High proportion of large genomic STK11 deletions in Peutz-Jeghers syndrome

Germline mutations in the STK11 gene have been identified in 10-70% of patients with Peutz-Jeghers syndrome (PJS), an autosomal-dominant hamartomatous polyposis syndrome. A second locus was assumed in a large proportion of PJS patients. To date, STK11 alterations comprise mainly point mutations; only a small number of large deletions have been reported. We performed a mutation analysis for the STK11 gene in 71 patients. Of these, 56 met the clinical criteria for PJS and 12 were presumed to have PJS because of mucocutaneous pigmentation only or bowel problems due to isolated PJS polyps. No clinical information was available for the remaining three patients. By direct sequencing of the coding region of the STK11 gene, we identified point mutations in 37 of 71 patients (52%). We examined the remaining 34 patients by means of the multiplex ligation-dependent probe amplification (MLPA) method, and detected deletions in 17 patients. In four patients the deletion extended over all 10 exons, and in eight patients only the promoter region and exon 1 were deleted. The remaining deletions encompassed exons 2-10 (in two patients), exons 2-3, exons 4-5, or exon 8. When only patients who met the clinical criteria for PJS are considered, the overall mutation detection rate increases to 94% (64% point mutations and 30% large deletions). No mutation was identified in any of the 12 presumed cases. In conclusion, we found that approximately one-third of the patients who met the clinical PJS criteria exhibited large genomic deletions that were readily detectable by MLPA. Screening for point mutations and large deletions by direct sequencing or MLPA, respectively, increased the mutation detection rate in the STK11 gene up to 94%. There may be still other mutations in the STK11 gene that are not detectable by the methods applied here. Therefore, it is questionable whether a second PJS locus exists at all.     

Mutations in the MTM1 gene implicated in X-linked myotubular myopathy. ENMC International Consortium on Myotubular Myopathy. European Neuro- Muscular Center

X-linked recessive myotubular myopathy (XLMTM) is characterized by severe hypotonia and generalized muscle weakness, with impaired maturation of muscle fibres. The gene responsible, MTM1, was identified recently by positional cloning, and encodes a protein (myotubularin) with a tyrosine phosphatase domain (PTP). Myotubularin is highly conserved through evolution and defines a new family of putative tyrosine phosphatases in man. We report the identification of MTM1 mutations in 55 of 85 independent patients screened by single-strand conformation polymorphism for all the coding sequence. Large deletions were observed in only three patients. Five point mutations were found in multiple unrelated patients, accounting for 27% of the observed mutations. The possibility of detecting mutations and determining carrier status in a disease with a high proportion of sporadic cases is of importance for genetic counselling. More than half of XLMTM mutations are expected to inactivate the putative enzymatic activity of myotubularin, either by truncation or by missense mutations affecting the predicted PTP domain. Additional mutations are missenses clustered in two regions of the protein. Most of these affect amino acids conserved in the homologous yeast and Caenorhabditis elegans proteins, thus indicating the presence of other functional domains.      

Genotype and laboratory and clinical phenotypes of protein s deficiency

The diagnosis of thrombophilia caused by protein S deficiency remains difficult. From 2005 to 2010, we documented 135 patients with suspected hereditary protein S deficiency for whom mutational analysis of the PROS1 gene had been performed by direct double-stranded sequencing of the amplified 15 exons including splice sites. Multiplex ligation-dependent probe amplification was performed on 12 of 15 exons in cases with no mutation found but a large deletion in the PROS1 gene was suspected. Mutations were identified in 49 patients, 9 by familial screening. Altogether, 17 new and 11 previously described mutations of PROS1 were identified among the 49 patients. After the exclusion of acquired protein S deficiency due to pregnancy or hormonal contraceptives, there remained only 1 case with protein S activity levels less than 40% that could not be explained by sequence variations or deletions in the examined regions of the PROS1 gene. After the exclusion of conditions associated with acquired protein S deficiency, persistently low protein S activity levels are highly indicative of a genetic alteration in PROS1. We observed a clear correlation between the laboratory phenotype and the type of mutation.     

