Method of sequence determination using sequence tags
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A technology of sequence tagging, tagging, applied in Renner and Macevicz, Nucleic Acid Population Based Steps: Obtaining T Cells from Individuals and Methods Fields
Inactive Publication Date: 2015-04-15
ADAPTIVE BIOTECH
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However, clonotypes are efficiently determined from sequence data because of the size of the populations to be analyzed, the similarity of sequences in such populations, the limited predictability of natural variation between sequences, and the noise introduced into the data by many sample preparation and measurement steps ( clonotype) and clonotype profile (clonotype profile) constitute a challenge, such as Warren et al., Genome Research, 21 (5): 790-797 (2011)
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[0019] 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 conventional 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 are also referred to in the examples herein below. However, other equivalent conventional methods may of course be used. Can be found in standard laboratory manuals such as Genome Analysis: A Laboratory Manual Series (Vols. I-IV), PCR primer: A Laboratory Manual, and Molecular Cloning: A Laboratory Manual (all from Cold Spring Harbor Laboratory Press), etc. Such conventional techniques and instructions.
[0020]In one aspect, the invention relates to methods for obtaining and analyzing sequence data from repertoires...
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Abstract
The invention is directed to the use of sequence tags to improve sequence determination of amplicons of related sequences, particularly large and complex amplicons, such as those comprising recombined nucleic acids encoding immune receptor molecules. In one aspect, sequence reads having the same sequence tags are aligned after which final base calls are determined from a (possibly weighted) average base call from sequence read base calls at each position. Similarly, in another aspect, sequence reads comprising series of incorporation signals are aligned by common sequence tags and base calls in homopolymer regions are made as a function incorporation signal values at each "flow" position.
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[0001] cross reference [0002] This application claims priority to U.S. Patent Application Serial No. 13 / 835,093 filed March 15, 2013, which claims priority to the following U.S. Provisional Patent Application: Serial filed June 11, 2012 Serial No. 61 / 658,317, Serial No. 61 / 738,277 filed December 17, 2012, and Serial No. 61 / 776,647 filed March 11, 2013, each of which is incorporated herein by reference in its entirety. This application also claims priority to US Provisional Patent Application Serial No. 61 / 829,054, filed May 30, 2013, which is incorporated herein by reference in its entirety. Background of the invention [0003] Analysis of biological or medical samples often requires determination of the nucleic acid sequence of large and complex populations of DNA and / or RNA, for example Gloor et al, PLoS ONE 5(10): el5406 (2010); Petrosino et al, Clinical Chemistry, 55(5 ):856-866 (2009); Arstila et al., Science, 286:958-961 (1999). In particular, nucleic acid profiles e...
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