Measures of short telomere abundance

Abstract

This invention provides methods and materials for measuring telomere abundance from chromosomes in a sample having telomeres within a pre-determined length range, e.g., short telomeres up to a certain length. The methods can involve a first step of performing a time-limited extension reaction calibrated to produce extension products from a double-stranded chromosomal DNA template of no more than a defined length, and a second step of amplifying, from the extension products, sequences bounded by a sub-telomeric sequence and the anchor sequence, to produce a length-limited telomere sequence product. The abundance of telomeric sequences in this product can be measured, and the measures can be correlated to a variety of indices.

What is claimed is: 
     
         1 .- 20 . (canceled) 
     
     
         21 . A method of amplifying telomeric repeat sequences and sub-telomeric sequences of a chromosome comprising:
 a) making a nucleic acid extension product by:
 i) hybridizing an extension primer to a telomeric repeat sequence in a 3′ overhang of double stranded chromosomal DNA, wherein:
 (1) the double stranded chromosomal DNA has a telomeric region comprising telomeric repeat sequences and a sub-telomeric region comprising sub-telomeric sequences; and 
 (2) the extension primer comprises:
 (A) a 3′ portion that hybridizes to a telomeric repeat sequence in the 3′ overhang under annealing conditions, and 
 (B) a 5′ portion having an anchor sequence that does not hybridize to a telomeric repeat sequence in the 3′ overhang under the annealing conditions; and 
 
 
 ii) performing a time-limited extension reaction to extend the extension primer towards the sub-telomeric region of the double stranded chromosomal DNA, wherein the extension reaction is timed to produce an extension product comprising both telomeric repeat sequences and sub-telomeric sequences only from double stranded chromosomal DNA having a telomeric region within a pre-determined length range 
   
     
     
         22 . The method of  claim 21 , further comprising: b) amplifying the sequences of the extension product using:
 (1) a first amplification primer that hybridizes to a sequence unique to the sub-telomeric region in the extension product under annealing conditions; and   (2) a second amplification primer that hybridizes to the anchor sequence under the annealing conditions.   
     
     
         23 . The method of  claim 22 , wherein the first amplification primer comprises the sequence 5′-GATGGATCCTGAGGGTGAGGGTGAGGG-3′ [SEQ ID NO: 2], 5′-CGGGCCGGCTGAGGGTACCGCGA-3′ [SEQ ID NO: 10] (chromosome 1), 5′-GCTAATGCACTCCCTCAATAC-3′ [SEQ ID NO: 11] (chromosome 5), or 5′-CATTCCTAATGCACACATGATACC-3′ [SEQ ID NO: 12] (Chromosome 9). 
     
     
         24 . The method of  claim 22 , wherein the first amplification primer comprises the sequence 5′-GATGGATCCTGAGGGTGAGGGTGAGGG-3′ [SEQ ID NO: 2] and the second primer comprises the sequence 5′-TGCTCGGCCGATCTGGCATC-3′ [SEQ ID NO: 8]. 
     
     
         25 . The method of  claim 21 , wherein the length range of the amplified telomere products can be determined by using a time-limited extension time in the PCR reaction. 
     
     
         26 . The method of  claim 21 , further comprising co-amplifying a control sequence. 
     
     
         27 . The method of  claim 26 , wherein the control sequence comprises a plurality of non-telomeric repeat sequences. 
     
     
         28 . (canceled) 
     
     
         29 . A method for determining short telomere abundance comprising:
 a) providing a sample comprising double-stranded chromosomal DNA comprising a 3′ overhang from a subject;   b) producing a length-limited amplification product from the double-stranded chromosomal DNA using the method of  claim 21 ; and   c) determining short telomere abundance from the length-limited amplified product.   
     
     
         30 . The method of  claim 29 , further comprising:
 d) comparing the short telomere abundance with a measure of total telomere abundance from the sample.   
     
     
         31 . (canceled) 
     
     
         32 . The method of  claim 30 , wherein step d) comprises determining short telomere abundance as a function of total telomere abundance. 
     
     
         33 . The method of  claim 29 , wherein determining short telomere abundance is performed using qPCR. 
     
     
         34 . The method of  claim 33 , wherein qPCR is performed using a first and a second primer,
 i) wherein said first primer hybridizes to at least one repetitive unit of said first strand and said second primer hybridizes to at least one repetitive unit of said second strand,   ii) wherein said hybridized primers are capable of primer extension when hybridized to their respective strands, and wherein at least one nucleotide of said first primer produces an internal base pair mismatch between said first primer and a nucleotide of said repetitive unit when said first primer is hybridized to at least one repetitive unit of said first strand,   iii) wherein said first primer also produces a mismatch with the 3′ terminal nucleotide of said second primer when first and second primers hybridize to each other,   iv) wherein at least one nucleotide of said second primer produces an internal base pair mismatch between said second primer and a nucleotide of said repetitive unit when said second primer is hybridized to at least one repetitive unit of said second strand.   
     
     
         35 . The method of  claim 29 , wherein determining short telomere abundance comprises measuring average telomere length in the sample by Southern blot, dot blot, slot blot, immunochemistry, nucleic acid sequencing, or digital PCR. 
     
     
         36 . The method of  claim 29 , wherein the short telomere abundance is a measure of relative abundance. 
     
     
         37 . The method of  claim 30 , wherein the total telomere abundance is measured relative to abundance of a genomic reference sequence. 
     
     
         38 . The method of  claim 37 , wherein the genomic reference sequence comprises a single copy reference nucleotide sequence or a non-telomere repetitive DNA sequence. 
     
     
         39 . The method of  claim 38 , wherein the single copy reference nucleotide sequence is human beta-globin. 
     
     
         40 .- 65 . (canceled) 
     
     
         66 . A kit comprising:
 (1) a first amplification primer comprising:
 (A) a 3′ portion that hybridizes to a telomeric repeat sequence in a 3′ overhang of double-stranded chromosomal DNA under annealing conditions, and 
 (B) a 5′ portion having an anchor sequence that does not hybridize under the annealing conditions to a sequence in the telomeric region or to a sequence in the sub-telomeric region in the chromosomal DNA; and 
   (2) a second amplification primer that hybridizes to a sub-telomeric sequence under annealing conditions.   
     
     
         67 . The kit of  claim 66 , further comprising:
 (3) a third amplification primer that hybridizes to a complement of the anchor sequence under annealing conditions.   
     
     
         68 . The kit of  claim 66 , further comprising:
 (3) reagents to carry out the hybridization, extension, amplification and quantification steps of the short telomere measurement.   
     
     
         69 . The kit of  claim 66 , further comprising:
 (3) a control sample and a reference sample comprising chromosomal DNA with known telomere lengths.   
     
     
         70 . The method of  claim 21 , wherein the time-limited extension reaction is a time-controlled strand displacement extension reaction. 
     
     
         71 . The method of  claim 21 , further comprising:
 b) amplifying by means of a subsequent PCR reaction sequences of the extension product using:
 (1) a first amplification primer that hybridizes to a sequence unique to the sub-telomeric region in the extension product under annealing conditions; and 
 (2) a second amplification primer that hybridizes to the anchor sequence under the annealing conditions. 
   
     
     
         72 . The method of  claim 70 , wherein the time-controlled strand displacement extension reaction is timed to produce a length-limited extension product. 
     
     
         73 . The method of  claim 72 , wherein the time-controlled strand displacement extension reaction is timed to be 0.1-30 minutes, 0.1-30 minutes, 0.1-5 minutes, 0.1-4 minutes, 0.1-3 minutes, 0.1-2 minutes, 0.1-1 minute or 0.1-0.5 minutes.