IP Library › Granted Patent US 7,794,983
Granted Patent B2
US 7,794,983 · App. 11/826,020 · Granted Sep 14, 2010

Method for genetic detection using interspersed genetic elements

Assignee: Life Genetics Lab, LLC.
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Quick Facts
Patent No.
US 7,794,983
App. No.
11/826,020
Granted
Sep 14, 2010
Kind
B2
Abstract

The way to design a “filled” site (which contains an interspersed element) primer set to target a particular locus is to design one of the two primers such that it encompasses that unique information (e.g., interspersed element+flanking genomic sequence+direct repeat). The way to design an “empty” site primer is to design one of the two primers such that the entire direct repeat sequence in addition to flanking genomic sequence is included on both sides. To improve efficiency, the “empty” site primer designed around the direct repeat should not be too long. This primer design of the present invention allows for the ability to test any type of interspersed genetic element containing characteristic direct repeat sequences (direct repeats). This gives the option of many new polymorphic marker sites because Alu elements are not the only interspersed genetic elements having direct repeats flanking their core sequence.

Claims (1791)

1. A method for genetic detection, comprising:

carrying out a polymerase chain reaction (PCR) on a DNA sample with a primer set to produce amplified DNA products, the primer set comprising a first primer for both a filled site containing an interspersed element and an empty site which does not contain the interspersed element, a second primer for the filled site, and a third primer for the empty site, the first primer complementary to a first flanking genomic sequence in the filled site and the empty site, the second primer complementary to a sequence comprised of a second flanking genomic sequence, a direct repeat sequence next to the second flanking genomic sequence and a part of the interspersed element next to the direct repeat sequence in the filled site, the third primer complementary to a sequence comprised of the direct repeat sequence and third flanking genomic sequences on both sides of the direct repeat sequence in the empty site; and

analyzing the amplified DNA products to detect presence or absence of the interspersed element insertion at the site.

2. The method of claim 1 , wherein the direct repeat sequence is not more than about 14 base pairs in length, the third flanking sequences include at least three bases on either side of the direct repeat sequence, and the third primer is less than or equal to about 20 base pairs in length.

3. The method of claim 1 , wherein the first primer is a forward primer for the filled site and the empty site, the second primer is a reverse primer for the filled site, and the third primer is a reverse primer for the empty site.

4. The method of claim 1 , wherein, in the filled site, the first flanking genomic sequence is in front of the second flanking genomic sequence, the direct repeat is present on the 5′ flanking side of the interspersed element and the part of the interspersed element included in the sequence complementary to the second primer is part of the 5′ sequence of the interspersed element.

5. The method of claim 1 , wherein the amplified DNA products from the filled site and the empty site have substantially the same length.

6. The method of claim 1 , wherein the interspersed element is selected from the group consisting of an Alu sequence, a long interspersed element (LINE), a short interspersed element (SINE), a human endogenous retrovirus (HERV), and a combination thereof.

7. The method of claim 6 , wherein the interspersed element is an Alu sequence.

8. The method of claim 1 , wherein the interspersed element is 50 to 200 base pairs in length.

9. The method of claim 1 , wherein the analysis of the amplified DNA products comprises sequencing the amplified DNA products.

10. The method of claim 1 , wherein the analysis of the amplified DNA products comprises quantitating the filled site and the empty site.

11. The method of claim 1 , wherein the analysis of the amplified DNA products is one selected from the group consisting of identifying paternity in human or animal, identifying a plant, a seed or a genetically modified product, detecting an agent of bio-terrorism, and identifying ethnic affiliation of an individual.

12. The method of claim 1 , wherein the analysis of the amplified DNA products comprises using at least one of a real-time PCR system, a DNA sequencer, a laser detection system, a detection platform, a gene chip, or capillary electrophoresis of the amplified DNA products which are fluorescently labeled.

13. The method of claim 1 , wherein the analysis of the amplified DNA products comprises using fluorescently labeled hybridization probes.

14. The method of claim 1 , wherein the analysis of the amplified DNA products comprises using an identical hybridization probe for the filled site and the empty site to hybridize to a homologous region in front of the interspersed element in view of a 5′ to 3′ orientation of the DNA sequence.

15. The method of claim 1 , further comprising, before or after the polymerase chain reaction, cleaving a genetic material in the DNA sample with a restriction enzyme specific for sequences within the interspersed element.

16. The method of claim 15 , wherein the restriction enzyme is ALU I.

17. The method of claim 1 , wherein the polymerase chain reaction is a multiplex polymerase chain reaction with multiple primer sets.

18. The method of claim 1 , wherein the interspersed element is Yb8AC1197, and the primer set comprises the first primer containing the sequence of TGCTGCCCTTAATCTTTACCA (SEQ ID NO: 3), the filled site second primer containing the sequence of CCCGGCCTTCATTTCTAAG (SEQ ID NO: 4), and the empty site third primer containing the sequence of GAGACTTTCATTTCTAAGATGTCTGG (SEQ ID NO: 5).

19. The method of claim 1 , wherein the interspersed element is Yb8AC1439, and the primer set comprises the first primer containing the sequence of TGCTGAGCTCCATGCTATTC (SEQ ID NO: 6), the filled site second primer containing the sequence of AGACGGGGTACCAGCTCTTG (SEQ ID NO: 7), and the empty site third primer containing the sequence of GCTCACCAGCTCTTGACGTA (SEQ ID NO: 8).

20. The method of claim 1 , wherein the interspersed element is Yb8NBC126, and the primer set comprises the first primer containing one of the sequence of AGCTCCTGGAAAAGGGAAAG (SEQ ID NO: 9) and the sequence of CTGTGAAGGCTCACCTGGAG (SEQ ID NO: 42), the filled site second primer containing the sequence of ATCCGATTGGGGCACCTTA (SEQ ID NO: 10), and the empty site third primer containing the sequence of ATGATGATTGGGGCACCTTA (SEQ ID NO: 11).

21. The method of claim 1 , wherein the interspersed element is Yb8AC1197, and the primer set comprises the first primer containing the sequence of CCTCCCTACAGAA (SEQ ID NO: 479), the filled site second primer containing the sequence of CGCCCGGCCTTCATTTCT (SEQ ID NO: 480), and the empty site third primer containing the sequence of GAGACTTTCATTTCTAAGATG (SEQ ID NO: 481).

22. The method of claim 17 , wherein the interspersed element comprises Yb8AC1197, Yb8AC1439, and Yb8NBC126, and the primer sets comprise:

a primer set for Yb8AC1197 comprising a first primer containing the sequence of TGCTGCCCTTAATCTTTACCA (SEQ ID NO: 3), a filled site second primer containing the sequence of CCCGGCCTTCATTTCTAAG (SEQ ID NO: 4), and an empty site third primer containing the sequence of GAGACTTTCATTTCTAAGATGTCTGG (SEQ ID NO: 5);

a primer set for Yb8AC1439 comprising a first primer containing the sequence of TGCTGAGCTCCATGCTATTC (SEQ ID NO: 6), a filled site second primer containing the sequence of AGACGGGGTACCAGCTCTTG (SEQ ID NO: 7), and an empty site third primer containing the sequence of GCTCACCAGCTCTTGACGTA (SEQ ID NO: 8); and

a primer set for Yb8NBC126 comprising a first primer containing the sequence of AGCTCCTGGAAAAGGGAAAG (SEQ ID NO: 9), a filled site second primer containing the sequence of ATCCGATTGGGGCACCTTA (SEQ ID NO: 10), and an empty site third primer containing the sequence of ATGATGATTGGGGCACCTTA (SEQ ID NO: 11).

