DNA Diagnosis Research Articles

Applying and testing the conveniently optimized enzyme mismatch cleavage method to clinical DNA diagnosis

Establishing a simple and effective mutation screening method is one of the most compelling problems with applying genetic diagnosis to clinical use. Because there is no reliable and inexpensive screening system, amplifying by PCR and performing direct sequencing of every coding exon is the gold standard strategy even today. However, this approach is expensive and time consuming, especially when gene size or sample number is large. Previously, we developed CEL nuclease mediated heteroduplex incision with polyacrylamide gel electrophoresis and silver staining (CHIPS) as an ideal simple mutation screening system constructed with only conventional apparatuses and commercially available reagents. In this study, we evaluated the utility of CHIPS technology for genetic diagnosis in clinical practice by applying this system to screening for the COL2A1, WRN and RPS6KA3 mutations in newly diagnosed patients with Stickler syndrome (autosomal dominant inheritance), Werner syndrome (autosomal recessive inheritance) and Coffin–Lowry syndrome (X-linked inheritance), respectively. In all three genes, CHIPS detected all DNA variations including disease causative mutations within a day. Direct sequencing of all coding exons of these genes confirmed 100% sensitivity and specificity. We demonstrate high sensitivity, high cost performance and reliability of this simple system, with compatibility to all inheritance modes. Because of its low technology, CHIPS is ready to use and potentially disseminate to any laboratories in the world.

The spectrum of CLCN1 gene mutations in patients with nondystrophic Thomsen’s and Becker’s myotonias

Thomsen's and Becker's diseases are the most prevalent nondystrophic myotonias. Their frequency varies, according to different sources, from 1 : 100 000 to 1 : 10 000. Thomsen's myotonia is autosomal dominant, and Becker's myotonia is autosomal recessive. Both diseases result from mutations of the CLCN1 gene encoding chloride ion channels of skeletal muscles. Molecular genetic analysis of the CLCN1 gene has been performed in patients with diagnoses of nondystrophic Thomsen's and Becker's myotonias living in the Russian Federation. A sample of 79 unrelated probands with nondystrophic Thomsen's and Becker's myotonias and 44 their relatives has been formed in the Laboratory of DNA Diagnosis of the Medical Genetic Research Center of the Russian Academy of Medical Sciences. Forty CLCN1 gene mutations have been found in a total of 118 chromosomes of 66 probands, including 21 familial and 45 sporadic cases. About half the mutations detected (45%) have been found for the first time; they are not described in the SNP database (ncbi.nlm.nih.gov). The following mutations (substitutions) have been detected in more than one chromosome, accounting for a total of 59.3% of chromosomes with mutations: Glyl90Ser (5.9%), c.1437-1450del14 (9.3%), Ala493Glu (5.1%), Thr550Met (3.4%), Tyr686Stop (5.1%), and Arg894Stop (30.5%).

Organizational and Functional Status of the Y-linked Genes and Loci in the Infertile Patients Having Normal Spermiogram

Male fertility is an orchestrated interplay of loci on the Y chromosome with a number of genes from across the other chromosomes. In this context, micro-deletions in the Y chromosome have been correlated with spermatogenic failure often leading to infertility. However, causes of infertility in the patients with the normal spermiogram have remained unclear and therefore pose another level of challenge. In the present study, we analyzed 64 STSs, studied different Y-linked genes and loci and conducted single nucleotide variant (SNV) analyses in 31 infertile males with normal spermiogram along with 67 normal fertile males (NFMs) to gain an insight into the organization of their Y chromosome. Further, employing quantitative real-time PCR (qPCR), we studied copy number variation of DYZ1 arrays and three genes and mutational status of SRY by direct sequence analyses. STS analyses of the AZFa, b and c regions in these patients showed known and new mutations. Further, copies of DAZ and BPY2 in the patients were found to be affected compared to those in NFMs. All the patients had normal copy number of the SRY however its sequence analysis (in silico) showed mutations in eight patients. In four of these eight patients, SRY mutations resulted into truncated proteins. Similarly, DYZ1 analysis showed micro-deletions and it's much reduced copy number as compared to those in NFMs. Present study in males with unexplained infertility revealed deletions similar to those observed in oligospermic and azoospermic patients. Thus, there are some common but still unknown factors underlying infertility in these patients irrespective of their spermatogenic status. This work is envisaged to augment DNA diagnosis, proving beneficial in the context of in vitro fertilization (IVF) and genetic counselling.

