|ggt|aCC|AAG|Gtt|g-3′ (SEQ ID NO: 77)

TABLE 42P

Variegated DNA for lambda chains

!------------------------

! For CDR1,

! <1> = 0.27 T, 0.27 G, 0.027 {ADEFHIKLMNPQRSVWY} no C

! <2> = 0.27 D, 0.27 N, 0.027 {AEFGHIKLMPQRSTVWY} no C

! <3> = 0.36 Y, 0.0355{ADEFGHIKLMNPQRSTVW} no C

! <4> = equimolar {ADEFGHIKLMNPQRSTVWY} no C

! <5> = 0.36 S, 0.0355{ADEFGHIKLMNPQRTVWY} no C

(Lm1vg710) 5′-gt|atc|act|att|tct|TGT|ACA|ggt|<1>|tct|tct|<2>|gtt|ggc|-

|<1>|<3>|<2>|<3>|gtt|tct|tgg|tat|caa|caa|caC|CC-3′ (SEQ ID NO: 83)

!------------------------------------------------

(Lm2vg750) 5′-G|CCg|aag|ttg|atg|atc|tac|-

<4>|<4>|<4>|<2>|cgt|cct|tct|ggt|gtc|agc|aat|c-3′ (SEQ ID NO: 88)

(Lm3vg817) 5′- gac|gag|gct|gac|tac|tat|tgt|-

|<4>|<5>|<4>|<2>|<4>|tct|<4>|<4>|<4>|<4>|gtc|ttc|ggc|ggt|GGT|-

|ACC|aaa|ctt|ac-3′ (SEQ ID NO: 93)

!----------------------------------------------------------------

TABLE 43P

Constant DNA for Synthetic Library

! CDR3 library components

(Ctop25) 5′-gctctggtcaa C|TTA|AGg|gct|gag|g-3′ (SEQ ID NO: 58)

(CtprmA) 5′-gctctggtcaa C|TTA|AGg|gct|gag|gac-

! AflII...

|acc|gct|gtc|tac|tac|tgc|gcc-3′ (SEQ ID NO: 59)

!

(CBprmB)[RC] 5′-|tac|ttc|gat|tac|ttg|ggc|caa|GGT|ACC|ctG|GTC|ACC|tcgctccacc-3′ (SEQ ID NO: 60)

! BstEII . . .

(CBot25)[RC] 5′-|GGT|ACC|ctG|GTC|ACC|tcgctccacc-3′ (SEQ ID NO: 61)

!----------------------------------------------------------------

! Kappa chains

(Ka1Top610) 5′-ggtctcagtt-

G|CTA|AGC|CCG|GGt|gaa|cgt|gct|acC|TTA|AGt|tgc|cgt|gct|tcc|cag-3′ (SEQ ID NO: 62)

(Ka1STp6l5) 5′-ggtctcagtt-

G|CTA|AGC|CCG|GGt|g-3′ (SEQ ID NO: 63)

(Ka1Bot620) [RC] 5′-ctt|gct|tgg|tat|caa|cag|aaA|-

CCt|GGT|caG|GCG|CC aagtcgtgtc-3′ (SEQ ID NO: 64)

(KalSB625) [RC] 5′-cct |GGT|caG|GCG|CC|aagtcgtgtc-3′ (SEQ ID NO: 65)

!

(Ka2Tshort657) 5′-cacgagtcctA|CCT|GGT|-

caG|GC-3′ (SEQ ID NO: 68)

(Ka2Tlong655) 5′-cacgagtcctA|CCT|GGT|-

caG|GCG|CCg|cgt|tta|ctt|att|tat-3′ (SEQ ID NO: 69)

(Ka2Bshort660) [RC] 5′- |GAC|CGt|ttc|tct|ggt|tctcacc-3′ (SEQ ID NO: 70)

!-----------------------------------------------------------------

(Ka3Tlon672)5′- gacgagtcct TCT|AGA|ttg|gaa|cct|gaa|gac|ttc|gct|gtt|-

|tat|tat|tgC|CAa|c|-3′ (SEQ ID NO: 72)

