Mixed lymphocyte culture and HLA typing in a family with a recombination between loci of the major HLA histocompatibility system]

A new case of recombination at the HLA region has been established by mixte lymphocyte culture in the family of potential kidney recipient. Serological family study, MLC and HLA typing were performed to localize the recombination. This corroborates the primordial interest of MLC in family pretransplant matching.     

Neonatal lupus erythematosus: five new cases with HLA typing.

In two of five infants with neonatal lupus erythematosus the signs of the disease did not appear until the children had been exposed to direct sunlight. This suggests that an environmental factor may be required for the development of the disease in some patients. Three of the five patients, together with their mothers, had the HLA (histocompatibility) antigens A1 and B8, which supports the concept that individuals may be genetically susceptible to lupus erythematosus.     

Congenital deficiency of factor VII in a canine family

Prolonged prothrombin time in the blood coagulation test was seen in some beagle dogs whose activated partial prothrombin times were distributed within the normal range. This phenomenon suggested possible abnormalities in coagulation factors II, V, VII, and/or X. Therefore, a revised cross-matching test was given and a determination of coagulation factors related to the extrinsic system was performed. We also determined whether or not factor VII inhibitor was present. The results were as follows: 1) In the revised cross-matching test, the prolonged prothrombin times were revised when normal canine serum was added to the plasma that showed prolongation of prothrombin time, but not when pooled normal canine plasma absorbed with BaSO4 was added to it. 2) The level of factor VII in the plasma with prolonged prothrombin time was 5 approximately 10% of the level in normal canine plasma. 3) Factor VII inhibitor was not detected in the plasma with prolonged prothrombin time or in normal plasma. Consequently, the prolongation of prothrombin time was attributed to a deficiency in factor VII. This abnormality was confirmed to be congenital.     

A fault-tolerant method for HLA typing with PacBio data

Background

Human leukocyte antigen (HLA) genes are critical genes involved in important biomedical aspects, including organ transplantation, autoimmune diseases and infectious diseases. The gene family contains the most polymorphic genes in humans and the difference between two alleles is only a single base pair substitution in many cases. The next generation sequencing (NGS) technologies could be used for high throughput HLA typing but in silico methods are still needed to correctly assign the alleles of a sample. Computer scientists have developed such methods for various NGS platforms, such as Illumina, Roche 454 and Ion Torrent, based on the characteristics of the reads they generate. However, the method for PacBio reads was less addressed, probably owing to its high error rates. The PacBio system has the longest read length among available NGS platforms, and therefore is the only platform capable of having exon 2 and exon 3 of HLA genes on the same read to unequivocally solve the ambiguity problem caused by the “phasing” issue.

Results

We proposed a new method BayesTyping1 to assign HLA alleles for PacBio circular consensus sequencing reads using Bayes’ theorem. The method was applied to simulated data of the three loci HLA-A, HLA-B and HLA-DRB1. The experimental results showed its capability to tolerate the disturbance of sequencing errors and external noise reads.

Conclusions

The BayesTyping1 method could overcome the problems of HLA typing using PacBio reads, which mostly arise from sequencing errors of PacBio reads and the divergence of HLA genes, to some extent.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-296) contains supplementary material, which is available to authorized users.     

Nasopharyngeal carcinoma and Burkitt's lymphoma in a Canadian family. I. HLA typing,EBV antibodies and serum immunoglobulins.

Two nasopharyngeal carcinomas of the lymphoepithelioma type and two Burkitt''s lymphomas with the characteristic histopathologic features developed in three siblings and one first-degree cousin in a large French-Canadian family. Epstein-Barr virus antibody titres in the two lymphoepithelioma cases but not in the Burkitt''s lymphoma cases were, as expected, greatly elevated. HLA typing of the family members failed to disclose HLA antigens A2 and B Sin-2, which have been associated with lymphoepithelioma in Asia. The occurrence, however, of a plasmacytoma in one other first-degree cousin and low serum IgA values in several siblings and cousins suggests the possibility of a genetically determined predisposing B-cell dysfunction in the development of these tumours.     

HLA antigens in patients with and without a family history of schizophrenia

Frequencies of HLA antigens (A, B, C and DR) were studied in patients with (n = 49) and without (n = 67) a family history of schizophrenia and in controls. Among the patients with a family history of schizophrenia significant increases were found in the A3 and B5 antigens while significant decreases were observed for the A1, A11 and B8 antigens. In a material of schizophrenic siblings the sharing of HLA haplotypes was consistent with normal segregation.     