Systematic Review on Epstein-Barr Virus (EBV) DNA in Diagnosis of Nasopharyngeal Carcinoma in Asian Populations

To conduct a meta-analysis to investigate the value of EBV DNA in diagnosis of nasopharyngeal cancer (NPC) in Asian populations, and provide important evidence for screening. Prospective or respective case-control or cohort studies regarding the detection role of EBV DNA for NPC were included in our study. We conducted a comprehensive literature search in PubMed, EMBASE, and the Chinese Biomedical Database (CBM database between January 1980 and March 2012. A total of 18 studies with 1492 NPC cases and 2641 health controls were included. Almost of the included studies were conducted in China, and only one other conducted in Thailand. The overall results demonstrated that the pooled sensitivity, specificity, positive likelihood (+ LR) and negative likelihood (-LR) were 0.73 (0.71-0.75), 0.89 (0.88-0.90), 8.84 (5.65-13.84) and 0.19(0.11-0.32), respectively. The overall EBV DNA detection showed the largest area of 0.932 under the summary receiver operator curve (SROC). The accuracy of detection by plasma for NPC (0.86) was higher than in serum (0.81), with largest areas under the SROC of 0.97 and 0.91, respectively. Our results demonstrated the EBV DNA detection in plasma or serum has high sensitivity and specificity in diagnosis of NPC, especially in Chinese populations with a high risk of cancer.

Diagnosis and Quantitative Detection of Herpes Simplex Virus DNA in Corneal Ulcers

Diagnosis and Quantitative Detection of Herpes Simplex Virus DNA in Corneal Ulcers

Hereditary deafness in Kirov oblast: Estimation of the incidence rate and DNA diagnosis in children

Genetic analysis of hereditary deafness (HD) has been performed in the city of Kirov and ten rural districts of Kirov oblast (administrative region). The analysis employed the methods used in audiology, medical genetic counseling, and DNA diagnosis. Deafness has been established to be hereditary in 143 children from 100 unrelated families. The incidence rates of isolated and syndromic HDs in the period studied (1995-2001) have been estimated at 1.25 and 0.36 per 1000 newborns, respectively, the total incidence rate of all HD forms being 1.61 per 1000 newborns (1 case per 621 newborns). DNA analysis for the detection of seven frequent mutations in the genes GJB2 (the 35delG, 167delT, 235delC, and M34T mutations), GJB6 (the del(GJB6-D13S1854) and del(GJB6-D13S1830) mutations), and TMC1 (the R34X mutation) has been performed in families with isolated neurosensory deafness. Molecular genetic analysis has detected mutations in 51 children (48.6%); in 54 children (51.4%), no mutations have been found. The following genotypes have been identified in children with HD: 35delG/35delG in 32 probands (30.5%), 35delG/+ in 16 probands (15.2%), 35delG/235delC in 1 proband (0.95%), M34T/+ in 1 proband (0.95%), and M34T/35delG in 1 proband (0.95%). The 167delT mutation has not been found. The frequency of the 35delG mutation in the GJB2 gene has been estimated to be 39.05%. In the group with a family history of HD, mutations have been found in 66.7% of patients; in the group without a family history of HD, in 37.5% of patients. No mutation has been found in the GJB6 or TMC1 gene. Molecular genetic analysis has been performed in a family with clinically diagnosed Treacher Collins-Franceschetti syndrome. Sequencing has been used to find the 748-69C>T polymorphism in intron 6 (in the homozygous state) and the 3635C>G mutation in exon 23 leading to the substitution of glycine for alanine at position 1176 of the amino acid sequence (Ala1176Gly, in the heterozygous state), which have not been described before.

Association of single nucleotide polymorphisms of nicotinic acetylcholine receptor subunits with cervical neoplasia

AimsCholinergic signaling, particularly in response to non-physiological ligands like nicotine, stimulates carcinogenesis of a variety of tissue types including epithelia of the cervix uteri. Cholinergic signaling is mediated by nicotinic acetylcholine receptors (nAChRs), which are pentamers formed by subsets of 16 nAChR subunits. Recent literature suggests that single nucleotide polymorphisms (SNPs) of some of these subunits, notably alpha5, are risk factors for developing lung cancer in smokers as well as in non-smokers. Main methodsWe have studied the prevalence of four SNPs in the alpha5, alpha9, and beta1 subunits, which are expressed in cervical cells, in 456 patients with cervical cancers, precursor lesions, and healthy controls from two cohorts in Mexico. Key findingsA SNP in the alpha9 subunit, the G allele of rs10009228 (alpha9, A>G) shows a significant trend in the combined cohort, indicating that this allele constitutes a risk factor for neoplastic progression. The A allele of the SNP rs16969968 (alpha5, G>A), which correlates with the development of lung cancer, shows a non-significant trend to be associated with cervical lesions. Two other SNPs, rs55633891 (alpha9, C>T) and rs17856697 (beta1, A>G), did not exhibit a significant trend. SignificanceOur study points to a potential risk factor of cervical carcinogenesis with importance for DNA diagnosis and as a target for intervention.

