Somatic mosaicism in Fanconi anemia: molecular basis and clinical significance

Approximately 25% of patients with Fanconi anemia (FA) have evidence of spontaneously occurring mosaicism as manifest by the presence of two subpopulations of lymphocytes, one of which is hypersensitive to cross-linking agents (e.g. mitomycin C) while the other behaves normally in response to these agents. The molecular basis of this phenotypic reversion has not yet been determined. We have investigated 8 FA patients with evidence of mosaicism. Epstein-Barr virus-immortalized lymphoblastoid cell lines established from these patients exhibited an IC50 for mitomycin C of 25 to > 100 nM compared to a mean of 2 +/- 2 nM for 20 nonmosaic FA patients and 49 +/- 11 nM for 8 healthy controls. In 3 patients who were compound heterozygotes for pathogenic FAC gene mutations the molecular mechanism of the mosaicism was investigated by haplotype analysis. The results indicated that an intragenic mitotic recombination must have occurred leading to a segregation of a wild-type allele in the reverted cells and suggested two patterns of recombination. In 1 patient a single intragenic crossover between the maternally and paternally inherited mutations occurred associated with markers located distally to the FAC gene; in the other 2 patients (sibs) the mechanism appears to have been gene conversion resulting in segregants which have lost one pathogenic mutation. In 6 of the 8 patients the hematological symptoms were relatively mild despite an age range of 9-30 years.

The genomic organization of the Fanconi anemia group A (FAA) gene

Fanconi anemia (FA) is a genetically heterogenous disease involving at least five genes on the basis of complementation analysis (FAA to FAE). The FAA gene has been recently isolated by two independent approaches, positional and functional cloning. In the present study we describe the genomic structure of the FAA gene. The gene contains 43 exons spanning approximately 80 kb as determined by the alignment of four cosmids and the fine localization of the first and the last exons in restriction fragments of these clones. Exons range from 34 to 188 bp. All but three of the splice sites were consistent with the ag-gt rule. We also describe three alternative splicing events in cDNA clones that result in the loss of exon 37, a 23-bp deletion at the 5' end of exon 41, and a GCAG insertion at the 3' portion also in exon 41. Sequence analysis of the 5' region upstream of the putative transcription start site showed no obvious TATA and CAAT boxes, but did show a GC-rich region, typical of housekeeping genes. Knowledge of the structure of the FAA gene will provide an invaluable resource for the discovery of mutations in the gene that accounts for about 60-66% of FA patients.

Clinical, cytogenetic, and molecular analysis of three families with FRAXE

The probe StB12.3 has been used to screen the FMR-1 gene in 42 pedigrees with a distal Xq fragile site for expansion of the CCG repeat and aberrant methylation of the FRAXA locus. Four families did not have a FRAXA mutation and were investigated further. Fluorescent in situ hybridisation (FISH) and molecular analyses showed that three of these families had an expansion at FRAXE and one at FRAXE. Detailed psychiatric, psychological, and behavioural features of three families with FRAXE identified in the study are presented. All the males who expressed FRAXE had a large methylated CCG repeat at FRAXF. All males with the mutation had some degree of mental handicap. This study illustrates the need for the FRAXE phenotype to be defined further.

Sequence variants of the estrogen receptor (ER) gene found in breast cancer patients with ER negative and progesterone receptor positive tumors

Thirteen pairs of tumor and blood DNAs from breast cancer patients with estrogen receptor (ER) negative and progesterone receptor (PgR) positive tumors were screened for mutation analysis using SSCP method. Although neither germline nor somatic mutation of the ER gene in this series was detected, we found two types of sequence variants in exon 1 and exon 4, indicating two silent mutations in codon 10 (TCT to TCC) and codon 325 (CCC to CCG), respectively. These variants were recognized as polymorphic sites. Although the frequency of these polymorphic sites was not correlated with hormone receptor status, the variant in codon 325 tended to be seen more frequently in breast cancer patients than in non-cancer control cases (P = 0.057).

