COMPOSITIONS AND METHODS FOR IDENTIFYING A SINGLE-NUCLEOTIDE VARIANT

1 . A method of identifying a single-nucleotide variant (SNV) in a single cell, the method comprising:

(a) purifying genomic DNA from a single cell;

(b) amplifying the genomic DNA;

(c) sequencing the amplified genomic DNA;

(d) detecting a variant nucleotide on forward and reverse strands, wherein the presence of the variant nucleotide on the forward and reverse strands identifies a double-stranded mutation that is a single-nucleotide variant.

2 . The method of claim 1 , wherein the single-nucleotide variant is a somatic mutation.

3 . The method of claim 1 , wherein detecting the variant nucleotide is in proximity to a germline variant.

4 . The method of claim 1 , wherein the cell is a neuron, cardiac cell, muscle cell, or skin cell.

5 . The method of claim 1 , wherein the purifying step comprises alkaline lysis on ice or comprises isolating the nucleus from the single cell.

6 . The method of claim 1 , comprising eliminating from a sequence read a variant nucleotide that is not present on forward and reverse strands, wherein the absence of the variant nucleotide on a forward or reverse strand identifies an error in genomic sequencing.

7 . The method of claim 6 , wherein the error is a DNA lesion that is biologically induced pre-mortem, biologically induced post-mortem, or generated during DNA purification, nuclear isolation, cell lysis, DNA amplification, DNA library preparation, or DNA sequencing.

8 . A method of determining the genomic age of a subject, the method comprising:

(a) purifying genomic DNA from a single cell obtained from the subject;

(b) amplifying the genomic DNA;

(c) sequencing the amplified genomic DNA;

(d) measuring the number of somatic variant nucleotides on forward and reverse strands, wherein the presence of the somatic variant nucleotide on the forward and reverse strands identifies a double-stranded mutation that is a somatic single-nucleotide variant; and

(e) determining a genomic age from the number of somatic variant nucleotides relative to a reference, wherein increased somatic variant nucleotides relative to a reference indicates advanced genomic age.

9 . The method of claim 8 , comprising measuring the number of somatic variant nucleotides in at least 2, 3, 4, 5 or more cells.

10 . The method of claim 8 , wherein the somatic variant nucleotide is in proximity to a germline variant.

11 . The method of claim 8 , wherein the subject has or is identified as having a progeroid disease.

12 . The method of claim 11 , wherein the progeroid disease is Cockayne syndrome (CS) or Xeroderma pigmentosum (XP).

13 . The method of claim 8 , comprising measuring the rate of accumulation of genome-wide somatic SNVs.

14 . A method of measuring the rate of accumulation of genome-wide somatic single-nucleotide variants (SNVs), the method comprising:

identifying double-stranded mutations in a genomic sequence derived from a biological sample, wherein the double-stranded mutations comprise a variant nucleotide on forward and reverse strands; and

performing linkage analysis to obtain a frequency of observed double-stranded mutations adjusted for the number of regions linked to a germline heterozygous variant, thereby measuring the rate of accumulation of genome-wide somatic SNVs.

15 . The method of claim 14 , wherein the biological sample is a single cell or single nucleus.

16 . The method of claim 15 , wherein the cell is a neuron, cardiac cell, muscle cell, or skin cell.

17 . A method of measuring the somatic mutation burden of a subject, the method comprising:

identifying double-stranded mutations in a genomic sequence from a biological sample from the subject, wherein the double-stranded mutations comprise a variant nucleotide on forward and reverse strands; and

performing linkage analysis to obtain a frequency of observed double-stranded mutations adjusted for the number of regions linked to a germline heterozygous variant, thereby measuring the somatic mutation burden in the subject.

18 . The method of claim 17 , wherein increased somatic mutation burden in the subject indicates advanced age and/or increased DNA damage.

19 . The method of claim 18 , wherein the rate of somatic mutation burden of greater than about 20 SNVs per year in the prefrontal cortex (PFC) and/or greater than about 40 SNVs per year in the hippocampal dentate gyrus (DG) is indicative of neuronal degeneration in the subject.

20 . The method of claim 19 , wherein the neuronal degeneration is associated with Cockayne syndrome (CS) or Xeroderma pigmentosum (XP).