23. The method of claim 1 , wherein a set of the interspersed element, the first primer, the second primer, and the third primer are one of a set as shown in the below table:

Inter-

spersed

Primer

Element

Sequence

Yb8NBC67

First primer

TGTGTCAAAGAGCGAGATGAACA

(SEQ ID NO: 18)

Second primer

GGGTTCACGCCATTCTAGC

(SEQ ID NO: 19)

Third primer

TTCATAGCAGCCTATTCTAGCAG

(SEQ ID NO: 20)

Ya5NBC241

First primer

aaacataatttagttccccacaa

(SEQ ID NO: 21)

Second primer

cccggccaagatccattc

(SEQ ID NO: 22)

Third primer

cccccagaagaaccattct

(SEQ ID NO: 23)

Yb8NBC237

First primer

GCCACTCGTAGGCAGTCATT

(SEQ ID NO: 24)

Second primer

GCCCGGCCGTTACGGTTT

(SEQ ID NO: 25)

Third primer

AGCATGTCAACTGTTACGTATG

(SEQ ID NO: 26)

YC1NBC60

First primer

CATAGCACCAGGTGACCACA

(SEQ ID NO: 27)

Second primer

GCGCCCGGCCTCTTTCTT

(SEQ ID NO: 28)

Third primer

AAAGGTTAAACCATCTTCTTTCTACA

(SEQ ID NO: 29)

First primer

GCACTTCACACCATTTCTGC

(SEQ ID NO: 30)

Second primer

GCGCCCGGCCTCTTTCTT

(SEQ ID NO: 31)

Third primer

AAAGGTTAAACCATCTTCTTTCTACA

(SEQ ID NO: 32)

Ya5AC2305

First primer

AGGACAGGTTAATAATCCAGAAAAA

(SEQ ID NO: 33)

Second primer

CGGCCCCAATTACAACTCT

(SEQ ID NO: 34)

Third primer

CTTTGATTACAACTCTTAAGGAAACG

(SEQ ID NO: 35)

Ya5ACA1736

First primer

CCTGCTCTGCACACTTCTTG

(SEQ ID NO: 36)

Second primer

CCGGCCCGAGAAGGCAAT

(SEQ ID NO: 37)

Third primer

GACCTTGACCTAGAGAAGGCAAT

(SEQ ID NO: 38)

First primer

CAACGTCCTCCCTAACTACCC

(SEQ ID NO: 39)

Second primer

(SEQ ID NO: 37)

Third primer

TGACCTTGACCTAGAGAAGGCAA

(SEQ ID NO: 40)

First primer

CCACCTCATGAACTCCCACT

(SEQ ID NO: 41)

Second primer

(SEQ ID NO: 37)

Third primer

(SEQ ID NO: 40)

Yb8AC1197

First primer

TGCTGCCCTTAATCTTTACCA

(SEQ ID NO: 3)

Second primer

CCCGGCCTTCATTTCTAAG

(SEQ ID NO: 4)

Third primer

GAGACTTTCATTTCTAAGATGTCTGG

(SEQ ID NO: 5)

Yb8NBC126

First primer

AGCTCCTGGAAAAGGGAAAG

(SEQ ID NO: 9)

Second primer

ATCCGATTGGGGCACCTTA

(SEQ ID NO: 10)

Third primer

ATGATGATTGGGGCACCTTA

(SEQ ID NO: 11)

First primer

CTGTGAAGGCTCACCTGGAG

(SEQ ID NO: 42)

Second primer

(SEQ ID NO: 43)

Third primer

(SEQ ID NO: 44)

Ya5ac2458

First primer

AGGGGGAATCGAGTGCTTAT

(SEQ ID NO: 45)

Second primer

GGCCCCCTGGAATCTTAAC

(SEQ ID NO: 46)

Third primer

GACCCTCCTGGAATCTTAACC

(SEQ ID NO: 47)

First primer

TGTTGGATATCCTGGCTGAA

(SEQ ID NO: 48)

Second primer

(SEQ ID NO: 46)

Third primer

(SEQ ID NO: 47)

First primer

AGGGGGAATCGAGTGCTTAT

(SEQ ID NO: 49)

Second primer

GGCCCCCTGGAATCTTAAC

(SEQ ID NO: 50)

Third primer

GACCCTCCTGGAATCTTAACC

(SEQ ID NO: 51)

Ya5ACA1736

First primer

TTCCATCTACCTAGAAGTTCCTCA

(SEQ ID NO: 52)

Second primer

CGAGAAGGCAATTTTCTACTTAGG

(SEQ ID NO: 53)

Third primer

TTGACCTAGAGAAGGCAATTTTC

(SEQ ID NO: 54)

First primer

CCACCTCATGAACTCCCACT

(SEQ ID NO: 55)

Second primer

CCGGCCCGAGAAGGCAAT

(SEQ ID NO: 56)

Third primer

GACCTTGACCTAGAGAAGGCAAT

(SEQ ID NO: 57)

First primer

CAACGTCCTCCCTAACTACCC

(SEQ ID NO: 58)

Second primer

(SEQ ID NO: 59)

Third primer

(SEQ ID NO: 60)

First primer

CCTGCTCTGCACACTTCTTG

(SEQ ID NO: 61)

Second primer

(SEQ ID NO: 59)

Third primer

(SEQ ID NO: 60)

Ya5ac2265

First primer

CAGCTCAGTCCTAAGCCACA

(SEQ ID NO: 62)

Second primer

CCGGCCCAGTTTCTTAATG

(SEQ ID NO: 63)

Third primer

CATGAATTCAGTTTCTTAATGATAAG

G

(SEQ ID NO: 64)

First primer

AGAAGAGTGAATGCACATTTATGA

(SEQ ID NO: 65)

Second primer

CCGGCCCAGTTTCTTAATG

(SEQ ID NO: 66)

Third primer

CATGAATTCAGTTTCTTAATGATAAG

G

(SEQ ID NO: 67)

Ya5aca1153

First primer

CAGTGAAAGCTTCTTAGGGGAAT

(SEQ ID NO: 68)

Second primer

CCGGCCCTGTGTCTTCTT

(SEQ ID NO: 69)

Third primer

TGTCCTTCTGTGTCTTCTTAAATATC

(SEQ ID NO: 70)

Yb7AD155

First primer

GTACACATTAAGCACATGGAAGTCA

(SEQ ID NO: 71)

Second primer

GCCCGGCCGTTCTTTTTC

(SEQ ID NO: 72)

Third primer

GCATGAAATGTTCTTTTTCATCTC

(SEQ ID NO: 73)

Yb8NBC622

First primer

TCAAAACTTGCGGATTTTCC

(SEQ ID NO: 74)

Second primer

GCGCAATCTCGGCTCCTT

(SEQ ID NO: 75)

Third primer

TGTGCAGGGGAATTCCTTCTAA

(SEQ ID NO: 76)

First primer

TGGAATACAATGTAACTGGGGATATG

(SEQ ID NO: 77)

