Error correction in amplification of samples
Disclosed herein are methods and systems for correcting errors in sample amplification, including the errors occurred in determining the number of targets in samples. In some embodiments, the method comprises: stochastically barcoding a plurality of targets in the samples using oligonucleotides comprising stochastic barcodes to generate stochastically barcoded targets; contacting one or more defined barcoded primers with each of the one or more samples; and determining an amplification noise.
1. A method comprising:
stochastically barcoding a plurality of targets in a sample using a plurality of stochastic barcodes to generate stochastically barcoded targets, wherein each stochastic barcode comprises a molecular label and an identical sample label, and wherein the molecular labels of at least two stochastic barcodes differ from one another by at least one nucleotide;
pooling the stochastically barcoded targets to generate a pool of stochastically barcoded targets;
contacting one or more defined barcoded primers with the pool of stochastically barcoded targets, wherein each of the one or more defined barcoded primers comprises a defined sample label and a defined molecular label, and wherein the defined barcoded primers are variants of the stochastic barcodes;
amplifying the stochastically barcoded targets and the one or more defined barcoded primers to generate a plurality of amplified stochastically barcoded targets and a plurality of amplified defined barcoded primers; and
detecting the plurality of amplified stochastically barcoded targets and the plurality of amplified defined barcoded primers by detecting the molecular labels present on the plurality of amplified stochastically barcoded targets and the defined molecular labels present on the plurality of amplified defined barcoded primers,
wherein the number of molecular labels with different sequences associated with each of the plurality of targets in the plurality of amplified stochastically barcoded targets detected indicates a pre-correction number of the target,
wherein the number of defined molecular labels in the plurality of amplified defined barcoded primers indicate an amplification noise, and
wherein a difference between the number of molecular labels with different sequences associated with each of the plurality of targets and number of defined molecular labels with different sequences indicate the number of copies of the target.
2. The method of claim 1 , wherein contacting the one or more defined barcoded primers with the plurality of stochastic barcodes comprises introducing the one or more defined barcoded primers at the same concentration of the plurality of stochastic barcodes.
3. The method of claim 1 , wherein the defined molecular label is 5-20 nucleotides in length, or wherein the defined molecular label and the molecular label have the same length.
4. The method of claim 1 , wherein the molecular label of one or more of the stochastic barcodes and the defined molecular labels of one or more of the one or more defined barcoded primers have the same sequence.
5. The method of claim 1 , wherein the one or more defined barcoded primers comprise one or more types of defined barcoded primers.
6. The method of claim 5 , wherein the defined molecular labels of one type of defined barcoded primers differ from one another by at least one nucleotide.
7. The method of claim 6 ,
wherein some defined molecular labels of different types of defined barcoded primers have the same sequence,
wherein different types of defined barcoded primers have the same length,
wherein the lengths of different types of defined barcoded primers differ by at most 10 nucleotides, or
wherein the defined sample labels of different types of defined barcoded primers have different sequences.
8. The method of claim 6 , wherein the stochastic barcodes and the one or more types of defined barcoded primers have the same length.
9. The method of claim 1 , wherein: (i) the Hamming distance between the sample labels of the stochastic barcodes and the defined sample labels of the defined barcoded primers is at least 2; and/or (ii) the sample label and the defined sample label have the same length.
10. The method of claim 1 , further comprising removing at least 50% of the stochastic barcodes not incorporated into the stochastically barcoded targets and the one or more defined barcoded primers from the sample.
11. The method of claim 10 ,
wherein less than 10% of the unincorporated stochastic barcodes are not removed from the sample,
wherein the percentage of the one or more defined barcoded primers not removed from the sample is within 10% of the percentage of the plurality of the stochastic barcodes not removed from the sample.
12. The method of claim 1 ,
wherein determining the pre-correction number of each of the plurality of targets using the molecular label comprises:
determining sequences of molecular labels of the amplified stochastically barcoded targets; and
determining the number of the molecular labels with different sequences, and
wherein determining the number of defined molecular labels with different sequences in the plurality of amplified defined barcoded primers comprises:
determining sequences of the defined molecular labels of the amplified defined barcoded primers; and
determining the number of defined molecular labels with different sequences.
