Three submicroscopic deletions at the APC locus and their rapid detection by quantitative-PCR analysis.

We describe three unrelated kindreds, affected by familial adenomatous polyposis (FAP), with 5q submicroscopic deletions that encompass the entire adenomatous polyposis coli (APC) gene and the adjacent DP1 gene. In one family the deletion encompasses also the MCC (mutated in colon cancer) gene. Affected members of these families had dysplastic adenomatous polyps and congenital hypertrophy of the retinal pigment epithelium (CHRPE); no individual was affected by mental retardation or facial dysmorphism. The deletions were detected by linkage analysis with several intragenic and closely flanking polymorphic markers and confirmed by a quantitative PCR analysis. This procedure could have an impact on the detection of the molecular defect in FAP patients in whom mutational analysis fails to identify the specific mutation.     

Linkage analysis in adenomatous polyposis coli: the use of four closely linked DNA probes in 20 UK families.

Linkage analysis was carried out on 20 unselected UK families segregating for adenomatous polyposis coli (APC) using four closely linked DNA probes. Significant lod scores were obtained between APC and three markers: pi 227 (D5S37) theta = 0.16; C11p11 (D5S71) theta = 0.10; and YN5.48 (D5S81) theta = 0.00. The fourth, ECB27 (D5S98), gave low lod scores. The APC gene showed linkage with at least one of the probes used in all families, which is in agreement with previous publications. Combined lod scores are now sufficiently high to allow the use of these probes in presymptomatic diagnosis. Despite the fact that 61% of persons at risk were informative for at least one DNA marker, only 15% were informative with flanking probes. One prenatal diagnosis was performed where the initial request had been for sterilisation.     

Presymptomatic diagnosis in families with adenomatous polyposis using highly polymorphic dinucleotide CA repeat markers flanking the APC gene.

A panel of five multiallelic and highly informative dinucleotide CA repeat markers flanking the APC gene was used for presymptomatic diagnosis of familial adenomatous polyposis coli (FAP). Marker regions were amplified by PCR. DNA fragments were separated by electrophoresis in denaturing polyacrylamide gels and visualised by ethidium bromide staining. Two or more markers were found to be informative in all nine families tested, and all 23 persons at risk could be diagnosed as affected or unaffected by the disease gene, the probability being > 99.9% in 14 cases from six families in which flanking markers were informative. We found no indication for locus heterogeneity of the disease in our sample. The polyposis phenotype and its extracolonic manifestations co-segregated with a distinct haplotype determined by the markers flanking the APC gene. In one family with no remaining living affected members, we could infer the high risk haplotype from genotyping of first degree relatives. The segregation of this haplotype is consistent with the occurrence of CHRPEs in the progeny. In a sporadic case we made use of the typical early extracolonic manifestations of the disease (osteomas, desmoids) to identify the high risk haplotype. We conclude from our experience that indirect genotyping of FAP with this particular panel of closely linked and highly polymorphic microsatellite markers is a rapid, efficient, and highly reliable method for presymptomatic diagnosis of FAP.     

Improved DNA markers for efficient analysis of fragile X families

We report the characteristics of two new probes that detect BclI RFLPs useful for analysis of fragile X families. With these two probes and a single blot, 34% of women are heterozygous both for the proximal marker DXS105 (closer to the fragile X locus than the factor IX gene) and for the distal markers DXS52 or the factor VIII gene. Combined with the analysis of previously described polymorphic markers, it is possible to have a majority of families fully informative for flanking markers using a limited number of probes and restriction digests.     

RFLP analysis for diagnosis of haemophilia A in the German Democratic Republic

The frequencies of Bcl I, Hind III and Xba I intragenic polymorphic sites in the population of the GDR were found to be 0.68, 0.38 and 0.48, respectively. No differences in composition and frequencies were detectable at DXS 52 locus in comparison with other Caucasian populations. A strong linkage disequilibrium between the intragenic Bcl I and Hind III sites could be confirmed. The observed heterozygosity for the flanking marker DXS 52 in combination with intragenic Bcl I and Xba I polymorphisms was 0.97. Using these three RFLPs, 122 females at risk in 41 independent haemophilia A families were investigated; 86 of them could be identified and 27 excluded as carriers; 9 females could not be classified. So far, four prenatal diagnoses in the first trimester of gestation have been performed by RFLP analysis.     

