Haplotype distribution and mutations at the PAH locus in Croatia

Summary Restriction fragment length polymorphism (RFLP) haplotypes and mutations at the phenylalanine hydroxylase (PAH) locus have been studied in 25 unrelated families from Croatia. The results of RFLP analysis demonstrated that 80% of the mutant alleles were associated with three haplotypes (1, 2 and 4). Eight mutations were detected on the background of six mutant haplotypes, comprising 68% of phenylketonuria (PKU) alleles in Croatia. The mutation in codon 408 was most frequent, as was the haplotype 2 allele with which it was associated. These data are in accordance with formerly published population genetic analyses at the PAH locus, and with studies revealing the molecular basis of the phenotypic heterogeneity of PKU. The codon 281 mutation was more frequent in Croatia than previously observed in other populations.     

Genetic heterogeneity in five Italian regions: analysis of PAH mutations and minihaplotypes

Molecular analysis of 289 chromosomes has been performed in a cohort of phenylketonuria (PKU) patients whose ancestors lived in five Italian regions, Calabria, Campania, Piemonte, Puglia/Basilicata and Sicilia. Phenylalaninehydroxylase (PAH) gene mutations and minihaplotypes (combinations of PAH gene STR and VNTR systems) have been determined for 78.5 and 64%, respectively, of the chromosomes studied. 21 different minihaplotypes and 24 PKU mutations were found. Heterogeneity tests carried out for the frequencies of mutations and minihaplotypes show that the distribution of eight mutations and four minihaplotypes is statistically heterogeneous in the five Italian regions. Although the evolutionary rate of microsatellites or the age of these mutations is difficult to estimate with accuracy, our findings taken together show a genetic stratification of the Italian population. These results rule out allelic homogeneity of PKU at the molecular level between regions of Italy, yet minihaplotype data may be of practical use for a multistep approach to PAH gene genotyping.     

Phenylketonuria mutations and their relation to RFLP haplotypes at the PAH locus in Czech PKU families

A detailed study of the mutant phenylalanine hydroxylase (PAH) gene from the eastern part of the Czech Republic (Moravia) is reported. A total of 190 mutant alleles from 95 phenylketonuria (PKU) families were analyzed for 21 prevalent Caucasian mutations and restriction fragment length polymorphism /variable number of tandem repeats (RFLP/VNTR) haplotypes. Eighty per cent of all mutant alleles were found to carry 11 mutations. The most common molecular defect was the mutation R408W (55.3%), with a very high degree of homozygosity (34.6%). Each of four other mutations (R158Q, R243X, G272X, IVS12nt1) accounted for more than 3% of PKU alleles. Rarely present were mutations IVS10nt546 (2.6%), R252W (2.6%), L48S (2.1%), R261Q (1.6%), Y414C (1.0%) and I65T (0.5%). Mutations that have been predominantly described in southern Europe (IVS7nt1, A259V, Y277D, R241H, T278N) were not detected. A total of 14 different mutant haplotypes were observed. Three unusual genotype-haplotype associations were identified (R158Q on haplotypes 2.3 and 7.8 and R252W on haplotype 69.3). There was a strong association between the mutation R408W and haplotype 2.3 (54.7%). Heterogeneity was found at mutations R408W (haplotypes 2.3 and 5.9), R158Q (haplotypes 4.3, 2.3 and 7.8) and IVS10nt546 (haplotypes 6.7 and 34.7). The molecular basis of PKU in the Moravian area appears to be relatively homogeneous in comparison with other southern and western European populations, thus providing a good starting point for prenatal diagnosis and early clinical classification.     

