METHODS AND COMPOSITIONS FOR ANALYZING NUCLEIC ACIDS
Provided herein are methods and compositions for analyzing nucleic acids within partitions loaded with a high occupancy. In some cases, partitions may be provided that include portions of a nucleic acid sample, The partitions may also include processing materials. The portions of the nucleic acid sample may be reacted with the processing materials. In some cases an imaging system may be used to scan the partitions. Signals generated from scanning the partitions may be used to identify a plurality of nucleic acid molecules.
1 . A method comprising:
(a) providing a plurality of partitions comprising at least 1,000 partitions, wherein each partition of said plurality of partitions comprises:
(i) a portion of a nucleic acid sample; and
(ii) processing materials,
wherein a distribution of nucleic acid material of said nucleic acid sample to partition has an average of at least 10 femtograms of said nucleic acid material per partition and wherein each partition comprises an average volume of said plurality of partitions is less than or equal to 10 picolitre (pl);
(b) reacting said processing materials of each partition of said plurality of partitions with said portion of said nucleic acid sample of each partition of said plurality of partitions;
(c) detecting signals from at least a subset of said plurality of partitions; and
(d) using said signals detected in (c) to identify a plurality of nucleic acid molecules of said nucleic acid sample.
2 . The method of claim 1 , wherein said plurality of partitions comprises at least 10,000 partitions.
3 . The method of claim 1 , wherein said plurality of partitions comprises at least 1,000,000 partitions.
4 . The method of claim 1 , wherein said distribution of nucleic acid material to partition has an average of at least 100 femtograms of said nucleic acid sample per partition.
5 . The method of claim 1 , wherein said distribution of nucleic acid material to partition has an average of at least 200 femtograms of said nucleic acid sample per partition.
6 . The method of claim 1 , wherein said average volume of said plurality of partitions is less than or equal to 5 pl.
7 . The method of claim 1 , wherein said average volume of said plurality of partitions is less than or equal to 1 pl.
8 . The method of claim 1 , wherein said nucleic acid sample comprises at least 0.1 microgram of nucleic acid material.
9 . The method of claim 1 , wherein said nucleic acid sample comprises at least 0.5 microgram of nucleic acid material.
10 . The method of claim 1 , wherein said nucleic acid sample comprises at least 1.0 microgram of nucleic acid material.
11 . The method of claim 1 , wherein said plurality of partitions are part of a gel matrix.
12 . The method of claim 1 , wherein said plurality of partitions are part of an emulsion.
13 . The method of claim 1 , wherein said nucleic acid sample comprise cell-free nucleic acid molecules.
14 . The method of claim 13 , wherein said cell-free nucleic acid molecules comprise deoxyribonucleic acid molecules.
15 . The method of claim 13 , wherein said cell-free nucleic acid molecules comprise ribonucleic acid molecules.
16 . A method comprising:
(a) providing a plurality of partitions comprising at least 1,000,000 partitions, wherein each partition of said plurality of partitions comprises:
(i) a portion of a nucleic acid sample; and
(ii) processing materials,
wherein a distribution of nucleic acid material of said nucleic acid sample to partition has an average of at least 10 femtograms of said nucleic acid material per partition;
(b) reacting said processing materials of each partition of said plurality of partitions with said portion of said nucleic acid sample of each partition of said plurality of partitions;
(c) detecting signals from at least a subset of said plurality of partitions; and
(d) using said signals detected in (c) to identify a plurality of nucleic acid molecules of said nucleic acid sample.
17 . The method of claim 16 , wherein said plurality of partitions comprises at least 10,000,000 partitions.
18 . The method of claim 17 , wherein said plurality of partitions comprises at least 20,000,000 partitions.
19 . The method of claim 16 , wherein said distribution of nucleic acid material to partition has an average of at least 100 femtograms of said nucleic acid sample per partition.
20 . The method of claim 16 , wherein said distribution of nucleic acid material to partition has an average of at least 200 femtograms of said nucleic acid sample per partition.