Analysis of the contribution of HLA genes to genetic predisposition in inflammatory bowel disease

Crohn disease (CD) and ulcerative colitis (UC) are chronic inflammatory bowel diseases (IBDs) of unknown etiology. First-degree relatives of IBD patients have a 10-fold increase in risk of developing the same disease, and distinct associations between specific HLA types and both CD and UC have been reported. We have evaluated the contribution of genes at the HLA locus to susceptibility in IBD by linkage analysis of highly informative microsatellite polymorphisms in 43 families with multiple affected cases. No evidence for linkage of HLA to IBD was obtained under any of the four models tested. Analysis of HLA haplotype sharing in affected relatives indicated that the relative risk to a sibling conferred by the HLA locus was 1.11 in UC and 0.75 in CD, with upper (95%) confidence limits of 2.41 and 1.37, respectively. This suggests that other genetic or environmental factors are responsible for most of the familial aggregation in IBD.

Fanconi's anaemia presenting as acute myeloid leukaemia in adulthood

We describe a 28-year-old male patient who presented with apparently de novo acute myeloid leukaemia (AML) who was subsequently found to have Fanconi's anaemia (FA). The gene for complementation group A (FAA) has recently been localized to chromosome 16q24.3 and utilizing genetic markers closely linked to this locus we were able to conclude that this patient was likely to belong to complementation group A. FA presenting as AML is an exceptionally rare event and all previously described cases have occurred in patients less than 21 years of age. We conclude that the diagnosis of FA should always be considered in younger patients presenting with AML. It is important that the correct diagnosis is made in these individuals because the administration of conventional chemotherapy may well have devastating consequences for them. Correlations between the specific mutations causing FA and clinical phenotypes are likely to become apparent as more genetic analyses are performed in this group of patients.

Accurate diagnosis of carriers of deletions and duplications in Duchenne/Becker muscular dystrophy by fluorescent dosage analysis

We have developed a semiautomated approach to amplify 25 exons of the dystrophin gene using two fluorescent multiplex PCR assays which detect over 98% of reported deletions and 90% of duplications causing Duchenne/Becker muscular dystrophy. The 5' multiplex detects 11 exons from the proximal deletion hotspot of the gene while the 3' multiplex detects 14 exons from the central deletion hotspot. The PCR products are accurately sized and quantified by a fluorescent DNA sequencer after only 18 cycles of amplification. The amount of product amplified from each exon in a multiplex is divided by that from each of the other exons, and this ratio is compared with those from control samples to obtain a series of dosage quotients (DQ), from which the copy number of each exon is determined. No overlap was observed between the DQ values obtained from single and double copy loci. The assays can be used to screen both affected males and at risk female relatives for a mutation. The method has been evaluated as a female carrier test by conducting a blind trial on 150 coded samples. Sixty-three deletion carriers, two duplication carriers, and 84 normal female controls were all correctly identified, showing that carrier diagnosis is possible even in families where the nature of the mutation is unknown. Additionally the analysis showed a non-pathogenic duplication involving the muscle specific promoter and exon 1. Together these two multiplex assays detect over 70% of all mutations in the dystrophin gene, greatly simplifying and partly automating molecular diagnosis in Duchenne and Becker muscular dystrophy.

Positive diepoxybutane test in only one of two brothers found to be compound heterozygotes for Fanconi's anaemia complementation group C mutations

Fanconi's anaemia (FA) is an autosomal recessive disorder characterized by diverse congenital abnormalities, the development of progressive bone marrow failure, and an increased predisposition to malignancy, particularly acute leukaemia. The FA phenotype is so variable that diagnosis on the basis of clinical manifestations alone can be difficult. The modern diagnosis of FA no longer rests entirely on the constellation of clinical and haematological abnormalities first described by Fanconi, but depends on finding elevated chromosomal breakage after incubation of peripheral blood lymphocytes with the chemical clastogens diepoxybutane (DEB) or mitomycin-C (MMC). The cloning of the gene for FA complementation group C [FAC] provides an opportunity to test the validity of the "DEB test' which in recent times has become the main arbiter as to whether a patient is classified as FA or non-FA. We report on two brothers with similar clinical and haematological features who have both been identified as compound heterozygotes for the FAC mutations L554P and delta G322, but only one of the brothers has a positive DEB test. On the basis of the DEB test one would be classified as FA and the other as non-FA. The time has come to re-evaluate the diagnostic criteria of "Fanconi's anaemia'.

