Detection of factor VIII gene mutations by high-resolution melting analysis

BACKGROUND: Single base-pair substitution mutations in the gene for coagulation factor VIII, procoagulant component (hemophilia A) (F8) account for approximately 50% of severe cases of hemophilia A (HA), and almost all moderate or mild cases. Because F8 is a large gene, mutation screening using denaturing HPLC or DNA sequencing is time-consuming and expensive. METHODS: We evaluated high-resolution melting analysis as an option for screening for F8 gene mutations. The melting curves of amplicons heterozygous for known F8 gene mutations were compared with melting curves of the corresponding normal amplicons to assess whether melting analysis could detect these variants. We examined 2 platforms, the Roche LightCycler 480 (LC480) and the Idaho Technology LightScanner. RESULTS: On both instruments, 18 (90%) of the 20 F8 gene variants we examined were resolved by melting analysis. For the other 2 mutations, the melting curves of the heterozygous amplicons were similar to the corresponding normal amplicons, suggesting these variants may not be detected by this approach in a mutation-scanning screen. CONCLUSION: High-resolution melting analysis is an appealing technology for F8 gene screening. It is rapid and quickly identifies mutations in the majority of HA patients; samples in which no mutation is detected require further testing by DNA sequencing. The LC480 and LightScanner platforms performed similarly.     

A highly informative, multiplexed assay for the indirect detection of hemophilia A using five-linked microsatellites

BACKGROUND: Hemophilia A is a severe bleeding disorder caused by almost 1000 different known mutations in the F8C gene. Direct mutation analysis is sometimes difficult for this disorder. When a mutation cannot be found, linkage analysis can be used for prenatal and carrier diagnosis. AIM: To develop a rapid and effective system for carrier detection and prenatal diagnosis of hemophilia A based on a single-multiplexed polymerase chain reaction (PCR) reaction utilizing five microsatellite markers. PATIENTS AND METHODS: Two intronic microsatellites and three other markers flanking the factor VIII gene were ascertained, and primers were designed for multiplex PCR amplification. A kindred with Hemophilia A was tested for linkage using the panel of primers, and informativity in the general population was ascertained by testing 50 unrelated females. RESULTS: Co-amplification of all microsatellites was optimized using DNA extracted by standard methods. Rapid detection and sizing of products were carried out using an automated DNA sequencer. The combined microsatellite panel was informative in each of the kindreds tested, and in 100% of the 50 unrelated females (95% CI 94.2-100%). CONCLUSIONS: This method enables the indirect detection of hemophilia A for patients in whom mutations cannot be found, facilitating carrier testing and prenatal analysis. It is rapid and straightforward compared with many other published protocols, and offers a high degree of informativity.     

两个同源重组血友病家系的基因诊断

目的探讨特殊血友病家系的基因诊断。方法通过FⅧ基因内含子22倒位及内含子1倒位的直接检测与遗传连锁分析的间接诊断相结合对1个血友病A（HA）家系进行基因诊断；采用核酸直接测序法对FⅨ各外显子及其侧翼序列进行检测，并联合FⅨ基因相关的6个微卫星（STR）位点对1个血友病B（HB）家系进行基因诊断。结果HA家系先证者为FⅧ内含子1倒位阳性，家系中要求做携带者诊断的女性成员为内含子1倒位携带者；而FⅧ基因内外8个多态性位点遗传连锁分析证实该女性成员发生同源染色体重组。HB家系先证者除7号外显子测序未成功外，其余部分均未找到突变，家系中要求做携带者与产前诊断的女性，其羊水细胞经直接核酸测序未找到突变，利用FⅨ相关的6个STR位点进行遗传连锁分析发现该女性有染色体同源重组现象存在，胎儿为正常男性。结论在应用间接诊断方法进行HA和HB的携带者及产前基因诊断时，要考虑到染色体同源重组现象的发生可能导致误诊与漏诊的情况。在中国人群中应该开发更多的FⅧ和FⅨ分子中信息量大的多态性位点，以提高HA和HB的携带者及产前诊断的准确率。     

