Biomedical subjects

B Budowle

Publications and source records attributed to B Budowle.

At least 127 records · Page 7Linked to original sources

PubMed1996

Hungarian population data on six STR loci--HUMVWFA31, HUMTH01, HUMCSF1PO, HUMFES/FPS, HUMTPOX, and HUMHPRTB--derived using multiplex PCR amplification and manual typing.

We present a Hungarian population study for six tetrameric short tandem repeat (STR) loci employing multiplex PCR amplification, electrophoresis of the PCR products in DNA sequencing gels and subsequent detection of allelic fragments by silver staining. The loci were HUMVWFA31, HUMTH01, HUMCSF1PO, HUMFES/ FPS, HUMTPOX, and HUMHPRTB. All loci met Hardy-Weinberg expectations in the examined Hungarian Caucasian population sample (N = 223 individuals). In addition, there was no evidence for association of alleles among the five autosomal loci HUMVWFA31, HUMTH01, HUMCSF1PO, HUMFES/FPS, and HUMTPOX.

Alleles↗

PubMed1996

Estimating minimum allele frequencies for DNA profile frequency estimates for PCR-based loci.

In order that there can be confidence that DNA profile frequency estimates will not place undue bias against a defendant, 2 methods are described for estimating minimum allele frequency bounds for PCR-based loci. One approach estimates minimum allele frequencies for VNTR and STR loci using sample size and the observed heterozygosity at a locus, while the second approach, appropriate for loci typed with allele-specific oligonucleotide probes, is based only on sample size. The use of a minimum allele frequency enables compensation for sparse sampling of infrequent alleles in population databases.

DNA Fingerprinting↗

PubMed1996

Hungarian population data on the loci HLA-DQ alpha, LDLR, GYPA, HBGG, D7S8 and GC.

Population data studies for HLA-DQ alpha and PM loci (LDLR, GYPA, HBGG, D7S8, GC) were carried out on a Hungarian Caucasian population sample of 163 unrelated individuals. Whereas the observed PM allele frequencies were similar to those reported for Caucasians, significant differences were found for HLA-DQ alpha between the Hungarian and some Caucasian population data. All six loci meet Hardy-Weinberg expectations and there is no evidence for association between any pairs of loci.

Alleles↗

PubMed1996

Hinf I/Tsp509 I and BsoF I polymorphisms in the flanking regions of the human VNTR locus D1S80.

The minisatellite locus D1S80 (1p35-p36), is a highly polymorphic VNTR that also contains a Hinf I polymorphism in the 5' flanking region. Our data suggest that the Hinf I polymorphism is a G > T transversion 58 bases downstream from the forward primer. This G > T transversion also creates a Tsp509 I restriction site. Additionally, a G > C transversion polymorphism was identified in the 3' flanking region by the creation of a BsoF I restriction site immediately adjacent to the repeat region.

Chromosomes, Human, Pair 1↗

PubMed1996

Multiplex amplification and typing procedure for the loci D1S80 and amelogenin.

A method has been developed that enables multiplex amplification and simultaneous typing of the loci D1S80 and amelogenin using discontinuous polyacrylamide gel electrophoresis and silver staining. The protocol is sensitive, simple, rapid, and relatively inexpensive. The results of the multiplex analysis of the D1S80 and amelogenin loci were comparable to those obtained when each locus was analyzed individually. A small validation study was undertaken to evaluate the forensic applicability of this multiplex system. The data demonstrate that DNA exposed to a variety of environmental insults yields reliable multiplex typing results.

Amelogenin↗

PubMed1996

Hungarian population data on seven PCR-based loci.

Hungarian population data for the loci LDLR, GYPA, HBGG, D7S8, Gc, HLA-DQA1, and D1S80 were generated. The genotype frequency distributions for the loci do not deviate from Hardy Weinberg expectations. Furthermore, there was little evidence for departures from expectations of independence between the loci. Using a test for homogeneity all the loci were similar between two Hungarian population samples and only the HLA-DQA1 locus was statistically different between Hungarians and US Caucasians. There generally would be little forensic differences, whether a Hungarian or a US Caucasian database was used, for estimating multiple locus profile frequencies for the seven PCR-based loci.

DNA↗

PubMed1996

Navajo, Pueblo, and Sioux population data on the Loci HLA-DQA1, LDLR, GYPA, HBGG, D7S8, Gc, and D1S80.

Navajo, Pueblo, and Sioux population databases were established for the loci HLA-DQA1, LDLR, GYPA, HBGG, D7S8, Gc, and D1S80. With the exception of HLA-DQA1, the loci appear to be almost as informative in the Native American population samples as for Caucasians, for identity testing purposes. HLA DQA1 is not as informative as the other loci, due to the high frequencies of the '3' and '4' alleles in these Native American groups. Except for GYPA in Navajos, the distribution of the genotype frequencies for the various loci meet Hardy Weinberg expectations. The deviation at the GYPA locus had no affect on generating statistical estimates. Also, there is little evidence for departures from expectations of independence of alleles across loci. The data demonstrate that estimates of multiple locus profile frequencies can be obtained from the Native American databases for identity testing purposes using the product rule under the assumption of independence. In addition, the Navajo, Pueblo, and Sioux databases were more similar to each other than to U.S. Caucasians and African Americans.

