Multiple DNA fragment polymorphisms associated with immunoglobulin mu chain switch-like regions in man

Chromosome-wide haplotype sharing: a measure integrating recombination information to reconstruct the phylogeny of human populations

The vast amount of recombination information in the human genome has long been ignored or deliberately avoided in studies on human population genetic relationships. One reason is that estimation of the recombination parameter from genotyping data is computationally challenging and practically difficult. Here we propose chromosome-wide haplotype sharing (CHS) as a measure of genetic similarity between human populations, which is an indirect approach to integrate recombination information. We showed in both empirical and simulated data that recombination differences and genetic differences between human populations are strongly correlated, indicating that recombination events in different human populations are evolutionarily related. We further demonstrated that CHS can be used to reconstruct reliable phylogenies of human populations and the majority of the variation in CHS matrix can be attributed to recombination. However, for distantly related populations, the utility of CHS to reconstruct correct phylogeny is limited, suggesting that the linear correlation of CHS and population divergence could have been disturbed by recurrent recombination events over a large time scale. The CHS we proposed in this study is a practical approach without involving computationally challenging and time-consuming estimation of recombination parameter. The advantage of CHS is rooted in its integration of both drift and recombination information, therefore providing additional resolution especially for populations separated recently.

Ongoing immunoglobulin class switch DNA recombination in lupus B cells: analysis of switch regulatory regions

Inflammation and tissue damage in systemic lupus erythematosus (SLE) are mediated by class-switched autoantibodies reactive with nucleic acids, nucleic acid-binding proteins, phospholipids and other self-antigens. While some healthy individuals produce IgM antibodies with specificities similar to those of lupus patients, immunoglobulin class switching to mature downstream isotypes appears to be required for the generation of pathogenic autoantibodies. To characterize the cellular and molecular basis of pathogenic autoantibody production in SLE, we studied the capacity of peripheral blood B cells of naive phenotype from patients with SLE, rheumatoid arthritis (RA) or healthy control subjects to spontaneously switch to IgG and IgA. In addition, we determined the DNA sequences of the upstream evolutionary conserved sequence (ECS)-Igamma promoter regulatory regions that control germline IH-CH transcription and class switch DNA recombination (CSR) to IgG1, IgG2 and IgG4. IgM+IgD+ B cells from patients with SLE, but not those from RA or healthy control subjects, underwent spontaneous CSR, as assessed by expression of germline Igamma1-Cgamma1, Igamma2-Cgamma2, Igamma3-Cgamma3, Igamma4-Cgamma4 and Ialpha1-Calpha1 transcripts, mature (switched) VHDJH-Cgamma1, VHDJH-Cgamma2, VHDJH-Cgamma3 and VHDJH-Calpha1 transcripts and secreted IgG and IgA. Although polymorphic DNA sequences were identified in the ECS-Igamma1, ECS-Igamma2 and ECS-Igamma4 promoter regions, the transcription factor-binding sites that mediate germline Igamma-Cgamma transcription were conserved in patients and controls. However, distinct patterns of nuclear protein binding to an ECS-Igamma promoter sequence that contains both positive and negative regulatory elements were observed in SLE patients and controls. These results support a role for exogenous signals, such as through CD40 ligation, rather than altered genomic sequence, in the increased production of class switched autoantibodies in SLE.

Clinical and molecular analysis of patients with defects in micro heavy chain gene

Autosomal recessive disorders of B cell development are rare and heterogeneous. To determine the proportion of affected patients who have defects in the micro heavy chain (IGHM) gene, we used single-stranded conformational polymorphism analysis to screen genomic DNA from 40 unrelated patients with early onset infections, profound hypogammaglobulinemia, and absent B cells. All of the patients were genotypically normal in BTK, the gene that underlies X-linked agammaglobulinemia. Eight different mutations in the micro heavy chain were identified in 19 members of 12 unrelated families. Four of the mutations were large deletions that removed more than 40 kb of DNA in the IGHM locus. In six of the 12 families, the affected patients had an identical single base pair substitution, a G-->A, at the -1 position of the alternative splice site. Immunoglobulin haplotype analysis showed that this mutation occurred on at least three different haplotypes, indicating that this is a hot spot for mutations. Compared with patients with mutations in Btk, patients with defects in the micro heavy chain had an earlier onset of disease and more complications. Our study indicates that at least 20-30% of patients with autosomal recessive defects in B cell development have mutations in the micro heavy chain.

Regulation of switching and production of IgA in human B cells in donors with duplicated alpha1 genes

IgA is the predominant immunoglobulin class synthesized in humans and can be subdivided into two subclasses, IgA1 and IgA2, each encoded by a separate gene and differentially expressed depending on age and anatomical localization of the producing cells. Duplication of the alpha1 gene is frequently observed in selected populations. As this duplication may serve to enhance IgA-mediated immunity, we determined its effect on switching and production of IgA in human B cells. We developed a nested PCR strategy, involving sequencing the switch (S) alpha2 region, the only human S region not sequenced to date, to assess the proportion of cells switching to IgA1 and IgA2 in vivo. Our results show that there is no difference in the serum and salivary levels of IgA1 and IgA or rate of switching to IgA1 and IgA between normal donors and individuals carrying alpha1 gene duplications, suggesting involvement of a regulatory step in the production of IgA.

Normal isotype switching in B cells lacking the I mu exon splice donor site: evidence for multiple I mu-like germline transcripts

Ig class switch recombination (CSR) in activated B cells is preceded by the generation of "switch" transcripts from the heavy chain constant region (CH) genes targeted for rearrangement. Switch transcripts include a sterile "I" exon spliced onto the first CH exon. Targeted mutations disrupting the expression or splicing of I exons severely hamper CSR to all tested CH loci, except mu. However, all mu switch transcript mutations tested so far have left the I mu exon splice donor site intact. To test the possibility that the residual CSR activity in I mu mutants could be due to splicing of a truncated I mu exon, we generated new mutants specifically lacking the I mu splice donor site. Surprisingly, normal CSR was observed in the I mu splice donor mutants even in the absence of detectable spliced I mu transcripts. In a search for potential alternative sources of switch-like transcripts in the mu locus, we identified two novel exons which map just upstream of the Smu region and splice onto the C mu 1 exon. Their expression is detectable from early B cell developmental stages, and, at least in hybridomas, it does not require the Emu enhancer. These studies highlight a unique structure for the mu locus I exon region, with multiple nested switch transcript-like exons mapping upstream of Smu. We propose that all of these transcripts directly contribute to mu class switching activity.

