发明名称 |
Compositions and method for measuring and calibrating amplification bias in multiplexed PCR reactions |
摘要 |
Compositions and methods are described for standardizing the DNA amplification efficiencies of a highly heterogeneous set of oligonucleotide primers as may typically be used to amplify a heterogeneous set of DNA templates that contains rearranged lymphoid cell DNA encoding T cell receptors (TCR) or immunoglobulins (IG). The presently disclosed embodiments are useful to overcome undesirable bias in the utilization of a subset of amplification primers, which leads to imprecision in multiplexed high throughput sequencing of amplification products to quantify unique TCR or Ig encoding genomes in a sample. Provided is a composition comprising a diverse plurality of template oligonucleotides in substantially equimolar amounts, for use as a calibration standard for amplification primer sets. Also provided are methods for identifying and correcting biased primer efficiency during amplification. |
申请公布号 |
US9371558(B2) |
申请公布日期 |
2016.06.21 |
申请号 |
US201514594007 |
申请日期 |
2015.01.09 |
申请人 |
Adaptive Biotechnologies Corp. |
发明人 |
Robins Harlan Saul;Carlson Christopher Scott;Livingston Robert J.;Emerson Ryan O.;Sherwood Anna M. |
分类号 |
C12Q1/68;C07H21/04 |
主分类号 |
C12Q1/68 |
代理机构 |
Cooley LLP |
代理人 |
Cooley LLP |
主权项 |
1. A method for determining non-uniform nucleic acid amplification potential among members of a set of oligonucleotide primers that is capable of amplifying rearranged nucleic acid molecules encoding one or more adaptive immune receptors in a biological sample from a mammalian subject, the method comprising:
(a) amplifying a composition comprising a plurality of synthetic template oligonucleotides comprising sequences of rearranged nucleic acid molecules encoding one or more adaptive immune receptors and one or more additional unique random polynucleotide sequences using a set of oligonucleotide primers in a single multiplex PCR reaction to obtain a plurality of amplified synthetic template oligonucleotides; (b) sequencing said plurality of amplified synthetic template oligonucleotides to determine, for each unique synthetic template oligonucleotide comprising said plurality,
(i) a synthetic template oligonucleotide sequence and(ii) a frequency of occurrence of said synthetic template oligonucleotide sequence; and (c) comparing a frequency of occurrence of each of said synthetic template oligonucleotide sequences to an expected distribution, wherein a deviation between said frequency of occurrence of said synthetic template oligonucleotide sequences and said expected distribution indicates a non-uniform nucleic acid amplification potential among members of the set of oligonucleotide amplification primers. |
地址 |
Seattle WA US |