甲基丙二酸血症患儿MUT基因突变分析

目的 检测甲基丙二酸血症(methylmalonic acidemia,MMA)患儿MUT基因突变类型及突变频率,探讨基因型与临床表型之间的关系.方法 依据串联质谱检测血酰基肉碱、气相色谱-质谱检测尿甲基丙二酸以及维生素B_(12)负荷试验等,诊断21例单纯MMA患儿;采用聚合酶链反应和直接测序法对这些患儿进行MUT基因突变检测分析.结果 在21例单纯MMA患儿中14例检测到17种MUT基因突变,其中8种为未报道突变.以c.323G>A(R108H)、c.729_730insTT(D244LfsX39)与c.1630_1631GG>TA(G544X)较为常见,突变频率分别为14.3%、10.7%及14.3%,以错义突变多见(64.7%).14例MUT突变患儿中10例为早发型,1例为迟发型,3例由新生儿出生筛查检出;11例为维生素B_(12)无效型,3例为有效型.结论 揭示了中国MMA患儿中MUT基因的部分突变谱,MUT基因突变患儿发病较早,多为维生素B_(12)无效型.     

非小细胞肺癌患者肿瘤组织中EGFR和KARS基因突变的分子病理检测分析

目的：探讨非小细胞肺癌患者肿瘤组织中EGFR和KRAS基因各亚型突变情况。方法：应用直接测序方法检测非小细胞肺癌石蜡组织中1273例EGFR基因和1062例KRAS基因突变情况。结果：非小细胞肺癌肿瘤组织中EGFR基因总突变率为36.68%(467/1273),外显子18、19、20和21的突变率分别为1.02%(13/1273)、18.93%(241/1273)、2.59%(33/1273)和15.95%(203/1273);EGFR基因各外显子之间双重突变共17例(1.34%),其中18外显子与20外显子双重突变3例(0.24%),19外显子与20外显子双重突变7例(0.55%),19外显子与21外显子双重突变4例(0.31%)和20外显子与21外显子双重突变3例(0.24%);EGFR基因各外显子内双重突变共2例(2.18%),均为21外显子双重突变。KRAS基因总突变率为3.01%(32/1062),外显子2的密码子5、12、13和25的突变率分别为0.09%(1/1062)、2.64%(28/1062)、0.18%(2/1062)和0.09%(1/1062),外显子3密码子61的突变率为0.09%(1/1062)。结论：非小细胞肺癌患者中EGFR基因存在较高的突变率,尤其为19和21外显子突变,其基因突变亚型分类能指导EGFR-TKI的肿瘤靶向治疗,KRAS基因突变率虽低但不容忽视,其基因突变预示着EGFR-TKI原发耐药。     

先天性视网膜劈裂症基因突变分析

目的 阐明先天性视网膜劈裂症（X－linked juvenile retinoschisis,RS or XLRS)的发病机理,为建立基因诊断的方法提供理论依据。方法 采用聚合酶链反应－单链构象多态性分析,对6个独立XLRS病例进行了XLRS1基因突变筛选,并对发现的异常泳动带进行DNA测序,以明确突变位点;对发现的缺失突变进行Southern印迹证实。结果 在5个病例中发现基因突变。在家系1中发现缺失突变,家系中的4个患者均缺失了1、2和3外显子。在外显子4上检出3种异常泳动带,分别为3种突变,Glu72Lys,Glu72Gln,Gly70Ser。结论 XLRS1基因突变是导致中国人患RS的主要原因。本研究结果可直接应用于RS的遗传咨询和产前基因诊断。     

Heterogeneous spectrum of mutations in the Fanconi anaemia group A gene

Fanconi anaemia (FA) is a genetically heterogeneous autosomal recessive disorder associated with chromosomal fragility, bone-marrow failure, congenital abnormalities and cancer. The gene for complementation group A (FAA), which accounts for 60-65% of all cases, has been cloned, and is composed of an open reading frame of 4.3 kb, which is distributed among 43 exons. We have investigated the molecular pathology of FA by screening the FAA gene for mutations in a panel of 90 patients identified by the European FA research group, EUFAR. A highly heterogeneous spectrum of mutations was identified, with 31 different mutations being detected in 34 patients. The mutations were scattered throughout the gene, and most are likely to result in the absence of the FAA protein. A surprisingly high frequency of intragenic deletions was detected, which removed between 1 and 30 exons from the gene. Most microdeletions and insertions occurred at homopolymeric tracts or direct repeats within the coding sequence. These features have not been observed in the other FA gene which has been cloned to date (FAC) and may be indicative of a higher mutation rate in FAA. This would explain why FA group A is much more common than the other complementation groups. The heterogeneity of the mutation spectrum and the frequency of intragenic deletions present a considerable challenge for the molecular diagnosis of FA. A scan of the entire coding sequence of the FAA gene may be required to detect the causative mutations, and scanning protocols will have to include methods which will detect the deletions in compound heterozygotes.     