幽门螺杆菌克拉霉素耐药基因芯片的制备和应用

目的 建立一种寡核苷酸微阵列检测幽门螺杆菌23S rRNA基因A2142G、A2143G及C2182T点突变的方法.方法 根据23S rRNA基因A2142G、A2143G及C2182T突变位点设计相应探针,样本经不对称PCR扩增后,其产物与芯片杂交.非荧光标记引物扩增PCR产物克隆至T载体,测序验证芯片结果,并结合临床最低抑菌浓度实验判断该方法的正确性.结果 寡核苷酸微阵列技术与测序检测幽门螺杆菌23S rRNA基因多态性结果完全一致.经培养及鉴定幽门螺杆菌阳性的54份标本,杂交结果显示A2142位点均为野生型(54/54);A2143G突变率为11.11%(6/54),尚未发现A2143C和A2143T的突变;C2182T突变率为12.96%(7/54),尚未发现C2182A和C2182G的突变,其余均为野生型,上述结果与菌株体外试验MIC结果完全一致.结论 建立一种寡核苷酸微阵列技术检测幽门螺杆菌克拉霉素耐药的23S rRNA基因多态性的方法,可以高通量并直接检测胃黏膜而不需进行细菌培养,推动个体化治疗方案的实施.     

一例凝血因子Ⅷ B区错义突变导致重型血友病A

目的：检测一例重型血友病Ａ患者（ＳＨ９）的基因突变。方法：用ＰＣＲ、变性梯度凝胶电泳（ＤＧＧＥ）和ＤＮＡ测序检测因子Ⅷ基因突变。先用Ｓｏｕｔｈｅｒｎｂｌｏｔｉｎｇ排除内含子２２倒位，然后应用ＰＣＲ对凝血因子Ⅷ基因进行扩增。扩增范围包括所有外显子及其侧翼内含子序列。结果：片段１４２在ＤＧＧＥ中泳动异常。ＤＮＡ测序证实Ｃ２５３５Ａ导致Ｂ区错义突变８２６Ａｓｐ（ＧＡＣ）→Ｇｌｕ（ＧＡＡ）。结论：该突变可能是导致重型血友病Ａ的原因，但有待进一步研究证实。     

40例血友病乙患者的基因分析及发病机制研究

血友病乙(Hemophilia B,HB)为X染色体连锁的隐性遗传性出血性疾病,其发病机制多为凝血因子IX(F9)基因突变致凝血因子IX缺乏或结构功能的异常。本研究对40例明确诊断为血友病乙的男性患者进行基因序列分析以寻找其分子发病机制并为遗传学咨询奠定基础。2009年6月-2012年6月收集血友病乙男性患者40例,均根据临床表现、血浆凝血因子IX活性检测及家族史等资料确诊。常规方法收集患者及亲属血样,分离血细胞和血浆,提取DNA,用聚合酶联反应(PCR)扩增结合直接测序法分析先证者的F9基因的所有外显子及其侧翼序列,并将测序结果和国际F9基因突变数据库进行比对,发现突变后排除多态性。结果表明,对40例HB患者基因分析共发现34种基因突变,突变类型包括插入框移突变2种,无义突变6种,剪切位点的突变2种,错义突变24种,其中29种突变为已报道的突变类型,5种突变在国际上未见报道。34种突变中发生在信号肽序列的有2种,前肽及γ-羧基化结构域的有7种突变,表皮生长因子样结构域有7种,活化肽区域有3种,丝氨酸蛋白酶催化结构域有15种突变。结论:40例HB患者的基因分析表明F9基因突变具有明显的异质性,且错义突变仍是目前F9基因的主要突变方式,与重型HB有更密切的联系。F9基因突变所常见的外显子部位与他们编码的氨基酸在蛋白行使功能时所起的作用有关。直接进行基因测序及短串联重复序列连锁分析将会对血友病乙的携带者诊断及产前诊断提供了一种快速、准确的诊断方法。     