Alleles↗

PubMed1996

Using multiplex PCR amplification and typing kits for the analysis of DNA evidence in a serial killer case.

Analysis of DNA evidence in a serial killer case was performed using the AmpliType HLA-DQ alpha-, AmpliType PM-, and the GenePrint STR Multiplex System PCR Amplification Kits. In addition, a sex typing procedure using the X-Y homologous gene amelogenin was carried out. DNA profiles from a single hair with attached sheath material, recovered from underneath the seat cover of the suspect's car seat were compared with DNA profiles derived from reference head hairs from a homicide victim. From the evidentiary sample only 9 ng of human DNA could be recovered. In a sample, where the quantity of DNA becomes a critical issue a powerful route is the simultaneous amplification of several loci (multiplex PCR). This is the first report where commercially available multiplex PCR amplification and typing kits have been introduced for the analysis of DNA evidence in a serial killer case and the analysis has been admitted in court.

Adult↗

PubMed1995

Chinese population data on three tetrameric short tandem repeat loci--HUMTHO1, TPOX, and CSF1PO--derived using multiplex PCR and manual typing.

Allele and genotype frequencies for three tetrameric short tandem repeat (STR) loci were determined in a Chinese sample population using multiplex polymerase chain reaction (PCR), electrophoresis of the PCR products in DNA sequencing gels and subsequent detection by silver staining. The loci are HUMTHO1, TPOX, and CSF1PO. All loci meet Hardy-Weinberg expectations. In addition, there is no evidence for association of alleles among the three loci. The allelic frequency data can be used in human identity testing to estimate the frequency of a multiple STR locus DNA profile in the Chinese population.

Alleles↗

PubMed1995

Application of dual internal standards for precise sizing of polymerase chain reaction products using capillary electrophoresis.

Capillary electrophoresis (CE) is an analytical technique which provides rapid, high resolution analysis of amplified DNA fragments produced by the polymerase chain reaction (PCR). In this study, two internal standards are used as size markers to bracket und precisely size PCR products. The technique is applied to typing PCR products from the short tandem repeat locus HUMTH01. HUMTH01 consists of five to seven major alleles in the size range of 179-203 bp, with each allele four bp apart. Using this genetic marker, a population containing 97 individuals was examined with both polyacrylamide gel electrophoresis and CE. Identical genotypes were obtained with both techniques demonstrating the reliability of CE in DNA typing applications. The DNA analysis took place in sets of 10 with a calibration of the CE being performed between each set of samples. For the 97 samples examined, the pooled standard deviation was 0.3 bp. The observed genotype frequencies determined from the sample set did not deviate significantly from Hardy-Weinberg expectations. From these CE results, we conclude that HUMTH01 PCR products can be accurately and precisely sized by capillary electrophoresis using the method described.

Base Sequence↗

PubMed1995

Simple protocols for typing forensic biological evidence: chemiluminescent detection for human DNA quantitation and restriction fragment length polymorphism (RFLP) analyses and manual typing of polymerase chain reaction (PCR) amplified polymorphisms.

Methods for identity testing are described that enable extraction of DNA from biological samples, determination of the quantity of human DNA, and genetic analyses of the materials using restriction fragment length polymorphism (RFLP) typing and/or amplified fragment length polymorphism (AMP-FLP) typing of PCR products. The salient features of the procedures are simplicity, manual typing, nonradioactive chemiluminescent assays or silver staining for detection, and low cost. Most application-oriented laboratories involved in forensic and/or paternity testing should be able to implement these procedures.

Base Sequence↗

PubMed1995

Swiss population data and forensic efficiency values on 3 tetrameric short tandem repeat loci-HUMTH01, TPOX, and CSF1PO-derived using a STR multiplex system.

Allele and genotype frequencies for 3 tetrameric short tandem repeat loci were determined in a Swiss population sample (n = 100) using the GenePrint STR Multiplex System, electrophoresis of the PCR products in DNA sequencing gels and subsequent detection of allelic fragments by silver staining. The loci are HUMTH01, TPOX, and CSF1PO. The observed heterozygosities are 83.0%, 60.0%, and 72.0%, respectively. The discrimination power determined for the individual loci is 0.914, 0.780, and 0.860, respectively, and the combined discrimination power for the triplex is 0.997. All loci meet Hardy-Weinberg expectations and after Bonferroni correction there was no evidence that the population sample deviates from expectations of independence. Moreover, independence of alleles at these STR loci with other PCR-based loci derived from the same Swiss population sample, previously reported, were considered. These loci were DQA1, LDLR, GYPA, HBGG, D7S8, GC and D1S80. Again, after Bonferroni correction there was no evidence that the population sample deviates from expectations of independence among alleles at the 10 different PCR-based loci. Thus, the allelic frequency data can be used in human identity testing to estimate the frequency of a multiple PCR-based DNA profile in the Swiss population.