Constant denaturant gel electrophoresis (CDGE) in BRCA1 mutation screening

Screening for mutations in the breast and ovarian cancer susceptibility gene, BRCA1, is complicated by the wide spectrum of mutations found in this large gene. In the present study a constant denaturant gel electrophoresis (CDGE) mutation screening strategy was established for ˜80% of the genomic coding sequence (exons 2, 11, 13–16, 20, 24). This strategy was applied to screen genomic DNA from 50 familial breast and/or ovarian cancer patients who had previously been examined for BRCA1 mutations by SSCP. A total of 14 carriers of 12 distinct disease-associated mutations and 7 carriers of 6 distinct rare substitutions leading to amino acid substitutions were identified. The SSCP failed to detect 40% of the different deletions/insertions (4/10) and 75% (6/8) of the different base substitutions leading to terminating codons or rare amino acid changes. SSCP did, however, identify one rare base substitution that could not be detected in the CDGE screening. To evaluate the CDGE mutation screening strategy further, 25 unrelated patients from Norwegian breast and/or ovarian cancer families were examined for BRCA1 mutations using a combined genomic DNA/cDNA approach covering the entire coding sequence of the gene. A total of six mutation carriers were detected, all of whom had cases of ovarian cancer in their families. Three patients from independent families carried an 1135insA mutation in exon 11, two others had a Gly484ter and an 1675delA mutation, respectively, and the sixth carried a splice mutation (5194-2 a→c) causing deletion of exon 18. CDGE may become an efficient tool in diagnostic and population based screening for BRCA1 mutations. Hum Mutat 11:166–174, 1998. © 1998 Wiley-Liss, Inc.     

Spectrum of mutations in mut methylmalonic acidemia and identification of a common Hispanic mutation and haplotype

Cobalamin nonresponsive methylmalonic acidemia (MMA, mut complementation class) results from mutations in the nuclear gene MUT, which codes for the mitochondrial enzyme methylmalonyl CoA mutase (MCM). To better elucidate the spectrum of mutations that cause MMA, the MUT gene was sequenced in 160 patients with mut MMA. Sequence analysis identified mutations in 96% of disease alleles. Mutations were found in all coding exons, but predominantly in exons 2, 3, 6, and 11. A total of 116 different mutations, 68 of which were novel, were identified. Of the 116 different mutations, 53% were missense mutations, 22% were deletions, duplications or insertions, 16% were nonsense mutations, and 9% were splice-site mutations. Sixty-one of the mutations have only been identified in one family. A novel mutation in exon 2, c.322C>T (p.R108C), was identified in 16 of 27 Hispanic patients. SNP genotyping data demonstrated that Hispanic patients with this mutation share a common haplotype. Three other mutations were seen exclusively in Hispanic patients: c.280G>A (p.G94R), c.1022dupA, and c.970G>A (p.A324T). Seven mutations were seen almost exclusively in black patients, including the previously reported c.2150G>T (p.G717V) mutation, which was identified in 12 of 29 black patients. Two mutations were seen only in Asian patients. Some frequently identified mutations were not population-specific and were identified in patients of various ethnic backgrounds. Some of these mutations were found in mutation clusters in exons 2, 3, 6, and 11, suggesting a recurrent mutation.     

