Genome fractioning

Abstract

Disclosed herein are compositions and methods related to the elimination of molecules of a selected sequence from a nucleic acid sample or from an sequence dataset resulting from the sequencing of a sample, for example to exclude such molecules from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.

1 .- 12 . (canceled) 
     
     
         13 . A composition comprising:
 a first plurality of double stranded nucleic acid molecules, wherein the double stranded nucleic acid molecule of the first plurality comprises a first nucleic acid sequence comprising a sequence of interest and adaptors at a 5′ end and a 3′ end of the first nucleic acid sequence;   a second plurality of double stranded nucleic acid molecules, wherein the double stranded nucleic acid molecule of the second plurality comprises a second nucleic acid sequence comprising an unwanted sequence and adaptors at a 5′ end and a 3′ end of the second nucleic acid sequence; and   a nucleic acid guided nuclease and a guide nucleic acid specifically bound to the unwanted sequence.   
     
     
         14 . The composition of  claim 13 , wherein the guide nucleic acid is RNA. 
     
     
         15 . The composition of  claim 13 , wherein the unwanted sequence comprises ribosomal RNA sequences, sequences encoding globin proteins, sequences encoding a transposon, sequences encoding retroviral sequences, sequences comprising telomere sequences, sequences comprising sub-telomeric repeats, sequences comprising centromeric sequences, sequences comprising intron sequences, sequences comprising Alu repeats, sequences comprising SINE repeats, sequences comprising LINE repeats, sequences comprising dinucleic acid repeats, sequences comprising trinucleic acid repeats, sequences comprising tetranucleic acid repeats, sequences comprising poly-A repeats, sequences comprising poly-T repeats, sequences comprising poly-C repeats, sequences comprising poly-G repeats, sequences comprising AT-rich sequences, sequences comprising GC-rich sequences, or a combination thereof. 
     
     
         16 . The composition of  claim 13 , wherein the unwanted sequence comprises ribosomal RNA sequences. 
     
     
         17 . The composition of  claim 13 , wherein the nucleic acid guided nuclease is a Cas9 endonuclease. 
     
     
         18 . The composition of  claim 13 , wherein the second plurality of double stranded nucleic acid molecules comprises at least 10% of the composition. 
     
     
         19 . The composition of  claim 13 , wherein the double stranded nucleic acid molecule is a cDNA. 
     
     
         20 . The composition of  claim 13 , wherein the double stranded nucleic acid molecule is a genomic DNA. 
     
     
         21 . The composition of  claim 13 , wherein the double stranded nucleic acid molecule is about 100 to about 1000 nucleotides in length. 
     
     
         22 . The composition of  claim 13 , wherein the adaptor comprises T7 promoter sequence. 
     
     
         23 . The composition of  claim 13 , wherein the adaptor comprises a universal adaptor.