Validation of a multiplex amplification system of 19 autosomal STRs and 27 Y-STRs

This article describes a newly devised autosomal short tandem repeat(STR)multiplex polymer-ase chain reaction(PCR)system for 19 autosomal loci(D12S391,D13S317,D16S539,D18S51,D19S433,D2S1338,D21S11,D3S1358,D5S818,D6S1043,D7S820,D8S1179,CSF1PO,FGA,TH01,TPOX,vWA,Penta D and Penta E),27 Y-chromosome STR loci(DYS19,DYS385,DYS3891,DYS38911,DYS390,DYS391,DYS392,DYS393,DYS437,DYS438,DYS439,DYS448,DYS449,DYS456,DYS458,DYS460,DYS481,DYS518,DYS533,DYS570,DYS576,DYS635,DYS627,YGATAH4 and DYF387S1)and amelogenin with six-colour fluorescent labelling.Various parameters were evaluated,such as its accuracy,sensitivity,specificity,stability,ability to ana-lysis of mixtures and effects of changes in the PCR-based procedures.All of the 47 selected STR loci were accurately and robustly amplified from 282 bloodstain samples.The species-spe-cificity was high and some ability to inhibit Hematin was identified.The lowest detectable DNA amount was ≥0.125 ng.All of the male loci of the secondary component were revealed precisely when the control DNA was mixed at male/female and male/male ratios of 1:4 or more.We conclude that the present 19-plex autosomal STR and 27 Y-STR assay is both accur-ate and sensitive.It constitutes an additional powerful tool for forensic applications.

A Study of Radiation-Induced Telomere Instability Using Multiplex Ligation-Dependent Probe Amplification (MLPA)

The integrity of the chromosomes for two WIL2-derived lymphoblastoid cell lines (TK6 and WTK1) in the presence and absence of ionizing radiation was analyzed by Multiplex Ligation-Dependent Probe Amplification (MLPA). The TK6 cell line has the native p53 tumor-suppressor gene, whereas WTK1 cells contain a p53 mutation. Each cell line was isolated pre- and post-irradiation (2 and 3 Gy) and analyzed by MLPA. The impact of irradiation on these two cell lines was investigated using probes that target specific regions on chromosomes associated with subtelomeric regions. Results indicate that WTK1 and TK6 are impacted differently after irradiation, and that each cell line presents its own unique MLPA profile. The most notable differences are the appearance of a number of probes in the post-irradiated MLPA profile that are not present in the controls, and two unique probe signals only seen in WTK1 cells. These results build on our previous studies that indicate how different human cell lines can be affected by radiation in significantly different ways depending on the presence or absence of wild type p53.

A Study of Radiation-Induced Instability for the Gene Locus Associated with Intellectual Disorders or Developmental Delays

Multiplex Ligation-Dependent Probe Amplification (MLPA) was used to study the integrity of the chromosomes for two WIL2-derived lymphoblastoid cell lines (TK6 and WTK1) in the presence and absence of ionizing radiation. WTK1 cells contain a p53 mutation, whereas the TK6 cell line has the native p53 tumor-suppressor gene. Each cell line was isolated pre- and post-irradiation (2 and 3 Gy) and analyzed by MLPA. Using probes that target specific regions on chromosomes associated with a distinct subset of microdeletions and microduplications either established or thought to be responsible for intellectual disability or developmental delay, we have demonstrated that WTK1 and TK6 are not impacted in the same way by irradiation. Instead, each cell line presents its own unique MLPA profile. The most notable differences are the appearance of nine unique probe signals only seen in WTK1 cells. These results are important in the study of how different cell lines can be affected in significantly different ways depending on the presence or absence of wild type p53.

APC gene mutations in Chinese familial adenomatous polyposis patients

AIM:To study the characteristics of APC(adenomatous polyposis coli)gene germline mutation in Chinese patients with familial adenomatous polyposis(FAP).METHODS:APC gene from 14 FAP families was amplified by polymerase chain reaction(PCR)and underwent direct sequencing to determine the micromutation type.For the samples without micromutation,the large fragment deletion of APC gene was examined by multiplex ligation-dependent probe amplification(MLPA).RESULTS:There were gene micromutations in 9 families with a micromutation detection rate of 64.3%(9/14),including 6 frameshift mutations(66.7%),1 nonsense mutation(11.1%)and 2 splicing mutations(22.2%).Large fragment deletions were detected by MLPA in 2 families.The total mutation detection rate of micromutations and large fragment deletions was 78.6%(11/14).CONCLUSION:The detection rate of APC gene germline mutation can be improved by direct sequencing combined with MLPA large fragment deletion detection.