应用蝎形探针扩增阻滞突变系统检测非小细胞肺癌表皮生长因子受体基因突变与病理改变的关系

目的 探讨非小细胞肺癌(NSCLC)肿瘤组织中表皮生长因子受体(EGFR)基因突变的检出率,比较蝎形探针扩增阻滞突变系统(scorpions amplifieation refractory mutation system,以下简称Scorpions ARMS)即时荧光PCR和直接测序检测EGFR基因突变的敏感性.方法 应用显微切割术、Scorpions ARMS及直接测序检测82例NSCLC石蜡包埋肿瘤组织以及癌旁正常肺组织中EGFR基因的第18、19、20和2l外显子的突变.结果 Scorpions ARMS检测82例NSCLC中42例的瘤组织中存在EGFR突变,突变检出率为51.2%,其中20例为EGFR第19外显子框架内多核苷酸的缺失,18例为EGFR第21外显子L858R点突变,1例为EGFR第21外显子L861Q点突变,2例为EGFR第20外显子插入突变,另外1例为EGFR第20外显子$7681点突变.而PCR反应后行直接测序,82例标本中仅58例得到可分析的测序结果,其中25例瘤组织中出现EGFR突变,因此82例的突变检出率为30.5%,25例中13例为EGFR第19外显子框架内多核苷酸的缺失,10例为EGFR第21外显子L858R点突变,1例为EGFR第21外显子L861Q点突变,另外1例为EGFR第20外显子$768I点突变.直接测序检测出25例突变模式与Scorpions ARMS检测结果一致.结果 显示Scorpions ARMS具有很高的敏感度,部分直接测序阴性的病例经Scorpions ARMS检测出EGFR突变.结论 EGFR基因的点突变或缺失在中国NSCLC的患者中的检出率明显高于其他国家,以女性、腺癌和细支气管肺泡以及不吸烟患者突变率较高.Scorpions ARMS技术能快速、敏感、准确检测EGFR突变,能为临床冶疗及预后提供重要信息.     

Biallelic inactivation of TP53 rarely contributes to the development of malignant peripheral nerve sheath tumors

About 10% of the patients with neurofibromatosis type 1 (NF1) develop malignant peripheral nerve sheath tumors (MPNSTs), accounting for half of all MPNST cases. Several nonrandom chromosomal aberrations have been found, but the target genes remain mostly unrecognized. Mutations in the NF1 and TP53 genes have been found in some MPNSTs, and recent data from mouse models support a synergistic effect of these two genes in the development of MPNST. In the present study, we have analyzed 16 MPNSTs, including 11 from patients with NF1 and 5 sporadic cases, for mutations in the coding sequence of the TP53 gene (exons 2-11). We applied denaturing gradient gel electrophoresis and modifications of this technique for analyses of 12 genomic fragments, followed by direct sequencing for identification of the mutated base(s). None of the MPNSTs revealed mutations. The detection of control mutants for each fragment analyzed, the high sensitivity of the technique, the detection of polymorphisms in some samples, and the high content of tumor tissue in the biopsies imply that false negatives are highly unlikely. Although we cannot exclude that deletions including large parts of the gene remain undetected by the mutation analyses, previous comparative genomic hybridization (CGH), cytogenetic banding analysis, and/or loss of heterozygosity studies on 14 of the cases included here had revealed 17p deletions in only three. We thus conclude that TP53 biallelic inactivation is rare in MPNST, and that the potential impact of an altered TP53 pathway on the malignant transformation of a neurofibroma into an MPNST may more frequently occur by changes in other components of that pathway.     

Deletion and insertion in vivo somatic mutations in the hypoxanthine phosphoribosyltransferase (hprt) gene of human T-lymphocytes

Deletion and insertion mutations have been found to be a major component of the in vivo somatic mutation spectrum in the hypoxanthine phosphoribosyltransferase (hprt) gene of T-lymphocytes. In apopulation of 172 healthy people (average age, 34; mutant frequency, 10.3 × 10⁻⁶), deletion/in sertion mutations constituted 41% (89) of the 217independent mutations, the remainder being base substitutions. Mutations were identified by multiplex PCR assay of genomic DNA for exon regions, by sequencing cDNA, or sequencing genomic DNA. The deletion and insertion mutations were divided among ±1 to 2 basepair (bp) frameshifts (14%, 30), small deletions and insertions of 3–200 bps (13%, 28), large deletions of one or more exons (12%, 27), and complex events (2%, 4). Frameshift mutations were dominated by −1 bp deletions (21 of 30). Exon 3 contained five frameshift mutations in the run of 6 Gs, the only site in the coding region with multiple frameshift mutations, possibly caused by strand dislocation during replication. Both end points were sequenced for 23 of the 28 small deletions/insertions including two tandem duplication events in exon 6. More small deletions (8/28), pos sibly mediated by trinucleotide repeats, occurred in exon 2 than in the other exons. Large deletions included total gene deletions (6), exon 2 + 3 dele tions (4), and loss of multiple (9) and single exons (8) in genomic DNA. The diverse mutation spectrum indicates that multiple mechanisms operated at many different sequences and provides a resource for examination of deletion mutation. Environ. Mol. Mutagen. 30:371–384, 1997 © 1997 Wiley-Liss, Inc.     