Improved access to life insurance after genetic diagnosis of familial hypercholesterolaemia: cross-sectional postal questionnaire study

A decade ago, in the initial stage of genetic testing for familial hypercholesterolaemia (FH) in The Netherlands, it was reported that such screening decreased access to affordable life insurance for mutation carriers. In 2003, in order to improve access to insurance for FH mutation carriers, insurers agreed to underwrite according to a set of guidelines. In this cross-sectional study, we assessed whether access to insurance has improved since the advent of these guidelines. We approached 2825 subjects that had participated in the genetic testing for FH between 1998 and 2003. We compared unconditional acceptance rates before and after FH diagnosis and before and after the guidelines were issued by means of logistic regression analysis. Our study outcome pertains to 414 FH patients who applied for life insurance. Unconditional acceptance of a policy before DNA diagnosis and before the issue of guidelines occurred in 182 out of 255 (71%) cases, versus 27 out of 35 (77%) cases after DNA diagnosis, but before the issue of guidelines. De facto, 107 out of 124 (86%) patients received unconditional acceptance after DNA diagnosis and after the issue of guidelines (P for trend=0.002). Access to life insurance improved for FH patients after molecular diagnosis and it improved even further after the guidelines were issued. Therefore, we argue that limited access to life insurance on the basis of 'DNA discrimination' is no longer a valid argument against genetic cascade testing for FH, at least not in our country.

Four novel and two recurrent NHLRC1 (EPM2B) and EPM2A gene mutations leading to Lafora disease in six Turkish families

Lafora disease (LD) is a type of autosomal recessive, progressive myoclonus epilepsy resulting mostly from mutations in the EPM2A and NHLRC1 genes. Mutational analysis in both genes was initiated with the aim of establishing LD DNA diagnosis in Turkey. Four novel NHLRC1 (p.G131X, p.P69S and p.D82H) and EPM2A (p.V7A) and two recurrent NHLRC1 (p.D146N) and EPM2A (p.R241X) mutations were identified in six families. The delineation of causative mutations in patients provided early disease diagnosis for other family members and contributed to the knowledge of LD pathogenesis.

Protein characterization by LC–MS/MS may be required for the DNA identification of a fusion hemoglobin: The example of Hb P-Nilotic

DNA analysis is currently the easiest way to identify a hemoglobin variant in most cases. Nevertheless, in case of complex gene rearrangements, mass spectrometry studies may be required to orientate the DNA diagnosis. The present report shows the use of mass spectrometry techniques prior to DNA analysis for the identification of the rare P-Nilotic fusion hemoglobin. Complete protein analysis is performed by liquid chromatography–tandem mass spectrometry on the abnormal globin chain isolated by reversed-phase liquid chromatography.

Ιnflammatory or septic arthritis associated with mycoplasma pneumonia in children: Two case reports and review of the literature.

Inflammatory or septic arthritis due to Mp is an extremely unusual manifestation in children, and the functional outcome of the joints is difficult to be predicted. Two cases with Mp infection are presented. The first patient had positive PCR for Mp after hip aspiration and arthrotomy with thorough irrigation and debridement. A flattened femoral head was detected during the follow-up, which became quite spherical a year after. An arthrotomy with medial synovectomy of the knee was performed in the second patient. Lack of full knee extension was presented during the first 3months, which gradually decreased to 7° in the final follow-up. The suspicion of Mp infection with extra-pulmonary involvement in children is mainly based on clinical, epidemiological and radiological data, but laboratory testing is required for confirmation. Rapid diagnosis of probability consists of serum tests, and their results are essential for early therapeutic planning. The direct diagnosis of Mp DNA through polymerase chain reaction (PCR) provides specificity and sensitivity. Very few cases of arthritis associated with Mp infection have been published but not with the severity of our cases. Clinical suspicion of Mp infection is of great importance, and the outcome depends on early diagnosis and specific treatment.

