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PubMed1999

A simple procedure for polymerase chain reaction of the PSBA gene in algae: application to the screening of mutations conferring atrazine resistance and discrimination of natural populations of Porphyra linearis.

A simplified procedure is described for polymerase chain reaction (PCR) of a partial sequence (bp 601-893) of the plastid gene psbA in the rhodophyte Porphyra linearis and the diatoms Haslea ostreria and Skeletonema costatum. This procedure involves the use of all tissues of P. linearis and live cell suspensions of H. ostreria or S. costatum, as DNA templates, without any further purification of DNA. As in the case of PCR with DNA extracts, a single major band of the expected size (292 bp) was obtained after PCR for the three species. Sequences of the amplified fragments were aligned, confirming that the amplified products were part of the psbA gene. The method was then used to screen mutations in partial psbA genes of 23 samples of P. linearis collected at four different stations along the mid-Atlantic coast of France. An alignment was obtained indicating the existence of mutations, though not in codons known for herbicide resistance. All mutations found were silent. However, genetic polymorphism discriminated between samples collected from two stations. The method employed allows rapid amplification of the herbicide target gene and simplifies the procedure for screening mutations or populations in algae. Its application to other genes and species is considered.

Atlantic Ocean↗
PubMedDate not supplied

Screening for mutations in a genetically heterogeneous disorder: DHPLC versus DNA sequence for mutation detection in multiple genes causing Charcot-Marie-Tooth neuropathy.

PURPOSE: To determine the efficacy of denaturing high-performance liquid chromatography (DHPLC) for mutation detection in genetically heterogeneous diseases using Charcot-Marie-Tooth neuropathy as a model. METHODS: (1) Identification of the optimal conditions for mutation scanning by DHPLC using 50 known variants of PMP22, MPZ, GJB1 and EGR2. (2) Comparison of DHPLC with DNA sequencing for mutation detection in 168 patient DNA samples. RESULTS: We established the optimal conditions for screening PMP22, MPZ, GJB1, and EGR2 for mutations. Under optimized conditions, DHPLC was as sensitive as DNA sequencing and detected two mutations that were not identified by automated DNA sequence. CONCLUSIONS: DHPLC increases the efficiency and sensitivity of mutation screening in genetically heterogeneous diseases.

Adult↗
PubMed1999

Screening for germ-line rearrangements and regulatory mutations in BRCA1 led to the identification of four new deletions.

Most previous BRCA1 mutation screening studies conducted on breast cancer families were aimed at identifying mutations in the coding sequence and splice sites. Mutations in the promoter and untranslated regions, and large rearrangements are missed by standard mutation detection strategies. To look specifically for such germ-line mutations in the BRCA1 gene, we have analyzed a series of 27 American and 51 French breast cancer families in which no BRCA1 mutation was identified by classical techniques. No mutations were detected in either the promoter or untranslated regions, and we did not find any deletion of the whole gene. Four families were found to carry distinct deletions. Two of them, probably generated by Alu-mediated homologous recombination, were internal deletions of 3 and 23.8 kb, encompassing exon 15 and exons 8-13, respectively. These alterations both lead to a frameshift in the mutant mRNA and to premature stop codon-mediated mRNA decay. The other two deletions encompass exons 1 and 2. On the basis of previous and present analyses, rearrangements represent 8% (3/37) of all mutations in our set of BRCA1 American families. Consequently, the search for rearrangements appears mandatory in BRCA1 mutation screening studies.

3' Untranslated Regions↗
PubMedDate not supplied

Spectrum and distribution of MECP2 mutations in 424 Rett syndrome patients: a molecular update.

Mutations in the MECP2 (Methyl-CpG-binding protein) gene have been reported to cause Rett syndrome (RTT), an X-linked progressive encephalopathy. Recent studies have identified large gene rearrangements that escape the common PCR-based mutation screening strategy and mutations in a novel MeCP2 isoform (named MECP2B). We have collected the results of MECP2 mutational analysis concerning 424 RTT patients conducted in eight laboratories in France. In total, 121 different MECP2 mutations were identified. R168X (11.5%) is the most common of MECP2 mutations, followed by R270X (9%), R255X (8.7%), T158 M (8.3%) and R306C (6.8%). Only eight mutations had relative frequency>3%. Large and complex rearrangements not previously detected using only a PCR-based strategy represent 5.8% of MECP2 mutations. On the contrary, mutation in exon 1 appears to be rare (less than 0.5%). These data demonstrate the high allelic heterogeneity of RTT in France and suggest that routine mutation screening in MECP2 should include quantitative analysis of the MECP2 gene. This study represents an important instrument for molecular diagnosis strategy and genetic counseling in RTT families.

