Hemizygous Amplification and Sanger Sequencing of HLA-B*35:433 From an Umbilical-Cord Blood Sample.
HLA-B*35:433 was fully characterised using sequence-based typing after haplo-specific amplification.
Humans↗
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HLA Allele and Haplotype Frequencies Among Registered Unrelated Donors in the Western Region of Saudi Arabia.
The Saudi stem cell donor registry (SSCDR) has successfully recruited over 92,000 unrelated potential stem cell donors through nationwide campaigns. The Western region of Saudi Arabia is characterized by its unique ethnic diversity, shaped by centuries of immigration and pilgrimage. This study aimed to determine the distribution of HLA alleles and haplotypes among donors from this region. A total of 1112 donors registered with SSCDR were included, all recruited during campaigns conducted in the Western region between 2019 and 2021. Participants provided ancestry information to confirm their city of origin. High-resolution HLA typing for loci A, B, C, DRB1 and DQB1 was performed using sequence-based typing (SBT). Allele and haplotype frequencies were estimated for each subgroup using Arlequin 3.5 software. Distinct haplotype patterns were observed across cities. The most common haplotypes in the 1112 potential stem cell donors in the Western Region of Saudi Arabia were HLA-A*02:01∼C*07:02∼B*07:02∼DRB1*15:01∼DQB1*06:02 and HLA-A*02:01∼C*06:02∼B*50:01∼DRB1*07:01∼DQB1*02:01 in Jeddah; A*23:01∼C*06:02∼B*50:01∼DRB1*07:01∼DQB1*02:01 in Al-Madinah; HLA-A*26:01∼C*07:02∼B*08:01∼DRB1*03:01∼DQB1*02:01, HLA-A*30:01∼C*06:02∼B*13:02∼DRB1*07:01∼DQB1*02:01 and HLA-A*02:01∼C*06:02∼B*50:01∼DRB1*07:01∼DQB1*02:01 in Makkah; HLA-A*02:01∼C*15:02∼B*51:01∼DRB1*13:01∼DQB1*06:03 and HLA-A*02:01∼C*07:02∼B*07:02∼DRB1*15:01∼DQB1*06:02 in Al-Baha; and HLA-A*31:01∼C*15:02∼B*51:01∼DRB1*13:01∼DQB1*06:03 in Taif. HLA data are available in the Allele Frequencies Net Database (AFND: 3854, 3855, 3856, 3857 and 3858) under the population name 'Saudi Western Region'. In western Saudi Arabia, HLA allele and haplotype distributions demonstrate marked city-specific variation. Our research identifies DR7-, DR13- and DR15-based haplotypes as the most prevalent across the region. These findings are critical for optimizing unrelated donor searches for patients lacking compatible familial matches. Understanding these local frequencies allows for more targeted recruitment and better matching probabilities in stem cell registries.
Humans↗
HLA-DRB1*15:01 Is Associated and Linked With Kawasaki Disease, With DRB1*14:01 Conferring Risk to Coronary Artery Lesions: Case-Control and Family-Based Studies.