Alleles↗

PubMed1995

Validation of mitochondrial DNA sequencing for forensic casework analysis.

Two sets of studies were performed to evaluate the forensic utility of sequencing human mitochondrial DNA (mtDNA) derived from various tissues and amplified by the polymerase chain reaction (PCR). Sequencing was performed on a Perkin-Elmer/Applied Biosystems Division (PE/ABD) automated DNA sequencer (model 373A). The first set of experiments included typical validation studies that had previously been conducted on forensic DNA markers, such as: chemical contaminant effects on DNA from blood and semen and the effect of typing DNA extracted from body fluid samples deposited on various substrates. A second set of experiments was performed strictly on human hair shafts. These studies included typing mtDNA from hairs that were: (1) from different body areas, (2) chemically treated, (3) from deceased individuals, and (4) deliberately contaminated with various body fluids. The data confirm that PCR-based mtDNA typing by direct automated sequencing is a valid and reliable means of forensic identification.

Animals↗

PubMed1995

The effects of inbreeding on DNA profile frequency estimates using PCR-based loci.

Estimates of inbreeding were determined using Wright's FST for loci used for PCR-based forensic analyses. The populations analyzed were African Americans, Caucasians, Hispanics, and Orientals. In most cases the FST values at each locus were less than 0.01. The FST values over all loci for African Americans, Caucasians, and Orientals ranged from 0.0015 to 0.0048. No substantial differences were observed for DNA profile frequency estimates when calculated under the assumption of independence or with the incorporation of FST.

Consanguinity↗

PubMed1995

Spanish population data on 7 tetrameric short tandem repeat loci.

Allele and genotype frequencies for 7 tetrameric short tandem repeat loci were determined in a Spanish population sample (N = 186-244) using PCR and subsequent analysis of the PCR products by denaturing polyacrylamide gel electrophoresis followed by silver staining. The loci were HUMFES/FPS, HUMVWA, HUMTHO1, HUMF13B, HUMCSF1PO, HUMF13A1 and HUMTPOX and all loci met Hardy-Weinberg expectations. In addition, little evidence was found for association of alleles among the 7 loci. Thus the allele frequency data can be used in identity testing to estimate the frequency of a multiple PCR-based DNA profile in the Spanish population.

Gene Frequency↗

PubMed1995

Korean population data on the PCR-based loci LDLR, GYPA, HBGG, D7S8, Gc, HLA-DQA1, and D1S80.

Korean population data was generated for the loci LDLR, GYPA, HBGG, D7S8, Gc, HLA-DQA1, and D1S80. The genotype frequency distributions for the loci do not deviate from Hardy Weinberg expectations. Furthermore, there was no evidence for departures from expectations of independence between the loci. Using a test for homogeneity all the loci, except for D1S80, were similar between the Korean population sample and a Chinese population sample.

DNA↗

PubMed1995

A method for the purification and recovery of genomic DNA from an HLA DQA1 amplification product and its subsequent amplification and typing with the AmpliType PM PCR Amplification and Typing Kit.

DNA from plucked single hairs from ten individuals was extracted by two different methods and subsequently amplified and typed using the AmpliType HLA DQ alpha Forensic DNA Amplification and Typing Kit. The remaining untyped portions of the DQA1 amplification products were stored refrigerated or frozen for two weeks and subsequently purified using Centricon 100 microconcentrators. Genomic DNA was recovered from the DQA1 amplification PCR and used again as a template for a subsequent multiplex PCR. Twenty microL of each retentate were amplified and typed with the AmpliType PM PCR Amplification and Typing Kit. All typing results were consistent with DQA1 and PM results of control hairs and reference blood samples from the donors and all results were consistent with those obtained when the samples were typed solely for PM. The DQA1-Centricon 100-PM approach is useful when the genomic DNA from an evidentiary sample has been used completely for HLA-DQA1 typing, so that only the amplified product is remaining. The typing of five more genetic markers can be achieved from a HLA-DQA1 sample, so additional information for identification purposes could be provided. However, genomic DNA as well as the DQA1 product are recovered and the latter will also serve as a template in the subsequent PM amplifications. Therefore there will be more DQA1 product after the PM amplification than would be expected when only genomic DNA was used as a template. Thus certain practices should be considered when reading the types from PM probe strips if this DQA1-Centricon 100-PM approach is used.

DNA↗

PubMed1995

Confirmation of the identity of human skeletal remains using Multiplex PCR Amplification and Typing Kits.

The identify of human skeletal remains found in a wooded area approximately one year after the person was reported missing was provisionally established by routine methods and circumstantial evidence. Multiplex PCR systems--the AmpliType PM PCR Amplification and Typing Kit and the GenePrint STR Triplex Amplification and Typing Kit--were used to confirm the identification. DNA profiles from femur bone from the remains were compared with profiles derived from head hairs from a hairbrush recovered in the missing woman's apartment. In addition, a sex typing procedure using the X-Y homologous gene amelogenin was carried out. This is the first report of a case using commercially available multiplex PCR amplification and typing kits to confirm the identity of skeletal remains.

Bone and Bones↗