Detection of the HLA-A*11:127N allele in a Taiwanese individual.

A nucleotide mutation in codon 171 of HLA-A*11:01:01:01 results in a novel allele HLA-A*11:127N.

Discovery of a novel HLA-A*11 null allele, HLA-A*11:466N, in a Taiwanese individual.

A nucleotide deletion in the residue 371 of HLA-A*11:01:01:01 results in a novel allele HLA-A*11:466N.

Identification of the novel null allele HLA-DPB1*1449:01N by next-generation sequencing.

The novel HLA-DPB1*1449:01N allele differs from HLA-DPB1*16:01:01:01 by a nucleotide at codon 92 in exon 2.

HLA-C*05:292N, a novel HLA-C null allele identified by next-generation sequencing.

HLA-C*05:292N differs from HLA-C*05:01:01:08 by a frameshift mutation, a deletion at gDNA position 758.

Discovery of the novel HLA-A*11:452N allele by next-generation sequencing in a Chinese individual.

HLA-A*11:452N differs from A*11:01:01:01 by a single nucleotide exchange in exon 1.

Genomic sequence of the novel HLA-A*26:206:02N allele, identified in a patient with hepatitis B infection.

HLA-A*26:206:02N differs from A*26:01:01:01 by a single nucleotide exchange in exon 3.

Relation between αS1-casein, genotype, and quality traits of milk from Swedish dairy goats.

Locally produced food is becoming popular among Swedish consumers. One product that has increased in popularity is artisan-manufactured goat cheese, and although the dairy goat industry in Sweden is small-scale, production is gradually increasing. In goats, the CSN1S1 gene regulates expression of the protein αS1-casein (αS1-CN), which has been found to be important for cheese yield. Over the years, breeding animals have been imported to Sweden from Norway. Historically, a high frequency of the Norwegian goat population carried a polymorphism at the CSN1S1 gene. This polymorphism, called the Norwegian null allele (D), leads to zero or significantly reduced expression of αS1-CN. Using milk samples from 75 goats, this study investigated associations between expression of αS1-CN and genotype at the CSN1S1 gene on milk quality traits from Swedish Landrace goats. Milk samples were grouped according to relative level of αS1-CN (low: 0-6.9% of total protein; medium-high: 7-25% of total protein) and genotype (DD, DG, DA/AG/AA). While the D allele leads to extremely low expression of αS1-CN, the G allele is low expressing and the A allele is highly expressing for this protein. Principal component analysis was used to explore the total variation in milk quality traits. To evaluate the effect of different allele groups on milk quality attributes, 1-way ANOVA and Tukey pairwise comparison tests were used. The majority (72%) of all goat milk samples investigated showed relative αS1-CN content of 0% to 6.82% of total protein. The frequency of individuals homozygous for the Norwegian null allele (DD) was 59% in the population of sampled goats, and only 15% carried at least one A allele. A low relative concentration of αS1-CN was associated with lower total protein, higher pH, and higher relative concentration of ß-casein and levels of free fatty acids. Milk from goats homozygous for the null allele (DD) showed a similar pattern as milk with low relative concentration of αS1-CN, but total protein was only numerically lower, and somatic cell count and αS2-CN were higher than for the other genotypes. The associations between levels of αS1-CN and the investigated genotype at the CSN1S1 gene indicate a need for a national breeding program for Swedish dairy goats.

Genetic inconsistency at the D6S1043 locus caused by microdeletion at 6q15.

In the practice of parentage testing, short tandem repeat (STR) genetic inconsistencies occasionally occur and are usually treated as genetic mutations. However, they arise for various reasons. To elucidate the reasons for their occurrence, this study investigates a typical trio. For the D6S1043 locus, the genotype of the biological mother comprised the heterozygous alleles "7,20"; that of the child, allele 20; and that of the alleged father, a heterozygous allele "11,13," revealing a 7-step mutation. Different kits were first used to verify the data. The locus map, primers, and core sequences were then analyzed. Ultimately, the STR and single nucleotide polymorphisms of 6q were tested to determine the microdeletion range. The results revealed that this was indeed a true trio, and the underlying cause of the genetic inconsistency at this locus was a microdeletion of approximately 0.74-1.78 Mb in 6q15. Overall, genetic inconsistencies detected during practical work, and particularly rare multi-step mutations, cannot be directly identified as STR mutations. Different tools should be used to examine the causes of genetic inconsistencies from various perspectives and improve the effectiveness of genetic evidence.

Characterization of a novel HLA-C allele, HLA-C*05:278N.

The novel HLA-C*05:278N allele has a premature stop codon in exon 4.

Identification of two new HLA-DRB1*07 alleles: HLA-DRB1*07:143N and HLA-DRB1*07:144.

HLA-DRB1*07:143N and HLA-DRB1*07:144 differ from DRB1*07:01:01:01 by single mismatches in exons 3 and 2 respectively.

