Illumina Corporation

Alex So

Chen Zhao

Kevin Eric Wu

Han-Yu Chuang

Frank J Steemers

Alex Aravanis

Stephen Tanner

Shannon Kaplan

Byoungsok Jung

Emrah Kostem

Stephen M Gross

Dwight Baker

Tatjana Singer

Zhihong Zhang

Xuyu Cai

Jennifer Lococo

Sante Gnerre

Li Liu

Min-Jui Richard Shen

Bala Murali Venkatesan

Sean M Ramirez

Rigo Pantoja

Kathryn M Stephens

Justin Fullerton

Shile Zhang

Kristina Kruglyak

Steven Modiano

Timothy J Wilson

Anne Jager

Sven Bilke

Neeraj Salathia

Timothy Wilson

Kevin Wu

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

The disclosed embodiments concern methods, systems and computer program products for determining sequences of interest using unique molecular indexes (UMIs) that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies or long sequence length. In some implementations, the UMIs include variable-length nonrandom UMIs (vNRUMIs). Methods and systems for making and using sequencing adapters comprising vNRUMIs are also provided.

Universal short adapters with variable length non-random unique molecular identifiers

The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index (UMI) sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

Error suppression in sequenced DNA fragments using redundant reads with unique molecular indices (UMIS)

The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the unique molecular index sequences include variable-length nonrandom sequences. In some implementations, the unique molecular index sequences are associated with the individual polynucleotide fragments based on alignment scores indicating similarity between the unique molecular index sequences and subsequences of sequence reads obtained from the individual polynucleotide fragments. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

Methods and systems for generation and error-correction of unique molecular index sets with heterogeneous molecular lengths

Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.

Spatial mapping of nucleic acid sequence information

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San Diego, CA, United States of America

Alex So