Segregation of HLA haplotypes in a family with infants having spina bifida]

The search for HLA association in spina bifida is particularly interesting since this condition can be associated with the effect of the T locus in mice. Gene and haplotype frequencies in 32 unrelated patients suffering from spina bifida were studied. Patients and families were examined clinically and radiologically. A high frequency of spina bifida occulta and other vertebral abnormalities was found suggesting genetic determinism but no evidence of linkage with HLA genes or haplotypes was found.     

Discrepancies in HLA typing by PCR-SSOP and SBT techniques: a case study

Six hundred twenty-one samples from Portugal, the Cabo Verde archipelago, and Guinea-Bissau were typed for HLA-A, HLA-B, and HLA-DRB1 using the polymerase chain reaction-sequence-specific oligonucleotide probe (PCR-SSOP) method and the sequence-based typing (SBT) method to characterize and compare discrepancies between the two methods. Fifty-three alleles (4.27% of 1242 chromosomes typed) identified by the PCR-SSOP method were not concordant with the results obtained using the SBT method. Thirty-four (2.74% of total chromosomes typed) PCR-SSOP mistyping results were discrepancies inside the same allele group and 19 others (1.53% of total chromosomes typed) were relative to nonconcordant results between different groups. PCR-SSOP allele mistyping is the result of interpretation difficulties resulting from less intense, absent, or dubious hybridization patterns. Noncommercial PCR-SSOP procedures are highly exigent on the technicians' experience and the availability of properly calibrated high-precision equipment.     

Red blood cell sorbitol dehydrogenase deficiency in a family with cataracts

Summary Sorbitol dehydrogenase (SORD) was quantitatively assayed in a family in which four out of five brothers and their father had bilateral cataracts. Three sibs (two of them with cataracts) and both their father and paternal grandfather had SORD activity of about 25% of the reference values; of the other two affected sibs one had about 50% and the other had 75%; the mother and two paternal uncles had about 75%. These results do not define a clear cataract-SORD deficiency etiopathogenic relationship, nevertheless, they strongly suggest activity polymorphism in human red cell SORD, which would be highly relevant not only to the study of cataracts but of other major complications in diabetes.     

G-6PD "ankara". a new G-6PD variant with deficiency found in a Turkish family.

A new G-6PD varient with enzyme deficiency is described in a 7-month-old Turkish boy without any hemolytic manifestation, except neonatal hyperbilirubinemia. The main characteristics of this variant were the following: Severe enzyme deficiency in erythrocytes (8% of normal), fast starch-gel-electrophoretic mobility (110% of normal), increased Ki NADPH with respect to NADP+, slightly biphasic pH curve, enzyme instability, in vivo and in vitro, decreased molecular specific activity (58% of normal).     

G6PD ciudad de la habana: A new slow variant with deficiency found in a cuban family

Summary A new G6PD variant has been detected in a Cuban male and there is no evidence of associated hematological abnormalities.The main characteristics of this variant, moderate deficiency, slow electrophoretic mobility, increased utilization of the substrate analogues, and a different chromatographic behavior, indicate that it is a variant that has not been previously described.     

The importance of HLA typing in cases of disputed paternity

In dispute paternity, the biologists must reply to two questions: 1. Is the paternity excluded or possible? 2. If it is possible, what is its probability? Valid answers can be given, using several genetic markers, among which HLA genes are specially interesting. Looking at HLA-A, B, C, DR typing of child, mother and presumed father, we propose a method which allows a direct calculation of paternity probability. Crossing over between HLA genes in presumed father and in mother are also considered in this method. In our experience, adding the date provided by the HLA genes and other genetic markers, we obtained, either formal exclusions, or possible paternities with a probability almost always higher than 90%.     

The importance of HLA DQB1*0602 typing in Slovene patients with narcolepsy

The HLA class II region genes DQB1*0602 and DQA1*0102 are currently the best genetic predictors for narcolepsy in humans (1(. The aim of this study was to identify the HLA DQ alleles (DQB1*0602 and DQA1*0102) in Slovene sporadic narcoleptic patients. 11 patients who fulfilled ICSD criteria for narcolepsy entered the study. DRB1*1501 DQB1*0602 was present in all the patients while DQA1*0102 was absent in 2 patients. We propose that DQB1*0602 typing is important in diagnosing narcolepsy in Slovene patients