[Molecular analysis of the estrogen receptor (ER) gene in association with ER negativity in breast cancer]

DNA from ninety-eight primary breast cancer biopsies has been examined for loss of heterozygosity (LOH). Thirteen of seventy-two informative cases (18.1%) were positive for LOH, which correlated with age at operation but not with ER status. This result suggests that LOH of the ER gene does not have an important role in the lack of ER function in breast cancer tissues. Thirteen breast cancers with ER negative/progesterone receptor (PgR) positive were screened for mutation analysis of the ER gene using single strand conformational polymorphism (SSCP). We found 2 polymorphisms in codon 10 (C to G) codon 325 (C to T), although neither germline nor somatic mutation was detected. Since the sequence variant of codon 325 tends to be more frequently seen in ER negative/PgR negative breast cancer patients than non-cancer control patients, it is suggested that this polymorphism was related to negativity and function of ER in breast cancer tissues.

Mapping of a susceptibility locus for Crohn's disease on chromosome 16

Crohn's disease (CD) and ulcerative colitis are the major forms of chronic inflammatory bowel diseases in the western world, and occur in young adults with an estimated prevalence of more than one per thousand inhabitants. The causes of inflammatory bowel diseases remain unknown, but genetic epidemiology studies suggest that inherited factors may contribute in part to variation in individual susceptibility to Crohn's disease. A genome-wide search performed on two consecutive and independent panels of families with multiple affected members, using a non-parametric two-point sibling-pair linkage method, identified a putative CD-susceptibility locus on chromosome 16 (P less than 0.01 for each panel). The localization was centered around loci D16S409 and D16S419 by using multipoint sibpair analysis (P less than 1.5x10(-5)). This region of the genome contains candidate genes which may be relevant to the pathogenic mechanism of inflammatory bowel diseases.

Novel mutations and polymorphisms in the Fanconi anemia group C gene

Fanconi anemia (FA) is an autosomal recessive disorder associated with hypersensitivity to DNA cross-linking agents and bone marrow failure. At least four complementation groups have been defined, and the FA group C gene (FAC) has been cloned. We have screened 76 unrelated FA patients of diverse ethnic and geographic origins and from unknown complementation groups for mutations in the FAC gene either by chemical cleavage mismatch analysis or by single-strand conformational polymorphism (SSCP). Five mutations were detected in four patients (5.3%), including two novel mutations (W22X and L496R). Nine polymorphisms were detected, seven of which have not been described previously (663A-->G, L190F, IVS6 + 30C-->T, I312V, V449M, Q465R, and 1974G-->A). Six of the nine polymorphisms occurred in patients or controls from the Tswana or Sotho chiefdoms of South Africa and were not found in 50 unrelated European controls. Restriction site assays were established for all 8 pathogenic mutations identified in the FAC gene to date and used to screen a total of 94 unrelated FA patients. This identified only one other group C patient, who was homozygons for the mutation IVS4 + 4A-->T. This study indicates that the proportion of FA patients from complementation group C is generally likely to be less than 10%. Guidelines for the selection of FA patients for FAC mutation screening are proposed.

A rapid, non-radioactive screening test for fragile X mutations at the FRAXA and FRAXE loci

Screening of referrals for the mutations associated with the fragile X syndrome constitutes a significant workload in many genetics laboratories. Since the great majority of these referrals will be negative, there is a need for a rapid and inexpensive screening test. We have developed an assay which allows simultaneous amplification of the triplet repeat sequences at the FRAXA and FRAXE loci by polymerase chain reaction, and detection of the products on non-denaturing gels stained with ethidium bromide. Alleles of normal size are detected, leaving a small minority of samples to be tested by Southern blotting. A PCR based assay for detection of methylation at the CpG island upstream of the FMR-1 gene has also been devised.

