Closest Matching Allele Research Articles

Using Next-Generation Sequencing Technology to Confirm the HLA Rare Alleles Detected by PCR-SSOP

To confirm the HLA genotypes of the samples including 4 cases of magnetic bead probe HLA genotyping result pattern abnormality and 3 cases of ambiguous result detected by PCR sequence-specific oligonudeotide probe (SSOP) method. All samples derived from HLA high-resolution typing laboratory were detected by PCR-SSOP. A total of 4 samples of magnetic bead probe HLA genotyping result pattern abnormality and 3 samples of ambiguous result were further confirmed by PCR sequence-based typing (SBT) technology and next-generation sequencing (NGS) technology. A total of 4 samples of magnetic bead probe HLA genotyping result pattern abnormality were detected by PCR-SSOP method. The results of SBT and NGS showed that the HLA-A genotype of sample 1 did not match any known genotypes. NGS analysis revealed that the novel allele was different from the closest matching allele A*31:01:02:01at position 154 with G>A in exon 2, which resulting in one amino acid substitution at codon 28 from Valine to Methionine (p.Val28Met). The HLA-C genotype of sample 2 was C*03:119, 06:02, sample 3 was C*03:03, 07:137, and sample 4 was B*55:02, 55:12. A total of 3 samples with ambiguous result were initially detected by PCR-SSOP method. The re-examination results of SBT and NGS showed that the HLA-B genotype of sample 5 was B*15:58, 38:02, sample 6 was DRB1*04:05, 14:101, and sample 7 was DQB1*03:34, 05:02. Among them, alleles C*03:119, C*07:137 and DRB1*14:101 were not included in the Common and Well-documented Alleles (CWD) v2.4 of the Chinese Hematopoietic Stem Cell Donor Database. The abnormal pattern of HLA genotyping results of magnetic probe by PCR-SSOP method suggests that it may be a rare allele or a novel allele, which needs to be verified by sequencing.

Sequence analysis and 3D molecular structure simulation of a novel HLA allele B*51:159

To identify a novel human leukocyte antigen (HLA) B allele in a Chinese Han individual and construct its three-dimensional structure. The initial HLA genotyping was performed by PCR-sequence-based typing (PCR-SBT). The ambiguous allele was confirmed with single-strand DNA sequencing. The DNA sequence was analyzed to identify the difference between the novel allele and its closest matching allele. Finally, the three-dimensional molecular structure of the novel allele was constructed using a Swiss-Model. One allele of the subject at the HLA-B locus was B*44:03:01, whilst the other was a novel allele which differed from the closest matching allele B*51:01:01:01 by nucleotide (nt) 329 A to C in exon 2, resulting in an amino acid change at codon 86 (p.Asn86Thr). A novel HLA-B allele has been identified and officially named as HLA-B*51:159 by the WHO Nomenclature Committee for Factors of the HLA System. The three-dimensional structure of B*51:159 was simulated.

A novel HLA-A allele, HLA-A*68:01:42, identified by next-generation sequencing in a Chinese individual.

The novel HLA-A*68:01:42 allele differs from the closest matching allele, HLA-A*68:01:02:02 by one nucleotide substitution.

Discovery of a novel HLA-B*07 variant, HLA-B*07:294, in a Chinese individual.

The novel HLA-B*07:294 allele differs from the closest matching allele, HLA-B*07:02:01 by 1 nucleotide substitution.

Identification of a novel HLA‐DQB1 allele, DQB1*05:19, in an African American family by sequence‐based typing

The novel allele, DQB1*05:19, differs from the closest matching allele, DQB1*05:02:01, by one nucleotide substitution.

Identification of a novel HLA allele HLA-B*55:35

To identify a novel human leukocyte antigen (HLA) B allele and explore its family heritage. A novel HLA allele was suspected upon routine HLA typing using a polymerase chain reaction-sequence specific oligonucleotide probe (PCR-SSOP) assay. The sequence was confirmed with DNA sequencing and compared with its closest matching allele, B*55:02. The family was also investigated. An unusual reaction pattern was detected during routine HLA typing. The sequence was confirmed to be a novel HLA-B allele, which differed from the closest matching allele, B*55:02 in 7 nt positions in exon 2. Among the 7 mutations from 6 codons, there were two amino acids changes including 69Glu→Met and 70Glu→Ala. A novel HLA-B allele has been identified and officially named as B*55:35 by the WHO Nomenclature Committee for Factors of the HLA System (GenBank accession number FJ898284).

