Illumina Corporation

Sven Bilke

Chen Zhao

Kevin Eric Wu

Shannon Kaplan

Shile Zhang

Alex So

Kristina Kruglyak

Johann Felix Wilhelm Schlesinger

Kristina M Kruglyak

Alex S So

Disclosed herein are systems and methods for collapsing sequencing reads and identifying similar sequencing reads. In one example, a method includes generating a plurality of first identifier subsequences from a first identifier sequence of each nucleotide sequencing read and generating a first signature for the nucleotide sequencing read by applying hashing to the plurality of first identifier subsequences. The method may include assigning the nucleotide sequencing read to a first particular bin of a first data structure based on the first signature and determining a nucleotide sequence for each first particular bin of the first data structure with one or more nucleotide sequencing reads assigned.

Systems and methods for grouping and collapsing sequencing reads

Presented herein are techniques for determining microsatellite instability. The techniques include generating a reference sample dataset representative of or mimicking a hypothetical matched sample for an individual sample of interest. The reference sample dataset may be generated from a set of reference normal samples that are not matched to the sample of interest. For samples of interest lacking a matched sample, the reference sample dataset may be used to determine microsatellite instability and to provide an indication of a presence, absence, or degree of microsatellite instability of the sample of interest. The reference sample dataset may be generated such that individual microsatelliate regions associated with a high degree of variability between ethnic groups are filtered out, masked, or otherwise not considered.

Systems and methods for determining microsatellite instability

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Bethesda, MD, United States of America

Sven Bilke