Cohort Studies↗
PubMed2006

Cost-effectiveness of screening BRCA1/2 mutation carriers with breast magnetic resonance imaging.

CONTEXT: Women with inherited BRCA1/2 mutations are at high risk for breast cancer, which mammography often misses. Screening with contrast-enhanced breast magnetic resonance imaging (MRI) detects cancer earlier but increases costs and results in more false-positive scans. OBJECTIVE: To evaluate the cost-effectiveness of screening BRCA1/2 mutation carriers with mammography plus breast MRI compared with mammography alone. DESIGN, SETTING, AND PATIENTS: A computer model that simulates the life histories of individual BRCA1/2 mutation carriers, incorporating the effects of mammographic and MRI screening was used. The accuracy of mammography and breast MRI was estimated from published data in high-risk women. Breast cancer survival in the absence of screening was based on the Surveillance, Epidemiology and End Results database of breast cancer patients diagnosed in the prescreening period (1975-1981), adjusted for the current use of adjuvant therapy. Utilization rates and costs of diagnostic and treatment interventions were based on a combination of published literature and Medicare payments for 2005. MAIN OUTCOME MEASURES: The survival benefit, incremental costs, and cost-effectiveness of MRI screening strategies, which varied by ages of starting and stopping MRI screening, were computed separately for BRCA1 and BRCA2 mutation carriers. RESULTS: Screening strategies that incorporate annual MRI as well as annual mammography have a cost per quality-adjusted life-year (QALY) gained ranging from less than 45,000 dollars to more than 700,000 dollars, depending on the ages selected for MRI screening and the specific BRCA mutation. Relative to screening with mammography alone, the cost per QALY gained by adding MRI from ages 35 to 54 years is 55,420 dollars for BRCA1 mutation carriers, 130,695 dollars for BRCA2 mutation carriers, and 98,454 dollars for BRCA2 mutation carriers who have mammographically dense breasts. CONCLUSIONS: Breast MRI screening is more cost-effective for BRCA1 than BRCA2 mutation carriers. The cost-effectiveness of adding MRI to mammography varies greatly by age.

Adult↗
PubMed1992

Trapped-oligonucleotide nucleotide incorporation (TONI) assay, a simple method for screening point mutations.

We present a simple screening method for detecting a known point mutation, using only one 5'-biotinylated oligonucleotide primer, with its 3' end adjacent to the mutation site. In parallel reactions, an amplified DNA template encompassing the biotinylated oligonucleotide and mutation site undergoes 40 step-cycles of single nucleotide incorporation using Taq thermostable DNA polymerase and only one radioactive [alpha-32P]dNTP, specified by either the normal or mutant sequence. The oligonucleotides, now radioactively labelled at the 3' end according to the template sequence, are then trapped by streptavidin-coated magnetic beads, and the percent of radiolabel incorporated is determined directly by the Cerenkov method in a scintillation counter. The trapped-oligonucleotide nucleotide incorporation (TONI) assay has been used for the screening of a mitochondrial polymorphism, and has also been shown to distinguish the genotypes of hemoglobin A/C, A/A, A/S, and S/S. It is reproducible over at least a 100-fold range of radioisotope and a 10-fold range of oligonucleotide primer. This method is particularly useful for diagnosing mutations which do not produce alterations detectable by restriction enzyme analysis, since optimization of conditions is rarely necessary. In addition, it requires only a single oligonucleotide, and no electrophoretic separation of the allele-specific products. It thus represents an improved and simplified modification of the existing allele-specific primer extension methods (Kuppuswamy et al., Proc Natl Acad Sci USA 88:1143-1147, 1991; Sokolov, Nucl Acids Res 18:3671, 1989; Syvanen et al., Genomics 8:684-692, 1990).

