US 12,658,284 B2 · Reference marks storing embedded oligo index in DNA data storage

Abstract

Example systems and methods for embedding an oligo index in a series of reference marks along the oligo for DNA data storage are described. A data unit may be encoded in oligos that include reference marks at predetermined intervals along the length of each oligo that encode the oligo index, generally in multiple copies encoded with varying symmetries. During decoding, the reference marks may be analyzed through multiple correlation matrices to determine a most likely set of values for the oligo index. In some configurations, the same reference marks may be processed through another correlation matrix to determine and correct insertions and deletions based on multiple copies of the oligo, as identified by the decoded oligo indices in those copies.

Claims20

Dependent claims

A system, comprising:

an encoder configured to:
determine an oligo for encoding a data unit, wherein the oligo encodes a number of symbols corresponding to user data in the data unit;
insert a plurality of reference marks at a predetermined interval along a length of the oligo, wherein:
at least one set of reference marks in the plurality of reference marks encodes an oligo index;
and
the predetermined interval equals a fixed data length between sequential reference marks;
and
output write data for the oligo for synthesis of the oligo.

5 more elements

A system comprising:

an index decoder configured to:
receive read data determined from sequencing an oligo, wherein:
the oligo encodes:
a number of symbols corresponding to user data in a data unit;
and
a plurality of reference marks at a predetermined interval along a length of the oligo;
at least one set of reference marks in the plurality of reference marks encodes an oligo index;
and
the predetermined interval equals a fixed data length between sequential reference marks;
determine, from the read data, a convolutional matrix for the oligo, wherein each column of the convolutional matrix corresponds to a base pair offset of the read data for the oligo;
determine, from the read data, a first reference matrix based on a first sequence of reference positions at an encoded frequency of the plurality of reference marks;
determine, from the read data, a second reference matrix based on a second sequence of reference positions at the encoded frequency of the plurality of reference marks;
determine a first correlation matrix based on a comparison of the convolutional matrix to the first reference matrix;
determine a second correlation matrix based on a comparison of the convolutional matrix and the second reference matrix;
determine a most likely path through a combination of the first correlation matrix and the second correlation matrix based on:
a series of probabilities of moving between corresponding rows in the first correlation matrix and the second correlation matrix;
and
loop decoding for different symmetries of a plurality of copies of the oligo index;
and
decode the oligo index based on the most likely path and the plurality of copies of the oligo index.

17 more elements

Dependencies are inferred from the claim text.

Facts

Application

18/750,586Filed 21 Jun 2024

Published

US 2025/0391513 A125 Dec 2025

Granted

16 Jun 2026

Term ends

Not estimatedThe source records don’t support an estimate.

Classification10 codes

G16B 50/50
ICT programming tools or database systems specially adapted for bioinformatics: compression of genetic data
G16B 30/00
Ict specially adapted for sequence analysis involving nucleotides or amino acids
H03M 13/1515
Using error location or error correction polynomials: reed-Solomon codes
G11C 13/02
Digital stores characterised by the use of storage elements not covered by groups G11C11/00, G11C23/00, or G11C25/00: using elements whose…

Reference marks storing embedded oligo index in DNA data storage

Life of this patent

Reference marks storing embedded oligo index in DNA data storage

Life of this patent

Abstract

Claims20