Molecular diagnosis of the fragile X [Fra (X)] syndrome: calculation of risks based on flanking DNA markers in small phase-unknown families

We studied two small, two-generation families with the fragile X [Fra (X)] syndrome. The absolute phase of the DNA markers in relation to the disease in the mother was not known in either family. We present the derivation of risks for these families using flanking markers, taking into account the uncertainty regarding maternal phase. Since the use of flanking markers fails to yield useful counseling data in the 1/3 to 1/7 of all cases where a single recombination event occurs between the two flanking markers, we calculate the probability that this method is likely to be successful or unsuccessful when prenatal diagnosis is attempted using linked RFLPs.     

Lack of linkage and association between autoimmune thyroid diseases and the CTLA-4 gene in a large Tunisian family.

The autoimmune thyroid diseases (AITDs) including Graves' disease and Hashimoto's thyroiditis are inherited as complex traits. We have performed linkage and association studies to investigate the role of CTLA-4 gene in the AITDs development using the D2S311, D2S143, the intragenic CTLA-4 (AT)(n) microsatellite markers and the CTLA-4 (A/G) dimorphism in exon 1. Four extended pedigrees belonging to a large Tunisian family named Akr and including 154 individuals from which 20 were affected with Hashimoto's thyroiditis and 26 with Graves' disease, were used in this investigation. No evidence for linkage with none of the markers was found under neither dominant nor recessive models [Z=-7.14 and Z=-14.32 at theta=0.0, respectively for the CTLA-4 (AT)(n) marker]. A family-based association study on 51 nuclear families derived from the Akr pedigree was performed by the FBAT approach applied to the CTLA-4 (AT)(n) marker and the CTLA-4 (A/G) dimorphism. We found no association of individual alleles to disease for both markers. These results showed no evidence for the involvement of the CTLA-4 locus in the AITDs pathogenesis.     

Hemophilia A: genetic prediction and linkage studies in all available families in Finland

RFLP studies were done in 82 (75%) of all known hemophilia A families in the Finnish population (approximately 5 million). Two intragenic RFLPs (Bc1I/F8A, XbaI/p482.6) and two extragenic markers (TaqI/St14, Bg1II/DX13) were used. Among 263 females at risk, carriership could be evaluated with an intragenic marker in 47% and with an extragenic marker in 26%. In 27% of the females, carriership could be neither excluded nor confirmed; 68% of these females were relatives of an isolated patient. Eight recombinations between the factor VIII gene (F8C) and DXS52 (lod 25.02 at theta max 0.06), eight recombinations between F8C and DXS15 (lod 21.91 at theta max 0.05), and two recombinations between DXS52 and DXS15 (lod 33.56 at theta max 0.01) were found. Using multipoint linkage analysis, the most likely order of loci supported by the data was: F8C-DXS15-DXS52-DXS134. RFLP segregation analysis provides a highly useful method of carrier detection and prenatal diagnosis of hemophilia A, but its limitations must be carefully taken into account.     

Genotype analysis of the NF1 gene in the French Canadians from the Québec population.

We genotyped 19 NF1 families from the French Canadians of the Québec population with six intragenic polymorphic markers including 2 RFLPs (EcoRI and RsaI) and 4 microsatellites (IVS26-2.3, IVS27AC28.4, IVS27AC33.1, and IVS38GT53.0). Genotype analysis indicated families 7610 and 7473 bear deletions. In Family 7610 the deletion removed the entire NF1 gene except exons 1 to 4b. The breakpoint of the deletion is located between exons 4a and 4b. The deletion 7473 was derived from the maternal chromosome and exons 1 to 5 were deleted. The breakpoint of the deletion is located between exons 7 and 13. Their phenotypes are reported. The allele frequencies of microsatellites IVS27AC28.4 and IVS38GT53.0 are compared to previously reported data from Caucasians, including Spanish and Italians. The difference is statistically significant (P < 0.0036) for marker IVS27AC28.4 between the Québec French Canadian and the Italian population.     

