Granted Patent
B2
US 12,380,337 · App. 17/069,247 · Granted Aug 5, 2025
Coded trace reconstruction
Inventors:
Olgica Milenkovic (Urbana, IL); Ryan Gabrys (San Diego, CA); João Ribeiro (London, GB); Mahdi Cheraghchi Bashi Astaneh (London, GB)
Assignees:
the Board of Trustees of the University of Illinois; Imperial College Innovations Limited
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Abstract
The present disclosure provides systems and methods that relate to storing encoded information in, and reading the encoded information from, nucleotide sequences. An example method includes receiving, at a DNA readout system, a nucleotide sequence. The method also includes reading the nucleotide sequence based on an alphabet consisting of {adenine (A), cytosine (C), guanine (G), and thymine (T)}. The method further includes determining positions of unique markers between a plurality of encoded blocks in the nucleotide sequence. The method yet further includes decoding each encoded block of the plurality of encoded blocks according to an inner code, so as to form a plurality of decoded blocks. The method also includes appending the decoded blocks to one another to provide a decoded message with message length n bits.
Claims (26)
1. A method, comprising:
partitioning a message having a message length n bits into a plurality of blocks with a maximum block length of O(log 2 n);
encoding each block to provide a plurality of encoded blocks;
inserting unique markers between the encoded blocks so as to form an encoded message, wherein the markers each have a minimum marker length O(log n); and
synthesizing a DNA having a nucleotide sequence based on the encoded message.
2. The method of claim 1 , wherein encoding each block comprises encoding according to an inner code, wherein the inner code comprises an alphabet consisting of adenine (A), cytosine (C), guanine (G), and thymine (T).
3. The method of claim 2 , wherein each unique marker is of the form M=(AC) l ∥(TG) l , where l=25 log n.
4. The method of claim 2 , wherein the encoded blocks consist of 50% guanine and cytosine content.
5. The method of claim 1 , wherein encoding each block comprises encoding each block according to a Hamming encoding with a relative Hamming distance.
6. The method of claim 1 , further comprising:
further partitioning each block into a plurality of subblocks; and
inserting a second level of markers between each subblock, wherein the second level of markers is different than the unique markers.
7. A DNA-based data storage system comprising:
a DNA synthesizer; and
a controller configured to carry out operations, the operations including:
partitioning a message having a message length n bits into a plurality of blocks with a maximum block length of O(log 2 n);
encoding each block to provide a plurality of encoded blocks;
inserting unique markers between the encoded blocks so as to form an encoded message, wherein the markers each have a minimum marker length O(log n); and
informing the DNA synthesizer to synthesize a nucleotide sequence based on the encoded message.
8. The DNA-based data storage system of claim 7 , wherein encoding each block comprises encoding according to an inner code, wherein the inner code comprises an alphabet consisting of adenine (A), cytosine (C), guanine (G), and thymine (T).
9. The DNA-based data storage system of claim 8 , wherein each unique marker is of the form M=(AC) l ∥(TG) l , where l=25 log n.
10. The DNA-based data storage system of claim 8 , wherein the encoded blocks consist of 50% guanine and cytosine content.
11. The DNA-based data storage system of claim 7 , wherein encoding each block comprises encoding each block according to a Hamming encoding with a relative Hamming distance.
12. The DNA-based data storage system of claim 7 , wherein the operations further comprise:
further partitioning each block into a plurality of subblocks; and
inserting a second level of markers between each subblock, wherein the second level of markers is different than the unique markers.
Assignments (5)
CONFIRMATORY LICENSE
Recorded Jun 1, 2023
From: UNIVERSITY OF ILLINOIS
To: NATIONAL SCIENCE FOUNDATION
Reel/Frame 063821/0646 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Apr 26, 2022
From: MILENKOVIC, OLGICA; GABRYS, RYAN
To: THE BOARD OF TRUSTEES OF THE UNIVERSITY OF ILLINOIS
Reel/Frame 059729/0966 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Apr 26, 2022
From: ASTANEH, MAHDI CHERAGHCHI BASHI; RIBEIRO, JOAO MIGUEL LOURENCO
To: IMPERIAL COLLEGE OF SCIENCE, TECHNOLOGY AND MEDICINE
Reel/Frame 059732/0145 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Apr 26, 2022
From: IMPERIAL COLLEGE OF SCIENCE, TECHNOLOGY AND MEDICINE
To: IMPERIAL COLLEGE INNOVATIONS LIMITED
Reel/Frame 059732/0186 →
CONFIRMATORY LICENSE
Recorded Jan 26, 2021
From: UNIVERSITY OF ILLINOIS, URBANA-CHAMPAIGN
To: NATIONAL SCIENCE FOUNDATION
Reel/Frame 055107/0409 →
Continuity (2)
Provisional Application
62925332
· Oct 24, 2019
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