Second primer

(SEQ ID NO: 75)

Third primer

(SEQ ID NO: 76)

Ya5NBC327

First primer

CTGGGGATATTTTCATAGATGC

(SEQ ID NO: 78)

Second primer

GCCCGGCCCTCATTATTC

(SEQ ID NO: 79)

Third primer

CCCATTCTCATTATTCTTATTCAACA

(SEQ ID NO: 80)

First primer

TGATGTCATGTACAAACAGGGATA

(SEQ ID NO: 81)

Second primer

GCCCGGCCCTCATTATTC

(SEQ ID NO: 82)

Third primer

CAAGGATACCCATTCTCATTATTCTT

A

(SEQ ID NO: 83)

SVA

First primer

aagcccctgaaaagtgaaat

(chr 2)

(SEQ ID NO: 84)

Second primer

GGAGAGGGGTCAAATTCTTa

(SEQ ID NO: 85)

Third primer

tttctggtTCAAATTCTTatctatca

a

(SEQ ID NO: 86)

HS-1

First primer

aaacaggaagcatttcgaggt

(chr 1)

(SEQ ID NO: 87)

Second primer

GCCCAGCCTCACATAGAt

(SEQ ID NO: 88)

Third primer

aaaaatgGCACATAGAtgttgaa

(SEQ ID NO: 89)

Y

First primer

ccctgaatctgagtgggact

(chr 1)

(SEQ ID NO: 90)

Second primer

CCGGCCGGCACTTTTatg

(SEQ ID NO: 91)

Third primer

tgcatGGCACTTTTatgact

(SEQ ID NO: 92)

First primer

(SEQ ID NO: 90)

Second primer

(SEQ ID NO: 91)

Third primer

cagaaatgcatGGCACTTTTat

(SEQ ID NO: 93)

YC1

First primer

ttcctctttttctccattttgtt

(Chr 1

(SEQ ID NO: 94)

or 2)

Second primer

GGCCTCCCAAGGATTCTTTa

(SEQ ID NO: 95)

Third primer

ccttgcttggGGATTCTTTa

(SEQ ID NO: 96)

YE5

First primer

ggtgtagcagaacagacaggag

(Chr1 or

(SEQ ID NO: 97)

2)

Second primer

AAGTGCTGGCTGTTCACCAc

(SEQ ID NO: 98)

Third primer

ggtttCTGTTCACCActttca

(SEQ ID NO: 99)

First primer

tagcagaacagacaggagacca

(SEQ ID NO: 100)

Second primer

(SEQ ID NO: 98)

Third primer

ttggggtttCTGTTCACCAc

(SEQ ID NO: 101)

First primer

ggtgtagcagaacagacaggag

(SEQ ID NO: 102)

Second primer

AAGTGCTGGCTGTTCACCAc

(SEQ ID NO: 103)

Third primer

ggtttCTGTTCACCActttca

(SEQ ID NO: 104)

YG6

First primer

acagctgggcaatacgttct

(chr 1

(SEQ ID NO: 105)

or 2)

Second primer

CCGGCCAAGATTTTCATTt

(SEQ ID NO: 106)

Third primer

gagccaAAGATTTTCATTttgatg

(SEQ ID NO: 107)

First primer

(SEQ ID NO: 105)

Second primer

(SEQ ID NO: 106)

Third primer

cagagccaAAGATTTTCATTtt

(SEQ ID NO: 108)

YG6

First primer

ttgcagaatgggtttggaag

(chr 1

(SEQ ID NO: 109)

or 2)

Second primer

CCGGCCTTTACCAAACTT

(SEQ ID NO: 110)

Third primer

gctgaacTTTACCAAACTTttaaaga

a

(SEQ ID NO: 111)

YA1

First primer

agaaggaagaagctccaaacgtg

(chr 1

(SEQ ID NO: 112)

or 2)

Second primer

CTCCTGCGTGGCTTCATT

(SEQ ID NO: 113)

Third primer

tgacttGGCTTCATTCTTcggtga

(SEQ ID NO: 114)

First primer

(SEQ ID NO: 112)

Second primer

(SEQ ID NO: 113)

Third primer

actgacttGGCTTCATTCTTcg

(SEQ ID NO: 115)

YA4

First primer

ttaagaaagtcagcagaaaacttc

(chr 1)

(SEQ ID NO: 116)

Second primer

CCCGGCCCAGATTTTACT

(SEQ ID NO: 117)

Third primer

ggtcttaCAGATTTTACTTttatttg

c

(SEQ ID NO: 118)

YA5

First primer

acagaggccaccctgtaggt

(chr 2)

(SEQ ID NO: 119)

Second primer

ACCTGGCCTGGGTGACTg

(SEQ ID NO: 120)

Third primer

tgagaCTGGGTGACTgtgtttt

(SEQ ID NO: 121)

First primer

(SEQ ID NO: 119)

Second primer

(SEQ ID NO: 120)

Third primer

tgaaatgagaCTGGGTGACTgt

(SEQ ID NO: 122)

SVA

First primer

aaagctgggtttccttttgc

(chr 3)

(SEQ ID NO: 123)

Second primer

GCTGGCCGGAAGTCTTaat

(SEQ ID NO: 124)

Third primer

tgaaggataGAAGTCTTaatgcag

(SEQ ID NO: 125)

YC1

First primer

cccaataaaatcagcaaatatga

(chr 3)

(SEQ ID NO: 126)

Second primer

CCGGCCCCCACATTTCTT

(SEQ ID NO: 127)

Third primer

tgacttttCCACATTTCTTacattg

(SEQ ID NO: 128)

YB8

First primer

tgctgcccttaatctttacca

(chr 3)

(SEQ ID NO: 129)

Second primer

CCCGGCCTTCATTTCTaag

(SEQ ID NO: 130)

Third primer

ataagagactTTCATTTCTaagatgt

c

(SEQ ID NO: 131)

YA5

First primer

ccattaaaggaacaagaatgga

(chr 4)

(SEQ ID NO: 132)

Second primer

GCCCGGCCAGTAATCTTTa

(SEQ ID NO: 133)

Third primer

ctggtcCAGTAATCTTTaatacact

(SEQ ID NO: 134)

Y

First primer

gtttacctgccttctggctct

(chr 5)

(SEQ ID NO: 135)

Second primer

GCCCAGCCTACTCTTGTTa

(SEQ ID NO: 136)

Third primer

attacctcTACTCTTGTTaaccaacc

a

(SEQ ID NO: 137)

YA5

First primer

tttcttagttctttaacaacagatgc

(chr 5)

(SEQ ID NO: 138)

Second primer

TATCCTTGCTAGAAGTTactgga

(SEQ ID NO: 139)

Third primer

attccaaaaAGAAGTTactggat

(SEQ ID NO: 140)

YA5

First primer

aatacagccaaatgaactggaga

(chr 5)

(SEQ ID NO: 141)

Second primer

TCTGGCCTCCATTTAGTatttt

(SEQ ID NO: 142)

Third primer

gcactctctATTTAGTattttctcg

(SEQ ID NO: 143)

LINE

First primer

tgcacacgtatgtttattgcag

(chr 7)

(SEQ ID NO: 144)

Second primer

TCCTCCCCTCCATTTTCTTa

(SEQ ID NO: 145)