Fabry disease: Molecular carrier detection and prenatal diagnosis by analysis of closely linked polymorphisms at Xq22.1

Fabry disease is an X-linked recessive inborn error of glycosphingolipid catabolism that results from the deficient activity of the lysosomal enzyme α-galactosidase A (α-Gal A). A rapid, reliable, and universal linkage method was developed for molecular carrier detection and prenatal diagnosis. By determining the informativeness and phase of amplifiable intragenic RFLPs (NcoI and SacI), flanking RFLPs (DXS94 and DXS17), and flanking microsatellite polymorphisms at Xq22.1 (DXS458, DXS454, DXS7424, DXS178, and DXS101), accurate carrier detection, and/or prenatal diagnosis was accomplished in three prototypic, unrelated Fabry families. All linkage diagnoses were confirmed by identification and analysis of the specific α-Gal A lesion in each family. Thus, molecular carrier detection and prenatal diagnoses can be performed rapidly and reliably by linkage analysis with intragenic and closely-linked polymorphisms at Xq22.1 in Fabry families whose specific Gal A lesions have not been determined. Am. J. Med. Genet. 71:329–335, 1997. © 1997 Wiley-Liss, Inc.     

Genetic heterogeneity in familial hypobetalipoproteinemia: Linkage and non-linkage to the apoB gene in caucasian families

Familial hypobetalipoproteinemia (FHBL) is an autosomal dominant disorder of lipid metabolism characterized by extremely low plasma levels of apolipoprotein B (apoB), and total-, and low-density lipoprotein (LDL) cholesterol. Various truncated forms of apoB have been found to cosegregate with the FHBL phenotype in more than 30 kindreds. By contrast, no truncated forms of apoB protein were detected with sensitive immunoblotting in the plasmas of any of the 6 kindreds reported here. Individuals with apoB levels in the 5th centile for their age and sex were considered as affected with FHBL. Linkage analysis was performed using 3 microsatellite markers flanking the apoB gene (D2S131, D2S149, and D2S144), a 3′ variable number of tandem repeats (VNTR) marker and one intragenic marker. Two-point linkage of FHBL was established to the 3′ VNTR marker with a combined maximum LOD score of 8.5 at θ = 0 for 5 of the 6 families. Maximum LOD scores for flanking microsatellite markers were 5.0, 2.4, 1.3, 1.2 and 2.1 for these kindreds (D, T, De, C and Z, respectively). A test of homogeneity differentiated the 6th family (F kindred) from the other five. LOD scores of −25.2 at the 3′ VNTR and −7.8 at the intragenic apoB/Xbal marker at θ = 0 excluded linkage to the apoB gene in the F kindred. These kindreds demonstrate the heterogeneity of FHBL and also offer the possibility to investigate as yet undescribed mutations of apoB, resulting in alterations of apoB metabolism. The F kindred may shed light on novel gene(s) contributing to the low apoB-phenotype. Am. J. Med. Genet. 76:79–86, 1998. © 1998 Wiley-Liss, Inc.     

Development of a microsatellite-based approach to co-segregation analysis of familial hypercholesterolaemic kindreds

Co-segregation studies based on a selection of intragenic restriction fragment length polymorphisms of the low density lipoprotein receptor (LDLR) gene have been used extensively both for research and diagnostic studies of familial hypercholesterolaemia (FH) families, because direct mutation screening remains complex. Here we describe the development and application of a more efficient approach to co-segregation studies based on highly informative dinucleotide and tetranucleotide repeats flanking the LDLR gene. A series of microsatellites (D19S391, D19S394, D19S221 and D19S179) were selected for study on the basis of linkage analysis in the CEPH families using intragenic polymorphisms for a TA repeat (exon 18) in the LDLR gene, and earlier data for a Pvu II polymorphism (intron 15). A physical map of the region of chromosome 19 also contributed to this selection. One marker in particular, D19S394, sited 150 kilobases telomeric to the gene, was extremely useful, displaying 90% heterozygosity, robust PCR of tetranucleotide repeats without stutter bands, and no recombination with the LDLR gene (θ=0, LOD 68). Use of this marker in the families of twenty-three FH probands from Hampshire demonstrated co-segregation of the hyperlipidaemia phenotype with the LDLR gene region, except in one family with defective apolipoprotein B-100, and a family turning out to display familial combined hyperlipidaemia. This approach should facilitate the search for any families where FH does not co-segregate with the LDLR gene, and will enhance the repertoire of molecular diagnostic tools available for FH.     

