Cell free DNA diagnostic testing standards
Embodiments of the invention include methods and compositions for producing standards for noninvasive prenatal genetic diagnostics and for the detection and monitoring of cancer. The compositions can include a plurality of different nucleosomal DNA fragments derived from either primary cells or cell lines and can include one or more synthetic oligonucleotides. The amount of the different nucleosomal DNA fragments can be varied so as to simulate naturally occurring cell free DNA samples obtained from the blood of the pregnant woman or naturally occurring cell free DNA samples obtained from the blood of cancer patients.
1. A kit, comprising two or more nucleic acid standard compositions for analyzing circulating tumor DNA, each standard composition comprising a mixture of a first nucleosomal ladder nucleic acid preparation generated in vitro from a cancer cell source and a second nucleosomal ladder nucleic acid preparation generated in vitro from a matched non-cancer cell source, wherein the first nucleosomal ladder nucleic acid preparation and the second nucleosomal ladder nucleic acid preparation are generated in vitro by MNase treatment, wherein the ratio of the quantity of the first nucleosomal ladder nucleic acid preparation and the quantity of the second nucleosomal ladder nucleic acid preparation in each nucleic acid standard composition is different, wherein the first nucleosomal ladder nucleic acid preparation comprises between 0.01% to 20% of the total nucleosomal nucleic acids in at least two of the nucleic acid standard compositions, and wherein a copy number of a chromosomal region known to exhibit copy number variation in cancer is different in the first nucleosomal ladder nucleic acid preparation compared to the second nucleosomal ladder nucleic acid preparation.
2. The kit of claim 1 , wherein the kit comprises between 2 and 20 nucleic acid standard compositions.
3. The kit of claim 1 , wherein the kit comprises between 5 and 10 nucleic acid standard compositions.
4. The kit of claim 1 , wherein the kit comprises at least one nucleic acid standard composition in which the quantity of the first nucleosomal ladder nucleic acid preparation comprises between 0.01% to 10% of the total nucleic acids of the nucleic acid standard composition.
5. The kit of claim 1 , wherein the kit comprises at least two nucleic acid standard composition in which the quantity of the first nucleosomal ladder nucleic acid preparation comprises between 0.01% to 1% of the total nucleic acids of the nucleic acid standard composition.
6. The kit of claim 1 , wherein the kit comprises at least two nucleic acid standard composition in which the quantity of the first nucleosomal ladder nucleic acid preparation comprises between 1% to 10% of the total nucleic acids of the nucleic acid standard composition.
7. The kit of claim 1 , wherein at least one of the nucleic acid standard compositions further comprises between 0.01 and 10% of total nucleic acids in the nucleic acid standard composition, of a synthetic oligonucleotide between 50 and 500 base pairs in length comprising at least 50 contiguous nucleotides having a sequence that is at least 90% identical to a genomic sequence comprising or flanking a mutation correlated with cancer selected from a single nucleotide variant, an indel, or a gene fusion junction.
8. A kit comprising:
(a) two or more nucleic acid standard compositions each in a separate chamber, tube, or vessel and each standard composition comprising a mixture of a first nucleosomal ladder nucleic acid preparation generated in vitro from a cancer cell source and a second nucleosomal ladder nucleic acid preparation generated in vitro from a matched non-cancer cell source, wherein the first nucleosomal ladder nucleic acid preparation and the second nucleosomal ladder nucleic acid preparation are generated in vitro by MNase treatment, wherein the ratio of the quantity of the first nucleosomal ladder nucleic acid preparation and the quantity of the second nucleosomal ladder nucleic acid preparation in each nucleic acid standard composition is different, wherein the first nucleosomal ladder nucleic acid preparation comprises between 0.01% to 20% of the total nucleosomal nucleic acid in at least two of the nucleic acid standard compositions, and wherein a copy number of a chromosomal region known to exhibit copy number variation in cancer is different in the first nucleosomal ladder nucleic acid preparation compared to the second nucleosomal ladder nucleic acid preparation; and
(b) one or more primers for amplifying at least a portion of the chromosomal region known to exhibit copy number variation in cancer.
9. The kit of claim 8 , wherein the kit comprises at least one nucleic acid standard composition in which the quantity of the first nucleosomal ladder nucleic acid preparation comprises between 0.01% and 1% of the total nucleic acids of the nucleic acid standard composition preparations.