Third primer

atatatgCCATTTTCTTaatccagtc

(SEQ ID NO: 146)

YB8

First primer

taatatgaggtgatgggggtta

(chr 7)

(SEQ ID NO: 147)

Second primer

CCGGCCGCCAGTTTCTTa

(SEQ ID NO: 148)

Third primer

cccagaaCCAGTTTCTTaaatagc

(SEQ ID NO: 149)

YB8

First primer

tcttgataacatagggaaaatcactt

(chr 7)

c

(SEQ ID NO: 150)

Second primer

CCGGCCCAGAGTTCTTaat

(SEQ ID NO: 151)

Third primer

tgttttgtaCAGAGTTCTTaattgca

g

(SEQ ID NO: 152)

YB8

First primer

ggctagccatatggagaagaa

(chr 7)

(SEQ ID NO: 153)

Second primer

CCGGCCGGAATTCTTatag

(SEQ ID NO: 154)

Third primer

ttcttctGGAATTCTTatagtttgag

g

(SEQ ID NO: 155)

LINE

First primer

agcttgagggtggctgtgt

(chr 8)

(SEQ ID NO: 156)

Second primer

GCTCACGCTCTGTGAGTGtt

(SEQ ID NO: 157)

Third primer

agagagattTGTGAGTGtttaaagat

g

(SEQ ID NO: 158)

SG1

First primer

ttttcggttgtgaactgaagg

(chr 8)

(SEQ ID NO: 159)

Second primer

CCCAGCCTTAAACTGACCat

(SEQ ID NO: 160)

Third primer

gccccTAAACTGACCattctt

(SEQ ID NO: 161)

First primer

(SEQ ID NO: 159)

Second primer

(SEQ ID NO: 160)

Third primer

ccagccccTAAACTGACCat

(SEQ ID NO: 162)

LINE

First primer

aagacccaaattagcgaaagaa

(chr 9)

(SEQ ID NO: 163)

Second primer

AAACCTAGGCATTACCTTTTCaa

(SEQ ID NO: 164)

Third primer

catttgtcgtTTACCTTTTCaa

(SEQ ID NO: 165)

YG9

First primer

ctctatatgcactacagttttgtga

(chr 9)

(SEQ ID NO: 166)

Second primer

CCGGCCCCAAGTGTTtta

(SEQ ID NO: 167)

Third primer

ccccagaattaCCAAGTGTTtt

(SEQ ID NO: 168)

YG6

First primer

gaacatccagcaccaaatcc

(chr 10)

(SEQ ID NO: 169)

Second primer

CCCGGCCCTACCTTCtta

(SEQ ID NO: 170)

Third primer

cctggttgtgtgtTACCTTCtt

(SEQ ID NO: 171)

YC1

First primer

aggcaggcagatcacttgag

(chr 10)

(SEQ ID NO: 172)

Second primer

CGCGCCCCTAATTCTTTct

(SEQ ID NO: 173)

Third primer

ccatgcctggCTAATTCTTTc

(SEQ ID NO: 174)

YC1

First primer

agggggtgagggataaaaga

(chr 10)

(SEQ ID NO: 175)

Second primer

TGAGCCACCGATGAATAAGTT

(SEQ ID NO: 176)

Third primer

ggtatttggttacATGAATAAGTTCt

(SEQ ID NO: 177)

YC2

First primer

gagcacattacctataggcagaca

(chr 12)

(SEQ ID NO: 178)

Second primer

GCCCGGCCTTATTTTAGttt

(SEQ ID NO: 179)

Third primer

tgggttgatagttattTTATTTTAGt

t

(SEQ ID NO: 180)

YA5

First primer

gggattggatagaatgaagaaagg

(chr 13)

(SEQ ID NO: 181)

Second primer

GCCCGGCCTCTCTCTTTag

(SEQ ID NO: 182)

Third primer

cgcgctctctcTCTCTCTTTag

(SEQ ID NO: 183)

YA5

First primer

agaagagtgaatgcacatttatga

(chr 13)

(SEQ ID NO: 184)

Second primer

CCCGGCCCAGTTTCTTaat

(SEQ ID NO: 185)

Third primer

gggagtcatgaattCAGTTTCTTa

(SEQ ID NO: 186)

LINE

First primer

tcctactctcatttcttcacattca

(chr 15)

(SEQ ID NO: 187)

Second primer

CTTGTAAATTTGTCTTGAGTTcattg

(SEQ ID NO: 188)

Third primer

ggctgtgtgctttTTGAGTTc

(SEQ ID NO: 189)

Sp

First primer

gggaggacattgaaggtaaaca

(chr 17)

(SEQ ID NO: 190)

Second primer

ACCTGGCTGATTGCAGtttt

(SEQ ID NO: 191)

Third primer

gggccattTGATTGCAGtt

(SEQ ID NO: 192)

Y

First primer

gaggctgcagtgagctatga

(chr 17)

(SEQ ID NO: 193)

Second primer

GCCCGGCCAATTTACAGc

(SEQ ID NO: 194)

Third primer

aagaactcattcagaAATTTACAGc

(SEQ ID NO: 195)

Y

First primer

tagagtgctgctgtggcaaa

(chr 19)

(SEQ ID NO: 196)

Second primer

GCCCAGCCTAGTGTCCTCT

(SEQ ID NO: 197)

YA5

Third primer

ttctcctggttacTAGTGTCCTCTc

(SEQ ID NO: 198)

YA5

First primer

ccaagtcaggtataagcctcaga

(chr 20)

(SEQ ID NO: 199)

Second primer

GCCGGATGTCCACTCttaaa

(SEQ ID NO: 200)

Third primer

acagaaaggatgtCCACTCtta

(SEQ ID NO: 201)

YA5

First primer

caggcctggtggtaacaaat

(chr 3)

(SEQ ID NO: 202)

Second primer

CTCGGCCTCCCAATCAAC

(SEQ ID NO: 203)

Third primer

ggccaatatTCAACATTCTTa

(SEQ ID NO: 204)

YA5

First primer

ccctggacttaccctatctca

(chr 3)

(SEQ ID NO: 205)

Second primer

TGCTGGGATTACATGGATTTT

(SEQ ID NO: 206)

Third primer

ggagaatgtgtgTGGATTTTATTc

(SEQ ID NO: 207)

SP

First primer

ctttggccctgagagagatg

Chr 22

(SEQ ID NO: 208)

Second primer

ACACCCCACCAAAACTGAAT

(SEQ ID NO: 209)

Third primer

ttttaaaaccGAATGCCTTt

(SEQ ID NO: 210)

YE

First primer

agcagctctgggtgtagcag

(chr 1)

(SEQ ID NO: 211)

Second primer

CCAAAGTGCTGGCTGTTCA

(SEQ ID NO: 212)

Third primer

tggggtttCTGTTCACCAct

(SEQ ID NO: 213)

YG6

First primer

acagctgggcaatacgttct

(chr 2)

(SEQ ID NO: 214)

Second primer

CGCCCGGCCAAGATTTTC

(SEQ ID NO: 215)

Third primer

cagagccaAAGATTTTCATTtt

(SEQ ID NO: 216)

YC1

First primer

tctttcctctttttctccattttg

(chr 2)

(SEQ ID NO: 217)

Second primer

CTCGGCCTCCCAAGGATT

(SEQ ID NO: 218)

