HLA class I nucleotide sequences, 1992

The HLA class I sequences included in this compilation are taken from publications listed in the papers: Nomenclature for factors of the HLA system, 1991 (Bodmer et al. 1992); Nomenclature for factors of the HLA system, 1990 (Bodmer et al. 1991); and Nomenclature for factors of the HLA system, 1989 (Bodmer et al. 1990). Due to the increased number of sequences we have only included sequences for exons 2, 3, and 4 in this compilation. Where discrepancies have arisen between reported sequences, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments, identify between nucleotides is indicated by a hyphen (-). An unavailable sequence is indicated by a period (.). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number. *** DIRECT SUPPORT *** A4903038 00002     

HLA class II nucleotide sequences, 1991

The HLA class II sequences included in this compilation are taken from publications listed in the accompanying paper, Nomenclature for factors of the HLA system, 1990 (Bodmer et al. 1991) and Nomenclature for factors of the HLA system, 1989 (Bodmer et al. 1990). Where discrepancies have arisen between reported sequences the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments identity between residues is indicated by a hyphen (-). Unavailable sequence is indicated by an asterisk (*). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number.     

HLA class I nucleotide sequences, 1991

The HLA class I sequences included in this compilation are taken from publications listed in the accompanying paper, Nomenclature for factors of the HLA system, 1990 (Bodmer et al. 1991) and Nomeclature for factors of the HLA system, 1989 (Bodmer et al. 1990). Where discrepancies have arisen between reported sequences the original authors have been contavted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments identify between residues is indicated by a hyphen (-). Unavailable sequence is indicated by a period (.). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number.     

Sequence of a novel HLA-DQB1 allele

The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence data base and have been assigned the accesion number M74842. The name DQB1*0304 has been officially assigned by the WHO Nomenclature Committee in November 1991. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report (WHO Nomenclature Committee for factors of the HLA system, 1991), names will be assigned to new sequences as they are identified. List of such new names will be published in the following WHO Nomenclature Report.     

DPB1 * BR: an Mhc class II DPB1 allele (DPB1 * 6601) of negroid origin

The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession number X96986. The nameDPB1 ^* 6601 was officially assigned by the WHO Nomenclature Committee in May 1996. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report (Bodmer et al. 1995), names will be assigned to new sequences as they are identified. Lists of such sequences will be published in the following WHO Nomenclature Report     

A new HLA-B44 subtype,B*4406, differing in exon 2

The name B ^*4406 was officially assigned by the WHO Nomenclature Committee in February 1995. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report (Bodmer et al. 1994), names will be assigned to new sequences as they are identified. Lists of such new names will be published in the following WHO Nomenclature Report. The nucleotide sequences reported in this Papers have been submitted to the EMBL nucleotide sequence database and have been assigned the accession numbers X83400 (HLA-B promoter region), X83401 (exon 1), X83402 (exon 2), and X83403 (exon 3)     

Human KIR sequences 2003

We have compiled the nucleotide sequences and their amino acid translations from a total of 89 Killer Immunoglobulin-like Receptor (KIR) alleles, derived from 17 different KIR genes. The alignments use the KIR3DL2*001 allele as a reference sequence. Each of the KIR sequences included in these alignments has been checked and where discrepancies have arisen between reported sequences, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation.     

Cw * 1505: a novel HLA-C allele isolated from a B * 7301 haplotype

The nucleotide sequence data reported in this paper have been submitted to the EMBL database and have been assigned the accession number X78343. The name Cw ^*1505 was officially assigned by the WHO Nomenclature Committee in May 1994. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report (The WHO Nomenclature Committee 1992), names will be assigned to new sequences as they are identified. Lists of such new names will be published in he following WHO Nomenclature Report     

A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes

Background  

Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the multiple alignment or profile as a whole, S is compared and aligned to individual sequences from A. Within this alignment, S can jump between different sequences from A, so different parts of S can be aligned to different sequences from the input multiple alignment. This approach is particularly useful for dealing with recombination events.     