Mutations in the mu heavy-chain gene in patients with agammaglobulinemia

BACKGROUND

Most patients with congenital hypogammaglobulinemia and absent B cells are males with X-linked agammaglobulinemia, which is caused by mutations in the gene for Bruton's tyrosine kinase (Btk); however, there are females with a similar disorder who do not have mutations in this gene. We studied two families with autosomal recessive defects in B-cell development and patients with presumed X-linked agammaglobulinemia who did not have mutations in Btk.

METHODS

A series of candidate genes that encode proteins involved in B-cell signal-transduction pathways were analyzed by linkage studies and mutation screening.

RESULTS

Four different mutations were identified in the mu heavy-chain gene on chromosome 14. In one family, there was a homozygous 75-to-100-kb deletion that included D-region genes, J-region genes, and the mu constant-region gene. In a second family, there was a homozygous base-pair substitution in the alternative splice site of the mu heavy-chain gene. This mutation would inhibit production of the membrane form of the mu chain and produce an amino acid substitution in the secreted form. In addition, a patient previously thought to have X-linked agammaglobulinemia was found to have an amino acid substitution on one chromosome at an invariant cysteine that is required for the intrachain disulfide bond and, on the other chromosome, a large deletion that included the immunoglobulin locus.

CONCLUSIONS

Defects in the mu heavy-chain gene are a cause of agammaglobulinemia in humans. This implies that an intact membrane-bound mu chain is essential for B-cell development.

Molecular analysis redefines three human chromosome 14 deletions

We have used a panel of 13 DNA markers in the distal region of chromosome 14q to characterize deletions in three patients determined cytogenetically to have a ring or terminally deleted chromosome 14. We have characterized one patient with a ring chromosome 14 [r (14) (p13q32.33)] and two with terminal deletions [del (14) (pter-->q32.3:)]. The two patients with cytogenetically identical terminal deletions of chromosome 14 were found to differ markedly when characterized with molecular markers. In one patient, none of the markers tested were deleted, indicating that the apparent terminal deletion is actually due to either an undetected interstitial deletion or a cryptic translocation event. In the other patient, the deletion was consistent with the cytogenetic observations. The deleted chromosome was shown to be of paternal origin. The long-arm breakpoint of the ring chromosome was mapped to within a 350-kb region of the immunoglobulin heavy chain gene cluster (IGH). This breakpoint was used to localize markers D14S20 and D14S23, previously thought to lie distal to IGH, to a more proximal location. The ring chromosome represents the smallest region of distal monosomy 14q yet reported.

Interferon alfa therapy in an infant with juvenile chronic myelogenous leukemia

We describe an infant with juvenile chronic myelogenous leukemia (JCML), the diagnosis of which was made by the characteristic clinical and hematologic findings. The absence of a related HLA-compatible donor for bone marrow transplantation coupled with the awareness that chemotherapy is usually ineffective prompted our decision to treat the patient with lymphoblastoid interferon-alpha [alpha(Ly)-IFN]. During the 26-month course of treatment with alpha(Ly)-IFN an incomplete regression of hematologic and clinical findings was achieved. The above results, along with the easy administration and absence of considerable side effects, suggest that alpha(Ly)-IFN may be a useful therapeutic tool in patients affected by JCML awaiting bone marrow transplantation.

The immunoglobulin heavy chain and disease association: application to pemphigus vulgaris

Genes involved in the immune response are generally encoded from a complex cluster of gene segments. Studies of the association of diseases with such genes require well-defined genetic markers throughout the selected region. A set of 15 polymorphic loci that span 1500 kb of the immunoglobulin heavy chain (IGH) complex, 8 in the variable (VH) region and 7 in the constant (CH) region, were selected for the study of disease association. We present a protocol for the use of multiple immunoglobulin heavy chain (IGH) polymorphisms for general application in disease association studies. No microsatellite repeat markers are available for this region. To demonstrate the applicability of this approach, we have examined these IGH polymorphisms in families with individuals affected with pemphigus vulgaris (PV), an autoimmune dermatologic disease. Allele frequencies in 12 patients with PV were compared with those found in their spouses, and with those in a white Canadian control population. A significant difference was found between PV patients and both control groups for the presence of the VH gene VH3f-R4, and possibly for the absence of VH3f-R3, suggesting the possibility of susceptibility factors in these regions. Examination of the frequencies of the IGH region C gamma-haplotypes of PV patients indicated that, while the patients did not differ significantly from their spouses (chi 2 = 1.79), both groups were found to differ significantly from the white Canadian control group (chi 2 = 10.10), emphasizing the importance of matching the ethnic background of controls with that of the patient test group in disease association studies. Unexpectedly, two patients had large deletions of genes in the IGH constant region, which could play a role in the development of PV and require further investigation.

Immunoglobulin light chain restriction and clonal rearrangement in nodular paragranuloma

B-cell clonality was demonstrated in a typical nodular paragranuloma case (NP) by both immunoglobulin (Ig) surface analysis and Ig genes rearrangement studies. On frozen sections, immunostaining for Ig light chain expression revealed a clear-cut predominance of Ig lambda-expressing cells, recognizable as both small lymphocytes and lympho-histiocytic (L&H) cells. Accordingly, molecular analysis of the Ig genes showed a monoclonal rearrangement of the lambda chain gene, although no specific pattern of heavy chain gene rearrangement could be detected by JH analysis. The C lambda rearranged band was identified with two different restriction enzymes, excluding the hypothesis of a genomic polymorphism. Furthermore, the C kappa gene was almost completely deleted, indicating that the developmental hierarchy of Ig genes rearrangement has been respected. The molecular pattern of the C lambda hybridizing band was consistent with monoallelic rearrangement of almost the entire DNA sample, indicating that clonal proliferation was not limited to L&H cells, but also involved surrounding lymphocytes. This finding is in keeping with the immunohistochemical evidence of a lambda light chain restriction on both L&H cells and small lymphocytes, pointing to a close relationship between these two cell types. Our results as a whole suggest that L&H cells and B lymphocytes share a common origin and may both be involved in clonal proliferation in NP.