Kawasaki disease (KD), also known as mucocutaneous lymph node syndrome, is a leading cause of vasculitis in children aged < 5 years. The HLA complex has been investigated for its association with KD since 1978 without conclusive results due to limitations such as small sample sizes. This study aimed to evaluate the associations and genetic linkage between HLA-DRB1 and KD, as well as its complications. The case-control and family-based studies enrolled 795 patients with KD and 946 healthy controls. Of the 795 patients, 180 trios were included. Genotypes of HLA-DRB1 were identified by sequence-based typing according to the International ImMunoGeneTics database. Allele frequencies were calculated using PyPop 7.0. The transmission/disequilibrium test (TDT) was used to verify the genetic linkage between HLA-DRB1 and KD. HLA-DRB1*15:01 was significantly associated with KD (OR, 1.44, Pc = 0.03) and with KD without CALs (OR = 1.46, Pc = 0.04). HLA-DRB1*14:01 was a risk factor for KD with CALs (OR = 2.47, Pc = 0.004) whereas HLA-DRB1*12:02 was a protective factor against CALs (OR = 0.49, Pc = 0.01). In the family-based study, HLA-DRB1*15:01 demonstrated significant overtransmission to KD patients (OR = 3.35; 95% CI, 2.20-5.78; Pc = 1.19E-06) and to KD patients without CALs (OR = 4.42; 95% CI, 2.59-10.08; Pc = 6.24E-06). The overtransmission remained significant in male KD patients (OR = 2.81; 95% CI, 1.68-5.58; Pc = 0.003), and in male KD patients without CALs (OR = 3.22; 95% CI, 1.69-8.84; Pc = 0.02). Our study identified significant associations between HLA-DRB1*15:01, *14:01, and *12:02 with KD. The association between HLA-DRB1*15:01 and KD was further verified by TDT, indicating a genetic linkage between the HLA-DRB1 locus and KD susceptibility.
Humans↗
Next-Generation Sequencing-Based High-Resolution Typing of HLA-A, -B, -C and HPA Genes in Jilin Province: Building a Platelet Donor Database and Identifying Novel Alleles.
To systematically analyse HLA-A, -B and -C and human platelet antigen (HPA) genotypes of platelet donors in Jilin Province using next-generation sequencing (NGS) technology, a comprehensive donor database was established. Additionally, potential novel alleles were identified, providing a scientific basis for enhancing the safety of clinical blood transfusions. DNA fragments from 200 platelet donor samples in Jilin Province were amplified using locus-specific primers. Comprehensive sequencing of HLA and HPA genes was performed via NGS. Bioinformatics analysis was employed to process genotyping results and screen for novel genetic variants. Newly discovered alleles were validated by Sanger sequencing to ensure accuracy and reliability. HLA genotyping achieved three-field allele resolution, revealing the highest-frequency alleles are as follows: HLA-A*11:01:01, HLA-B*13:02:01, HLA-C*01:02:01 and C*03:04:01. A novel allele B*49:91 (mutation: E2 24T>C) was identified. For the HPA systems (HPA-1, -2, -3, -5, -6, -15, -21), high heterozygosity was observed in HPA-3 and HPA-15, while no bb homozygosity was detected in HPA-1, -2, -5, -6 or -21. The application of NGS in constructing a platelet HLA/HPA gene database enables high-resolution genotyping, laying a critical foundation for precise platelet matching. This significantly reduces the risk of platelet transfusion refractoriness (PTR) and facilitates the discovery of novel allelic variants. The database provides essential theoretical and practical guidance for future donor screening and personalised transfusion strategies.
Humans↗
The Novel HLA-B*15:751 Allele Identified Through Next Generation Sequencing in an Individual From Tamil Nadu, India.
HLA-B*15:751 differs from HLA-B*15:02:01:01 by a single nucleotide in exon 3, changing residue 103 from Valine to Leucine.
Humans↗
The HLA-C*12:04:04 Allele Identified by Next Generation Sequencing in an Individual From Tamil Nadu, India.
Novel HLA-C*12:04:04 differs from HLA-C*12:04:02:02 by a single synonymous nucleotide substitution in exon 5 (ATC>ATT).
Humans↗
Analysis with restriction endonucleases recognizing 4- or 5-base-pair sequences of human adenovirus type 3 isolated from ocular diseases in Sapporo, Japan.
A total of 49 adenovirus type 3 (Ad3) strains from patients with epidemic keratoconjunctivitis at an eye clinic in Sapporo, Japan, from 1983 to 1986 were classified into either genome type Ad3f (26 strains) or Ad3g (23 strains). By the use of Hinf1 and TaqI restriction endonucleases, they were classified into 11 and 3 subgenome types, respectively. During this observation period, two epidemics of Ad3 infection relating to epidemic keratoconjunctivitis occurred. The prevalent Ad3g strains isolated during the epidemic in 1983 belonged to a single subgenome type. However, in the course of the Ad3f epidemic in 1986, alteration of one subgenome type of the prevalent strain to a different subgenome type which was presumed to be a derivative of the former was observed. In the years in which only a few Ad3 strains were isolated, such Ad3f strains were classified into different subgenome types. However, all Ad3g strains except two belonged to the same subgenome type.