Identification of the novel HLA-DPB1*1455:01N allele in a French living organ donor.

The novel HLA-DPB1*1455:01N allele differs from DPB1*05:01:01:01 by one amino acid deletion in exon 3.

Generation of Conditional Knockout Alleles for PRUNE-1.

PRUNE1 is a member of the aspartic acid-histidine-histidine (DHH) protein superfamily, which could display an exopolyphosphatase activity and interact with multiple cellular proteins involved in the cytoskeletal rearrangement. It is widely expressed during embryonic development and is essential for embryogenesis. PRUNE1 could also be critical for postnatal development of the nervous system as it was found to be mutated in patients with microcephaly, brain malformations, and neurodegeneration. To determine the cellular function of PRUNE1 during development and in disease, we have generated conditional mouse alleles of the Prune1 in which loxP sites flank exon 6. Crossing these alleles with a ubiquitous Cre transgenic line resulted in a complete loss of PRUNE1 expression and embryonic defects identical to those previously described for Prune1 null embryos. In addition, breeding these alleles with a Purkinje cell-specific Cre line (Pcp2-Cre) resulted in the loss of Purkinje cells similar to that observed in patients carrying a mutation with loss of PRUNE1 function. Therefore, the Prune1 conditional mouse alleles generated in this study provide important genetic tools not only for dissecting the spatial and temporal roles of PRUNE1 during development but also for understanding the pathogenic role of PRUNE1 dysfunction in neurodegenerative or neurodevelopmental disease. In addition, from this work, we have described an approach that allows one to efficiently generate conditional mouse alleles based on mouse zygote electroporation.

Detection and characterization of the novel HLA-DPA1*02:66:02N allele, with a premature stop codon in exon 2.

The failure to identify HLA null alleles in bone marrow transplantation could be life-threatening because this could result in an HLA mismatch with the ability to trigger the graft-vs-host disease (GVHD) and to reduce patient's survival. In this report we describe the identification and characterization of the novel HLA-DPA1*02:66:02N allele with a non-sense codon in exon 2. This new allele was discovered in two unrelated bone marrow donors during routine HLA-typing using next-generation sequencing (NGS). DPA1*02:66:02N is homologous to DPA1*02:01:01:03 with a single nucleotide difference in exon 2, codon 50, where the replacement of C located at genomic position 3825 by T, causes the formation of a premature stop codon (TGA), resulting in a null allele. This description illustrates the benefits of HLA typing by NGS since it permits to reduce ambiguities, identify new alleles, analyze multiple HLA loci and improve transplantation outcome.

Identification of a novel HLA-C allele, HLA-C*03:618N.

The novel HLA-C*03:618N allele has one change in exon 1 leading to a premature stop codon.

Identification of three new HLA alleles, HLA-A*68:298, HLA-C*07:1054N and HLA-DRB1*15:216.

Three new HLA alleles characterized by next-generation sequencing, HLA-A*68:298, HLA-C*07:1054N and HLA-DRB1*15:216.

A novel null-allele, HLA-B*35:574N, containing a mutation in the start-codon.

HLA-B*35:574N contains a single nucleotide substitution at nucleotide position 2 (ATG to ACG).

Identification of a novel HLA-A null allele, HLA-A*01:420N allele.

The novel HLA-A*01:420N allele has two changes in exon 4 leading to premature stop codon.

Large fragment Sanger sequencing identifies the newly encountered variant that caused null alleles in parentage testing.

Short tandem repeat (STR) is regarded as a crucial tool for personal identification as well as parentage testing. Thus, genotyping errors of STRs could have negative effects on the reliability of forensic identification. A null allele at the combined DNA index system (CODIS) core loci D2S1338 was found in a father-daughter pair with the AGCU Expressmarker 22 kit which was a commonly used commercial kit during our daily laboratory work. This null allele caused the father and daughter to not conform to the laws of inheritance, thus potentially generating erroneous conclusions that excluded parentage. To figure out the reason for this phenomenon, re-amplification with new primers and then large fragment Sanger sequencing was conducted. We found a G to G/T variation at the position which is fifty-nine bases away from the 3' end of the core repeat in both samples. This probably could be considered a novel variant at the primer binding region which had not been reported that resulted in the emergence of the null allele. We also found that there was more than one single-nucleotide polymorphism (SNP) with minor allele frequency (MAF) greater than 0.1 in the upstream and downstream sequences of D2S1338. When designing primers for amplification of D2S1338, the possible adverse results of these SNPs should be taken into account and avoided.

Identification of a novel allele with a frameshift mutation, HLA-DRB4*01:165N, using next-generation sequencing.

HLA-DRB4*01:165N exhibits deletion of a nucleotide in exon 3, producing a premature stop codon.

Discovery of a novel HLA-C*04 null allele, HLA-C*04:279N, in a Singaporean individual.

A nucleotide mutation in codon 75 of HLA-C*04:01:01:01 results in a novel allele HLA-C*04:279N.