Method of analysis of genetic markers

Abstract

A method of analyzing genetic markers includes binding a set of probes to a segment of single stranded nucleic acids. The segment of single stranded nucleic acids includes a repeat region formed of at least two of a repeat unit. The repeat unit can include at least two nucleic acids. The set of probes includes a first probe complementary to the repeat unit. The method can further include directing the segment through a nanopore device and measuring a signal through the nanopore device. The signal can be indicative of the number of repeat units.

What is claimed is: 
     
         1 . A method of detecting an allele of a human identification panel, the method comprising:
 binding specifically a set of probes to a single stranded nucleic acid segment derived from a locus of the human identification panel, the segment including a microsatellite region having between 5 and 30 k-mer repeat units, wherein k is in a range of 2 to 6, the set of probes including a first subset of k-mer binding probes complementary to the k-mer repeat units;   directing the segment through a nanopore of a nanopore device with an applied voltage, the bound set of probes being stripped from the segment as the segment passes through the nanopore, the nanopore comprising a hole fabricated in a solid state membrane;   measuring with the nanopore device an ion current signal including current spikes corresponding to the stripping of probes of the first subset of k-mer binding probes as the segment passes through the nanopore of the nanopore device, a number of current spikes of the ion current signal indicative of the number of k-mer repeat units;   detecting the allele based on a characteristic of the current spikes of the ion current signal, wherein the characteristic includes the number of the current spikes.   
     
     
         2 . The method of  claim 1 , wherein the set of probes includes a second subset of k-mer binding probes complementary to a mutation of the k-mer repeat units. 
     
     
         3 . The method of  claim 1 , wherein the first subset of k-mer binding probes complementary to the k-mer repeat units is complementary to at least two consecutive k-mer repeat units. 
     
     
         4 . The method of  claim 1 , wherein the first subset of k-mer binding probes complementary to the k-mer repeat units is complementary to a subset of consecutive nucleotides in at least two adjacent k-mer repeat units. 
     
     
         5 . The method of  claim 1 , wherein the segment further includes a common region and a variant region and wherein the set of probes includes a second subset of probes complementary to the common region and a third subset of probes complementary to the variant region. 
     
     
         6 . The method of  claim 5 , wherein the segment further includes a second common region, the set of probes further including a fourth subset of probes complementary to the second common region. 
     
     
         7 . The method of  claim 1 , wherein the first subset of k-mer binding probes includes an appended chemical group. 
     
     
         8 . The method of  claim 7 , wherein the appended chemical group is larger than a pore opening of the nanopore device. 
     
     
         9 . The method of  claim 7 , wherein the appended chemical group is reactive with the nanopore device. 
     
     
         10 . The method of  claim 1 , wherein the set of probes includes second and third subsets of probes complementary to regions of the single stranded nucleic acid segment different than the microsatellite region. 
     
     
         11 . The method of  claim 1 , wherein the nanopore includes a passive circuit. 
     
     
         12 . The method of  claim 1 , wherein the nanopore includes an active circuit. 
     
     
         13 . A method of determining an allele of a human identification panel, the method comprising:
 mixing a set of binding probes with a set of single stranded nucleic acid segments, the set of single stranded nucleic acid segments including a first segment and a second segment, the first segment including a first repeating section having between 5 and 30 first k-mer repeating units, the second segment including a second repeating section having between 5 and 30 second k-mer repeating units, the set of binding probes including first probes complementary to the first k-mer repeating units, second probes to uniquely associate with the first segment and complementary to a region of the first segment other than the first repeating section, and third probes complementary to the second k-mer repeating units, the first probes specifically binding to the first repeating section, the second probes specifically binding to the region of the first segment, the third probes specifically binding to the second repeating section;   directing the segments through a nanopore of a nanopore device, the nanopore comprising a hole fabricated in a solid state membrane;   stripping the first, second, and third probes of the set of probes from the first and second segments; and   measuring with the nanopore device an ion current signal including current spikes corresponding to the stripping of the first probes or the second probes as the first or second segment passes through the nanopore of the nanopore device, a number of current spikes of the ion current signal indicative of the number of first or second k-mer repeating units in the first or second segment;   detecting the allele based on a characteristic of the current spikes of the ion current signal, wherein the characteristic includes the number of the current spikes.   
     
     
         14 . The method of  claim 13 , wherein the set of binding probes includes fourth probes to uniquely associate with and complementary to a region of the second segment other than the second repeating section. 
     
     
         15 . The method of  claim 13 , wherein the set of binding probes includes fourth probes uniquely associated with and complementary to a second region of the first segment other than the first repeating section and the region of the first segment. 
     
     
         16 . The method of  claim 13 , wherein the first probes are complementary to at least two consecutive first k-mer repeating units. 
     
     
         17 . The method of  claim 13 , wherein the first probes complementary are complementary to a subset of consecutive nucleotides in at least two adjacent first k-mer repeat units. 
     
     
         18 . The method of  claim 13 , wherein the first segment further includes a common region and a variant region and wherein the second probes are complementary to the common region and fourth probes are complementary to the variant region. 
     
     
         19 . The method of  claim 13 , wherein the nanopore includes a passive circuit. 
     
     
         20 . The method of  claim 13 , wherein the nanopore includes an active circuit.