(Ka3BotL682) [RC] 5′-act|ttc|ggt|caa|-

|ggt|aCC|AAG|Gtt|gaa|atc|aag| |CGT|ACG| tcacaggtgag-3′ (SEQ ID NO: 73)

(Ka3Bsho694) [RC]5′- gaa|atc|aag| |CGT|ACG| tcacaggtgag-3′ (SEQ ID NO: 74)

!-----------------------------------------------------------------

(Lm1TPri75) 5′-gacgagtcct GG|TcA|CCt|GGT|-3′ (SEQ ID NO: 78)

(Lm1TLo715) 5′-gacgagtcct GG|TcA|CCt|GGT|-

caa|agt|atc|act|att|tct|TGT|ACA|ggt-3′ (SEQ ID NO: 79)

(Lm1BLo724)[RC] 5′-gtt|tct|tgg|tat|caa|caa|caC|CCG|GGc|aaG|GCG|-

AGA TCT tcacaggtgag-3′ (SEQ ID NO: 80)

(Lm1BSh737) [RC] 5′- Gc|aaG|GCG -

AGA TCT tcacaggtgag-3′ (SEQ ID NO: 81)

!-------------------------------------------------

(Lm2TSh757) 5′-gagcagagga C|CCG|GGc|aaG|GC-3′ (SEQ ID NO: 84)

(Lm2TLo753) 5′-gagcagagga C|CCG|GGc|aaG|GCG|CCg|aag|ttg|atg|atc|tac|-3′ (SEQ ID NO: 85)

(Lm2BLo762)[RC] 5′-cgt|cct|tct|ggt|gtc|agc|aat|cgt|ttc|TCC|GGA|tcacaggtgag-3′ (SEQ ID NO: 86)

(Lm2BSh765)[RC] 5′- cgt|ttc|TCC|GGA|tcacaggtgag-3′ (SEQ ID NO: 87)

!-------------------------------------------------

(Lm3TSh822) 5′-CTG|CAG|gct|gaa|gac|gag|gct|gac -3′ (SEQ ID NO: 89)

(Lm3TLo819) 5′-CTG|CAG|gct|gaa|gac|gag|gct|gac|tac|tat|tgt|-3′ (SEQ ID NO: 90)

(Lm3BLo825) [RC] 5′-gtc|ttc|ggc|ggt|GGT|-

|ACC|aaa|ctt|act|gtc|ctc|gGT|CAA|CCT|aAG|G acacaggtgag-3′ (SEQ ID NO: 91)

(Lm3BSh832) [RC] 5′- c|gGT|CAA|CCT|aAG|G acacaggtgag-3′ (SEQ ID NO: 92)

TABLE 48P

Synthtic human lambda-chain gene with stuffers in place of CDRs

TABLE 50P

3-23::CDR3::JH4 Stuffers in place of CDRs

Claims

1.-43. (canceled)

44. A library, comprising a first set of variegated DNA molecules encoding a collection of antibody heavy chains (HC), wherein each comprises a CDR1 region, a CDR2 region, and a CDR3 region, and wherein at least a heavy chain portion of the collection comprises a plurality of components that contain HC CDR3 regions, the components being selected from the group consisting of:

(i) YYCA21111YFDYWG (SEQ ID NO:6), wherein 1 is any amino acid residue except C, and 2 is a mixture of K and R;

(ii) YYCA2111111YFDYWG (SEQ ID NO:7), wherein 1 is any amino acid residue except C, and 2 is a mixture of K and R;

(iii) YYCA211111111YFDAYTG (SEQ ID NO:8), wherein 1 is any amino acid residue except C, and 2 is a mixture of K and R;

(iv) YYCAR111S2S3111YFDYWG (SEQ ID NO:9), wherein 1 is any amino acid residue except C, 2 is a mixture of S and G, and 3 is a mixture of Y and W;

