Detection and quantitation of sample contamination in immune repertoire analysis
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A technique for tissue samples and molecules, applied in the determination/inspection of microorganisms, biochemical equipment and methods, etc., which can solve problems such as limitation, sensitivity cross-contamination, etc.
Inactive Publication Date: 2015-03-04
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[0022] The practice of the present invention will employ, unless otherwise indicated, conventional techniques and descriptions of molecular biology (including recombinant techniques), bioinformatics, cell biology, and biochemistry, which are within the skill of the art. Such routine techniques include, but are not limited to, sampling and analysis of blood cells, nucleic acid sequencing and analysis, and the like. Specific illustrations of suitable techniques can be found by reference to the Examples herein below. However, other equivalent conventional methods can of course also be used. Such general techniques and descriptions can be found in standard laboratory manuals such as Genome Analysis: A Laboratory Manual Series (Vol. I-IV); PCR Primer: A Laboratory Manual; and Molecular Cloning: A Laboratory Manual (all published by Cold Spring Harbor Laboratory );Wait.
[0023] The present invention relates to a method for detecting and quantifying nucleic acid contamination in a...
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Abstract
The invention is directed to methods for detecting and quantifying nucleic acid contamination in a tissue sample of an individual containing T cells and/or B cells, which is used for generating a sequence-based clonotype profile. In one aspect, the invention is implemented by measuring the presence and/or level of an endogenous or exogenous nucleic acid tag by which nucleic acid from an intended individual can be distinguished from that of unintended individuals. Endogenous tags include genetic identity markers, such as short tandem repeats, rare clonotypes or the like, and exogenous tags include sequence tags employed to determine clonotype sequences from sequence reads.
Description
[0001] This application is a continuation-in-part of each of the following U.S. patent applications: Serial No. 13 / 835,093, filed March 15, 2013, and Serial No. 13 / 834,794, filed March 15, 2013, And claims priority from: U.S. Provisional Application Serial No. 61 / 624,002, filed April 13, 2012; Serial No. 61 / 658,317, filed June 11, 2012; Serial No. 61, filed December 17, 2012 / 738,277; and Serial No. 61 / 768,269, filed February 22, 2013; each of the foregoing applications is hereby incorporated by application in its entirety. Background of the invention [0002] As the cost per base of DNA sequencing has fallen and sequencing technologies have become more reliable and accessible, an increasing number of diagnostic and prognostic applications are being developed using large-scale DNA sequencing, eg, Faham and Willis, U.S. Patent Publication 2010 / 0151471; Freeman et al., Genome Research, 19:1817-1824 (2009); Boyd et al., Sci.Transl.Med., 1(12):12ra23 (2009); He et al., Oncotarget ...
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