Loss of heterozygosity of the oestrogen receptor gene in breast cancer

DNA from 67 primary breast carcinoma biopsies has been examined for loss of heterozygosity (LOH) using the microsatellite (TA)n repeat marker positioned 1 kb upstream of the oestrogen receptor (ER) gene. Forty-seven (70.1%) of the cases were informative; nine of these (19.1%) were positive for LOH. In three of the nine cases, there was total loss, and in the other six cases there was a marked reduction in the intensity of signal from one allele. LOH correlated weakly with histological grade and age, but not with ER status. This result suggests that LOH of the ER gene does not have an important role in the lack of ER function in breast cancer tissues.

Rapid molecular method for prenatal detection of Down's syndrome

We have evaluated a rapid method that allows prenatal detection of Down's syndrome in less than 24 hours. DNA from uncultured amniotic fluid, fetal blood, and tissue samples was amplified with the small tandem repeat (STR) marker D21S11. Quantitative analysis of fluorescent STR products with evaluation of their sizes provided clear evidence for trisomy 21. Whilst most normal samples showed two amplification peaks of equal size, Down's syndrome samples were characterised by either three STR peaks or two peaks with a ratio of 2:1. Co-amplification with a non-polymorphic sequence allowed analysis of samples that were homozygous for the 21-derived STRs.

Mutation analysis of the Fanconi anemia gene FACC

Fanconi anemia (FA) is a genetically heterogeneous autosomal recessive disorder characterized by a unique hypersensitivity of cells to DNA cross-linking agents; a gene for complementation group C (FACC) has recently been cloned. We have amplified FACC exons with their flanking intron sequences from genomic DNA from 174 racially and ethnically diverse families in the International Fanconi Anemia Registry and have screened for mutations by using SSCP analysis. We identified eight different variants in 32 families; three were detected in exon 1, one in exon 4, one in intron 4, two in exon 6, and one in exon 14. Two of the eight variants, in seven families, did not segregate with the disease allele in multiplex families, suggesting that these variants represented benign polymorphisms. Disease-associated mutations in FACC were detected in a total of 25 (14.4%) of 174 families screened. The most frequent mutations were IVS4 + 4 A-->T (intron 4; 12 families) and 322delG (exon 1; 9 families). Other, less common mutations include Q13X in exon 1, R185X and D195V in exon 6, and L554P in exon 14. The polymorphisms were S26F in exon 1 and G139E in exon 4. All patients in our study with 322delG, Q13X, R185X, and D195V are of northern or eastern European or southern Italian ancestry, and 18 of 19 have a mild form of the disease, while the 2 patients with L554P, both from the same family, have a severe phenotype. All 19 patients with IVS4 + 4 A-->T have Jewish ancestry and have a severe phenotype.

Cytogenetic versus DNA diagnosis in routine referrals for fragile X syndrome

The molecular cloning of the gene that causes the fragile X syndrome, and the demonstration that the causative mutation is an expansion of an unstable trinucleotide repeat, suggests that cytogenetic testing could be replaced by a molecular test. We compared the two methods in 525 routine referrals. 12 cases were positive in both tests. 1 case that had a negative DNA test for the fragile site at Xq27.3 (FRAXA), but a positive cytogenetic result, was shown to be caused by a mutation at the FRAXE locus on chromosome Xq28. DNA analysis is a sensitive, reliable, and cost-effective diagnostic alternative.

