Systems and methods to detect rare mutations and copy number variation
The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.
1. A method, comprising:
a) providing a population of circulating cell-free DNA (“cfDNA”) molecules obtained from a bodily sample from a subject;
b) converting the population of circulating cfDNA molecules into a population of non-uniquely tagged parent polynucleotides, wherein each of the non-uniquely tagged parent polynucleotides comprises (i) a sequence from a circulating cfDNA molecule of the population of circulating cfDNA molecules, and (ii) an identifier sequence comprising one or more polynucleotide barcodes;
c) amplifying the population of non-uniquely tagged parent polynucleotides to produce a corresponding population of amplified progeny polynucleotides;
d) sequencing the population of amplified progeny polynucleotides to produce a set of sequence reads;
e) mapping sequence reads of the set of sequence reads to a reference sequence from a human genome;
f) grouping the sequence reads into families, each of the families comprising sequence reads comprising the same identifier sequence and having (1) the same start positions at which the sequencing reads are determined to start mapping to the reference sequence and (2) the same stop positions at which the given sequencing read is determined to stop mapping to the reference sequence, whereby each of the families comprises sequence reads amplified from the same non-uniquely tagged parent polynucleotide;
g) at each genetic locus of a plurality of genetic loci in the reference sequence, collapsing sequence reads in each family to yield a base call for each family at the genetic locus; and
h) determining a frequency of one or more bases called at the locus from among the families.
2. The method of claim 1 , further comprising detecting, at one or more loci, at least one single nucleotide variant and at least one copy number variant.
3. The method of claim 1 , wherein converting comprises any of blunt-end ligation or sticky end ligation.
4. The method of claim 1 , wherein determining the frequency comprises detecting a rare mutation.
5. The method of claim 1 , further comprising generating a set of consensus sequences from the sequence reads, and detecting a presence of sequence variations in the set of consensus sequences compared with the reference sequence.
6. The method of claim 1 , wherein mapping the sequence reads comprises using information about a length of each of the sequence reads.
7. The method of claim 1 , further comprising filtering out sequence reads that fail to meet a quality threshold.
8. The method of claim 1 , wherein the population of circulating cfDNA molecules is tagged with from 10 to 100,000 different identifiers.
9. The method of claim 1 , further comprising selectively enriching regions from a genome or transcriptome of the subject prior to sequencing.
10. The method of claim 1 , further comprising removing a subset of the sequence reads from further analysis prior to (f).
11. The method of claim 1 , wherein the population of circulating cfDNA molecules is tagged with from 50 to 10,000 different identifiers.