Third primer

ccttgcttggGGATTCTTTa

(SEQ ID NO: 219)

Ya5/8

First primer

gtctgcagcttcactcctga

(Chr 1)

(SEQ ID NO: 220)

Second primer

CATTCTCCTGCGTGGCTTC

(SEQ ID NO: 221)

Third primer

tgacttGGCTTCATTCTTcg

(SEQ ID NO: 222)

Ya5

First primer

tcctaacaagggactttgcag

(Chr 1)

(SEQ ID NO: 402)

Second primer

CGGCCTCCCAAAGAAGAT

(SEQ ID NO: 403)

Third primer

gatgggaAAGATTCTCCACTTt

(SEQ ID NO: 404)

YA5

First primer

caggcctggtggtaacaaat

(chr 3)

(SEQ ID NO: 405)

Second primer

TCGGCCTCCCAATCAAC

(SEQ ID NO: 406)

Third primer

ggccaatatTCAACATTCTTa

(SEQ ID NO: 407)

Ya5ACA1050

First primer

ccctggacttaccctatctca

(chr 3)

(SEQ ID NO: 408)

Second primer

TGCTGGGATTACATGGATTTT

(SEQ ID NO: 409)

Third primer

ggagaatgtgtgTGGATTTTATTc

(SEQ ID NO: 410)

Ya5

First primer

aaaaacaagcaatggggaaa

(chr 3)

(SEQ ID NO: 411)

Second primer

GTGTCCGGCCACGTTTAAG

(SEQ ID NO: 412)

Third primer

gttttaggtctaACGTTTAAGTCTTt

(SEQ ID NO: 413)

YB7

First primer

tgccaggaatggacttacaa

(chr 3)

(SEQ ID NO: 414)

Second primer

CCCGGCCATGAACTTCTaat

(SEQ ID NO: 415)

Third primer

tgacctgcATGAACTTCTaataaaat

(SEQ ID NO: 416)

First primer

(SEQ ID NO: 414)

Second primer

(SEQ ID NO: 415)

Third primer

ttcatgacctgcATGAACTTCTa

(SEQ ID NO: 417)

YB7

First primer

ggtaatcaacagaagatcataagagg

(chr 3)

a

(SEQ ID NO: 418)

Second primer

gttAAGACTTGAGGCCGGG

(SEQ ID NO: 419)

Third primer

cttctctcctccCTCAAGTCTTa

(SEQ ID NO: 420)

Yd8

First primer

caagtgctggggattacagg

(chr 4)

(SEQ ID NO: 421)

Second primer

AGACGGGGTTTCACCGTTAG

(SEQ ID NO: 422)

Third primer

gcagagagacTAGGAGGCATtc

(SEQ ID NO: 423)

Y

First primer

ccatggactcatggaatgct

(chr 4)

(SEQ ID NO: 424)

Second primer

AGCCTGCCACACTTCTTtag

(SEQ ID NO: 425)

Third primer

ttccatgacggCACTTCTTt

(SEQ ID NO: 426)

YA8

First primer

tgtaggcaaaactttagtttcat

(chr 4)

(SEQ ID NO: 427)

Second primer

CCCGGCCCAGAAAGAACt

(SEQ ID NO: 428)

Third primer

ctcccattatcttCAGAAAGAACt

(SEQ ID NO: 429)

YA5

First primer

ccattaaaggaacaagaatgga

(chr 4)

(SEQ ID NO: 430)

Second primer

GCCCGGCCAGTAATCTTTa

(SEQ ID NO: 431)

Third primer

ctggtcCAGTAATCTTTaatacact

(SEQ ID NO: 432)

YA5

First primer

ctgagctggaggcataggtc

(chr 4)

(SEQ ID NO: 433)

Second primer

CCGGCCCGGCTATTTTTa

(SEQ ID NO: 434)

Third primer

tgttgcccaGGCTATTTTTa

(SEQ ID NO: 435)

YA5

First primer

tggagagcattgacagttcat

(chr 4)

(SEQ ID NO: 436)

Second primer

CCGGCCCCTGCTTCTTat

(SEQ ID NO: 437)

Third primer

acacactcacCCTGCTTCTTa

(SEQ ID NO: 438)

YB3A2

First primer

caggagaacatggccttcac

(chr 4)

(SEQ ID NO: 223)

Second primer

CGCCCAGCCTATCCTTTT

(SEQ ID NO: 224)

Third primer

atgtctTATCCTTTTgccttttg

(SEQ ID NO: 225)

First primer

(SEQ ID NO: 223)

Second primer

(SEQ ID NO: 224)

Third primer

ttgcctttatgtctTATCCTTTTg

(SEQ ID NO: 226)

YB10

First primer

agatatgcccaaaggacacaa

(chr 5)

(SEQ ID NO: 227)

Second primer

GCCCGGCCGAAACTATTa

(SEQ ID NO: 228)

Third primer

tccccttccatgtGAAACTATTa

(SEQ ID NO: 229)

Y

First primer

ctcattccctttccccactc

(chr 5)

(SEQ ID NO: 230)

Second primer

GCCCAGCCTACTCTTGTTa

(SEQ ID NO: 231)

Third primer

attacctcTACTCTTGTTaaccaacc

a

(SEQ ID NO: 232)

Y

First primer

(SEQ ID NO: 230)

(chr 5)

Second primer

(SEQ ID NO: 231)

Third primer

tgctaacattacctcTACTCTTGTTa

(SEQ ID NO: 233)

YB8

First primer

gtcaacagcctggtgtcatc

(chr 5)

(SEQ ID NO: 234)

Second primer

AGCCACCGCTCCTTGTAAC

(SEQ ID NO: 235)

Third primer

actggcctcCTTGTAACTTTCc

(SEQ ID NO: 236)

Ya5

First primer

tttcttagttctttaacaacagatgc

(chr 5)

(SEQ ID NO: 237)

Second primer

TATCCTTGCTAGAAGTTactgga

(SEQ ID NO: 238)

Third primer

attccaaaaAGAAGTTactggat

(SEQ ID NO: 239)

Ya5

First primer

aatacagccaaatgaactggaga

(chr 5)

(SEQ ID NO: 240)

Second primer

TCTGGCCTCCATTTAGTatttt

(SEQ ID NO: 241)

Third primer

gcactctctATTTAGTattttctcg

(SEQ ID NO: 242)

First primer

aagtgtcaaggagaacaaaatgc

(SEQ ID NO: 243)

Second primer

GCCTCTGGCCTCCATTTA

(SEQ ID NO: 244)

Third primer

gctccaagagcactctctATTTAGTa

(SEQ ID NO: 245)

YB3A1

First primer

cccttttgtgtccctcttca

(chr 5)

(SEQ ID NO: 246)

Second primer

ACCGCGCCTGGCCTAAAGT

(SEQ ID NO: 247)

Third primer

catgtatcccagaactTAAAGTAAAa

(SEQ ID NO: 248)

YA5

First primer

ttgccacttaggcaattaagg

(chr 6)

(SEQ ID NO: 249)

Second primer

GCCTCGGCCTCCCACAAG

(SEQ ID NO: 250)

Third primer

ctctgtgcaCACAAGTTTTTCa

(SEQ ID NO: 251)

YA5

First primer

aaagggaagcccatcagact

(chr 6)

