US 12,486,542 B2
Detecting mutations and ploidy in chromosomal segments
Joshua Babiarz, Castro Valley, CA (US); Tudor Pompiliu Constantin, Berkeley, CA (US); Lane A. Eubank, San Carlos, CA (US); George Gemelos, Portland, OR (US); Matthew Micah Hill, Belmont, CA (US); Huseyin Eser Kirkizlar, Los Angeles, CA (US); Matthew Rabinowitz, San Francisco, CA (US); Onur Sakarya, Redwood City, CA (US); Styrmir Sigurjonsson, San Jose, CA (US); and Bernhard Zimmermann, Manteca, CA (US)
Assigned to Natera, Inc., San Carlos, CA (US)
Filed by Natera, Inc., San Carlos, CA (US)
Filed on Jun. 4, 2024, as Appl. No. 18/733,681.
Application 18/733,681 is a continuation of application No. 17/692,469, filed on Mar. 11, 2022.
Application 17/692,469 is a continuation of application No. 15/898,145, filed on Feb. 15, 2018, granted, now 11,319,595, issued on May 3, 2022.
Application 15/898,145 is a continuation of application No. 14/692,703, filed on Apr. 21, 2015, granted, now 10,179,937, issued on Jan. 15, 2019.
Claims priority of provisional application 62/148,173, filed on Apr. 15, 2015.
Claims priority of provisional application 62/147,377, filed on Apr. 14, 2015.
Claims priority of provisional application 62/146,188, filed on Apr. 10, 2015.
Claims priority of provisional application 62/066,514, filed on Oct. 21, 2014.
Claims priority of provisional application 61/994,791, filed on May 16, 2014.
Claims priority of provisional application 61/987,407, filed on May 1, 2014.
Claims priority of provisional application 61/982,245, filed on Apr. 21, 2014.
Prior Publication US 2024/0318263 A1, Sep. 26, 2024
Int. Cl. C12Q 1/6886 (2018.01); C12Q 1/6869 (2018.01); G06N 7/01 (2023.01); G06N 20/00 (2019.01); G16B 15/00 (2019.01); G16B 20/00 (2019.01); G16B 20/10 (2019.01); G16B 20/20 (2019.01); G16B 25/00 (2019.01); G16B 25/20 (2019.01); G16B 40/00 (2019.01); G16B 40/20 (2019.01); G16H 10/40 (2018.01); G16H 50/20 (2018.01); G16Z 99/00 (2019.01)
CPC C12Q 1/6886 (2013.01) [C12Q 1/6869 (2013.01); G06N 7/01 (2023.01); G06N 20/00 (2019.01); G16B 15/00 (2019.02); G16B 20/00 (2019.02); G16B 20/10 (2019.02); G16B 20/20 (2019.02); G16B 25/00 (2019.02); G16B 40/00 (2019.02); G16B 40/20 (2019.02); G16H 10/40 (2018.01); G16H 50/20 (2018.01); G16Z 99/00 (2019.02); C12Q 2539/10 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/158 (2013.01); C12Q 2600/16 (2013.01); C12Q 2600/172 (2013.01); G16B 25/20 (2019.02)] 15 Claims
OG exemplary drawing
 
1. A method for preparing a DNA fraction from a biological sample of a subject useful for analyzing methylation patterns involved with cancer, comprising:
(a) extracting cell-free DNA from the biological sample;
(b) producing an enriched DNA fraction by: (i) treating the extracted cell-free DNA or DNA derived therefrom with an agent that discriminates between methylated and unmethylated cytosines, wherein the extracted DNA or its derivative or the treated DNA or its derivative is further tagged with at least one adaptor containing a universal priming sequence, thereby producing adapted treated DNA, (ii) performing universal amplification on at least some of the adapted treated DNA using the universal priming sequence and producing amplified adapted treated DNA, and (iii) selectively enriching for a subset of the amplified adapted treated DNA or its derivative that contain one or more preselected loci and producing enriched DNA that contain one or more preselected loci, wherein the enrichment comprises selectively enriching for at least 1,000 preselected loci in a single reaction volume using at least 1,000 target-specific oligonucleotides; and
(c) performing massively parallel sequencing on the enriched DNA or its derivative and obtaining sequence reads in a sequencer and obtaining an identification of one or more methylation patterns involved with cancer.