(v) YYCA2111CSG11CY1YFDYWG (SEQ ID NO:10), wherein 1 is any amino acid residue except C, and 2 is a mixture of K and R;

(vi) YYCA211S1TIFG11111YFDYWG (SEQ ID NO:11), wherein 1 is any amino acid residue except C, and 2 is a mixture of K and R;

(vii) YYCAR111YY2S3344111YFDYWG (SEQ ID NO:12), wherein 1 is any amino acid residue except C, 2 is D or S, and 3 is a mixture of S and G;

(viii) YYCAR1111YC2231CY111YFDYWG (SEQ ID NO:13), wherein 1 is any amino acid residue except C, 2 is a mixture of S and G, and 3 is a mixture of T, D and G; and

(ix) a mixture of any of (i) to (viii) set forth above.

45. The library of claim 44, wherein:

the complexity of component (i) is 2×10⁵,

the complexity of component (ii) is 9.4×10⁷,

the complexity of component (iii) is 3.4×10¹⁰,

the complexity of component (iv) is 1.9×10⁸,

the complexity of component (v) is 9.4×10⁷,

the complexity of component (vi) is 1.7×10¹⁰,

the complexity of component (vii) is 3.8×10⁸, and

the complexity of component (viii) is 2.0×10¹¹.

46. The library of claim 44, wherein:

in one or more of components (i), (ii), (iii), (v), and (vi), 1 is (a) an equimolar mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; or (b) a mixture of 0.095 Y, 0.095 G, and 0.048 each of A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, and W; and 2 is an equimolar mixture of K and R;

in (iv), 1 is (a) an equimolar mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; or (b) a mixture of 0.095 Y, 0.095 G, and 0.048 each of A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, and W; 2 is an equimolar mixture of S and G; and 3 is an equimolar mixture of Y and W;

in (vii), 1 is (a) an equimolar mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; or (b) a mixture of 0.095 Y, 0.095 G, and 0.048 each of A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, and W; 2 is an equimolar mixture of D and G; and 3 is an equimolar mixture of S and G; or

in (viii), 1 is (a) an equimolar mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; or (b) a mixture of 0.095 Y, 0.095 G, and 0.048 each of A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, and W; 2 is an equimolar mixture of S and G; and 3 is an equimolar mixture of T, D, and G.

47. The library of claim 44, wherein components (i) through (viii) are present in the library in the following proportions: (i) 0.10, (ii) 0.14, (iii) 0.25, (iv) 0.13, (v) 0.13, (vi) 0.11, (vii) 0.04, and (viii) 0.10.

48. The library of claim 44, wherein components (i) through (viii) are present in the library in the following proportions: (i) 0.02, (ii) 0.14, (iii) 0.25, (iv) 0.14, (v) 0.14, (vi) 0.12, (vii) 0.08, and (viii) 0.11.

49. The library of claim 44, wherein the heavy chain portion further comprises a plurality of HC CDR1 regions selected from the group consisting of:

(1) <1>₁Y₂<1>₃M₄<1>₅(SEQ ID NO:100), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y;

(2) (S/T)₁(S/G/X)₂(S/G/X)₃Y₄Y₅W₆(S/G/X)₇(SEQ ID NO:101), wherein (SIT) is a 1:1 mixture of S and T residues, (S/G/X) is a mixture of 0.2025 S, 0.2025, G and 0.035 of each of amino acid residues A, D, E, F, H, I, K, L, M, N, P, Q, R, T, V, W, and Y;

(3) V₁S₂G₃G₄S₅I₆S₇<<1>₈<1>₉<1>₁₀Y₁₁Y₁₂W₁₃<1>₁₄(SEQ ID NO:1), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and

(4) a mixture of any of (1) to (3) set forth above.