Nucleotide sequencing analysis of the swine 433-kb genomic segment located between the non-classical and classical<Emphasis Type="Italic"> SLA</Emphasis> class I gene clusters

Genome analysis of the swine leukocyte antigen (SLA) region is needed to obtain information on the MHC genomic sequence similarities and differences between the swine and human, given the possible use of swine organs for xenotransplantation. Here, the genomic sequences of a 433-kb segment located between the non-classical and classical SLA class I gene clusters were determined and analyzed for gene organization and contents of repetitive sequences. The genomic organization and diversity of this swine non-class I gene region was compared with the orthologous region of the human leukocyte antigen (HLA) complex. The length of the fully sequenced SLA genomic segment was 433 kb compared with 595 kb in the corresponding HLA class I region. This 162-kb difference in size between the swine and human genomic segments can be explained by indel activity, and the greater variety and density of repetitive sequences within the human MHC. Twenty-one swine genes with strong sequence similarity to the corresponding human genes were identified, with the gene order from the centromere to telomere of HCR - SPR1 - SEEK1 - CDSN - STG - DPCR1 - KIAA1885 - TFIIH - DDR - IER3 - FLOT1 - TUBB - KIAA0170 - NRM - KIAA1949 - DDX16 - FLJ13158 - MRPS18B - FB19 - ABCFI - CAT56. The human SEEK1 and DPCR1 genes are pseudogenes in swine. We conclude that the swine non-class I gene region that we have sequenced is highly conserved and therefore homologous to the corresponding region located between the HLA-C and HLA-E genes in the human.The nucleotide sequence data reported in this paper have been submitted to DDBJ, EMBL and GenBank databases under accession numbers AB113354, AB113355, AB113356, AB113357     

An HLA-C-specific DNA probe

Analysis of available nucleotide sequence data for class I HLA genes has established that the seventh intron is one of the gene regions which expresses the highest degree of locus specificity (the percentage sequence divergence between nonallelic genes minus the percentage sequence divergence between allelic genes). We have subcloned short DNA sequences including this region from the HLA-Cw3 gene. Two clones, pC250 and pC800, were tested by hybridizing them at high stringency to a panel of clones containing class I HLA genes. Under conditions permitting a strong hybridization signal with a C-locus gene, pC800 also expressed a weak but significant hybridization to other class I genes, while pC250 appeared to hybridize exclusively to the C-locus gene. Hybridization of the pC250 probe at high stringency to Hind III-digested genomic DNA from a panel of unrelated individuals and homozygous typing cell lines revealed a single band in all cases. However, equivalent hybridization against Eco RI-digested DNA revealed two hybridization bands, one at 7.9 kb which correlated with the serologically defined Cw5 and Cw8 alleles, and one at 7.6 kb which correlated with the Cw1, Cw2, Cw3, Cw4, Cw6, and Cw7 alleles.     

A new DRB1 allele (DRB1 * 0811) identified in Native Americans

The nucleotide sequence data reported here have been submitted to the Genome Sequence Database and have been assigned the accession number L32810. The name DRB1 ^*0811 was officially assigned by the WHO Nomenclature Committee in March 1994. This follows the policy that, subject to the conditions stated in the most recent Nomenclature Report (Bodmer et al. 1992), names will be assigned to new sequences as they are identified. Lists of such new names will be published in the following WHO Nomenclature Report     

HLA class II haplotype and sequence analysis support a role for DQ in narcolepsy

 A systematic haplotype and sequencing analysis of the HLA-DR and -DQ region in patients with narcolepsy was performed. Five new (CA)_n microsatellite markers were generated and positioned on the physical map across the HLA-DQB1-DQA1-DRB1 interval. Haplotypes for these new markers and the three HLA loci were established using somatic cell hybrids generated from patients. A four-marker haplotype surrounding the DQB1 ^* 0602 gene was found in all narcolepsy patients, and was identical to haplotypes observed on random chromosomes harboring the DQB1 ^* 0602 allele. Eighty-six kilobases of contiguous genomic sequence across the region did not reveal new genes, and analysis of this sequence for single nucleotide polymorphisms did not reveal sequence variation among DQB1 ^* 0602 chromosomes. These results are consistent with other studies, suggesting that the HLA-DQ genes themselves are among the predisposing factors in narcolepsy. Received: 18 March 1997 / Revised: 23 April 1997     

