Methods for indexing samples and sequencing multiple polynucleotide templates
First Claim
1. A method for preparing nucleic acid sequences for sequencing on an array and identifying subsets of nucleic acid sequences on the array, wherein each subset of nucleic acid sequences is isolated from a different source, said method comprising the steps of:
- (a) providing at least two samples of randomly fragmented double stranded nucleic acid targets, wherein each sample is isolated from a different source;
(b) ligating a universal adaptor to each end of each target of each sample to generate adaptor-target-adaptors, wherein said universal adaptor comprises a region of double stranded nucleic acid and at least one region of single stranded nucleic acid;
(c) amplifying the adaptor-target-adaptors with two or more sample specific amplification primers to generate amplified adaptor-target-adaptors, wherein one of said amplification primers comprises a sample specific tag sequence, and wherein said sample specific tag sequence differentiates amplified adaptor-target-adaptors originating from different samples;
(d) pooling the amplified adaptor-target-adaptors of the different samples;
(e) immobilizing the amplified adaptor-target-adaptors on a solid surface to generate an array of immobilized adaptor-target adaptors;
(f) sequencing the immobilized adaptor-target-adaptors on the array to determine a sequence read of each immobilized adaptor-target-adaptor comprising hybridizing a first sequencing primer to the adaptor-target-adaptors, performing a first sequencing read, and removing the first sequencing primer; and
(g) sequencing the sample specific tag sequence of each immobilized adaptor-target-adaptor by hybridizing a second sequencing primer to the adaptor-target-adaptors and performing a second sequencing read, thereby determining both a nucleic acid sequence of said immobilized adaptor-target-adaptors and identifying the immobilized adaptor-target-adaptors as a member of a subset of nucleic acid sequences on the array.
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Abstract
The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like.
260 Citations
33 Claims
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1. A method for preparing nucleic acid sequences for sequencing on an array and identifying subsets of nucleic acid sequences on the array, wherein each subset of nucleic acid sequences is isolated from a different source, said method comprising the steps of:
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(a) providing at least two samples of randomly fragmented double stranded nucleic acid targets, wherein each sample is isolated from a different source; (b) ligating a universal adaptor to each end of each target of each sample to generate adaptor-target-adaptors, wherein said universal adaptor comprises a region of double stranded nucleic acid and at least one region of single stranded nucleic acid; (c) amplifying the adaptor-target-adaptors with two or more sample specific amplification primers to generate amplified adaptor-target-adaptors, wherein one of said amplification primers comprises a sample specific tag sequence, and wherein said sample specific tag sequence differentiates amplified adaptor-target-adaptors originating from different samples; (d) pooling the amplified adaptor-target-adaptors of the different samples; (e) immobilizing the amplified adaptor-target-adaptors on a solid surface to generate an array of immobilized adaptor-target adaptors; (f) sequencing the immobilized adaptor-target-adaptors on the array to determine a sequence read of each immobilized adaptor-target-adaptor comprising hybridizing a first sequencing primer to the adaptor-target-adaptors, performing a first sequencing read, and removing the first sequencing primer; and (g) sequencing the sample specific tag sequence of each immobilized adaptor-target-adaptor by hybridizing a second sequencing primer to the adaptor-target-adaptors and performing a second sequencing read, thereby determining both a nucleic acid sequence of said immobilized adaptor-target-adaptors and identifying the immobilized adaptor-target-adaptors as a member of a subset of nucleic acid sequences on the array. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
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18. A method for sequencing nucleic acid sequences on an array and identifying subsets of nucleic acid sequences on an array, wherein each subset of nucleic acid sequences is isolated from a different source, said method comprising the steps of:
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(a) providing at least two samples of randomly fragmented double stranded nucleic acid targets, wherein each sample is isolated from a different source; (b) ligating a sample specific tagged adaptor to each end of each target fragment of each sample to generate adaptor-target-adaptors, wherein said tagged adaptor comprises a region of double stranded nucleic acid and at least one region of single stranded nucleic acid and a sample specific tag that differentiates adaptor-target-adaptors originating from different samples; (c) pooling the adaptor-target-adaptors of different samples to generate a pooled sample of adaptor-target adaptors; (d) amplifying the adaptor-target-adaptors with a pair of universal amplification primers to generate amplified adaptor-target-adaptors; (e) immobilising the amplified adaptor-target-adaptors on a solid surface to generate an array of immobilised adaptor-target-adaptors; (f) sequencing the array to determine a sequence read of each immobilised adaptor-target-adaptor comprising hybridizing a first sequencing primer to the adaptor-target-adaptors, performing a first sequencing read, and removing the first sequencing primer and; (g) sequencing the sample specific tag sequence of each immobilised adaptor-target-adaptor by hybridizing a second sequencing primer to the adaptor-target-adaptors and performing a second sequencing read, thereby determining both a nucleic acid sequence of said immobilized adaptor-target-adaptor and identifying the immobilized adaptor-target-adaptor as a member of a subset of nucleic acids on the array. - View Dependent Claims (19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33)
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Specification