Carrier analysis and prenatal diagnosis of haemophilia A in North India

The feasibility of DNA diagnosis for haemophilia A in North India was evaluated using intragenic polymorphic DNA markers in factor VIII gene for linkage analysis as well as direct detection of inversion mutation in intron 22 of the gene. The informativity of RFLP (HindIII, BclI and XbaI) and STR (introns 13 and 22) markers for linkage analysis in factor VIII gene was determined in 100 normal individuals. The observed heterozygosity for RFLP markers HindIII, BclI and XbaI was 0.63, 0.60 and 0.48 while that of STR markers introns 13 and 22 were 0.60 and 0.40 respectively. Six and four alleles were identified for introns 13 and 22 and the most frequent allele was 13(CA)26 and 22(AG)n(GT)26 with an allele frequency of 0.53 and 0.62 respectively. The heterozygosities observed for RFLP markers was higher (>70%) than the STR markers (50%) in the affected families with haemophilia A. Inversion mutation was detected in 37% of severely affected patients. Based on present and previous studies from India, a strategy has been proposed to provide molecular diagnosis to a large number of undiagnosed cases of haemophilia A.     

Further refinement of the Usher 2A locus at 1q41.

Usher syndrome (USH) is characterised by congenital sensorineural hearing loss and progressive pigmentary retinopathy. All three subtypes (USH1, USH2, and USH3) are inherited as recessive traits. People with Usher type 2 (USH2) have normal vestibular responses and moderate to severe hearing loss. These syndromes have been found to be genetically heterogeneous, with a single locus for USH2 at 1q41 (USH2A), six loci for USH1, and one for USH3. Some USH2 families have been excluded from the 1q41 locus suggesting that a second, as yet unidentified, locus (USH2B) must exist. Linkage studies suggest that around 90% of USH2 families are USH2A. Four USH2 families were analysed for linkage to markers flanking the USH2A locus. In one of these families a recombination event was observed in an affected subject which excludes the USH2A gene from proximal to the marker AFM143XF10 and defines this as the new centromeric flanking marker for the USH2A locus. A further recombination event in another patient from this family confirmed AFM144XF2 as the telomeric flanking marker. The interval between these polymorphic markers is estimated to be 400 kb. This region is completely contained in each of three YACs from the CEPH library: 867g9, 919h3, and 848b9. This refinement more than halves the critical genetic interval and will greatly facilitate positional cloning of the USH2A gene.     

Common origin of the I1307K APC polymorphism in Ashkenazi and non-Ashkenazi Jews.

A common germline missense mutation within the APC gene, I1307K, has recently been described in Ashkenazi Jews. We detected this polymorphism in two non-Ashkenazi Jewish women using denaturing gradient gel electrophoresis (DGGE), and hypothesized that in Jewish individuals it might not be restricted to Ashkenazim, and actually reflect a common ancestral polymorphism. To test this notion we performed allelic pattern determination using APC-linked markers in these two women and in nine Ashkenazi carrier controls. The pattern of the intragenic markers, as well as a single downstream marker 30-70 Kb from the APC gene was identical in all individuals, regardless of ethnic origin. We conclude that the I1307K polymorphism in Jewish individuals, is not restricted to Ashkenazim and probably reflects a founder mutation.     

Genotype analysis of the NF1 gene in the French Canadians from the Québec population

We genotyped 19 NF1 families from the French Canadians of the Québec population with six intragenic polymorphic markers including 2 RFLPs (EcoRI and RsaI) and 4 microsatellites (IVS26‐2.3, IVS27AC28.4, IVS27AC33.1, and IVS38GT53.0). Genotype analysis indicated families 7610 and 7473 bear deletions. In Family 7610 the deletion removed the entire NF1 gene except exons 1 to 4b. The breakpoint of the deletion is located between exons 4a and 4b. The deletion 7473 was derived from the maternal chromosome and exons 1 to 5 were deleted. The breakpoint of the deletion is located between exons 7 and 13. Their phenotypes are reported. The allele frequencies of microsatellites IVS27AC28.4 and IVS38GT53.0 are compared to previously reported data from Caucasians, including Spanish and Italians. The difference is statistically significant (P < 0.0036) for marker IVS27AC28.4 between the Québec French Canadian and the Italian population. © 2001 Wiley‐Liss, Inc.     