HLA-B alleles of the Cayapa of Ecuador: new B39 and B15 alleles

Recent data suggest that HLA-B locus alleles can evolve quickly in native South American populations. To investigate further this phenomenon of new HLA-B variants among Amerindians, we studied samples from another South American tribe, the Cayapa from Ecuador. We selected individuals for HLA-B molecular typing based upon their HLA class II typing results. Three new variants of HLA-B39 and one new variant of HLA-B15 were found in the Cayapa: HLA-B ^*3905, HLA-B^*3906, HLA-B^*3907, and HLA-B ^*1522. A total of thirteen new HLA-B alleles have now been found in the four South American tribes studied. Each of these four tribes studied, including the Cayapa, had novel alleles that were not found in any of the other tribes, suggesting that many of these new HLA-B alleles may have evolved since the Paleo-Indians originally populated South America. Each of these 13 new alleles contained predicted amino acid replacements that were located in the peptide binding site. These amino acid replacements may affect the sequence motif of the bound peptides, suggesting that these new alleles have been maintained by selection. New allelic variants have been found for all common HLA-B locus antigenic groups present in South American tribes with the exception of B48. In spite of its high frequency in South American tribes, no evidence for variants of B48 has been found in all the Amerindians studied, suggesting that B48 may have unique characteristics among the B locus alleles.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers U14756 (HLA-B ^*1522), U15683 (HLA-B ^*3905), U15639 (HLA-B ^*3906), and U15640 (HLA-B ^*3907)The names listed for these sequences were officially assigned by the WHO nomenclature Committee in September 1994, B ^*3905, and November 1994, B ^*1522, B^*3906, and B ^*3907. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report (Bodmer et al. 1994), names will be assigned to the new sequences as they are identified. Lists of such new names will be published in the following WHO Nomenclature Report.     

The HLA-AW24 gene: Sequence,surroundings and comparison with the HLA-A2 and HLA-A3 genes

A cosmid clone containing two class I sequences was found to cause expression of the HLA-AW24 protein after transfection into mouse L cells. The restriction map of this cosmid shows extensive homology over 26 kb with the map of the HLA-A3 region obtained from cosmids of the same library, constructed with DNA from an HLA-A3/HLA-AW24 heterozygote, but diverges over the remaining 14 kb. The HLA-AW24 gene was subcloned from this cosmid and its nucleotide sequence was determined. Amino acid and, more strikingly, nucleotide sequence comparisons with other HLA alleles indicate that the A locus alleles are more closely related to each other than to alleles from other HLA loci. A very skewed distribution of silent substitutions is apparent, and the occurrence of clustered multiple substitutions hints at gene-conversion-like events.     

An improved algorithm for statistical alignment of sequences related by a star tree

The insertion-deletion model developed by Thorne, Kishino and Felsenstein (1991, J. Mol. Evol., 33, 114–124; the TKF91 model) provides a statistical framework of two sequences. The statistical alignment of a set of sequences related by a star tree is a generalization of this model. The known algorithm computes the probability of a set of such sequences in O(l ^2k ) time, where l is the geometric mean of the sequence lengths and k is the number of sequences. An improved algorithm is presented whose running time is only O(2^2k l ^k).     