(SEQ ID NO: 252)

Second primer

CCCGGCCGAAAATTCTTt

(SEQ ID NO: 253)

Third primer

ctgggttGAAAATTCTTttcttt

(SEQ ID NO: 254)

YB7

First primer

tgtccaggttaaacttcagttgc

(chr 6)

(SEQ ID NO: 255)

Second primer

GCCCGGCCCGAAAGAAGT

(SEQ ID NO: 256)

Third primer

ggggcaatGAAAGAAGTTt

(SEQ ID NO: 257)

YI6

First primer

aggtgctggcactgatgac

(chr 6)

(SEQ ID NO: 439)

Second primer

CTGGGATTACAAGCGTGAGG

(SEQ ID NO: 440)

Third primer

tctcacaagtaagcaAGGTAGAt

(SEQ ID NO: 441)

YB8

First primer

ccttaagacctaagccctagtaga

(chr 6)

(SEQ ID NO: 442)

Second primer

CAGGCGTGAGCCACTAACTT

(SEQ ID NO: 443)

Third primer

gtttcccaagccaCTAACTTTTa

(SEQ ID NO: 444)

Y

First primer

gaatgcaagtaaaaaccatgagg

(chr 7)

(SEQ ID NO: 445)

Second primer

TTTAGTAGAGACGGGGTTAGCA

(SEQ ID NO: 446)

Third primer

tccttgtgtctAGCATGTTTTTg

(SEQ ID NO: 447)

Y

First primer

aaccaaagtgactctgaagaagaaa

(chr 7)

(SEQ ID NO: 448)

Second primer

TCCTGGGTTCACGTATGATG

(SEQ ID NO: 449)

Third primer

ttggaactggcTATGATGTTTg

(SEQ ID NO: 450)

YA5

First primer

ggttgatcatctgccgaaag

(chr 7)

(SEQ ID NO: 451)

Second primer

GCCACCGCGCCCTCTACT

(SEQ ID NO: 452)

Third primer

cacctttaccacctTCTACTGTCTa

(SEQ ID NO: 453)

YA5

First primer

cttgagcccaggagtttgag

(chr 7)

(SEQ ID NO: 454)

Second primer

CGCCCGGCCTTATTTTTC

(SEQ ID NO: 455)

Third primer

gagaggcccCCTTATTTTTCt

(SEQ ID NO: 456)

YA5

First primer

aacaaaattccctttcctcca

(chr 7)

(SEQ ID NO: 457)

Second primer

CGCCCGGCCAGAAGTTAG

(SEQ ID NO: 458)

Third primer

ggatatatgctagCAGAAGTTAGATt

(SEQ ID NO: 459)

YB8

First primer

cctgaggtgtgtgcttaatcttc

(chr 7)

(SEQ ID NO: 460)

Second primer

CCCGGCCGCCAGTTTCTT

(SEQ ID NO: 461)

Third primer

ttttcccagaaCCAGTTTCTTa

(SEQ ID NO: 462)

YA5

First primer

ctctcctgtgcccacttagg

(chr 8)

(SEQ ID NO: 463)

Second primer

ACGCCCGGCCATATTCTT

(SEQ ID NO: 464)

Third primer

tggagtcatgtccatATATTCTTg

(SEQ ID NO: 465)

SG1

First primer

ttttcggttgtgaactgaagg

(chr 8)

(SEQ ID NO: 466)

Second primer

CGCCCAGCCITAAACTGA

(SEQ ID NO: 467)

Third primer

accagccccTAAACTGACCa

(SEQ ID NO: 468)

YA8

First primer

caggccatgtaagagtagaagga

(chr 8)

(SEQ ID NO: 469)

Second primer

GCCCGGCCAGAACACTAC

(SEQ ID NO: 470)

Third primer

caaccctatgagattAGAACACTACa

(SEQ ID NO: 471)

Y

First primer

cattgaatgaatggggaagaa

(chr 10)

(SEQ ID NO: 472)

Second primer

GCCTGGCGCAAAGATAtg

(SEQ ID NO: 473)

Third primer

ttggaaccaaaGCAAAGATAtg

(SEQ ID NO: 474)

Y

First primer

ggcaaagagtgaactagaatcca

(chr 10)

(SEQ ID NO: 475)

Second primer

GCGCCCGGCCTCAACTAC

(SEQ ID NO: 476)

Third primer

ggaagagcacacTCAACTACTTTTa

(SEQ ID NO: 477)

YA5

First primer

ttagctgagggagtcactgga

(chr 10)

(SEQ ID NO: 258)

Second primer

CCCGGCCGAAGATTTgtt

(SEQ ID NO: 259)

Third primer

gcatgtctcctgtGAAGATTTg

(SEQ ID NO: 260)

YB7

First primer

tggccaacaaatacgtgaaa

(chr 10)

(SEQ ID NO: 261)

Second primer

GCGCCCGGCCCTTAACTT

(SEQ ID NO: 262)

Third primer

cagcatctgttgtttCTTAACTTtt

(SEQ ID NO: 263)

YC1

First primer

aggcaggcagatcacttg

(chr 10)

(SEQ ID NO: 264)

Second primer

CGCGCCCCTAATTCTTTct

(SEQ ID NO: 265)

Third primer

ccatgcctggCTAATTCTTTc

(SEQ ID NO: 266)

YC1

First primer

tgaaatggactgtggggact

(chr 10)

(SEQ ID NO: 267)

Second primer

CGTGAGCCACCGATGAATA

(SEQ ID NO: 268)

Third primer

tggtatttggttacATGAATAAGGTC

t

(SEQ ID NO: 269)

YG6

First primer

ctcggcataaataaaactttaagga

(chr 10)

(SEQ ID NO: 270)

Second primer

GCGCCCGGCCAATTCTAC

(SEQ ID NO: 271)

Third primer

ggcttgctcagAATTCTACCTTc

(SEQ ID NO: 272)

YG6

First primer

gaacatccagcaccaaatcc

(chr 10)

(SEQ ID NO: 273)

Second primer

CCCGGCCCTACCTTCtta

(SEQ ID NO: 274)

Third primer

cctggttgtgtgtTACCTTCtt

(SEQ ID NO: 275)

YA5

First primer

ccttgacaggcactaaccact

(chr 11)

(SEQ ID NO: 276)

Second primer

CTCCCAAAGTGCGGTTCTC

(SEQ ID NO: 277)

Third primer

gaatgtggagtacatGGTTCTCTTTa

(SEQ ID NO: 278)

YA5

First primer

aggagaattgcttgaacctg

(chr 11)

(SEQ ID NO: 279)

Second primer

TCCCAAGCTGAGATCCTTTC

(SEQ ID NO: 280)

Third primer

ggtatgctgagaTCCTTTCTc

(SEQ ID NO: 281)

YA5

First primer

ggttttaccaggaatgtagtttgg

(chr 11)

(SEQ ID NO: 282)

Second primer

GCCCGGCCTCATCCATTC

(SEQ ID NO: 283)

Third primer

gcctccctTCATCCATTCTTa

(SEQ ID NO: 284)

YX

First primer

ccagatggaagacatgcaca

(chr 11)

(SEQ ID NO: 285)

Second primer

GCCCGGCCCATTCAGTCT

(SEQ ID NO: 286)