13. The method of claim 1 , wherein determining the amplification noise comprises one or more of:
determining the number of defined molecular labels in the plurality of amplified defined barcoded primers with different sequences for each type of amplified defined barcoded primers,
determining the average number of defined molecular labels in the plurality of amplified defined barcoded primers with different sequences for different types of amplified defined barcoded primers, and
determining the maximum number of defined molecular labels in the plurality of amplified stochastically barcoded targets and the plurality of amplified defined barcoded primers with different sequences for different types of amplified defined barcoded primers.
14. The method of claim 1 , wherein the amplification noise comprises noise caused by PCR crossover.
15. The method of claim 1 , wherein (i) the sample comprises a single cell, (ii) the sample comprises a single cell, and wherein the method comprises lysing the single cell, or (iii) the sample comprises a lysate of a single cell.
16. A method comprising:
stochastically barcoding a plurality of targets in a sample using a plurality of stochastic barcodes, in the presence of one or more defined barcoded primers, to generate stochastically barcoded targets, wherein each stochastic barcode comprises a molecular label, wherein the molecular labels of at least two stochastic barcodes differ from one another by at least one nucleotide, wherein each of the one or more defined barcoded primers comprises a defined molecular label, and wherein the defined barcoded primers are variants of the stochastic barcodes;
amplifying the stochastically barcoded targets and the one or more defined barcoded primers to generate a plurality of amplified stochastically barcoded targets and a plurality of amplified defined barcoded primers; and
detecting the plurality of amplified stochastically barcoded targets and the plurality of amplified defined barcoded primers by detecting the molecular labels present on the plurality of amplified stochastically barcoded targets and the defined molecular labels present on the plurality of amplified defined barcoded primers,
wherein the number of molecular labels with different sequences associated with each of the plurality of targets in the plurality of amplified stochastically barcoded targets detected indicates a pre-correction number of the target,
wherein the number of defined molecular labels in the plurality of amplified defined barcoded primers indicate an amplification noise, and
wherein a difference between the number of molecular labels with different sequences associated with each of the plurality of targets and number of defined molecular labels with different sequences indicate the number of copies of the target.
17. A method comprising:
stochastically barcoding a plurality of targets in a sample in a plurality of partitions using a plurality of stochastic barcodes to generate stochastically barcoded targets, wherein for each partition, each stochastic barcode comprises a molecular label and an identical sample label, and the molecular labels of at least two stochastic barcodes differ from one another by at least one nucleotide;
pooling the stochastically barcoded targets from the plurality of partitions to generate a pool of stochastically barcoded targets;
contacting defined barcoded primers of one or more types of defined barcoded primers with the pool of stochastically barcoded targets, wherein each defined barcoded primer comprises a defined sample label and a defined molecular label, wherein the defined sample labels of defined barcoded primers of the same type of defined barcoded primers have the same sequence, wherein the defined sample labels of different types of defined barcoded primers have different sequences, wherein the sample labels of the stochastic barcodes and the defined sample labels are variants of the sample label;
amplifying the stochastically barcoded targets and the one or more defined barcoded primers to generate a plurality of amplified stochastically barcoded targets and a plurality of amplified defined barcoded primers; and
detecting the plurality of amplified stochastically barcoded targets and the plurality of amplified defined barcoded primers:
wherein the number of molecular labels with different sequences associated with each of the plurality of targets in the plurality of amplified stochastically barcoded targets detected indicates a pre-correction number of the target,
wherein the number of defined molecular labels with different sequences in the plurality of amplified defined barcoded primers detected indicates an amplification noise, and
wherein a difference between the number of molecular labels with different sequences associated with each of the plurality of targets and the number of defined molecular labels with different sequences indicate the number of copies of the target.
18. The method of claim 1 , wherein the sample comprises single cells comprising said targets, wherein the single cells comprise one or more cell types, and wherein the one or more cell types comprise one or more of brain cells, heart cells, cancer cells, circulating tumor cells, organ cells, epithelial cells, metastatic cells, benign cells, primary cells, and circulatory cells.
19. The method of claim 16 , wherein the sample comprises single cells comprising said targets, wherein the single cells comprise one or more cell types, and wherein the one or more cell types comprise one or more of brain cells, heart cells, cancer cells, circulating tumor cells, organ cells, epithelial cells, metastatic cells, benign cells, primary cells, and circulatory cells.
20. The method of claim 17 , wherein the sample comprises single cells comprising said targets, wherein the single cells comprise one or more cell types, and wherein the one or more cell types comprise one or more of brain cells, heart cells, cancer cells, circulating tumor cells, organ cells, epithelial cells, metastatic cells, benign cells, primary cells, and circulatory cells.