US 9,519,650 B2Granted

Systems and methods for genetic data compression

AssigneePresident and Fellows of Harvard College

InventorsChristoph Lange, Dandi Qiao

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Abstract

Genetic data may be compressed efficiently by selecting for each bi-allelic marker, from among multiple compression algorithms with different associated storage requirements that depend on the minor allele frequency of the respective marker, the algorithm that has the lowest storage requirements. Efficient approaches compress, store, and load pedigree file data. A hybrid method is used that selects between multiple alternative compression algorithms whose performance depends on the frequency of certain observable genetic variations. The hybrid method may achieve higher compression ratios than PLINK or PBAT. Further, it results in a compressed data format that, generally, does not require any overhead memory space and CPU time for decompression, and, consequently, has shorter loading times for compressed files than the binary format in PLINK or PBAT. Moreover, the compressed data fonnat supports parallel loading of genetic information, which decreases the loading time by a factor of the number of parallel jobs.

Claims11

Dependent claims

A computer-implemented method of compressing, for a plurality of subjects, genetic data corresponding to at least one bi-allelic marker having at least one minor allele frequency associated therewith, the method utilizing at least two compression algorithms and comprising:

for each of the at least one bi-allelic marker,
using a computer processor to (i) compute storage requirements associated with each of the at least two compression algorithms, the storage requirement of at least one of the compression algorithms depending, at least in part, on the minor allele frequency associated with the marker, and (ii) compress the genetic data for the marker using only the compression algorithm having the lowest storage requirement associated therewith, and
storing the compressed genetic data;
and
using the computer processor, analyzing the compressed genetic data without decompression,
wherein the at least two compression algorithms are selected from (i) a binary-encoding algorithm, (ii) an algorithm wherein total numbers and unique indices of (a) all subjects having a rare homozygous genotype for a marker, (b) all subjects having a heterozygous genotype for the marker, and (c) all subjects having an unknown genotype for the marker are expressed in binary numbers, and (iii) an algorithm wherein the total numbers and unique indices of (a) all subjects having a rare homozygous genotype for a marker and (b) all subjects having an unknown genotype for the marker are expressed in binary numbers, and the unique indices of all subjects having a heterozygous genotype for the marker are expressed in a single n-digit number, where n is the number of subjects.

3 more elements

A computer system for compressing genetic data, the system comprising:

at least one data storage medium for storing (i) original genetic data for a plurality of subjects, the data corresponding to at least one bi-allelic marker having at least one minor allele frequency associated therewith, and (ii) compressed genetic data;
and
a computer processor, in communication with the at least one data storage medium, for (i) computing, for each of the at least one bi-allelic marker, computer storage requirements associated with each of at least two compression algorithms, the storage requirement of at least one of the compression algorithms depending, at least in part, on the minor allele frequency associated with the marker, and (ii) compressing the genetic data for each of the at least one bi-allelic markers using only the compression algorithm having the lowest storage requirement associated therewith,
wherein:
the computer processor is further configured to analyze the compressed genetic data without decompression;
and
the at least two compression algorithms are selected from (i) a binary-encoding algorithm, (ii) an algorithm wherein total numbers and unique indices of (a) all subjects having a rare homozygous genotype for a marker, (b) all subjects having a heterozygous genotype for the maker, and (c) all subjects having an unknown genotype for the marker are expressed in binary numbers, and (iii) an algorithm wherein the total numbers and unique indices of (a) all subjects having an rare homozygous for a marker and (b) all subjects having an unknown genotype for the marker are expressed in binary numbers, and the unique indices of all subjects having a heterozygous genotype for the marker are expressed in a single n-digit number, where n is the number of subjects.

4 more elements

Dependencies are inferred from the claim text.

Facts

Application: 14/131,084Filed 6 Jul 2012 · us provisional application
Priority: 6 Jul 2011
Published: US 2014/0214780 A131 Jul 2014
Granted: 13 Dec 2016
Term ends: Not estimatedThe source records don’t support an estimate.

Classification6 codes

G16B 50/50
ICT programming tools or database systems specially adapted for bioinformatics: compression of genetic data
G06F 16/1744
Redundancy elimination performed by the file system: using compression, e.g. sparse files
G16B 20/00
Ict specially adapted for functional genomics or proteomics
G16B 20/20
ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations: allele or variant detection, e.g. single…

Family

Application61/504,838Us provisional application · filed 6 Jul 2011
US 2014/0214780 A1Pre-grant publication · published 31 Jul 2014
US 9,519,650 B2This patent

From the US filing history. Foreign family members aren’t listed.

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