Analyses of Genotypes and Phenotypes of Ten Chinese Patients with Wolf-Hirschhorn Syndrome by Multiplex Ligation-dependent Probe Amplification and Array Comparative Genomic Hybridization

Background： Wolf-Hirschhorn syndrome （WHS） is a contiguous gene syndrome that is typically caused by a deletion of the distal portion of the short arm of chromosome 4. However, there are few reports about the features of Chinese WHS patients. This study aimed to characterize the clinical and molecular cytogenetic features of Chinese WHS patients using the combination of multiplex ligation-dependent probe amplification （MLPA） and array comparative genomic hybridization （array CGH）. Methods： Clinical information was collected from ten patients with WHS. Genomic DNA was extracted from the peripheral blood of the patients. The deletions were analyzed by MLPA and array CGH. Results： All patients exhibited the core clinical symptoms of WHS, including severe growth delay, a Greek warrior helmet facial appearance, differing degrees of intellectual disability, and epilepsy or electroencephalogram anomalies. The 4p deletions ranged from 2.62 Mb to 17.25 Mb in size and included LETM1, WHSC1, and FGFR3. Conclusions： The combined use of MLPA and array CGH is an effective and specific means to diagnose WHS and allows for the precise identification of the breakpoints and sizes of deletions. The deletion of genes in the WHS candidate region is closely correlated with the core WHS phenotype.

Coexistent Charcot-Marie-Tooth type 1A and type 2 diabetes mellitus neuropathies in a Chinese family

Charcot-Marie-Tooth disease type 1A（CMT1A） is caused by duplication of the peripheral myelin protein 22（PMP22） gene on chromosome 17. It is the most common inherited demyelinating neuropathy. Type 2 diabetes mellitus is a common metabolic disorder that frequently causes predominantly sensory neuropathy. In this study, we report the occurrence of CMT1 A in a Chinese family affected by type 2 diabetes mellitus. In this family, seven individuals had duplication of the PMP22 gene, although only four had clinical features of polyneuropathy. All CMT1 A patients with a clinical phenotype also presented with type 2 diabetes mellitus. The other three individuals had no signs of CMT1 A or type 2 diabetes mellitus. We believe that there may be a genetic link between these two diseases.

Forensic Identification of Four Indian Snake Species Using Single Multiplex Polymerase Chain Reaction

Among different endangered animal species,snakes are the most neglected creature looked at with apathy and therefore,are ruthlessly killed,illegally trafficked,and poached for their venom,lucrative skin,meat,and bones for manufacturing of medicines,accessories,and food items.Establishing the identity of the endangered snake species is important for punishing the offenders under Wildlife Protection Act(WPA)(1972)but morphological characters fail to establish identity as they are often altered.The technique of identification of snake species at molecular level holds very effective conclusion in punishing offender.Here,we have constructed and demonstrated a novel multiplexing polymerase chain reaction technique,using 16S rRNA and C-mos gene for identification of four Indian snake species,namely Ptyas mucosa,Daboia russellii,Naja naja,and Xenochrophis piscator.They are listed in Appendix-II and III of convention on international trade in endangered species of wild fauna and flora and Schedule II;Part II of Indian WPA,1972.Therefore,it may be considered a functional tool for establishing species-specific identity of four Indian snake species and promising to be useful for their conservation.

一种新型6色荧光25个STR基因座复合扩增体系研究

To develop and validate a novel 6-dye STR(short tandem repeat)25-plex DNA typing system for forensic DNA profiling and databases.In this study,a novel STR 25-plex DNA typing system that includes 24 autosomal STRs(D1S1656,D2S1338,D2S441,D3S1358,D5S818,D6S1043,D7S820,D8S1179,D10S1248,D12S391,D13S317,D16S539,D18S51,D19S433,D21S11,D22S1045,CSF1PO,FGA,Penta D,Penta E,TH01,TPOX,vWA,D11S4463)and Amelogenin was developed.Validation studies demonstrated the sensitivity,accuracy,and reproducibility of our novel STR 25-plex DNA typing system.The sensitivity of the STR 25-plex DNA typing system was demonstrated by the ability to obtain complete profiles from as little as 0.125ng of human DNA.Specificity testing was demonstrated by the lack of cross-reactivity to a variety of commonly encountered animal species and microbial pool.For stability testing,full profiles were obtained with humic acid concentration≤60ng/μL and hematin≤600μM.For forensic evaluation,the selected 24 autosomal STRs followed the Hardy-Weinberg equilibrium.Since 24 autosomal STRs were independent from one another,PM(Probability matching)was 3.5434×10-28,TDP(Total Probability of Discrimination Power)was 0.999999999999999999999999969863,and CEP(Cumulative probability of exclusion)was 0.99999999375.The new STR 25-plex typing system is sensitive,reproducible,and stable,therefore it is highly applicable for use in national DNA database and can help to facilitate international data sharing.