The identification of two mis-sense mutations at the PAH gene locus in a Turkish patient with phenylketonuria

Summary DNA sequence analysis of the 13 exons and intron/exon boundaries of the phenylalanine hydroxylase (PAH) gene has detected two base transitions, resulting in mis-sense mutations, in the genomic DNA of a Turkish patient (E1) with phenylketonuria (PKU). The Leu⁴⁸Ser amino acid substitution was associated with the mutant haplotype 3 allele and the Glu²²¹Gly amino acid substitution with the mutant haplotype 4 allele of this family. Allele-specific oligonucleotide (ASO) dotblot analysis subsequently detected the Leu⁴⁸Ser mutation in the haplotype 4 PKU alleles of nine (18.8%) of the 48 unrelated Caucasian PKU families investigated. This mutation results in mild PKU in the homozygous state. The Glu²²¹Gly mutation has only been detected within patient E1 and his father.     

Haltere determination and mutations at the bithorax locus

Mutations at the bithorax locus transform anterior haltere tissue into anterior wing. These transformations could in principle be due to the mutations altering either the expression or cell heredity functions of determination. I have studied two alleles of the bithorax locus bx³ and bx^34e using disc culture techniques and found that both produce their transformations by altering the expression of the determined state. I have also found that the expression of the temperature-sensitive allele, bx^34e, can be altered by temperature shifts during the culture period. Evidence has been obtained that suggests that such changes in expression do not require growth or cell division.     

Identification of three novel PKU mutations among Chinese: evidence for recombination or recurrent mutation at the PAH locus.

Three novel mutations have been identified in the phenylalanine hydroxylase (PAH) genes of Chinese classical phenylketonuria (PKU) patients. Two of these substitutions (W326X and Y356X) result in the generation of a premature stop codon, while the third (IVS-7nt2) alters an invariant dinucleotide splicing signal. These mutations together account for about 10% of all PKU alleles in the Chinese population. The W326X mutation is associated with PAH RFLP haplotype 4, the most common haplotype in Orientals, while the IVS-7nt2 mutation occurs once on a haplotype 7 chromosome. The Y356X mutation is associated with multiple haplotypes, possibly due to crossover, gene conversion, or recurrent mutation.     

Two novel PAH gene mutations detected in Italian phenylketonuric patients

We report the identification by denaturing gradient gel electrophoresis and sequence analysis of two new phenylalanine hydroxylase (PAH) gene mutations (IVS4nt-2 and N207S) in single chromosomes of two unrelated Italian phenylketonuric (PKU) patients. Interestingly, mutation Y204C, found on the second mutant allele of family F1, has been previously detected in Chinese patients. Haplotype analysis showed that the latter mutation is linked to the same haplotype (H4) in both Chinese and Italian patients, suggesting a common origin. In vivo assessment of mutation severity indicates that N207S is associated with classic PKU. The identification of these two new mutations further extends the remarkable heterogeneity of the PAH locus in the Italian population. Received: 23 May 1996     

PAH Mutation Analysis Consortium Database: a database for disease-producing and other allelic variation at the human PAH locus.

The PAH Mutation Analysis Consortium (81 investigators, 26 countries) is engaged in mutation detection at the human PAH locus. Ascertainment of probands occurs largely through newborn screening for hyperphenylalaninemia. A relational database records allelic variation (disease-producing and polymorphic) at the locus. Information is distributed by Newsletter, diskette (WINPAHDB software stand-alone executable on IBM compatible hardware), and at a 'real' site on the Worldwide Web (http://www.mcgill.ca/pahdb). The database presently records (Sept. 27, 1995) 248 alleles in 798 different associations (with polymorphic haplotype, geographic region and population) along with additional information. The database, as a record of human genetic diversity, at a particular locus, contributes to the study of human evolution and demic expansion; it also has medical relevance.     

