Structural variant detection using spatially linked reads
AssigneeIllumina, Inc.
InventorsMitchell A. Bekritsky, Marzieh Eslami Rasekh, Vitor Ferreira Onuchic
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Abstract
Systems and methods are provided for detecting a structural variant using complementary sequencing information, where the complementary information includes the spatial location of the sequence and the links between sequences. A baseline metric for the distribution of links for a low probability of structural variants may be used to determine whether variations in the number or distribution of spatially linked sequences is significant and could indicate the presence of a structural variant.
Claims24
A system for detecting structural variants in a polynucleotide sequence comprising:
- one or more processors configured to execute instructions which cause the system to:
- retrieve genomic data comprising polynucleotide sequence reads and spatial locations of the polynucleotide sequences on a sequencing substrate to determine spatially linked read pairs;
- calculate a metric for spatially linked read pairs in a background region of the polynucleotide sequence that has a low probability of including a structural variant to generate a baseline metric;
- calculate the metric for spatially linked read pairs in a target region of the polynucleotide sequence to generate a target metric;
- detect the presence of a candidate structural variant based on a comparison of the target metric and the baseline metric;
- and
- store information on the presence of the candidate structural variant in the target region in a computer memory.
A method of detecting structural variants in a polynucleotide sequence, comprising:
- providing genomic data comprising polynucleotide sequence reads and spatial locations of the polynucleotide sequence on a sequencing substrate to determine spatially linked read pairs;
- calculating a metric for spatially linked read pairs in a background region of the polynucleotide sequence that has a low probability of including a structural variant to generate a baseline metric;
- calculating the metric for spatially linked read pairs in a target region of the polynucleotide sequence to generate a target metric;
- detecting the presence of a candidate structural variant based on a comparison of the target metric and the baseline metric;
- and
- storing information on the presence of the candidate structural variant in the target region in a computer memory.
Dependencies are inferred from the claim text.