The polymorphism of the immunoglobulin heavy chain switch region gene in IgA nephropathy, Henoch-Schönlein nephritis and idiopathic nephrotic syndrome

It is well known genetic predisposition may play an important role in the pathogenesis of renal diseases. Recently, there has been some controversy about the possible role of the polymorphism of the immunoglobulin heavy chain switch region gene. We have studied this gene by SstI restriction fragment length polymorphisms using DNA from 41 children with IgA nephropathy, 44 with Henoch-Schönlein nephritis and 60 with idiopathic nephrotic syndrome. There was no association of specific genotype with these diseases, in contrast to previous reports. These results are probably due to the differing genetic background of Japanese and Caucasoid patients as far as the switch region is concerned; no switch region genotype constitutes a genetic risk factor for the Japanese in these diseases.

Immunophenotype of acute lymphoblastic leukemia cells: the experience of the Italian Cooperative Group (Gimema)

The immunophenotype of 304 adult lymphoblastic leukemias (> 18 years) diagnosed on the basis of the FAB criteria was determined at the time of diagnosis using a panel of monoclonal antibodies. The series comprised cases diagnosed and immunophenotyped in 43 Italian centers (GIMEMA Cooperative Group) between April 1988 and June 1991. The immunophenotypic characterization consisted of two consecutive steps. The initial screening was based on the reactivity for TdT, HLA-Dr, CD7, CD10, CD13, CD19, CD24, CD33 and CD41. According to the results obtained, the second level of investigation assessed the positivity for intra cytoplasmic (Cy) Ig, CD1a, CD2, CD3, CD4, CD5, CD8 and CD20. Based on the hierarchical expression of the different B- and T-cell related antigens, each case was assigned to a given differentiation stage. B-lineage ALL were classified in five subgroups (B0-B4) and T-lineage ALL in four subgroups (T0-T3). Cases in which the blasts were lymphoid according to the FAB criteria, but expressed myeloid antigens in association with B- and T-lymphoid markers were defined as hybrid leukemias. As expected, CD10+ cases (B2-B3) were the most frequent within the B-lineage ALL (83.2% of cases). CyIg+ (B3) accounted for about 20% of CD10+ ALL. Twenty eight cases (13.4%) were at a pre-cALL stage (B0-B1) and of these, 8 (3.8% of the total series) were positive only for TdT and HLA-Dr (B0). Intermediate and mature thymic phenotypes (T2-T3) were predominant within the T-ALL (67.2%) groups. Five cases, were positive only for TdT and CD7 (CD5+), and classified as T0. 9.2% of cases fulfilled the definition of hybrid leukemia, largely in view of the co-expression of B-lymphoid and myeloid markers.(ABSTRACT TRUNCATED AT 250 WORDS)

Heterogeneous immunoglobulin gene rearrangement in a B-chronic lymphocytic leukemia progressing into non-Hodgkin lymphoma (Richter syndrome)

BACKGROUND

The relationship between chronic lymphocytic leukemia (CLL) and supervening non-Hodgkin lymphoma is debated, as is whether a particular genomic pattern is related to the emergence of the terminal lymphoma. To investigate these features, the molecular organization of the immunoglobulin (Ig) gene region in a case during both the B-CLL and Richter transformation phase was studied.

METHODS

B-CLL and non-Hodgkin lymphoma cells were processed for Southern blot analysis of Ig heavy- and light-chain gene configuration.

RESULTS

Molecular studies of B-CLL cells revealed the presence of a single Ig heavy-chain rearrangement with both kappa and lambda light-chain rearranged genes, which was consistent with the occurrence of multiple mutational events during the development of the B-CLL clone. Molecular analysis of the lymphoma DNA showed new Ig heavy- and kappa light-chain rearrangements in addition to the original ones related to the CLL phase, indicating that the lymphoma tissue consisted of two genotypically distinct populations of cells.

CONCLUSIONS

On the basis of the overall molecular configuration, this heterogeneous pattern of Ig gene rearrangement was interpreted as an inherent genetic instability of the CLL clone, in which multiple mutational events allowed a selective pressure toward more aggressive subclones, resulting in the emergence of the terminal lymphoma.

Immunoglobulin and HLA-DP genes contribute to the susceptibility to juvenile dermatitis herpetiformis

HLA-DQ genes and gluten diet are the main factors involved in the pathogenesis of Dermatitis Herpetiformis (DH), as well as Coeliac Disease (CD). However other genetic factors are probably relevant, since about 10% of the patients with DH and CD lack the DQA1*0501/B1*0201 heterodimer while the majority of individuals presenting this genotype and also being exposed to gluten diets did not suffer from these diseases. To evaluate the role of other genes, 36 Northern Italian children with DH were analysed for DNA polymorphisms at HLA-DP and immunoglobulin (Ig) heavy chain loci. DPA1*0201 and DPB1*1301 frequencies were higher in patients than in controls (Pc = 0.0357 and Pc = 0.0273). With respect to immunoglobulin heavy chain restriction fragment length polymorphisms (RFLP), the 4.6 kb SacI RFLP at the switch alpha 2 gene was more frequent in patients (0.13) than in controls (0.019; Pc = 0.036). Moreover, rare alleles or duplications in the switch regions occurred more frequently in the patients than in the controls. These results support the hypothesis of a multifactorial inheritance of DH, the HLA and Ig constant heavy chain genes being some of the loci contributing to the susceptibility. In accordance with previous CD studies, these data also confirm that DP subregion is probably involved in the pathogenesis of DH.

Unique genotypic features of infant acute lymphoblastic leukaemia at presentation and at relapse

Acute lymphoblastic leukaemia (ALL) of infants aged less than 1 year represents a group of patients with peculiar biological features, poor response to therapy and unfavourable prognosis. In order better to characterize this type of leukaemia, we have investigated the immunoglobulin (Ig) and T-cell receptor (TCR) genes configuration of 21 infants with ALL, and compared the genotypic features with the phenotypic and karyotypic data, as well as with the clinical outcome. All cases had a pre-B phenotype; 12 (57%) of them were pre-pre-B ALL (CD10-, CD19+). Six of the 16 cases evaluated (38%) displayed chromosomal abnormalities; five had the typical translocation t(4;11)(q21;23). Eleven cases presented with a white blood cell count greater than 100 x 10(9)/l. The clinical course was unfavourable in 14 patients. The genotype of this group of ALL revealed several peculiarities. (1) Of the 21 cases, six (29%) displayed a multiple rearrangement pattern at the IgH locus. (2) In three cases (15%), the light chain genes were rearranged. (3) The TCR beta and gamma genes were rearranged in only one case (one case at the TCR beta and one at the TCR gamma locus). (4) The TCR delta chain was rearranged in eight cases (40%) and rarely deleted; the rearrangements observed were those most frequently observed in B cell-precursor ALL. Two cases were evaluated both at presentation and at relapse. While the immunophenotype had remained unmodified, comparison of Ig heavy chain gene rearrangements revealed clonal variations in both cases. Taken together, these findings further underline the biological peculiarities of infant ALL compared to ALL which occurs in older children and in adults, and stress the need of differentiated and aggressive therapeutic approach for these patients.

