US 12,448,645 B2
Profiling expression at transcriptome scale
Peter J. Shepard, Carlsbad, CA (US); Joanne M. Yeakley, Encinitas, CA (US); and Bruce Seligmann, Tucson, CA (US)
Assigned to BioSpyder Technologies, Inc., Carlsbad, CA (US)
Filed by BioSpyder Technologies, Inc., Carlsbad, CA (US)
Filed on Mar. 1, 2021, as Appl. No. 17/188,319.
Application 15/920,381 is a division of application No. 14/595,069, filed on Jan. 12, 2015, granted, now 9,938,566, issued on Apr. 10, 2018.
Application 15/938,178 is a division of application No. 14/480,525, filed on Sep. 8, 2014, granted, now 9,957,550, issued on May 1, 2018.
Application 17/188,319 is a continuation of application No. 15/920,381, filed on Mar. 13, 2018, granted, now 10,934,576.
Application 14/595,069 is a continuation in part of application No. 14/480,525, filed on Sep. 8, 2014, granted, now 9,957,550, issued on May 1, 2018.
Application 17/188,319 is a continuation in part of application No. 15/938,178, filed on Mar. 28, 2018, granted, now 11,293,048.
Prior Publication US 2021/0189466 A1, Jun. 24, 2021
Int. Cl. C12Q 1/6813 (2018.01)
CPC C12Q 1/6813 (2013.01) 23 Claims
 
1. A method for selectively detecting target nucleic acid sequences of a plurality of full-length sequences of interest (FLSs) in a sample, wherein the FLSs are members of a defined set of full-length species that may be present in the sample, comprising the steps of
(a) selecting a target sequence for each FLS by
(1) defining a plurality of subsequences of the FLS as target sequence candidates (TSCs),
wherein each TSC has a downstream region (DR) and an upstream region (UR),
wherein the DR has ligation-selective bases (DLSB) at the 5′-end, or the UR has ligation-selective bases (ULSB) at the 3′-end, or both, collectively being the ligation-selective bases (TSC-LSB),
wherein the sequence of the TSC-LSB spans an exon or splice junction;
(2) identifying a similar full-length species (SFL) in the defined set that comprises regions that are similar to regions in the TSC, wherein the SFL has ligation-selective bases (SFL-LSB) that correspond to the ligation-selective bases of the target sequence candidate (TSC-LSB);
(3) selecting a TSC to be the target sequence based on the following factors:
(i) the difference of one or more bases of the TSC-LSB to the corresponding bases of the SFL-LSB;
(b) contacting the sample with pairs of target sequence oligos, each pair comprising
(1) a downstream detector oligo (DD) comprising a portion (DR′) complementary to the DR of the selected TSC, and
(2) an upstream detector oligo (UD) comprising a portion (UR′) complementary to the UR of the selected TSC;
(c) ligating the DD and UD if both are hybridized to the DR and UR of a target sequence in the sample;
whereby the ligation product indicates detection of the target sequence that is selective over SFLs in the sample.