US 2025/0051843 A1 · METHODS FOR HUMAN LEUKOCYTE ANTIGEN TYPING AND PHASING

Abstract

Provided herein are methods of obtaining phased human leukocyte antigen (HLA) types of a sample from an individual.

Dependent claims

A method of obtaining a phased human leukocyte antigen (HLA) type of a sample comprising:

(a) aligning a plurality of sequencing reads to a reference genome or a first variation graph, wherein at least a portion of said plurality of sequencing reads correspond to an HLA gene locus;
(b) identifying a plurality of single nucleotide polymorphisms (SNPs) or indels in said plurality of sequencing reads;
(c) sorting said plurality of SNPs or indels into phase blocks;
(d) aligning said plurality of sequencing reads to a second variation graph to identify a plurality of HLA types;
(e) comparing said plurality of HLA types to a plurality of known HLA alleles to obtain a SNP signature for each HLA allele;
and
(f) comparing said SNP signature of (e) to said phase blocks of (c) to obtain said phased HLA type.

4 more elements

Dependencies are inferred from the claim text.

Facts

Application

18/780,961Filed 23 Jul 2024

Priority

25 Jan 2022

Published

13 Feb 2025

Term ends

Not estimatedThe source records don’t support an estimate.

C12Q 1/6881
Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes: for tissue or cell typing, e.g. human leukocyte antigen [HLA]…
C12Q 1/6827
Hybridisation assays: for detection of mutation or polymorphism
C12Q 1/6874
Methods for sequencing: involving nucleic acid arrays, e.g. sequencing by hybridisation
G16B 20/20
ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations: allele or variant detection, e.g. single…

Provided herein are methods of obtaining phased human leukocyte antigen (HLA) types of a sample from an individual.

Dependent claims

A method of obtaining a phased human leukocyte antigen (HLA) type of a sample comprising:

(a) aligning a plurality of sequencing reads to a reference genome or a first variation graph, wherein at least a portion of said plurality of sequencing reads correspond to an HLA gene locus;
(b) identifying a plurality of single nucleotide polymorphisms (SNPs) or indels in said plurality of sequencing reads;
(c) sorting said plurality of SNPs or indels into phase blocks;
(d) aligning said plurality of sequencing reads to a second variation graph to identify a plurality of HLA types;
(e) comparing said plurality of HLA types to a plurality of known HLA alleles to obtain a SNP signature for each HLA allele;
and
(f) comparing said SNP signature of (e) to said phase blocks of (c) to obtain said phased HLA type.

4 more elements

Dependencies are inferred from the claim text.