Methods and compositions for direct chemical lysis

Abstract

A direct chemical lysis composition includes an assay compatible buffer composition and an assay compatible surfactant. When combined with a specimen storage composition, such compositions prevent undesired modifications to nucleic acid and proteins lysed from cells in the biological sample. Assays of samples from such compositions do not require expensive and time-consuming steps such as centrifugation and prolonged high temperature processing. The direct chemical lysis composition of the present invention permits direct nucleic acid extraction from the cells in the biological sample without the need to decant off the transport media or otherwise exchange the transport media with assay compatible buffers. There is no need to combine the sample with proteinase K or another enzyme to extract nucleic acids from the cells. A method for lysing cells to obtain target nucleic acid for assay and a kit for combining the direct chemical lysis composition with a sample are also contemplated.

What is claimed is: 
     
         1 . A direct chemical lysis composition for combination with a specimen storage composition, the direct chemical lysis composition comprising:
 a) an assay compatible buffer composition; and   b) an assay compatible surfactant.   
     
     
         2 . The direct chemical lysis composition of  claim 1  wherein the assay compatible buffer composition further comprises a buffer component and a metal salt component. 
     
     
         3 . The direct chemical lysis composition of  claim 2  wherein the pH is in the range of about 6.6 to about 10. 
     
     
         4 . The direct chemical lysis composition of  claim 2  wherein the metal salt component is selected from the group consisting of sodium chloride (NaCl), potassium chloride (KCl), sodium acetate (C 2 H 3 NaO 2 ) and ammonium sulfate ((NH 4 ) 2 SO 4 ) and the concentration of metal salt in the direct chemical lysis composition is at least about 0.01 M. 
     
     
         5 . The direct chemical lysis composition of  claim 4  wherein the buffer component concentration is in the range of about 0.2 M to about 2M. 
     
     
         6 . The direct chemical lysis composition of  claim 5  wherein the metal salt component is NaCl and the NaCl concentration is in the range of about 0.01 M to about 1 M. 
     
     
         7 . The direct chemical lysis composition of  claim 6  wherein the buffer component is selected from the group consisting of tris(hydroxymethyl)amino methane and the acid salt of tris(hydroxymethyl)amino methane. 
     
     
         8 . The direct chemical lysis composition of  claim 7  wherein the non-ionic surfactant is a polyethylene glycol based non-ionic surfactant. 
     
     
         9 . The direct chemical lysis composition of  claim 7  wherein the concentration of the non-ionic surfactant is in the range of about 0.01 to about 2 percent (v/v). 
     
     
         10 . The direct chemical lysis composition of  claim 9  wherein the non-ionic surfactant is selected from the group consisting of polyoxyethylene (20) sorbitan monolaurate and polyethylene glycol octylphenyl ether. 
     
     
         11 . The direct chemical lysis composition of  claim 10  wherein the buffer component is the acid salt of tris(hydroxymethyl)amino methane and the buffer component concentration is about 0.75 M, the NaCl concentration is about 0.19 M and the polyethylene glycol octylphenyl ether concentration is about 0.75 percent (v/v). 
     
     
         12 . The direct chemical lysis composition of  claim 11  further comprising glycine. 
     
     
         13 . A method for analyzing samples stored in a specimen storage composition comprising:
 combining the sample with a direct chemical lysis composition comprising a) an assay compatible buffer composition; and b) an assay compatible surfactant;   removing at least a portion of the sample from the specimen storage composition wherein the removed portion also includes the specimen storage composition;   incubating the removed portion of the sample at a temperature that is at least 80° C. for a time sufficient to lyse at least a portion of the cells in the removed portion of the sample;   extracting the target from the removed portion of the sample; and   assaying the target in the removed portion of the sample.   
     
     
         14 . The method of  claim 13  wherein the target is a target nucleic acid and the assay is an amplification assay for the target nucleic acid. 
     