First genotype characterization of Argentinean FAP patients: identification of 14 novel APC mutations

We examined the adenomatous polyposis coli (APC) gene for disease-causing mutations in 51 unrelated Argentinean probands affected by familial adenomatous polyposis (FAP). Using a combination of the protein truncation test, the single strand conformation polymorphism technique, DNA sequencing and quantitative PCR analysis, we identified the specific mutation in 39 (average age: 28.4 years) of the 51 probands (detection rate: 76.47%); 13 are novel germline mutations and one is a novel sequence variant. There were 27 small deletions, four small duplications, five nonsense mutations in exon 15, three nonsense mutations in exons 6, 11, and 12, and one sequence variant in exon 3 identified in a patient bearing a truncating mutation in exon 15. The most common mutation (found in 10 cases) was at codon 1309. All patients negative for APC mutations were also negative for the MutY homolog (MYH) gene mutation, as expected because of fully penetrant FAP cases. This study enlarges the spectrum of APC gene mutations, and reinforces the concept of mutation heterogeneity. It also sheds light on correlations between the site of APC germline mutations and the clinical manifestations of FAP. Our data indicate that the genotype/phenotype correlations in Argentinean patients are similar to those observed in other populations.     

Genetic mutations in von Willebrand disease identified by DHPLC and DNA sequence analysis

Von Willebrand disease (VWD) is a common inherited bleeding disorder caused by quantitative (types 1 and 3) and qualitative (type 2) defects in von Willebrand factor (VWF). The VWF gene is a large gene containing 52 exons; except for type 2 VWD, the majority of mutations causing VWD are not localized to specific exons. We have used denaturing high performance liquid chromatography (DHPLC) to scan the coding region of the VWF gene for sequence variations. Primers were designed to amplify all 52 exons while avoiding amplification of the VWF pseudogene. Exon-specific primers were designed with sequencing primers, allowing direct sequencing of each VWF exon. Sequence variations in 33 previously characterized von Willebrand disease (VWD) samples were all detected using DHPLC demonstrating the high sensitivity of this technique. In addition, we analyzed 42 patients or family members with VWD. Thirty-two novel sequence variations were identified (2 deletions, 2 nonsense, 15 missense, 6 silent, and 7 intronic), some with clear functional consequences. A previously described deletion in exon 18, 2435delC, was also found in two unrelated type 3 patients. This DHPLC and DNA sequencing technique will enable the full length assessment of the VWF gene necessary to detect mutations causing types 1 and 3 VWD.     

Comprehensive mutational analysis of a cohort of Swedish Cornelia de Lange syndrome patients

Cornelia de Lange syndrome (CdLS; OMIM 122470) is a rare multiple congenital anomaly/mental retardation syndrome characterized by distinctive dysmorphic facial features, severe growth and developmental delay and abnormalities of the upper limbs. About 50% of CdLS patients have been found to have heterozygous mutations in the NIPBL gene and a few cases were recently found to be caused by mutations in the X-linked SMC1L1 gene. We performed a mutation screening of all NIPBL coding exons by direct sequencing in 11 patients (nine sporadic and two familial cases) diagnosed with CdLS in Sweden and detected mutations in seven of the cases. All were de novo, and six of the mutations have not been previously described. Four patients without identifiable NIPBL mutations were subsequently subjected to multiplex ligation-dependent probe amplification analysis to exclude whole exon deletions/duplications of NIPBL. In addition, mutation analysis of the 5' untranslated region (5' UTR) of NIPBL was performed. Tiling resolution array comparative genomic hybridization analysis was carried out on these four patients to detect cryptic chromosome imbalances and in addition the boys were screened for SMC1L1 mutations. We found a de novo 9p duplication with a size of 0.6 Mb in one of the patients with a CdLS-like phenotype but no mutations were detected in SMC1L1. So far, two genes (NIPBL and SMC1L1) have been identified causing CdLS or CdLS-like phenotypes. However, in a considerable proportion of individuals demonstrating the CdLS phenotype, mutations in any of these two genes are not found and other potential loci harboring additional CdLS-causing genes should be considered.     