50. The library of claim 44, wherein the heavy chain portion further comprises a plurality of HC CDR2 regions selected from the group consisting of:

(1) <2>I<2><3>SGG<1>T<1>YADSVKG (SEQ ID NO:2), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; <2> is an equimolar mixture of each of amino acid residues Y, R, W, V, G, and S; and <3> is an equimolar mixture of each of amino acid residues P, S, and G or an equimolar mixture of P and S;

(2) <1>I<4><1><1><G><5><1><1>-<1>YADSVKG (SEQ ID NO:3), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; <4> is an equimolar mixture of residues D, I, N, S, W, Y; and <5> is an equimolar mixture of residues S, G, D and N;

(3) <1>I<4><1><1>G<5><1><1>YNPSLKG (SEQ ID NO:4), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; and <4> and <5> are as defined above;

(4) <1>I<8>S<1><1><1>GGYY<1>YAASVKG (SEQ ID NO:5), wherein <1> is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; <8> is 0.27 R and 0.027 of each of ADEFGHIKLMNPQSTVWY; and

(5) a mixture of any of (1) to (4) set forth above.

51. The library of claim 49, wherein the heavy chain portion further comprises a plurality of HC CDR2 regions selected from the group consisting of:

(1) <2>I<2><3>SGG<1>T<1>YADSVKG (SEQ ID NO:2), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, 1, K, L, M, N, P, Q, R, S, T, V, W, and Y; <2> is an equimolar mixture of each of amino acid residues Y, R, W, V, G, and S; and <3> is an equimolar mixture of each of amino acid residues P, S, and G or an equimolar mixture of P and S;

(4) <1>I<8>S<1><1><1>GGYY<1>YAASVKG (SEQ ID NO:5), wherein <1> is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; <8> is 0.27 R and 0.027 of each of A, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, and Y; and

(5) a mixture of any of (1) to (4) set forth above.

52. The focused library according to claim 49, wherein the HC CDR1s (1), (2) and (3) regions are present in the library in the ratio 0.80:0.17:0.02.

53. The focused library according to claim 50, wherein a mixture of HC CDR2s (1)/(2) (equimolar), (3) and (4) are present in the library in a ratio of 0.54:0.43:0.03.

54. The library of claim 44, further comprising a second set of variegated DNA molecules encoding a collection of antibody light chains (LC), wherein each comprises a CDR1 region, a CDR2 region, and a CDR3 region.

55. The library of claim 54, wherein at least a light chain portion of the collection are kappa light chains, each of which comprises a LC_κCDR1 region, a LC_κCDR2 region, and a LC_κCDR3 region.

56. The library of claim 55, wherein the light chain portion comprises a plurality of LC_κCDR3 regions selected from the group consisting of:

(1) QQ<3><1><1><1>P<1>T (SEQ ID NO:16), wherein <1> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY; and <3> is 0.2 Y and 0.044 each of A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, and W;

(2) QQ33111P (SEQ ID NO:103), wherein 1 and 3 are as defined in (1) above;

(3) QQ3211PP1T (SEQ ID NO:17), wherein 1 and 3 are as defined in (1) above and 2 is 0.2 S and 0.044 each of A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, and Y; and

(4) a mixture of any of (1) to (3) set forth above.

57. The library of claim 56, wherein the light chain portion further comprises a plurality of LC_κCDR1 regions selected from the group consisting of:

(1) RASQ<1>V<2><2><3>LA (SEQ ID NO:14), wherein <1> is an equimolar mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y; <2> is 0.2 S and 0.044 of each of A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, Y; and <3> is 0.2Y and 0.044 each of A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W and S; and

(2) RASQ<1>V<2><2><2><3>LA (SEQ ID NO:15); wherein <1>, <2>, and <3> are as defined in (1) above; and

(3) a mixture of (1) and (2) set forth above.

58. The library of claim 56, wherein the light chain portion further comprises a plurality of LC_κCDR2 regions <1>AS<2>R<4><1> (SEQ ID NO:102), wherein <1> is an equimolar mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; <2> is 0.2 S and 0.044 of each of A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, and Y; and <4> is 0.2 A and 0.044 each of D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y.