临床不同背景情况下血友病A的产前诊断方案

目的建立临床不同背景情况下HA患儿产前诊断方案.方法对前来要求作HA产前诊断的15例孕妇进行遗传咨询,根据孕周和临床资料不同采取不同诊断方法.孕妇孕周＜23周,有先证者且已明确基因突变类型,抽羊水进行直接基因诊断和间接遗传连锁分析;有先证者但未明确基因突变类型,抽脐血进行间接遗传连锁分析和FⅧ活性检测;孕妇孕周＞23周且无先证者,抽脐血做FⅧ活性检测和性别染色体检查,但不能诊断携带者.直接基因诊断采用长距离PCR技术,对F8基因内含子22和内含子1倒位进行检测,找不到倒位者,行核苷酸测序;连锁分析采用F8基因内外的7个位点(DXS1108,F8Civs13,INTRON22,DXS1073,DXS9901,DXS15,DXS8069)以及性别位点(Amelo).产前诊断标本均需做母血污染鉴定.结果 15例产前诊断标本均无母血污染.明确诊断血友病A胎儿5例,其中脐血FⅧ活性＜1%的3例,1例伴21三体;F8基因22内含子倒位1例;F8基因23外显子错义突变p.Arg2182Cys 1例.结论对临床不同背景情况下采取不同方案进行HA产前诊断,可提高HA患儿检出率和准确性,最大程度地预防出生缺陷儿的发生.     

DNA芯片快速检测耐利福平结核分枝杆菌rpoB基因突变

目的 开发快速检测耐利福平结核分枝杆菌(结核菌)rpoB基因突变的DNA芯片。方法 根据结核菌rpoB基因序列设计探针并制作基因芯片，从临床样品中分离出结核菌的基因组DNA，PCR扩增含有rpoB基因突变位点的特异DNA片段，荧光标记后与芯片上含有的检测特异突变位点的寡核苷酸探针进行杂交，同时与DNA直接测序法测定序列比较。结果 35株耐利福平结核菌中有91．4％(32／35)用直接测序法检测出存在rpoB基因突变，DNA芯片的检测效率为71．4％(25／35)。结论 用DNA芯片检测结核菌对利福平的耐药性具有较高的特异性和敏感性，可用于临床结核菌耐药性检测。     

应用多聚酶链反应和双链DNA循环测序对FIX基因点突变的研究

应用多聚酶链反应扩增因子ＩＸ（ＦＩＸ）基因外显子８的４８１ｂｐＤＮＡ片段，并利用双链ＤＮＡ循环测序，对两例血友病乙ＦＩＸ基因缺陷进行了研究。发现这两例都发生在３１１１９位的碱基替换，Ｇ（ＣＧＡ）→Ａ（ＣＡＡ）。该突变为ＦＩＸ基因ＣＧ双核苷酸突变热点，改变了正常ＦＩＸ的结构和凝血功能，因而导致血友病乙。重复点突变的发现，对血友病乙分子缺陷的发病机制研究十分重要。     

两种新的F8内含子突变导致剪接异常的机制研究

目的：分析从2个血友病A家系中检出的2个未报道的内含子突变对剪接的影响,明确这2种突变的致病性,为遗传咨询提供依据。方法：通过检测相关的凝血指标,明确血友病A的诊断。进行F8相关检测,包括PCR扩增及测序分析F8的26个外显子及其侧翼序列、拷贝数检测、内含子1和内含子22倒位检测,明确致病突变。采用巢式PCR扩增外周血中的mRNA,从异位转录水平分析内含子突变对剪接的影响。针对6个短串联重复序列（short tandem repeats, STR）位点F8Up226、F8Up146、F8Int13、F8Int25、F8Down48和DXS1073进行家系遗传连锁分析,用SNaPshot SNP分型技术检测外周血、口腔黏膜细胞和毛囊细胞嵌合情况,分析突变来源。结果：家系1中血友病A先证者1的 FⅧ：C为0.9%,检测到F8的9号内含子c.1444-2dupA突变,mRNA分析显示该突变导致F8的10号和11号外显子缺失;家系2中血友病A先证者2的 FⅧ：C为5.1%,检测到F8的18号内含子c.5999-29T>G突变,mRNA分析显示该突变产生2种转录本,即缺失19号外显子的异常转录本和少量正常转录本。家系1无血友病A家族史,遗传分析显示突变来源于先证者的外公,但外公的血液、毛发和口腔样本嵌合检测均未检出突变。结论：c.1444-2dupA和c.5999-29T>G突变均为国际首次报道,突变导致了不同程度的剪接异常,分别引起重型和轻型血友病A。家系1的c.1444-2dupA为新发突变,可能是在先证者外公的精子形成过程中发生。     

