Viewing Study NCT00155818



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Last Modification Date: 2024-10-26 @ 9:15 AM
Study NCT ID: NCT00155818
Status: COMPLETED
Last Update Posted: 2005-09-12
First Post: 2005-09-09

Brief Title: Mutation Screening and Translocation Detection of DISC1 Gene in Schizophrenia
Sponsor: National Taiwan University Hospital
Organization: National Taiwan University Hospital

Study Overview

Official Title: Mutation Screening and Translocation Detection of DISC1 Gene in Schizophrenia
Status: COMPLETED
Status Verified Date: 2003-08
Last Known Status: None
Delayed Posting: No
If Stopped, Why?: Not Stopped
Has Expanded Access: False
If Expanded Access, NCT#: N/A
Has Expanded Access, NCT# Status: N/A
Acronym: None
Brief Summary: Several chromosomal loci obtained from genetic linkage studies have been reported of relating to schizophrenia These areas include of 1q32-41 6p24-21 8p22-21 15q13-14 and 22q11-12 The names of these genes located in these loci have not been identified nor have the function and the relationship to the disease Our research team using genetic linkage studies has found a strong linkage NPL Z score 218 p001 between the D1S251 marker and schizophrenia disease This marker is about 4 kb away from DISC1 disrupted in schizophrenia gene 1 gene In a Scottish family a balanced translocation t111 q421q143 has cosegregated inside the schizophrenia affected members of the family LOD score 60 The breakpoint of the translocation is located at the intron area between exon 8 and exon 9 of DISC1 gene This translocation disrupted the gene and caused its malfunction A large molecular genetic study study recently in Finland has also demonstrated strong linkage evidence Zmax321 between the DIS2709 marker located among exon 4 and exon 5 of DISC1 gene and schizophrenia in a All these findings have indicated that DISC1 gene is a potential positional candidate gene and worth for further study

The main purposes of this proposal include 1 To evaluate the incidence rate of the balanced translocation between the chromosome 1q421 and 11q143 in approximately 500 schizophrenic patients in Taiwan Furthermore we will compare the clinical symptoms illness course and family genetic model to examine if any particular characters coexist with the translocation 2 To search for the genetic polymorphisms in DISC1 gene area where the thirteen exons the promoter regions 1 kb upstream the start codon and the breakpoint area 1 kb of both upstream and downstream area will be analyzed by the method of denaturing high performance liquid chromatography DHPLC Case-control association study will be performed further in each 200 schizophrenic patients and normal controls to evaluate the relationship between the disease and the clinical characteristics

This proposal is quite feasible and prospective with the following reasons 1 All the DNA samples and the clinical data have been collected and evaluated completely for further analysis 2 Our research team has built up an integrated andreliable molecular genetic laboratory All the facilities necessary for this study DHPLC had been setup with standard operating protocols and working routinely 3 DISC1 gene has strong linkage evidence with schizophrenia in Taiwanese sample The high prior probability of DISC1 gene as a positional candidate gene increases the successfulness of association study 4 Once the relationship among balance translocation genetic polymorphism and the schizophrenia have established further functional study will be evaluated to understand the possible mechanisms involved in the disease
Detailed Description: The grant proposal has two major research goals The first goal will be constructing an Ecoli plasmid carried with an approximately 14 kb of DNA sequences from each 700 bps of the chromosome 1q421 and 11q143 around the breakpoint The second goal will be establishing the denaturing high performance liquid chromatography DHPLC methods to screen the mutations or polymorphisms for all the exons of DISC1 gene the 1 kb at the promoter region and the sequences from 1 kb at the upstream and downstream of the breakpoint

Translocation 1q42111q143-Carried Plasmid DNA Construction

Human genomic DNA isolation All human genomic DNA will be used from these subjects collected in the past or subjects collected specific for the plasmid construction study with informed consents For the plasmid construction mononuclear leukocytes will be isolated by a modification of the method of Böyum 1968 Whole blood with EDTA as anticoagulant will be taken by venipuncture from healthy volunteers The collected blood will be diluted with an equal volume of phosphate buffered saline PBS and layered onto Histopaque-1077 After separation by centrifugation at 400xg for 40 min the mononuclear leukocyte layer will be removed and washed three times with PBS by centrifuging cells at 400xg for 10 min The freshly isolated cells will be further applied for genomic DNA isolation according to standard phenolchloroform extraction procedures Sambrook et al 1989