59. The library of claim 57, wherein the light chain portion further comprises a plurality of LC_κCDR2 regions <1>AS<2>R<4><1> (SEQ ID NO:102), wherein <1> is an equimolar mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; <2> is 0.2 S and 0.044 of each of A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, and Y; and <4> is 0.2 A and 0.044 each of D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y.

60. The library of claim 57, wherein the LC_κCDR1s (1) and (2) are present in the library in a ratio of 0.68:0.32.

61. The library of claim 56, wherein the LC_κCDR3s (1), (2) and (3) are present in the library in a ratio of 0.65:0.1:0.25.

62. The library of claim 54, wherein at least a light chain portion of the collection are lambda light chains, each of which comprises a LC_λCDR1 region, a LC_λCDR2 region, and a LC_λCDR3 region.

63. The library of claim 62, wherein the light chain portion further comprises a plurality of LC_λCDR3 regions selected from the group consisting of:

(1) <4><5><4><2><4>S<4><4><4><4>V (SEQ ID NO:106), wherein <2> is 0.27 D, 0.27 N, and 0.027 each of A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y; <4> is an equimolar mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W; and <5> is 0.36 S and 0.0355 each of A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, and Y;

(2) <5>SY<1><5>S<5><1><4>V (SEQ ID NO:19), wherein <1> is an equimolar mixture of A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and <4> and <5> are as defined in (1) above; and

(3) a mixture of (1) and (2) set forth above.

64. The library of claim 63, wherein the light chain portion further comprises a plurality of LC_λCDR1 regions selected from the group consisting of:

(1) TG<1>SS<2>VG<1><3><2><3>VS (SEQ ID NO:18), wherein <1> is 0.27 T, 0.27 G and 0.027 each of A, D, E, F, H, I, K, L, M, N, P, Q, R, S, V, W, and Y, <2> is 0.27 D, 0.27 N and 0.027 each of A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y, and <3> is 0.36 Y and 0.036 each of A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W;

(2) G<2><4>L<4><4><4><3><4><4> (SEQ ID NO:104), wherein <2> is as defined in (1) above and <4> is an equimolar mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and

(3) a mixture of (1) and (2) set forth above.

65. The library of claim 63, wherein the light chain portion further comprises a plurality of LC_λCDR2 regions <4><4><4><2>RPS (SEQ ID NO:105), wherein <2> is 0.27 D, 0.27 N, and 0.027 each of A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y and <4> is an equimolar mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W.

66. The library of claim 64, wherein the light chain portion further comprises a plurality of LC_λCDR2 regions <4><4><4><2>RPS (SEQ ID NO:105), wherein <2> is 0.27 D, 0.27 N, and 0.027 each of A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y and <4> is an equimolar mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W.

67. The library of claim 64, where the LC_λ CDR1s (1) and (2) are present in the library in a ratio of 0.67:0.33.

68. The library of claim 63, wherein the LC_λCDR3s (1) and (2) are present in the library in an equimolar mixture.

69. The library of claim 44, wherein the library is a library of vectors.

70. The library of claim 69, wherein the vectors are yeast vectors.

71. The library of claim 44, wherein the library is a library of genetic packages.

72. The library of claim 71, wherein the genetic packages are cells, spores, or viral particles.

73. The library of claim 72, wherein the genetic packages are phage particles or yeast cells.

74. The library of claim 73, wherein the genetic packages are yeast cells, which display the collection of antibody heavy chains encoded by the first set of variegated DNA molecules.

75. The library of claim 54, wherein the library is a library of vectors.

76. The library of claim 75, wherein the vectors are yeast vectors.

77. The library of claim 54, wherein the library is a library of genetic packages.

78. The library of claim 77, wherein the genetic packages are cells, spores, or viral particles.

79. The library of claim 78, wherein the genetic packages are phage particles or yeast cells.

80. The library of claim 79, wherein the genetic packages are yeast cells, which display the collection of antibody heavy chains encoded by the first set of variegated DNA molecules, the collection of antibody light chains encoded by the second set of variegated DNA molecules, or both.