     
         15 . The method of  claim 14  wherein the target nucleic acid is DNA. 
     
     
         16 . The method of  claim 14  wherein the target nucleic acid is RNA. 
     
     
         17 . The method of  claim 13  wherein the sample is a blood sample. 
     
     
         18 . The method of  claim 13  wherein the sample is cells selected from the group consisting of vaginal cells, cervical cells, endocervical cells, anal cells, exfoliated cells, oral cells, throat cells and peritoneal cells. 
     
     
         19 . The method of  claim 18  wherein the cells are collected by a swab, brush, broom, or biopsy. 
     
     
         20 . The method of  claim 13  wherein the specimen storage composition has at least one constituent selected from the group consisting of formaldehyde, formic acid, methanol, ethanol, buffered formalin, EDTA, polypeptides, poly amino acids, and polysaccharides. 
     
     
         21 . The method of  claim 20  wherein the transport medium comprises buffered formalin. 
     
     
         22 . The method of  claim 13  wherein the removed portion of the sample is not further separated from the specimen storage medium prior to the steps of lysing and extraction. 
     
     
         23 . The method of  claim 13  wherein the pH of the direct chemical lysis composition is in the range of about 6.6 to about 10. 
     
     
         24 . The method of  claim 13  wherein the assay compatible buffer composition comprises a buffer component and a metal salt. 
     
     
         25 . The method of  claim 22  where the metal salt is NaCl and the concentration of NaCl in the direct chemical lysis composition is at least about 0.01 M. 
     
     
         26 . The method of  claim 25  wherein the buffer component concentration is in the range of about 0.2 M to about 2M. 
     
     
         27 . The method of  claim 26  wherein the NaCl concentration is in the range of about 0.01 M to about 1 M. 
     
     
         28 . The method of  claim 13  wherein the concentration of the non-ionic surfactant is in the range of about 0.01 to about 2 percent (v/v). 
     
     
         29 . The method of  claim 26  wherein the buffer component is the acid salt of tris(hydroxymethyl)amino methane and the buffer concentration is about 0.75 M, the NaCl concentration is about 0.19 M and the polyethylene glycol octylphenyl ether concentration is about 0.75 percent (v/v). 
     
     
         30 . The method of  claim 13  wherein the step of extracting is performed by a manual process. 
     
     
         31 . The method of  claim 14  wherein the step of amplifying step is performed by a manual process. 
     
     
         32 . The method of  claim 14  wherein the step of extracting and amplifying steps are performed in an automated process. 
     
     
         33 . The method of  claim 13  wherein the target is a protein and the assay is a detection assay for the protein. 
     
     
         34 . The method of  claim 33  wherein the protein is a biomarker. 
     
     
         35 . The method of  claim 34  wherein the biomarker is selected from the group consisting of antibodies and antigens. 
     
     
         36 . The method of  claim 33  wherein the assay is an Enzyme Linked Immunosorbent Assay (ELISA). 
     
     
         37 . A diagnostic kit for extracting target molecules from cellular components comprising a specimen storage composition with a direct chemical lysis composition comprising a) an assay compatible buffer component; and b) a non-ionic surfactant, wherein the specimen storage is provided to preserve a tissue sample. 
     
     
         38 . The diagnostic kit of  claim 37  wherein the assay compatible buffer composition comprises a buffer component and a metal salt. 
     
     
         39 . The diagnostic kit of  claim 38  wherein the metal salt is NaCl and the concentration of NaCl in the direct chemical lysis composition is at least about 0.01 M. 
     
     
         40 . The diagnostic kit of  claim 37  wherein the buffer component concentration is in the range of about 0.2 M to about 2M. 
     
     
         41 . The diagnostic kit of  claim 40  wherein the direct chemical lysis composition has a pH in the range of about 7 to about 9. 
     
     
         42 . The diagnostic kit of  claim 40  wherein the concentration of the non-ionic surfactant is in the range of about 0.01 to about 2 percent (v/v).