US 11,702,685 B2
Methods for characterizing DNA sequence composition in a genome
Mary Beatty, Earlham, IA (US); Kevin Hayes, Urbandale, IA (US); Jenna Hoffman, Grimes, IA (US); Haining Lin, Clive, IA (US); and Gina Marie Zastrow-Hayes, Urbandale, IA (US)
Assigned to PIONEER HI-BRED INTERNATIONAL, INC.
Filed by PIONEER HI-BRED INTERNATIONAL, INC., Johnston, IA (US)
Filed on Feb. 8, 2021, as Appl. No. 17/169,609.
Application 17/169,609 is a continuation of application No. 16/598,341, filed on Oct. 10, 2019, granted, now 10,941,436.
Application 16/598,341 is a continuation of application No. 15/711,403, filed on Sep. 21, 2017, granted, now 10,487,352, issued on Nov. 26, 2019.
Application 15/711,403 is a continuation of application No. 14/255,144, filed on Apr. 17, 2014, granted, now 9,797,001, issued on Oct. 24, 2017.
Claims priority of provisional application 61/813,001, filed on Apr. 17, 2013.
Claims priority of provisional application 61/812,876, filed on Apr. 17, 2013.
Prior Publication US 2021/0238651 A1, Aug. 5, 2021
This patent is subject to a terminal disclaimer.
Int. Cl. C12P 19/34 (2006.01); C12Q 1/6806 (2018.01); C12Q 1/6869 (2018.01); C12Q 1/6895 (2018.01)
CPC C12Q 1/6806 (2013.01) [C12Q 1/6869 (2013.01); C12Q 1/6895 (2013.01); C12Q 2600/13 (2013.01)] 22 Claims
 
1. A method for characterizing a target sequence in the genome of an organism, the method comprising:
a) capturing DNA fragments comprising a region of a target sequence of interest from a genomic DNA fragment library by hybridization to a probe library comprising probes specific for different regions of the target sequence of interest, wherein said genomic DNA fragment library comprises the target sequence of interest, and wherein the library comprises a plurality of genomic DNA fragments, wherein each genomic DNA fragment has an adaptor at each end of the fragment, thereby enriching the library for DNA fragments having regions of the target sequence of interest;
b) amplifying the enriched DNA fragments using adaptor-specific PCR primers;
c) pooling the enriched library in equal molar ratios into sample pools;
d) sequencing the sample pools to obtain reads;
e) filtering and aligning the reads to the genomic sequence of a control and to the target sequence of interest;
f) selecting reads that align to the target sequence of interest;
g) determining junction sequences from the selected reads; and
h) using the junction sequences to characterize the integrity of the target sequence of interest in the genome of the sample.