Target-associated molecules for characterization associated with biological targets

1. A method for determining an abundance of a biological target from a biological sample, the method comprising:

providing a set of target-associated molecules comprising target-associated regions with sequence similarity to a target sequence region of the biological target;

generating at least one spike-in mixture, wherein the generation of the at least one spike-in mixture comprises amplification of the set of target-associated molecules and nucleic acid molecules from the biological sample, the nucleic acid molecules being associated with the target sequence region;

sequencing the at least one spike-in mixture to generate sequencing results; and

determining the abundance of the biological target based on the sequencing results.

2. The method of claim 1 , further comprising:

determining a characterization of a medical condition based on the abundance of the biological target.

3. The method of claim 2 , wherein the medical condition is a cancer condition and the target sequence region comprises a mutation associated with the cancer condition.

4. The method of claim 2 , wherein the medical condition is sickle cell disease.

5. The method of claim 2 , wherein:

generating the spike-in mixture further comprises amplification of reference-associated molecules having sequence similarity to a reference sequence region of a biological reference; and

the characterization of the medical condition is further based on an abundance of the reference sequence indicated by the sequencing results.

6. The method of claim 1 , wherein:

generating the spike-in mixture further comprises amplification of reference molecules that have an expected copy number of the biological target; and

determining the abundance of the biological target comprises determining a copy number for the biological target in the nucleic acid molecules from the biological sample based on a comparison of sequencing results associated with the reference molecules with sequencing results associated with the nucleic acid molecules from the biological sample.

7. The method of claim 1 , wherein the abundance of the biological target is further based on one or more temporal indicators that indicate different stages of generation of the spike-in mixture.

8. The method of claim 1 , wherein the abundance of the biological target is further based on a plurality of temporal indicators, each of the plurality of temporal indicators indicating a time associated with corresponding sequencing data, the method further comprising determining a change in abundance of the biological target over time using the temporal indicators.

9. The method of claim 1 , wherein sequence similarity means the target-associated region has at least a threshold proportion of nucleotides that match the target sequence region of the biological target.

10. The method of claim 1 , wherein the target-associated molecules further comprise target variation regions that have an insertion, deletion, or replacement relative to a corresponding region of the biological target.

11. The method of claim 1 , wherein the target-associated molecules further comprise a sequencing region that includes one or more sequencing primers or adapter sequences.

12. The method of claim 1 , further comprising:

generating a list of candidate target sequences;

filtering out candidate target sequences that have specified types of mutations or polymorphisms to obtain a filtered list of candidate sequences with relative invariance across subjects of a population;

identifying primers for the filtered list of candidate sequences; and

selecting one of the filtered list of candidate sequences as the target sequence based on the identified primers.

13. The method of claim 1 , further comprising causing, based on the abundance of the biological target, application of a treatment on a subject from which the biological sample was collected.

14. The method of claim 1 , wherein generating the at least one spike-in mixture comprises transforming at least a portion of one of the target-associated molecules or the nucleic acid molecules from the biological sample into another form.

15. The method of claim 1 , wherein determining the abundance of the biological target comprises performing a normalization based on sequencing data for the target-associated molecules.

16. The method of claim 1 , further comprising:

determining an initial abundance of the target-associated molecules; and

modifying the initial abundance of the target-associated molecules, based on an expected abundance of the target sequence, by at least one of dilution or amplification.

17. The method of claim 1 , further comprising:

determining an initial abundance of the target-associated molecules; and

determining a correction factor based on the initial abundance, wherein the determined abundance of the biological target is further based on the correction factor.

18. The method of claim 1 , wherein the abundance of the biological target is determined based on a statistical combination of abundances determined for multiple loci of the biological target.

19. The method of claim 1 , wherein generating the at least one spike-in mixture comprises:

pre-amplifying the biological sample using a set of non-specific primers;

dividing the pre-amplified sample into a plurality of portions; and

amplifying each portion using allele-specific PCR process to generate the at least one spike-in mixture.

20. A method for quantification of a biological target from a biological sample, the method comprising:

generating a first set of target-associated molecules comprising:

first target-associated regions with sequence similarity to a first target sequence region of the biological target; and

target variation regions with sequence dissimilarity to a sequence region of the biological target;

generating a first set of reference-associated molecules comprising:

first reference-associated regions with sequence similarity to a first reference sequence region of a biological reference; and

reference variation regions with sequence dissimilarity to a sequence region of the biological reference;

generating at least one spike-in mixture, wherein the generation of the at least one spike-in mixture comprises:

co-amplification of the first set of target-associated molecules and first nucleic acid molecules from the biological sample, wherein the first nucleic acid molecules are associated with the first target sequence region; and

co-amplification of the first set of reference-associated molecules and second nucleic acid molecules from the biological sample, wherein the second nucleic acid molecules are associated with the first reference sequence region;

determining a count for the biological target, a count for the first set of target-associated molecules, a count for the biological reference, and a count for the first set of reference-associated molecules, based on sequencing of the at least one spike-in mixture;

determining a first target-associated count ratio and a first reference-associated count ratio based on the count for the biological target, the count for the first set of target-associated molecules, the count for the biological reference, and the count for the first set of reference-associated molecules; and

quantifying the biological target in the biological sample based on the first target-associated count ratio and the first reference-associated count ratio.

21. The method of claim 20 , wherein quantifying the biological target comprises determining a copy number variation of the biological target.

22. The method of claim 21 , further comprising facilitating diagnosis of a medical condition using the copy number variation.

23. The method of claim 20 , wherein the co-amplification of the first set of target-associated molecules and first nucleic acid molecules comprises an allele-specific PCR process.

24. The method of claim 23 , wherein the allele-specific PCR process is for sickle cell disease detection.

25. The method of claim 20 , wherein the co-amplification of the first set of target-associated molecules and first nucleic acid molecules from the biological sample and the co-amplification of the first set of reference-associated molecules and second nucleic acid molecules from the biological sample occurs in a single container.