Base Sequence↗
PubMed1995

Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII.

Each of four possible sets of mismatches (G.A/C.T, C.C/G.G, A.A/T.T, and C.A/G.T) containing the 8 possible single-base-pair mismatches derived from isolated mutations were examined to test the ability of T4 endonuclease VII to consistently detect mismatches in heteroduplexes. At least two examples of each set of mismatches were studied for cleavage in the complementary pairs of heteroduplexes formed between normal and mutant DNA. Four deletion mutations were also included in this study. The various PCR-derived products used in the formation of heteroduplexes ranged from 133 to 1502 bp. At least one example of each set showed cleavage of at least one strand containing a mismatch. Cleavage of at least one strand of the pairs of heteroduplexes occurred in 17 of the 18 known single-base-pair mutations tested, with an A.A/T.T set not being cleaved in any mismatched strand. We propose that this method may be effective in detecting and positioning almost all mutational changes when DNA is screened for mutations.

Adenosine Triphosphate↗
PubMed2001

Junctional epidermolysis bullosa gravis (Herlitz): diagnostic and genetic aspects.

We report on a boy suffering from lethal junctional epidermolysis bullosa gravis (JEBH) (Herlitz-type) (OMIM 226700). Screening for mutations of LAMB3 gene with polymerase chain reaction (PCR) amplification of all exons from genomic DNA and subsequent heteroduplex analysis and dideoxynucleotide sequencing of heteroduplex forming PCR products disclosed two mutations: the recurrent maternal mutation R635X and the novel paternal mutation 1629insG, both in exon 14 of LAMB3. Both mutations lead to a premature termination code, non-sense mediated mRNA decay and to absence of the synthesis of the beta3 chain of laminin 5. During the mutation screening of the index patient a second pregnancy was ascertained. After amniocentesis (14 + 1 week of pregnancy), prenatal diagnosis from fetal cells was performed and compound heterozygosity for both mutations was evident. The consultants decided to have a termination of pregnancy shortly after the diagnosis. Remarkable skin fragility of the fetus was evident by clinical examination. Complete absence of laminin 5 could be demonstrated by immunofluorescence staining. By the third pregnancy of this couple so far screened for mutations by chorionic villus sampling for prenatal molecular diagnosis a healthy but heterozygous child is expected.

Epidermolysis Bullosa, Junctional↗
PubMed1998

DGGE screening of mutations in mismatch repair genes (hMSH2 and hMLH1) in 34 Swedish families with colorectal cancer.

Hereditary non-polyposis colorectal cancer (HNPCC) is an autosomal dominantly inherited syndrome which confers an increased risk for colorectal cancer and endometrial cancer as well as other tumors. It is caused by germline DNA mismatch repair (MMR) gene mutations in five MMR genes, hMSH2, hMLH1, hPMS1, hPMS2 and hMSH6. Finding mutations in these high risk families means that you can offer presymptomatic carrier diagnosis and thereby identify individuals with a very high risk for cancer. These persons benefit from counseling and should be offered surveillance. We have used DGGE to screen members from 34 families for mutations in hMLH1 and hMSH2. Six mutations in five families were found, five of these mutations are new. Besides, three new polymorphisms were identified. The mutations were found in two of seven Amsterdam criteria HNPCC families and in three of four families with at least one case of early onset of CRC (before 35), suggesting there are appropriate families to be chosen for mutation screening in MMR genes.

Adaptor Proteins, Signal Transducing↗
PubMedDate not supplied

Buccal cell DNA analysis in premature and term neonates: screening for mutations of the complete coding region for the cystic fibrosis transmembrane conductance regulator.