Adenoviruses, Human↗
HLA-DR, DQ and DP typing using PCR amplification and immobilized probes.
A simple, rapid, and precise method of typing HLA class II polymorphism would be valuable in the areas of disease susceptibility, tissue transplantation, individual identification and anthropological genetics. Here we describe a method of analysing class II sequence polymorphism based on polymerase chain reaction (PCR) amplification and hybridization with oligonucleotide probes. One valuable property of sequence-based HLA typing strategies, like oligonucleotide probe hybridization, is that they reveal how and where two alleles differ, not simply that they can be operationally distinguished. The nature and location of HLA polymorphisms appears to be critical in disease association studies and are likely to be important in tissue typing for transplantation. New alleles at the DRB1, DPB1 and DQB1 loci are likely to be identified as this technology is applied to more and more samples, particularly in non-Caucasian ethnic groups. A new allele is uncovered as an unusual pattern of probe binding and then confirmed by sequencing. This pattern is observed because class II polymorphism is localized to specific regions and virtually all 'new' alleles have polymorphisms in the region of probe binding. Obviously, any new allele with a new polymorphic sequence in a region for which typing probes are not available would not be revealed by oligonucleotide typing. With the PCR primers and probes described here, 7 DQA1 alleles, 15 DQB1 alleles, 18 DPB1 alleles, and 32 DRB1 alleles are distinguished. Additional primers and/or probes can, of course, increase the allelic discrimination of oligonucleotide dot blot typing. These horseradish peroxidase (HRP)-labelled oligonucleotide probes are stable (greater than 2 years when stored at 4 degrees C) and the typing system is simple and robust. Over 500 samples from the CEPH pedigrees (unpublished data; A. B. Begovich, et al., manuscript in preparation) and greater than 1000 unrelated samples have been typed by this procedure. Although this dot blot/oligonucleotide hybridization procedure is a powerful and precise method of HLA class II typing, the complexity of the procedure increases as the number of probes required for analysis increases. The reverse dot blot method, based on an array of immobilized probes, allows the typing of individual samples in one single hybridization reaction. In this approach, a panel of unlabelled oligonucleotides are immobilized to a nylon membrane. The PCR product is labelled during the amplification reaction by using biotinylated primers and hybridized to the membrane. The presence of bound PCR product specifically hybridized to a given probe is detected using streptavidin-HRP conjugates and either chromogenic or chemiluminescent substrates.(ABSTRACT TRUNCATED AT 400 WORDS)
Amino Acid Sequence↗
Typing of human rhinoviruses based on sequence variations in the 5' non-coding region.
Unambiguous assignment of restriction enzyme patterns to six individual serotypes of human rhinovirus was accomplished after amplification of a 380 bp DNA fragment derived from the 5' non-coding region. This was possible even though serotypes 1A and 1B and serotypes 2 and 49 differed only at 10 and 15 positions respectively. The method utilizes the conserved and variable components of this part of the genome and provides the basis for a simple and rapid method for typing of human rhinoviruses.
Base Sequence↗
Thirteen Novel HLA Class I Alleles Identified in a Brazilian Population Using NGS-Based Typing.
Eight nonsynonymous and five synonymous HLA class I variants identified in admixed Brazilian individuals.
Humans↗
Detection and typing of human papillomavirus in archival cervical cancer specimens by DNA amplification with consensus primers.
