Efficient algorithm for PCR testing of blood samples

Abstract

Systems, processes, and devices are provided which are useful for testing blood or plasma donations to detect those specific donations which are contaminated by a virus above a predetermined level. An apparatus and process is described which forms individual, separately sealed and connected sample containers from a flexible hollow tubing segment connected to a fluid donation container. The tubing segment is sealed at spaced-apart intervals along its length, with tubing segment portions in the intervals between the seals defining containers, each of which holds a portion of a plasma sample. The contents of the containers are formed into pools which are subsequently tested for virus contamination by a high-sensitivity test such as PCR. The pools are tested in accordance with an algorithm by which a sample from each donation is mapped to each element of an N-dimensional matrix or grid. Each element of the matrix is identified by a matrix identifier, X rcs , where rcs defines the dimensional index. An aliquot is taken from each sample, and subpools are formed, each subpool comprising aliquots of samples in which one dimensional index is fixed. All of the subpools are tested in one PCR test cycle. The dimensional indicia of each positive subpool is evaluated mathematically in accordance with a reduction by the method of minors, thereby unambiguously identifying a unique element in the grid, thereby unambiguously identifying a uniquely positive blood or plasma donation.

1 - 11 . (canceled)  
   
   
       12 . A method for screening a multiplicity of biological fluid donations to identify a subgroup of specific donations contaminated with a pathogen, said method comprising the steps: 
 (a) forming separate individual samples from each of said multiplicity of biological fluid donations;    (b) forming a first pool comprising an aliquot from each of said samples;    (c) testing said first pool with a high-sensitivity test for positive or negative pathogen indication;    (d) if said first pool tests negative for a pathogen then the screening method is complete;    (e) if said first pool tests positive for a pathogen, then assigning said samples making up said first pool into at least two subgroups;    (f) forming at least two second pools, each pool comprising an aliquot from each sample assigned to one subgroup of said at least two subgroups;    (g) testing said at least two second pools with a high-sensitivity test to determine which of said second pools tests positive for a pathogen, thereby identifying a subgroup of specific donations contaminated with a pathogen.    
   
   
       13 . The method according to  claim 12 , wherein said samples are collected concurrently with the collection of said multiplicity of biological fluid donations.  
   
   
       14 . The method according to  claim 12 , wherein said samples are collected after the collection of said multiplicity of biological fluid donations.  
   
   
       15 . The method according to  claim 12 , wherein said multiplicity of donations is more than 500 donations.  
   
   
       16 . The method according to  claim 12 , wherein the biological fluid is blood.  
   
   
       17 . The method according to  claim 12 , wherein the biological fluid is plasma.  
   
   
       18 . The method according to  claim 12 , wherein the pathogen is a viral pathogen.  
   
   
       19 . The method according to  claim 12 , wherein the high-sensitivity test is PCR.  
   
   
       20 . The method according to  claim 12  comprising the further step: 
 (h) repeating steps (e)-(g).    
   
   
       21 . The method according to  claim 20 , wherein said samples are collected concurrently with the collection of said multiplicity of biological fluid donations.  
   
   
       22 . The method according to  claim 20 , wherein said samples are collected after the collection of said multiplicity of biological fluid donations.  
   
   
       23 . The method according to  claim 20 , wherein said multiplicity of donations is more than 500 donations.  
   
   
       24 . The method according to  claim 20 , wherein the biological fluid is blood.  
   
   
       25 . The method according to  claim 20 , wherein the biological fluid is plasma.  
   
   
       26 . The method according to  claim 20 , wherein the pathogen is a viral pathogen.  
   
   
       27 . The method according to  claim 20 , wherein the high-sensitivity test is PCR.  
   
   
       28 . The method according to  claim 20 , wherein one or more of said multiplicity of biological fluid donations is uniquely identified as contaminated with a pathogen.  
   
   
       29 . The method according to  claim 28 , wherein said samples are collected concurrently with the collection of said multiplicity of biological fluid donations.  
   
   
       30 . The method according to  claim 28 , wherein said samples are collected after the collection of said multiplicity of biological fluid donations.  
   
   
       31 . The method according to  claim 28 , wherein said multiplicity of donations is more than 500 donations.  
   
   
       32 . The method according to  claim 28 , wherein the biological fluid is blood.  
   