The genetics of IgG4 deficiency: role of the immunoglobulin heavy chain constant region and HLA loci

IgG4 deficiency is very common (1/400 in the Italian population) and provides a good model for analyzing the genetic factors involved in Ig subclass deficiencies. We have previously reported an association between some immunoglobulin heavy chain constant region (IGHC) polymorphisms and the IgG4 deficiency. The associated polymorphisms spanned the region between the GP and the G4 genes. A larger sample composed of 50 healthy blood donors with IgG4 deficiency (less than 0.001 g/l IgG4), not carrying homozygous gene deletions, together with 82 first-degree relatives is now examined. The results confirmed the association of the deficiency with IGHC polymorphisms, and detected a new association with the HLA-D locus with a strong additive effect between the two systems. However, despite these associations and a highly significant risk for IgG4 deficiency within families, close linkage with either IGHC or HLA loci was not apparent by the affected sib pair method. These findings suggest that several concomitant, possibly cooperating, genetic factors may be involved in IgG4 deficiency.

Immunoglobulin heavy chain gene associations in myasthenia gravis: new evidence for disease heterogeneity

Susceptibility to myasthenia gravis (MG) is known to involve genes residing in the major histocompatibility complex class I and II regions (HLA-B8 and DR3). Immunoglobulin heavy chain constant region (IgCH) allotypes have also shown some associations with MG. We have used restriction fragment length polymorphism analysis with probes to the IgCH switch (S) regions mu and alpha 1 and the downstream marker D14S1 to investigate 189 Caucasoid patients with well-defined MG. A highly significant increase in the frequency of the 2.6 kilobase (kb) S mu homozygous genotype and the 2.6 kb S mu allele was found in patients with disease onset after the age of 40 years (late onset) compared with normal controls (P less than 0.00075 and P less than 0.025 respectively). No association was found at the S alpha 1 or D14S1 loci. In patients with an associated thymoma there was a moderate increase in the frequency of the 2.6 kb S mu and 7.4 kb S alpha 1 genotypes. These results independently support the previous separation of the late-onset subgroup. Finally, the stronger association at S mu rather than at the downstream S alpha 1, Gm and D14S1 loci suggest that the genes predisposing to MG are located within the variable region of the Ig heavy chain loci.

Genetic linkage of autosomal recessive canine narcolepsy with a mu immunoglobulin heavy-chain switch-like segment

Identification of genes determining narcolepsy susceptibility is important not only for understanding that disorder but also for possible clues to general sleep-control mechanisms. Studies in humans reveal at least one such gene related to the major histocompatibility complex and in dog an as-yet-unmapped single, autosomal recessive gene canarc-1. Gene markers for canarc-1 were therefore sought by DNA restriction fragment length polymorphisms in our colony of narcoleptic dogs. A human mu-switch immunoglobulin probe and the enzyme Hae III identified a gene cosegregating with canarc-1 in backcrossed animals (logarithm of odds scores: m = 24, Z max = 7.2 at theta = 0%). canarc-1 was also shown not to be tightly linked with the dog major histocompatibility complex (m = 40, Z less than -2 at theta less than 4.8%). These results represent the mapping of a non-major histocompatibility complex narcolepsy gene and strongly suggest involvement of the immune system in the pathophysiology of that disease.

Pulsed-field electrophoresis screening for immunoglobulin heavy-chain constant-region (IGHC) multigene deletions and duplications

Genome regions containing multiple copies of homologous genes, such as the immunoglobulin (Ig) heavy-chain constant-region (IGHC) locus, are often unstable and give rise to duplicated and deleted haplotypes. Analysis of such processes is fundamental to understanding the mechanisms of evolution of multigene families. In the IGHC region, a number of single and multiple gene deletions, derived from either unequal crossing-over or looping-out excision, have been described. To study these haplotypes at the population level, a simple and efficient method for preparing large numbers of DNA samples suitable for pulsed-field gel electrophoresis (PFGE) analysis was set up, and a sample of 110 blood donors was screened. Deletions were found to be frequent, as expected on the basis of previous serological surveys for homozygotes. Furthermore, a number of multigene duplications, never identified before, were detected. The total frequency of individuals bearing rearranged IGHC haplotypes was 10%. The genes involved in these deletions and duplications were assessed by densitometric analysis of standard Southern blots hybridized with several IGHC probes; two types of deletion and two types of duplication could thus be characterized. These data provide further evidence of the instability of the IGHC locus and demonstrate that unequal crossing-over is the most likely origin of rearranged IGHC haplotypes; they also suggest that such recombination events may be relatively frequent. Moreover, the simplicity and effectiveness of the large-scale PFGE screening approach will be of great help in the study of multigene families and of other loci involved in aberrant recombinations.

Susceptibility to multiple sclerosis is associated with the proximal immunoglobulin heavy chain variable region

15 immunoglobulin heavy chain constant (CH) and variable region (VH) polymorphisms were selected to span the entire length of the heavy chain cluster. These polymorphisms were examined in 34 sib pairs concordant for multiple sclerosis (MS) and in 23 sporadic MS patients. Allele frequencies were calculated for the 2 MS patient groups and compared with those found in a control population from the same geographical location and of similar ethnic background. No significant association was found between MS and the 7 CH region polymorphisms examined. However, a significant correlation between the MS phenotype and a VH2 family polymorphism was observed in both MS patient populations (familial MS patients chi 2 = 8.16, P less than 0.005; sporadic MS patients chi 2 = 8.90, P less than 0.005). One allele of the VH2-5 gene segment was found to be over-represented in both MS groups. VH2-5 has recently been physically mapped close to the CH region, between 180 and 360 kb away. These results indicate that a locus near or within the CH-proximal VH region is associated with increased susceptibility to MS.