Probing the Charge-Transfer Dynamics in DNA at the Single-Molecule Level

Photoinduced charge-transfer fluorescence quenching of a fluorescent dye produces the nonemissive charge-separated state, and subsequent charge recombination makes the reaction reversible. While the information available from the photoinduced charge-transfer process provides the basis for monitoring the microenvironment around the fluorescent dyes and such monitoring is particularly important in live-cell imaging and DNA diagnosis, the information obtainable from the charge recombination process is usually overlooked. When looking at fluorescence emitted from each single fluorescent dye, photoinduced charge-transfer, charge-migration, and charge recombination cause a "blinking" of the fluorescence, in which the charge-recombination rate or the lifetime of the charge-separated state (τ) is supposed to be reflected in the duration of the off time during the single-molecule-level fluorescence measurement. Herein, based on our recently developed method for the direct observation of charge migration in DNA, we utilized DNA as a platform for spectroscopic investigations of charge-recombination dynamics for several fluorescent dyes: TAMRA, ATTO 655, and Alexa 532, which are used in single-molecule fluorescence measurements. Charge recombination dynamics were observed by transient absorption measurements, demonstrating that these fluorescent dyes can be used to monitor the charge-separation and charge-recombination events. Fluorescence correlation spectroscopy (FCS) of ATTO 655 modified DNA allowed the successful measurement of the charge-recombination dynamics in DNA at the single-molecule level. Utilizing the injected charge just like a pulse of sound, such as a "ping" in active sonar systems, information about the DNA sequence surrounding the fluorescent dye was read out by measuring the time it takes for the charge to return.

Invitation to Gold 2012, Tokyo

The price of gold reached 1891.90 US dollars per ounce during August 2011, suggesting that gold has found a new prominence in global financial markets and economics. An increasing number of people are currently protecting their capital in an asset that offers a safe store of value to today's investor. At the same time, the industrial applications of gold, largely centered on electronics (bonding wires, electroplating, etc.), have been growing and currently occupy around 12% of total gold demand. So a new gold rush is underway at the cutting edge of nanoscience and -technology research. A typical example is catalysis by gold. For over a century, gold in bulk form had been considered too noble to work as a catalyst. However, it has recently been proved that gold exhibits surprisingly high catalytic activity for many reactions when deposited as nanoparticles on base metal oxides, carbons, and polymers. At the same time, gold colloids of different morphology are attracting growing interest owing to their special surface plasmonics; applications in DNA diagnosis, health care, and new paints are on the horizon. Coulomb blockade by quantum dots may present a new topic in electronics. Self-assembled monolayers on a substrate of gold are also an interesting area of research which functionalizes solid surfaces leading to catalysis, electrodes, and optoelectronics. These are just a part of the expanding science and technology of gold. Plenty of exciting discoveries and achievements are still emerging in other areas too, for example unexpected magnetism in gold nanostructures. To discuss and debate this rapid growth of gold science and technology, the Gold 2012 conference will be held at one of the biggest terminals in the center of Tokyo, Shinjuku. Participants will enjoy a magnificent view from the 42nd and 43rd floors of the conference venue, the Keio Plaza Hotel. You are cordially invited to join us for this 6th Gold Conference, the first in Asia, after Heidelberg (2009), Limerick (2006), Vancouver (2003), Cape Town (2001), and Hanau (1996). Japan was once called the island of gold, Zipang, and it is now moving to the island to nanogold. Please join us at Gold 2012 in Tokyo to discuss mutual interests in nanotechnology, chemistry, catalysis, and nanomaterials of gold and its applications (www.gold2012.org) M. Haruta Chairman of the GOLD 2012 Organising Committee

Early Prenatal Diagnosis of Thalassemia: The First Report of Experience in Mainland China

In this study, we report our experience with chorionic villus sampling (CVS) for prenatal diagnosis of thalassemia in mainland China. During a 4-year period, 308 pregnant women chose to have CVS for prenatal diagnosis. Chorionic villus sampling was successful in all cases, and post-CVS abortion was seen in only two cases (0.6%). DNA diagnosis was correctly done in 307 (99.7%) prenatal samples but maternal contamination was found in one (0.3%) subject. In total, 77 pregnancies were found with an affected fetus, and all of the affected pregnancies were terminated within 1 week after the CVS procedure. Our experience indicates that CVS is a feasible and effective technique for prenatal diagnosis of thalassemia.

