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US5364759A
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DNA typing with short tandem repeat polymorphisms and identification of polymorphic short tandem repeats
Assignee: Baylor College of Medicine
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Filing: 1991-01-31
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Granted: 1994-11-15
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Expires: 2011-01-31
Abstract
Abstract The present invention relates to a DNA profiling assay for detecting polymorphisms in a short tandem repeat. The method includes the steps of extracting DNA from a sample to be tested, amplifying the extracted DNA and identifying the amplified extension products for each different sequence. Each different sequence is differentially labeled. In the method, internal and external standards can also be used. The method is applicable to a wide variety of forensic and medical samples, including blood, semen, vaginal swaps, tissue, hair, saliva, urine and mixtures of body fluids. A short tandem repeat sequence which can be characterized by the formula (AwGxTyCz)n, wherein A, G, T and C represent the nucleotides, w, x, y and z represent the number of nucleotide and range from 0 to 7 and the sum of w+x+y+z ranges from 3 to 7 and n represents the repeat number and ranges from 5 to 50. The labels can be from a variety of groups, including fluorescers, radioisotopes, chemiluminescers, stains, enzymes and antibodies. Also described is a kit. Further, a method of detecting the polymorphic short tandem repeats comprising the steps of either searching for the repeats in a data base or comparing oligonucleotides and searching for the repeats in a genetic library.
Inventors
- 👤 Charles T. Caskey
- 👤 Albert O. Edwards
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-10-29 04:46
CPC Classifications
C; C12; C12Q; C12Q1/00; C12Q1/68; C12Q1/6876; C12Q1/6844; C12Q1/6858; B; B01; B01J; B01J2219/00; B01J2219/00274; B01J2219/00277; B01J2219/0054; B01J2219/00572; B01J2219/00574; B01J2219/00576; B01J2219/00578; B01J2219/00718; B01J2219/0072; B01J2219/00722; C12Q2600/00; C12Q2600/156; C12Q2600/16; Y; Y10; Y10S; Y10S435/00; Y10S435/81; Y10T; Y10T436/00; Y10T436/14; Y10T436/142222; Y10T436/143333
Claims Analysis
Total Claims: 31
Claim 1
Independent Claim
126 words
A DNA profiling assay for detecting polymorphisms in at least one short tandem repeat, comprising the steps of: extracting DNA from a sample to be tested; amplifying said at least one short tandem repeat in the extracted DNA, wherein the short tandem repeat sequence is characterized by the formula (A w G x T y C z ) n wherein A,G,T, and C represent the nucleotides; w, x, y and z represent the number of each nucleotide and range from 0 to 7; the sum of w+x+y+z ranges from 4 to 7; and n represents the repeat number and ranges from about 5 to 50; and detecting said polymorphisms by identifying said amplified extension products for each different sequence, wherein each different sequence is differentially labelled.
Claim 2
Dependent Claim
126 words
A DNA profiling assay for detecting polymorphisms in at least one short tandem repeat, comprising the steps of: extracting DNA from a sample to be tested; amplifying said at least one short tandem repeat in the extracted DNA, wherein the short tandem repeat sequence is characterized by the formula (A w G x T y C z ) n wherein A,G,T, and C represent the nucleotides; w, x, y and z represent the number of each nucleotide and range from 0 to 7; the sum of w+x+y+z ranges from 4 to 7; and n represents the repeat number and ranges from about 5 to 50; and detecting said polymorphisms by identifying said amplified extension products for each different sequence, wherein each different sequence is differentially labelled.
Claim 3
Dependent Claim
10 words
The method of claim 1, further comprising an external standard.
Claim 4
Dependent Claim
10 words
The method of claim 1, further comprising an internal standard.
Claim 5
Dependent Claim
36 words
The method of claim 1, wherein the sample to be tested is a forensic or medical sample selected from the group consisting of blood, semen, vaginal swabs, tissue, hair, saliva, urine, and mixtures of body fluids.
