Ultra-low coverage genome sequencing and uses thereof
Inventors
Pickrell, Joseph K. • Berisa, Tomaz • Jaini, Suma • Houck-Loomis, Brian • Wasik, Kaja
Assignees
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Publication Number
US-11124831-B2
Publication Date
2021-09-21
Expiration Date
Abstract
Methods are provided for analyzing one or more genetic samples, comprising procuring one or more genetic samples comprising genetic material from one or more individuals and sequencing the genetic material using non-targeted, ultra-low coverage sequencing to obtain genetic information for individual associated with the one or more genetic samples. Personal and genetic information associated with the individuals is stored in a database for retrieval and manipulation.
Core Innovation
The invention describes measuring a condition of an individual by procuring genetic samples comprising substantially non-ancient genetic material, where each genetic sample is associated with the individual from which it is procured. The method performs non-targeted, ultra-low coverage DNA sequencing with coverage of 1x or less relative to a first genome to determine genetic reads, and the reads are aligned to one or more reference genomes, which can be the same as or different from the first genome, to produce aligned genetic reads.
The method stores, in a database, a locus and a value of each allele in the aligned reads together with a unique identifier for the associated individual. The database storing further includes personal behavior or phenotype information provided for the associated individual, plus ancestry information and relatedness to other individuals. A likelihood for a condition of the associated individual is determined without imputing the genotype of any missing alleles.
The condition includes one or more biome species and/or new phenotype, new ancestry, new relatedness, or new behavior not provided for the associated individual. These new attributes are determined based on alleles in the aligned reads from the individual in the ultra-low sequencing data and ultra-low sequencing data in the database about second alleles in second aligned reads for a second individual. The condition is presented on a display device and steps are repeated until the likelihood for the condition meets or exceeds a predetermined threshold.
Claims Coverage
The independent claim covers an end-to-end method with seven main inventive features: sample acquisition, ultra-low non-targeted sequencing (1x or less), read alignment to one or more reference genomes, database storage of allele loci/values with individual identifiers plus ancestry/relatedness/behavior/phenotype, likelihood-based condition determination without genotype imputation (including biome species and/or new phenotype/ancestry/relatedness/behavior), presenting the condition on a display device, and repeating until a predetermined likelihood threshold is met.
Substantially non-ancient genetic samples for condition measurement
Procuring one or more genetic samples comprising genetic material from one or more individuals, where each genetic sample is associated with the individual and the genetic material is substantially non-ancient genetic material.
Non-targeted ultra-low coverage sequencing with 1x or less
Sequencing the genetic material from each genetic sample using only non-targeted, ultra-low coverage DNA sequencing with coverage of 1x or less relative to a first genome to determine a plurality of genetic reads.
Alignment of genetic reads to one or more reference genomes
Aligning the plurality of genetic reads for each genetic sample to one or more reference genomes, producing a plurality of aligned genetic reads for each genetic sample.
Database storage of allele loci/values linked to individuals plus ancestry/relatedness/behavior/phenotype
Storing in a database a locus and a value of each allele in the aligned reads along with a unique identifier for the associated individual and any personal behavior or phenotype information, plus any ancestry information and any relatedness to other individuals.
Likelihood-based condition determination without imputing missing alleles
Determining likelihood for a condition of the associated individual without imputing the genotype of any missing alleles, where the condition includes one or more biome species and/or any new phenotype, new ancestry, new relatedness, or new behavior, determined based on alleles in the aligned reads for the individual and alleles in aligned reads for second individuals in the database.
Presenting the determined condition on a display device
Presenting, on a display device, the condition of the associated individual.
Iterative repetition until likelihood meets a threshold
Repeating steps a through e until the likelihood for the condition meets or exceeds a predetermined threshold.
The claim coverage focuses on measuring a condition from non-targeted ultra-low sequencing of substantially non-ancient genetic material, aligning reads to reference genomes, storing allele locus/value data linked to individuals together with ancestry and relatedness, and determining a likelihood-based condition without imputing missing alleles, followed by display and iteration until a predetermined threshold is reached.
Stated Advantages
Not explicitly described in patent.
Documented Applications
Not explicitly described in patent.
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