Chronic myeloid leukaemia lymphoid blast crisis. Relevance of molecular analysis at the bcr and immunoglobulin heavy chain gene level in monitoring response to therapy and residual disease

Southern blot analyses were performed in sequential DNA samples from 4 patients with Ph' + chronic myeloid leukaemia (CML) who underwent lymphoid or mixed blast crisis (BC). Genomic rearrangements at the breakpoint cluster region (bcr) and immunoglobulin heavy chain (IgH) gene level provided, in these cases, a sensitive and specific evaluation of response to therapy both in terms of blasts and Ph' + cell suppression. Recurrent BC was molecularly characterized in the 4 patients, showing each time identical individual specific DNA rearrangement patterns. Residual blasts were detected in 2 cases during intervening chronic phases by IgH rearrangements. Such findings highlight the specificity of these molecular markers, clearly indicating the failure of ablative therapy in eradicating the neoplastic clone. Finally, molecular and phenotypic identity in individual recurrent BC also suggested, in our cases, a lack of clonal evolution during disease progression.

Sequencing of selected regions of the human immunoglobulin heavy-chain gene locus that completes the sequence from JH through the delta constant region

Much of the nucleotide sequence between the start of the joining region and the end of the immunoglobulin heavy chain delta gene has already been determined. However, two gaps existed in potentially functionally important regions in this sequence: the region between the 3' end of the joining region and the heavy chain enhancer region and that between the enhancer and the mu constant region. We have determined the nucleotide sequences of these regions. The 734 bp between the joining and enhancer regions contained no additional joining regions. The 4525 bp region between the heavy chain enhancer and the mu constant region contains the mu switch region, which consists of pentameric repeats. Approximately 60% of these repeats are GGGCT and GAGCT. With the determination of these sequences, the entire region of the heavy chain locus starting upstream of the joining region to downstream of the last exon of the delta constant region (a total of more than 29 kb) has now been sequenced.

Immunoglobulin constant heavy chain gene polymorphisms of Caucasoids of west European origin

We have used restriction fragment length polymorphism (RFLP) analysis to investigate the immunoglobulin constant heavy chain (IgCH) loci and the associated locus Dl4Sl, of Caucasoids from South East England and South-West. West Germany, Haplotypes were determined using probes to the Ig heavy chain switch loci S mu and S alpha 1, the IgC gamma 3 and IgC gamma 2 loci as well as the Dl4Sl locus which is 3' of the IgCH loci. The 6.3:1.7 kilobase (kb) Bst EII C gamma 3-C gamma 2 haplotype was the most prevalent in the population from South-East England (frequency 0.364), whilst the 2.3:3.7 kb C gamma 3-C gamma 2 haplotype was the major haplotype in the German population (frequency 0.400). With one exception, the major haplotypes of these two populations differed from the ones previously published for a Caucasoid population from California. This suggests that there may be a major ancestral IgCH haplotype which has been maintained in the population, whilst other haplotypes tend to be specific for a particular group of Caucasoids.

A multigene deletion in the immunoglobulin heavy chain region in a highly atopic individual

Highly atopic individuals, with marked allergy, have extremely elevated total plasma IgE levels. To determine if atopy could be associated with structural alterations involving the IGHE gene of the immunoglobulin heavy chain constant region, the genomic DNA from five atopic individuals was examined. We describe here the identification of a deletion of approximately 120kb, including the IGHA1, IGHGP, IGHG2, AGHG4, and IGHE genes of the IGH constant region, in one atopic patient. This deletion arose de novo from a maternally derived chromosome. The deletion, although apparently not the primary cause of the atopic phenotype of this patient, could be indirectly responsible for the phenotype by exposing aberrant immunoglobulin-regulating elements within the paternally derived IGH constant region.

Human IgE mRNA expression by peripheral blood lymphocytes stimulated with interleukin 4 and pokeweed mitogen

Expression of human IgE mRNA by peripheral blood lymphocytes (PBL) and an IgE-producing myeloma cell line, U-266, was examined by Northern blot hybridization and compared with IgE levels in culture supernatants. A 2.35-kb IgE mRNA was detected in unstimulated atopic PBL and U-266 cells but not in normal PBL, and its levels correlated with IgE protein levels in the supernatant. Upon stimulation with interleukin 4, a new 1.75-kb transcript was revealed in both atopic and normal PBL but not in U-266 cells. Its expression did not correlate with IgE levels in the supernatant. Pokeweed mitogen also induced the expression of the 1.75-kb transcript without concomitant induction of IgE synthesis by normal PBL and even suppressed the spontaneous expression of the 2.35-kb transcript and IgE protein synthesis by atopic PBL. Interferon-gamma, which suppressed both the 2.35-kb transcript and IgE protein production, had no inhibitory effect on the 1.75-kb transcript. Expression of the 1.75-kb transcript was already high after 2 days of stimulation and peaked around day 4. The length of the transcript is smaller than that of mRNA coding for secreted human IgG and IgA and contains all four C epsilon exon sequences, suggesting it might be a truncated transcript without v region and might be a human counterpart of the murine germ-line C epsilon transcript.

Immunoglobulin heavy chain switch region gene polymorphisms in glomerulonephritis

Much evidence suggests that primary IgA nephropathy (IgAN) and idiopathic membranous nephropathy (MN) are immune complex mediated diseases. Moreover, genetic factors may play an important role in their pathogenesis. Recently, restriction fragment length polymorphisms (RFLPs) of the immunoglobulin heavy chain genes have been described which appear to associate with glomerulonephritis. We have studied RFLPs of the switch region of the IgM (S mu) and IgA1 (S alpha 1) heavy chain in MN and IgAN. DNA obtained from British Caucasoids with IgAN (N = 75), MN (N = 43), and normal controls (N = 73), was digested with the restriction enzyme Sac1, and studied using Southern blot techniques and hybridization with a 32P labelled DNA probe homologous to S mu. This probe detects RFLPs at the S mu and S alpha 1 loci. The genotypic and allelic frequencies of the S mu and S alpha 1 alleles in IgAN and MN was similar to normal controls. Caucasoid subjects with IgAN from Northern and Southern Europe (Finland and Italy, respectively) were also studied to determine whether an ethnic variation in genetic susceptibility to IgAN exists. The frequency of the S mu and S alpha 1 alleles was similar between the patient groups and their respective local healthy controls. These results do not support the recent findings of an association with RFLPs of the S mu and S alpha 1 loci in IgAN and MN, and suggest that the immunoglobulin heavy chain switch region genes are not important in conferring disease susceptibility to IgAN or MN.

