US 12,227,803 B2
Methods and compositions for efficient base calling in sequencing reactions
Radoje Drmanac, Los Altos Hills, CA (US)
Assigned to Complete Genomics, Inc., San Jose, CA (US)
Filed by Complete Genomics, Inc., San Jose, CA (US)
Filed on Nov. 10, 2021, as Appl. No. 17/523,706.
Application 17/523,706 is a continuation of application No. 15/359,277, filed on Nov. 22, 2016, granted, now 11,214,832.
Application 15/359,277 is a continuation of application No. 14/094,630, filed on Dec. 2, 2013, granted, now 9,523,125.
Application 14/094,630 is a continuation of application No. 12/361,507, filed on Jan. 28, 2009, granted, now 8,617,811, issued on Dec. 31, 2013.
Claims priority of provisional application 61/024,396, filed on Jan. 29, 2008.
Claims priority of provisional application 61/024,110, filed on Jan. 28, 2008.
Prior Publication US 2022/0275442 A1, Sep. 1, 2022
This patent is subject to a terminal disclaimer.
Int. Cl. C12P 19/34 (2006.01); C12Q 1/686 (2018.01); C12Q 1/6869 (2018.01); C12Q 1/6874 (2018.01); C12Q 1/6876 (2018.01); C12Q 1/68 (2018.01)
CPC C12Q 1/6874 (2013.01) [C12Q 1/686 (2013.01); C12Q 1/6869 (2013.01); C12Q 1/6876 (2013.01); C12Q 1/68 (2013.01); C12Q 2565/102 (2013.01); C12Q 2565/1025 (2013.01)] 6 Claims
OG exemplary drawing
 
1. A method for determining nucleotide sequences from a plurality of different nucleic acid templates disposed at different array positions on a surface of a nucleic acid array, wherein each array position of the different array positions comprises a plurality of copies of one nucleic acid template of the plurality of different nucleic acid templates, wherein the method comprises conducting multiple cycles of sequencing-by-synthesis at each of the different array positions,
wherein in each cycle of the multiple cycles of sequencing-by-synthesis, at each array position of the different array positions, a nucleotide selected from A, T, G and C anneals to a complementary nucleotide at a detection position of the plurality of copies of the one nucleic acid template, wherein at least three of the nucleotides selected from A, T, G and C are labeled with a fluorescent label that produces a fluorescent signal or at least three of the nucleotides selected from A, T, G and C are labeled with a luminescent label that produces a luminescent signal,
wherein each cycle of the multiple cycles of sequencing-by-synthesis comprises
(i) at each of a plurality of first array positions of the different array positions, binding a first nucleotide selected from A, T, G and C to a first complementary nucleotide at the detection position of the plurality of copies of the one nucleic acid template disposed at the first array positions, wherein the first nucleotide is complementary to the first complementary nucleotide,
(ii) at each of a plurality of second array positions of the different array positions, binding a second nucleotide selected from A, T, G and C to a second complementary nucleotide at the detection position of the plurality of copies of the one nucleic acid template disposed at the second array positions, wherein the second nucleotide is complementary to the second complementary nucleotide,
(iii) at each of a plurality of third array positions of the different array positions, binding a third nucleotide selected from A, T, G and C to a third complementary nucleotide at the detection position of the plurality of copies of the one nucleic acid template disposed at the third array positions, wherein the third nucleotide is complementary to the third complementary nucleotide,
(iv) at each of a plurality of fourth array positions, binding a fourth nucleotide selected from A, T, G and C to a fourth complementary nucleotide at the detection position of the plurality of copies of the one nucleic acid template disposed at the fourth array positions, wherein the fourth nucleotide is complementary to the fourth complementary nucleotide,
wherein each of the first nucleotide, the second nucleotide, the third nucleotide and the fourth nucleotide is one of A, T, G and C,
wherein none of the first nucleotide, the second nucleotide, the third nucleotide and the fourth nucleotide is the same, wherein the plurality of first array positions, the plurality of second array positions, the plurality of third array positions and the plurality of fourth array positions are non-overlapping subsets of the different array positions on the surface of the nucleic acid array;
wherein the first nucleotide, the second nucleotide, the third nucleotide and the fourth nucleotide are labeled with the same fluorescent label or luminescent label but produce fluorescent or luminescent signals having different intensities, or
wherein three of the first nucleotide, the second nucleotide, the third nucleotide and the fourth nucleotide are labeled with the same fluorescent label or luminescent label but produce fluorescent or luminescent signals having different intensities and one of the first nucleotide, the second nucleotide, the third nucleotide and the four nucleotide has no fluorescent label or luminescent label,
wherein the first nucleotide, the second nucleotide, the third nucleotide and the fourth nucleotide are identified and distinguished from each other based on intensities of their fluorescent or luminescent signals, and
(v) determining whether a complementary nucleotide at a detection position of the plurality of copies of the one nucleic acid template at each of the plurality of first array positions, the plurality of second array positions, the plurality of third array positions and the plurality of fourth array positions is A, T, G or C, by detecting an intensity of fluorescent or luminescent signal at each of the plurality of first array positions, the plurality of second array positions, the plurality of third array positions and the plurality of fourth array positions.