<Emphasis Type="Italic">HLA-A</Emphasis> allele associations with viral <Emphasis Type="Italic">MER9-LTR</Emphasis> nucleotide sequences at two distinct loci within the <Emphasis Type="Italic">MHC alpha</Emphasis> block

The study of the association of the Human Leukocyte Antigen (HLA) alleles and polymorphic retrotransposons such as Alu, HERV, and LTR at various loci within the Major Histocompatibility Complex allows for a better identification and stratification of disease associations and the origins of HLA haplotypes in different populations. This paper provides sequence and association data on two structurally polymorphic MER9-LTR retrotransposons that are located 54 kb apart and in close proximity to the multiallelic HLA-A gene involved in the regulation of the human immune system. Direct DNA sequencing and analysis of the PCR products identified DNA nucleotide variations between the MER9-LTR sequences at the two loci and their associations with HLA-A alleles as potential haplotype and evolutionary markers. All MER9-LTR sequences were haplotypic when associated with common HLA-A alleles. The number of SNP loci was 2.5 times greater for the solo LTR at the AK locus, which is located closer to the HLA-A gene than the solo or 3′ LTR at the HG locus. Our study shows that the nucleotide variations of the MER9-LTR DNA sequences are additional informative markers in fine mapping HLA-A genomic haplotypes for future population, evolutionary, and disease studies.     

Recursive organizer (ROR): an analytic framework for sequence-based association analysis

The advent of next-generation sequencing technologies affords the ability to sequence thousands of subjects cost-effectively, and is revolutionizing the landscape of genetic research. With the evolving genotyping/sequencing technologies, it is not unrealistic to expect that we will soon obtain a pair of diploidic fully phased genome sequences from each subject in the near future. Here, in light of this potential, we propose an analytic framework called, recursive organizer (ROR), which recursively groups sequence variants based upon sequence similarities and their empirical disease associations, into fewer and potentially more interpretable super sequence variants (SSV). As an illustration, we applied ROR to assess an association between HLA-DRB1 and type 1 diabetes (T1D), discovering SSVs of HLA-DRB1 with sequence data from the Wellcome Trust Case Control Consortium. Specifically, ROR reduces 36 observed unique HLA-DRB1 sequences into 8 SSVs that empirically associate with T1D, a fourfold reduction of sequence complexity. Using HLA-DRB1 data from Type 1 Diabetes Genetics Consortium as cases and data from Fred Hutchinson Cancer Research Center as controls, we are able to validate associations of these SSVs with T1D. Further, SSVs consist of nine nucleotides, and each associates with its corresponding amino acids. Detailed examination of these selected amino acids reveals their potential functional roles in protein structures and possible implication to the mechanism of T1D.     

Index of new names of syntaxa published in 1991

This Index collects the new names of syntaxa (in the sense of the Code of Phytosociological Nomenclature,Barkman et al. 1986) above subassociation rank found in the literature received by the Library of the Conservatoire Botanique in Geneva. For the year 1991 591 names have been listed. Each one is accompanied by an appreciation about its validity with respect to the Code of Nomenclature. 25 names are given in addition to the Indexes 1988, 1989 and 1990 (Theurillat & Moravec 1991, 1992, 1993).     