Third primer

ggagggttCATrCAGTCTTttg

(SEQ ID NO: 287)

YB8

First primer

tcaaaaagactatctttccccatt

(chr 11)

(SEQ ID NO: 288)

Second primer

TGGGACTGGGACTTAGGA

(SEQ ID NO: 289)

Third primer

aaagttatgggagTTAGGATTTCaa

(SEQ ID NO: 290)

YC2

First primer

gcggaaaactaaaggcaaag

(chr 11)

(SEQ ID NO: 291)

Second primer

CGCCCGGCCTTATTTTAG

(SEQ ID NO: 292)

Third primer

tgggttgatagttattTTATTTTAGt

t

(SEQ ID NO: 293)

YA5

First primer

tgatccatgaacattcactctg

(chr 12)

(SEQ ID NO: 294)

Second primer

GCCCGGCCCAGATCTTTC

(SEQ ID NO: 295)

Third primer

cagtgcactttCAGATCTTTCTtta

(SEQ ID NO: 296)

YA5

First primer

gggattggatagaatgaagaaagg

(chr 13)

(SEQ ID NO: 297)

Second primer

GCCCGGCCTCTCTCTTTag

(SEQ ID NO: 298)

Third primer

cgcgctctctcTCTCTCTTTag

(SEQ ID NO: 299)

YA5

First primer

gggattggatagaatgaagaaagg

(chr 13)

(SEQ ID NO: 300)

Second primer

GCCCGGCCTCTCTCTTTag

(SEQ ID NO: 301)

Third primer

cgcgctctctcTCTCTCTTTag

(SEQ ID NO: 302)

YA5

First primer

acatggacacgcatgaaaga

(chr 13)

(SEQ ID NO: 303)

Second primer

CCGGCCACAACCCTCATT

(SEQ ID NO: 304)

Third primer

ggtagttaccttacaACCCTCATTTT

Ta

(SEQ ID NO: 305)

YA5

First primer

aagaagagtgaatgcacatttatga

(chr 13)

(SEQ ID NO: 306)

Second primer

CCCGGCCCAGTTTCTTaat

(SEQ ID NO: 307)

Third primer

gggagtcatgaattCAGTTTCTTa

(SEQ ID NO: 308)

YA1

First primer

cccaagtctaaaccaggaagaa

(chr 15)

(SEQ ID NO: 309)

Second primer

CCCAGCTACCAGTTCCTCTTT

(SEQ ID NO: 310)

Third primer

atggtaccagcgCCTCTTTg

(SEQ ID NO: 311)

YA5

First primer

tgtttttccttgccacactg

(chr 15)

(SEQ ID NO: 312)

Second primer

GCGCCCGGCCTTACTCTC

(SEQ ID NO: 313)

Third primer

tcttcgtggtcTTACTCTCTCTTc

(SEQ ID NO: 314)

Sp

First primer

agctgccaataaggctgaaa

(chr 17)

(SEQ ID NO: 315)

Second primer

CCGCACCTGGCTGATTGC

(SEQ ID NO: 316)

Third primer

gggccattTGATTGCAGtt

(SEQ ID NO: 317)

Y

First primer

cctagctactaggaagcctgag

(chr 17)

(SEQ ID NO: 318)

Second primer

CGCCCGGCCAATTTACAG

(SEQ ID NO: 319)

Third primer

aagaactcattcagaAATTTACAGc

(SEQ ID NO: 320)

Y

First primer

tagagtgctgctgtggcaaa

(chr 19)

(SEQ ID NO: 321)

Second primer

GCCCAGCCTAGTGTCCTCT

(SEQ ID NO: 322)

Third primer

tggttacCTAGTGGCCTCTct

(SEQ ID NO: 323)

YA5

First primer

ccaagtcaggtataagcctcaga

(chr 20)

(SEQ ID NO: 324)

Second primer

GCCGGATGTCCACTCttaaa

(SEQ ID NO: 325)

Third primer

acagaaaggatgtCCACTCtta

(SEQ ID NO: 326)

YA5

First primer

tggcttccttttctttcctta

(chr 20)

(SEQ ID NO: 327)

Second primer

GCCCGGCCAAAATGACTG

(SEQ ID NO: 328)

Third primer

caagcagtgagaAAAATGACTGTt

(SEQ ID NO: 329)

YA5

First primer

tgctgttccagaaacacacttt

(Y)

(SEQ ID NO: 330)

Second primer

GCCCGGCCGACACTTCTT

(SEQ ID NO: 331)

Third primer

cacaatcaccttGACACTTTTTa

(SEQ ID NO: 332)

YB8

First primer

tgatggggatagaggaagaaga

(Y)

(SEQ ID NO: 333)

Second primer

CGCCCGGCCTGTCTACCA

(SEQ ID NO: 334)

Third primer

gcatctctTGTCTACCAGTTTTaa

(SEQ ID NO: 335)

YB8

First primer

cctaaggtgagtaaggttaaatcctg

(Y)

(SEQ ID NO: 336)

Second primer

CGCCCGGCCTGGATTCTT

(SEQ ID NO: 337)

Third primer

tgttgtagctgtTGGATTCTTa

(SEQ ID NO: 338)

SC

First primer

ccgaattcaaagaaggatca

(X)

(SEQ ID NO: 339)

Second primer

ACGCCCAGTCCTTAGGCTAC

(SEQ ID NO: 340)

Third primer

tgaccaacactCTTAAGCTACTTtt

(SEQ ID NO: 341)

SC

First primer

ctgtatcctcatgttctgttgga

(X)

(SEQ ID NO: 342)

Second primer

CTGCCCACTCATTTTCTTagg

(SEQ ID NO: 343)

Third primer

ccactcgttttctcTTTCTTag

(SEQ ID NO: 344)

YA3A1

First primer

acttgttgaccgagccacat

(X)

(SEQ ID NO: 345)

Second primer

GCCCGGCCAAGAAACTGG

(SEQ ID NO: 346)

Third primer

tccagttAAGAAACTGGTCCCttc

(SEQ ID NO: 347)

YD8

First primer

cagccagaagtggcttccta

(X)

(SEQ ID NO: 348)

Second primer

CCCGGCCGTCCTTTCATT

(SEQ ID NO: 349)

Third primer

gccccaatTCCTTTCATTtt

(SEQ ID NO: 350)

YA4

First primer

tgctggtcagatagaccctgt

(X)

(SEQ ID NO: 351)

Second primer

GCCCGGCCAACACTGCTT

(SEQ ID NO: 352)

Third primer

ggggtgaagtAACACTGCTTTt

(SEQ ID NO: 353)

YG6

First primer

gaatctagcccttcccttgc

(X)

(SEQ ID NO: 354)

Second primer

CCCGGCAGCCAAGAAGTC

(SEQ ID NO: 355)

Third primer

aaccagAGCCAAGAAGTCTTatg

(SEQ ID NO: 356)

Y

First primer

tggtaaaaatggggtgacaaa

(X)

(SEQ ID NO: 357)

Second primer

CACCCGGCCTACAATTTTT

(SEQ ID NO: 358)

Third primer

gccacagatgatTACAATTTTTCaa

(SEQ ID NO: 359)

SVA

First primer

ccagtgcctgtgtatctaagtga

(Chr 1)

(SEQ ID NO: 360)