Diagnosis and quantitative detection of HSV DNA in samples from patients with suspected herpes simplex encephalitis

Diagnosis and quantitative detection of HSV DNA in samples from patients with suspected herpes simplex encephalitis

Clinical profile of hearing loss in children with congenital cytomegalovirus (CMV) infection: CMV DNA diagnosis using preserved umbilical cord

Conclusions: Congenital cytomegalovirus (CMV) infection is a major cause of bilateral and unilateral sensorineural hearing loss (SNHL) in children, accounting for 9.0% of SNHL cases. The diagnostic rate using combined genetic deafness test and CMV DNA detection test was determined to be 46.4% in bilateral profound SNHL. Objectives. The present study investigated the prevalence of congenital CMV infection diagnosed retrospectively by detection of CMV DNA in dried umbilical cord specimens from children with unilateral or bilateral SNHL up to the age of 12 years. Methods: Preserved dried umbilical cords were collected from 134 children with bilateral (46 children) or unilateral (88 children) SNHL. DNA was extracted from the dried umbilical cords and CMV DNA was detected by quantitative PCR. Genetic deafness tests based on the invader assay were performed in children with bilateral SNHL. Results: CMV DNA from the dried umbilical cords was detected in 8.7% of the bilateral SNHL and 9.1% of unilateral SNHL. Deafness gene mutations were identified in 21.7% (10/46) of children with bilateral SNHL.

USA - Doctors use sick boy’s DNA in diagnosis and treatment

USA - Doctors use sick boy’s DNA in diagnosis and treatment

Diagnosis and quantitative detection of HSV DNA in samples from patients with suspected herpes simplex encephalitis

Diagnosis of herpes simplex encephalitis (HSE) is based on the detection of herpes simplex virus (HSV) DNA in patients’ CSF samples. HSV DNA quantitation has the potential for estimating the effects of antiviral therapy. The aim of this study was to diagnose HSV DNA in HSE suspected patients and the quantitative analysis of its genome using real-time PCR to assess the value of the viral load in the course of antiviral treatment. The CSF samples were collected from 236 consecutive HSE suspected patients from November 2004 to May 2008. Upon DNA extraction, the samples were analyzed by Real-Time PCR assay. A set of primers amplified a common sequence of HSV glycoprotein B gene. The copy numbers of unknown samples were expressed via a standard curve drawn with a known amount of amplified cloned plasmid. Of the 236 samples, 137 (58%) came from males and 99 (42%) from females. The HSV genome was detected in 22 (9.3%) patients by PCR, 13 males/9 females. Serial CSF samples were available from 10 of the 22 patients. The range of the HSV DNA copy numbers in the clinical samples ranged from 2.5 × 102 to 1.7 × 106 copies/mL of CSF. Quantitative PCR results can be helpful in evaluating the efficacy of antiviral therapy in the above-mentioned patients. There is an association between the initial viral load and the duration of treatment course.

The first use of EaeI restriction enzyme in DNA diagnosis of Hb Q‐India

The α-chain variant Hb Q-India (c.193G>C) is caused by a point mutation GAC→CAC at codon 64 of the α1 globin gene and is clinically silent. Point mutations can be diagnosed easily by many simple polymerase chain reaction (PCR) techniques including PCR-restriction digest, but for Hb Q-India the restriction digest has never been described. In this work we aimed to develop a restriction enzyme digestion assay for DNA diagnosis of Hb Q-India, in order to increase the panel of restriction enzymes used in DNA diagnosis of haemoglobinopathies and also as a simple cheap alternative to the ARMS-PCR method. A restriction enzyme digestion assay was designed for diagnosis of Hb Q-India using the restriction enzyme EaeI enzyme as the Hb Q-India mutation abolishes the recognition site of this enzyme. Patients were screened for an abnormal haemoglobin by high performance liquid chromatography (HPLC) and those had an abnormal peak with a retention time between 4.7 and 4.8 minutes were selected for diagnosis at the molecular level. The α1 globin gene was amplified in 12 cases with a presumed diagnosis of Hb Q-India by HPLC and isoelectric focusing (IEF), and the amplified products were subjected to the EaeI digestion. All the 12 cases were diagnosed positive (100%) for Hb Q-India by the EaeI restriction enzyme digest. They were heterozygotes for the mutation. EaeI restriction enzyme digestion can be used as a simple and robust alternative method to ARMS-PCR for DNA diagnosis of Hb Q-India. The EaeI restriction enzyme can be added to the panel of restriction enzymes used in the DNA diagnosis of the abnormal Hb variants. Concomitant use of HPLC and IEF can be used efficiently for presumed diagnosis of this rare variant.

Detection of OSMR and TFPI2 gene methylation in stool DNA for diagnosis of colorectal cancer

Detection of OSMR and TFPI2 gene methylation in stool DNA for diagnosis of colorectal cancer