The DY sub-region of the sheep MHC contains an A/B gene pair

The major histocompatibility complex (MHC) class II region of ruminants appears to have a structure broadly similar to that of the human class II or HLA-D region. Restriction fragment length polymorphism (RFLP) studies of class II genes in cattle (Andersson et al. 1988; Anderson and Rask 1988; Sigurdardottir et al. 1988, 1991 b), and in sheep (Scott et al. 1987), have provided an estimate of the number and type of class II genes in these species. The subsequent cloning and sequencing of sheep and cattle class II genes (Muggli-Cockett and Stone 1989; Groenen et al. 1990; van der Poel et al. 1990; Andersson et al. 1991; Scott et al. 1991 a, b; Ballingall et al. 1992; Sigurdardottir et al. 1991 a, 1992), have demonstrated that they are highly homologous to their human counterparts. Of more interest, therefore, are loci within the ruminant MHC which differ from the HLA class II region.Three distinguishing features of the ruminant class II region described to date are, firstly, the apparent absence of a DP-like isotype, secondly, the variability in the number of DQ genes between haplotypes (Andersson and Rask 1988), and thirdly, the presence of class II genes presumed to be unique to the ruminant (Andersson et al. 1988). The presence of two such genes, designated DYA and DYB, was deduced from RFLP studies of cattle DNA. These genes were shown to segregate together with the DOB gene in one region separated by a recombination distance of 17 cM from the region which contains the DQA, DQB, DRB, DRA, and C4 loci (Andersson et al. 1988). Subsequently, Bota-DYA was cloned from a phage library and sequenced (van der Poel et al. 1990; Acc. Nos. m30119 and m30118). The sequence of part of a similar gene in the goat, obtained by PCR by using primers derived from the cattle sequence, has recently been reported (Mann et al. 1993; Acc. No. m94325). However, there has been no report of the cloning of a B gene partner for the DYA gene. A novel cattle class II B gene designated Bota-DIB was cloned from a phage library and sequenced by Stone and Muggli-Cockett (1990). This was shown to be a single copy gene of limited polymorphism, which on the basis of RFLP analysis was probably not Bota-DYB but did appear to be distinct from other known cattle class II genes. The species distribution of this B gene was shown to be restricted to Cervidae, Giraffidae, and Bovidae (Stone and Muggli-Cockett 1993). However, it is not known whether any of these novel genes are functional.Expressed human class II genes usually occur as A/B gene pairs situated close to each other on the chromosome. This is also the case with Bota-DQ genes (Groenen et al. 1990) and Ovar-DQ genes (Deverson et al. 1991; Wright and Ballingall 1994). We used the techniques of cosmid cloning and DNA-mediated gene transfection to determine whether there is a sheep equivalent of the Bota-DYA gene, whether there is a DYB gene partner, and whether there is a protein product.A cosmid library was constructed from DNA prepared from a Finnish Landrace ram. The library was screened with Ovar-DQA, Ovar-DQB, HLA-DQA, and HLA-DQB gene probes at low stringency. A cosmid clone, 365, was obtained which hybridized weakly to both the Ovar gene probes. Restriction maps of the clone were produced for the enzymes Eco R1, Bam HI, Hin dIII, Sac I and Sma I. When the maps were compared to those published for the phage clones containing the Bota-DYA (van der Poel et al. 1990) and the Bota-DIB gene (Stone and Muggli-Cockett 1990), there was an imperfect match (Figure 1 shows the Eco RI maps). However, the sequence data for the A and B genes in cosmid 365 are more convincing. The sequences of exons 2 and 3 of the A gene in cosmid 365 and the Bota-DYA gene, together with the partial sequence from the third exon of the Cahi-DYA gene are shown in Figure 2 A. The predicted amino acid translations of these genes together with those of other published sheep MHC class II A genes are shown in Figure 2 B. The A gene in cosmid 365 had all the salient features of an MHC class II A gene. It showed a high sequence similarity to the cattle and caprine DYA genes and much less so to the Ovar-DRA gene (Ballingall et al. 1992; Acc. No z11600) and the Ovar-DQA1 and DQA2 (Scott et al. 1991 a; Acc. Nos. m33304 and m33305), as detailed in Table 1. The cosmid A gene showed low sequence similarity to the sheep DNA (formerly DZA) gene (unpublished observations). The A gene described here is clearly the sheep homologue of the Bota-DYA gene.The sequences of the second, third, and fourth exons of the B gene in cosmid 365 are shown in Figure 3 A together with those of the Bota-DIB gene (Stone and Muggli-Cockett 1990). Unfortunately, the presence of a Bam HI site in exon 2 of the sheep gene caused a truncation at this point, during the cloning procedure and so a part of exon 2, the whole of exon 1, and all the upstream regulatory elements were missing. The predicted amino acid translations of exons 2, 3, and 4 are shown together with those of an Ovar-DQB (Scott et al. 1991 a; Acc. No. m33323) and an expressed Ovar-DRB gene (Ballingall et al. 1992; Acc. No. z11522) in Figure 3 B.