PCR amplification of 1q421 and 11q143 DNA sequences The amplification will be performed with AmpliTaq Gold DNA polymerase in a 50 ul reaction volume The reaction containing 50 ng DNA 1 U of enzyme 300 ng of each primer 200 mM of each dNTP 15 mM MgCl2 50 mM KCl and 10 mM Tris-HCl pH83 All reaction will be performed with an initial denaturing step of 5 min at 95 followed by 35 cycles of a denaturing step at 94 for 30 sec an annealing step of 1 min at a temperature appropriate for the primers used and a synthesis step at 72 for 10 min The primer sequence for the 738 bps of upstream breakpoint at 1q421 will be designed with an EcoRI cutting site at the breakpoint end The primer sequence for the 719 bps of downstream breakpoint at 11q143 will also be designed with an EcoRI cutting site at the breakpoint end

Ligating the two PCR DNA fragments and purification by gel electrophoresis The PCR product of both 1q421 and 11q143 will be reacted with EcoRI separately to reveal the cohesive ligation sites Two of the DNA fragments around 700 bps each will be ligated by T4 DNA ligase following the protocol provided from the InsTAcloneTM cloning kit MBI Fermentas USA The ligated 14 kb of DNA fragment will be re-amplified by above PCR procedure purified and recovered from agarose gel by electroelution and extraction with organic solvents Sambrook et al 1989

Cloning the isolated DNA fragments into E Coli plasmid The purified 14 kb of DNA fragment 054 pmol ends will be mixed with plasmid vector pTZ57RT DNA 0165 ug 018 pmole ends 10x ligation buffer PEG 4000 solution and T4 ligase 5U The mixture will be incubated at 22 for 1 hr A control ligation reaction will be performed using 4 ul 168 ng 054 pmol ends of control PCR fragment provided by the InsTAcloneTM cloning kit

Transformation of the plasmids into competent E Coli The transformation will follow the protocol provided by the InsTAcloneTM cloning kit Competent cells of Ecoli bacteria DH5α stain will be inoculate with 2 ml of TransformAid C medium from a frozen stock and incubate the culture overnight at 37 in a shaker A pre-warm culture tube containing TransformAid C medium 075 ml will be added up with 0075 ml of overnight cultured Ecoli and shaken at 37 for 20 min

Equal volumes 250 ul of TransformAid T-solution A and B will be mixed and kept on ice The 075 ml of Ecoli culture tube will be spun for 1 min at 4 and discarded the supernatant Adding in 300 ul of TransformAid T-solution mixture the Ecoli will be incubated on ice for 5 min and spun for 1 min The supernatant will be discarded and 120 ul of TransformAid T-solution will be added and incubated for another 5 min on ice The ligation plasmid 25 ul 10-20 ng and the control ligation mixture 2 ul 10 ng vector DNA will be prepared and sat on ice for 2 min The resuspended on ice of Ecoli cells 50 ul will be added to each of the ligation plasmid and incubated on ice for 5 min The cells with ligation plasmid will be plated on a pre-warmed LB-Ampicillin agar plate and incubate overnight at 37 The control ligation plasmid usually generates of about 90 of transformation efficiencies

Clone selection and isolation of the Ecoli plasmids The recombinant clones of Ecoli will be identified by the white selection because the vector carried the lacZ gene will be disrupted by the insertion The presence of correct plasmid insertion will be further confirmed by PCR reaction The plasmid will be isolated from Ecoli by the method of alkaline lysis Liou et al 1999 or by commercialized plasmid extraction kit A single cell colony picked up to a mixture with 30 ul of TE 10 mM Tris-HCl pH74 1 mM EDTA pH80 buffer and 60 ul of SDS-NaOH 1 SDS 01 M NaOH will be inverted gently and incubated for 5 min at room temperature A subsequent of 45 ul of 3M sodium acetate solution pH52 and 130 ul of chloroform will be added into the cell mixture and microcentrifuged for 5 min The upper phase will be collected and added 130 ul of isopropanol mixed and centrifuge for 10 min The plasmid DNA pellet will be washed with 70 ethanol 100 ul and dissolved in 10-20 ul of TE buffer

PCR the breakpoint area of genomic DNA from all patients The isolated plasmid DNA and the collect schizophrenic patients genomic DNA will be analyzed by further PCR reaction in the breakpoint area with the pair of primers coming from both chromosomes 1 and 11 PCR will be performed in a volume of 50 ul with AmpliTaq Gold DNA polymerase The reaction containing 50 ng DNA 1 U of enzyme 300 ng of each primer 200 mM of each dNTP 15 mM MgCl2 50 mM KCl and 10 mM Tris-HCl pH83 All reaction will be performed with an initial denaturation step of 5 min at 95 followed by 35 cycles of a denaturation step at 94 for 30 sec an annealing step of 1 min at a temperature appropriate for the primers used and a synthesis step at 72 for 10 min The primer sequences from both chromosome 1q421 and 11q143 will be used

Data Analysis PCR result with a band at approximately 14 kb of patient will be consider as having a balanced translocation at the chromosome 1q421 area The incidence rate will be calculated by dividing the numbers of patients with balanced translocation to the total patients analyzed in this experiment