Potential genetic functions of tandem repeated DNA sequence blocks in the human genome are based on a highly conserved "chromatin folding code"

This review is based on a thorough description of the structure and sequence organization of tandemly organized repetitive DNA sequence families in the human genome; it is aimed at revealing the locus-specific sequence organization of tandemly repetitive sequence structures as a highly conserved DNA sequence code. These repetitive so-called "super-structures" or "higher-order" structures are able to attract specific nuclear proteins. I shall define this code therefore as a "chromatin folding code". Since locus-specific superstructures of tandemly repetitive sequence units are present not only in the chromosome centromere or telomere region but also on the arms of the chromosomes, I assume that their chromatin folding code may contribute to, or even organize, the folding pathway of the chromatin chain in the nucleus. The "chromatin folding code" is based on its specific "chromatin code", which describes the sequence dependence of the helical pathway of the DNA primary sequence (i.e., secondary structure) entrapping the histone octamers in preferential positions. There is no periodicity in the distribution of the nucleosomes along the DNA chain. The folding pathway of the nucleosomal chromatin chain is however still flexible and determined by e.g., the length of the DNA chain between the nucleosomes. The fixation and stabilization of the chromatin chain in the space of the nucleus (i.e., its "functional state") may be mediated by additionally unique DNA protein interactions that are dictated by the "chromatin folding code". The unique DNA-protein interactions around the centromeres of human chromosomes are revealed for example by their "C-banding". I wish to stress that it is not my aim to relate each block of repetitive DNA sequences to a specific "chromatin folding code", but I shall demonstrate that there is an inherent potential for tandem repeated sequence units to develop a locus-specific repetitive higher order structure; this potential may create a specific chromatin folding code whenever a selection force exists at the position of this repetitive DNA structure in the genome.

CD7 positive acute myeloid leukaemia: a subtype associated with cell immaturity

Seventeen patients with acute myeloid leukaemia (AML) whose blasts co-expressed the T-cell associated CD7 antibody were identified among 160 consecutive AML cases. Fourteen had FAB defined AML according to morphocytochemical criteria, whereas three patients were classified as 'MO' on the basis of immunophenotype. The incidence of CD7 positively was particularly significant in the less differentiated subtypes M0 and M1 compared with other FAB groups (P less than 0.001). In all cases the myeloid determinants CD13 and/or CD33 were associated with CD7 expression. Other B-lymphoid (CD10, CD19) or T-lymphoid (CD2, surface and cytoplasmic CD3) markers were analysed and found to be negative. Five out of 15 cases examined were TdT+. Clonal rearrangements of the immunoglobulin heavy chain (IgH) and/or T-cell receptor (TcR) beta chain genes were identified in only three out of 13 cases. Among these, one out of five co-expressing TdT showed IgH rearrangement when analysed at the DNA level. Clinical features at presentation and response to induction therapy did not allow us to consider CD7+ AML patients as a distinct subgroup with prognostic significance. Our data indicate that CD7 expression is a common finding in immature AML, being generally found in the absence of other T-cell features. Rather than suggesting the occurrence of 'mixed leukaemia', such cases confirm a broader spectrum of CD7 reactivity and its possible identification of a particular subset of myeloid progenitors.

Genetic analysis of new restriction fragment length polymorphisms (RFLP) in the human IgH constant gene locus

The human immunoglobulin heavy chain constant gene locus (IGHC) is polymorphic at both the protein (Gm and A2m allotypes) and the DNA level [RFLP for the gamma genes (IGHG), the switch mu region (IGHSM) and the switch alpha regions (IGHSA)]. The polymorphisms have been a valuable tool for assessment of the IGHC locus organization and a variety of population genetics and immunological investigations. In this study three new probes, identifying regions related to the IGHG (IGHPG and IGHSG) or IGHA (IGHAT) genes, have been employed to describe 11 different loci, 6 of which were polymorphic. Most of the polymorphisms are probably due to short insertions/deletions, particularly the SG regions, due to their repetitive structure. Ten loci were assigned to the IGHC region on the basis of known restriction maps, deletion mapping and association with mapped RFLP; the 11th, despite a striking sequence similarity with the IGHPG regions, could not be assigned to any known IGHC subregion. Analysis of these and previously known IGHG RFLP in a sample of 65 unrelated subjects plus 15 families allowed us to draw a genetic map, with particularly high resolution in the GP-G2-G4 genes region, revealing a marked discontinuity in the linkage disequilibrium values between pairs of adjacent loci.

Polymorphisms of the immunoglobulin heavy-chain delta gene and association with other constant-region genes

Polymorphisms have previously been reported for the C mu, C alpha, C epsilon, and C gamma genes of the immunoglobulin heavy-chain (IGH) gene cluster. Here we report polymorphisms of the IGH C delta gene region, observed using the enzymes ApaI, AvaII, TaqI, and XbaI. The TaqI and XbaI polymorphisms were used in an investigation of linkage disequilibrium throughout the cluster of constant-region genes. The TaqI polymorphism, located 5' to the C delta gene, is in linkage disequilibrium with a polymorphism of the C mu switch region. The XbaI polymorphism, which is in the vicinity of the C delta 2 exon, is not strongly associated with any other polymorphisms, including the TaqI polymorphism and the Gm polymorphism of C gamma 3. Although there is a high degree of association between most genes of the IGH region, there is a lack of association between C delta and C gamma 3, which may indicate a hot spot for recombination.

Thyroglobulin antibodies in Graves' disease are associated with T-cell receptor beta chain and major histocompatibility complex loci

We have investigated the T-cell antigen receptor constant beta and alpha chain genes (TCR-C beta, -C alpha) and the immunoglobulin (Ig) heavy chain switch regions of patients with Graves' disease (GD) using restriction fragment length polymorphism (RFLP) analysis. No significant associations were found with RFLPs of either the TCR-C beta, -C alpha or Ig heavy chain switch region loci and GD. However, a significant association was found between the presence of anti-thyroglobulin (anti-Tg) antibodies in the serum of patients and the 10.0; 9.2 kb TCR-C beta genotype (P less than 0.02). Also, those patients with anti-Tg antibodies had an increased frequency of HLA-DR3 (P less than 0.025). These results suggest that genes residing in the TCR chain and major histocompatibility complex loci may be important in determining the immune response to thyroglobulin but not to the disease itself.

A specific switch alpha probe of the human immunoglobulin IGHA locus

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Inheritance of a large deletion within the human immunoglobulin heavy chain constant region gene complex and immunological implications

A deletion of the immunoglobulin heavy chain (IgH) pseudo-gamma, gamma-2, gamma-4, epsilon, and alpha-2 constant region gene segments was found to segregate unchanged in three generations of a family. The IgG1 locus on the IgH allele carrying the deletion was expressed to the same extent as its normal counterpart. One individual who was heterozygous for the deletion had an IgG2 deficiency, whereas the four other heterozygous individuals had serum levels of IgG2 and IgG4 within the normal ranges. IgA2 levels were low or below the normal range in all heterozygous individuals. The data indicate that the expression of some Ig isotypes can be decreased by hemizygous deletions, possibly due to a lower probability for switching.

