Sieving and profiling nucleic acid samples
AssigneeBioInventors & Entrepreneurs Network, LLC
InventorMichael Seul
Life of this patent
Estimating the term…
Abstract
A method of selecting nucleic acid samples including particular desired alleles from a plurality of nucleic acid samples including the steps of performing a first reaction in a plurality of pools containing the samples to produce reaction products including a source tag identifying said each pool; pooling the pools to provide pooled pools; for each of the desired alleles to be identified, performing a second reaction using said reaction products to produce allele-specific second reaction products comprising a marker tag and a derived source tag; identifying said allele-specific second reaction products, and further identifying nucleic acid samples with the desired alleles. A source tag sharing number “d” may be determined for each of the alleles. Alleles may also be binned together.
Claims20
A process of identifying alleles at a plurality of polymorphic sites for at least two nucleic acid samples, wherein the alleles of interest at particular polymorphic site are identified by a marker tag, the process comprising:
- (a) for each of the alleles of interest:
- (i) determining a value, d, representing a first maximum number of samples to be combined together, by finding first that the probability of at least one of d nucleic acid samples in any combination having at least one allele of interest does not exceed a predetermined probability threshold, wherein said alleles of interest are known to occur in the population at a specified frequency;
- (ii) if d of said allele of interest exceeds a maximum pool size, then setting the value d for said allele equal to the maximum pool size;
- (b) further limiting the first maximum number of samples to be combined together by grouping the said alleles of interest by their determined values of d, such that said alleles of interest having values of d within designated limits are placed into the same group(s);
- (c) for alleles of interest in at least one of the groups:
- (i) pooling aliquots from a number dgrp of the nucleic acid samples wherein dgrp is set equal to the smallest d value of at least one of the alleles of interest in said group, to form a plurality of sample pools;
- (ii) associating particular said alleles of interest in different sample pools with a source tag identifying the different sample pools;
- (iii) pooling aliquots from one or more of the different sample pools to form one or more combined pools wherein the total number of samples in each combined pool does not exceed the maximum pool size;
- and
- (iv) associating particular said desired alleles in combined pools each with a marker tag identifying the different alleles present (at said specific polymorphic sites) in the combined pools,
- (d) determining if any alleles of interest are in any combined pool by identifying the associated marker tags in the combined pools, and further determining:
- (i) whether the marker tags at the specific polymorphic sites are identical or different, and identifying the source tags to identify the sample pool(s) where samples including any alleles of interest bearing one of said identified marker tags originated;
- and
- (ii) if said marker tags are different, and if d for an identified sample pool exceeds 1, thereby raising ambiguity in identifying the nucleic acid sample(s) having the identified alleles, then making at least some of the ambiguous identifications unambiguous.
A process of identifying alleles at a plurality of polymorphic sites for at least two nucleic acid samples, wherein alleles of interest at particular polymorphic sites are identified by a marker tag, the process comprising:
- (a) for each of the alleles of interest:
- (i) determining a value, d, representing a first maximum number of samples to be combined together, by finding first that the probability of at least one of d nucleic acid samples in any combination having at least one allele of interest does not exceed a predetermined probability threshold, wherein said alleles of interest are known to occur in the population at a specified frequency;
- (ii) if d of said allele of interest exceeds a maximum pool size, then setting the value d for said allele equal to the maximum pool size;
- (b) further limiting the first maximum number of samples to be combined together by grouping the said alleles of interest by their determined values of d, such that said alleles of interest having values of d within designated limits are placed into the same group(s);
- (c) for alleles of interest in at least one of the groups:
- (i) pooling aliquots from a number dgrp of the nucleic acid samples wherein dgrp is set equal to the smallest d value of at least one the alleles of interest in said group, to form a plurality of sample pools;
- (ii) associating particular said the alleles of interest in different sample pools with a source tag identifying the different sample pools;
- (iii) pooling aliquots from one or more of the different sample pools to form one or more combined pools wherein the total number of samples in each combined pool does not exceed the maximum pool size;
- and
- (iv) associating particular said desired alleles in combined pools each with a marker tag identifying the different alleles present (at said specific polymorphic sites) in the combined pools,
- (d) determining if any alleles the alleles of interest are in any combined pool by the associated marker tags in the combined pools, and, further determining:
- (i) whether the marker tags at the specific polymorphic sites are identical or different, and identifying the source tags to identify the sample pool(s) where samples including any allele of interest bearing one of said identified marker tags originated, and;
- (ii) if said marker tags are different, and if d for any identified sample pool exceeds 1 then analyzing samples in the identified sample pools to determine which one(s) contain samples having the alleles of interest bearing the different marker tags.
Dependencies are inferred from the claim text.