核酸薄膜技术快速检测结核分枝杆菌katG突变的研究

目的研制一种新的核苷酸薄膜,通过导流杂交技术检测结核分枝杆菌katG基因突变类型,以快速判断结核分枝杆菌对异烟肼的耐受性,寻找一种快速简便检测耐异烟肼结核病的方法。方法根据结核分枝杆菌katG基因序列设计1个野生型及2个常见突变型寡核苷酸特异探针,探针5’末端连接亚甲基(-CH2)。同时设计1个人类基因组探针以及1个生物素探针。制作低密度核苷酸薄膜微阵距列,通过导流杂交技术进行杂交,将杂交结果与DNA测序法对照。结果核酸测序显示,突变位点分别出现在包括315位点在内的7个位点,315位点突变占75.0%(18/24),最常见突变形式为AGC315ACC所致Ser315Thr氨基酸改变。杂交结果与测序结果符合率为93.9%(31/33),与DNA测序相比,其阳性预测值、阴性预测值、敏感度、特异度分别为90.0%、100%、100%、86.7%。结论核酸薄膜导流杂交技术能快速、简便、高效地检测临床标本中有无结核分枝杆菌,并可提示结核分枝杆菌有无异烟肼耐药性,指导临床用药。     

74例血友病B患者FⅨ基因突变研究

目的 研究导致中国人血友病B的凝血因子Ⅸ（FⅨ）基因突变类型的分布,并比较与美国白种人群有何异同。方法 从患者外周血白细胞抽提基因组DNA,分9段扩增Ⅸ基因外显子序列,用基因扩增转录测序技术直接测序法检出突变。结果 74例患者中有69例查到了FⅨ基因58种突变。分析比较这69例患者FⅨ基因突变类型的分布特征与美国白种人无显著性。中国不同地区之间差异也无显著性。结论 中国人血友病B的FⅨ基因突变类型非常分散,呈高度异质性。与美国白种人之间相比差异无显著性。     

Evaluation of oligonucleotide arrays for sequencing of the p53 gene in DNA from formalin-fixed, paraffin-embedded breast cancer specimens

BACKGROUND: Routine tissue processing has generated banks of paraffin-embedded tissue that could be used in retrospective cohort studies to study the molecular changes that occur during cancer development. The purpose of this study was to determine whether a p53 microarray could be used to sequence the p53 gene in DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tissues. METHODS: DNA was extracted from 70 FFPE breast cancer tissue specimens. p53 was sequenced with an oligonucleotide microarray (p53 GeneChip; Affymetrix), and the results were compared with the results obtained from direct sequencing. RESULTS: DNA was extracted from 62 of 70 cases. We identified 26 mutations in 24 of the 62 cases by the p53 GeneChip. No polymorphisms were detected, and exon 4 could not be evaluated in 20 cases. There were 43 genetic alterations detected by direct sequencing in 35 of the 62 cases. These consisted of 26 polymorphisms and 17 mutations in exons or splice sites. Fifteen mutations were identified by both methods. Direct sequencing detected significantly more gene alterations (43 of 54) in DNA extracted from FFPE tissue than the p53 GeneChip (26 of 54; P = 0.018). However, if the changes in exon 4 were eliminated from this comparison, the p53 GeneChip detected 26 of 27 mutations compared with direct sequencing, which identified 16 of 27 mutations. (P = 0.016). CONCLUSIONS: A combination of oligonucleotide microarray and direct sequencing may be necessary to accurately identify p53 gene alterations in FFPE breast cancer. The p53 GeneChip cannot be used to detect exon 4 polymorphisms (codon 72) in FFPE breast cancer tissue.     

