10X Genomics, Inc.

Ancestry.com Dna, LLC

Nigel Delaney

Patrick Marks

Niranjan Srinivas

Lee M Silver

Nicolaus Lance Hepler

Ari Silver

Chaitanya Aluru

Methods for index hopping sequence read filtering are provided. Each read in a plurality of reads from a multiplexed reaction comprises an insert portion, and first (molecular identifier) and second (sample index) non-insert portions. For each of a plurality of hashes, a hash data structure is formed with a representation of each read. Each representation comprises a hash of the first non-insert portion of the corresponding read. Read pairs are identified in the hash data structures. Each pair includes a first and second read sharing a common hash value but differing index values. An entry is added into a heterogeneous data structure, for each such pair, that includes the first and second non-insert portions of the first and second reads of the pair. Reads with first non-insert portion values appearing more than a threshold number of times in the heterogeneous data structure are removed from the plurality of reads.

Systems and methods for index hopping filtering

A system, device and method for receiving multiple aligned genetic sequences obtained from genetic samples of multiple organisms of one or more different species. A measure of evolutionary variation may be computed for one or more alleles at each of one or more aligned genetic loci. The aligned genetic loci in the multiple organisms may be derived from one or more common ancestral genetic loci or may be otherwise related. The measure of evolutionary variation may be a function of variation in alleles at corresponding aligned genetic loci in the multiple aligned genetic sequences. One or more likelihoods may be computed that an allele mutation at each of the one or more genetic loci in a simulated virtual progeny will be deleterious based on the measure of evolutionary variation of alleles at the corresponding aligned genetic loci for the multiple organisms.

Evolutionary models of multiple sequence alignments to predict offspring fitness prior to conception

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San Francisco, CA, United States of America

Nigel Delaney