We developed a polymerase chain reaction DNA amplification system using two distinct consensus oligonucleotide primer sets for the improved detection and typing of a broad spectrum of human genital papillomavirus (HPV) sequences, including those of novel viruses. The system incorporates one primer set designed to amplify a highly conserved L1 domain and a second primer set designed to amplify a domain within the E6 gene. We used this system to analyze 48 fixed, paraffin-embedded tissue sections (41 specimens from 33 cervical carcinomas, four normal cervical tissues, and several control tissues) for the presence of HPV DNA. HPV sequences were detected in all carcinoma samples and none of the control samples. Hybridization analyses showed that the results obtained with the two amplification schemes concurred completely. This approach allowed rapid confirmation of typing results and may improve the likelihood of detecting a wide variety of HPV sequences, including those of novel HPVs.
Adenocarcinoma↗
Deletion of the HLA-B Gene in One of the Inherited Haplotypes in a Northern European Family.
Targeted next generation sequencing-based HLA typing of a 17-year-old female transplant patient showed homozygosity for the HLA-B allele. The segregation analysis of HLA haplotypes of family members only allowed the conclusion that the B-allele was deleted in the haplotype inherited from the father and accordingly paternal grandfather, resulting in false homozygous genotyping. The subsequent whole-genome sequencing of the patient and her father confirmed an approximately 85 kb deletion at 6p21.33 from the 5' end of the HLA-B to the 3' end of the HLA-C gene extending telomeric to HLA-C.
Adolescent↗
Rabbit surfactant protein C: cDNA cloning and regulation of alternatively spliced surfactant protein C mRNAs.
Surfactant protein C (SP-C), a hydrophobic protein of pulmonary surfactant is essential for surfactant function. Toward elucidating molecular mechanisms that mediate regulation of SP-C gene expression in rabbit lung, we isolated and characterized cDNAs encoding rabbit SP-C and studied the regulation of SP-C gene expression during fetal lung development and by adenosine 3',5'-cyclic monophosphate (cAMP) and dexamethasone in fetal lung tissues in vitro. We found that rabbit SP-C is highly homologous to SP-C of other species and is encoded by two mRNAs that differ by an insertion of 31 nucleotides in the 3' untranslated regions. SP-C mRNAs were classified into two types based on the nucleotide sequence; type I represents RNA without the 31 nucleotide insert and comprises approximately 80-90% of total SP-C mRNA content, whereas type II represents RNA containing the insert and comprises approximately 10-20% of total SP-C mRNA content. SP-C mRNAs were induced in a coordinate manner during fetal lung development and by cAMP and dexamethasone in fetal lung tissues in vitro. Southern hybridization analysis of genomic DNA suggested that SP-C mRNAs are encoded by a single gene. Polymerase [corrected] chain reaction-amplification of genomic DNA with oligonucleotide primers flanking the insertional sequence and sequence analysis of amplified DNA showed that SP-C mRNAs are produced by alternative use of 3' splice sites of intron 5 of SP-C gene.
Amino Acid Sequence↗
Detection of the HLA-A*02:924 Allele, a Variant of A*02:07:01:01, in a Taiwanese Individual.
One nucleotide mutation in exon 4 of HLA-A*02:07:01:01 results in the novel allele, HLA-A*02:924.
Humans↗
Detection of the HLA-B*15:88 Allele in a Taiwanese Individual.
Two nucleotide substitutions in codon 152 of HLA-B*15:02:01:01 result in a novel allele, HLA-B*15:88.
Humans↗
Recognition of the HLA-C*05:37 Allele in a Taiwanese Individual.
One nucleotide substitution in codon 186 of HLA-C*05:01:01:01 results in a novel allele, HLA-C*05:37.
Humans↗
Detection of the HLA-B*54:21 Allele, a Variant of B*54:01:01:01, in a Taiwanese Individual.
One nucleotide mutation in exon 2 of HLA-B*54:01:01:01 results in the novel allele, HLA-B*54:21.
Humans↗
The Novel HLA-DPB1*1772:01 Allele, Identified by Sanger Dideoxy Nucleotide Sequencing in a Chinese Individual.
The HLA-DPB1*1772:01 allele differs from HLA-DPB1*05:01:01:01 by a single non-synonymous nucleotide change in exon 2.
Humans↗