	US 12,347,526 B2
	BAMBAM: parallel comparative analysis of high-throughput sequencing data
John Zachary Sanborn, Santa Cruz, CA (US); and David Haussler, Santa Cruz, CA (US)
Assigned to THE REGENTS OF THE UNIVERSITY OF CALIFORNIA, Oakland, CA (US)
Filed by THE REGENTS OF THE UNIVERSITY OF CALIFORNIA, Oakland, CA (US)
Filed on May 14, 2020, as Appl. No. 16/874,470.
Application 15/476,337 is a division of application No. 13/373,550, filed on Nov. 18, 2011, granted, now 9,646,134, issued on Apr. 19, 2017.
Application 16/874,470 is a continuation of application No. 15/476,337, filed on Mar. 31, 2017, granted, now 10,726,945.
Application 13/373,550 is a continuation in part of application No. 13/134,047, filed on May 25, 2011, granted, now 9,652,587, issued on Apr. 26, 2017.
Claims priority of provisional application 61/396,356, filed on May 25, 2010.
Prior Publication US 2020/0279617 A1, Sep. 3, 2020
This patent is subject to a terminal disclaimer.
Int. Cl. G16B 50/30 (2019.01); G06F 3/04845 (2022.01); G06F 40/169 (2020.01); G06N 7/01 (2023.01); G16B 20/00 (2019.01); G16B 20/10 (2019.01); G16B 20/20 (2019.01); G16B 20/40 (2019.01); G16B 30/00 (2019.01); G16B 30/10 (2019.01); G16B 50/00 (2019.01); G16H 10/40 (2018.01); G16H 10/60 (2018.01); G16H 50/20 (2018.01); G16H 50/30 (2018.01)

CPC G16B 50/30 (2019.02) [G06F 3/04845 (2013.01); G06F 40/169 (2020.01); G06N 7/01 (2023.01); G16B 20/00 (2019.02); G16B 20/10 (2019.02); G16B 20/20 (2019.02); G16B 20/40 (2019.02); G16B 30/00 (2019.02); G16B 30/10 (2019.02); G16B 50/00 (2019.02); G16H 10/40 (2018.01); G16H 10/60 (2018.01); G16H 50/20 (2018.01); G16H 50/30 (2018.01); Y02A 90/10 (2018.01)]

19 Claims

1. A method of providing a health care service, the method comprising performing, by a computer system:

generating a differential genetic sequence object by:

for each common genomic location of a set of common genomic locations:

storing simultaneously, in a RAM of a sequence analysis system, a first subset of first reads corresponding to nucleic acids of a first tissue sample of two tissue samples and a second subset of second reads corresponding to nucleic acids from a second tissue sample of the two tissue samples, the first subset of first reads and the second subset of second reads overlapping a common genomic location;

aligning, using the sequence analysis system, the first subset of reads and the second subset of reads using the common genomic location; and

comparing the first subset of first reads to the second subset of second reads to determine a difference between the two tissue samples, thereby determining a plurality of local differential strings for at least one chromosome;

retrieving, from a medical records storage device, the differential genetic sequence object for a patient, the differential genetic sequence object including the plurality of local differential strings for the at least one chromosome, the plurality of local differential strings representing differences between the two tissue samples of the patient, the differences being in genetic status;

determining a patient-specific data set using a presence of a particular local differential string or a particular constellation of local differential strings in the differential genetic sequence object for the patient; and

producing a patient-specific instruction based on the patient-specific data set.