Molecular Analysis-Based Genetic Characterization of a Cohort of Patients with Duchenne and Becker Muscular Dystrophy in Eastern China

Background： Duchenne muscular dystrophy （DMD） and Becker muscular dystrophy （BMD） are common X-linked recessive neuromuscular disorders caused by mutations in dystrophin gene. Multiplex polymerase chain reaction （multiplex PCR） and multiplex ligation-dependent probe amplification （MLPA） are the most common methods for detecting dystrophin gene mutations, This study aimed to contrast the two methods and discern the genetic characterization of patients with DMD/BMD in Eastern China. Methods： We collected 121 probands, 64 mothers ofprobands, and 15 fetuses in our study. The dystrophin gene was detected by multiplex PCR primarily in 28 probands, and MLPA was used in multiplex PCR-negative cases subsequently. The dystrophin gene of the remaining 93 probands and 62 female potential carriers was tested by MLPA directly. In fetuses, multiplex PCR and MLPA were performed on 4 fetuses and 10 fetuses, respectively. In addition, sequencing was also performed in 4 probands with negative MLPA. Results： We found that 61.98% of the subjects had genetic mutations including deletions （50.41%） and duplications （11.57%）. There were 43.75% of mothers as carriers of the mutation. In 15 fetuses, 2 out of 7 male fetuses were found to be unhealthy and 2 out of 8 female fetuses were found to be carriers. Exons 3-26 and 45-52 have the maximum frequency in mutation regions. In the frequency ofexons individually, exon 47 and exon 50 were the most common in deleted regions and exons 5, 6, and 7 were found most frequently in duplicated regions. Conclusions： MLPA has better productivity and sensitivity than multiplex PCR. Prenatal diagnosis should be applied in DM D high-risk fetuses to reduce the disease incidence. Furthermore, it is the responsibility of physicians to inform female carriers the importance of prenatal diagnosis.

THREE NOVEL FOXL2 GENE MUTATIONS IN CHINESE PATIENTS WITH BLEPHAROPHIMOSIS-PTOSIS-EPICANTHUS INVERSUS SYNDROME

Blepharophimosis-ptosis-epicanthus inversus Psyndrome （BPES, OMIM # 110100） is a rare autosomal dominant disorder affecting the eyelid and ovarian development. When co-occurred together, it is type Ⅰ and when only the eyelid abnormalities are present, it is type Ⅱ. Both types had been mapped to the same locus 3q23 on the basis of cytogenetic rearrangements 1-3 and linkage analyses. 4-6 Subsequently,

A novel large deletion(exons 12,13)and a missense mutation(p.G46R)in the PAH in a Japanese patient with phenylketonuria

Background:Phenylketonuria(PKU)is caused by a defect in phenylalanine hydroxylase(PAH).More than 500 mutations have been reported for the gene encoding PAH.However,approximately l%-5%of these include large deletions and large duplications that cannot be detected by conventional methods.Methods:In this report we tried to fully characterize a PAH-deficient patient.The patient was a 2-year-old Japanese boy who was diagnosed with classical PKU at the time of neonatal screening,which was confirmed by the tetrahydrobiopterin-loading test.PCR-related direct sequencing and multiplex ligation-dependent probe amplification(MLPA)were used to analyze of the PAH of the patient.Results:Using PCR-related direct sequencing method,we could detect only a heterozygous novel missense mutation:p.136G>C(p.G46R).A second mutation was detected by MLPA.The patient was heterozygous for a novel large deletion of exons 12 and 13:c.1200-?_1359+?del(EX12_13del).For genetic counseling,an accurate genetic diagnosis is often necessary.Conclusions:Through a combination of MLPA and conventional methods,the success rate of PAH mutation identification can be close to 100%.