   
       33 . The method according to  claim 28 , wherein the biological fluid is plasma.  
   
   
       34 . The method according to  claim 28 , wherein the pathogen is a viral pathogen.  
   
   
       35 . The method according to  claim 28 , wherein the high-sensitivity test is PCR.  
   
   
       36 . The method according to  claim 12  wherein the statistical probability that viruses present at low concentrations will go undetected is minimized, comprising the further step of determining the number of multiplicity of biological fluid donations using criteria comprising: the aliquot volume, anticipated concentration of the pathogen in the biological fluid donations, and sensitivity of the high-sensitivity test for detection of the pathogen.  
   
   
       37 . The method according to  claim 36 , wherein said samples are collected concurrently with the collection of said multiplicity of biological fluid donations.  
   
   
       38 . The method according to  claim 36 , wherein said samples are collected after the collection of said multiplicity of biological fluid donations.  
   
   
       39 . The method according to  claim 36 , wherein said multiplicity of donations is more than 500 donations.  
   
   
       40 . The method according to  claim 36 , wherein the biological fluid is blood.  
   
   
       41 . The method according to  claim 36 , wherein the biological fluid is plasma.  
   
   
       42 . The method according to  claim 36 , wherein the pathogen is a viral pathogen.  
   
   
       43 . The method according to  claim 36 , wherein the high-sensitivity test is PCR.  
   
   
       44 . The method according to  claim 12 , wherein said at least two subgroups comprise approximately equal numbers of samples.  
   
   
       45 . The method according to  claim 44 , wherein said samples are collected concurrently with the collection of said multiplicity of biological fluid donations.  
   
   
       46 . The method according to  claim 44 , wherein said samples are collected after the collection of said multiplicity of biological fluid donations.  
   
   
       47 . The method according to  claim 44 , wherein said multiplicity of donations is more than 500 donations.  
   
   
       48 . The method according to  claim 44 , wherein the biological fluid is blood.  
   
   
       49 . The method according to  claim 44 , wherein the biological fluid is plasma.  
   
   
       50 . The method according to  claim 44 , wherein the pathogen is a viral pathogen.  
   
   
       51 . The method according to  claim 44 , wherein the high-sensitivity test is PCR.  
   
   
       52 . A method for screening a multiplicity of biological fluid donations to identify a subgroup of specific donations contaminated with a pathogen, said method comprising the steps: 
 (a) forming separate individual samples from each of said multiplicity of biological fluid donations;    (b) forming a first pool comprising an aliquot from each of said samples;    (c) testing said first pool with a high-sensitivity test for positive or negative pathogen indication;    (d) if said first pool tests negative for a pathogen then the screening method is complete;    (e) if said first pool tests positive for a pathogen, then assigning said samples making up said first pool into at least two subgroups;    (f) forming at least two second pools, each pool comprising an aliquot from each sample assigned to one subgroup of said at least two subgroups;    (g) testing said at least two second pools with a high-sensitivity test to determine which of said second pools tests positive for a pathogen; and    (h) repeating steps (e)-(g), wherein one or more of said multiplicity of biological fluid donations is uniquely identified as contaminated with a pathogen.    
   
   
       53 . The method according to  claim 52  wherein the statistical probability that viruses present at low concentrations will go undetected is minimized, comprising the further step of determining the number of multiplicity of biological fluid donations using criteria comprising: the aliquot volume, anticipated concentration of the pathogen in the biological fluid donations, and sensitivity of the high-sensitivity test for detection of the pathogen.  
   
   
       54 . The method according to  claim 52 , wherein said at least two subgroups comprise approximately equal numbers of samples.  
   
   
       55 . The method according to  claim 52 , wherein said samples are collected concurrently with the collection of said multiplicity of biological fluid donations.  
   
   
       56 . The method according to  claim 52 , wherein said samples are collected after the collection of said multiplicity of biological fluid donations.  
   
   
       57 . The method according to  claim 52 , wherein said multiplicity of donations is more than 500 donations.  
   
   
       58 . The method according to  claim 52 , wherein the biological fluid is blood.  
   
   
       59 . The method according to  claim 52 , wherein the biological fluid is plasma.  
   
   
       60 . The method according to  claim 52 , wherein the pathogen is a viral pathogen.  
   
   
       61 . The method according to  claim 52 , wherein the high-sensitivity test is PCR.