Association between the ABO locus and hematological traits in Korean

ABSTRACT: BACKGROUND: Recently, genomewide association studies identified a pleiotropic gene locus, ABO, as being significantly associated with hematological traits. To confirm the effects of ABO on hematological traits, we examined the link between the ABO locus and hematological traits in Korean population-based cohorts. RESULTS: Six tagging SNPs for ABO were analyzed with regard to their effects on hematological traits [white blood cell count (WBC), red blood cell count (RBC), platelet (Plat), mean corpuscular volume (MCV), and mean corpuscular haemoglobin concentration (MCHC)]. Linear regression analyses were performed, controlling for recruitment center, sex, and age as covariates. Of the 6 tagging SNPs, 3 (rs2073823, rs8176720, and rs495828) and 3 (rs2073823, rs8176717, and rs687289) were significantly associated with RBC and MCV, respectively (Bonferroni correction p-value criteria < 0.05/6 = 0.008). rs2073823 and a reported SNP (rs8176746), as well as rs495828 and a reported SNP (rs651007), showed perfect linkage disequilibrium status (r2s = 0.99). Of the remaining 3 SNPs (rs8176720, rs8176717 and rs687289), rs8176717 generated an independent signal with moderate p-value (= 0.045) when it was adjusted for by rs2073823 (the most significant SNP). We also identified a copy number variation (CNV) that was tagged by the SNP rs8176717, the minor allele of which correlated with the deletion allele of CNV. Our haplotype analysis indicated that the haplotype that contained the CNV deletion was significantly associated with MCV (beta +/- se = 0.363 +/- 0.118, p =2.09 x 10-3). CONCLUSIONS: Our findings confirm that ABO is one of the genetic factors that are associated with hematological traits in the Korean population. This result is notable, because GWASs fail to evaluate the link between a CNV and phenotype traits.     

APC gene mutations causing familial adenomatous polyposis in Polish patients

Familial adenomatous polyposis (FAP) is a well-known hereditary condition characterised by alimentary system tumours. Tens to thousands of polyps occur in the colon and rectum of the patients. There is a high heterogeneity with regard to the number and time of the occurrence of polyps. The occurrence of FAP is associated with mutations in theAPC tumour suppressor gene, which was described in 1991. Since then, many studies have been done to analyse the distribution of mutations in individual populations and to determine the function of the gene and a diagnostic approach to FAP. Here theAPC gene was studied with respect to the occurrence of small mutations and large rearrangements in 300 unrelated Polish FAP families. Ninety-seven mutations were identified in 164 families. Out of these mutations, 80 were small mutations, including 58 small mutations that were first identified in the Polish population (42 novel and 16 described previously). An increased frequency of mutation c.3927_3931delAAAGA was observed in 10% of the Polish group. Seventeen large rearrangements were found in 29 families. Out of those rearrangements, 8 repeat rearrangements occurred in 20 families. A problem in fast molecular diagnostics of FAP is a high heterogeneity of mutations in theAPC gene. It seems that a multiplex ligation-dependent probe amplification test and searching for small mutations by the use of screening methods at the 5’ end of exon 15 and exons 14, 9, 11, 13, 5, and 3, help to improve the molecular diagnostics of FAP in Polish patients.     

Analysis of ENU-induced mutations at the Adh locus in Drosophila melanogaster

N-Ethyl-N-nitrosourea (ENU) was used to induce mutations in the Drosophila melanogaster, alcohol dehydrogenase (Adh) gene. Flies were treated with ENU and mated to homozygous intragenic Adh null mutants; Adh null mutations were selected by exposure of the F1 generation to 1-penten-3-ol. Fourteen Adh null mutations were recovered which included 11 from spermatozoa, 2 from oocytes and 1 from a premeiotic spermatocyte. 2 mutations from spermatozoa and 1 of the mutations from oocytes were multilocus deficiencies which included the Adh locus as determined by complementation tests. The remaining 11 intragenic Adh null mutations were sequenced using the Sanger dideoxy method. One Adh null mutation induced in an oocyte was an AT to TA transversion and the mutation induced in a premeiotic spermatocyte was a GC to AT transition, both of which resulted in a single amino acid substitution. The 11 null mutations induced in spermatozoa were a data set in which both the dose of ENU and the treated germ-cell stage were held constant; therefore, only these 11 mutations were used to calculate the mutation frequency and compare the mutations at the Adh locus with those recovered in other studies. The dose of ENU induced a sex-linked recessive lethal frequency approximately 300 times that of the spontaneous frequency; therefore, these mutations were assumed to have been induced by ENU. 2 of the 11 mutations induced in spermatozoa were multilocus deficiencies and 9 were intragenic mutations. 7 of the 9 intragenic mutations were GC to AT transitions which resulted in 5 single amino acid substitutions, 1 premature translation termination codon, and 1 splice site mutation.(ABSTRACT TRUNCATED AT 400 WORDS)     

