US 12,065,703 B2
System and method for cleaning noisy genetic data and determining chromosome copy number
Matthew Rabinowitz, San Francisco, CA (US); Milena Banjevic, Los Altos Hills, CA (US); Zachary Demko, San Francisco, CA (US); David Johnson, San Francisco, CA (US); Dusan Kijacic, Los Altos Hills, CA (US); Dimitri Petrov, Stanford, CA (US); Joshua Sweetkind-Singer, San Jose, CA (US); and Jing Xu, Jersey City, NJ (US)
Assigned to Natera, Inc., San Carlos, CA (US)
Filed by Natera, Inc., San Carlos, CA (US)
Filed on Mar. 13, 2023, as Appl. No. 18/120,873.
Application 18/120,873 is a continuation of application No. 17/836,610, filed on Jun. 9, 2022.
Application 17/836,610 is a continuation of application No. 17/164,599, filed on Feb. 1, 2021.
Application 17/164,599 is a continuation of application No. 16/823,127, filed on Mar. 18, 2020, granted, now 11,111,544, issued on Sep. 7, 2021.
Application 16/823,127 is a continuation in part of application No. 16/411,507, filed on May 14, 2019, granted, now 10,597,724, issued on Mar. 24, 2020.
Application 16/823,127 is a continuation in part of application No. 16/399,911, filed on Apr. 30, 2019, abandoned.
Application 16/411,507 is a continuation of application No. 16/288,690, filed on Feb. 28, 2019, granted, now 11,306,359, issued on Apr. 19, 2022.
Application 16/288,690 is a continuation of application No. 15/187,555, filed on Jun. 20, 2016, granted, now 10,227,652, issued on Mar. 12, 2019.
Application 15/187,555 is a continuation of application No. 14/092,457, filed on Nov. 27, 2013, granted, now 9,430,611, issued on Aug. 30, 2016.
Application 14/092,457 is a continuation of application No. 13/793,133, filed on Mar. 11, 2013, granted, now 9,424,392, issued on Aug. 23, 2016.
Application 14/092,457 is a continuation of application No. 13/793,186, filed on Mar. 11, 2013, granted, now 8,682,592, issued on Mar. 25, 2014.
Application 13/793,133 is a continuation of application No. 11/603,406, filed on Nov. 22, 2006, granted, now 8,532,930, issued on Sep. 10, 2013.
Application 13/793,186 is a continuation of application No. 11/603,406, filed on Nov. 22, 2006, granted, now 8,532,930, issued on Sep. 10, 2013.
Application 16/399,911 is a continuation of application No. 15/887,746, filed on Feb. 2, 2018.
Application 15/887,746 is a continuation of application No. 15/446,778, filed on Mar. 1, 2017, granted, now 10,260,096, issued on Apr. 16, 2019.
Application 15/446,778 is a continuation of application No. 13/949,212, filed on Jul. 23, 2013, granted, now 10,083,273, issued on Sep. 25, 2018.
Application 13/949,212 is a continuation of application No. 12/076,348, filed on Mar. 17, 2008, granted, now 8,515,679, issued on Aug. 20, 2013.
Application 12/076,348 is a continuation in part of application No. 11/495,982, filed on Jul. 31, 2006, abandoned.
Application 12/076,348 is a continuation in part of application No. 11/603,406, filed on Nov. 22, 2006, granted, now 8,532,930, issued on Sep. 10, 2013.
Application 12/076,348 is a continuation in part of application No. 11/634,550, filed on Dec. 6, 2006, abandoned.
Application 11/603,406 is a continuation in part of application No. 11/496,982, filed on Jul. 31, 2006, abandoned.
Claims priority of provisional application 61/008,637, filed on Dec. 21, 2007.
Claims priority of provisional application 61/003,101, filed on Nov. 13, 2007.
Claims priority of provisional application 60/934,440, filed on Jun. 13, 2007.
Claims priority of provisional application 60/932,456, filed on May 31, 2007.
Claims priority of provisional application 60/926,198, filed on Apr. 25, 2007.
Claims priority of provisional application 60/918,292, filed on Mar. 16, 2007.
Claims priority of provisional application 60/846,610, filed on Sep. 22, 2006.
Claims priority of provisional application 60/817,741, filed on Jun. 30, 2006.
Claims priority of provisional application 60/789,506, filed on Apr. 4, 2006.
Claims priority of provisional application 60/774,976, filed on Feb. 21, 2006.
Claims priority of provisional application 60/754,396, filed on Dec. 29, 2005.
Claims priority of provisional application 60/742,305, filed on Dec. 6, 2005.
Claims priority of provisional application 60/739,882, filed on Nov. 26, 2005.
Claims priority of provisional application 60/703,415, filed on Jul. 29, 2005.
Prior Publication US 2023/0212693 A1, Jul. 6, 2023
Int. Cl. C12Q 1/68 (2018.01); C12Q 1/6806 (2018.01); C12Q 1/6827 (2018.01); C12Q 1/6855 (2018.01); C12Q 1/6869 (2018.01); C12Q 1/6876 (2018.01); C12Q 1/6883 (2018.01); C12Q 1/6886 (2018.01); G16B 20/00 (2019.01); G16B 25/00 (2019.01); G16B 30/00 (2019.01); G16B 40/00 (2019.01)
CPC C12Q 1/6883 (2013.01) [C12Q 1/6806 (2013.01); C12Q 1/6827 (2013.01); C12Q 1/6855 (2013.01); C12Q 1/6869 (2013.01); C12Q 1/6876 (2013.01); C12Q 1/6886 (2013.01); G16B 20/00 (2019.02); G16B 25/00 (2019.02); G16B 30/00 (2019.02); G16B 40/00 (2019.02); C12Q 2537/149 (2013.01); C12Q 2545/114 (2013.01); C12Q 2600/118 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/158 (2013.01)] 26 Claims
 
1. A method for determining genetic data for DNA from cancer cells, comprising:
obtaining cell-free DNA from a blood sample, wherein the cell-free DNA comprises DNA from cancer cells comprising one or more chromosome segments;
ligating at least one adapter to the chromosome segments, wherein the at least one adapter comprises a universal amplification sequence;
performing targeted amplification using a universal primer that binds to the universal amplification sequence, and target-specific primers, to generate amplified nucleic acid molecules; and
determining genetic data for the cell-free DNA from cancer cells by performing next-generation sequencing.