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 for tagging a population of 100 to 100,000 haploid human genome equivalents of cell-free deoxyribonucleic acid (cfDNA) molecules, comprising: ligating a set of tags containing 5-10,000 different molecular barcodes to the population of cfDNA molecules before any amplification of the cfDNA molecules to tag at least 20% of the cfDNA molecules, which ligating comprises using more than a 60× molar excess of tags as compared to the cfDNA molecules, and the method further comprises selectively enriching tagged cfDNA molecules for tagged cfDNA molecules comprising sequences of oncogenes or tumor suppressor genes.
2. The method of claim 1 , wherein the tags are components of adapters.
3. The method of claim 2 , wherein the adapters are blunt-ended.
4. The method of claim 1 , comprising enriching the tagged cfDNA for sequences comprising exon sequences of the oncogenes or the tumor suppressor genes.
5. The method of claim 1 , wherein the molecules of tags in the set comprise 5 to 100 different molecular barcode nucleic acid sequences.
6. The method of claim 5 , wherein the molecular barcodes have a length of 5 to 20 nucleotides.
7. The method of claim 1 , wherein the ligating comprises using more than a 100× molar excess of tags as compared to the cfDNA molecules.
8. The method of claim 7 , wherein at least 40% of the cfDNA molecules are tagged.
9. The method of claim 1 , wherein the number of molecules of tags in the set is in more than an 80× molar excess of the cfDNA molecules in the population.
10. The method of claim 2 , wherein the adapters have sticky ends.
11. The method of claim 1 , further comprising amplifying tagged cfDNA prior to the selectively enriching.