Polyclonal hyper-immunoglobulin G1(A1) syndrome. Evidence for a dominant immunoglobulin production regulator within the human immunoglobulin heavy chain gene complex

The hyper-IgG1(A1) syndrome entails a polyclonal selective increase of the serum levels of immunoglobulin (Ig) G1 and to a lesser extent of IgA1; this is not mediated by malignancy, infectious or autoimmune diseases or environmental agents. In three generations of a family, all the affected individuals carried an immunoglobulin heavy chain (IgH) allele distinguished by restriction fragment length polymorphism analysis; the IgH allele was not present in non-affected family members. A 32:1 chance for the linkage of this rare IgH haplotype with the hyper-IgG1(A1) syndrome in the family argues for a dominant regulator located at the human IgH locus having a selective influence on the production of IgG1 and IgA1.

Human T cells expressing the gamma/delta T-cell receptor (TcR-1): C gamma 1- and C gamma 2-encoded forms of the receptor correlate with distinctive morphology, cytoskeletal organization, and growth characteristics

BB3 and delta-TCS1 monoclonal antibodies identify two distinct nonoverlapping populations of T-cell receptor (TcR) gamma/delta (TcR-1)-positive cells, which express a disulfide-linked and a nondisulfide-linked form of TcR, respectively. BB3+ cells represented the majority of circulating TcR-1+ cells, but they were virtually undetectable in the thymus. On the other hand, delta-TCS1+ cells were largely predominant among TcR-1+ thymocytes but represented a minority in peripheral blood (PB). Similar distributions were observed by clonal analysis of thymocytes or PB TcR-1+ populations. The use of joining region (J)-specific probes indicated that BB3+ and delta-TCS1+ clones displayed different patterns of J rearrangement. Thus, the disulfide-linked form of TcR-1 (BB3+ clones) was associated with the expression of J segments upstream to the C gamma 1 gene segment, whereas the nondisulfide-linked form (delta-TCS1+ clones) was associated with the expression of J segments upstream to C gamma 2. delta-TCS1+ clones, in most instances, exhibited a growth pattern different from that of BB3+ or conventional TcR alpha/beta+ clones as they adhered promptly to surfaces, spread, and emitted long filopodia ending with adhesion plaques. Ultrastructural analyses showed, exclusively in delta-TCS1+ cells, nuclear deformations, uropod formation, and abundant cytoskeletal structures. In addition, immunofluorescence studies of this subset of TcR-1+ cells revealed the presence of abundant microtubules, intermediate filaments, and submembranous microfilaments. Thus, our findings suggest that delta-TCS1+ cells are capable of active motility.

T-cell receptor V alpha and C alpha alleles associated with multiple and myasthenia gravis

Polymorphic markers in genes encoding that alpha chain of the human T-cell receptor (TcR) have been detected by Southern blot analysis in Pss I digests. Polymorphic bands were observed at 6.3 and 2.0 kilobases (kb) with frequencies of 0.30 and 0.44, respectively, in the general population. Using the polymerase chain reaction (PCR) method, we amplified selected sequences derived from the full-length TcR alpha cDNA probe. These PCR products were used as specific probes to demonstrate that the 6.3-kb polymorphic fragment hybridizes to the variable (V)-region probe and the 2.0-kb fragment hybridizes to the constant (C)-region probe. Segregation of the polymorphic bands was analyzed in family studies. To look for associations between these markers and autoimmune diseases, we have studied the restriction fragment length polymorphism distribution of the Pss I markers in patients with multiple sclerosis, myasthenia gravis, and Graves disease. Significant differences in the frequency of the polymorphic V alpha and C alpha markers were identified between patients and healthy individuals.

New types of multiple and single gene deletions in the human IgCH locus

The locus for human immunoglobulin heavy chain constant region genes (IgCH) is characterized by a significant frequency of deleted or duplicated haplotypes, due to unequal crossing-over events. Four types of deletions and one duplication have been reported so far. We describe here a molecular study of four cases of IgCH deletions. Two of the three types of deletions are reported here for the first time. Analysis of genetic markers associated with the deleted haplotypes pointed to the independent origin of similar deletions and the involvement of intergenic sequences in the mispairing-recombination process. The reduced or absent transcription of the C gamma 4 gene in two C gamma 2-deleted haplotypes offers an insight into the requirements for the isotype switch mechanism.

Pst I restriction fragment length polymorphism of human placental alkaline phosphatase gene: Mendelian segregation and localization of mutation site in the gene

The pattern of inheritance of a Pst I restriction fragment length polymorphism (RFLP) of the human placental alkaline phosphatase gene was studied in nine nuclear families by Southern blot hybridization analysis of genomic DNA. The dimorphic RFLP is defined by the presence of allelic fragments 1.0 kilobase and 0.8 kilobase long. The results of this study show that the two alleles of the PstI RFLP of the placental alkaline phosphatase gene segregate as codominant traits according to Mendelian expectations. For a polymorphism to be useful as a genetic marker the probability that an offspring is informative (PIC) must be at least 0.15. The allelic frequency of the 1.0-kilobase allele is 0.21, which correlates to a probability that an offspring is informative of 0.275 and is indicative of a useful polymorphism. By using probes derived from different regions of the placental alkaline phosphatase cDNA, the mutated Pst I site causing the RFLP was located in the penultimate intron 2497 base pairs downstream from the transcriptional initiation site.

Immunoglobulin heavy chain switch region polymorphisms are not associated with type 1 diabetes

In order to ascertain whether the immunoglobulin heavy chain genes are important in the aetiology of Type 1 diabetes, we have used restriction fragment length polymorphism (RFLP) analysis of genomic DNA to study 148 Caucasoid subjects with Type 1 diabetes and 146 normal Caucasoid subjects. A DNA probe homologous to the switch regions for the IgM (S mu) and IgA1 (S alpha 1) genes when used in conjunction with the restriction endonuclease Sst I detects RFLPs at both these loci. There were no significant differences in phenotype or gene frequencies for the alleles of S mu or S alpha 1 in the patients when compared with control subjects; nor were there significant associations of S mu or S alpha 1 with HLA-DR type or gender.

