Computation pipeline of location-dependent variant calls
Inventors
Ye, Jun • Zhou, Wei • Chen, Luoqi • Feng, Hanying • Chen, Hong • Liu, Xiaofeng
Assignees
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Publication Number
US-10424396-B2
Publication Date
2019-09-24
Expiration Date
Abstract
The present disclosure provides a computer-implemented method for analyzing variants from a plurality of nucleic acid sequence reads using a computation pipeline, which comprises a module depending on a location-dependent parameter. The method comprises executing on a processor the steps of: receiving a plurality of nucleic acid sequence reads comprising at least a first nucleic acid sequence read and a second nucleic acid sequence read; mapping the first nucleic acid sequence read and the second nucleic acid sequence read to a first location and a second location in a genome, respectively; setting a first value and a second value for the location-dependent parameter on the basis of the first location and the second location in the genome, respectively; passing the first nucleic acid sequence read and the second nucleic acid sequence read through the module using the first value and the second value, respectively; and generating a variant call.
Core Innovation
The disclosure describes a genomic sequencing analysis computation pipeline in which nucleic acid sequence reads are mapped to locations in a genome, and a module in the pipeline uses a location-dependent parameter. The mapped reads are mapped to different genome locations, where the parameter values differ between the locations, and a parameter of SNP or Indel probability is set based on the locations in the genome.
The disclosure further describes generating parameter maps customized for different factors, including genomic region, ethnicity or regional group, disease status including cancer, and cell type. It explains performing a multi-pass iterative procedure for parameter map refinement and generating improved parameter values over multiple passes.
To reduce computation, the disclosure describes a single-pass multiple-parameter-map execution approach and incremental exploration using saved intermediates. The pipeline passes at least a thousand nucleic acid sequence reads through the computation pipeline using the location-dependent SNP or Indel probability values and generates a variant call.
Claims Coverage
The provided independent claims are clm-00001 and clm-00006. They cover two inventive features implemented as either a method or instructions on a non-transitory computer-readable medium.
Location-dependent SNP or Indel probability for variant calling after mapping
Receiving at least a thousand nucleic acid sequence reads; mapping the reads to locations in a genome, with a first location different from a second location; setting values for a parameter of SNP or Indel probability on the basis of the locations in the genome, with a first value different from a second value; passing the reads through the computation pipeline using the set values; and generating a variant call.
Non-transitory medium instructions implementing location-dependent SNP or Indel probability for variant calling
A non-transitory computer-readable medium with instructions for analyzing variants from a plurality of nucleic acid sequence reads using a computation pipeline stored thereon, the computation pipeline comprising a parameter of SNP or Indel probability, and the instructions when executed by a processor perform receiving at least a thousand nucleic acid sequence reads, mapping the reads to locations in a genome with different locations, setting location-based SNP or Indel probability values with different values at the different locations, passing the reads through the computation pipeline using the set values, and generating a variant call.
Across the independent claims, the core coverage is mapping reads to different genome locations and setting a SNP or Indel probability parameter with different values for the different locations, followed by running the computation pipeline to generate a variant call.
Stated Advantages
Improved variant call accuracy.
Reduced computation via single-pass multiple-parameter-map execution and incremental exploration using saved intermediates.
Documented Applications
Analyzing variants from a plurality of nucleic acid sequence reads using a computation pipeline to generate a variant call.
Customizing parameter maps using genomic region, ethnicity or regional group, disease status including cancer, and cell type.
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