US 12,084,724 B2
Computational method for detecting fusion events
Samuel Woodhouse, Cambridge (GB); Stefanie Lensing, Cambridge (GB); Tim Forshew, Stevenage (GB); Vincent Plagnol, Cambridge (GB); Matthew Edward Smith, Cambridge (GB); Karen Howarth, Cambridge (GB); and Michael Epstein, Cambridge (GB)
Assigned to INIVATA LTD., Cambridge (GB)
Filed by Inivata Ltd., Cambridge (GB)
Filed on Oct. 5, 2021, as Appl. No. 17/494,669.
Application 17/494,669 is a continuation of application No. 16/389,596, filed on Apr. 19, 2019, granted, now 11,168,371.
Application 16/389,596 is a continuation of application No. PCT/GB2018/051688, filed on Jun. 18, 2018.
Claims priority of application No. 1709675 (GB), filed on Jun. 16, 2017.
Prior Publication US 2022/0162707 A1, May 26, 2022
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6886 (2018.01); C12Q 1/6806 (2018.01); C12Q 1/6853 (2018.01); C12Q 1/686 (2018.01); G16B 20/00 (2019.01); G16B 30/00 (2019.01)
CPC C12Q 1/6886 (2013.01) [C12Q 1/6806 (2013.01); C12Q 1/6853 (2013.01); C12Q 1/686 (2013.01); C12Q 2600/106 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/16 (2013.01); G16B 20/00 (2019.02); G16B 30/00 (2019.02)] 16 Claims
 
1. A method for identifying a genomic fusion, comprising:
(a) performing a polymerase chain reaction (PCR) on a nucleic acid sample from a subject using a plurality of forward primers and a plurality of reverse primers to produce amplification products;
(b) sequencing the amplification products produced in step (a), or amplification product made from the same, to produce sequence reads; and
(c) identifying sequence reads that correspond to a fusion between the first and second regions by:
(i) identifying sequence reads which have the sequence of a forward primer used in step (a), or complement thereof, at one end and the sequence of a reverse primer used in step (a), or a complement thereof, at the other end;
(ii) for each sequence read identified in (c)(i), determining whether the sequence read comprises a sequence that matches a sequence in a first region of the reference human genome and is downstream of the sequence of the forward primer; and
(iii) for each sequence read identified in (c)(i), determining whether the sequence read comprises a sequence that matches a sequence in a second region of the reference human genome and is downstream of the sequence of the reverse primer;
wherein an amplification product that corresponds to a genomic fusion comprises the sequence of a forward primer used in step (a) at one end, the sequence of a reverse primer used in step (a) at the other end, a sequence that matches a sequence in the first region of the reference human genome, and a sequence that matches a sequence in the second region of the reference human genome.