Claim 6
Dependent Claim
137 words
The assay of claim 1, wherein at least one short tandem repeat sequence is selected from the non-duplicative alphabetical represented nucleotide sequence group consisting of: (AAAC) n , (AAAG) n , (AAAT) n , (AACC) n , (AACG) n , (AAGC) n , (AAGG) n , (AAGT) n , (AATC) n , (AATG) n , (AATT) n , (ACAG) n , (ACAT) n , (AGAT) n , (ACCC) n , (ACCG) n , (ACCT) n , (ACGC) n , (ACGG) n , (ACGT) n , (ACTC) n , (ACTG) n , (AGCC) n , (AGCG) n , (AGCT) n , (AGGC) n , (AGGG) n , (ATCC) n , (ATCG) n , (ATGC) n , (CCCG) n , (CCGG) n , and combinations thereof; wherein n is the repeat number and varies from about 5 to 50.
Claim 7
Dependent Claim
12 words
The assay of claim 1 wherein n ranges between 5 and 40.
Claim 8
Dependent Claim
13 words
The assay of claim 1, wherein n varies from about 5 to 20.
Claim 9
Dependent Claim
15 words
The assay of claim 1, wherein the DNA is amplified by PCR or multiplex PCR.
Claim 10
Dependent Claim
21 words
The assay of claim 1, wherein amplification is by multiplex PCR with primers to at least two short tandem repeat sequences.
Claim 11
Dependent Claim
22 words
The assay of claim 1, wherein the label is selected from the group consisting of fluorescers, radioisotopes, chemiluminescers, stains, enzymes and antibodies.
Claim 12
Dependent Claim
29 words
The method of claim 10, wherein the label is fluorescent and is selected from the group consisting of Texas Red, NBD aminoheanoic acid Tetramethylrhodamine-5- (and -6) isothiocyanate, and Fluorescein-5-isothiocyanate.
Claim 13
Dependent Claim
31 words
The DNA profiling assay of claim 1, further comprising the step of distinguishing simultaneously differential labels during the detecting step, wherein said labels are distinguished by an automated DNA label analyzer.
Claim 14
Dependent Claim
36 words
A kit for a DNA profiling assay to detect polymorphisms in at least one short tandom repeat sequence comprising a container which has oligonucleotide primer pairs for amplifying said at least one short tandem repeat sequence.
Claim 15
Dependent Claim
36 words
A kit for a DNA profiling assay to detect polymorphisms in at least one short tandom repeat sequence comprising a container which has oligonucleotide primer pairs for amplifying said at least one short tandem repeat sequence.
Claim 16
Dependent Claim
10 words
The kit of claim 13 further comprising a labelled standard.
Claim 17
Dependent Claim
16 words
The kit of claim 13 further comprising a container having reagents for multiplex polymerase chain reaction.
Claim 18
Independent Claim
138 words
A method of detecting a polymorphic short tandem repeat comprising the steps of: determining possible, non-duplicative nucleotide sequences of the formula (A w G x T y C z ), wherein A,G,T and C represents each nucleotide and w,x,y and z represent the number of each nucleotide and ranges between 0 and 7 with the sum of w+x+y+z ranging between 3 and 7; searching for (A w G x T y C z ) n in databases containing known genetic sequences, wherein n represents the number of tandem repeats of the genetic sequence and is at least 5; identifying the (A w G x T y C z ) n sequence and its flanking sequence; extracting each identified sequence found in the searching step and its flanking sequence; and identifying the extracted sequences which have unique flanking sequences.
Claim 19
Independent Claim
138 words
A method of detecting a polymorphic short tandem repeat comprising the steps of: determining possible, non-duplicative nucleotide sequences of the formula (A w G x T y C z ), wherein A,G,T and C represents each nucleotide and w,x,y and z represent the number of each nucleotide and ranges between 0 and 7 with the sum of w+x+y+z ranging between 3 and 7; searching for (A w G x T y C z ) n in databases containing known genetic sequences, wherein n represents the number of tandem repeats of the genetic sequence and is at least 5; identifying the (A w G x T y C z ) n sequence and its flanking sequence; extracting each identified sequence found in the searching step and its flanking sequence; and identifying the extracted sequences which have unique flanking sequences.
Claim 20
Dependent Claim
50 words
The method of claim 16, further comprising the steps of: synthesizing oligonucleotide primer pairs to the unique flanking sequences; performing a polymerase chain reaction with the primer pairs on DNA samples from a test population; and detecting polymorphic short tandem repeats in the extension products of the polymerase chain reaction.