Identification of a novel HLA‐B allele HLA‐B*55:34 in a Chinese individual

The HLA-B*55:34 allele differs from the closest matching allele B*55:02:01 by one nucleotide substitution in exon 2.

Identification of a new HLA allele, HLA‐DRB1*03:80, in a Chinese Han ethnic individual

The new allele DRB1*03:80 has a single nucleotide change at position 239(C→G) in exon 2 from the closest matching allele DRB1*03:06.

Identification of a novel HLA‐DRB1*11:129 allele in a Chinese individual by sequence‐based typing

The new DRB1*11:129 allele differs from the closest matching allele HLA-DRB1*11:06:01 by one nucleotide substitution in exon 3 at position 623 (G→A).

Identification of the novel HLA‐B allele, HLA‐B*39:42, in a Chinese individual

The HLA-B*39:42 allele differs from the closest matching allele B*39:01:01:01 by two nucleotide substitutions in exon 3.

Identification of a novel HLA‐A allele HLA‐A*02:227N

The HLA-A*02:227N allele differs from the closest matching allele A*02:01:01:01 by one nucleotide substitution in exon 3 at nt 610 (C→T).

Identification of a novel HLA‐B allele HLA‐B*13:20 in a Chinese individual

The HLA-B*13:20 allele differs from the closest matching allele B*13:01:01 by one nucleotide substitution in exon 3 at nt 527 (T→A).

Identification of the novel HLA‐A allele, HLA‐A*24:96, in a Chinese individual

The human leukocyte antigen (HLA)-A*24:96 allele differs from the closest matching allele A*24:01:01:01 by three nucleotide substitutions in exon 3 at nt 411(C->T), nt 412(C->A) and nt 419(A->T).

Identification of a novel HLA‐B allele, HLA‐B*13:19, in a Chinese individual

The HLA-B*13:19 allele differs from the closest matching allele B*13:02:01 by one nucleotide substitution in exon 3 at nt 268(A->G).

A novel HLA-B*40 allele, HLA-B*40:74, detected in a Chinese individual

The HLA-B*40:74 allele has two nucleotide changes at positions 103 and 106 of exon 2 from the closest matching allele HLA-B*40:01:01.

Identification of a novel HLA-C allele, HLA-C*04:82, by sequence-based typing in a Chinese individual

A novel HLA allele, C*04:82, was identified in a Chinese individual, which has nine nucleotides insertion compared with the closest matching allele HLA-C*04:01:01 in exon 5, resulting in three amino acid insertions: 301 Ala, 302 Val and 303 Leu.

Identification of a novel HLA-B*15 allele (B*9552) by sequence-based typing in a Chinese donor

A novel human leukocyte antigen B allele, B*9552, has been identified by sequence-based typing in a donor of Chinese Marrow Donor Program, which has one nucleotide change at position 272 (C-->A) in exon 2 from the closest matching allele B*15010101, resulting in an amino acid substitution from Ser to Tyr at codon 91.

A novel HLA-B allele, B*5535, was identified by sequence-based typing in a Chinese individual

A novel human leukocyte antigen (HLA)-B allele, B*5535, has been identified in a Chinese individual by sequence-based typing, which has seven nucleotide changes from the closest matching allele B*5502 resulting in two amino acids changes: 69 Glu-->Met; 70 Glu-->Ala.

Identification of a novel HLA allele HLA-B*9526

A novel human leukocyte antigen-B (HLA-B) allele, B*9526, was identified and analyzed by sequencing-based method in a Chinese donor. HLA typing was performed by PCR-sequence-specific oligonucleotide (SSO). Molecular cloning and DNA sequencing were used to identify the sequence of the potential novel allele and the difference between this new allele and other known alleles were analyzed. HLA genotyping of one sample gave different results. The sequencing result showed HLA-B alleles of the proband as B*5403 and a novel allele. The nucleotide sequence of the novel allele was different from all known B alleles and harbored one nucleotide change from the closest matching allele B*1507 at nucleotide 425 (A to G) in exon 3, resulting in an amino acid change from Y (TAC) to C (TGC) at codon 142. A novel HLA allele was identified and officially designated as HLA-B*9526 by WHO Nomenclature Committee for Factors of the HLA System.

A novel HLA‐B allele, B*4096 was identified by sequence‐based typing in a Chinese individual

A novel HLA-B allele, B*4096, has been identified in a Chinese individual by sequence-based typing, which has seven nucleotide changes from the closest matching allele B*40060101 resulting in five amino acid changes: 101Ser-->Asn; 104Ser-->Thr; 105Leu-->Ala; 106Arg--> Leu and 107Gly-->Arg.