Illumina Corporation

Institute for Systems Biology

Battelle Memorial Institute

The Ohio State University

Shile Zhang

Kai Hua Wang

David J Galas

Shannon Kaplan

Chen Zhao

Han-Yu Chuang

Kristina Kruglyak

Mengchi Wang

Alex So

Richard Evan Gelinas

Xiao Chen

Clay Braden Marsh

Tingting Jiang

Sven Bilke

Melissa Garnet Piper

Vitor Ferreira Onuchic

Han Kang

Aaron Wise

Bochao Zhang

Gwenn Berry

Jessica Gordon

Kristina M Kruglyak

Alex S So

Kai Wang

Provided is a computer-implemented method, including inputting to a trained machine learning classifier genomic information of a non-training subject that includes features from a tumor sample, wherein the trained machine learning classifier trained on features of tumor samples obtained from training subjects and their a responsiveness to checkpoint inhibition treatment and the machine-learning classifier is trained to predict responsiveness to the treatment, and generating a checkpoint inhibition responsiveness classification predictive of the subject's responding to the checkpoint inhibition with the trained machine-learning classifier, and reporting the checkpoint inhibition responsiveness classification using a graphical user interface. Also provided are a computer system for performing the method and a machine learning classifier trained by the method.

Method for administering a cancer treatment

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

Provided herein are systems and methods for quantitating the HLA diversity in a solid tissue or circulating tumor DNA sample that is predictive of a patient's responsiveness to immune checkpoint inhibitory therapies.

Quantitative score of HLA diversity

Display screen or portion thereof with graphical user interface

Improved methods to quantitate RNA in biological or other analytical samples employ extended RNAs containing adaptors at the 5' end and polyA sequences coupled to a tag at the 3&#x2032; end. The invention method is particularly useful in quantitating microRNAs as primers can be used that need not complement the non-conserved 3&#x2032; ends of these molecules.

Methods to detect and quantify RNA

Methods, compositions, and devices are disclosed which use microRNA to detect, predict, treat, and monitor physiological conditions such as disease or injury. microRNA are isolated and their differential expression is measured to provide diagnostic information. This information may then be utilized for evaluation and/or treatment purposes.

Methods, compositions, and devices utilizing MicroRNA to determine physiological conditions

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San Diego, CA, United States of America

Shile Zhang