Claim 21
Independent Claim
38 words
A method of detecting a polymorphic short tandem repeat comprising the steps of: synthesizing labelled oligonucleotide probes complementary to said short tandem repeat; hybridizing the labelled probes to total human λ phage libraries; and sequencing the hybridized plaques.
Claim 22
Independent Claim
38 words
A method of detecting a polymorphic short tandem repeat comprising the steps of: synthesizing labelled oligonucleotide probes complementary to said short tandem repeat; hybridizing the labelled probes to total human λ phage libraries; and sequencing the hybridized plaques.
Claim 23
Dependent Claim
17 words
The method of claim 18, wherein the sequencing step, includes the step of subcloning the hybridized plaque.
Claim 24
Dependent Claim
21 words
The method of claim 18, wherein the sequencing step, includes the step of direct polymerase chain reaction of the hybridized plaque.
Claim 25
Dependent Claim
12 words
The short tandem AGAT repeat as defined in SEQ ID. NO. 26.
Claim 26
Dependent Claim
12 words
The short tandem AGAT repeat as defined in SEQ ID. NO. 26.
Claim 27
Dependent Claim
101 words
The assay of claim 8, wherein the primer pairs are selected from the group consisting of SEQ ID. NO. 1 and 2, SEQ ID. NO. 3 and 4, SEQ ID. NO. 5 and 6, SEQ ID. NO. 7 and 8, SEQ ID. NO. 9 and 10, SEQ ID. NO. 11 and 12, SEQ ID. NO. 13 and 14, SEQ ID. NO. 15 and 16, SEQ ID. NO. 17 and 18, SEQ ID. NO. 19 and 20, SEQ ID. NO. 21 and 22, SEQ ID. NO. 5 and 24, SEQ ID. NO. 19 and 25 and Seq. ID NO. 13 and 23.
Claim 28
Dependent Claim
95 words
The assay of claim 13, wherein the primer pairs are selected from the group consisting of SEQ ID. o NO. 1 and 2, SEQ ID. NO. 3 and 4, SEQ ID. NO. 5 and 6, SEQ ID. NO. 7 and 8, SEQ ID. NO. 9 and 10, SEQ ID. NO. 11 and 12, SEQ ID. NO. 13 and 14, SEQ ID. NO. 15 and 16, SEQ ID. NO. 17 and 18, SEQ ID. NO. 19 and 20, SEQ ID. NO. 21 and 22, SEQ ID. NO. 5 and 23, SEQ ID. NO. 19 and 24.
Claim 29
Dependent Claim
28 words
The sequences of SEQ ID. NO. 1, SEQ ID. NO. 2, SEQ ID. NO. 3, and SEQ ID. NO. 4 for determining flanking sequences of short tandem repeat.
Claim 30
Dependent Claim
28 words
The sequences of SEQ ID. NO. 1, SEQ ID. NO. 2, SEQ ID. NO. 3, and SEQ ID. NO. 4 for determining flanking sequences of short tandem repeat.
Claim 31
Dependent Claim
55 words
The assay of claim 1, wherein the short tandem repeat sequence further includes sequences selected from the non-duplicative alphabetical represented nucleotide sequence group consisting of (AAC) n , (AAG) n , (AAT) n , (ACC) n , (ACG) n , (ACT) n (AGC) n , (AGG) n , (ATC) n , and (CCG) n .
References Cited (Backward Citations)
USPTO Annuity & Maintenance Windows
| Annuity Stage | Window Opens | Payment Deadline | Surcharge Period Until | Estimated Fee | Status |
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| 3.5 Years (Year 4) | 1997-11-14 | 1998-05-16 | 1998-11-15 | $2000.00 | Window Closed / Lapsed |
| 7.5 Years (Year 8) | 2001-11-14 | 2002-05-16 | 2002-11-15 | $3760.00 | Window Closed / Lapsed |
| 11.5 Years (Year 12) | 2005-11-14 | 2006-05-16 | 2006-11-15 | $7700.00 | Window Closed / Lapsed |