Identification of Polynucleotides Associated with a Sample

Abstract

Disclosed herein are compositions and methods for sequencing, analyzing, and utilizing samples such as single samples. Also disclosed herein are compositions and methods for matching together two or more sequences from a sample. Also disclosed herein are compositions and methods for expressing and screening molecules of interest.

1 - 385 . (canceled) 
     
     
         386 . A method for producing one or more polynucleotides of interest, comprising:
 obtaining a polynucleotide composition library comprising a plurality of compositions,   wherein each composition is present in a separate container,   wherein each composition comprises a single sample-derived cDNA region comprising a variable region,   wherein each composition comprises a sample identification region,   wherein the nucleotide sequence of each sample identification region is distinct from the nucleotide sequence of the sample identification region of the other sample identification regions present in each separate container in the library, and   wherein the sample identification region is attached to the cDNA region; and   amplifying the polynucleotide library with a set of primers to produce the one or more polynucleotides of interest.   
     
     
         387 . The method of  claim 386 , further comprising: sequencing the one or more polynucleotides of interest; and selecting one or more polynucleotides of interest. 
     
     
         388 . The method of  claim 386 , wherein the set of primers comprises one or more 3′ gene specific primers and, optionally, a 5′ universal primer. 
     
     
         389 . The method of  claim 386 , wherein the cDNA region is attached to the sample identification region by an adapter region. 
     
     
         390 . The method of  claim 389 , wherein the adapter region comprises the nucleotide dG at its 3′ end and the cDNA region comprises the nucleotide C at its 3′ end. 
     
     
         391 . The method of  claim 390 , wherein the adapter region is attached to the cDNA region by binding between the C and dG. 
     
     
         392 . The method of  claim 386 , wherein the variable region is a B cell immunoglobulin variable region. 
     
     
         393 . The method of  claim 386 , wherein the variable region is a T cell receptor variable region. 
     
     
         394 . The method of  claim 386 , wherein each composition further comprises a universal primer region attached to the sample identification region, and wherein the universal primer region is substantially identical in each separate container. 
     
     
         395 . The method of  claim 386 , wherein the single sample comprises a plurality of B cells, a single B cell and one or more other cells, a single B cell, or a single T cell. 
     
     
         396 . The method of  claim 395 , wherein the single B cell is a single plasmablast. 
     
     
         397 . A method for analyzing sequencing data, comprising:
 obtaining a dataset associated with a plurality of polynucleotides, wherein the dataset comprises sequencing data for the plurality of polynucleotides, wherein each polynucleotide in the plurality of polynucleotides comprises a sample identification region, and wherein each sample identification region on each polynucleotide is unique to a single sample, wherein the sequence of the sample identification region of each polynucleotide from a first single sample is distinct from the sequence of the sample identification region of the other polynucleotides in the plurality of polynucleotides from one or more samples distinct from the first single sample; and   analyzing, by a computer, the dataset to match together data associated with polynucleotides with identical sample identification regions, wherein a match indicates that the polynucleotides originated from the same sample.   
     
     
         398 - 433 . (canceled) 
     
     
         434 . The method of  claim 386 , wherein each composition comprising the single sample-derived cDNA region comprises cDNA molecules that encode (a) cognate pairs of immunoglobulin heavy and light chain variable regions, or (b) cognate pairs of T cell receptor alpha and beta chain sequences. 
     
     
         435 . The method of  claim 434 , where each cDNA encoding the cognate pair independently comprises an identical sample identification region. 
     
     
         436 - 440 . (canceled) 
     
     
         441 . The method of  claim 397 , wherein one or both polynucleotides comprise a variable region. 
     
     
         442 . The method of  claim 397 , wherein obtaining the dataset comprises obtaining the plurality of polynucleotides and sequencing the plurality of polynucleotides to experimentally determine the dataset. 
     
     
         443 . The method of  claim 397 , wherein obtaining the dataset comprises receiving the dataset directly or indirectly from a third party that has sequenced the plurality of polynucleotides to experimentally determine the dataset. 
     
     
         444 . The method of  claim 397 , wherein the single sample is a single cell or comprises a single cell. 
     
     
         445 . The method of  claim 397 , wherein the single sample comprises a plurality of B cells, a single B cell and one or more other cells, a single B cell, or a single T cell. 
     
     
         446 . The method of  claim 397 , wherein one or both polynucleotides encode (a) cognate pairs of immunoglobulin heavy and light chain variable regions, or (b) cognate pairs of T cell receptor alpha and beta chain sequences.