# US 2019/0172553 A1 · Using k-mers for rapid quality control of sequencing data without alignment

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- Number: US 2019/0172553 A1
- Document ID: US20190172553A1
- Status: Published application
- Kind: A1
- Application number: 16/177,684
- Filed: 2018-11-01
- Published: 2019-06-06
- Earliest claimed: 2017-11-08
- Assignees: Koninklijke Philips N.V.
- Applicants: Koninklijke Philips N.V.
- Inventors: Jie Wu; Yee Him Cheung
- Web page: https://patentgrep.com/patent/US20190172553A1

## CPC

- G16B 30/00: ICT specially adapted for sequence analysis involving nucleotides or amino acids
- C12Q 1/68: involving nucleic acids
- G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B 45/00: ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
- G16B 50/30: Data warehousing; Computing architectures
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES

## Abstract

A method for evaluating nucleic acid sequencing data using a quality control analysis system, comprising: receiving a plurality of reads of a nucleic acid sequence; extracting a plurality of k-mers from the plurality of reads; identifying, using the plurality of extracted k-mers, one or more of a plurality of annotated k-mers found in the plurality of reads, wherein the plurality of extracted k-mers are stored in an annotation database, and further wherein the annotated k-mers are annotated with annotation information about the one or more nucleic acid sequences from which the annotated k-mers are generated; gathering, based on the identified annotated k-mers found in the plurality of reads, annotation information about the plurality of reads; and determining, based on the gathered annotation information, a quality control metric for at least some of the plurality of reads.

## Claims

### Claim 1

A method for evaluating nucleic acid sequencing data using a quality control analysis system, comprising:
receiving, by the quality control analysis system, a plurality of reads of a nucleic acid sequence;
extracting, by a processor of the quality control analysis system, a plurality of k-mers from the plurality of reads;
identifying, using the plurality of extracted k-mers, one or more of a plurality of annotated k-mers found in the plurality of reads, wherein the plurality of annotated k-mers are generated from one or more nucleic acid sequences and stored in an annotation database of the quality control analysis system, and further wherein the annotated k-mers are annotated with annotation information about the one or more nucleic acid sequences from which the annotated k-mers are generated;
gathering, based on the identified annotated k-mers found in the plurality of reads, annotation information about the plurality of reads; and
determining, based on the gathered annotation information, a quality control metric for at least some of the plurality of reads.

### Claim 2 (depends on 1)

The method of claim 1, further comprising the step of reporting the determined quality control metric.

### Claim 3 (depends on 1)

The method of claim 1, further comprising the step of responding to the determined quality control metric.

### Claim 4 (depends on 1)

The method of claim 1, further comprising the steps of:
generating, from a nucleic acid sequence, the plurality of annotated k-mers;
storing the generated plurality of k-mers in the annotation database; and
annotating one or more of the stored plurality of k-mers with annotation information.

### Claim 5 (depends on 4)

The method of claim 4, wherein the annotation information comprises information about a location of the annotated k-mer within the nucleic acid sequence.

### Claim 6 (depends on 4)

The method of claim 4, wherein the annotation information comprises information about a characteristic of the nucleic acid sequence from which the annotated k-mer was generated.

### Claim 7 (depends on 1)

The method of claim 1, wherein the quality control metric is a measurement of contamination of the reads, depth or coverage of the plurality of reads, and/or an identification of one or more species from which the plurality of reads were generated.

### Claim 8 (depends on 1)

The method of claim 1, wherein the quality control metric is determined prior to alignment of the received reads to a genomic sequence.

### Claim 9

A system configured to evaluate nucleic acid sequencing data, comprising:
an annotation database comprising a plurality of annotated k-mers generated from one or more nucleic acid sequences, wherein the plurality of annotated k-mers are annotated with annotation information about the one or more nucleic acid sequences from which the annotated k-mers are generated; and
a processor comprising:
a k-mer extractor configured to extract a plurality of k-mers from a plurality of reads of a nucleic acid sequence;
a k-mer analyzer configured to: (i) identify, using the plurality of extracted k-mers, one or more of the plurality of annotated k-mers in the annotation database found in the plurality of reads; (ii) gather, based on the identified annotated k-mers found in the plurality of reads, annotation information about the plurality of reads; and (iii) determine, based on the gathered annotation information, a quality control metric for at least some of the plurality of reads.

### Claim 10 (depends on 9)

The system of claim 9, further comprising an annotator configured to: (i) generate the plurality of annotated k-mers from the one or more nucleic acid sequences; (ii) store the generated plurality of k-mers in the annotation database; and (iii) annotate one or more of the stored plurality of k-mers with annotation information.

### Claim 11 (depends on 9)

The system of claim 9, wherein the processor is configured to respond to the determined quality control metric.

### Claim 12 (depends on 9)

The system of claim 9, further comprising a user interface configured to provide the determined quality control metric to a user.

### Claim 13 (depends on 9)

The system of claim 9, wherein the annotation information comprises information about a location of the annotated k-mer within the nucleic acid sequence, and/or about a characteristic of the nucleic acid sequence from which the annotated k-mer was generated.

### Claim 14 (depends on 9)

The system of claim 9, wherein the quality control metric is determined prior to alignment of the received reads to a genomic sequence.

### Claim 15 (depends on 9)

The system of claim 9, wherein the k-mer extractor is configured to extract k-mers from the plurality of reads using a sliding window method.