Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics
S Ardui, A Ameur, JR Vermeesch… - Nucleic acids …, 2018 - academic.oup.com
Short read massive parallel sequencing has emerged as a standard diagnostic tool in the
medical setting. However, short read technologies have inherent limitations such as GC …
medical setting. However, short read technologies have inherent limitations such as GC …
Major histocompatibility complex genomics and human disease
J Trowsdale, JC Knight - Annual review of genomics and human …, 2013 - annualreviews.org
Over several decades, various forms of genomic analysis of the human major
histocompatibility complex (MHC) have been extremely successful in picking up many …
histocompatibility complex (MHC) have been extremely successful in picking up many …
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
The human reference genome represents only a small number of individuals, which limits its
usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for …
usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for …
OptiType: precision HLA typing from next-generation sequencing data
A Szolek, B Schubert, C Mohr, M Sturm… - …, 2014 - academic.oup.com
Motivation: The human leukocyte antigen (HLA) gene cluster plays a crucial role in adaptive
immunity and is thus relevant in many biomedical applications. While next-generation …
immunity and is thus relevant in many biomedical applications. While next-generation …
Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes
SA Shukla, MS Rooney, M Rajasagi, G Tiao… - Nature …, 2015 - nature.com
Detection of somatic mutations in human leukocyte antigen (HLA) genes using whole-
exome sequencing (WES) is hampered by the high polymorphism of the HLA loci, which …
exome sequencing (WES) is hampered by the high polymorphism of the HLA loci, which …
Imputing amino acid polymorphisms in human leukocyte antigens
DNA sequence variation within human leukocyte antigen (HLA) genes mediate susceptibility
to a wide range of human diseases. The complex genetic structure of the major …
to a wide range of human diseases. The complex genetic structure of the major …
Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
ET Lam, A Hastie, C Lin, D Ehrlich, SK Das… - Nature …, 2012 - nature.com
We describe genome mapping on nanochannel arrays. In this approach, specific sequence
motifs in single DNA molecules are fluorescently labeled, and the DNA molecules are …
motifs in single DNA molecules are fluorescently labeled, and the DNA molecules are …
HLA-B*13:01 and the Dapsone Hypersensitivity Syndrome
Background Dapsone is used in the treatment of infections and inflammatory diseases. The
dapsone hypersensitivity syndrome, which is associated with a reported mortality of 9.9 …
dapsone hypersensitivity syndrome, which is associated with a reported mortality of 9.9 …
A genomic perspective on HLA evolution
Several decades of research have convincingly shown that classical human leukocyte
antigen (HLA) loci bear signatures of natural selection. Despite this conclusion, many …
antigen (HLA) loci bear signatures of natural selection. Despite this conclusion, many …
HLA typing from RNA-Seq sequence reads
S Boegel, M Löwer, M Schäfer, T Bukur, J De Graaf… - Genome medicine, 2013 - Springer
We present a method, seq2HLA, for obtaining an individual's human leukocyte antigen
(HLA) class I and II type and expression using standard next generation sequencing RNA …
(HLA) class I and II type and expression using standard next generation sequencing RNA …