UNLABELLED: Traditionally, cystic fibrosis (CF) is diagnosed either by measuring sweat electrolyte levels or by screening for mutations using genomic DNA isolated from leucocytes. The aim of this work was to develop a modified fast and non-invasive tool for the collection of cell samples and the genetic analysis of the entire coding region for the cystic fibrosis transmembrane conductance regulator (CFTR) in newborns, especially premature infants. Cell samples were taken by scraping the buccal mucus with tiny dental brushes, followed by DNA isolation and mutation analysis using SSCP-heteroduplex (single-strand conformation polymorphism) screening and sequencing. We have demonstrated that buccal cell DNA collected from premature and term newborns yields sufficient DNA (at least 60 ng) to perform a mutation screening of the complete CFTR coding region, independently of the patients' weight (mean 2200 g) or gestational age (mean 35 weeks). The high stability of the samples at room temperature admits the possibility of dry shipment of samples collected elsewhere to the diagnostic laboratory. CONCLUSION: This fast, non-invasive sampling and DNA isolation method allows for early diagnosis of CF, initiation of therapy and minimisation of parental uncertainty and offers a technique for mutation analysis in any other monogenic disorder.

Cheek↗
PubMed1998

Efficient neurophysiologic selection of X-linked Charcot-Marie-Tooth families: ten novel mutations.

OBJECTIVE: To devise a neurophysiologic strategy to select X-linked Charcot-Marie-Tooth neuropathy syndrome (CMTX) families for connexin 32 mutation screening. BACKGROUND: Once the common chromosome 17 DNA duplication (CMT1A syndrome) has been excluded, clinical features are not sufficiently distinctive to select which of three genes (PMP22, Po, or connexin 32) should be screened for mutations. DESIGN: The yield of connexin 32 mutations was compared in possible CMTX families with clinical and genetic features of CMTX and probable CMTX families, defined by additional characteristic neurophysiologic features of CMTX. Of 232 CMT families with median motor nerve conduction velocities below 50 m/second (s) in affected men, 50 were found to have no CMT1A duplication and a pattern of inheritance compatible with CMTX (no man-to-man inheritance of CMT). These families were divided into 23 probable CMTX families (defined as having electrophysiologic indicators of CMTX), 23 possible CMTX families (with no neurophysiologic features of CMTX), and five unlikely CMTX families (with normal brainstem evoked auditory potentials [BAEPs]). RESULTS: The yield of mutations in the whole group was 25 mutations in 51 families (50%). Most probable CMTX families (21 of 23; 91%) had connexin 32 coding region mutations. Included in this group were 14 families with obligate female carriers; 11 of these had intermediate conduction velocities (>42 m/s) and nine (81%) had connexin 32 mutations. Only 3 of 23 (13%) possible CMTX families had connexin 32 mutations. One of five families with normal BAEPs in affected men had a connexin 32 mutation, and one had a Po Ala112Val mutation. Seventeen different mutations were found among 24 families, including 10 previously undescribed mutations (Leu9Trp, Ile28Thr, Ile30Thr, Ile127Met, Leu131Pro, Tyr154 stop, Pro158Ala, one base deletion of codon 158 causing stop at codon 195, Val192Phe, and Leu239Ile). CONCLUSIONS: The yield of connexin 32 mutations can be increased from approximately 6% of all CMT type I families to 91% of nonduplicated nondominant families with characteristic electrophysiologic changes of CMTX.

Amino Acid Substitution↗
PubMed2005

Screening for exonic copy number mutations at MSH2 and MLH1 by MAPH.

BACKGROUND: Exonic deletions in MSH2 and MLH1 are significant contributors to the mutation spectrum in HNPCC, and heterozygous changes in exon copy number are not detected by conventional mutation screening methods. AIMS: We aimed to develop methods for screening copy number changes in all the exons of the MLH1 and MSH2 genes using a single multiplex amplifiable probe hybridisation (MAPH) assay. METHODS: We developed a probe set consisting of probes from the 19 exons of MLH1 and 16 exons of MSH2, and 3 control probes, and applied it to screening for deletions and duplications using fluorescent detection of amplified fragments. RESULTS: We tested 73 DNA samples from controls and 50 from HNPCC patients in whom no point mutations had been found, and detected 10 copy number changes among the patient samples. A deletion of about 1.4 kb including exon 3 of MSH2 was confirmed by amplification of a junction fragment, and was shown to be the result of an unequal recombination between intronic Alu elements. CONCLUSIONS: MAPH can detect exonic copy number changes in MLH1 and MSH2 in DNA from HNPCC patients. Since finding an exonic deletion or duplication makes full sequence analysis unnecessary, it may be most cost-effective to pre-screen samples by MAPH or MLPA before screening for point mutations.