Osteogenesis imperfecta type III: mutations in the type I collagen structural genes, COL1A1 and COL1A2, are not necessarily responsible

Most forms of osteogenesis imperfecta are caused by dominant mutations in either of the two genes, COL1A1 and COL1A2, that encode the pro alpha 1(I) and pro alpha 2(I) chains of type I collagen, respectively. However, a severe, autosomal recessive form of OI type III with a comparatively high frequency has been recognised in the black populations of southern Africa. We preformed linkage analyses in eight OI type III families using RFLPs associated with the COL1A1 and COL1A2 loci to determine whether mutations in the genes for type I collagen were responsible for this form of OI. Recombination between the OI phenotype and polymorphic markers at both loci was shown in three of the eight families investigated. The combined lod scores for the eight families were -10.6 for COL1A1 and -11.2 for COL1A2. Further, we examined the type I procollagen produced by skin fibroblast cultures derived from 15 affected and 12 unaffected subjects from the above eight families plus one further family. We found no evidence for defects in the synthesis, structure, secretion, or post-translational modification of the chains of type I procollagen produced by any of the family members. These results suggest that mutations within or near the type I collagen structural genes are not responsible for this form of OI.

A nonsense mutation and exon skipping in the Fanconi anaemia group C gene

Fanconi anaemia (FA) is an autosomal recessive disorder associated with bone-marrow failure and hypersensitivity to DNA cross-linking agents. At least four complementation groups have been defined, and a cDNA which corrects the defect in group C cells (FACC) has recently been isolated. We have screened the FACC coding sequence for mutations in FA patients and found one patient to be homozygous for a nonsense mutation in exon 6 of the FACC coding sequence (R185X). Exon 6 was spliced out of a proportion of this patient's transcripts, providing further support for the proposal that nonsense mutations may alter splice site selection. Alternatively spliced transcripts which lacked exon 13 were detected in both patients and controls.

Genetic events in tumour initiation and progression in multiple endocrine neoplasia type 2

Multiple endocrine neoplasia type 2 (MEN 2) is a familial cancer syndrome arising from mutation at a locus or loci in chromosome region 10p11.2-q11.2. The disease is characterized by medullary thyroid carcinoma (MTC) and pheochromocytoma (Pheo). To assess the genetic events in tumour initiation and progression in this disease, we have compiled an allelotype for MTC and Pheo tumours using polymorphic marker loci from each chromosome arm. Using a panel of 58 tumours, we found frequent allele losses on chromosome arms 1p (42%), 3p (30%), 3q (38%), 11p (11%), 13q (10%), 17p (8%), and 22q (29%). Loss of heterozygosity (LOH) for loci on chromosome 10 was detected in a single tumour where one whole chromosome copy was lost. We used a panel of polymorphic markers for each of chromosomes 1, 3, 11, and 17 to define a shortest region of overlap for these regions. The most frequent allele losses were on chromosome 1, spanning the entire short arm of the chromosome but not loci on 1q. LOH on chromosome 3 encompassed a minimal common region of 3q12-qter. The regions of allelic deletion on chromosome 11 (11pter-p13), 17 (17pter-p11.2), and 13 (13q) encompass known tumour suppressor loci (WTI, TP53, RBI) which must therefore be candidates for genes contributing to MTC and Pheo development. Our data suggest allele loss on chromosome 11, 13, or 17 occurs predominantly in tumours with losses on chromosome 3, potentially reflecting the accumulation of genetic change in tumour progression. These events may be associated with more advanced disease in MTC. We suggest that at least 7 genes contribute to tumour development in MEN 2, including an initiating locus on chromosome 10 and loci on chromosomes 1, 3, 11, 13, 17, and 22 which have a progressional role in these tumours.

Direct diagnosis of carriers of point mutations in Duchenne muscular dystrophy

In about one-third of patients with Duchenne/Becker muscular dystrophy, the causative mutation does not involve gross alterations in the structure of the dystrophin gene. Prenatal diagnosis and carrier detection for such families is therefore dependent on the indirect method of linkage analysis with polymorphic DNA markers, a method that is subject to error. The identification of point mutations in the dystrophin gene in six affected males enabled us to develop direct assays, based on the polymerase chain reaction, that are specific for each of the mutations. In all six cases, the assays allowed us to offer families accurate carrier testing and prenatal diagnosis.