三个新的PAH基因短串联重复序列多态性及其在苯丙酮尿症产前诊断中的应用

目的提高经典型苯丙酮尿症的产前诊断的成功率。方法在苯丙氨酸羟化酶（phenylalanine hydroxylase，PAH）基因附近选择了3个新的短串联重复序列（short tandem repeat，STR）位点（PAH26、PAH32和PAH9），进行扩增长度片段多态性分析，确定它们在中国人群的分布及在诊断中的应用价值。结果3个新的STR位点的多态信息含量分别为0．518（PAH26）、0．413（PAH32）和0．362（PAH9）。这3个位点之间，PAH9与第3内含子中的STR位点（TCTA）n之间存在连锁不平衡，其他位点组合不存在连锁不平衡。联合第3内含子中的STR位点（TCTA）n和2个新的位点，可以对家系中突变基因标记进行95％N断，并成功地用于4例产前诊断中。结论选择性地应用PAH基因中的3个STR位点组合，可以95％地区分经典型苯丙酮尿症家系中父母的两个基因，从而准确地进行快速产前诊断。     

Multimarkerhaplotypes within the serotonin transporter gene suggest evidence of an association with bipolar disorder

Previously we obtained modest linkage evidence implicating 17q11. 1-12 in bipolar disorder. A modified genome screen, based on gene-rich regions, on a collection of Irish sib-pair nuclear families revealed excess allele sharing at markers flanking the gene encoding the serotonin transporter (5-HTT; hSERT). Here we describe a study designed to combine the advantages of family-based association studies with the consideration of multiple polymorphic markers within a candidate gene. Ninety-two Irish families, with a total of 106 proband-parent trios, have been genotyped for 3 previously known polymorphisms within hSERT (5-HTTLPR, intron 2 VNTR, and 3' UTR G/T). Data from two and three polymorphic marker haplotypes revealed a number of marker combinations that showed evidence supportive of association; the most significant being for polymorphisms 5-HTTLPR and 3' UTR G/T (global chi(2), 12.91, df 3, P = 0.005). In addition, modest evidence of association also was observed for 5-HTTLPR alone. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:845-849, 2000.     

Absence of linkage and linkage disequilibrium to chromosome 15q11-q13 markers in 139 multiplex families with autism.

Chromosomal region 15q11-q13 has been implicated to harbor a susceptibility gene or genes underlying autism. Evidence has been derived from the existence of cytogenetic anomalies in this region associated with autism, and the report of linkage in a modest collection of multiplex families. Most recently, linkage disequilibrium with the marker GABRB3-155CA2 in the candidate locus GABRB3, located in this region, has been reported. We searched for linkage using eight microsatellite markers located in this region of chromosome 15 in 147 affected sib-pairs from 139 multiplex autism families. We also tested for linkage disequilibrium in the same set of families with the same markers. We found no evidence for excess allele sharing (linkage) for the markers in this region. Also, we found no evidence of linkage disequilibrium, including for the locus GABRB3-155CA2. Thus, it appears that the role of this region of chromosome 15 is minor, at best, in the majority of individuals with autism.     

Loss of mutation at the FMR1 locus through multiple exchanges between maternal X chromosomes

The mutation observed in the fragile X syndrome, an X-linkedinherited disorder causing mental retardation, is almost exclusivelyan expanded CGG repeat in the first exon of the FMR1 gene. Herewe describe a daughter of a female carrier, who inherited thefragile X premutation chromosome based on haplotype analysisusing flanking markers. However, the CGG repeat sequence andthe intragenic polymorphic marker FMRb showed the normal maternalalleles, while two other intragenic markers, FMRa and FRAXAC2and other, more distant markers, showed the risk haplotype.Since FMRa and FRAXAC2 are located in between the markers CGGand FMRb, this results in patches of normal and fragile X sequencesin the FMR1 gene of the daughter. This observation is very likelydue to gene conversion. As this daughter received a normal CGGrepeat region, we expect that her risk to have affected offspringis the same as the population risk. The observed phenomenonwould therefore represent a back mutation at the FMR1 locus.