Adaptor Proteins, Signal Transducing↗
PubMed1999

Screening for mutations of the APC gene in 66 Italian familial adenomatous polyposis patients: evidence for phenotypic differences in cases with and without identified mutation.

Germline mutations in the APC gene are responsible for familial adenomatous polyposis (FAP), a dominantly inherited syndrome characterized by the development of hundreds to thousands of polyps in the colon and in the rectum of affected individuals and by variable extracolonic manifestations (gastric and duodenal polyps, osteomas, retinal lesions, and desmoid tumors). Through the combined use of single-strand conformation polymorphism (SSCP) analysis and the protein truncation test (PTT), we have screened 66 Italian FAP patients and found 29 different APC mutations in a total of 34 cases. Of the identified mutations, 15 were nonsense, 12 were 1- to 5-bp deletions or insertions and two were complex rearrangements, all leading to the formation of premature stop codons. Only 10 mutations had been already previously described at the germline level, confirming the high heterogeneity of the APC mutational spectrum. The mean age of diagnosis in mutation positive cases and their affected relatives was significantly lower than in cases without identified mutation (30.6 vs 39.1 years, respectively; p = 0.003). In addition, among patients without a family history of polyposis, all mutation-positive cases displayed at least one of the extracolonic manifestations usually associated with FAP, whereas in one-half of the cases without identified mutation, none of these phenotypes was observed. Although a fraction of apparently mutation-negative cases were likely to be due to limitations of the mutation screening strategy, our results suggest, in agreement with previous reports, that allelic and/or genetic heterogeneity might be responsible for the phenotypic variability observed in FAP patients.

Adenomatous Polyposis Coli↗
PubMed1999

Identification of a D579G homozygote cystic fibrosis patient with pancreatic sufficiency and minor lung involvement. Mutations in brief no. 221. Online.

Here we describe the identification of an italian patient homozygote for the D579G mutation affected by a mild form of Cystic Fibrosis with pancreatic sufficiency, minor lung involvement and marked viscosity of the cervical mucous. The D579G mutation causes an A1868G transition, a substitution of an aspartic acid to a glycine residue, generating an important amino acid change (charged to hydrophobic) in the nucleotide-binding domain (NBD). The mutation was first described by Brancolini et al. (1995) on two pancreatic sufficient CF patients, compound heterozygotes for delta508F. Patients were from Southern Italy (Puglia) as the D579G homozygote one, who is a 30 years old woman from Taranto (Puglia), daughter of second cousins born in Bari (Puglia). The identification of a homozygote D579G patient might confirm that this mutation does correlate with pancreatic sufficiency and a mild pulmonary phenotype.

Adult↗
PubMed1998

Screening for mutations in the neuropeptide Y Y5 receptor gene in cohorts belonging to different weight extremes.

OBJECTIVE: The neuropeptide Y (NPY) Y5 receptor is presumed to be involved in the regulation of food intake. DESIGN: To investigate the possible role of this receptor in weight regulation, the whole coding region of the NPY Y5 receptor gene was screened for mutations using temperature gradient gel electrophoresis (TGGE). Detected mutations were screened in extended cohorts. STUDY COHORTS AND METHODS: Cohorts of 87 extremely obese children and adolescents, 15 underweight subjects and 25 patients with anorexia nervosa (AN) were initially screened by TGGE. Extended samples of these cohorts (160 obese children and adolescents; mean body mass index (BMI) 33.5 +/- 6.4 kg/m2, 128 underweight subjects; mean BMI 18.4 +/- 1.0 kg/m2 and 58 patients with AN; mean BMI 14.6 +/- 1.7 kg/m2) were screened to determine the frequencies of a detected mutation and a detected polymorphism in the NPY Y5 receptor gene. In addition, a previously described polymorphism in the first intron of the NPY Y1 receptor gene was analysed. RESULTS: The coding region of the NPY Y5 receptor gene encompasses one exon. A single mutation, which results in a non-conservative amino acid substitution in the first extracellular domain of the receptor (Glu-4-Ala), and one silent polymorphism (Gly-426-Gly-Gly) at nucleotide position 1278 (G-->A) were detected by TGGE. Both tests for association and linkage to the NPY Y1 and NPY Y5 receptor polymorphisms were negative among all cohorts. The Glu-4-Ala mutation was found only in a single patient with AN and her mother. CONCLUSION: The results do not support a major role of the NPY Y5 receptor gene in the variability of body weight in children and adolescents.