Immunogenetics of Graves' ophthalmopathy

We have performed an immunogenetic analysis of 53 patients with severe Graves' ophthalmopathy, 51 patients with Graves' disease but little or no clinically apparent eye disease, and 90 controls. The distribution of restriction fragment length polymorphisms was analysed in the three groups, using probes for the HLA-DQ alpha and DR beta regions, the T-cell receptor C alpha, V alpha, C beta and J gamma genes and the immunoglobulin gene switch regions, S alpha and S mu. There was no abnormal distribution of these polymorphisms in either group of Graves' patients, or differences between the Graves' patients with or without eye disease. It was possible to assign HLA-DR types in most patients using the polymorphisms found after probing with DQ alpha and DR beta; there was no abnormal distribution of DR types (including HLA-DR3) assigned by restriction fragment polymorphisms in the two Graves' groups. These results fail to confirm the reported associations between ophthalmopathy and HLA-DR3 and between Graves' disease and the T-cell receptor C beta polymorphism; they also argue against a strong influence of Gm allotypes in Graves' disease since these genes are in linkage disequilibrium with the S alpha polymorphisms. The association of Graves' disease with HLA-DR3, defined hitherto using serological reagents, may be less strong than previously described.

Linkage disequilibrium analyses and restriction mapping of four RFLPs at the pro alpha 2(I) collagen locus: lack of correlation between linkage disequilibrium and physical distance

Restriction fragment length polymorphisms (RRLPs) located at short distances may demonstrate linkage disequilibrium. Under the assumption that the distances between the loci of the RFLPs are inversely related to the linkage disequilibria, gene order may be deduced. However, if the assumption is invalid, the results may be incorrect. We have studied four different DNA polymorphisms at the COLIA2 locus in 180 unrelated Norwegian individuals. Observed frequencies (presence/absence) for the different polymorphic sites were as follows: site A (EcoRI) 0.30/0.70, site B (MspI) 0.83/0.16, site C (StuI) 0.86/0.14, and site D (RsaI) 0.66/0.34. Of 16 possible haplotypes 12 were demonstrated, and 2 additional were deduced to be present. Restriction mapping of the four polymorphic sites gave the following order of the sites from the 5' to the 3' of the gene: A-D-B-C. Linkage disequilibrium was not found between the sites A and D; strong disequilibrium was found between sites A and C, and B and C; and less strong, between A and B, B and D, and C and D. Analysis of linkage disequilibrium coefficients between all pairs of loci demonstrated that there is no consistent relationship between linkage disequilibrium and physical distance (tau = -0.07). These results suggest that for a small region of the genome, factors such as deviating mutation rate and gene conversion may add significantly to rearrangements by recombination. Thus, a deduced gene order from linkage disequilibrium data has to be regarded with great caution.

Arthritis in patients with psoriasis is associated with an immunoglobulin gene polymorphism

Using a DNA probe for the switch region of immunoglobulin heavy chain genes, together with the restriction endonuclease Sst I, we detected a particular polymorphic DNA pattern in 17 of 28 patients (60.7%) with psoriatic arthropathy but in only 5 of 41 patients (12.2%) with psoriasis alone. Our findings suggest that genes in the immunoglobulin region confer susceptibility to the development of arthropathy in patients with psoriasis.

Relation of mesangial IgA glomerulonephritis to polymorphism of immunoglobulin heavy chain switch region

We have investigated the switch regions of Ig heavy chain genes of patients with IgA glomerulonephritis (IgA-GN) using restriction fragment length polymorphism (RFLP) analysis. Genomic DNA from patients and controls was digested with the restriction endonuclease Sst I and transferred to nylon membranes using the Southern blot procedure and hybridized with a probe homologous to the switch region of the Ig C mu gene (S mu) which detects RFLPs in both S mu and the switch region of the Ig C alpha 1 gene (S alpha 1). A significant decrease in the frequency of the 2.6;2.1 kb heterozygous S mu phenotype was found in patients with IgA-GN (P = 0.003). With respect to the S alpha 1 region, there was a significant increase in the frequency of the 7.4 kb S alpha 1 phenotype (P = 0.002). In addition, a significant increase in the frequency of the 7.4 kb S alpha 1 allele was found (P = 0.0002). These results suggest that gene(s) within the Ig heavy chain loci may be important in the pathogenesis of IgA-GN.

Association of membranous nephropathy with T-cell receptor constant beta chain and immunoglobulin heavy chain switch region polymorphisms

We have investigated T-cell antigen receptor constant beta chain genes (Tcr C beta) and immunoglobulin (Ig) heavy chain switch region genes of HLA-DR-typed patients with membranous nephropathy (MN) employing DNA restriction fragment length polymorphism (RFLP) analysis. When a Tcr C beta probe in conjunction with the restriction endonuclease Bgl II was used, a significant increase in the frequency of a 10.0; 9.2 kb heterozygous RFLP phenotype was found in MN (75.0% versus 42.1% in controls; P = 0.002). When Sst I-restricted DNA from MN patients was hybridized with a DNA probe homologous to the switch region flanking the Ig C mu heavy chain gene (S mu), there was a significant decrease in the frequency of the 2.1; 2.6 kb heterozygous RFLP phenotype in MN (24.0% versus 54.6% in controls; P = 0.004). These results suggest that Tcr beta and Ig heavy chain loci, as well as HLA antigens, may be important in the pathogenesis of MN.

Characterisation and uses of a hypervariable DNA polymorphism associated with the human JH immunoglobulin gene locus

A DNA hypervariable polymorphism associated with the human immunoglobulin JH gene locus on chromosome 14 is described. Its potential applications include the distinguishing of cells as host or donor in a transplantation situation as well as characterisation of immunoglobulin gene rearrangements.

A deductive method of haplotype analysis in pedigrees

Derivation of haplotypes from pedigree data by means of likelihood techniques requires large computational resources and is thus highly limited in terms of the complexity of problems that can be analyzed. The present paper presents 20 rules of logic that are both necessary and sufficient for deriving haplotypes by means of nonstatistical techniques. As a result, automated haplotype analysis that uses these rules is fast and efficient, requiring computer memory that increases only linearly (rather than exponentially) with family size and the number of factors under analysis. Some error analysis is also possible. The rules are completely general with regard to any system of completely linked, discrete genetic markers that are autosomally inherited. There are no limitations on pedigree structure or the amount of missing data, although the existence of incomplete data usually reduces the fraction of haplotypes that can be completely determined.