Second primer

GAGAGGGAGAGGGAACTGAA

(SEQ ID NO: 361)

Third primer

tcaatggagtacaGAACTGAATCTTa

(SEQ ID NO: 362)

SVA

First primer

gaaatgaataagcttcttggatagtg

(Chr 1)

(SEQ ID NO: 363)

Second primer

GGGAGAGGGAGAGGTCATTA

(SEQ ID NO: 364)

Third primer

cggccaatcTCATTATTTTCa

(SEQ ID NO: 365)

SVA

First primer

aaagctgggtttccttttgc

(Chr 3)

(SEQ ID NO: 366)

Second primer

GGCTGGCCGGAAGTCTTa

(SEQ ID NO: 367)

Third primer

tggtgtcttgaaggataGAAGTCTTa

(SEQ ID NO: 368)

SVA

First primer

cgtggtgatgtgcactttta

(Chr 19)

(SEQ ID NO: 369)

Second primer

TTAAATTTTTGACCGGGTTT

(SEQ ID NO: 370)

Third primer

gaaggaaaagtagttaaGGGTTTTTg

(SEQ ID NO: 371)

SVA

First primer

ccctgctatcctaaatgctg

(Chr 22)

(SEQ ID NO: 372)

Second primer

GTGATGGCGGGCTTAACCT

(SEQ ID NO: 373)

Third primer

cagcccaccCTTAACCTCTa

(SEQ ID NO: 374)

LINE

First primer

tttcctcttgttcgtgatgg

(Chr 2)

(SEQ ID NO: 375)

Second primer

GGTGGTTCCAAGCTGTTTTC

(SEQ ID NO: 376)

Third primer

ccaaaaacccatAGCTGTTTTCTa

(SEQ ID NO: 377)

LINE

First primer

tgggcatcactcagctctaa

(Chr 2)

(SEQ ID NO: 378)

Second primer

CTCCTCCTTCCGGCACTG

(SEQ ID NO: 379)

Third primer

acttctCGGCACTGGCTTt

(SEQ ID NO: 380)

LINE

First primer

ttgctcagagcccataagga

(Chr 5)

(SEQ ID NO: 381)

Second primer

TGGCTCCTCCAAGCCTTC

(SEQ ID NO: 382)

Third primer

ctacacattaaattAAGCCTTCAAAt

t

(SEQ ID NO: 383)

LINE

First primer

tgaataccatgatatgccaaa

(Chr 6)

(SEQ ID NO: 384)

Second primer

TGATTGCCATTCACACTCC

(SEQ ID NO: 385)

Third primer

gaaattgcCACACTCCTTTTc

(SEQ ID NO: 386)

LINE

First primer

agcagcatgatttataatccttt

(Chr 7)

(SEQ ID NO: 387)

Second primer

GGTCCCCTAACAGGAGCAC

(SEQ ID NO: 388)

Third primer

tgtggagaaatatGAACACTTTTac

(SEQ ID NO: 389)

LINE

First primer

taacatttgaccaaacagttgag

(Chr 8)

(SEQ ID NO: 390)

Second primer

CCCACTTTTTGACCTTTCa

(SEQ ID NO: 391)

Third primer

ccgctgcttctaACCTTTCa

(SEQ ID NO: 392)

LINE

First primer

ttctcttcttccctctctgagc

(Chr 8)

(SEQ ID NO: 393)

Second primer

CTTGGCTCCTCCTGCAAAT

(SEQ ID NO: 394)

Third primer

tctctgctcatTGCAAATCTTa

(SEQ ID NO: 395)

LINE

First primer

ctctggagaagggtgcattg

(Chr 8)

(SEQ ID NO: 396)

Second primer

CGTCGCTCACGCTCTGTG

(SEQ ID NO: 397)

Third primer

ttagagagagagattTGTGAGTGtt

(SEQ ID NO: 398)

LINE

First primer

tgctagtagaacccacgaggt

(Chr 10)

(SEQ ID NO: 399)

Second primer

GGCACAAGACAGGGATGC

(SEQ ID NO: 400)

Third primer

gaaaagacaaaGTTGCATTGTTa

(SEQ ID NO: 401).

24. A method for genetic detection, comprising:

carrying out a polymerase chain reaction (PCR) on a DNA sample with primer sets to produce amplified DNA products, the primer sets comprising:

a primer set for a filled site which contains an interspersed element, the primer set for the filled site comprising:

a forward primer complementary to a first flanking genomic sequence; and

a reverse primer complementary to a sequence comprised of a second flanking genomic sequence, a direct repeat sequence flanking the 3′ side of the second flanking genomic sequence and the 5′ side of the interspersed element, and a part of the 5′ sequence of the interspersed element next to the direct repeat sequence; and

a primer set for an empty site which does not contain the interspersed element, the primer set for the empty site comprising:

said forward primer complementary to the first flanking genomic sequence existing in the empty site and the filled site; and

a reverse primer complementary to a sequence comprised of the direct repeat sequence and third flanking genomic sequences on both sides of the direct repeat sequence in the empty site; and

analyzing the amplified DNA products to detect presence or absence of the interspersed element insertion at the site.

25. A primer set for a polymorphic marker site, comprising:

a first primer for a filled site containing an interspersed element and an empty site which does not contain the interspersed element, the first primer complementary to a first flanking genomic sequence in the filled site and the empty site;

a second primer for the filled site, the second primer complementary to a sequence having a second flanking genomic sequence, a direct repeat sequence next to the second flanking genomic sequence and a part of the interspersed element next to the direct repeat sequence in the filled site; and

a third primer for the empty site, the third primer complementary to a sequence having the direct repeat sequence and third flanking genomic sequences on both sides of the direct repeat sequence in the empty site.

26. The primer set of claim 25 , wherein the direct repeat sequence is not more than about 14 base pairs in length, and the third primer is less than or equal to about 20 base pairs in length.

27. The primer set of claim 25 , wherein the first primer is a forward primer for the filled site and the empty site, the second primer is a reverse primer for the filled site, and the third primer is a reverse primer for the empty site.

28. The primer set of claim 25 , wherein in the filled site, the first flanking genomic sequence is in front of the second flanking genomic sequence, the direct repeat is present on the 5′ flanking side of the interspersed element and the part of the interspersed element included in the sequence complementary to the second primer is part of the 5′ sequence of the interspersed element.

29. The primer set of claim 25 , wherein the amplified DNA products for the filled site and the empty site have substantially the same length.

30. A kit for genetic detection, comprising a polymerase and the primer set of claim 25 .

Assignments (2)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Sep 22, 2008
From: ORCHID CELLMARK INC.
To: LIFE GENETICS LAB, LLC, A BODY CORPORATE CHARTERED IN AND EXISTING UNDER THE LAWS OF THE STATE OF LOUISIANA, THAT MAINTAINS ITS PRINCIPAL OFFICES AT:
Reel/Frame 021570/0816 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Nov 6, 2007
From: SINHA, SUDHIR K; CARTER, ANTHONY B.
To: RELIAGENE TECHNOLOGIES INC., A CORPORATION CHARTERED IN AND EXISTING UNDER THE LAWS OF THE STATE OF LOUISIANA
Reel/Frame 020110/0958 →
Continuity (2)
Provisional Application 6090285000 · Feb 23, 2007
Related Publication 20080206755A1 · Aug 28, 2008