Gene probes: application to prenatal and postnatal diagnosis of genetic disease

Gene probes can now be used to detect a variety of mutations that produce single-gene disorders. In present clinical practice, restriction endonuclease analysis is used for the prenatal diagnosis of sickle cell anemia, alpha-thalassemia, and beta-thalassemia. Direct detection of the mutation is possible in alpha-thalassemia, where a deletion has usually occurred, and in sickle cell anemia, where the mutation alters the recognition sequence of the restriction endonuclease, Mst II. Indirect detection of beta-thalassemia is based on using normal variations in DNA (DNA polymorphisms) to track normal and affected beta-globin genes in families. This latter kind of analysis is also useful in detecting the phenylalanine hydroxylase genes affected in phenylketonuria and will often be used in disorders where the mutations are unknown. In cases where the mutation is known, direct analysis by use of oligonucleotide probes is a new and important advance. An example of this type of gene detection in a family with classical hemophilia is presented. In addition, with chorion villus biopsy, detection of these inherited diseases is feasible by the 12th week of pregnancy.     

建立检测细胞色素P450酶与紫杉醇代谢相关突变位点的基因芯片分型方法

目的 建立针对与临床抗癌药物紫杉醇代谢相关的细胞色素P450(CYP450)酶基因多态性位点的快速、准确、高通量的基因芯片基因分型方法.方法 选取CYP450酶2C8*3、3A4* 18、3A5*3C等3个与紫杉醇代谢相关突变位点,根据基因库中报道的序列,设计每个基因多态性位点的野生型和突变型探针,在突变位点2侧设计PCR扩增引物,PCR片段长度应＜200 bp,并构建标准质粒.探针在3'端氨基修饰,下游引物标记荧光素Cy3,将探针按一定顺序点样于经醛基化处理的玻片制备成基因芯片.人体血液DNA样本分别通过3对引物扩增后与基因芯片上的探针杂交,通过扫描图像和配套软件对结果进行分析和判断.同时,对50份血液样本进行检测.结果 通过标准质粒杂交结果显示,每个位点对应的1对探针均能将野生型和突变型质粒进行准确地区分,无非特异性杂交信号出现;检测50份血液样本,CYP2C8 * 3位点的突变率为2%,CYP3A4 * 18位点均为野生型,CYP3A5 * 3C位点的突变率为62%.同时,通过测序法进行验证,基因芯片方法与测序方法的结果完全一致.结论 建立的同时检测抗癌药物紫杉醇代谢相关的CYP450酶基因多态性位点CYP2C8*3、CYP3A4 * 18、CYP3A5 * 3C的基因芯片分型方法快速、准确,结果可靠,重复性好,可用于指导紫杉醇患者的个体化用药,并为分析个体患者对于紫杉醇药物体内代谢提供了一个高通量技术平台.     

嗜铬细胞瘤基因突变检测芯片的开发和验证

目的：开发一种低通量的基因芯片,以识别和诊断嗜铬细胞瘤基因突变。方法：将人工合成的寡核苷酸探针点样于玻片介质上,制成嗜铬细胞瘤基因突变检测芯片。此芯片包含与嗜铬细胞瘤相关的SDHB、SDHD、VHI。和RET4个基因的87个突变位点,应用于35例已测序的嗜铬细胞瘤患者DNA样本以验证芯片检测的准确性。结果：该芯片的内参照结果能做到绝对阳性和绝对阴性,91％的样本芯片杂交与基因测序结果一致。35例嗜铬细胞瘤患者中,基因测序证实的29例突变样本用基因芯片技术检出26例;在6例无突变的样本中两种方法检出结果一致。结论：制作的基因芯片可准确识别嗜铬细胞瘤相关的基因突变,为筛查嗜铬细胞瘤基因突变提供一种快速的方法。     

