SAMPLE SERIES TO DIFFERENTIATE TARGET NUCLEIC ACIDS FROM CONTAMINANT NUCLEIC ACIDS
This disclosure provides methods, compositions and kits for determining if nucleic acids detected in a sample such as a clinical sample are derived from contaminant pathogens or clinically-relevant pathogens.
1 .- 135 . (canceled)
136 . A composition comprising: a plurality of containers comprising a first container, a second container, and a third container, wherein:
(a) the first container comprises a first plasma comprising a first concentration of cell-free nucleic acids;
(b) the second container comprises a second plasma comprising a second concentration of cell-free nucleic acids, wherein the second plasma comprises a dilution of the first plasma;
(c) the third container comprises a third plasma comprising a third concentration of cell-free nucleic acids, wherein the third plasma comprises a dilution of the second plasma; and
wherein intact bacteria, fungus, or parasites have been removed from the first plasma, the second plasma, and the third plasma.
137 . The method of claim 136 , wherein the intact bacteria, fungus, or parasites have been removed by centrifugation.
138 . The method of claim 136 , wherein the intact bacteria, fungus, or parasites have been removed by filtration.
139 . The composition of claim 136 , wherein the first concentration of cell-free nucleic acids, the second concentration of cell-free nucleic acids, and the third concentration of cell-free nucleic acids comprise microbial cell-free nucleic acids (mcfNA).
140 . The composition of claim 139 , wherein the mcfNA comprises microbial cell-free DNA (mcfDNA).
141 . The composition of claim 139 , wherein the mcfNA comprises microbial cell-free RNA (mcfRNA).
142 . The composition of claim 136 , wherein the first plasma comprises a concentration of spike-in synthetic nucleic acids, the second plasma comprises a concentration of spike-in synthetic nucleic acids, and the third plasma comprises a concentration of spike-in synthetic nucleic acids.
143 . The composition of claim 142 , wherein a dilution factor between the concentration of spike-in synthetic nucleic acids in the first container and the concentration of spike-in synthetic nucleic acids in the second container is about the same as a dilution factor between the cell-free nucleic acid concentration of the first container and the cell-free nucleic acid concentration of the second container.
144 . The composition of claim 142 , wherein the spike-in synthetic nucleic acids in the first plasma comprise at least 1000 unique sequences.
145 . The composition of claim 142 , wherein the spike-in synthetic nucleic acids comprise less than 500 base pairs or nucleotides in length.
146 . The composition of claim 142 , wherein the spike-in synthetic nucleic acids comprise DNA.
147 . The composition of claim 142 , wherein the spike-in synthetic nucleic acids comprise RNA.
148 . The composition of claim 136 , wherein the first plasma, the second plasma, and the third plasma each further comprise reagents for processing a sample type.
149 . The composition of claim 136 , wherein the first plasma, the second plasma, and the third plasma each comprises a buffer.
150 . The composition of claim 149 , wherein the buffer comprises a dilution buffer.