US 12,110,554 B2
Methods for classification of tissue samples as positive or negative for cancer
Giulia C. Kennedy, San Francisco, CA (US); Bonnie H. Anderson, Half Moon Bay, CA (US); Darya I. Chudova, San Jose, CA (US); Eric T. Wang, Milpitas, CA (US); Hui Wang, San Bruno, CA (US); Moraima Pagan, San Francisco, CA (US); Nusrat Rabbee, South San Francisco, CA (US); and Jonathan I. Wilde, Burlingame, CA (US)
Assigned to VERACYTE, INC., South San Francisco, CA (US)
Filed by VERACYTE, INC., South San Francisco, CA (US)
Filed on Jan. 25, 2021, as Appl. No. 17/157,876.
Application 17/157,876 is a continuation of application No. 14/153,219, filed on Jan. 13, 2014, granted, now 10,934,587.
Application 14/153,219 is a continuation of application No. 13/318,751, granted, now 8,669,057, issued on Mar. 11, 2014, previously published as PCT/US2010/034140, filed on May 7, 2010.
Claims priority of provisional application 61/176,471, filed on May 7, 2009.
Prior Publication US 2021/0238686 A1, Aug. 5, 2021
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6883 (2018.01); C12Q 1/6886 (2018.01)
CPC C12Q 1/6883 (2013.01) [C12Q 1/6886 (2013.01); C12Q 2600/112 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/158 (2013.01)] 21 Claims
 
1. A method for processing or analyzing a tissue sample of a subject, comprising:
(a) obtaining said tissue sample from said subject;
(b) subjecting at least a portion of said tissue sample to a diagnostic screening process which indicates said tissue sample as ambiguous or indeterminate;
(c) assaying one or more nucleic acid molecules derived from a nucleic acid sample from said tissue sample of said subject to generate a data set;
(d) using a programmed computer to process said data set to identify (i) a level of expression of one or more gene expression products in said nucleic acid sample, and (ii) one or more genetic mutations in said nucleic acid sample;
(e) using a trained algorithm, computer processing said level of expression and said one or more genetic mutations identified in (d) to generate a classification of said tissue sample as positive or negative for a cancer; and
(f) electronically outputting a report that identifies said classification of said tissue sample as positive or negative for said cancer.