Adolescent↗
PubMed2000

Screening for mutations in exon 4 of the LDL receptor gene in Thai subjects with primary hypercholesterolemia: detection of a novel mutation D151Y by PCR-CFLP.

A mutation in low density lipoprotein (LDL) receptor gene causes an autosomal codominant disorder namely familial hypercholesterolemia (FH). Mutations in the LDL receptor gene are very heterogeneous at the DNA levels, occurring in all 18 exons of the gene. However, exon 4 has been found to be the hot spot for mutational events. In this study DNA from 45 Thai subjects with primary hypercholesterolemia was screened for mutations in the hot spot exon 4. The DNA samples were amplified by Polymerase Chain Reaction (PCR) and screened for mutation by Cleavase Fragment Length Polymorphism (CFLP) technique. Identification of mutation was performed by direct sequencing of PCR product. From this screening, one female patient was found to be heterozygous for a novel mutation which was due to a G to T transversion at nucleotide 514. This transversion would change the species-conserved amino acid at codon 151 from charged R group aspatic (GAC) to uncharged R group tyrosine (TAC), termed D151Y. From the same screening strategy, we found that this mutation was absent in 33 healthy normolipidemic subjects. In this index subject, Arg 3500 Gln mutation in apo B-100 gene, causing hypercholesterolemia namely familial defective apo B-100 (FDB), was not found. Therefore, hypercholesterolemia in this index subject was possibly caused by the D151Y mutation in the LDL receptor gene.

DNA Mutational Analysis↗
PubMed2001

Mitotic checkpoint genes hBUB1, hBUB1B, hBUB3 and TTK in human bladder cancer, screening for mutations and loss of heterozygosity.

Chromosomal instability is common in bladder cancer and could be caused by mutations of mitotic checkpoint genes. Therefore we screened for mutations of the mitotic checkpoint genes hBUB1, hBUB1B, hBUB3 and TTK in six aneuploid bladder cancer cell lines and 15 human bladder tumours. The screening was performed by sequence analysis of the entire coding regions of the four genes. No mutations were detected in any of the four genes. We detected several sequence variations in hBUB1, hBUB1B and TTK both new and previously published. The genetic stability of the four gene loci were tested by loss of heterozygosity (LOH) analysis in the 15 patient samples, showing one LOH for each of the hBUB1B, hBUB3 and TTK loci (6.7%) of the cases, all in different tumour samples. No LOH was detected at hBUB1. We conclude that both mutational inactivation, and loss of one allele, of the examined mitotic checkpoint genes are relatively uncommon.

Genes, cdc↗
PubMed2001

Screening for mutations in exons encoding the ligand-binding domain of the LDL receptor gene using PCR-CFLP and PCR-SSCP.

Primary hypercholesterolemia includes both monogenic disorders and polygenic conditions. Two well defined monogenic disorders are familial hypercholesterolemia (FH) and familial defective apolipoprotein (apo) B-100 (FDB). Both disorders convey high risk of premature coronary artery disease. FH and FDB are caused by mutations in LDL receptor and apo B-100 genes, respectively. In the present study, mutations in both genes in Thai subjects with primary hypercholesterolemia were screened. For apo B-100 gene, a common mutation R3500Q was screened. This mutation was not observed in the patients (n = 45). For LDL receptor gene, mutations in the exons encoding the ligand-binding domain were screened. By PCR-CFLP analysis, 18 abnormal CFLP patterns in exon 4, the hot spot for mutations, were found in patients (n=45). One of the DNA samples with abnormal CFLP patterns was previously identified and reported as a possible disease-causing mutation, namely D151Y. For the other exons, the screening technique was PCR-SSCP. Abnormal SSCP patterns in DNA samples from patients (n=20) were found as follows, two in exon 3, one in exon 5 and another one in exon 6. Further characterization by DNA sequencing and family studies for these abnormal patterns are underway.

Adult↗