Heterozygote detection in MLD. Allelic mutations at the ARA locus

Summary The syndrome caused by partial trisomy for 11q is reviewed on the basis of a patient of our own and 20 cases (including a stillbirth) from the literature. The main symptoms are presented in Tables 1 and 2. The syndrome can be suspected when, in addition to mental retardation, the following characteristics are present: short nose, long philtrum, micrognathia, retracted lower lip, and micropenis in males. In 15 families, the mother was a balanced translocation carrier and in four the father. The translocation had arisen de novo in two patients. The chromosome number was 46 in 13 affected individuals (including the stillbirth) and 47 in eight. In seven of the latter patients the other translocation chromosome was 22, and in one, chromosome 9. The breakpoints on 11q ranged from 11q121 to 11q232 (Fig. 5). There is no apparent correlation between the length of the trisomic segment and the number or severity of the symptoms (Table 2). This could be explained by assuming that most, if not all, symptoms are caused by trisomy for the Q-dark region distal to 11q232, whereas trisomy for the rest of the 11q up to q121 has few phenotypic effects. These observations support the idea that Q-dark segments, and especially certain hot spots, have a high gene density in contrast with Q-brighter regions.     

SURF1 gene mutations in Polish patients with COX-deficient Leigh syndrome

One of the most frequent forms of Leigh syndrome (LS), a severe neurodegenerative, genetically heterogenous disease, is associated with cytochrome c oxidase (COX) deficiency. No mutations in any of the 13 polypeptide subunits of human COX have been detected in LS patients. Recently, SURF1, a positional candidate gene for LS has been identified on chromosome 9q34. We present the identification of SURF1 mutations in a randomly chosen group of Polish patients with a classical form of LS. Sequence analysis revealed the presence of a novel 704T-->C transition (Met235Thr), and two recurrent dinucleotide deletions (758delCA, 845delCT), as well as one novel polymorphic 573C-->G transversion (Thr191Thr). 845delCT was identified in 66% of all our patients in homozygous or heterozygous form. Our study confirms the recent observations that SURF1 is consistently involved in disorders of the mitochondrial respiratory chain in patients with typical Leigh syndrome.     

Haplotypes and linkage disequilibrium at the phenylalanine hydroxylase locus, PAH, in a global representation of populations

Because defects in the phenylalanine hydroxylase gene (PAH) cause phenylketonuria (PKU), PAH was studied for normal polymorphisms and linkage disequilibrium soon after the gene was cloned. Studies in the 1980s concentrated on European populations in which PKU was common and showed that haplotype-frequency variation exists between some regions of the world. In European populations, linkage disequilibrium generally was found not to exist between RFLPs at opposite ends of the gene but was found to exist among the RFLPs clustered at each end. We have now undertaken the first global survey of normal variation and disequilibrium across the PAH gene. Four well-mapped single-nucleotide polymorphisms (SNPs) spanning approximately 75 kb, two near each end of the gene, were selected to allow linkage disequilibrium across most of the gene to be examined. These SNPs were studied as PCR-RFLP markers in samples of, on average, 50 individuals for each of 29 populations, including, for the first time, multiple populations from Africa and from the Americas. All four sites are polymorphic in all 29 populations. Although all but 5 of the 16 possible haplotypes reach frequencies >5% somewhere in the world, no haplotype was seen in all populations. Overall linkage disequilibrium is highly significant in all populations, but disequilibrium between the opposite ends is significant only in Native American populations and in one African population. This study demonstrates that the physical extent of linkage disequilibrium can differ substantially among populations from different regions of the world, because of both ancient genetic drift in the ancestor common to a large regional group of modern populations and recent genetic drift affecting individual populations.