US 12,331,361 B2
Methods and systems for identification and prioritization of mutation-derived neoantigens
Victor Velculescu, Baltimore, MD (US); Theresa Zhang, Baltimore, MD (US); James Robert White, Baltimore, MD (US); and Luis Diaz, Ellicott City, MD (US)
Assigned to Personal Genome Diagnostics Inc., Baltimore, MD (US)
Filed by Personal Genome Diagnostics Inc., Baltimore, MD (US)
Filed on Dec. 31, 2019, as Appl. No. 16/731,724.
Application 16/731,724 is a continuation of application No. 15/210,489, filed on Jul. 14, 2016, granted, now 10,563,266.
Claims priority of provisional application 62/192,373, filed on Jul. 14, 2015.
Prior Publication US 2020/0160939 A1, May 21, 2020
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6886 (2018.01); C12N 15/10 (2006.01); G01N 33/574 (2006.01); G01N 33/68 (2006.01); G16B 20/00 (2019.01); G16B 20/20 (2019.01); G16B 20/30 (2019.01); G16B 20/40 (2019.01); G16B 35/00 (2019.01); G16B 35/20 (2019.01); G16C 20/20 (2019.01); G16C 20/50 (2019.01); G16C 20/60 (2019.01); G16C 20/70 (2019.01); G16H 10/40 (2018.01)
CPC C12Q 1/6886 (2013.01) [C12N 15/1068 (2013.01); C12N 15/1089 (2013.01); G01N 33/574 (2013.01); G01N 33/57484 (2013.01); G01N 33/6878 (2013.01); G16B 20/00 (2019.02); G16B 20/20 (2019.02); G16B 20/30 (2019.02); G16B 20/40 (2019.02); G16B 35/00 (2019.02); G16B 35/20 (2019.02); G16C 20/20 (2019.02); G16C 20/50 (2019.02); G16C 20/60 (2019.02); G16C 20/70 (2019.02); G16H 10/40 (2018.01); C12Q 2600/136 (2013.01); C12Q 2600/156 (2013.01); G01N 2333/70539 (2013.01)] 21 Claims
 
1. A method for prioritizing candidate neoantigens for a patient, the method comprising the steps of:
obtaining a plurality of candidate neoantigens;
determining self-similarity of members of said plurality;
determining similarity of members of said plurality to known antigens;
determining a level of expression of members of said plurality;
identifying a mutant allele frequency in exons encoding members of said plurality;
applying a rule to the results of the determining steps and identifying step to rank members of said plurality according to a likelihood of clinical significance; and
experimentally validating a subset of said plurality of candidate neoantigens based on the ranking.