Reliable low-density DNA array based on allele-specific probes for detection of 118 mutations causing familial hypercholesterolemia

BACKGROUND: Patients with familial hypercholesterolemia (FH) have a high risk of premature cardiovascular disease (PCVD). Mutations in the LDL receptor (LDLR) gene and the R3500Q mutation in the apolipoprotein B (APOB) gene are known to cause FH, but lack of high-throughput methods makes routine genetic diagnosis difficult. The objective of this work was to develop a DNA array for large-scale identification of mutant LDLR alleles. METHODS: We developed a low-density oligonucleotide microarray to identify 118 DNA sequence variations (117 for the LDLR gene and 1 for the APOB gene). We verified specificity and sensitivity by analyzing 1180 previously sequenced DNA samples, and conducted a blind study screening 407 Spanish patients with a clinical diagnosis of FH. RESULTS: The DNA array confirmed the previous genotyping results in almost all cases. In the blind study, the microarray detected at least 1 mutation in 51% of the patients for whom clinical diagnosis was classified as certain according to Dutch FH-MEDPED criteria; it also identified mutations in 37% of those with a diagnosis of probable/possible FH, thus giving a definite diagnosis. Patients harboring null mutations had shorter PCVD-free survival times and higher relative risk of PCVD than patients with a missense mutation. CONCLUSIONS: The proposed DNA array allows large-scale population screening and provides molecular information regarding mutation type and its correlation with clinical severity of FH, which can be used to develop therapeutic strategies.     

An oligonucleotide microarray for high-throughput sequencing of the mitochondrial genome

Previously we developed an oligonucleotide sequencing microarray (MitoChip) as an array-based sequencing platform for rapid and high-throughput analysis of mitochondrial DNA. The first generation MitoChip, however, was not tiled with probes for the noncoding D-loop region, a site frequently mutated in human cancers. Here we report the development of a second-generation MitoChip (v2.0) with oligonucleotide probes to sequence the entire mitochondrial genome. In addition, the MitoChip v2.0 contains redundant tiling of sequences for 500 of the most common haplotypes including single-nucleotide changes, insertions, and deletions. Sequencing results from 14 primary head and neck tumor tissues demonstrated that the v2.0 MitoChips detected a larger number of variants than the original version. Multiple coding region variants detected only in the second generation MitoChips, but not the earlier chip version, were further confirmed with conventional sequencing. Moreover, 31 variations in noncoding region were identified using MitoChips v2.0. Replicate experiments demonstrated >99.99% reproducibility in the second generation MitoChip. In seven head and neck cancer samples with matched lymphocyte DNA, the MitoChip v2.0 detected at least one cancer-associated mitochondrial mutation in four (57%) samples. These results indicate that the second generation MitoChip is a high-throughput platform for identification of mitochondrial DNA mutations in primary tumors.     

A microarray to analyze methylation patterns of p16(Ink4a) gene 5'-CpG islands

OBJECTIVES: Aberrant DNA methylation of the CpG site is among the earliest and most frequent alterations in cancer. Several studies suggest that aberrant methylation on the CpG sites of the tumor suppressor gene is closely associated with carcinogenesis. However, large-scale analysis of candidate genes has so far been hampered by the lack of high throughput approach for analyzing methylation patterns. The aim of this study was to develop a new method to analyze methylation patterns of p16(Ink4a) gene. DESIGN AND METHODS: We selected a 336 bp segment of the 5' untranslated region and the first exon of the p16(Ink4a) gene, as the target sequence, which include the most densely packed CpG fragment of the islands containing 32 CpG sites. A set of oligonucleotide probes was designed to assemble a DNA microarray to discriminate the methylation patterns of several adjacent CpG sites. RESULTS: Methylation patterns of human p16(Ink4a) gene were mapped and the results were validated by bisulphite DNA sequencing. A good reproducibility was observed in several parallel experiments. CONCLUSIONS: The methylation oligonucleotide microarray can be applied as a useful and powerful tool to map methylation patterns in multiple CpG island sites.