Method for cloning of a rare, specifically mutated cell
First Claim
1. A method of detecting and isolating a cell in a culture, which cell is mutated by a sequence-specific process, the method comprising:
- a) treating the culture with a sequence-specific process that introduces a 3′ and
a 5′
mutation in a genomic target, wherein the 3′ and
5′
mutations are separated by not more than 100 nucleotides;
b) forming replicate subcultures of the treated culture;
c) making a first polymerase chain reaction (PCR) product that contains the site of the 3′ and
5′
mutations using a sample of genomic DNA from a replicate of at least two subcultures of the treated culture;
d) making a second PCR product that contains the site of the 5′
mutation using the first PCR product, an allele-specific polymerase chain reaction (AS-PCR) primer that encodes the 3′
mutation and a forward primer that is not homologous to the site of the 5′
mutation;
e) identifying a positive subculture by the presence of the 5′
mutation in the second PCR product using template from the subculture;
f) subdividing a replicate of the positive subculture;
g) identifying a positive subdivision of the positive subculture by the presence of the 5′
mutation in cells of the subdivision; and
h) verifying that the positive subdivision contains a doubly substituted cell having both the 3′ and
5′
mutations and cloning the doubly substituted cell, wherein the sequence-specific process is short fragment homologous replacement (SFHR), the SFHR comprising the use of an exogenous nucleic acid having a sense strand, an antisense strand, or both.
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Abstract
The invention concerns a new method of detecting a rare product of a directed genetic alteration of a cultured cell. The method is applicable to any method of making the alteration provided that a pair of closely linked alterations can be made. The method consists of sequentially using allele specific polymerase chain reaction (PCR) to preferentially amplify sequences containing one of the two linked alterations coupled with a second method that detects the second change in the PCR product. The second method can be restriction digestion, traditional sequencing or pyro-sequencing. Experiments indicate that alterations as rare as one correctly altered copy in 10,000 cells can be detected.
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Citations
27 Claims
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1. A method of detecting and isolating a cell in a culture, which cell is mutated by a sequence-specific process, the method comprising:
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a) treating the culture with a sequence-specific process that introduces a 3′ and
a 5′
mutation in a genomic target, wherein the 3′ and
5′
mutations are separated by not more than 100 nucleotides;
b) forming replicate subcultures of the treated culture;
c) making a first polymerase chain reaction (PCR) product that contains the site of the 3′ and
5′
mutations using a sample of genomic DNA from a replicate of at least two subcultures of the treated culture;
d) making a second PCR product that contains the site of the 5′
mutation using the first PCR product, an allele-specific polymerase chain reaction (AS-PCR) primer that encodes the 3′
mutation and a forward primer that is not homologous to the site of the 5′
mutation;
e) identifying a positive subculture by the presence of the 5′
mutation in the second PCR product using template from the subculture;
f) subdividing a replicate of the positive subculture;
g) identifying a positive subdivision of the positive subculture by the presence of the 5′
mutation in cells of the subdivision; and
h) verifying that the positive subdivision contains a doubly substituted cell having both the 3′ and
5′
mutations and cloning the doubly substituted cell,wherein the sequence-specific process is short fragment homologous replacement (SFHR), the SFHR comprising the use of an exogenous nucleic acid having a sense strand, an antisense strand, or both. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21)
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22. A method of detecting and isolating a cell in a culture, the cell having a 3′
- and a 5′
mutation in a genomic target, the method comprising;a) forming replicate subcultures of a culture comprising the cell;
b) making a first polymerase chain reaction (PCR) product that contains the site of the 3′ and
5′
mutations using a sample of genomic DNA from a replicate of at least two subcultures of the culture;
c) making a second PCR product that contains the site of the 5′
mutation using the first PCR product, an allele-specific polymerase chain reaction (AS-PCR) primer that encodes the 3′
nucleotide mutation and a forward primer that is not homologous to the site of the 5′
mutation;
d) identifying a positive subculture by the presence of the 5′
mutation in the second PCR product using template from the subculture;
e) subdividing a replicate of the positive subculture;
f) identifying a positive subdivision of the positive subculture by the presence of the 5′
mutation in cells of the subdivision; and
g) verifying that the positive subdivision contains a doubly substituted cell having both the 3′ and
5′
mutations and cloning the doubly substituted cell. - View Dependent Claims (23, 24, 25, 26, 27)
- and a 5′
Specification