Expected Difficulties and Solutions

If balanced translocation did not happen in any schizophrenic patients of Taiwan The following inferences will be made

1 No balanced translocation at the 1q421 and 11q143 has occurred in the patients collected by this laboratory
2 The balanced translocation rate in the population is quite low almost zero
3 This result may not rule out the possibility of a relationship between DISC1 gene and schizophrenia
4 It indicates that further experiments need to be carried out to evaluate if any mutation or polymorphisms in this area relating to the disease because in our previous experiment we have demonstrate a strong correlation between this chromosome area and the disease

Denaturing High Performance Liquid Chromatography DHPLC DHPLC is a technique with benefits of fully automated high throughput analysis accommodated to the primers and the specific reagent arrays of PCR and required no sample pretreatment other than PCR Xiao and Oefner 2001 Using this technique to screen the breakpoint area of DNA sequence will speed up the finding in the possibility of having single nucleotide polymorphism or insertions and deletions relating to schizophrenia disease

PCR the upstream and downstream breakpoint area exon 8 and exon 9 DNA fragments All the collected schizophrenic patients genomic DNA will be analyzed by PCR reaction at the upstream and downstream 1 kb of the breakpoint and the exon 8 and the exon 9 covered parts of introns toward the breakpoint As the optima DNA fragment length for the DHPLC analysis is around 500 bps therefore seven pairs of primers will be designed for each PCR reaction PCR will be performed in a volume of 50 ul with AmpliTaq Gold DNA polymerase The reaction containing 50 ng DNA 1 U of enzyme 300 ng of each primer 200 mM of each dNTP 15 mM MgCl2 50 mM KCl and 10 mM Tris-HCl pH83 All reaction will be performed with an initial denaturation step of 5 min at 95 followed by 35 cycles of a denaturation step at 94 for 30 sec an annealing step of 1 min at a temperature appropriate for the primers used and a synthesis step at 72 for 10 min PCR reaction condition will be adjusted according to the Tm predicted from each primer

Denaturing HPLC analysis The DNA fragment of a PCR product will be first screened by the DHPLC chromatograph to evaluate a pure and concentrated PCR product generated from the PCR process Mutation and polymorphism analysis will be performed according to the method on an analysis system from Transgenomic WAVE HPLC Transgenomic Oefner and Underhill 1998 The PCR products of each of the 500 bps will be denatured at 95 for 5 min and cooled to 65 for the formation of heteroduplexes DHPLC will be carried out using a DNASep column Transgenomic as described Kuklin et al 1997 The composition of buffer A will be 01M triethylammonium acetate TEAA Transgenomic and buffer B will contain 01 M TEAA 25 acetonitrile Analysis will be carried out at a flow rate of 09 mlmin and a buffer B gradient increase of 2 per min for 4 min Start and end concentrations of buffer B will be determined empirically for each fragment Elution of DNA from the column will be detected by absorbance at 260 nm The optimum temperature for mutation detection for each fragment will be approximately 1-2 before or after Tm and will be determined empirically for each fragment Where the Wavemaker software will be used to indicate that the numbers of melting domains existed in an amplicon HPLC will be conducted at that numbers of temperatures A Wave Sizing standard and a Wave Mutation standard will evaluate the column resolution and the column oven efficiency every week

RFLP and Direct sequencing of PCR fragments Differences in the elution profiles of DHPLC chromatograms will be compared between schizophrenic patients and controls The detail mutation or polymorphism sequences will be sent out to biotechnology company for further analysis or by restriction fragment length polymorphism RFLP to verify certain mutations or polymorphisms

Data Analysis DHPLC data analysis will be based upon a subjective comparison of sample and reference chromatograms In the present proposal we will use controls and diseased patients to be references and samples Peak number will be the most important criterion for assigning the presence of a mutation In the majority of cases a single peak seen in a control sample will produce two three or four peaks in the presence of a mutation The shape of the peak will help to identify mutations Some mutations will be seen only as changes in the shape of a single peak

Results will be scored based upon the elution profile of the DHPLC chromatogram Different profiles will be correlated to the disease symptom or disease status Highly correlation of elution profile as the part of mutation or polymorphisms will be sequenced

Expected Difficulties and Solutions

1 Further sequencing and comparing to our previous work will be used to verify the mutation results of DHPLC
2 Restriction fragment length polymorphism RFLP will also be used if a specific mutation has been detected by DHPLC

The DHPLC will be used following the regulations in the common research office

Study Oversight

Has Oversight DMC: None
Is a FDA Regulated Drug?: None
Is a FDA Regulated Device?: None
Is an Unapproved Device?: None
Is a PPSD?: None
Is a US Export?: None
Is an FDA AA801 Violation?: None