中国乳腺癌患者BRCA1基因突变的研究

目的　在中国乳腺癌患者 BRCA1基因外显子 2、2 0和 11部分序列中寻找突变位点 ,探讨其与乳腺癌发病的关系。方法收集 86例无血缘关系的乳腺癌患者 ,用聚合酶链反应 -双链四色荧光标记的方法 ,分析 BRCA1基因的外显子 2和 2 0的全长序列和外显子 11的部分序列。结果　外显子 2、2 0和 11的序列中均未发现有突变 ,仅在外显子 11A的序列上有一个 C/ T多态 ,基因型频率高达 4 2 %。对这个高频单核苷酸多态 (single nucleotide ploymorphism,SNP)位点 ,先作了 Hardy- Weinberg检测 ,P>0 .0 5 ,确定这个 SNP的频率不受杂合性缺失的影响。再进行 χ2检测 ,与正常对照组进行比较 ,P>0 .1,两者差异无显著性。结论　这个高频 SNP位点与乳腺癌的发生无显著相关 ;在中国人群中没有发现其他乳腺癌患者人群中普遍存在的这几个突变热点 ,说明外显子 2、2 0和 11上的这部分序列对中国人群的乳腺癌发生影响不大。     

Mutations in gastrointestinal stromal tumors--a population-based study from Northern Norway

Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the gastrointestinal tract. This tumor typically expresses KIT, and has KIT or PDGFRA activating mutation. In this study we evaluated 89 GISTs diagnosed in Northern Norway during a 30-year period. KIT exons 8, 9, 11, 13, and 17 were analyzed by PCR amplification and direct sequencing. Subsequently PDGRA exons 12, 14, and 18 were evaluated in KIT wild-type cases. KIT mutations were found in 66 cases (75%), and PDGFRA mutations in 9 cases (10%). Most common were KIT exon 11 mutations, with 58 cases. Tumors with Kit exon 11 point mutations had a significantly better prognosis than those with deletions. There were five KIT exon 9 duplications, three exon 13 point mutations, and one point mutation in exon 17. There were nine PDGFGRA mutations: seven in exon 18 and two in exon 12. All but one PDGFRA mutant GISTs were gastric tumors with epithelioid morphology, and these tumors were on average smaller than those with KIT mutations. KIT and PDGFRA wild type was found in 15% of cases. Analysis of KIT and PDGFRA mutations is of significance for treatment with tyrosine kinase inhibitors, and may also have value when assessing the biological potential of GIST.     

Mutation screening of EXT1 and EXT2 by direct sequence analysis and MLPA in patients with multiple osteochondromas: splice site mutations and exonic deletions account for more than half of the mutations

Multiple osteochondromas (MO) is an autosomal dominant condition, caused by mutations in either the EXT1 or the EXT2 gene. The DNA of a cohort of 35 patients, clinically suspected to be affected with MO, was screened for mutations by a combination of direct sequence analysis and multiplex ligation-dependent probe amplification (MLPA). In this cohort, 26 pathogenic gene alterations were found (74%). With sequence analysis mutations were detected in 22 patients (63%). In total, 10 mutations were detected in the EXT1 and 12 in the EXT2 gene. The number of the splice site mutations detected was larger than expected from the literature. In addition, with the MLPA four deletions of one or more exons were found in this cohort. Two patients, of whom one had a negative family history, showed deletions of exon 1 of the EXT1 gene, which is possibly a deletion hot spot. In patients suspected to be affected by MO, we recommend a quantitative analysis such as MLPA, followed by direct sequence analysis for the screening of the EXT1 and EXT2 genes.