Data communication and storage systems and methods

Patent metadata

Field	Value
Publication number	US-10409791-B2
Application number	US-201715669401-A
Country	US
Kind code	B2
Filing date	Aug 4, 2017
Priority date	Aug 5, 2016
Publication date	Sep 10, 2019
Grant date	Sep 10, 2019

Abstract

This disclosure relates to systems and methods for communicating and storing data that may include genomic data. In certain embodiments, a sample genome may be stored and/or communicated as a list of variants relative to a reference dataset. Transmission and/or storage of a set of variants relative to a reference genome may allow for more efficient storage and/or communication of the sample genome. Systems and methods are further disclosed that allow for the efficient selection and computation of a reference dataset used to represent a set of sample genomes.

First claim

What is claimed is:

1. A method for communicating genomic information performed by a first computing system comprising a processor and a non-transitory computer-readable medium storing instructions that, when executed by the processor, cause the processor to perform the method, the method comprising:
receiving a first sample genomic dataset for transfer to a second computing system;
generating a first reference dataset;
generating, based on the first sample genomic dataset and the first reference dataset, a first variant list, the first variant list comprising entries indicating differences between the first sample genomic dataset and the first reference dataset;
receiving an nth sample genomic dataset for transfer to the second computing system;
generating, based on the first sample genomic dataset and the nth sample genomic dataset, an ith reference dataset;
generating, based on at least the first sample genomic dataset and the ith reference dataset, an updated first variant list comprising entries indicating differences between the first sample genomic dataset and the ith reference dataset;
generating, based on the nth sample genomic dataset and the ith reference dataset, an nth variant list comprising entries indicating differences between the nth sample genomic dataset and the ith reference dataset; and
transmitting the first variant list and the nth variant list from the first computing system to the second computing system.

2. The method of claim 1 , wherein generating the first reference dataset comprises assigning the first sample genomic dataset as the first reference dataset.

3. The method of claim 2 , wherein entries of the first variant list comprise null values.

4. The method of claim 1 , wherein generating the first reference dataset comprises accessing a standard genomic reference dataset.

5. The method of claim 1 , wherein the first variant list comprises a reference to the first reference dataset.

6. The method of claim 1 , wherein the nth variant list comprises a reference to the ith reference dataset.

7. The method of claim 1 , wherein prior to generating the ith reference dataset, the method further comprises determining that an updated reference dataset should be generated.

8. The method of claim 7 , wherein determining that the updated reference dataset should be generated comprises determining that a threshold number of sample genomic datasets are represented using the first reference dataset.

9. The method of claim 7 , wherein determining that the updated reference dataset should be generated comprises determining that a size of a variant list generated based on the first reference dataset and the nth sample genomic dataset exceeds a threshold size.

10. The method of claim 7 , wherein determining that the updated reference dataset should be generated comprises determining that a collective size of variant lists generated based on the first reference dataset and the nth sample genomic dataset exceeds a threshold size.

11. The method of claim 1 , wherein the method further comprises transmitting the ith reference dataset from the first computing system to the second computing system.

12. The method of claim 1 , wherein the method further comprises generating an ith reference variant list comprising entries indicating differences between the ith reference dataset and the first reference dataset.

13. The method of claim 12 , wherein the method further comprises transmitting the ith reference variant list from the first computing system to the second computing system.

14. The method of claim 1 , wherein generating the ith reference dataset is further based on contextual information associated with the first sample genomic dataset and the nth sample genomic dataset.

15. The method of claim 14 , wherein the contextual information comprises an indication of a genealogical relatedness between an individual associated with the first sample genomic dataset and an individual associated with the nth sample genomic dataset.

16. The method of claim 14 , wherein the contextual information comprises an indication of an ethnical relatedness between an individual associated with the first sample genomic dataset and an individual associated with the nth sample genomic dataset.

17. The method of claim 1 , wherein generating the ith reference dataset comprises selecting the ith reference dataset from one or more existing genomic datasets.

Assignees

• Intertrust Tech Corp

Inventors

• Carey W Knox
• Nilsson Jarl A
• Swenson Eric
• Grantham Bart

Classifications

• G16B30/10

  Sequence alignment; Homology search · CPC title

• G06F16/2282

  Tablespace storage structures; Management thereof · CPC title

• G16B50/50

  Compression of genetic data · CPC title

• G16B50/00 Primary

  ICT programming tools or database systems specially adapted for bioinformatics · CPC title

• G06F16/1873

  Versioning file systems, temporal file systems, e.g. file system supporting different historic versions of files · CPC title